From 79bb309872658e240c7f5d9e189b9b5fe0d3d094 Mon Sep 17 00:00:00 2001 From: Daniele Rapetti <5535617+Iximiel@users.noreply.github.com> Date: Mon, 15 Sep 2025 14:42:43 +0200 Subject: [PATCH 1/2] Separating the PTM openACC implementation from the mpi+openMP preparing distance for the new plugin Setting up the new ptm in the new plugin deactivating a check in ActionShortcut::readInputLine setting up USEGPU for distance_vector Templatization of Angle and Torsion Mixed precision in Pbcs Mixed precision for GetInputData moved the multicolvar with openacc in a plugin Starting the migration of multicolvars to a template adding some templatization to the PTM updating the PTM accelerated now multicolvar is ready to be compiled in the openacc plugin adding the plugins to the modulemap setting up secondaryStructure for the plugin setting up secondary structure to target the plugin addressing some codecheck problems moving some of the volume kw in the headers moved Volumes to the plugin added the spherical harmonic to the plugin adding the matrixtimes family fixing a warning added Combine Between and <= and >= setting up contact matrix separating the GPU from the PTM moved the openACC tests updating some tests adding a way to get the dl handles in the actions addressed some codechek problems now checkin if an action is registered do note expose the vector of LOADed handles now the tests for existing GPU implementation pass, added fccubic, and better test compler guard to fccubic removing an unecessary shadowed variable now also the gpu-torsion test is checked against the CPU deactivated the quaternion tests small changes after the rebase deleted a support file --- plugins/openaccPTM/.gitignore | 4 + plugins/openaccPTM/ACCParallelTaskManager.h | 364 ++++++++++++++++ plugins/openaccPTM/Angle.cpp | 30 ++ plugins/openaccPTM/Between.cpp | 37 ++ plugins/openaccPTM/Combine.cpp | 38 ++ plugins/openaccPTM/ContactMatrix.cpp | 34 ++ plugins/openaccPTM/DihedralCorrelation.cpp | 30 ++ plugins/openaccPTM/Dipole.cpp | 30 ++ plugins/openaccPTM/Distance.cpp | 30 ++ plugins/openaccPTM/Fccubic.cpp | 34 ++ plugins/openaccPTM/LessThan.cpp | 38 ++ plugins/openaccPTM/Makefile | 62 +++ plugins/openaccPTM/MatrixTimesMatrix.cpp | 37 ++ plugins/openaccPTM/MatrixTimesVectorBase.cpp | 35 ++ plugins/openaccPTM/MoreThan.cpp | 39 ++ plugins/openaccPTM/Plane.cpp | 30 ++ plugins/openaccPTM/Position.cpp | 30 ++ .../openaccPTM/SecondaryStructureDRMSD.cpp | 33 ++ plugins/openaccPTM/SphericalHarmonic.cpp | 36 ++ plugins/openaccPTM/Torsion.cpp | 30 ++ plugins/openaccPTM/VolumeAround.cpp | 31 ++ plugins/openaccPTM/VolumeInCylinder.cpp | 36 ++ plugins/openaccPTM/VolumeInSphere.cpp | 33 ++ plugins/openaccPTM/configure.sh | 32 ++ plugins/openaccPTM/module.type | 0 plugins/openaccPTM/plumed | 1 + plugins/openaccPTM/regtest/.gitignore | 2 + plugins/openaccPTM/regtest/Makefile | 1 + plugins/openaccPTM/regtest/scripts | 1 + plugins/openaccPTM/regtest/targetGPU/Makefile | 2 + 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.../targetGPU/rt-symfunc-nbonds-q6/config | 2 +- .../rt-symfunc-nbonds-q6/forces.reference | 66 +++ .../targetGPU/rt-symfunc-nbonds-q6/plumed.dat | 71 +++ .../targetGPU/rt-symfunc-ntwo-lq6/Makefile | 0 .../rt-symfunc-ntwo-lq6/colvar.reference | 0 .../targetGPU/rt-symfunc-ntwo-lq6/config | 0 .../rt-symfunc-ntwo-lq6/forces.reference | 0 .../targetGPU/rt-symfunc-ntwo-lq6/plumed.dat | 1 + .../targetGPU/rt-symfunc-q6-nochain/Makefile | 0 .../rt-symfunc-q6-nochain/colv.reference | 0 .../rt-symfunc-q6-nochain/colv3.reference | 0 .../targetGPU/rt-symfunc-q6-nochain/config | 0 .../rt-symfunc-q6-nochain/forces.reference | 0 .../rt-symfunc-q6-nochain/plumed.dat | 1 + .../targetGPU/rt-symfunc-q6-subset/Makefile | 0 .../rt-symfunc-q6-subset/colv3.reference | 0 .../targetGPU/rt-symfunc-q6-subset/config | 0 .../rt-symfunc-q6-subset/forces.reference | 0 .../targetGPU/rt-symfunc-q6-subset/plumed.dat | 1 + .../regtest}/targetGPU/rt-symfunc-q6/Makefile | 0 .../targetGPU/rt-symfunc-q6/colv.reference | 0 .../targetGPU/rt-symfunc-q6/colv2.reference | 0 .../targetGPU/rt-symfunc-q6/colv3.reference | 0 .../targetGPU/rt-symfunc-q6/colv4.reference | 0 .../regtest}/targetGPU/rt-symfunc-q6/config | 0 .../targetGPU/rt-symfunc-q6/forces.reference | 0 .../targetGPU/rt-symfunc-q6/plumed.dat | 1 + .../targetGPU/rt-symfunc-simplecubic/Makefile | 0 .../rt-symfunc-simplecubic/colv.reference | 0 .../rt-symfunc-simplecubic/colv2.reference | 0 .../rt-symfunc-simplecubic/colv3.reference | 0 .../rt-symfunc-simplecubic/colv4.reference | 0 .../targetGPU/rt-symfunc-simplecubic/config | 0 .../rt-symfunc-simplecubic/forces.reference | 0 .../rt-symfunc-simplecubic/plumed.dat | 1 + .../targetGPU/rt-symfunc-small-lq6/Makefile | 0 .../rt-symfunc-small-lq6/colvar.reference | 0 .../targetGPU/rt-symfunc-small-lq6/config | 0 .../rt-symfunc-small-lq6/forces.reference | 0 .../targetGPU/rt-symfunc-small-lq6/plumed.dat | 1 + .../targetGPU/rt-symfunc-small-q6/Makefile | 0 .../rt-symfunc-small-q6/colvar.reference | 0 .../targetGPU/rt-symfunc-small-q6/config | 0 .../rt-symfunc-small-q6/forces.reference | 0 .../targetGPU/rt-symfunc-small-q6/plumed.dat | 1 + .../targetGPU/rt-symfunc-two-lq6/Makefile | 0 .../rt-symfunc-two-lq6/colvar.reference | 0 .../targetGPU/rt-symfunc-two-lq6/config | 0 .../rt-symfunc-two-lq6/forces.reference | 0 .../targetGPU/rt-symfunc-two-lq6/plumed.dat | 1 + .../targetGPU/rt-symfunc-two-q6/Makefile | 0 .../rt-symfunc-two-q6/colvar.reference | 0 .../targetGPU/rt-symfunc-two-q6/config | 0 .../rt-symfunc-two-q6/forces.reference | 0 .../targetGPU/rt-symfunc-two-q6/plumed.dat | 1 + .../targetGPU/rt-volume-around/Makefile | 0 .../rt-volume-around/colvar.reference | 0 .../targetGPU/rt-volume-around/config | 0 .../targetGPU/rt-volume-around/gentraj.cpp | 0 .../targetGPU/rt-volume-around/plumed.dat | 1 + .../targetGPU/rt-volume-around/trajectory.xyz | 0 plugins/openaccPTM/regtest/trajectories | 1 + plugins/openaccPTM/src/plumed | 1 + .../secondarystructure/rt33-mpi/plumed.dat | 2 +- regtest/secondarystructure/rt33/plumed.dat | 2 +- regtest/targetGPU/distribuitedMCBiasTests.sh | 181 -------- regtest/targetGPU/distribuitedMCTests.sh | 132 ------ regtest/targetGPU/distribuitedTests.sh | 126 ------ regtest/targetGPU/rt-GPU-DISTANCE/plumed.dat | 8 - .../rt-GPU-TORSION-biasIsSUM/colvar.reference | 20 - .../rt-GPU-TORSION-biasIsSUM/plumed.dat | 6 - .../rt-GPU-TORSION-biasIsSUM/tors.reference | 20 - .../rt-adjmat-basic-matrix/coords.reference | 18 - .../rt-adjmat-basic-matrix/forces.reference | 272 ------------ .../rt-symfunc-nbonds-one-q6/colv1.reference | 2 - .../rt-symfunc-nbonds-one-q6/forces.reference | 66 --- .../rt-symfunc-nbonds-one-q6/plumed.dat | 17 - .../rt-symfunc-nbonds-q6/colv1.reference | 2 - .../rt-symfunc-nbonds-q6/colv2.reference | 2 - .../rt-symfunc-nbonds-q6/forces.reference | 66 --- .../targetGPU/rt-symfunc-nbonds-q6/plumed.dat | 35 -- regtest/tools/rt-make-angle/main.cpp | 84 ++-- regtest/tools/rt-make-angle/output.reference | 39 +- src/adjmat/AdjacencyMatrixBase.h | 104 +++-- src/adjmat/ContactMatrix.cpp | 359 +++++++++++++--- src/adjmat/ContactMatrix.h | 82 +++- src/adjmat/ContactMatrixShortcut.cpp | 393 +---------------- src/adjmat/ContactMatrixShortcut.h | 145 +++++++ src/adjmat/Neighbors.cpp | 2 + src/adjmat/TorsionsMatrix.cpp | 33 ++ src/colvar/Angle.cpp | 112 +---- src/colvar/Angle.h | 135 ++++++ src/colvar/ColvarInput.cpp | 48 --- src/colvar/ColvarInput.h | 73 +++- src/colvar/ColvarShortcut.h | 10 +- src/colvar/DihedralCorrelation.cpp | 137 +----- src/colvar/DihedralCorrelation.h | 163 +++++++ src/colvar/Dipole.cpp | 166 +------ src/colvar/Dipole.h | 197 +++++++++ src/colvar/Distance.cpp | 231 +--------- src/colvar/Distance.h | 254 +++++++++++ src/colvar/MultiColvarTemplate.h | 131 +++--- src/colvar/Plane.cpp | 146 +------ src/colvar/Plane.h | 176 ++++++++ src/colvar/Position.cpp | 165 +------ src/colvar/Position.h | 192 +++++++++ src/colvar/RMSDVector.h | 2 + src/colvar/Torsion.cpp | 188 +------- src/colvar/Torsion.h | 215 ++++++++++ src/contour/FindContour.h | 2 + src/contour/FindContourSurface.cpp | 2 + src/contour/FindSphericalContour.cpp | 2 + src/core/AccelerableShortcut.cpp | 23 + src/core/AccelerableShortcut.h | 59 +++ src/core/ActionShortcut.cpp | 8 +- src/core/ActionWithMatrix.cpp | 38 ++ src/core/ActionWithMatrix.h | 4 + src/core/ActionWithVector.cpp | 49 +++ src/core/ActionWithVector.h | 5 + src/core/ParallelTaskManager.h | 406 +++++------------- src/core/PlumedMain.cpp | 5 +- src/core/PlumedMain.h | 2 + src/crystdistrib/Quaternion.cpp | 10 +- .../QuaternionBondProductMatrix.cpp | 5 +- src/dimred/ProjectPoints.cpp | 2 + src/function/Between.cpp | 93 +--- src/function/Between.h | 123 ++++++ src/function/Combine.cpp | 159 +------ src/function/Combine.h | 189 ++++++++ src/function/FunctionOfMatrix.h | 137 ++++-- src/function/FunctionOfVector.h | 129 ++++-- src/function/FunctionSetup.h | 4 +- src/function/FunctionShortcut.h | 74 +++- src/function/LessThan.cpp | 106 +---- src/function/LessThan.h | 133 ++++++ src/function/MoreThan.cpp | 105 +---- src/function/MoreThan.h | 135 ++++++ src/gridtools/FunctionOfGrid.h | 2 + src/gridtools/InterpolateGrid.cpp | 2 + src/gridtools/KDE.h | 2 + src/gridtools/Marginal.cpp | 2 + src/maketools/makeModuleMap | 19 +- src/matrixtools/MatrixDissimilarities.cpp | 111 +++++ src/matrixtools/MatrixDissimilarities.h | 111 +++++ src/matrixtools/MatrixProduct.cpp | 137 ++++++ src/matrixtools/MatrixProduct.h | 69 +++ src/matrixtools/MatrixTimesMatrix.cpp | 297 ------------- src/matrixtools/MatrixTimesMatrix.h | 108 +++-- src/matrixtools/MatrixTimesVector.cpp | 27 +- src/matrixtools/MatrixTimesVectorBase.cpp | 63 +-- src/matrixtools/MatrixTimesVectorBase.h | 170 +++++--- src/matrixtools/OuterProduct.h | 2 + src/refdist/MatrixProductDiagonal.cpp | 2 + src/secondarystructure/AlphaRMSD.cpp | 6 +- src/secondarystructure/AntibetaRMSD.cpp | 6 +- src/secondarystructure/ParabetaRMSD.cpp | 6 +- .../SecondaryStructureBase.h | 120 ++++-- .../SecondaryStructureDRMSD.cpp | 195 +-------- .../SecondaryStructureDRMSD.h | 206 +++++++++ .../SecondaryStructureRMSD.cpp | 14 +- src/symfunc/Fccubic.cpp | 70 +-- src/symfunc/Fccubic.h | 118 +++++ src/symfunc/SphericalHarmonic.cpp | 331 +------------- src/symfunc/SphericalHarmonic.h | 360 ++++++++++++++++ src/symfunc/ThreeBodyGFunctions.cpp | 2 + src/tools/Angle.cpp | 46 -- src/tools/Angle.h | 50 ++- src/tools/ColvarOutput.cpp | 8 - src/tools/ColvarOutput.h | 38 +- src/tools/Pbc.cpp | 62 +++ src/tools/Pbc.h | 6 + src/tools/SwitchingFunction.cpp | 2 + src/tools/Tools.h | 17 +- src/tools/Torsion.cpp | 57 --- src/tools/Torsion.h | 68 ++- src/tools/TypeUtils.cpp | 22 + src/tools/TypeUtils.h | 32 ++ src/volumes/ActionVolume.h | 148 ++++--- src/volumes/VolumeAround.cpp | 132 +----- src/volumes/VolumeAround.h | 167 +++++++ src/volumes/VolumeBetweenContours.cpp | 3 + src/volumes/VolumeCavity.cpp | 3 + src/volumes/VolumeInCylinder.cpp | 130 +----- src/volumes/VolumeInCylinder.h | 178 ++++++++ src/volumes/VolumeInSphere.cpp | 86 +--- src/volumes/VolumeInSphere.h | 121 ++++++ src/volumes/VolumeShortcut.h | 15 +- src/volumes/VolumeTetrapore.cpp | 3 + 403 files changed, 7574 insertions(+), 5409 deletions(-) create mode 100644 plugins/openaccPTM/.gitignore create mode 100644 plugins/openaccPTM/ACCParallelTaskManager.h create mode 100644 plugins/openaccPTM/Angle.cpp create mode 100644 plugins/openaccPTM/Between.cpp create mode 100644 plugins/openaccPTM/Combine.cpp create mode 100644 plugins/openaccPTM/ContactMatrix.cpp create mode 100644 plugins/openaccPTM/DihedralCorrelation.cpp create mode 100644 plugins/openaccPTM/Dipole.cpp create mode 100644 plugins/openaccPTM/Distance.cpp create mode 100644 plugins/openaccPTM/Fccubic.cpp create mode 100644 plugins/openaccPTM/LessThan.cpp create mode 100644 plugins/openaccPTM/Makefile create mode 100644 plugins/openaccPTM/MatrixTimesMatrix.cpp create mode 100644 plugins/openaccPTM/MatrixTimesVectorBase.cpp create mode 100644 plugins/openaccPTM/MoreThan.cpp create mode 100644 plugins/openaccPTM/Plane.cpp create mode 100644 plugins/openaccPTM/Position.cpp create mode 100644 plugins/openaccPTM/SecondaryStructureDRMSD.cpp create mode 100644 plugins/openaccPTM/SphericalHarmonic.cpp create mode 100644 plugins/openaccPTM/Torsion.cpp create mode 100644 plugins/openaccPTM/VolumeAround.cpp create mode 100644 plugins/openaccPTM/VolumeInCylinder.cpp create mode 100644 plugins/openaccPTM/VolumeInSphere.cpp create mode 100755 plugins/openaccPTM/configure.sh create mode 100644 plugins/openaccPTM/module.type create mode 120000 plugins/openaccPTM/plumed create mode 100644 plugins/openaccPTM/regtest/.gitignore create mode 120000 plugins/openaccPTM/regtest/Makefile create mode 120000 plugins/openaccPTM/regtest/scripts create mode 100644 plugins/openaccPTM/regtest/targetGPU/Makefile rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-DISTANCE/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-DISTANCE/colvar.reference (100%) rename {regtest/targetGPU/rt-GPU-TORSION-biasIsSUM => plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE}/config (73%) create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/diff.reference rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-DISTANCE/dists.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-DISTANCE/forces.reference (100%) create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/plumed.dat rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-PLANE-bias/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-PLANE-bias/config (80%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-PLANE-bias/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-PLANE-bias/planes.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-PLANE-bias/plumed.dat (77%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-TORSION-biasIsSUM/Makefile (100%) rename {regtest/targetGPU/rt-GPU-DISTANCE => plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM}/config (73%) create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/diff.reference rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-TORSION-biasIsSUM/forces.reference (54%) create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/plumed.dat create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/tors.reference rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/angles.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/cdipoles.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/cdists.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/ctorsions.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/ctorsions2.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/dipoles.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/dists.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/plumed.dat (98%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/pos.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/scdists.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/spos.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/test.pdb (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-multicolvar-print/torsions.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product-deriv/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product-deriv/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product-deriv/config (82%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product-deriv/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product-deriv/plumed.dat (95%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product-only/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product-only/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product-only/config (84%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product-only/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product-only/plumed.dat (92%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product/config (84%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-quaternion-bond-product/plumed.dat (90%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure-DRMSD/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure-DRMSD/ala12_trajectory.xyz (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure-DRMSD/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure-DRMSD/colvar10.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure-DRMSD/config (82%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure-DRMSD/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure-DRMSD/helix.pdb (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure-DRMSD/plumed.dat (96%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure/ala12_trajectory.xyz (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure/colvar10.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure/helix.pdb (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-GPU-secondarystructure/plumed.dat (95%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix-mtv/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix-mtv/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix-mtv/config (100%) create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/diff.reference rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix-mtv/fcolvar.reference (100%) create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/forces.reference rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix-mtv/isomers.xyz (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix-mtv/plumed.dat (52%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix/config (100%) rename {regtest/targetGPU/rt-adjmat-basic-matrix-mtv => plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix}/coords.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix/fcolvar.reference (100%) rename {regtest/targetGPU/rt-adjmat-basic-matrix-mtv => plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix}/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix/isomers.xyz (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix/plumed.dat (89%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix2/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix2/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix2/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix2/coords.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix2/fcolvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix2/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix2/plumed.dat (90%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix3/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix3/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix3/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix3/coords.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix3/fcolvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix3/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix3/gas-one.xyz (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix3/plumed.dat (91%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix4/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix4/cmcolvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix4/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix4/fcolvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix4/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix4/gas-one.xyz (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-basic-matrix4/plumed.dat (87%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-eigvals/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-eigvals/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-eigvals/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-eigvals/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-eigvals/plumed.dat (82%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-eigvecs/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-eigvecs/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-eigvecs/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-eigvecs/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-eigvecs/plumed.dat (93%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-join-eigvals/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-join-eigvals/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-join-eigvals/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-join-eigvals/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-join-eigvals/plumed.dat (91%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-join-eigvecs/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-join-eigvecs/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-join-eigvecs/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-join-eigvecs/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-join-eigvecs/plumed.dat (97%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-matmult/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-matmult/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-matmult/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-matmult/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-matmult/isomers.xyz (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-matmult/plumed.dat (84%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-prod/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-prod/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-prod/config (87%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-prod/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-adjmat-prod/plumed.dat (89%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-coordination-insphere-nochain/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-coordination-insphere-nochain/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-coordination-insphere-nochain/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-coordination-insphere-nochain/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-coordination-insphere-nochain/plumed.dat (94%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-coordination-insphere/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-coordination-insphere/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-coordination-insphere/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-coordination-insphere/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-coordination-insphere/plumed.dat (94%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-cylinder/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-cylinder/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-cylinder/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-cylinder/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-cylinder/gentraj.cpp (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-cylinder/plumed.dat (87%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-cylinder/trajectory.xyz (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-landmarks-calc-dissims/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-landmarks-calc-dissims/analysis.1.mymatrix3.dat.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-landmarks-calc-dissims/colv_in (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-landmarks-calc-dissims/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-landmarks-calc-dissims/mymatrix.dat.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-landmarks-calc-dissims/mymatrix2.dat.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-landmarks-calc-dissims/mymatrix3.dat.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-landmarks-calc-dissims/output-fps.pdb.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-landmarks-calc-dissims/output-stride.pdb.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-landmarks-calc-dissims/plumed.dat (94%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-multicolvar-filters/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-multicolvar-filters/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-multicolvar-filters/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-multicolvar-filters/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-multicolvar-filters/plumed.dat (98%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-averaged-q6-spAspB/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-averaged-q6-spAspB/colvar_aq6.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-averaged-q6-spAspB/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-averaged-q6-spAspB/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-averaged-q6-spAspB/plumed.dat (87%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-averaged-q6-spAspB/traj_md-10.xyz (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-averaged-q6/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-averaged-q6/colv.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-averaged-q6/colv3.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-averaged-q6/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-averaged-q6/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-averaged-q6/plumed.dat (85%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-nbonds-one-q6/Makefile (100%) create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/colv1.reference rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-nbonds-one-q6/config (100%) create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/forces.reference create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/plumed.dat rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-nbonds-q6/Makefile (100%) create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/colv1.reference create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/colv2.reference rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-nbonds-q6/config (78%) create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/forces.reference create mode 100644 plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/plumed.dat rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-ntwo-lq6/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-ntwo-lq6/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-ntwo-lq6/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-ntwo-lq6/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-ntwo-lq6/plumed.dat (95%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6-nochain/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6-nochain/colv.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6-nochain/colv3.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6-nochain/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6-nochain/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6-nochain/plumed.dat (84%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6-subset/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6-subset/colv3.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6-subset/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6-subset/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6-subset/plumed.dat (88%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6/colv.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6/colv2.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6/colv3.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6/colv4.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-q6/plumed.dat (92%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-simplecubic/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-simplecubic/colv.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-simplecubic/colv2.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-simplecubic/colv3.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-simplecubic/colv4.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-simplecubic/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-simplecubic/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-simplecubic/plumed.dat (97%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-small-lq6/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-small-lq6/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-small-lq6/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-small-lq6/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-small-lq6/plumed.dat (94%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-small-q6/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-small-q6/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-small-q6/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-small-q6/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-small-q6/plumed.dat (92%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-two-lq6/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-two-lq6/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-two-lq6/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-two-lq6/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-two-lq6/plumed.dat (92%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-two-q6/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-two-q6/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-two-q6/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-two-q6/forces.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-symfunc-two-q6/plumed.dat (91%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-volume-around/Makefile (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-volume-around/colvar.reference (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-volume-around/config (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-volume-around/gentraj.cpp (100%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-volume-around/plumed.dat (99%) rename {regtest => plugins/openaccPTM/regtest}/targetGPU/rt-volume-around/trajectory.xyz (100%) create mode 120000 plugins/openaccPTM/regtest/trajectories create mode 120000 plugins/openaccPTM/src/plumed delete mode 100644 regtest/targetGPU/distribuitedMCBiasTests.sh delete mode 100644 regtest/targetGPU/distribuitedMCTests.sh delete mode 100644 regtest/targetGPU/distribuitedTests.sh delete mode 100644 regtest/targetGPU/rt-GPU-DISTANCE/plumed.dat delete mode 100644 regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/colvar.reference delete mode 100644 regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/plumed.dat delete mode 100644 regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/tors.reference delete mode 100644 regtest/targetGPU/rt-adjmat-basic-matrix/coords.reference delete mode 100644 regtest/targetGPU/rt-adjmat-basic-matrix/forces.reference delete mode 100644 regtest/targetGPU/rt-symfunc-nbonds-one-q6/colv1.reference delete mode 100644 regtest/targetGPU/rt-symfunc-nbonds-one-q6/forces.reference delete mode 100644 regtest/targetGPU/rt-symfunc-nbonds-one-q6/plumed.dat delete mode 100644 regtest/targetGPU/rt-symfunc-nbonds-q6/colv1.reference delete mode 100644 regtest/targetGPU/rt-symfunc-nbonds-q6/colv2.reference delete mode 100644 regtest/targetGPU/rt-symfunc-nbonds-q6/forces.reference delete mode 100644 regtest/targetGPU/rt-symfunc-nbonds-q6/plumed.dat create mode 100644 src/adjmat/ContactMatrixShortcut.h create mode 100644 src/colvar/Angle.h create mode 100644 src/colvar/DihedralCorrelation.h create mode 100644 src/colvar/Dipole.h create mode 100644 src/colvar/Distance.h create mode 100644 src/colvar/Plane.h create mode 100644 src/colvar/Position.h create mode 100644 src/colvar/Torsion.h create mode 100644 src/core/AccelerableShortcut.cpp create mode 100644 src/core/AccelerableShortcut.h create mode 100644 src/function/Between.h create mode 100644 src/function/Combine.h create mode 100644 src/function/LessThan.h create mode 100644 src/function/MoreThan.h create mode 100644 src/matrixtools/MatrixDissimilarities.cpp create mode 100644 src/matrixtools/MatrixDissimilarities.h create mode 100644 src/matrixtools/MatrixProduct.cpp create mode 100644 src/matrixtools/MatrixProduct.h create mode 100644 src/secondarystructure/SecondaryStructureDRMSD.h create mode 100644 src/symfunc/Fccubic.h create mode 100644 src/symfunc/SphericalHarmonic.h create mode 100644 src/tools/TypeUtils.cpp create mode 100644 src/tools/TypeUtils.h create mode 100644 src/volumes/VolumeAround.h create mode 100644 src/volumes/VolumeInCylinder.h create mode 100644 src/volumes/VolumeInSphere.h diff --git a/plugins/openaccPTM/.gitignore b/plugins/openaccPTM/.gitignore new file mode 100644 index 0000000000..f11b086c1d --- /dev/null +++ b/plugins/openaccPTM/.gitignore @@ -0,0 +1,4 @@ +Makefile.conf +extra/ +.deps/ + diff --git a/plugins/openaccPTM/ACCParallelTaskManager.h b/plugins/openaccPTM/ACCParallelTaskManager.h new file mode 100644 index 0000000000..3036e70659 --- /dev/null +++ b/plugins/openaccPTM/ACCParallelTaskManager.h @@ -0,0 +1,364 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2017-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_acc_ParallelTaskManager_h +#define __PLUMED_acc_ParallelTaskManager_h +#include "plumed/core/ActionWithVector.h" +#include "plumed/core/ActionWithMatrix.h" +#include "plumed/core/ParallelTaskManager.h" +#include "plumed/tools/Communicator.h" +#include "plumed/tools/OpenMP.h" +#include "plumed/tools/View.h" +#include "plumed/tools/View2D.h" + +#include "plumed/tools/ColvarOutput.h" +#include "plumed/tools/OpenACC.h" + +namespace PLMD { + +template +class AccParallelTaskManager : public ParallelTaskManager { + using ParallelTaskManager::action; + using ParallelTaskManager::myinput; + using ParallelTaskManager::argumentsMap; + using ParallelTaskManager::value_stash; + using ParallelTaskManager::comm; + using ParallelTaskManager::actiondata; + using ParallelTaskManager::nderivatives_per_task; + using ParallelTaskManager::workspace_size; + using ParallelTaskManager::omp_forces; + using ParallelTaskManager::input_buffer; + using ParallelTaskManager::serial; + using ParallelTaskManager::useacc; + using ParallelTaskManager::getValueStashSize; +public: + typedef typename ParallelTaskManager::ParallelActionsInput ParallelActionsInput; + typedef typename ParallelTaskManager::ParallelActionsOutput ParallelActionsOutput; + typedef typename ParallelTaskManager::ForceInput ForceInput; + typedef typename ParallelTaskManager::ForceOutput ForceOutput; + typedef typename ParallelTaskManager::precision precision; + static void registerKeywords( Keywords& keys ) { + ParallelTaskManager::registerKeywords(keys); + } + AccParallelTaskManager(ActionWithVector* av): + PLMD::ParallelTaskManager(av) { + useacc=true; + } +/// This runs all the tasks + void runAllTasks(); +/// Apply the forces on the parallel object + void applyForces( std::vector& forcesForApply ); +}; + +struct ACCPTM { + template + using PTM=AccParallelTaskManager; +}; + +//use the __PLUMED_USE_OPENACC_TASKSMINE macro to debug the ptm ins a single file +//so that compiling witha a small modification will be faster (the ptm is included nearly everywhere) +#ifndef __PLUMED_USE_OPENACC_TASKSMINE +template +void runAllTasksACC(typename T::input_type actiondata, + ParActionsInput myinput, + std::vector& value_stash, + const std::vector & partialTaskList, + const unsigned nactive_tasks, + const std::size_t nderivatives_per_task, + const std::size_t workspace_size + ) { + auto myinput_acc = OpenACC::fromToDataHelper(myinput); + auto actiondata_acc = OpenACC::fromToDataHelper(actiondata); + + //template type is deduced + OpenACC::memoryManager vs{value_stash}; + auto value_stash_data = vs.devicePtr(); + + OpenACC::memoryManager ptl{partialTaskList}; + auto partialTaskList_data = ptl.devicePtr(); + + OpenACC::memoryManager buff{workspace_size*nactive_tasks}; + + auto buffer = buff.devicePtr(); + OpenACC::memoryManager dev(nderivatives_per_task*nactive_tasks); + auto derivatives = dev.devicePtr(); +#pragma acc parallel loop present(myinput, actiondata) \ + copyin(nactive_tasks, \ + nderivatives_per_task, \ + workspace_size)\ + deviceptr(derivatives, \ + partialTaskList_data, \ + value_stash_data, \ + buffer) \ + default(none) + for(unsigned i=0; i::create (myinput.nscalars, + value_stash_data+val_pos, + nderivatives_per_task, + derivatives+nderivatives_per_task*i, + workspace_size, + (workspace_size>0)? + buffer+workspace_size*i + :nullptr ); + // Calculate the stuff in the loop for this action + T::performTask( task_index, actiondata, myinput, myout ); + } + vs.copyFromDevice(value_stash.data()); +} +#else +template +void runAllTasksACC(typename T::input_type actiondata, + ParActionsInput myinput, + std::vector& value_stash, + const std::vector & partialTaskList, + const unsigned nactive_tasks, + const std::size_t nderivatives_per_task, + const std::size_t workspace_size + ) ; +#endif //__PLUMED_USE_OPENACC_TASKSMINE + +template +void AccParallelTaskManager::runAllTasks() { + // Get the list of active tasks + std::vector & partialTaskList( action->getListOfActiveTasks( action ) ); + unsigned nactive_tasks=partialTaskList.size(); + // Get all the input data so we can broadcast it to the GPU + myinput.noderiv = true; + action->getInputData( input_buffer ); + myinput.dataSize = input_buffer.size(); + myinput.inputdata = input_buffer.data(); + // Transfer all the bookeeping information about the arguments + argumentsMap.setupArguments( action ); + myinput.setupArguments( argumentsMap ); + // Reset the values at the start of the task loop + std::size_t totalvals=getValueStashSize(); + if( value_stash.size()!=totalvals ) { + value_stash.resize(totalvals); + } + std::fill (value_stash.begin(),value_stash.end(), 0.0); + if (comm.Get_rank()== 0) {// no multigpu shenanigans until this works + runAllTasksACC( + actiondata, + myinput, + value_stash, + partialTaskList, + nactive_tasks, + nderivatives_per_task, + workspace_size + ); + } + comm.Bcast( value_stash.data(), value_stash.size(), 0); + + // MPI Gather everything + if( !serial ) { + this->comm.Sum( this->value_stash ); + } + +// And transfer the value to the output values + action->transferStashToValues( partialTaskList, value_stash ); +} + +//use the __PLUMED_USE_OPENACC_FORCESMINE macro to debug the ptm ins a single file +//so that compiling witha a small modification will be faster (the ptm is included nearly everywhere) +#ifndef __PLUMED_USE_OPENACC_FORCESMINE +template +void applyForcesWithACC(PLMD::View forcesForApply, + typename T::input_type actiondata, + ParActionsInput myinput, + const std::vector& value_stash, + const std::vector & partialTaskList, + const unsigned nactive_tasks, + const std::size_t nderivatives_per_task, + const std::size_t workspace_size + ) { + auto myinput_acc = OpenACC::fromToDataHelper(myinput); + auto actiondata_acc = OpenACC::fromToDataHelper(actiondata); + + //template type is deduced + OpenACC::memoryManager vs{value_stash}; + auto value_stash_data = vs.devicePtr(); + + OpenACC::memoryManager ptl{partialTaskList}; + auto partialTaskList_data = ptl.devicePtr(); + + OpenACC::memoryManager ffa {forcesForApply}; + auto forcesForApply_data = ffa.devicePtr(); + const auto forcesForApply_size = ffa.size(); + const auto nind_per_scalar = ForceIndexHolder::indexesPerScalar(myinput); + //nscalars is >=ncomponents (see setupParallelTaskManager ) + const auto nind_per_task = nind_per_scalar*myinput.nscalars; + + OpenACC::memoryManager dev{nderivatives_per_task*nactive_tasks}; + auto derivatives = dev.devicePtr(); + OpenACC::memoryManager ind{nind_per_task*nactive_tasks}; + auto indices = ind.devicePtr(); + OpenACC::memoryManager vtmp{myinput.sizeOfFakeVals()*nactive_tasks}; + auto valstmp = vtmp.devicePtr(); + OpenACC::memoryManager buff{workspace_size*nactive_tasks}; + auto buffer = buff.devicePtr(); + +#define forces_indicesArg(taskID,scalarID) ForceIndexHolder::create(myinput, \ + indices + taskID*nind_per_task + scalarID*nind_per_scalar) +#define derivativeDrift(taskID,scalarID) taskID*nderivatives_per_task \ + + scalarID*myinput.ncomponents*myinput.nderivatives_per_scalar +#define stashDrift(taskID,scalarID) taskID*myinput.nscalars \ + + scalarID*myinput.ncomponents + +#pragma acc data present(myinput,actiondata) \ + copyin(nactive_tasks, \ + forcesForApply_size, \ + nderivatives_per_task, nind_per_task,nind_per_scalar, \ + workspace_size) \ + deviceptr(derivatives, \ + indices, \ + value_stash_data, \ + partialTaskList_data, \ + forcesForApply_data, \ + valstmp, \ + buffer) \ + default(none) + { +#pragma acc parallel loop + for(unsigned t=0; t::create( myinput.nscalars, + valstmp+myinput.nscalars*t, + nderivatives_per_task, + derivatives+nderivatives_per_task*t, + workspace_size, + (workspace_size>0)?buffer+workspace_size*t:nullptr); + // Calculate the stuff in the loop for this action + T::performTask( task_index, actiondata, myinput, myout ); + // If this is a matrix this returns a number that isn't one as we have to loop over the columns + const std::size_t nvpt = T::getNumberOfValuesPerTask( task_index, actiondata ); +#pragma acc loop seq + for(unsigned vID=0; vID::create ( myinput.nscalars, + value_stash_data + stashDrift(task_index,vID), + myinput.nderivatives_per_scalar, + derivatives + derivativeDrift(t,vID)); + + // Gather forces that can be gathered locally + ParallelTaskManager::gatherThreadSafeForces( myinput, + force_indices, + finput, + View(forcesForApply_data, + forcesForApply_size)); + } + } + +#pragma acc parallel loop + for(unsigned v=myinput.threadunsafe_forces_start; v::create( myinput.nscalars, + value_stash_data + stashDrift(task_index,vID), + myinput.nderivatives_per_scalar, + derivatives + derivativeDrift(t,vID)); + for(unsigned i=0; i +void applyForcesWithACC(PLMD::View forcesForApply, + typename T::input_type actiondata, + ParActionsInput myinput, + const std::vector& value_stash, + const std::vector & partialTaskList, + const unsigned nactive_tasks, + const std::size_t nderivatives_per_task, + const std::size_t workspace_size + ); +#endif //__PLUMED_USE_OPENACC_FORCESMINE + +template +void AccParallelTaskManager::applyForces( std::vector& forcesForApply ) { + // Get the list of active tasks + std::vector & partialTaskList= action->getListOfActiveTasks( action ); + unsigned nactive_tasks=partialTaskList.size(); + forceData forces(forcesForApply); + // Clear force buffer + std::fill (forces.ffa.begin(),forces.ffa.end(), precision(0.0)); + // Get all the input data so we can broadcast it to the GPU + myinput.noderiv = false; + // Retrieve the forces from the values + action->transferForcesToStash( partialTaskList, value_stash ); + + std::fill (omp_forces[0].begin(),omp_forces[0].end(), 0.0); + if (comm.Get_rank() == 0) { + applyForcesWithACC( + PLMD::View { forces.ffa.data(), forces.ffa.size() }, + actiondata, + myinput, + value_stash, + partialTaskList, + nactive_tasks, + nderivatives_per_task, + workspace_size + ); + } + forces.update(); + // MPI Gather everything (this must be extended to the gpu thing, after makning it mpi-aware) + if( !serial ) { + this->comm.Sum( forcesForApply ); + } +} + +} // namespace PLMD +#endif // __PLUMED_acc_ParallelTaskManager_h + + diff --git a/plugins/openaccPTM/Angle.cpp b/plugins/openaccPTM/Angle.cpp new file mode 100644 index 0000000000..9fcb021a24 --- /dev/null +++ b/plugins/openaccPTM/Angle.cpp @@ -0,0 +1,30 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/core/ActionRegister.h" +#include "plumed/colvar/MultiColvarTemplate.h" +#include "plumed/colvar/Angle.h" + +#include "ACCParallelTaskManager.h" + +typedef PLMD::colvar::MultiColvarTemplate,PLMD::ACCPTM> AngleMultiAcc; + +PLUMED_REGISTER_ACTION(AngleMultiAcc,"ANGLE_VECTORACC") diff --git a/plugins/openaccPTM/Between.cpp b/plugins/openaccPTM/Between.cpp new file mode 100644 index 0000000000..2e6b2cb58f --- /dev/null +++ b/plugins/openaccPTM/Between.cpp @@ -0,0 +1,37 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2017 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/function/Between.h" +#include "plumed/function/FunctionOfVector.h" +#include "plumed/function/FunctionOfMatrix.h" +#include "plumed/core/ActionRegister.h" + +#include "ACCParallelTaskManager.h" + +namespace PLMD { +namespace function { + +typedef FunctionOfVector VectorBetween; +PLUMED_REGISTER_ACTION(VectorBetween,"BETWEEN_VECTORACC") +typedef FunctionOfMatrix MatrixBetween; +PLUMED_REGISTER_ACTION(MatrixBetween,"BETWEEN_MATRIXACC") +} +} diff --git a/plugins/openaccPTM/Combine.cpp b/plugins/openaccPTM/Combine.cpp new file mode 100644 index 0000000000..dc9a411cb6 --- /dev/null +++ b/plugins/openaccPTM/Combine.cpp @@ -0,0 +1,38 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/function/Combine.h" +#include "plumed/function/FunctionOfVector.h" +#include "plumed/function/FunctionOfMatrix.h" +#include "plumed/core/ActionRegister.h" + +#include "ACCParallelTaskManager.h" + +namespace PLMD { +namespace function { + +typedef FunctionOfVector VectorCombine; +PLUMED_REGISTER_ACTION(VectorCombine,"COMBINE_VECTORACC") +typedef FunctionOfMatrix MatrixCombine; +PLUMED_REGISTER_ACTION(MatrixCombine,"COMBINE_MATRIXACC") + +} // namespace function +} // namespace PLMD diff --git a/plugins/openaccPTM/ContactMatrix.cpp b/plugins/openaccPTM/ContactMatrix.cpp new file mode 100644 index 0000000000..858a48b7e5 --- /dev/null +++ b/plugins/openaccPTM/ContactMatrix.cpp @@ -0,0 +1,34 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2015-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/adjmat/ContactMatrix.h" +#include "plumed/core/ActionRegister.h" + +#include "ACCParallelTaskManager.h" + +namespace PLMD { +namespace adjmat { + +typedef AdjacencyMatrixBase cmap; +PLUMED_REGISTER_ACTION(cmap,"CONTACT_MATRIX_PROPERACC") + +} // namespace adjmat +} // namespace PLMD diff --git a/plugins/openaccPTM/DihedralCorrelation.cpp b/plugins/openaccPTM/DihedralCorrelation.cpp new file mode 100644 index 0000000000..045bf770c9 --- /dev/null +++ b/plugins/openaccPTM/DihedralCorrelation.cpp @@ -0,0 +1,30 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/core/ActionRegister.h" +#include "plumed/colvar/MultiColvarTemplate.h" +#include "plumed/colvar/DihedralCorrelation.h" + +#include "ACCParallelTaskManager.h" + +typedef PLMD::colvar::MultiColvarTemplate,PLMD::ACCPTM> DihedralCorrelationMultiAcc; + +PLUMED_REGISTER_ACTION(DihedralCorrelationMultiAcc,"DIHEDRALCORRELATION_VECTORACC") diff --git a/plugins/openaccPTM/Dipole.cpp b/plugins/openaccPTM/Dipole.cpp new file mode 100644 index 0000000000..4bfa9650fb --- /dev/null +++ b/plugins/openaccPTM/Dipole.cpp @@ -0,0 +1,30 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/core/ActionRegister.h" +#include "plumed/colvar/MultiColvarTemplate.h" +#include "plumed/colvar/Dipole.h" + +#include "ACCParallelTaskManager.h" + +typedef PLMD::colvar::MultiColvarTemplate,PLMD::ACCPTM> DipoleMultiAcc; + +PLUMED_REGISTER_ACTION(DipoleMultiAcc,"DIPOLE_VECTORACC") diff --git a/plugins/openaccPTM/Distance.cpp b/plugins/openaccPTM/Distance.cpp new file mode 100644 index 0000000000..0b21d85ac2 --- /dev/null +++ b/plugins/openaccPTM/Distance.cpp @@ -0,0 +1,30 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/core/ActionRegister.h" +#include "plumed/colvar/MultiColvarTemplate.h" +#include "plumed/colvar/Distance.h" + +#include "ACCParallelTaskManager.h" + +typedef PLMD::colvar::MultiColvarTemplate,PLMD::ACCPTM> DistanceMultiAcc; + +PLUMED_REGISTER_ACTION(DistanceMultiAcc,"DISTANCE_VECTORACC") diff --git a/plugins/openaccPTM/Fccubic.cpp b/plugins/openaccPTM/Fccubic.cpp new file mode 100644 index 0000000000..2de1a582e4 --- /dev/null +++ b/plugins/openaccPTM/Fccubic.cpp @@ -0,0 +1,34 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2014-2020 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/symfunc/Fccubic.h" +#include "plumed/function/FunctionOfMatrix.h" +#include "plumed/core/ActionRegister.h" + +#include "ACCParallelTaskManager.h" +namespace PLMD { +namespace symfunc { + +typedef function::FunctionOfMatrix,PLMD::ACCPTM> MatrixFccubic; +PLUMED_REGISTER_ACTION(MatrixFccubic,"FCCUBIC_FUNC_MATRIXACC") + +} +} diff --git a/plugins/openaccPTM/LessThan.cpp b/plugins/openaccPTM/LessThan.cpp new file mode 100644 index 0000000000..aea09c395b --- /dev/null +++ b/plugins/openaccPTM/LessThan.cpp @@ -0,0 +1,38 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2017 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/function/LessThan.h" +#include "plumed/function/FunctionOfVector.h" +#include "plumed/function/FunctionOfMatrix.h" +#include "plumed/core/ActionRegister.h" + +#include "ACCParallelTaskManager.h" + +namespace PLMD { +namespace function { + +typedef FunctionOfVector VectorLessThan; +PLUMED_REGISTER_ACTION(VectorLessThan,"LESS_THAN_VECTORACC") +typedef FunctionOfMatrix MatrixLessThan; +PLUMED_REGISTER_ACTION(MatrixLessThan,"LESS_THAN_MATRIXACC") + +} +} diff --git a/plugins/openaccPTM/Makefile b/plugins/openaccPTM/Makefile new file mode 100644 index 0000000000..6f5b7413fd --- /dev/null +++ b/plugins/openaccPTM/Makefile @@ -0,0 +1,62 @@ +include ./Makefile.conf + +#Dependency tracking based on https://make.mad-scientist.net/papers/advanced-auto-dependency-generation/#tldr +#this assumes gcc +DEPDIR := .deps +DEPFLAGS = -MT $@ -MMD -MP -MF $(DEPDIR)/$*.d +#tested with nvcc with :"Build cuda_11.7.r11.7/compiler.31442593_0" +#-dc adds relocatable device code +#-dlto Perform link-time optimization of device code. +CVS_OBJS = $(wildcard *.cpp) +TOOLS_OBJS = extra/colvar/ColvarInput.o extra/tools/Pbc.o extra/tools/SwitchingFunction.o extra/tools/HistogramBead.o + +OBJS = $(CVS_OBJS:.cpp=.o) $(TOOLS_OBJS) +ADDCPPFLAGS=$(PLUMED_INCLUDE) -D__PLUMED_HAS_OPENACC=1 -acc -acc="gpu" +ADDCLDFLAGS=-acc -static-nvidia + +ifeq ($(SOEXT),dylib) + SONAME_OPTION:=-Xlinker -install_name +else + SONAME_OPTION:=-Xlinker -soname +endif + +PLUGIN=plumedOpenACC.$(SOEXT) + +NVCXX ?= nvc++ +NVLDSHARED = $(LDSHARED:$(CXX)=$(NVCXX)) +all: $(PLUGIN) + +%.o: %.cpp $(DEPDIR)/%.d | $(DEPDIR) + @echo Compiling object $@ + $(NVCXX) -c $(DEPFLAGS) $(CPPFLAGS) $(ADDCPPFLAGS) $(CXXFLAGS) $< -o $@ + +extra/colvar/%.o: plumed/colvar/%.cpp $(DEPDIR)/extra/colvar/%.d | $(DEPDIR)/extra/colvar extra/colvar + @echo Compiling object $@ + $(NVCXX) -c $(DEPFLAGS) $(CPPFLAGS) $(ADDCPPFLAGS) $(CXXFLAGS) $< -o $@ + +extra/tools/%.o: plumed/tools/%.cpp $(DEPDIR)/extra/tools/%.d | $(DEPDIR)/extra/tools extra/tools + @echo Compiling object $@ + $(NVCXX) -c $(DEPFLAGS) $(CPPFLAGS) $(ADDCPPFLAGS) $(CXXFLAGS) $< -o $@ + + +$(DEPDIR): ; @mkdir -p $@ +$(DEPDIR)/extra/colvar: ; @mkdir -p $@ +$(DEPDIR)/extra/tools: ; @mkdir -p $@ +extra/colvar: ; mkdir -p $@ +extra/tools: ; mkdir -p $@ + +DEPFILES := $(OBJS:%.o=$(DEPDIR)/%.d) +$(DEPFILES): +include $(wildcard $(DEPFILES)) + +$(PLUGIN): $(OBJS) + @echo Linking $@ + $(NVLDSHARED) $(ADDCLDFLAGS) $(SONAME_OPTION),"$(notdir $@)" $(DYNAMIC_LIBS) $(PLUMED_KERNEL) -o $@ $^ + +clean: + @rm -fv $(OBJS) $(PLUGIN) + @rm -rf .deps + +check: all + $(MAKE) -C regtest + $(MAKE) -C regtest checkfail diff --git a/plugins/openaccPTM/MatrixTimesMatrix.cpp b/plugins/openaccPTM/MatrixTimesMatrix.cpp new file mode 100644 index 0000000000..c646cdbcd9 --- /dev/null +++ b/plugins/openaccPTM/MatrixTimesMatrix.cpp @@ -0,0 +1,37 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/matrixtools/MatrixDissimilarities.h" +#include "plumed/matrixtools/MatrixProduct.h" +#include "plumed/core/ActionRegister.h" + +#include "ACCParallelTaskManager.h" + +namespace PLMD { +namespace matrixtools { + +typedef MatrixTimesMatrix mtimes; +PLUMED_REGISTER_ACTION(mtimes,"MATRIX_PRODUCT_ACC") +typedef MatrixTimesMatrix dissims; +PLUMED_REGISTER_ACTION(dissims,"DISSIMILARITIES_ACC") + +} +} diff --git a/plugins/openaccPTM/MatrixTimesVectorBase.cpp b/plugins/openaccPTM/MatrixTimesVectorBase.cpp new file mode 100644 index 0000000000..935915387c --- /dev/null +++ b/plugins/openaccPTM/MatrixTimesVectorBase.cpp @@ -0,0 +1,35 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/matrixtools/MatrixTimesVectorBase.h" +#include "plumed/core/ActionRegister.h" + +#include "ACCParallelTaskManager.h" +namespace PLMD { +namespace matrixtools { +typedef MatrixTimesVectorBase,PLMD::ACCPTM> mycr; +PLUMED_REGISTER_ACTION(mycr,"MATRIX_VECTOR_PRODUCT_ROWSUMSACC") +typedef MatrixTimesVectorBase,PLMD::ACCPTM> mycp; +PLUMED_REGISTER_ACTION(mycp,"MATRIX_VECTOR_PRODUCT_PROPERACC") + + +} +} diff --git a/plugins/openaccPTM/MoreThan.cpp b/plugins/openaccPTM/MoreThan.cpp new file mode 100644 index 0000000000..42abb9dec2 --- /dev/null +++ b/plugins/openaccPTM/MoreThan.cpp @@ -0,0 +1,39 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2017 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/function/MoreThan.h" +#include "plumed/function/FunctionOfVector.h" +#include "plumed/function/FunctionOfMatrix.h" +#include "plumed/core/ActionRegister.h" + +#include "ACCParallelTaskManager.h" + +namespace PLMD { +namespace function { + + +typedef FunctionOfVector VectorMoreThan; +PLUMED_REGISTER_ACTION(VectorMoreThan,"MORE_THAN_VECTORACC") +typedef FunctionOfMatrix MatrixMoreThan; +PLUMED_REGISTER_ACTION(MatrixMoreThan,"MORE_THAN_MATRIXACC") + +} +} diff --git a/plugins/openaccPTM/Plane.cpp b/plugins/openaccPTM/Plane.cpp new file mode 100644 index 0000000000..d9bf70b781 --- /dev/null +++ b/plugins/openaccPTM/Plane.cpp @@ -0,0 +1,30 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/core/ActionRegister.h" +#include "plumed/colvar/MultiColvarTemplate.h" +#include "plumed/colvar/Plane.h" + +#include "ACCParallelTaskManager.h" + +typedef PLMD::colvar::MultiColvarTemplate,PLMD::ACCPTM> PlaneMultiAcc; + +PLUMED_REGISTER_ACTION(PlaneMultiAcc,"PLANE_VECTORACC") diff --git a/plugins/openaccPTM/Position.cpp b/plugins/openaccPTM/Position.cpp new file mode 100644 index 0000000000..f14f8ed5a4 --- /dev/null +++ b/plugins/openaccPTM/Position.cpp @@ -0,0 +1,30 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/core/ActionRegister.h" +#include "plumed/colvar/MultiColvarTemplate.h" +#include "plumed/colvar/Position.h" + +#include "ACCParallelTaskManager.h" + +typedef PLMD::colvar::MultiColvarTemplate,PLMD::ACCPTM> PositionMultiAcc; + +PLUMED_REGISTER_ACTION(PositionMultiAcc,"POSITION_VECTORACC") diff --git a/plugins/openaccPTM/SecondaryStructureDRMSD.cpp b/plugins/openaccPTM/SecondaryStructureDRMSD.cpp new file mode 100644 index 0000000000..32a0de05d1 --- /dev/null +++ b/plugins/openaccPTM/SecondaryStructureDRMSD.cpp @@ -0,0 +1,33 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2017-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/secondarystructure/SecondaryStructureDRMSD.h" +#include "plumed/core/ActionRegister.h" +#include "ACCParallelTaskManager.h" + +namespace PLMD { +namespace secondarystructure { + +typedef SecondaryStructureBase,PLMD::ACCPTM> colv; +PLUMED_REGISTER_ACTION(colv,"SECONDARY_STRUCTURE_DRMSD_ACC"); + +} +} diff --git a/plugins/openaccPTM/SphericalHarmonic.cpp b/plugins/openaccPTM/SphericalHarmonic.cpp new file mode 100644 index 0000000000..a5c9a5d15f --- /dev/null +++ b/plugins/openaccPTM/SphericalHarmonic.cpp @@ -0,0 +1,36 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2012-2017 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/symfunc/SphericalHarmonic.h" +#include "plumed/function/FunctionOfMatrix.h" +#include "plumed/core/ActionRegister.h" + +#include "ACCParallelTaskManager.h" + +namespace PLMD { +namespace symfunc { + +typedef function::FunctionOfMatrix MatrixSpHarm; +PLUMED_REGISTER_ACTION(MatrixSpHarm,"SPHERICAL_HARMONIC_MATRIXACC") + +} +} + diff --git a/plugins/openaccPTM/Torsion.cpp b/plugins/openaccPTM/Torsion.cpp new file mode 100644 index 0000000000..c49f0c9cbd --- /dev/null +++ b/plugins/openaccPTM/Torsion.cpp @@ -0,0 +1,30 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/core/ActionRegister.h" +#include "plumed/colvar/MultiColvarTemplate.h" +#include "plumed/colvar/Torsion.h" + +#include "ACCParallelTaskManager.h" + +typedef PLMD::colvar::MultiColvarTemplate,PLMD::ACCPTM> TorsionMultiAcc; + +PLUMED_REGISTER_ACTION(TorsionMultiAcc,"TORSION_VECTORACC") diff --git a/plugins/openaccPTM/VolumeAround.cpp b/plugins/openaccPTM/VolumeAround.cpp new file mode 100644 index 0000000000..f59c4cad01 --- /dev/null +++ b/plugins/openaccPTM/VolumeAround.cpp @@ -0,0 +1,31 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2013-2020 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/volumes/VolumeAround.h" +#include "plumed/core/ActionRegister.h" + +#include "ACCParallelTaskManager.h" +namespace PLMD { +namespace volumes { +typedef ActionVolume Vola; +PLUMED_REGISTER_ACTION(Vola,"AROUND_ACC") +} +} diff --git a/plugins/openaccPTM/VolumeInCylinder.cpp b/plugins/openaccPTM/VolumeInCylinder.cpp new file mode 100644 index 0000000000..c3d0bf46ed --- /dev/null +++ b/plugins/openaccPTM/VolumeInCylinder.cpp @@ -0,0 +1,36 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2015-2020 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/volumes/VolumeInCylinder.h" +#include "plumed/volumes/ActionVolume.h" +#include "plumed/core/ActionRegister.h" + +#include "ACCParallelTaskManager.h" + +namespace PLMD { +namespace volumes { + + +typedef ActionVolume Volc; +PLUMED_REGISTER_ACTION(Volc,"INCYLINDER_ACC") + +} +} diff --git a/plugins/openaccPTM/VolumeInSphere.cpp b/plugins/openaccPTM/VolumeInSphere.cpp new file mode 100644 index 0000000000..d700a910f1 --- /dev/null +++ b/plugins/openaccPTM/VolumeInSphere.cpp @@ -0,0 +1,33 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2015-2020 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "plumed/volumes/VolumeInSphere.h" +#include "plumed/volumes/VolumeShortcut.h" +#include "plumed/core/ActionRegister.h" + +#include "ACCParallelTaskManager.h" +namespace PLMD { +namespace volumes { + +typedef ActionVolume Vols; +PLUMED_REGISTER_ACTION(Vols,"INSPHERE_ACC") +} // namespace PLMD +} // namespace volumes diff --git a/plugins/openaccPTM/configure.sh b/plugins/openaccPTM/configure.sh new file mode 100755 index 0000000000..09ebb2b162 --- /dev/null +++ b/plugins/openaccPTM/configure.sh @@ -0,0 +1,32 @@ +#! /usr/bin/env bash + +if [[ -z $PLUMED_KERNEL ]]; then + echo "$(basename $0) can work only if \"PLUMED_KERNEL\" is defined" + echo "either via module load or sourceme.sh" +fi + +{ + plumed config makefile_conf + echo "PLUMED_INCLUDE=-I$(plumed info --include-dir)" + echo "PLUMED_KERNEL=-L${PLUMED_KERNEL}" +} >Make.tmp + +#pendantic adds a unuseful FOR EACH line with +#"" warning: style of line directive is a GCC extension" +{ + # grep CXXFLAGS Make.tmp \ + # | sed -e 's/-f/-Xcompiler -f/g' \ + # -e 's/-pedantic//g' \ + # -e 's/-W/-Xcompiler -W/g' + # grep -eDYNAMIC_LIBS -eLDFLAGS Make.tmp \ + # | sed -e 's/-rdynamic/-Xcompiler -rdynamic/g' \ + # -e 's/-Wl,/-Xlinker /g' \ + # -e 's/-f/-Xcompiler -f/g' + # #prints the rest of the file + # grep -eDYNAMIC_LIBS -eLDFLAGS -eCXXFLAGS Make.tmp -v + sed -e 's/-fno-gnu-unique//g' -e 's/-Wno-unknown-pragmas//g' \ + -e 's/ -Wno-unknown-pragmas//g' \ + Make.tmp +} >Makefile.conf + +rm Make.tmp diff --git a/plugins/openaccPTM/module.type b/plugins/openaccPTM/module.type new file mode 100644 index 0000000000..e69de29bb2 diff --git a/plugins/openaccPTM/plumed b/plugins/openaccPTM/plumed new file mode 120000 index 0000000000..929cb3dc9b --- /dev/null +++ b/plugins/openaccPTM/plumed @@ -0,0 +1 @@ +../../src \ No newline at end of file diff --git a/plugins/openaccPTM/regtest/.gitignore b/plugins/openaccPTM/regtest/.gitignore new file mode 100644 index 0000000000..1774e730ac --- /dev/null +++ b/plugins/openaccPTM/regtest/.gitignore @@ -0,0 +1,2 @@ +tmp +report.txt diff --git a/plugins/openaccPTM/regtest/Makefile b/plugins/openaccPTM/regtest/Makefile new file mode 120000 index 0000000000..c99f3d3431 --- /dev/null +++ b/plugins/openaccPTM/regtest/Makefile @@ -0,0 +1 @@ +../../../regtest/Makefile \ No newline at end of file diff --git a/plugins/openaccPTM/regtest/scripts b/plugins/openaccPTM/regtest/scripts new file mode 120000 index 0000000000..efaa4c5613 --- /dev/null +++ b/plugins/openaccPTM/regtest/scripts @@ -0,0 +1 @@ +../../../regtest/scripts \ No newline at end of file diff --git a/plugins/openaccPTM/regtest/targetGPU/Makefile b/plugins/openaccPTM/regtest/targetGPU/Makefile new file mode 100644 index 0000000000..42480767ae --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/Makefile @@ -0,0 +1,2 @@ +include ../scripts/module.make + diff --git a/regtest/targetGPU/rt-GPU-DISTANCE/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/Makefile similarity index 100% rename from regtest/targetGPU/rt-GPU-DISTANCE/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/Makefile diff --git a/regtest/targetGPU/rt-GPU-DISTANCE/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-DISTANCE/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/colvar.reference diff --git a/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/config b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/config similarity index 73% rename from regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/config rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/config index 63c2256362..be65c62ebc 100644 --- a/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/config +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/config @@ -1,8 +1,7 @@ type=driver -plumed_modules=adjmat -plumed_needs=openacc +#plumed_modules=adjmat # this is to test a different name arg="--plumed plumed.dat --ixyz isomers.xyz --dump-forces forces --dump-forces-fmt=%8.4f" # --debug-forces forces.num" extra_files="../../trajectories/isomers.xyz" -#export NVCOMPILER_ACC_NOTIFY=31 \ No newline at end of file +#export NVCOMPILER_ACC_NOTIFY=31 diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/diff.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/diff.reference new file mode 100644 index 0000000000..7710dbd875 --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/diff.reference @@ -0,0 +1,18 @@ +#! FIELDS time diff_x.1 diff_x.2 diff_x.3 diff_x.4 diff_y.1 diff_y.2 diff_y.3 diff_y.4 diff_z.1 diff_z.2 diff_z.3 diff_z.4 + 0.000000 -0.0000 -0.0000 -0.0000 0.0000 -0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 + 1.000000 -0.0000 0.0000 -0.0000 -0.0000 0.0000 -0.0000 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 + 2.000000 -0.0000 -0.0000 0.0000 -0.0000 -0.0000 0.0000 -0.0000 0.0000 -0.0000 -0.0000 0.0000 0.0000 + 3.000000 -0.0000 0.0000 -0.0000 -0.0000 -0.0000 -0.0000 -0.0000 0.0000 -0.0000 0.0000 -0.0000 -0.0000 + 4.000000 0.0000 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 0.0000 -0.0000 0.0000 0.0000 0.0000 + 5.000000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 -0.0000 0.0000 -0.0000 -0.0000 0.0000 0.0000 + 6.000000 0.0000 -0.0000 -0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 -0.0000 0.0000 -0.0000 -0.0000 + 7.000000 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000 -0.0000 -0.0000 0.0000 -0.0000 -0.0000 + 8.000000 -0.0000 -0.0000 0.0000 0.0000 0.0000 -0.0000 0.0000 0.0000 -0.0000 -0.0000 0.0000 0.0000 + 9.000000 0.0000 0.0000 -0.0000 0.0000 -0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000 0.0000 0.0000 + 10.000000 -0.0000 -0.0000 -0.0000 0.0000 0.0000 -0.0000 0.0000 -0.0000 0.0000 -0.0000 -0.0000 -0.0000 + 11.000000 -0.0000 -0.0000 -0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 + 12.000000 0.0000 0.0000 -0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000 -0.0000 -0.0000 0.0000 + 13.000000 -0.0000 -0.0000 -0.0000 0.0000 -0.0000 -0.0000 -0.0000 -0.0000 0.0000 0.0000 -0.0000 0.0000 + 14.000000 0.0000 0.0000 0.0000 0.0000 0.0000 -0.0000 -0.0000 0.0000 0.0000 -0.0000 0.0000 -0.0000 + 15.000000 -0.0000 0.0000 -0.0000 -0.0000 -0.0000 0.0000 -0.0000 -0.0000 0.0000 -0.0000 -0.0000 -0.0000 + 16.000000 0.0000 0.0000 0.0000 -0.0000 -0.0000 0.0000 0.0000 -0.0000 -0.0000 -0.0000 -0.0000 0.0000 diff --git a/regtest/targetGPU/rt-GPU-DISTANCE/dists.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/dists.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-DISTANCE/dists.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/dists.reference diff --git a/regtest/targetGPU/rt-GPU-DISTANCE/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/forces.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-DISTANCE/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/forces.reference diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/plumed.dat new file mode 100644 index 0000000000..3e97668424 --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-DISTANCE/plumed.dat @@ -0,0 +1,15 @@ +LOAD FILE=../../../../plumedOpenACC.so +#original test was 3 task of 3 components, this is 4 task of 3 componets, so I can manage better where the 3 comes from + +d1cpu: DISTANCE COMPONENTS ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 ATOMS4=1,6 +d1: DISTANCE USEGPU COMPONENTS ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 ATOMS4=1,6 +v: VSTACK ARG=d1.x,d1.y,d1.z +vT: TRANSPOSE ARG=v +s: SUM ARG=vT PERIODIC=NO +diff_x: CUSTOM ARG=d1.x,d1cpu.x FUNC=y-x PERIODIC=NO +diff_y: CUSTOM ARG=d1.y,d1cpu.y FUNC=y-x PERIODIC=NO +diff_z: CUSTOM ARG=d1.z,d1cpu.z FUNC=y-x PERIODIC=NO +PRINT ARG=diff_x,diff_y,diff_z FILE=diff FMT=%8.4f +PRINT ARG=d1.* FILE=dists FMT=%8.4f +PRINT ARG=s FILE=colvar FMT=%8.4f +BIASVALUE ARG=s diff --git a/regtest/targetGPU/rt-GPU-PLANE-bias/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-PLANE-bias/Makefile similarity index 100% rename from regtest/targetGPU/rt-GPU-PLANE-bias/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-PLANE-bias/Makefile diff --git a/regtest/targetGPU/rt-GPU-PLANE-bias/config b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-PLANE-bias/config similarity index 80% rename from regtest/targetGPU/rt-GPU-PLANE-bias/config rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-PLANE-bias/config index 6fdf46b014..f97288130a 100644 --- a/regtest/targetGPU/rt-GPU-PLANE-bias/config +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-PLANE-bias/config @@ -1,7 +1,6 @@ type=driver # this is to test a different name -plumed_needs=openacc arg="--plumed plumed.dat --ixyz isomers.xyz --dump-forces forces --dump-forces-fmt=%8.4f" # --debug-forces forces.num" extra_files="../../trajectories/isomers.xyz" -#export NVCOMPILER_ACC_NOTIFY=31 \ No newline at end of file +#export NVCOMPILER_ACC_NOTIFY=31 diff --git a/regtest/targetGPU/rt-GPU-PLANE-bias/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-PLANE-bias/forces.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-PLANE-bias/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-PLANE-bias/forces.reference diff --git a/regtest/targetGPU/rt-GPU-PLANE-bias/planes.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-PLANE-bias/planes.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-PLANE-bias/planes.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-PLANE-bias/planes.reference diff --git a/regtest/targetGPU/rt-GPU-PLANE-bias/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-PLANE-bias/plumed.dat similarity index 77% rename from regtest/targetGPU/rt-GPU-PLANE-bias/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-PLANE-bias/plumed.dat index 4aed89d401..ca707aa1fd 100644 --- a/regtest/targetGPU/rt-GPU-PLANE-bias/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-PLANE-bias/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so plns: PLANE ATOMS1=1,2,3 ATOMS2=2,3,4 ATOMS3=3,4,5 ATOMS4=4,5,6 USEGPU PRINT ARG=plns.* FILE=planes FMT=%8.4f diff --git a/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/Makefile similarity index 100% rename from regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/Makefile diff --git a/regtest/targetGPU/rt-GPU-DISTANCE/config b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/config similarity index 73% rename from regtest/targetGPU/rt-GPU-DISTANCE/config rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/config index 63c2256362..f97288130a 100644 --- a/regtest/targetGPU/rt-GPU-DISTANCE/config +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/config @@ -1,8 +1,6 @@ type=driver -plumed_modules=adjmat -plumed_needs=openacc # this is to test a different name arg="--plumed plumed.dat --ixyz isomers.xyz --dump-forces forces --dump-forces-fmt=%8.4f" # --debug-forces forces.num" extra_files="../../trajectories/isomers.xyz" -#export NVCOMPILER_ACC_NOTIFY=31 \ No newline at end of file +#export NVCOMPILER_ACC_NOTIFY=31 diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/diff.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/diff.reference new file mode 100644 index 0000000000..cbf54ebe76 --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/diff.reference @@ -0,0 +1,20 @@ +#! FIELDS time diff.1 diff.2 diff.3 diff.4 +#! SET min_diff -pi +#! SET max_diff pi + 0.000000 -0.0000 0.0000 0.0000 -0.0000 + 1.000000 -0.0000 0.0000 0.0000 0.0000 + 2.000000 0.0000 -0.0000 -0.0000 -0.0000 + 3.000000 -0.0000 -0.0000 0.0000 -0.0000 + 4.000000 0.0000 0.0000 -0.0000 0.0000 + 5.000000 -0.0000 0.0000 0.0000 -0.0000 + 6.000000 0.0000 -0.0000 -0.0000 -0.0000 + 7.000000 -0.0000 0.0000 0.0000 -0.0000 + 8.000000 -0.0000 0.0000 0.0000 -0.0000 + 9.000000 -0.0000 -0.0000 0.0000 0.0000 + 10.000000 -0.0000 0.0000 0.0000 0.0000 + 11.000000 0.0000 0.0000 -0.0000 0.0000 + 12.000000 -0.0000 -0.0000 0.0000 0.0000 + 13.000000 0.0000 -0.0000 0.0000 0.0000 + 14.000000 -0.0000 -0.0000 0.0000 0.0000 + 15.000000 -0.0000 -0.0000 0.0000 0.0000 + 16.000000 0.0000 0.0000 -0.0000 -0.0000 diff --git a/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/forces.reference similarity index 54% rename from regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/forces.reference index 19f5db1db7..eab1e53f5c 100644 --- a/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/forces.reference +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/forces.reference @@ -1,11 +1,11 @@ 14 - -0.0290 0.1212 -0.0923 -X 0.1006 1.5995 -0.1145 -X -0.1319 -1.2124 0.1541 -X 0.0524 0.8326 -0.0311 -X -0.0169 -0.8257 -0.0295 -X 0.0128 1.2690 -0.0084 -X -0.0171 -1.6630 0.0293 + -0.0000 -0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X -0.0000 0.0000 0.0000 +X 0.0000 0.0000 -0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -15,13 +15,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - 0.0785 -0.0331 -0.0454 -X 0.2158 1.3049 -0.9419 -X -0.1537 -0.9743 0.6638 -X 0.1086 0.6284 -0.4659 -X -0.1125 -0.6577 0.5264 -X 0.2144 0.9642 -0.7501 -X -0.2725 -1.2656 0.9678 + -0.0000 0.0000 -0.0000 +X 0.0000 -0.0000 0.0000 +X -0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X 0.0000 0.0000 -0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -31,13 +31,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - -0.3511 0.2909 0.0603 -X 0.4188 1.4836 -0.6721 -X -0.2839 -0.9001 0.3353 -X -0.0423 0.6835 -0.3062 -X -0.0994 -0.9064 0.6462 -X 0.1886 1.0002 -1.1852 -X -0.1816 -1.3608 1.1820 + 0.0000 0.0000 0.0000 +X -0.0000 0.0000 -0.0000 +X 0.0000 0.0000 0.0000 +X 0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 0.0000 +X -0.0000 -0.0000 0.0000 +X -0.0000 0.0000 -0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -47,13 +47,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - 0.3706 -1.0189 0.6483 -X 0.2307 1.4725 -0.5202 -X -0.2011 -1.3333 0.5600 -X 0.2789 0.6681 -0.1430 -X -0.3780 -0.7172 0.0903 -X 0.8866 1.1315 0.1918 -X -0.8171 -1.2217 -0.1789 + 0.0000 -0.0000 0.0000 +X 0.0000 -0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X -0.0000 0.0000 0.0000 +X -0.0000 -0.0000 0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 -0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -63,13 +63,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - 0.4326 -1.0978 0.6652 -X 0.1811 1.5460 -0.6850 -X -0.1781 -1.6765 0.8279 -X 0.3207 0.9242 -0.3230 -X -0.3594 -0.6699 0.1941 -X 0.8989 1.0411 0.1193 -X -0.8632 -1.1649 -0.1333 + -0.0000 0.0000 -0.0000 +X 0.0000 -0.0000 0.0000 +X -0.0000 0.0000 -0.0000 +X 0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X 0.0000 0.0000 -0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -79,13 +79,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - -0.0008 0.0008 0.0000 -X -0.5075 1.6222 0.0002 -X 0.2428 -0.7767 -0.0001 -X 0.4892 -1.5668 -0.0002 -X -0.0019 0.0084 0.0000 -X -0.6202 1.9870 0.0003 -X 0.3977 -1.2740 -0.0002 + 0.0000 -0.0000 0.0000 +X -0.0000 -0.0000 0.0000 +X 0.0000 -0.0000 -0.0000 +X 0.0000 -0.0000 0.0000 +X 0.0000 -0.0000 0.0000 +X -0.0000 0.0000 0.0000 +X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -95,13 +95,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - -0.1510 0.3674 -0.2163 -X -1.0194 1.3928 0.9151 -X 0.5310 -0.7944 -0.4920 -X -0.4694 0.4567 0.4297 -X 0.6484 -0.5638 -0.9757 -X 1.0320 -0.8043 -0.7424 -X -0.7225 0.3129 0.8653 + -0.0000 -0.0000 -0.0000 +X 0.0000 -0.0000 -0.0000 +X -0.0000 0.0000 0.0000 +X 0.0000 -0.0000 0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X -0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -111,13 +111,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - -0.5645 -0.0111 0.5755 -X -0.5835 0.6844 0.9123 -X 0.8234 -0.9086 -0.4350 -X 0.2753 0.3739 0.9490 -X -0.4685 0.2937 -0.9094 -X -0.1809 -1.2291 -0.0613 -X 0.1341 0.7857 -0.4557 + 0.0000 -0.0000 0.0000 +X 0.0000 -0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 0.0000 +X -0.0000 -0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -127,13 +127,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - 0.6866 0.2955 -0.9821 -X -1.1139 0.2655 1.2948 -X 0.6793 -0.1844 -0.0713 -X -0.4537 0.1030 0.5161 -X 0.3366 -0.0925 -0.4063 -X 0.5421 0.0650 -0.3531 -X 0.0096 -0.1567 -0.9800 + -0.0000 0.0000 -0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X -0.0000 0.0000 0.0000 +X 0.0000 -0.0000 -0.0000 +X -0.0000 0.0000 -0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -143,13 +143,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - 0.5502 0.4314 -0.9816 -X -0.4701 -0.2929 1.6608 -X 0.3111 0.1111 -0.6959 -X -0.1757 -0.1174 0.6634 -X 0.1374 -0.0873 -0.9179 -X 0.2751 0.4587 0.1799 -X -0.0777 -0.0722 -0.8903 + 0.0000 -0.0000 -0.0000 +X 0.0000 -0.0000 0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -159,13 +159,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - -0.0001 0.0000 0.0001 -X -0.6213 1.5536 0.6698 -X 0.2343 -0.5859 -0.2526 -X -0.2409 0.6023 0.2596 -X 0.4195 -1.0491 -0.4521 -X -0.1414 0.3538 0.1524 -X 0.3497 -0.8747 -0.3770 + -0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 0.0000 0.0000 +X -0.0000 -0.0000 0.0000 +X 0.0000 -0.0000 -0.0000 +X -0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -176,12 +176,12 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 0.0000 0.0000 0.0000 -X 0.0000 -3.1362 0.0000 -X 0.0000 1.4635 0.0000 -X 0.0000 1.0361 0.0000 -X 0.0000 31.2032 0.0000 -X 0.0000 -62.8267 0.0000 -X 0.0000 32.2602 0.0000 +X 0.0000 0.0000 0.0000 +X 0.0000 -0.0000 0.0000 +X 0.0000 -0.0000 0.0000 +X 0.0000 -0.0001 0.0000 +X 0.0000 0.0001 0.0000 +X 0.0000 -0.0001 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -191,13 +191,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - 0.0097 0.0756 -0.0853 -X 0.4533 -0.3424 1.8456 -X 0.6530 -0.7103 2.1238 -X 0.1838 -0.1365 0.7451 -X -0.1007 0.0742 -0.4144 -X -0.5683 0.5126 -2.1123 -X -0.6212 0.6024 -2.1879 + 0.0000 0.0000 0.0000 +X 0.0000 0.0000 0.0000 +X -0.0000 0.0000 0.0000 +X -0.0000 0.0000 -0.0000 +X 0.0000 -0.0000 0.0000 +X 0.0000 0.0000 -0.0000 +X 0.0000 -0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -207,13 +207,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - -0.0009 -0.0002 0.0012 -X -0.0009 0.0092 1.7670 -X -0.0011 0.0167 2.8515 -X -0.0001 0.0037 0.6931 -X 0.0000 -0.0018 -0.2743 -X 0.0007 -0.0129 -2.3673 -X 0.0013 -0.0149 -2.6699 + -0.0000 -0.0000 0.0000 +X 0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 -0.0000 +X 0.0000 0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X -0.0000 0.0000 0.0000 +X 0.0000 -0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -223,13 +223,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - 0.6007 0.2090 -0.8097 -X -0.8209 0.0098 1.7049 -X 0.7935 -1.0465 -0.2523 -X -0.3154 0.0155 0.6608 -X 0.2265 -0.0078 -0.3634 -X 0.3498 0.3172 -1.0656 -X -0.2335 0.7117 -0.6843 + 0.0000 -0.0000 0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 0.0000 0.0000 +X 0.0000 0.0000 -0.0000 +X 0.0000 0.0000 0.0000 +X -0.0000 -0.0000 0.0000 +X 0.0000 -0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -240,12 +240,12 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 0.0000 -0.0000 -0.0000 -X 0.0052 -0.0409 -1.6635 -X -0.0038 0.0302 1.2264 -X 0.0025 -0.0197 -0.7995 -X -0.0026 0.0203 0.8268 -X 0.0038 -0.0297 -1.2056 -X -0.0050 0.0397 1.6155 +X -0.0000 0.0000 -0.0000 +X -0.0000 0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X -0.0000 0.0000 0.0000 +X 0.0000 -0.0000 -0.0000 +X -0.0000 0.0000 -0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 @@ -255,13 +255,13 @@ X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 14 - -0.0131 0.0912 -0.0781 -X -0.9206 0.4456 -0.5210 -X 0.7036 0.0588 0.7675 -X -0.1849 0.6894 -0.2128 -X 0.1348 -0.7273 -0.1915 -X -0.5138 0.0289 0.8430 -X 0.7809 -0.4955 -0.6852 + -0.0000 0.0000 -0.0000 +X 0.0000 -0.0000 0.0000 +X -0.0000 0.0000 -0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X 0.0000 -0.0000 -0.0000 +X -0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 X 0.0000 0.0000 0.0000 diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/plumed.dat new file mode 100644 index 0000000000..c0ff4d9ddf --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/plumed.dat @@ -0,0 +1,11 @@ +LOAD FILE=../../../../plumedOpenACC.so +trs_cpu: TORSION ATOMS1=1,2,3,4 ATOMS2=3,4,5,6 ATOMS3=2,3,4,5 ATOMS4=1,2,5,6 +trs: TORSION ATOMS1=1,2,3,4 ATOMS2=3,4,5,6 ATOMS3=2,3,4,5 ATOMS4=1,2,5,6 USEGPU + +diff: CUSTOM ARG=trs,trs_cpu FUNC=y-x PERIODIC=-pi,pi +PRINT ARG=diff FILE=diff FMT=%8.4f +#note that if TORSION is compiled in floating precision the test will give some periodicity errors (namely -pi instead of pi and vice versa) +s: SUM ARG=diff PERIODIC=-pi,pi +PRINT ARG=diff FILE=tors FMT=%8.4f +PRINT ARG=s FILE=colvar FMT=%8.4f +BIASVALUE ARG=s diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/tors.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/tors.reference new file mode 100644 index 0000000000..cbf54ebe76 --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/tors.reference @@ -0,0 +1,20 @@ +#! FIELDS time diff.1 diff.2 diff.3 diff.4 +#! SET min_diff -pi +#! SET max_diff pi + 0.000000 -0.0000 0.0000 0.0000 -0.0000 + 1.000000 -0.0000 0.0000 0.0000 0.0000 + 2.000000 0.0000 -0.0000 -0.0000 -0.0000 + 3.000000 -0.0000 -0.0000 0.0000 -0.0000 + 4.000000 0.0000 0.0000 -0.0000 0.0000 + 5.000000 -0.0000 0.0000 0.0000 -0.0000 + 6.000000 0.0000 -0.0000 -0.0000 -0.0000 + 7.000000 -0.0000 0.0000 0.0000 -0.0000 + 8.000000 -0.0000 0.0000 0.0000 -0.0000 + 9.000000 -0.0000 -0.0000 0.0000 0.0000 + 10.000000 -0.0000 0.0000 0.0000 0.0000 + 11.000000 0.0000 0.0000 -0.0000 0.0000 + 12.000000 -0.0000 -0.0000 0.0000 0.0000 + 13.000000 0.0000 -0.0000 0.0000 0.0000 + 14.000000 -0.0000 -0.0000 0.0000 0.0000 + 15.000000 -0.0000 -0.0000 0.0000 0.0000 + 16.000000 0.0000 0.0000 -0.0000 -0.0000 diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/Makefile similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/Makefile diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/angles.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/angles.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/angles.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/angles.reference diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/cdipoles.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/cdipoles.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/cdipoles.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/cdipoles.reference diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/cdists.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/cdists.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/cdists.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/cdists.reference diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/config b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/config similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/config rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/config diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/ctorsions.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/ctorsions.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/ctorsions.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/ctorsions.reference diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/ctorsions2.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/ctorsions2.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/ctorsions2.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/ctorsions2.reference diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/dipoles.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/dipoles.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/dipoles.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/dipoles.reference diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/dists.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/dists.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/dists.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/dists.reference diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/plumed.dat similarity index 98% rename from regtest/targetGPU/rt-GPU-multicolvar-print/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/plumed.dat index 2a5aaf602f..16c6af1c08 100644 --- a/regtest/targetGPU/rt-GPU-multicolvar-print/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so d1: DISTANCE ATOMS=1,2 d2: DISTANCE ATOMS=3,4 d3: DISTANCE ATOMS=5,6 diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/pos.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/pos.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/pos.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/pos.reference diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/scdists.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/scdists.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/scdists.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/scdists.reference diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/spos.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/spos.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/spos.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/spos.reference diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/test.pdb b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/test.pdb similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/test.pdb rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/test.pdb diff --git a/regtest/targetGPU/rt-GPU-multicolvar-print/torsions.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/torsions.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-multicolvar-print/torsions.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-multicolvar-print/torsions.reference diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/Makefile similarity index 100% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/Makefile diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/colvar.reference diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/config b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/config similarity index 82% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/config rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/config index a539a80b0f..562c2a274c 100644 --- a/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/config +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/config @@ -1,5 +1,5 @@ type=driver -plumed_modules="adjmat crystdistrib" +plumed_modules="adjmat crystdistrib notImplemented" arg="--plumed plumed.dat --ixyz short.xyz --dump-forces forces --dump-forces-fmt=%8.4f" #--debug-forces=forces.num" extra_files="../../crystdistrib/rt-quaternion-bond-product-deriv/short.xyz" diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/forces.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/forces.reference diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/plumed.dat similarity index 95% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/plumed.dat index 33e95844cb..f38ff1b347 100644 --- a/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-deriv/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so quat: QUATERNION ATOMS1=1,2,3 ATOMS2=4,5,6 ATOMS3=7,8,9 ATOMS4=10,11,12 ATOMS5=13,14,15 ATOMS6=16,17,18 ATOMS7=19,20,21 ATOMS8=22,23,24 ATOMS9=25,26,27 ATOMS10=28,29,30 ATOMS11=31,32,33 ATOMS12=34,35,36 ATOMS13=37,38,39 ATOMS14=40,41,42 ATOMS15=43,44,45 ATOMS16=46,47,48 ATOMS17=49,50,51 ATOMS18=52,53,54 ATOMS19=55,56,57 ATOMS20=58,59,60 ATOMS21=61,62,63 ATOMS22=64,65,66 ATOMS23=67,68,69 ATOMS24=70,71,72 ATOMS25=73,74,75 c1: DISTANCE_MATRIX GROUP=1,4,7,10,13,16,19,22,25,28,31,34,37,40,43,46,49,52,55,58,61,64,67,70,73 CUTOFF=100.0 COMPONENTS diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/Makefile similarity index 100% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product-only/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/Makefile diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product-only/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/colvar.reference diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/config b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/config similarity index 84% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product-only/config rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/config index 4f006d22d5..10ef3b597f 100644 --- a/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/config +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/config @@ -1,5 +1,5 @@ type=driver -plumed_modules="adjmat crystdistrib" +plumed_modules="adjmat crystdistrib notImplemented" arg="--plumed plumed.dat --ixyz small.xyz --timestep=0.001 --trajectory-stride=25 --dump-forces forces --dump-forces-fmt=%8.4f" # --debug-forces=forces.num" extra_files="../../crystdistrib/rt-quaternion-bond-product-only/small.xyz" diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/forces.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product-only/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/forces.reference diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/plumed.dat similarity index 92% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product-only/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/plumed.dat index e388f89820..f3c385502a 100644 --- a/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product-only/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so quat: QUATERNION ATOMS1=1,2,3 ATOMS2=4,5,6 ATOMS3=7,8,9 c1: DISTANCE_MATRIX GROUP=1,4,7 CUTOFF=100.0 COMPONENTS qp: QUATERNION_BOND_PRODUCT_MATRIX ARG=quat.*,c1.* USEGPU diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product/Makefile similarity index 100% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product/Makefile diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product/colvar.reference diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product/config b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product/config similarity index 84% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product/config rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product/config index 5213556460..0f1b56ecc6 100644 --- a/regtest/targetGPU/rt-GPU-quaternion-bond-product/config +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product/config @@ -1,5 +1,5 @@ type=driver -plumed_modules="adjmat crystdistrib" +plumed_modules="adjmat crystdistrib notimplemented" arg="--plumed plumed.dat --ixyz small.xyz --timestep=0.001 --trajectory-stride=25 --dump-forces forces --dump-forces-fmt=%8.4f" # --debug-forces=forces.num" extra_files="../../crystdistrib/rt-quaternion-bond-product/small.xyz" diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product/forces.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product/forces.reference diff --git a/regtest/targetGPU/rt-GPU-quaternion-bond-product/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product/plumed.dat similarity index 90% rename from regtest/targetGPU/rt-GPU-quaternion-bond-product/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product/plumed.dat index b905997bee..047904732d 100644 --- a/regtest/targetGPU/rt-GPU-quaternion-bond-product/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-quaternion-bond-product/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so quat: QUATERNION ATOMS1=1,2,3 ATOMS2=4,5,6 ATOMS3=7,8,9 c1: DISTANCE_MATRIX GROUP=1,4,7 CUTOFF=100.0 COMPONENTS qp: QUATERNION_BOND_PRODUCT_MATRIX ARG=quat.*,c1.* USEGPU diff --git a/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/Makefile similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/Makefile diff --git a/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/ala12_trajectory.xyz b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/ala12_trajectory.xyz similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/ala12_trajectory.xyz rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/ala12_trajectory.xyz diff --git a/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/colvar.reference diff --git a/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/colvar10.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/colvar10.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/colvar10.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/colvar10.reference diff --git a/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/config b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/config similarity index 82% rename from regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/config rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/config index 64ee15151e..5079009dfd 100644 --- a/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/config +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/config @@ -1,4 +1,4 @@ type=driver arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f" -export NVCOMPILER_ACC_NOTIFY=31 +#export NVCOMPILER_ACC_NOTIFY=31 diff --git a/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/forces.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/forces.reference diff --git a/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/helix.pdb b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/helix.pdb similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/helix.pdb rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/helix.pdb diff --git a/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/plumed.dat similarity index 96% rename from regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/plumed.dat index 2a2bf529dc..9b396f233b 100644 --- a/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure-DRMSD/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so MOLINFO STRUCTURE=helix.pdb ALPHARMSD RESIDUES=ALL TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=a USEGPU ANTIBETARMSD RESIDUES=all TYPE=DRMSD STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=b USEGPU diff --git a/regtest/targetGPU/rt-GPU-secondarystructure/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/Makefile similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/Makefile diff --git a/regtest/targetGPU/rt-GPU-secondarystructure/ala12_trajectory.xyz b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/ala12_trajectory.xyz similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure/ala12_trajectory.xyz rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/ala12_trajectory.xyz diff --git a/regtest/targetGPU/rt-GPU-secondarystructure/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/colvar.reference diff --git a/regtest/targetGPU/rt-GPU-secondarystructure/colvar10.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/colvar10.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure/colvar10.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/colvar10.reference diff --git a/regtest/targetGPU/rt-GPU-secondarystructure/config b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/config similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure/config rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/config diff --git a/regtest/targetGPU/rt-GPU-secondarystructure/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/forces.reference similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/forces.reference diff --git a/regtest/targetGPU/rt-GPU-secondarystructure/helix.pdb b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/helix.pdb similarity index 100% rename from regtest/targetGPU/rt-GPU-secondarystructure/helix.pdb rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/helix.pdb diff --git a/regtest/targetGPU/rt-GPU-secondarystructure/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/plumed.dat similarity index 95% rename from regtest/targetGPU/rt-GPU-secondarystructure/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/plumed.dat index de008a2ab1..afec80f2ba 100644 --- a/regtest/targetGPU/rt-GPU-secondarystructure/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-GPU-secondarystructure/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so MOLINFO STRUCTURE=helix.pdb ALPHARMSD RESIDUES=ALL TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=a USEGPU ANTIBETARMSD RESIDUES=all TYPE=DRMSD STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=b USEGPU diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/Makefile similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix-mtv/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/Makefile diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix-mtv/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/colvar.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/config b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/config similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix-mtv/config rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/config diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/diff.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/diff.reference new file mode 100644 index 0000000000..4bc27c962d --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/diff.reference @@ -0,0 +1,18 @@ +#! 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regtest/targetGPU/rt-adjmat-basic-matrix-mtv/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/plumed.dat index d3d24e3d08..1b7ed2a625 100644 --- a/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c1: CONTACT_MATRIX ... GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} @@ -6,9 +7,19 @@ PRINT ARG=c1 FILE=colvar FMT=%8.4f ones: ONES SIZE=7 cc: MATRIX_VECTOR_PRODUCT ARG=c1,ones USEGPU +cc_cpu: MATRIX_VECTOR_PRODUCT ARG=c1,ones PRINT ARG=cc FILE=coords FMT=%8.5f +diff: CUSTOM ARG=cc,cc_cpu PERIODIC=NO FUNC=y-x +print arg=diff file=diff + mtc: MORE_THAN ARG=cc SWITCH={RATIONAL D_0=3 R_0=1} s: SUM ARG=mtc PERIODIC=NO PRINT ARG=s FILE=fcolvar FMT=%8.5f BIASVALUE ARG=s + +mtc_cpu: MORE_THAN ARG=cc_cpu SWITCH={RATIONAL D_0=3 R_0=1} +s_cpu: SUM ARG=mtc_cpu PERIODIC=NO +inv: CUSTOM ARG=s_cpu FUNC=-x PERIODIC=NO +BIASVALUE ARG=inv + diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/Makefile similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/Makefile diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/colvar.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix/config b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/config similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix/config rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/config diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/coords.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/coords.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix-mtv/coords.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/coords.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix/fcolvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/fcolvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix/fcolvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/fcolvar.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix-mtv/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/forces.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix-mtv/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/forces.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix/isomers.xyz b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/isomers.xyz similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix/isomers.xyz rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/isomers.xyz diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/plumed.dat similarity index 89% rename from regtest/targetGPU/rt-adjmat-basic-matrix/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/plumed.dat index 7aa5ce18ef..5d232243e6 100644 --- a/regtest/targetGPU/rt-adjmat-basic-matrix/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c1: CONTACT_MATRIX ... GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix2/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/Makefile similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix2/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/Makefile diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix2/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix2/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/colvar.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix2/config b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/config similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix2/config rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/config diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix2/coords.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/coords.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix2/coords.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/coords.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix2/fcolvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/fcolvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix2/fcolvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/fcolvar.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix2/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/forces.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix2/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/forces.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix2/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/plumed.dat similarity index 90% rename from regtest/targetGPU/rt-adjmat-basic-matrix2/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/plumed.dat index f8a4d27c84..8b03fc368a 100644 --- a/regtest/targetGPU/rt-adjmat-basic-matrix2/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix2/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c1: CONTACT_MATRIX ... GROUPA=1-3 GROUPB=1-108 diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix3/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/Makefile similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix3/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/Makefile diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix3/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix3/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/colvar.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix3/config b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/config similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix3/config rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/config diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix3/coords.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/coords.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix3/coords.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/coords.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix3/fcolvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/fcolvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix3/fcolvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/fcolvar.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix3/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/forces.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix3/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/forces.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix3/gas-one.xyz b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/gas-one.xyz similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix3/gas-one.xyz rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/gas-one.xyz diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix3/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/plumed.dat similarity index 91% rename from regtest/targetGPU/rt-adjmat-basic-matrix3/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/plumed.dat index 1a3acb6084..561c2ead47 100644 --- a/regtest/targetGPU/rt-adjmat-basic-matrix3/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix3/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c1: CONTACT_MATRIX ... GROUPA=1-3 GROUPB=1-512 diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix4/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/Makefile similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix4/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/Makefile diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix4/cmcolvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/cmcolvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix4/cmcolvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/cmcolvar.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix4/config b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/config similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix4/config rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/config diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix4/fcolvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/fcolvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix4/fcolvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/fcolvar.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix4/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/forces.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix4/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/forces.reference diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix4/gas-one.xyz b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/gas-one.xyz similarity index 100% rename from regtest/targetGPU/rt-adjmat-basic-matrix4/gas-one.xyz rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/gas-one.xyz diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix4/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/plumed.dat similarity index 87% rename from regtest/targetGPU/rt-adjmat-basic-matrix4/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/plumed.dat index 9746f698ea..6d8ef7ca58 100644 --- a/regtest/targetGPU/rt-adjmat-basic-matrix4/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-basic-matrix4/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c1: CONTACT_MATRIX ... GROUPA=1-3 GROUPB=1-512 diff --git a/regtest/targetGPU/rt-adjmat-eigvals/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvals/Makefile similarity index 100% rename from regtest/targetGPU/rt-adjmat-eigvals/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvals/Makefile diff --git a/regtest/targetGPU/rt-adjmat-eigvals/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvals/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-eigvals/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvals/colvar.reference diff --git a/regtest/targetGPU/rt-adjmat-eigvals/config b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvals/config similarity index 100% rename from regtest/targetGPU/rt-adjmat-eigvals/config rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvals/config diff --git a/regtest/targetGPU/rt-adjmat-eigvals/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvals/forces.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-eigvals/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvals/forces.reference diff --git a/regtest/targetGPU/rt-adjmat-eigvals/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvals/plumed.dat similarity index 82% rename from regtest/targetGPU/rt-adjmat-eigvals/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvals/plumed.dat index 23de49783e..071352c277 100644 --- a/regtest/targetGPU/rt-adjmat-eigvals/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvals/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c1: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} USEGPU diag: DIAGONALIZE ARG=c1 VECTORS=1 PRINT ARG=diag.vals-1 FILE=colvar FMT=%8.4f diff --git a/regtest/targetGPU/rt-adjmat-eigvecs/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvecs/Makefile similarity index 100% rename from regtest/targetGPU/rt-adjmat-eigvecs/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvecs/Makefile diff --git a/regtest/targetGPU/rt-adjmat-eigvecs/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvecs/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-eigvecs/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvecs/colvar.reference diff --git a/regtest/targetGPU/rt-adjmat-eigvecs/config b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvecs/config similarity index 100% rename from regtest/targetGPU/rt-adjmat-eigvecs/config rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvecs/config diff --git a/regtest/targetGPU/rt-adjmat-eigvecs/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvecs/forces.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-eigvecs/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvecs/forces.reference diff --git a/regtest/targetGPU/rt-adjmat-eigvecs/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvecs/plumed.dat similarity index 93% rename from regtest/targetGPU/rt-adjmat-eigvecs/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvecs/plumed.dat index 66c1772156..f496dd7a89 100644 --- a/regtest/targetGPU/rt-adjmat-eigvecs/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-eigvecs/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c1: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} USEGPU diag: DIAGONALIZE ARG=c1 VECTORS=1 eigv1: SELECT_COMPONENTS ARG=diag.vecs-1 COMPONENTS=1 @@ -7,6 +8,6 @@ eigv4: SELECT_COMPONENTS ARG=diag.vecs-1 COMPONENTS=4 eigv5: SELECT_COMPONENTS ARG=diag.vecs-1 COMPONENTS=5 eigv6: SELECT_COMPONENTS ARG=diag.vecs-1 COMPONENTS=6 eigv7: SELECT_COMPONENTS ARG=diag.vecs-1 COMPONENTS=7 -cc: COMBINE ARG=eigv1,eigv2,eigv3,eigv4,eigv5,eigv6,eigv7 COEFFICIENTS=1,2,3,4,5,6,7 POWERS=2,2,3,4,3,2,1 PERIODIC=NO NORMALIZE USEGPU +cc: COMBINE ARG=eigv1,eigv2,eigv3,eigv4,eigv5,eigv6,eigv7 COEFFICIENTS=1,2,3,4,5,6,7 POWERS=2,2,3,4,3,2,1 PERIODIC=NO NORMALIZE USEGPU PRINT ARG=cc FILE=colvar FMT=%8.4f BIASVALUE ARG=cc diff --git a/regtest/targetGPU/rt-adjmat-join-eigvals/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvals/Makefile similarity index 100% rename from regtest/targetGPU/rt-adjmat-join-eigvals/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvals/Makefile diff --git a/regtest/targetGPU/rt-adjmat-join-eigvals/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvals/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-join-eigvals/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvals/colvar.reference diff --git a/regtest/targetGPU/rt-adjmat-join-eigvals/config b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvals/config similarity index 100% rename from regtest/targetGPU/rt-adjmat-join-eigvals/config rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvals/config diff --git a/regtest/targetGPU/rt-adjmat-join-eigvals/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvals/forces.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-join-eigvals/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvals/forces.reference diff --git a/regtest/targetGPU/rt-adjmat-join-eigvals/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvals/plumed.dat similarity index 91% rename from regtest/targetGPU/rt-adjmat-join-eigvals/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvals/plumed.dat index af572f8679..c9cfb35cf4 100644 --- a/regtest/targetGPU/rt-adjmat-join-eigvals/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvals/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c11: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} USEGPU c12: CONTACT_MATRIX GROUPA=1-7 GROUPB=8-14 SWITCH={RATIONAL R_0=2.2 NN=6 MM=12} USEGPU c21: TRANSPOSE ARG=c12 diff --git a/regtest/targetGPU/rt-adjmat-join-eigvecs/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvecs/Makefile similarity index 100% rename from regtest/targetGPU/rt-adjmat-join-eigvecs/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvecs/Makefile diff --git a/regtest/targetGPU/rt-adjmat-join-eigvecs/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvecs/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-join-eigvecs/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvecs/colvar.reference diff --git a/regtest/targetGPU/rt-adjmat-join-eigvecs/config b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvecs/config similarity index 100% rename from regtest/targetGPU/rt-adjmat-join-eigvecs/config rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvecs/config diff --git a/regtest/targetGPU/rt-adjmat-join-eigvecs/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvecs/forces.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-join-eigvecs/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvecs/forces.reference diff --git a/regtest/targetGPU/rt-adjmat-join-eigvecs/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvecs/plumed.dat similarity index 97% rename from regtest/targetGPU/rt-adjmat-join-eigvecs/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvecs/plumed.dat index bab317834a..be23a93a98 100644 --- a/regtest/targetGPU/rt-adjmat-join-eigvecs/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-join-eigvecs/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c11: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} USEGPU c12: CONTACT_MATRIX GROUPA=1-7 GROUPB=8-14 SWITCH={RATIONAL R_0=2.2 NN=6 MM=12} USEGPU c21: TRANSPOSE ARG=c12 diff --git a/regtest/targetGPU/rt-adjmat-matmult/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/Makefile similarity index 100% rename from regtest/targetGPU/rt-adjmat-matmult/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/Makefile diff --git a/regtest/targetGPU/rt-adjmat-matmult/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-matmult/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/colvar.reference diff --git a/regtest/targetGPU/rt-adjmat-matmult/config b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/config similarity index 100% rename from regtest/targetGPU/rt-adjmat-matmult/config rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/config diff --git a/regtest/targetGPU/rt-adjmat-matmult/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/forces.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-matmult/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/forces.reference diff --git a/regtest/targetGPU/rt-adjmat-matmult/isomers.xyz b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/isomers.xyz similarity index 100% rename from regtest/targetGPU/rt-adjmat-matmult/isomers.xyz rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/isomers.xyz diff --git a/regtest/targetGPU/rt-adjmat-matmult/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/plumed.dat similarity index 84% rename from regtest/targetGPU/rt-adjmat-matmult/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/plumed.dat index 5094e1d5f0..699edffa69 100644 --- a/regtest/targetGPU/rt-adjmat-matmult/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-matmult/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c1: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} c12: MATRIX_PRODUCT ARG=c1,c1 USEGPU diag: DIAGONALIZE ARG=c12 VECTORS=1 diff --git a/regtest/targetGPU/rt-adjmat-prod/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-prod/Makefile similarity index 100% rename from regtest/targetGPU/rt-adjmat-prod/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-prod/Makefile diff --git a/regtest/targetGPU/rt-adjmat-prod/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-prod/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-prod/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-prod/colvar.reference diff --git a/regtest/targetGPU/rt-adjmat-prod/config b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-prod/config similarity index 87% rename from regtest/targetGPU/rt-adjmat-prod/config rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-prod/config index f7cb2dce13..e95183481c 100644 --- a/regtest/targetGPU/rt-adjmat-prod/config +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-prod/config @@ -4,4 +4,4 @@ plumed_modules=adjmat arg="--plumed plumed.dat --ixyz isomers.xyz --dump-forces forces --dump-forces-fmt=%8.4f" # --debug-forces forces.num" extra_files="../../trajectories/isomers.xyz" -# export NVCOMPILER_ACC_NOTIFY=31 \ No newline at end of file +# export NVCOMPILER_ACC_NOTIFY=31 diff --git a/regtest/targetGPU/rt-adjmat-prod/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-prod/forces.reference similarity index 100% rename from regtest/targetGPU/rt-adjmat-prod/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-prod/forces.reference diff --git a/regtest/targetGPU/rt-adjmat-prod/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-prod/plumed.dat similarity index 89% rename from regtest/targetGPU/rt-adjmat-prod/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-adjmat-prod/plumed.dat index ae57b2c7f7..9ff0003334 100644 --- a/regtest/targetGPU/rt-adjmat-prod/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-adjmat-prod/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c1: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} USEGPU c2: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=3.2 NN=4 MM=8 } USEGPU prod: CUSTOM ARG=c1,c2 FUNC=x*y PERIODIC=NO diff --git a/regtest/targetGPU/rt-coordination-insphere-nochain/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere-nochain/Makefile similarity index 100% rename from regtest/targetGPU/rt-coordination-insphere-nochain/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere-nochain/Makefile diff --git a/regtest/targetGPU/rt-coordination-insphere-nochain/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere-nochain/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-coordination-insphere-nochain/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere-nochain/colvar.reference diff --git a/regtest/targetGPU/rt-coordination-insphere-nochain/config b/plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere-nochain/config similarity index 100% rename from regtest/targetGPU/rt-coordination-insphere-nochain/config rename to plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere-nochain/config diff --git a/regtest/targetGPU/rt-coordination-insphere-nochain/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere-nochain/forces.reference similarity index 100% rename from regtest/targetGPU/rt-coordination-insphere-nochain/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere-nochain/forces.reference diff --git a/regtest/targetGPU/rt-coordination-insphere-nochain/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere-nochain/plumed.dat similarity index 94% rename from regtest/targetGPU/rt-coordination-insphere-nochain/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere-nochain/plumed.dat index 4cb1733aa3..511f811c9e 100644 --- a/regtest/targetGPU/rt-coordination-insphere-nochain/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere-nochain/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so # Water oxygens: atoms 1-N with stride 4 (TIP4P geometry) ow: GROUP ATOMS=1-16500:4 diff --git a/regtest/targetGPU/rt-coordination-insphere/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere/Makefile similarity index 100% rename from regtest/targetGPU/rt-coordination-insphere/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere/Makefile diff --git a/regtest/targetGPU/rt-coordination-insphere/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-coordination-insphere/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere/colvar.reference diff --git a/regtest/targetGPU/rt-coordination-insphere/config b/plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere/config similarity index 100% rename from regtest/targetGPU/rt-coordination-insphere/config rename to plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere/config diff --git a/regtest/targetGPU/rt-coordination-insphere/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere/forces.reference similarity index 100% rename from regtest/targetGPU/rt-coordination-insphere/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere/forces.reference diff --git a/regtest/targetGPU/rt-coordination-insphere/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere/plumed.dat similarity index 94% rename from regtest/targetGPU/rt-coordination-insphere/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere/plumed.dat index e21da71002..1e211c19a0 100644 --- a/regtest/targetGPU/rt-coordination-insphere/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-coordination-insphere/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so # Water oxygens: atoms 1-N with stride 4 (TIP4P geometry) ow: GROUP ATOMS=1-16500:4 diff --git a/regtest/targetGPU/rt-cylinder/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-cylinder/Makefile similarity index 100% rename from regtest/targetGPU/rt-cylinder/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-cylinder/Makefile diff --git a/regtest/targetGPU/rt-cylinder/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-cylinder/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-cylinder/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-cylinder/colvar.reference diff --git a/regtest/targetGPU/rt-cylinder/config b/plugins/openaccPTM/regtest/targetGPU/rt-cylinder/config similarity index 100% rename from regtest/targetGPU/rt-cylinder/config rename to plugins/openaccPTM/regtest/targetGPU/rt-cylinder/config diff --git a/regtest/targetGPU/rt-cylinder/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-cylinder/forces.reference similarity index 100% rename from regtest/targetGPU/rt-cylinder/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-cylinder/forces.reference diff --git a/regtest/targetGPU/rt-cylinder/gentraj.cpp b/plugins/openaccPTM/regtest/targetGPU/rt-cylinder/gentraj.cpp similarity index 100% rename from regtest/targetGPU/rt-cylinder/gentraj.cpp rename to plugins/openaccPTM/regtest/targetGPU/rt-cylinder/gentraj.cpp diff --git a/regtest/targetGPU/rt-cylinder/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-cylinder/plumed.dat similarity index 87% rename from regtest/targetGPU/rt-cylinder/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-cylinder/plumed.dat index f5581d2d08..38497db56a 100644 --- a/regtest/targetGPU/rt-cylinder/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-cylinder/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c1: CENTER ATOMS=1-200 d2: INCYLINDER ATOMS=2-201 CENTER=c1 DIRECTION=Z RADIUS={TANH R_0=1.5} SIGMA=0.1 LOWER=-0.1 UPPER=0.1 SUM USEGPU diff --git a/regtest/targetGPU/rt-cylinder/trajectory.xyz b/plugins/openaccPTM/regtest/targetGPU/rt-cylinder/trajectory.xyz similarity index 100% rename from regtest/targetGPU/rt-cylinder/trajectory.xyz rename to plugins/openaccPTM/regtest/targetGPU/rt-cylinder/trajectory.xyz diff --git a/regtest/targetGPU/rt-landmarks-calc-dissims/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/Makefile similarity index 100% rename from regtest/targetGPU/rt-landmarks-calc-dissims/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/Makefile diff --git a/regtest/targetGPU/rt-landmarks-calc-dissims/analysis.1.mymatrix3.dat.reference b/plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/analysis.1.mymatrix3.dat.reference similarity index 100% rename from regtest/targetGPU/rt-landmarks-calc-dissims/analysis.1.mymatrix3.dat.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/analysis.1.mymatrix3.dat.reference diff --git a/regtest/targetGPU/rt-landmarks-calc-dissims/colv_in b/plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/colv_in similarity index 100% rename from regtest/targetGPU/rt-landmarks-calc-dissims/colv_in rename to plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/colv_in diff --git a/regtest/targetGPU/rt-landmarks-calc-dissims/config b/plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/config similarity index 100% rename from regtest/targetGPU/rt-landmarks-calc-dissims/config rename to plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/config diff --git a/regtest/targetGPU/rt-landmarks-calc-dissims/mymatrix.dat.reference b/plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/mymatrix.dat.reference similarity index 100% rename from regtest/targetGPU/rt-landmarks-calc-dissims/mymatrix.dat.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/mymatrix.dat.reference diff --git a/regtest/targetGPU/rt-landmarks-calc-dissims/mymatrix2.dat.reference b/plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/mymatrix2.dat.reference similarity index 100% rename from regtest/targetGPU/rt-landmarks-calc-dissims/mymatrix2.dat.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/mymatrix2.dat.reference diff --git a/regtest/targetGPU/rt-landmarks-calc-dissims/mymatrix3.dat.reference b/plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/mymatrix3.dat.reference similarity index 100% rename from regtest/targetGPU/rt-landmarks-calc-dissims/mymatrix3.dat.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/mymatrix3.dat.reference diff --git a/regtest/targetGPU/rt-landmarks-calc-dissims/output-fps.pdb.reference b/plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/output-fps.pdb.reference similarity index 100% rename from regtest/targetGPU/rt-landmarks-calc-dissims/output-fps.pdb.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/output-fps.pdb.reference diff --git a/regtest/targetGPU/rt-landmarks-calc-dissims/output-stride.pdb.reference b/plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/output-stride.pdb.reference similarity index 100% rename from regtest/targetGPU/rt-landmarks-calc-dissims/output-stride.pdb.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/output-stride.pdb.reference diff --git a/regtest/targetGPU/rt-landmarks-calc-dissims/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/plumed.dat similarity index 94% rename from regtest/targetGPU/rt-landmarks-calc-dissims/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/plumed.dat index 6f162118ff..273230a411 100644 --- a/regtest/targetGPU/rt-landmarks-calc-dissims/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-landmarks-calc-dissims/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so d1: READ FILE=colv_in VALUES=data ff: COLLECT_FRAMES ARG=d1 STRIDE=1 diff --git a/regtest/targetGPU/rt-multicolvar-filters/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-multicolvar-filters/Makefile similarity index 100% rename from regtest/targetGPU/rt-multicolvar-filters/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-multicolvar-filters/Makefile diff --git a/regtest/targetGPU/rt-multicolvar-filters/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-multicolvar-filters/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-multicolvar-filters/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-multicolvar-filters/colvar.reference diff --git a/regtest/targetGPU/rt-multicolvar-filters/config b/plugins/openaccPTM/regtest/targetGPU/rt-multicolvar-filters/config similarity index 100% rename from regtest/targetGPU/rt-multicolvar-filters/config rename to plugins/openaccPTM/regtest/targetGPU/rt-multicolvar-filters/config diff --git a/regtest/targetGPU/rt-multicolvar-filters/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-multicolvar-filters/forces.reference similarity index 100% rename from regtest/targetGPU/rt-multicolvar-filters/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-multicolvar-filters/forces.reference diff --git a/regtest/targetGPU/rt-multicolvar-filters/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-multicolvar-filters/plumed.dat similarity index 98% rename from regtest/targetGPU/rt-multicolvar-filters/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-multicolvar-filters/plumed.dat index 0377f989d9..12719d385b 100644 --- a/regtest/targetGPU/rt-multicolvar-filters/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-multicolvar-filters/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so d1: DISTANCE ... ATOMS1=1,2 ATOMS2=1,3 diff --git a/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/Makefile diff --git a/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/colvar_aq6.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/colvar_aq6.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/colvar_aq6.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/colvar_aq6.reference diff --git a/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/config similarity index 100% rename from regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/config diff --git a/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/forces.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/forces.reference diff --git a/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/plumed.dat similarity index 87% rename from regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/plumed.dat index fbb730dec8..8498d5eb86 100644 --- a/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so q6: Q6 SPECIES=1-500 SWITCH={RATIONAL R_0=0.01 D_0=0.415 D_MAX=0.45} MEAN USEGPU aq6: LOCAL_AVERAGE SPECIESA=q6 SPECIESB=q6 SWITCH={RATIONAL R_0=0.01 D_0=0.415 D_MAX=0.45} MEAN USEGPU diff --git a/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/traj_md-10.xyz b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/traj_md-10.xyz similarity index 100% rename from regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/traj_md-10.xyz rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6-spAspB/traj_md-10.xyz diff --git a/regtest/targetGPU/rt-symfunc-averaged-q6/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-averaged-q6/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/Makefile diff --git a/regtest/targetGPU/rt-symfunc-averaged-q6/colv.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/colv.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-averaged-q6/colv.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/colv.reference diff --git a/regtest/targetGPU/rt-symfunc-averaged-q6/colv3.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/colv3.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-averaged-q6/colv3.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/colv3.reference diff --git a/regtest/targetGPU/rt-symfunc-averaged-q6/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/config similarity index 100% rename from regtest/targetGPU/rt-symfunc-averaged-q6/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/config diff --git a/regtest/targetGPU/rt-symfunc-averaged-q6/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/forces.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-averaged-q6/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/forces.reference diff --git a/regtest/targetGPU/rt-symfunc-averaged-q6/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/plumed.dat similarity index 85% rename from regtest/targetGPU/rt-symfunc-averaged-q6/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/plumed.dat index 49f15ab8ef..81578593b7 100644 --- a/regtest/targetGPU/rt-symfunc-averaged-q6/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-averaged-q6/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MM=24 MEAN LABEL=q6 USEGPU PRINT ARG=q6.* FILE=colv diff --git a/regtest/targetGPU/rt-symfunc-nbonds-one-q6/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-nbonds-one-q6/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/Makefile diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/colv1.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/colv1.reference new file mode 100644 index 0000000000..d0cfe3c253 --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/colv1.reference @@ -0,0 +1,2 @@ +#! FIELDS time diff + 0.000000 -0.0000 diff --git a/regtest/targetGPU/rt-symfunc-nbonds-one-q6/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/config similarity index 100% rename from regtest/targetGPU/rt-symfunc-nbonds-one-q6/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/config diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/forces.reference new file mode 100644 index 0000000000..2e600497ca --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/forces.reference @@ -0,0 +1,66 @@ +64 + -0.0001 -0.0000 0.0001 +X 0.0000 0.0000 0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X 0.0000 -0.0000 -0.0000 +X 0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 -0.0000 +X 0.0000 -0.0000 -0.0000 +X -0.0000 0.0000 -0.0000 +X -0.0000 0.0000 -0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X 0.0000 -0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X 0.0000 -0.0000 0.0000 +X 0.0000 0.0000 0.0000 +X -0.0000 0.0000 -0.0000 +X -0.0000 0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 0.0000 +X -0.0000 0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X 0.0000 -0.0000 0.0000 +X -0.0000 -0.0000 0.0000 +X -0.0000 -0.0000 0.0000 +X -0.0000 0.0000 0.0000 +X 0.0000 0.0000 0.0000 +X 0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X 0.0000 0.0000 0.0000 +X 0.0000 0.0000 0.0000 +X 0.0000 -0.0000 0.0000 +X -0.0000 0.0000 -0.0000 +X 0.0000 0.0000 0.0000 +X -0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X -0.0000 -0.0000 0.0000 +X 0.0000 0.0000 0.0000 +X 0.0000 0.0000 0.0000 +X 0.0000 0.0000 -0.0000 +X 0.0000 0.0000 -0.0000 +X 0.0000 0.0000 0.0000 +X 0.0000 -0.0000 -0.0000 +X -0.0000 -0.0000 -0.0000 +X -0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 0.0000 0.0000 +X 0.0000 0.0000 0.0000 +X 0.0000 -0.0000 0.0000 +X 0.0000 -0.0000 0.0000 +X -0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 -0.0000 +X 0.0000 0.0000 0.0000 +X -0.0000 0.0000 0.0000 +X 0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 -0.0000 +X -0.0000 -0.0000 -0.0000 +X -0.0000 -0.0000 -0.0000 +X 0.0000 0.0000 0.0000 +X -0.0000 0.0000 0.0000 +X 0.0000 -0.0000 0.0000 diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/plumed.dat new file mode 100644 index 0000000000..3a6eeb9957 --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-one-q6/plumed.dat @@ -0,0 +1,33 @@ +LOAD FILE=../../../../plumedOpenACC.so +q6: Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MEAN USEGPU + +# Create a normalising matrix +q6_uones: ONES SIZE=26 +q6_nmat: OUTER_PRODUCT ARG=q6_norm,q6_uones +udata6: VSTACK ARG=q6_sp.* +data6: CUSTOM ARG=udata6,q6_nmat FUNC=x/y PERIODIC=NO +data6T: TRANSPOSE ARG=data6 + +con6: CONTACT_MATRIX GROUP=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} USEGPU +dot6: MATRIX_PRODUCT ARG=data6,data6T MASK=con6 USEGPU +ww6: CUSTOM ARG=con6,dot6 FUNC=x*y PERIODIC=NO +w6: SUM ARG=ww6 PERIODIC=NO +#on the CPU: +q6c: Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MEAN + +# Create a normalising matrix +q6c_uones: ONES SIZE=26 +q6c_nmat: OUTER_PRODUCT ARG=q6c_norm,q6c_uones +udata6c: VSTACK ARG=q6c_sp.* +data6c: CUSTOM ARG=udata6c,q6c_nmat FUNC=x/y PERIODIC=NO +data6Tc: TRANSPOSE ARG=data6 + +con6c: CONTACT_MATRIX GROUP=q6c SWITCH={RATIONAL D_0=3.0 R_0=1.5} +dot6c: MATRIX_PRODUCT ARG=data6c,data6Tc MASK=con6c +ww6c: CUSTOM ARG=con6c,dot6c FUNC=x*y PERIODIC=NO +w6c: SUM ARG=ww6c PERIODIC=NO + +diff: CUSTOM ARG=w6,w6c FUNC=y-x PERIODIC=NO +PRINT ARG=diff FILE=colv1 FMT=%8.4f + +RESTRAINT ARG=diff AT=30 KAPPA=1 diff --git a/regtest/targetGPU/rt-symfunc-nbonds-q6/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-nbonds-q6/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/Makefile diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/colv1.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/colv1.reference new file mode 100644 index 0000000000..4caa598c7b --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/colv1.reference @@ -0,0 +1,2 @@ +#! FIELDS time w6d + 0.000000 -0.0000 diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/colv2.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/colv2.reference new file mode 100644 index 0000000000..a4269a0d46 --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/colv2.reference @@ -0,0 +1,2 @@ +#! FIELDS time w4d + 0.000000 0.0000 diff --git a/regtest/targetGPU/rt-symfunc-nbonds-q6/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/config similarity index 78% rename from regtest/targetGPU/rt-symfunc-nbonds-q6/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/config index 4654aeb728..f37b86ed5a 100644 --- a/regtest/targetGPU/rt-symfunc-nbonds-q6/config +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/config @@ -1,5 +1,5 @@ type=driver plumed_modules="adjmat symfunc" # this is to test a different name -arg="--plumed plumed.dat --ixyz 64.xyz --dump-forces forces --dump-forces-fmt=%8.4f" # --debug-forces forces.num" +arg="--plumed plumed.dat --ixyz 64.xyz --dump-forces forces --dump-forces-fmt=%8.3f" # --debug-forces forces.num" extra_files="../../trajectories/64.xyz" diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/forces.reference new file mode 100644 index 0000000000..a9482b974a --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/forces.reference @@ -0,0 +1,66 @@ +64 + -0.001 0.001 0.001 +X -0.000 -0.000 -0.000 +X 0.000 0.000 0.000 +X 0.000 -0.000 0.000 +X -0.000 0.000 -0.000 +X 0.000 -0.000 0.000 +X 0.000 -0.000 0.000 +X -0.000 0.000 0.000 +X 0.000 0.000 0.000 +X -0.000 0.000 0.000 +X 0.000 0.000 0.000 +X -0.000 0.000 0.000 +X 0.000 -0.000 -0.000 +X 0.000 0.000 -0.000 +X -0.000 -0.000 0.000 +X -0.000 0.000 -0.000 +X 0.000 -0.000 0.000 +X 0.000 0.000 0.000 +X -0.000 0.000 -0.000 +X 0.000 -0.000 -0.000 +X 0.000 0.000 0.000 +X -0.000 0.000 0.000 +X 0.000 0.000 -0.000 +X -0.000 -0.000 0.000 +X -0.000 -0.000 0.000 +X -0.000 -0.000 -0.000 +X -0.000 -0.000 -0.000 +X 0.000 -0.000 -0.000 +X 0.000 -0.000 -0.000 +X 0.000 -0.000 -0.000 +X -0.000 -0.000 0.000 +X 0.000 -0.000 0.000 +X -0.000 -0.000 -0.000 +X 0.000 -0.000 0.000 +X -0.000 0.000 0.000 +X -0.000 0.000 -0.000 +X 0.000 0.000 0.000 +X 0.000 -0.000 -0.000 +X 0.000 0.000 -0.000 +X -0.000 0.000 -0.000 +X -0.000 -0.000 0.000 +X 0.000 0.000 -0.000 +X 0.000 -0.000 -0.000 +X 0.000 -0.000 -0.000 +X 0.000 0.000 0.000 +X -0.000 0.000 0.000 +X 0.000 0.000 0.000 +X 0.000 -0.000 0.000 +X -0.000 -0.000 0.000 +X -0.000 -0.000 -0.000 +X -0.000 -0.000 -0.000 +X 0.000 0.000 -0.000 +X 0.000 0.000 0.000 +X 0.000 -0.000 0.000 +X -0.000 -0.000 -0.000 +X 0.000 0.000 -0.000 +X -0.000 -0.000 0.000 +X 0.000 0.000 -0.000 +X -0.000 0.000 -0.000 +X -0.000 0.000 0.000 +X -0.000 0.000 -0.000 +X -0.000 0.000 0.000 +X -0.000 -0.000 0.000 +X 0.000 0.000 -0.000 +X 0.000 0.000 0.000 diff --git a/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/plumed.dat new file mode 100644 index 0000000000..ac955721aa --- /dev/null +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-nbonds-q6/plumed.dat @@ -0,0 +1,71 @@ +LOAD FILE=../../../../plumedOpenACC.so +q6: Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MEAN USEGPU +q4: Q4 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MEAN USEGPU + +# Create a normalising matrix +q6_uones: ONES SIZE=26 +q6_nmat: OUTER_PRODUCT ARG=q6_norm,q6_uones +udata6: VSTACK ARG=q6_sp.* +data6: CUSTOM ARG=udata6,q6_nmat FUNC=x/y PERIODIC=NO +data6T: TRANSPOSE ARG=data6 + +# Create a normalising matrix +q4_uones: ONES SIZE=18 +q4_nmat: OUTER_PRODUCT ARG=q4_norm,q4_uones +udata4: VSTACK ARG=q4_sp.* +data4: CUSTOM ARG=udata4,q4_nmat FUNC=x/y PERIODIC=NO +data4T: TRANSPOSE ARG=data4 + +con6: CONTACT_MATRIX GROUP=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} +dot6: MATRIX_PRODUCT ARG=data6,data6T MASK=con6 USEGPU + +ww6: CUSTOM ARG=con6,dot6 FUNC=x*y PERIODIC=NO + +w6: SUM ARG=ww6 PERIODIC=NO + + +dot4: MATRIX_PRODUCT ARG=data4,data4T MASK=con6 USEGPU + +ww4: CUSTOM ARG=con6,dot4 FUNC=x*y PERIODIC=NO + +w4: SUM ARG=ww4 PERIODIC=NO + + +#CPU references +q6c: Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MEAN +q4c: Q4 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MEAN + +# Create a normalising matrix +q6c_uones: ONES SIZE=26 +q6c_nmat: OUTER_PRODUCT ARG=q6c_norm,q6c_uones +udata6c: VSTACK ARG=q6c_sp.* +data6c: CUSTOM ARG=udata6c,q6c_nmat FUNC=x/y PERIODIC=NO +data6Tc: TRANSPOSE ARG=data6c + +# Create a normalising matrix +q4c_uones: ONES SIZE=18 +q4c_nmat: OUTER_PRODUCT ARG=q4c_norm,q4c_uones +udata4c: VSTACK ARG=q4c_sp.* +data4c: CUSTOM ARG=udata4c,q4c_nmat FUNC=x/y PERIODIC=NO +data4Tc: TRANSPOSE ARG=data4c + +dot6c: MATRIX_PRODUCT ARG=data6c,data6Tc MASK=con6 + +ww6c: CUSTOM ARG=con6,dot6c FUNC=x*y PERIODIC=NO + +w6c: SUM ARG=ww6c PERIODIC=NO + +dot4c: MATRIX_PRODUCT ARG=data4c,data4Tc MASK=con6 USEGPU + +ww4c: CUSTOM ARG=con6,dot4c FUNC=x*y PERIODIC=NO + +w4c: SUM ARG=ww4c PERIODIC=NO +######## + +w6d: CUSTOM ARG=w6,w6c FUNC=y-x PERIODIC=NO +w4d: CUSTOM ARG=w4,w4c FUNC=y-x PERIODIC=NO + +PRINT ARG=w6d FILE=colv1 FMT=%8.4f +PRINT ARG=w4d FILE=colv2 FMT=%8.4f + +RESTRAINT ARG=w6d,w4d AT=30,66 KAPPA=1,1 diff --git a/regtest/targetGPU/rt-symfunc-ntwo-lq6/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-ntwo-lq6/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-ntwo-lq6/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-ntwo-lq6/Makefile diff --git a/regtest/targetGPU/rt-symfunc-ntwo-lq6/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-ntwo-lq6/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-ntwo-lq6/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-ntwo-lq6/colvar.reference diff --git a/regtest/targetGPU/rt-symfunc-ntwo-lq6/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-ntwo-lq6/config similarity index 100% rename from regtest/targetGPU/rt-symfunc-ntwo-lq6/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-ntwo-lq6/config diff --git a/regtest/targetGPU/rt-symfunc-ntwo-lq6/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-ntwo-lq6/forces.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-ntwo-lq6/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-ntwo-lq6/forces.reference diff --git a/regtest/targetGPU/rt-symfunc-ntwo-lq6/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-ntwo-lq6/plumed.dat similarity index 95% rename from regtest/targetGPU/rt-symfunc-ntwo-lq6/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-ntwo-lq6/plumed.dat index d9e1cfb212..48f96890ea 100644 --- a/regtest/targetGPU/rt-symfunc-ntwo-lq6/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-ntwo-lq6/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so q1: Q1 SPECIESA=1,2 SPECIESB=1-64 D_0=3.0 R_0=1.5 NN=12 SUM USEGPU norm_q1_rm-n1: CUSTOM ARG=q1_sp.rm-n1,q1_norm FUNC=x/y PERIODIC=NO diff --git a/regtest/targetGPU/rt-symfunc-q6-nochain/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6-nochain/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/Makefile diff --git a/regtest/targetGPU/rt-symfunc-q6-nochain/colv.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/colv.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6-nochain/colv.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/colv.reference diff --git a/regtest/targetGPU/rt-symfunc-q6-nochain/colv3.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/colv3.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6-nochain/colv3.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/colv3.reference diff --git a/regtest/targetGPU/rt-symfunc-q6-nochain/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/config similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6-nochain/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/config diff --git a/regtest/targetGPU/rt-symfunc-q6-nochain/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/forces.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6-nochain/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/forces.reference diff --git a/regtest/targetGPU/rt-symfunc-q6-nochain/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/plumed.dat similarity index 84% rename from regtest/targetGPU/rt-symfunc-q6-nochain/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/plumed.dat index 2342f3be01..c641e345d4 100644 --- a/regtest/targetGPU/rt-symfunc-q6-nochain/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-nochain/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MEAN LABEL=q6 USEGPU PRINT ARG=q6.* FILE=colv diff --git a/regtest/targetGPU/rt-symfunc-q6-subset/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-subset/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6-subset/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-subset/Makefile diff --git a/regtest/targetGPU/rt-symfunc-q6-subset/colv3.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-subset/colv3.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6-subset/colv3.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-subset/colv3.reference diff --git a/regtest/targetGPU/rt-symfunc-q6-subset/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-subset/config similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6-subset/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-subset/config diff --git a/regtest/targetGPU/rt-symfunc-q6-subset/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-subset/forces.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6-subset/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-subset/forces.reference diff --git a/regtest/targetGPU/rt-symfunc-q6-subset/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-subset/plumed.dat similarity index 88% rename from regtest/targetGPU/rt-symfunc-q6-subset/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-subset/plumed.dat index e5fb80b83f..cb84c4c069 100644 --- a/regtest/targetGPU/rt-symfunc-q6-subset/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6-subset/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so Q6 SPECIESA=1-5 SPECIESB=1-64 D_0=3.0 R_0=1.5 NN=12 MM=24 LABEL=q6a USEGPU Q6 SPECIESA=6-64 SPECIESB=1-64 D_0=3.0 R_0=1.5 NN=12 MM=24 LABEL=q6b USEGPU diff --git a/regtest/targetGPU/rt-symfunc-q6/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/Makefile diff --git a/regtest/targetGPU/rt-symfunc-q6/colv.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/colv.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6/colv.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/colv.reference diff --git a/regtest/targetGPU/rt-symfunc-q6/colv2.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/colv2.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6/colv2.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/colv2.reference diff --git a/regtest/targetGPU/rt-symfunc-q6/colv3.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/colv3.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6/colv3.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/colv3.reference diff --git a/regtest/targetGPU/rt-symfunc-q6/colv4.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/colv4.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6/colv4.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/colv4.reference diff --git a/regtest/targetGPU/rt-symfunc-q6/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/config similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/config diff --git a/regtest/targetGPU/rt-symfunc-q6/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/forces.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-q6/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/forces.reference diff --git a/regtest/targetGPU/rt-symfunc-q6/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/plumed.dat similarity index 92% rename from regtest/targetGPU/rt-symfunc-q6/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/plumed.dat index 731e32d51b..21bbc19736 100644 --- a/regtest/targetGPU/rt-symfunc-q6/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-q6/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so COORDINATIONNUMBER SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LABEL=c PRINT ARG=c.* FILE=colv2 diff --git a/regtest/targetGPU/rt-symfunc-simplecubic/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-simplecubic/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/Makefile diff --git a/regtest/targetGPU/rt-symfunc-simplecubic/colv.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/colv.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-simplecubic/colv.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/colv.reference diff --git a/regtest/targetGPU/rt-symfunc-simplecubic/colv2.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/colv2.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-simplecubic/colv2.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/colv2.reference diff --git a/regtest/targetGPU/rt-symfunc-simplecubic/colv3.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/colv3.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-simplecubic/colv3.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/colv3.reference diff --git a/regtest/targetGPU/rt-symfunc-simplecubic/colv4.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/colv4.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-simplecubic/colv4.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/colv4.reference diff --git a/regtest/targetGPU/rt-symfunc-simplecubic/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/config similarity index 100% rename from regtest/targetGPU/rt-symfunc-simplecubic/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/config diff --git a/regtest/targetGPU/rt-symfunc-simplecubic/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/forces.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-simplecubic/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/forces.reference diff --git a/regtest/targetGPU/rt-symfunc-simplecubic/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/plumed.dat similarity index 97% rename from regtest/targetGPU/rt-symfunc-simplecubic/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/plumed.dat index 74991cec91..82f22fa758 100644 --- a/regtest/targetGPU/rt-symfunc-simplecubic/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-simplecubic/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so SIMPLECUBIC SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LABEL=c USEGPU #SIMPLECUBIC SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN NUMERICAL_DERIVATIVES LABEL=cn PRINT ARG=c.* FILE=colv2 FMT=%8.4f diff --git a/regtest/targetGPU/rt-symfunc-small-lq6/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-lq6/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-small-lq6/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-lq6/Makefile diff --git a/regtest/targetGPU/rt-symfunc-small-lq6/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-lq6/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-small-lq6/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-lq6/colvar.reference diff --git a/regtest/targetGPU/rt-symfunc-small-lq6/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-lq6/config similarity index 100% rename from regtest/targetGPU/rt-symfunc-small-lq6/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-lq6/config diff --git a/regtest/targetGPU/rt-symfunc-small-lq6/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-lq6/forces.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-small-lq6/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-lq6/forces.reference diff --git a/regtest/targetGPU/rt-symfunc-small-lq6/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-lq6/plumed.dat similarity index 94% rename from regtest/targetGPU/rt-symfunc-small-lq6/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-lq6/plumed.dat index 1ce5a4efdb..9142ed5069 100644 --- a/regtest/targetGPU/rt-symfunc-small-lq6/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-lq6/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so q1a: Q1 SPECIESA=1 SPECIESB=2-64 D_0=3.0 R_0=1.5 NN=12 SUM USEGPU q1b: Q1 SPECIESA=2 SPECIESB=1,3-64 D_0=3.0 R_0=1.5 NN=12 SUM USEGPU diff --git a/regtest/targetGPU/rt-symfunc-small-q6/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-q6/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-small-q6/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-q6/Makefile diff --git a/regtest/targetGPU/rt-symfunc-small-q6/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-q6/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-small-q6/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-q6/colvar.reference diff --git a/regtest/targetGPU/rt-symfunc-small-q6/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-q6/config similarity index 100% rename from regtest/targetGPU/rt-symfunc-small-q6/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-q6/config diff --git a/regtest/targetGPU/rt-symfunc-small-q6/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-q6/forces.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-small-q6/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-q6/forces.reference diff --git a/regtest/targetGPU/rt-symfunc-small-q6/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-q6/plumed.dat similarity index 92% rename from regtest/targetGPU/rt-symfunc-small-q6/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-q6/plumed.dat index acda4ec985..b67045cf68 100644 --- a/regtest/targetGPU/rt-symfunc-small-q6/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-small-q6/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so q1a: Q1 SPECIESA=1 SPECIESB=2-64 D_0=3.0 R_0=1.5 NN=12 SUM USEGPU q1b: Q1 SPECIESA=2 SPECIESB=1,3-64 D_0=3.0 R_0=1.5 NN=12 SUM USEGPU diff --git a/regtest/targetGPU/rt-symfunc-two-lq6/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-lq6/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-two-lq6/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-lq6/Makefile diff --git a/regtest/targetGPU/rt-symfunc-two-lq6/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-lq6/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-two-lq6/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-lq6/colvar.reference diff --git a/regtest/targetGPU/rt-symfunc-two-lq6/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-lq6/config similarity index 100% rename from regtest/targetGPU/rt-symfunc-two-lq6/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-lq6/config diff --git a/regtest/targetGPU/rt-symfunc-two-lq6/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-lq6/forces.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-two-lq6/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-lq6/forces.reference diff --git a/regtest/targetGPU/rt-symfunc-two-lq6/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-lq6/plumed.dat similarity index 92% rename from regtest/targetGPU/rt-symfunc-two-lq6/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-lq6/plumed.dat index fdb1f8484d..0d35cd4eb6 100644 --- a/regtest/targetGPU/rt-symfunc-two-lq6/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-lq6/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so q1: Q1 SPECIESA=1,2 SPECIESB=1-64 D_0=3.0 R_0=1.5 NN=12 SUM USEGPU ddA: VSTACK ARG=q1_sp.rm-n1,q1_sp.im-n1,q1_sp.rm-0,q1_sp.im-0,q1_sp.rm-p1,q1_sp.im-p1 diff --git a/regtest/targetGPU/rt-symfunc-two-q6/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-q6/Makefile similarity index 100% rename from regtest/targetGPU/rt-symfunc-two-q6/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-q6/Makefile diff --git a/regtest/targetGPU/rt-symfunc-two-q6/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-q6/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-two-q6/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-q6/colvar.reference diff --git a/regtest/targetGPU/rt-symfunc-two-q6/config b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-q6/config similarity index 100% rename from regtest/targetGPU/rt-symfunc-two-q6/config rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-q6/config diff --git a/regtest/targetGPU/rt-symfunc-two-q6/forces.reference b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-q6/forces.reference similarity index 100% rename from regtest/targetGPU/rt-symfunc-two-q6/forces.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-q6/forces.reference diff --git a/regtest/targetGPU/rt-symfunc-two-q6/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-q6/plumed.dat similarity index 91% rename from regtest/targetGPU/rt-symfunc-two-q6/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-q6/plumed.dat index 5f78fc1438..2d7986878f 100644 --- a/regtest/targetGPU/rt-symfunc-two-q6/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-symfunc-two-q6/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so q1: Q1 SPECIESA=1,2 SPECIESB=1-64 D_0=3.0 R_0=1.5 NN=12 SUM USEGPU dda: VSTACK ARG=q1_sp.rm-n1,q1_sp.im-n1,q1_sp.rm-0,q1_sp.im-0,q1_sp.rm-p1,q1_sp.im-p1 diff --git a/regtest/targetGPU/rt-volume-around/Makefile b/plugins/openaccPTM/regtest/targetGPU/rt-volume-around/Makefile similarity index 100% rename from regtest/targetGPU/rt-volume-around/Makefile rename to plugins/openaccPTM/regtest/targetGPU/rt-volume-around/Makefile diff --git a/regtest/targetGPU/rt-volume-around/colvar.reference b/plugins/openaccPTM/regtest/targetGPU/rt-volume-around/colvar.reference similarity index 100% rename from regtest/targetGPU/rt-volume-around/colvar.reference rename to plugins/openaccPTM/regtest/targetGPU/rt-volume-around/colvar.reference diff --git a/regtest/targetGPU/rt-volume-around/config b/plugins/openaccPTM/regtest/targetGPU/rt-volume-around/config similarity index 100% rename from regtest/targetGPU/rt-volume-around/config rename to plugins/openaccPTM/regtest/targetGPU/rt-volume-around/config diff --git a/regtest/targetGPU/rt-volume-around/gentraj.cpp b/plugins/openaccPTM/regtest/targetGPU/rt-volume-around/gentraj.cpp similarity index 100% rename from regtest/targetGPU/rt-volume-around/gentraj.cpp rename to plugins/openaccPTM/regtest/targetGPU/rt-volume-around/gentraj.cpp diff --git a/regtest/targetGPU/rt-volume-around/plumed.dat b/plugins/openaccPTM/regtest/targetGPU/rt-volume-around/plumed.dat similarity index 99% rename from regtest/targetGPU/rt-volume-around/plumed.dat rename to plugins/openaccPTM/regtest/targetGPU/rt-volume-around/plumed.dat index d00e47866b..0492b2dfea 100644 --- a/regtest/targetGPU/rt-volume-around/plumed.dat +++ b/plugins/openaccPTM/regtest/targetGPU/rt-volume-around/plumed.dat @@ -1,3 +1,4 @@ +LOAD FILE=../../../../plumedOpenACC.so c1: CENTER ATOMS=2,3 c2: CENTER ATOMS=4,5 c3: CENTER ATOMS=6,7 diff --git a/regtest/targetGPU/rt-volume-around/trajectory.xyz b/plugins/openaccPTM/regtest/targetGPU/rt-volume-around/trajectory.xyz similarity index 100% rename from regtest/targetGPU/rt-volume-around/trajectory.xyz rename to plugins/openaccPTM/regtest/targetGPU/rt-volume-around/trajectory.xyz diff --git a/plugins/openaccPTM/regtest/trajectories b/plugins/openaccPTM/regtest/trajectories new file mode 120000 index 0000000000..ea70cfb850 --- /dev/null +++ b/plugins/openaccPTM/regtest/trajectories @@ -0,0 +1 @@ +../../../regtest/trajectories \ No newline at end of file diff --git a/plugins/openaccPTM/src/plumed b/plugins/openaccPTM/src/plumed new file mode 120000 index 0000000000..dabb0e15a9 --- /dev/null +++ b/plugins/openaccPTM/src/plumed @@ -0,0 +1 @@ +../../../src \ No newline at end of file diff --git a/regtest/secondarystructure/rt33-mpi/plumed.dat b/regtest/secondarystructure/rt33-mpi/plumed.dat index f565596144..faf0776395 100644 --- a/regtest/secondarystructure/rt33-mpi/plumed.dat +++ b/regtest/secondarystructure/rt33-mpi/plumed.dat @@ -9,7 +9,7 @@ COMBINE ARG=b.lessthan,p.lessthan PERIODIC=NO LABEL=sum RESTRAINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum KAPPA=1.,1.,1.,1,1,1,1 AT=0,0,0,0,0,0,0 SLOPE=0,0,0,0,0,0,0 -DUMPFORCES ARG=b.lessthan,brf.lessthan,br.lessthan,p.lessthan,prf.lessthan,pr.lessthan,sum,@75.* FILE=forces STRIDE=1 +DUMPFORCES ARG=b.lessthan,brf.lessthan,br.lessthan,p.lessthan,prf.lessthan,pr.lessthan,sum,@77.* FILE=forces STRIDE=1 PRINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum STRIDE=1 FILE=colvar FMT=%8.4f diff --git a/regtest/secondarystructure/rt33/plumed.dat b/regtest/secondarystructure/rt33/plumed.dat index f565596144..faf0776395 100644 --- a/regtest/secondarystructure/rt33/plumed.dat +++ b/regtest/secondarystructure/rt33/plumed.dat @@ -9,7 +9,7 @@ COMBINE ARG=b.lessthan,p.lessthan PERIODIC=NO LABEL=sum RESTRAINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum KAPPA=1.,1.,1.,1,1,1,1 AT=0,0,0,0,0,0,0 SLOPE=0,0,0,0,0,0,0 -DUMPFORCES ARG=b.lessthan,brf.lessthan,br.lessthan,p.lessthan,prf.lessthan,pr.lessthan,sum,@75.* FILE=forces STRIDE=1 +DUMPFORCES ARG=b.lessthan,brf.lessthan,br.lessthan,p.lessthan,prf.lessthan,pr.lessthan,sum,@77.* FILE=forces STRIDE=1 PRINT ARG=b.*,brf.*,br.*,p.*,prf.*,pr.*,sum STRIDE=1 FILE=colvar FMT=%8.4f diff --git a/regtest/targetGPU/distribuitedMCBiasTests.sh b/regtest/targetGPU/distribuitedMCBiasTests.sh deleted file mode 100644 index 0bcaeb190f..0000000000 --- a/regtest/targetGPU/distribuitedMCBiasTests.sh +++ /dev/null @@ -1,181 +0,0 @@ -#!/bin/bash -# checked with shellcheck -# formatted with shfmtv3.36.0 - -action="run" -initialize="false" -USEGPU="USEGPU" -basedir="rt-GPU-MCVT-Bias-" -if [[ $1 = "prepare" ]]; then - action="prepare" -elif [[ $1 = "reset" ]]; then - action="prepare" - initialize="true" - USEGPU="" -elif [[ $1 = "clean" ]]; then - action="clean" -elif [[ $1 = "usage" ]]; then - cat <"$dir"/plumed.dat -v: $line -PRINT ARG=v STRIDE=1 FILE=colvar FMT=%8.4f -RESTRAINT ARG=v AT=2 KAPPA=3 SLOPE=3 -EOF - if [[ $initialize = "true" ]]; then - ( - cd "$dir" || exit - #touch forces.reference - touch colvar.reference - - echo "include ../../scripts/test.make" >Makefile - - cat <config -type=driver -arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f --pdb print_pdb_test.pdb" - -extra_files="../../trajectories/trajectory.xyz ../../trajectories/print_pdb_test.pdb" - -#export NVCOMPILER_ACC_NOTIFY=31 -EOF - make reset - grep -vzq FAILURE report.txt - ) >>/dev/null || echo "fail: $i, \"$line\"" - fi - i=$((i + 1)) - done - - for line in "${inputLineComponents[@]}"; do - echo "$i $line" - dir=${basedir}$i - mkdir -pv "$dir" - - cat <"$dir"/plumed.dat -v: $line -PRINT ARG=v.* STRIDE=1 FILE=colvar FMT=%8.4f -RESTRAINT ARG=v.x AT=2 KAPPA=3 SLOPE=3 -RESTRAINT ARG=v.y AT=2 KAPPA=3 SLOPE=3 -RESTRAINT ARG=v.z AT=2 KAPPA=3 SLOPE=3 -EOF - if [[ $initialize = "true" ]]; then - ( - cd "$dir" || exit - # touch forces.reference - touch colvar.reference - - echo "include ../../scripts/test.make" >Makefile - - cat <config -type=driver -arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f --pdb print_pdb_test.pdb" - -extra_files="../../trajectories/trajectory.xyz ../../trajectories/print_pdb_test.pdb" - -#export NVCOMPILER_ACC_NOTIFY=31 -EOF - make reset - grep -vzq FAILURE report.txt - ) >>/dev/null || echo "fail: $i, \"$line\"" - fi - i=$((i + 1)) - done - -for line in "${inputLineScaledComponents[@]}"; do - echo "$i $line" - dir=${basedir}$i - mkdir -pv "$dir" - - cat <"$dir"/plumed.dat -v: $line -PRINT ARG=v.* STRIDE=1 FILE=colvar FMT=%8.4f -RESTRAINT ARG=v.a AT=2 KAPPA=3 SLOPE=3 -RESTRAINT ARG=v.b AT=2 KAPPA=3 SLOPE=3 -RESTRAINT ARG=v.c AT=2 KAPPA=3 SLOPE=3 -EOF - if [[ $initialize = "true" ]]; then - ( - cd "$dir" || exit - # touch forces.reference - touch colvar.reference - - echo "include ../../scripts/test.make" >Makefile - - cat <config -type=driver -arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f --pdb print_pdb_test.pdb" - -extra_files="../../trajectories/trajectory.xyz ../../trajectories/print_pdb_test.pdb" - -#export NVCOMPILER_ACC_NOTIFY=31 -EOF - make reset - grep -vzq FAILURE report.txt - ) >>/dev/null || echo "fail: $i, \"$line\"" - fi - i=$((i + 1)) - done - -fi - - -if [[ $action = "run" ]]; then - for dir in rt-GPU-MCVT-B*; do - - ( - cd "$dir" || exit - make - grep -vzq FAILURE report.txt - ) >>/dev/null || { - echo "####" - echo "FAILURE in:" - echo "$dir" - grep 'v:' "${dir}/plumed.dat" - } && { - echo -n "" - # tail "$dir/tmp/out" | grep 'Cycles Total Average Minimum MaximumCalculating' - # tail "$dir/tmp/out" | grep Calculating -A1 - } - done -fi - -if [[ $action = "clean" ]]; then - for dir in rt-GPU-secondarystructure-DRMSD-play-*; do - ( - cd "$dir" || exit - make clean - - ) - done -fi diff --git a/regtest/targetGPU/distribuitedMCTests.sh b/regtest/targetGPU/distribuitedMCTests.sh deleted file mode 100644 index a495eb108e..0000000000 --- a/regtest/targetGPU/distribuitedMCTests.sh +++ /dev/null @@ -1,132 +0,0 @@ -#!/bin/bash -# checked with shellcheck -# formatted with shfmtv3.36.0 - -action="run" -initialize="false" -USEGPU="USEGPU" -basedir="rt-GPU-MCVT-" -if [[ $1 = "prepare" ]]; then - action="prepare" -elif [[ $1 = "reset" ]]; then - action="prepare" - initialize="true" - USEGPU="" -elif [[ $1 = "clean" ]]; then - action="clean" -fi - -if [[ $action = "prepare" ]]; then - inputLine=() - inputLineComponents=() - inputLine[${#inputLine[@]}]="DISTANCE ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 $USEGPU" - inputLineComponents[${#inputLineComponents[@]}]="DISTANCE ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 COMPONENTS $USEGPU" - inputLineComponents[${#inputLineComponents[@]}]="DISTANCE ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 SCALED_COMPONENTS $USEGPU" - inputLine[${#inputLine[@]}]="ANGLE ATOMS1=1,2,3 ATOMS2=4,5,6,7 ATOMS3=8,9,10 $USEGPU" - inputLine[${#inputLine[@]}]="TORSION ATOMS1=1,2,3,4 VECTORA2=5,6 AXIS2=7,8 VECTORB2=9,10 ATOMS3=11,12,13,14 $USEGPU" - inputLine[${#inputLine[@]}]="TORSION ATOMS1=1,2,3,4 VECTORA2=5,6 AXIS2=7,8 VECTORB2=9,10 ATOMS3=11,12,13,14 COSINE $USEGPU" - #inputLine[${#inputLine[@]}]="TORSION ATOMS1=1,2,3,4 VECTORA2=5,6 AXIS2=7,8 VECTORB2=9,10 ATOMS3=11,12,13,14 $USEGPU" - #ct5: CUSTOM ARG=tt4 FUNC=cos(x) PERIODIC=NO - - inputLineComponents[${#inputLineComponents[@]}]="POSITION ATOM1=1 ATOM2=3 ATOM3=5 $USEGPU" - inputLineComponents[${#inputLineComponents[@]}]="POSITION ATOM1=1 ATOM2=3 ATOM3=5 SCALED_COMPONENTS $USEGPU" - inputLine[${#inputLine[@]}]="DIPOLE GROUP1=1-6 GROUP2=7-12 $USEGPU" - inputLineComponents[${#inputLineComponents[@]}]="DIPOLE GROUP1=1-6 GROUP2=7-12 COMPONENTS $USEGPU" - - i=0 - for line in "${inputLine[@]}"; do - echo "$i $line" - dir=${basedir}$i - mkdir -pv "$dir" - - cat <"$dir"/plumed.dat -v: $line -PRINT ARG=v STRIDE=1 FILE=colvar FMT=%8.4f -#RESTRAINT ARG=v AT=2 KAPPA=3 SLOPE=3 -EOF - if [[ $initialize = "true" ]]; then - ( - cd "$dir" || exit - #touch forces.reference - touch colvar.reference - - echo "include ../../scripts/test.make" >Makefile - - cat <config -type=driver -arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f --pdb print_pdb_test.pdb" - -extra_files="../../trajectories/trajectory.xyz ../../trajectories/print_pdb_test.pdb" - -#export NVCOMPILER_ACC_NOTIFY=31 -EOF - make reset - grep -vzq FAILURE report.txt - ) >>/dev/null || echo "fail: $i, \"$line\"" - fi - i=$((i + 1)) - done - - for line in "${inputLineComponents[@]}"; do - echo "$i $line" - dir=${basedir}$i - mkdir -pv "$dir" - - cat <"$dir"/plumed.dat -v: $line -PRINT ARG=v.* STRIDE=1 FILE=colvar FMT=%8.4f -EOF - if [[ $initialize = "true" ]]; then - ( - cd "$dir" || exit - # touch forces.reference - touch colvar.reference - - echo "include ../../scripts/test.make" >Makefile - - cat <config -type=driver -arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f --pdb print_pdb_test.pdb" - -extra_files="../../trajectories/trajectory.xyz ../../trajectories/print_pdb_test.pdb" - -#export NVCOMPILER_ACC_NOTIFY=31 -EOF - make reset - grep -vzq FAILURE report.txt - ) >>/dev/null || echo "fail: $i, \"$line\"" - fi - i=$((i + 1)) - done - -fi - -if [[ $action = "run" ]]; then - for dir in rt-GPU-MCVT*; do - - ( - cd "$dir" || exit - make - grep -vzq FAILURE report.txt - ) >>/dev/null || { - echo "####" - echo "FAILURE in:" - echo "$dir" - grep 'v:' "${dir}/plumed.dat" - } && { - echo -n "" - # tail "$dir/tmp/out" | grep 'Cycles Total Average Minimum MaximumCalculating' - # tail "$dir/tmp/out" | grep Calculating -A1 - } - done -fi - -if [[ $action = "clean" ]]; then - for dir in rt-GPU-secondarystructure-DRMSD-play-*; do - ( - cd "$dir" || exit - make clean - - ) - done -fi diff --git a/regtest/targetGPU/distribuitedTests.sh b/regtest/targetGPU/distribuitedTests.sh deleted file mode 100644 index c4565f42a6..0000000000 --- a/regtest/targetGPU/distribuitedTests.sh +++ /dev/null @@ -1,126 +0,0 @@ -#!/bin/bash -# checked with shellcheck -# formatted with shfmtv3.36.0 - -action="run" -initialize="false" -USEGPU="USEGPU" -basedir="rt-GPU-secondarystructure-DRMSD-" -if [[ $1 = "prepare" ]]; then - action="prepare" -elif [[ $1 = "reset" ]]; then - action="prepare" - initialize="true" - USEGPU="" -elif [[ $1 = "clean" ]]; then - action="clean" -fi - -if [[ $action = "prepare" ]]; then - inputLine=() - inputLineNoBias=() - inputLine[${#inputLine[@]}]="ALPHARMSD RESIDUES=ALL TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} $USEGPU" - inputLine[${#inputLine[@]}]="ANTIBETARMSD RESIDUES=all TYPE=DRMSD STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} $USEGPU" - inputLine[${#inputLine[@]}]="PARABETARMSD RESIDUES=all TYPE=DRMSD STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} $USEGPU" - inputLine[${#inputLine[@]}]="ANTIBETARMSD RESIDUES=3-5,8-10 TYPE=DRMSD STYLE=inter LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} $USEGPU" - inputLine[${#inputLine[@]}]="PARABETARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} $USEGPU" - - inputLineNoBias[${#inputLineNoBias[@]}]="ALPHARMSD RESIDUES=2-7 TYPE=DRMSD R_0=0.08 NN=8 MM=12 $USEGPU" - inputLineNoBias[${#inputLineNoBias[@]}]="ALPHARMSD RESIDUES=ALL TYPE=DRMSD $USEGPU" - inputLineNoBias[${#inputLineNoBias[@]}]="PARABETARMSD RESIDUES=all TYPE=DRMSD NN=8 MM=12 R_0=0.08 $USEGPU" - - i=0 - for line in "${inputLine[@]}"; do - dir=${basedir}$i - mkdir -pv "$dir" - - cat <"$dir"/plumed.dat -MOLINFO STRUCTURE=helix.pdb -v: $line -PRINT ARG=v.* STRIDE=1 FILE=colvar FMT=%8.4f -RESTRAINT ARG=v.lessthan AT=2 KAPPA=3 SLOPE=3 -EOF - if [[ $initialize = "true" ]]; then - ( - cd "$dir" || exit - touch forces.reference - touch colvar.reference - cp ../rt-GPU-secondarystructure-DRMSD/*.pdb . - cp ../rt-GPU-secondarystructure-DRMSD/*.xyz . - echo "include ../../scripts/test.make" >Makefile - - cat <config -type=driver -arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f" - -#export NVCOMPILER_ACC_NOTIFY=31 -EOF - make reset - grep -vzq FAILURE report.txt - ) >>/dev/null || echo "fail: $i, \"$line\"" - fi - i=$((i + 1)) - done - - for line in "${inputLineNoBias[@]}"; do - dir=${basedir}$i - mkdir -pv "$dir" - - cat <"$dir"/plumed.dat -MOLINFO STRUCTURE=helix.pdb -v: $line -PRINT ARG=v.* STRIDE=1 FILE=colvar FMT=%8.4f -EOF - if [[ $initialize = "true" ]]; then - ( - cd "$dir" || exit - touch forces.reference - touch colvar.reference - cp ../rt-GPU-secondarystructure-DRMSD/*.pdb . - cp ../rt-GPU-secondarystructure-DRMSD/*.xyz . - echo "include ../../scripts/test.make" >Makefile - - cat <config -type=driver -arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz ala12_trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f" - -#export NVCOMPILER_ACC_NOTIFY=31 -EOF - make reset - grep -vzq FAILURE report.txt - ) >>/dev/null || echo "fail: $i, \"$line\"" - fi - i=$((i + 1)) - done - -fi - -if [[ $action = "run" ]]; then - for dir in rt-GPU-*; do - - ( - cd "$dir" || exit - make - grep -vzq FAILURE report.txt - ) >>/dev/null || { - echo "####" - echo "FAILURE in:" - echo "$dir" - grep 'v:' "${dir}/plumed.dat" - } && { - echo -n "" - # tail "$dir/tmp/out" | grep 'Cycles Total Average Minimum MaximumCalculating' - # tail "$dir/tmp/out" | grep Calculating -A1 - } - done -fi - -if [[ $action = "clean" ]]; then - for dir in rt-GPU-secondarystructure-DRMSD-play-*; do - ( - cd "$dir" || exit - make clean - - ) - done -fi diff --git a/regtest/targetGPU/rt-GPU-DISTANCE/plumed.dat b/regtest/targetGPU/rt-GPU-DISTANCE/plumed.dat deleted file mode 100644 index c1e9dfc0b6..0000000000 --- a/regtest/targetGPU/rt-GPU-DISTANCE/plumed.dat +++ /dev/null @@ -1,8 +0,0 @@ -#original test was 3 task of 3 components, this is 4 task of 3 componets, so I can manage better where the 3 comes from -d1: DISTANCE COMPONENTS ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 ATOMS4=1,6 USEGPU -v: VSTACK ARG=d1.x,d1.y,d1.z -vT: TRANSPOSE ARG=v -s: SUM ARG=vT PERIODIC=NO -PRINT ARG=d1.* FILE=dists FMT=%8.4f -PRINT ARG=s FILE=colvar FMT=%8.4f -BIASVALUE ARG=s diff --git a/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/colvar.reference b/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/colvar.reference deleted file mode 100644 index c0c647ec2a..0000000000 --- a/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/colvar.reference +++ /dev/null @@ -1,20 +0,0 @@ -#! FIELDS time s -#! SET min_s -pi -#! SET max_s pi - 0.000000 0.1232 - 1.000000 -0.0261 - 2.000000 0.1719 - 3.000000 -1.3292 - 4.000000 -1.4901 - 5.000000 0.0010 - 6.000000 -1.1835 - 7.000000 -0.3836 - 8.000000 -1.4126 - 9.000000 -1.0617 - 10.000000 0.0000 - 11.000000 -3.1416 - 12.000000 -0.1065 - 13.000000 0.0012 - 14.000000 -1.5912 - 15.000000 -0.0000 - 16.000000 -0.0676 diff --git a/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/plumed.dat b/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/plumed.dat deleted file mode 100644 index dc561d505d..0000000000 --- a/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/plumed.dat +++ /dev/null @@ -1,6 +0,0 @@ -trs: TORSION ATOMS1=1,2,3,4 ATOMS2=3,4,5,6 ATOMS3=2,3,4,5 ATOMS4=1,2,5,6 USEGPU - -s: SUM ARG=trs PERIODIC=-pi,pi -PRINT ARG=trs FILE=tors FMT=%8.4f -PRINT ARG=s FILE=colvar FMT=%8.4f -BIASVALUE ARG=s diff --git a/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/tors.reference b/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/tors.reference deleted file mode 100644 index e1e0c14395..0000000000 --- a/regtest/targetGPU/rt-GPU-TORSION-biasIsSUM/tors.reference +++ /dev/null @@ -1,20 +0,0 @@ -#! FIELDS time trs.1 trs.2 trs.3 trs.4 -#! SET min_trs -pi -#! SET max_trs pi - 0.000000 0.1667 0.0000 -0.0834 0.0400 - 1.000000 0.0682 -0.0085 -0.0574 -0.0283 - 2.000000 0.0814 -0.5201 0.3719 0.2387 - 3.000000 -0.0831 -0.1011 -0.4395 -0.7055 - 4.000000 0.0081 -0.1375 -0.5609 -0.7998 - 5.000000 -0.0000 -3.1416 -3.1406 -0.0000 - 6.000000 0.0200 2.6856 -0.1632 2.5572 - 7.000000 1.2403 -1.7220 0.1118 -0.0136 - 8.000000 -0.0103 -0.4899 0.0174 -0.9298 - 9.000000 -0.0183 -0.5304 0.0000 -0.5130 - 10.000000 -0.0001 0.0001 0.0000 -0.0000 - 11.000000 0.0000 -3.1416 -3.1416 -3.1416 - 12.000000 0.0055 -0.0112 -0.0034 -0.0975 - 13.000000 0.0009 0.0005 -0.0009 0.0006 - 14.000000 0.0286 -0.3142 -0.0169 -1.2887 - 15.000000 0.0000 0.0000 -0.0000 -0.0000 - 16.000000 -1.1854 1.1178 0.0003 -0.0003 diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix/coords.reference b/regtest/targetGPU/rt-adjmat-basic-matrix/coords.reference deleted file mode 100644 index a02d335502..0000000000 --- a/regtest/targetGPU/rt-adjmat-basic-matrix/coords.reference +++ /dev/null @@ -1,18 +0,0 @@ -#! FIELDS time cc.1 cc.2 cc.3 cc.4 cc.5 cc.6 cc.7 - 0.000000 4.46566 4.10850 3.63302 3.57930 3.63245 4.11256 2.37411 - 1.000000 3.91738 4.43991 4.35299 3.87437 3.65999 3.65829 3.17390 - 2.000000 3.54957 3.74537 3.61167 3.61935 3.61214 3.59171 3.50725 - 3.000000 3.79237 3.56206 3.61228 3.63247 3.65638 3.57460 3.61015 - 4.000000 3.57150 3.81183 3.59765 3.60209 3.66333 3.68429 3.62085 - 5.000000 3.50112 3.50112 3.49697 3.49697 3.50777 3.50777 3.49693 - 6.000000 3.80643 3.56238 3.85363 5.03687 4.92002 3.50579 3.36274 - 7.000000 3.59722 4.99874 3.58017 3.90625 4.84507 3.55930 3.72120 - 8.000000 4.57943 4.58007 3.88238 3.60851 3.88263 4.30509 2.17297 - 9.000000 4.68555 3.90649 3.44913 3.44909 3.90647 3.33067 1.74511 - 10.000000 4.67865 3.81642 3.37773 3.39538 3.91952 3.29259 1.71067 - 11.000000 2.64515 1.68995 3.26061 3.18501 3.17662 2.60149 1.58498 - 12.000000 3.91745 4.85212 3.91728 3.44451 3.44455 3.16351 1.89748 - 13.000000 3.97196 4.78409 3.93409 3.40543 3.38665 3.18219 1.95781 - 14.000000 4.08288 4.73992 3.91445 3.46537 3.48869 3.27422 2.07807 - 15.000000 3.66878 4.10845 4.44719 4.20548 3.60765 3.59714 2.23526 - 16.000000 4.16870 5.00342 4.16888 4.19368 4.91772 4.19356 4.47857 diff --git a/regtest/targetGPU/rt-adjmat-basic-matrix/forces.reference b/regtest/targetGPU/rt-adjmat-basic-matrix/forces.reference deleted file mode 100644 index 61d13f94ab..0000000000 --- a/regtest/targetGPU/rt-adjmat-basic-matrix/forces.reference +++ /dev/null @@ -1,272 +0,0 @@ -14 --11.7529 -0.0185 -12.0120 -X -1.2086 -0.0122 -0.7014 -X -2.2206 0.1846 2.4328 -X 0.0612 -0.0123 2.0864 -X 1.8111 -0.0390 1.0415 -X 1.8363 -0.0321 -0.9934 -X 0.9931 -0.0595 -3.1271 -X -1.2726 -0.0295 -0.7387 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 --15.4835 -4.0233 -10.1720 -X 4.1853 -1.1156 0.1042 -X 0.6947 -1.3034 -1.5482 -X -1.8950 -0.7696 -1.3017 -X -3.7924 1.2436 1.2682 -X -0.8266 1.4965 1.8540 -X 1.9284 0.5908 1.4056 -X -0.2943 -0.1424 -1.7821 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 - -8.9763 -2.5817 -7.0672 -X 1.1577 -0.3744 0.0623 -X 1.6093 -1.2648 -1.6179 -X -1.6860 -0.2058 -0.5389 -X -1.5571 0.2912 0.6552 -X -0.2886 0.9872 1.3454 -X 0.9399 0.6956 1.1962 -X -0.1752 -0.1290 -1.1022 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 --12.1661 -0.7729 -9.5142 -X 3.0752 -0.0004 -0.0961 -X 0.7727 -0.3687 -1.1722 -X -0.7341 -0.1650 -1.8716 -X -1.8278 0.5488 -0.6796 -X -1.9553 0.4153 0.9757 -X -0.5468 -0.5079 1.6756 -X 1.2160 0.0780 1.1683 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 --11.2306 -1.1175 -12.6378 -X 1.6243 0.1528 -0.1406 -X 1.8110 -0.7205 -2.7990 -X -0.4177 -0.2493 -1.6891 -X -1.8791 0.6672 -0.5919 -X -1.9732 0.6129 1.0999 -X -0.5267 -0.6099 2.4684 -X 1.3614 0.1467 1.6522 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 - -3.1932 -0.3115 -3.5041 -X -0.5418 -0.1694 -0.2520 -X -0.5419 -0.1694 0.2520 -X -0.1168 -0.0363 0.5894 -X -0.1168 -0.0362 -0.5894 -X 0.3741 0.1168 0.5078 -X 0.3741 0.1170 -0.5078 -X 0.5691 0.1775 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 - -6.1016 -6.1116 -5.1466 -X -1.6176 -2.4456 0.9183 -X 0.1723 -0.3829 0.6216 -X 2.8315 0.7255 1.4982 -X 0.3465 0.7312 -0.5812 -X -0.7805 -0.2384 -0.8416 -X -0.3728 1.0549 -0.9107 -X -0.5794 0.5553 -0.7045 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 --10.5457 -8.3226 -0.7069 -X -1.5828 -0.6758 -0.2480 -X -0.6039 -0.9498 0.4270 -X 0.9527 0.1283 -0.2721 -X 1.8731 3.0858 -0.3648 -X -0.6030 0.6552 0.4300 -X -1.6086 0.0735 -0.1698 -X 1.5724 -2.3172 0.1978 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 --10.9705 -8.8664 -2.8882 -X 0.9176 -0.4528 1.1395 -X 0.4501 1.4201 0.3530 -X -2.5779 2.3720 -1.7199 -X -1.1749 -0.5566 -0.6280 -X -1.0712 -3.6636 0.8130 -X 2.7006 0.7653 0.2176 -X 0.7558 0.1156 -0.1750 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 - -7.8056 -8.7204 -0.6692 -X 0.4583 -0.0332 0.1815 -X -0.5352 3.1831 0.9143 -X -0.7866 0.8316 -0.0458 -X -0.7861 -0.7616 -0.3384 -X -0.5331 -3.3006 -0.2764 -X 1.6346 0.0701 -0.3784 -X 0.5481 0.0106 -0.0569 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 - -6.9259 -2.1034 -6.7351 -X -0.2296 0.0319 -0.2869 -X -1.7249 -1.5363 1.9635 -X 0.1208 -0.3867 1.0092 -X 0.9165 0.2913 0.1746 -X 2.3048 1.5304 -1.4125 -X -1.0492 0.0514 -1.0924 -X -0.3384 0.0180 -0.3555 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 - -0.0043 0.0000 -0.0337 -X 0.0008 0.0000 0.0015 -X 0.0010 0.0000 0.0044 -X -0.0003 0.0000 0.0022 -X 0.0007 0.0000 -0.0009 -X -0.0008 0.0000 -0.0046 -X -0.0009 0.0000 -0.0018 -X -0.0005 0.0000 -0.0007 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 - -7.9176 -8.5214 -0.6659 -X -0.5252 -3.2121 -0.5459 -X 0.3441 0.0185 -0.0996 -X -0.5278 3.1962 0.6298 -X -0.7623 0.7447 0.3250 -X -0.7616 -0.8122 0.0394 -X 1.5651 0.0750 -0.4047 -X 0.6677 -0.0100 0.0560 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 - -8.8629 -8.5241 -0.0003 -X -0.2000 -3.3301 0.0176 -X 0.3076 0.1505 -0.0006 -X -0.8131 3.0850 -0.0176 -X -0.9330 0.5915 -0.0032 -X -0.7526 -0.7947 0.0042 -X 1.5930 0.2863 -0.0006 -X 0.7980 0.0115 0.0003 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 - -8.0421 -8.4845 -0.7712 -X -0.3029 -3.0058 0.6902 -X 0.4250 0.1021 0.2841 -X -1.0888 3.1436 0.0021 -X -0.7966 0.5694 -0.3740 -X -0.6221 -1.0061 -0.2491 -X 1.5442 0.2101 -0.0824 -X 0.8411 -0.0132 -0.2709 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 --11.3834 -11.0342 -0.0068 -X -1.1413 1.8689 -0.0495 -X 0.8421 2.9433 -0.0697 -X 1.4435 -0.1361 0.0079 -X 0.6087 -2.7364 0.0692 -X -1.0312 -1.7207 0.0391 -X -2.0449 -0.0707 -0.0046 -X 1.3231 -0.1484 0.0077 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -14 --10.8672 -9.2775 -5.9309 -X 1.5136 2.5965 -1.5726 -X 0.1837 -0.4081 -1.0603 -X -3.0363 -1.2158 -0.8956 -X -2.5575 -1.1194 1.5926 -X 0.4993 -0.3944 1.1399 -X 1.7725 2.5083 0.9489 -X 1.6246 -1.9670 -0.1529 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 -X 0.0000 0.0000 0.0000 diff --git a/regtest/targetGPU/rt-symfunc-nbonds-one-q6/colv1.reference b/regtest/targetGPU/rt-symfunc-nbonds-one-q6/colv1.reference deleted file mode 100644 index 65e2cc8c1a..0000000000 --- a/regtest/targetGPU/rt-symfunc-nbonds-one-q6/colv1.reference +++ /dev/null @@ -1,2 +0,0 @@ -#! FIELDS time w6 - 0.000000 31.2882 diff --git a/regtest/targetGPU/rt-symfunc-nbonds-one-q6/forces.reference b/regtest/targetGPU/rt-symfunc-nbonds-one-q6/forces.reference deleted file mode 100644 index d7788a757f..0000000000 --- a/regtest/targetGPU/rt-symfunc-nbonds-one-q6/forces.reference +++ /dev/null @@ -1,66 +0,0 @@ -64 --106.7571 77.1605 -2.3060 -X -1.9360 -2.2745 -6.2646 -X 9.1140 -1.2294 20.5367 -X -5.3464 -3.0208 22.3305 -X 4.8957 -1.2996 -7.6059 -X 0.0209 -0.1193 -0.0225 -X 0.6590 8.6035 0.6692 -X 7.9899 0.4593 -0.1673 -X 1.9363 1.3545 2.2160 -X -8.3855 4.3400 6.6035 -X -2.1788 8.7509 -1.4810 -X 3.4280 -14.8706 -3.6056 -X -3.2670 0.5906 -7.9737 -X -0.1695 0.3182 6.3447 -X -1.9290 -4.6495 -7.1641 -X 2.2993 -5.6411 -1.6758 -X -12.9872 -2.5351 -4.4377 -X 4.2751 1.2023 4.9743 -X 3.0469 -4.8951 7.2375 -X 0.8919 -7.8115 -9.2222 -X 0.5335 3.8606 6.7507 -X 1.0973 12.0449 2.7568 -X 9.5187 -11.0087 -8.0466 -X 0.0755 -3.2723 8.1532 -X -4.7208 5.4793 2.0939 -X -5.1874 -10.5065 -10.6462 -X 4.8058 8.3682 1.0234 -X -6.8109 11.6990 1.2832 -X 3.6819 3.4047 -0.9343 -X -4.2988 -1.1830 1.0438 -X 0.6230 8.0716 -22.2132 -X -1.5530 -4.2628 -6.3275 -X -7.9129 -3.0261 12.4253 -X -7.6973 -7.1771 1.4027 -X -0.6930 -2.6421 3.4878 -X 4.9328 6.0213 1.7788 -X -16.7645 -0.0890 -7.7296 -X -0.7179 -13.6532 1.0868 -X -1.2952 -2.2488 3.4969 -X -10.1070 4.8564 12.9132 -X -9.8394 -1.1509 -13.1097 -X 5.7940 6.0021 -2.8803 -X -3.7998 5.5769 14.4462 -X 3.5659 4.3264 -1.5596 -X -0.1006 15.3403 4.0990 -X 4.2663 -0.5217 9.2966 -X -7.2712 2.5225 -10.0530 -X -11.3184 0.4627 1.2938 -X 2.4396 -2.8740 -13.6829 -X -3.4174 -1.3823 -1.3163 -X 9.0495 -0.9796 3.1617 -X 5.8471 -8.0591 -11.1142 -X 5.9064 -0.0601 8.1531 -X -7.1817 1.8354 15.4212 -X 7.7601 7.3024 4.7172 -X 8.8340 10.0608 -13.4993 -X -7.2098 4.4126 -14.9404 -X -6.7263 -9.9006 -7.8963 -X 1.2421 -13.7278 -0.5332 -X 0.6479 10.6837 -16.5880 -X 12.1371 -2.8863 -1.0563 -X 0.8573 -1.1242 20.7123 -X 2.7276 11.8767 -2.5897 -X 8.6666 0.4273 -0.7667 -X 17.2560 -20.1724 5.1936 diff --git a/regtest/targetGPU/rt-symfunc-nbonds-one-q6/plumed.dat b/regtest/targetGPU/rt-symfunc-nbonds-one-q6/plumed.dat deleted file mode 100644 index d565bd11e6..0000000000 --- a/regtest/targetGPU/rt-symfunc-nbonds-one-q6/plumed.dat +++ /dev/null @@ -1,17 +0,0 @@ -q6: Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MEAN USEGPU - -# Create a normalising matrix -q6_uones: ONES SIZE=26 -q6_nmat: OUTER_PRODUCT ARG=q6_norm,q6_uones -udata6: VSTACK ARG=q6_sp.* -data6: CUSTOM ARG=udata6,q6_nmat FUNC=x/y PERIODIC=NO -data6T: TRANSPOSE ARG=data6 - -con6: CONTACT_MATRIX GROUP=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} USEGPU -dot6: MATRIX_PRODUCT ARG=data6,data6T MASK=con6 USEGPU -ww6: CUSTOM ARG=con6,dot6 FUNC=x*y PERIODIC=NO -w6: SUM ARG=ww6 PERIODIC=NO - -PRINT ARG=w6 FILE=colv1 FMT=%8.4f - -RESTRAINT ARG=w6 AT=30 KAPPA=1 diff --git a/regtest/targetGPU/rt-symfunc-nbonds-q6/colv1.reference b/regtest/targetGPU/rt-symfunc-nbonds-q6/colv1.reference deleted file mode 100644 index 65e2cc8c1a..0000000000 --- a/regtest/targetGPU/rt-symfunc-nbonds-q6/colv1.reference +++ /dev/null @@ -1,2 +0,0 @@ -#! FIELDS time w6 - 0.000000 31.2882 diff --git a/regtest/targetGPU/rt-symfunc-nbonds-q6/colv2.reference b/regtest/targetGPU/rt-symfunc-nbonds-q6/colv2.reference deleted file mode 100644 index f9606fdf81..0000000000 --- a/regtest/targetGPU/rt-symfunc-nbonds-q6/colv2.reference +++ /dev/null @@ -1,2 +0,0 @@ -#! FIELDS time w4 - 0.000000 67.6239 diff --git a/regtest/targetGPU/rt-symfunc-nbonds-q6/forces.reference b/regtest/targetGPU/rt-symfunc-nbonds-q6/forces.reference deleted file mode 100644 index 21512b5264..0000000000 --- a/regtest/targetGPU/rt-symfunc-nbonds-q6/forces.reference +++ /dev/null @@ -1,66 +0,0 @@ -64 - 35.6178 233.2021 594.1096 -X -1.1090 -8.0931 -10.8826 -X 20.1914 9.1972 33.1012 -X -7.2433 -4.7241 24.1188 -X -0.5613 6.5246 -21.6037 -X -1.6585 -10.4122 2.5490 -X -27.6995 -1.9626 -14.2509 -X 7.4933 4.8792 -2.1363 -X -5.0379 -2.3678 -3.5793 -X -0.2218 -3.0763 16.8300 -X 9.1047 9.2066 -2.5416 -X -18.0789 -14.0220 3.8151 -X -6.3715 11.7773 -2.2729 -X 16.1859 -6.9319 25.5446 -X -0.6996 18.4939 -8.1891 -X -5.1562 -1.1171 -3.2800 -X -18.5409 -1.9242 -12.5475 -X 23.3042 15.1516 8.2474 -X 16.1888 -13.8679 5.4119 -X 2.2552 -10.1397 -14.0183 -X 0.3735 8.3007 -14.7275 -X 11.2690 5.6741 -10.3180 -X -1.4197 -27.6537 -11.4799 -X 8.7529 -9.6092 18.1892 -X -15.7129 -6.0096 10.4283 -X -9.6871 -7.6271 -21.2446 -X 23.9197 31.8715 7.6719 -X -10.7465 2.9191 7.8935 -X 4.5999 8.6750 -2.9585 -X -8.4942 -10.9668 -23.7202 -X 7.0508 5.3489 -42.5071 -X 2.5450 -9.7580 -22.3195 -X -7.7330 -24.2511 32.0889 -X -4.3825 -8.3764 24.3058 -X 2.3715 2.5780 -28.4529 -X 20.2640 -2.9183 27.5157 -X -34.8277 -4.0827 -20.2956 -X 6.6003 -11.7928 7.9191 -X -0.1759 3.8699 -0.3237 -X -7.1729 13.0739 24.2590 -X -22.6281 -1.3048 -16.5224 -X 22.0167 15.1831 -4.2115 -X -9.4277 15.3892 15.3749 -X -2.4917 -2.3009 5.3769 -X 8.6785 7.0673 5.0115 -X -0.9090 9.5521 14.5193 -X -9.7282 -9.5758 -12.6614 -X -13.6139 1.1621 4.6502 -X -1.2772 -7.7462 -17.0120 -X -1.8947 6.2766 -21.6470 -X -1.0801 6.0876 -5.8118 -X 13.9424 3.9885 -5.4200 -X 19.3351 5.6165 17.5935 -X -11.6539 6.2622 39.0639 -X 11.9032 8.2731 3.7823 -X 2.7352 20.5966 4.4860 -X 4.5448 -17.3924 -24.1895 -X -25.7250 1.4864 -15.5689 -X -5.9445 -18.2450 2.0745 -X 12.3993 25.3743 -12.8354 -X 8.4740 -5.7727 -18.3089 -X -1.2052 1.3296 32.2614 -X 2.5622 7.9696 -2.6587 -X -1.1658 -7.0903 9.6047 -X 12.4146 -28.0434 16.8084 diff --git a/regtest/targetGPU/rt-symfunc-nbonds-q6/plumed.dat b/regtest/targetGPU/rt-symfunc-nbonds-q6/plumed.dat deleted file mode 100644 index 9da204a08d..0000000000 --- a/regtest/targetGPU/rt-symfunc-nbonds-q6/plumed.dat +++ /dev/null @@ -1,35 +0,0 @@ -q6: Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MEAN USEGPU -q4: Q4 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MEAN USEGPU - -# Create a normalising matrix -q6_uones: ONES SIZE=26 -q6_nmat: OUTER_PRODUCT ARG=q6_norm,q6_uones -udata6: VSTACK ARG=q6_sp.* -data6: CUSTOM ARG=udata6,q6_nmat FUNC=x/y PERIODIC=NO -data6T: TRANSPOSE ARG=data6 - -# Create a normalising matrix -q4_uones: ONES SIZE=18 -q4_nmat: OUTER_PRODUCT ARG=q4_norm,q4_uones -udata4: VSTACK ARG=q4_sp.* -data4: CUSTOM ARG=udata4,q4_nmat FUNC=x/y PERIODIC=NO -data4T: TRANSPOSE ARG=data4 - -con6: CONTACT_MATRIX GROUP=q6 SWITCH={RATIONAL D_0=3.0 R_0=1.5} -dot6: MATRIX_PRODUCT ARG=data6,data6T MASK=con6 USEGPU - -ww6: CUSTOM ARG=con6,dot6 FUNC=x*y PERIODIC=NO - -w6: SUM ARG=ww6 PERIODIC=NO - -PRINT ARG=w6 FILE=colv1 FMT=%8.4f - -dot4: MATRIX_PRODUCT ARG=data4,data4T MASK=con6 USEGPU - -ww4: CUSTOM ARG=con6,dot4 FUNC=x*y PERIODIC=NO - -w4: SUM ARG=ww4 PERIODIC=NO - -PRINT ARG=w4 FILE=colv2 FMT=%8.4f - -RESTRAINT ARG=w6,w4 AT=30,66 KAPPA=1,1 diff --git a/regtest/tools/rt-make-angle/main.cpp b/regtest/tools/rt-make-angle/main.cpp index 51dc1ecc28..3591864c0b 100644 --- a/regtest/tools/rt-make-angle/main.cpp +++ b/regtest/tools/rt-make-angle/main.cpp @@ -5,71 +5,83 @@ using namespace PLMD; +template +using myVector=PLMD::VectorTyped; +//by removing the \n the diff becames clearer +template int testCompute2Vectors90Degrees(std::ofstream &ofs) { - ofs << "testCompute2Vectors90Degrees" << std::endl; - Vector vector1(1.0, 0.0, 0.0); - Vector vector2(0.0, 1.0, 0.0); + ofs << "testCompute2Vectors90Degrees "; + myVector vector1(1.0, 0.0, 0.0); + myVector vector2(0.0, 1.0, 0.0); Angle angle; - double result = angle.compute(vector1, vector2); + auto result = angle.compute(vector1, vector2); ofs << result << std::endl; return 0; } +template int testCompute2Vectors45Degrees(std::ofstream &ofs) { - ofs << "testCompute2Vectors45Degrees" << std::endl; - Vector vector1(1.0, 0.0, 0.0); - Vector vector2(1.0, 1.0, 0.0); + ofs << "testCompute2Vectors45Degrees "; + myVector vector1(1.0, 0.0, 0.0); + myVector vector2(1.0, 1.0, 0.0); Angle angle; - double result = angle.compute(vector1, vector2); + auto result = angle.compute(vector1, vector2); ofs << result << std::endl; return 0; } +template int testCompute4Vectors45Degrees(std::ofstream &ofs) { - ofs << "testCompute4Vectors45Degrees" << std::endl; - Vector vector1(1.0, 1.0, 0.0); - Vector vector2(1.0, 0.0, 0.0); - Vector d1, d2; + ofs << "testCompute4Vectors45Degrees "; + myVector vector1(1.0, 1.0, 0.0); + myVector vector2(1.0, 0.0, 0.0); + myVector d1, d2; Angle angle; - double result = angle.compute(vector1, vector2, d1, d2); + auto result = angle.compute(vector1, vector2, d1, d2); ofs << result << std::endl; - ofs << d1 << std::endl; - ofs << d2 << std::endl; + ofs << "testCompute4Vectors45Degrees d1= " << d1 << std::endl; + ofs << "testCompute4Vectors45Degrees d2= " << d2 << std::endl; return 0; } +template int testCompute4VectorsParallel(std::ofstream &ofs) { - ofs << "testCompute4VectorsParallel" << std::endl; - Vector vector1(1.0, 1.0, 0.0); - Vector vector2(1.0, 1.0, 0.0); - Vector d1, d2; - Angle angle; - double result = angle.compute(vector1, vector2, d1, d2); + ofs << "testCompute4VectorsParallel "; + myVector vector1(1.0, 1.0, 0.0); + myVector vector2(1.0, 1.0, 0.0); + myVector d1, d2; + auto result = Angle::compute(vector1, vector2, d1, d2); ofs << result << std::endl; - ofs << d1 << std::endl; - ofs << d2 << std::endl; + ofs << "testCompute4VectorsParallel d1= " << d1 << std::endl; + ofs << "testCompute4VectorsParallel d2= " << d2 << std::endl; return 0; } - +template int testCompute4VectorsAntiParallel(std::ofstream &ofs) { - ofs << "testCompute4VectorsAntiParallel" << std::endl; - Vector vector1(1.0, 1.0, 0.0); - Vector vector2(-1.0, -1.0, 0.0); - Vector d1, d2; + ofs << "testCompute4VectorsAntiParallel "; + myVector vector1(1.0, 1.0, 0.0); + myVector vector2(-1.0, -1.0, 0.0); + myVector d1, d2; Angle angle; - double result = angle.compute(vector1, vector2, d1, d2); + auto result = angle.compute(vector1, vector2, d1, d2); ofs << result << std::endl; - ofs << d1 << std::endl; - ofs << d2 << std::endl; + ofs << "testCompute4VectorsAntiParallel d1= " << d1 << std::endl; + ofs << "testCompute4VectorsAntiParallel d2= " << d2 << std::endl; return 0; } int main() { std::ofstream ofs("output"); - testCompute2Vectors90Degrees(ofs); - testCompute2Vectors45Degrees(ofs); - testCompute4Vectors45Degrees(ofs); - testCompute4VectorsParallel(ofs); - testCompute4VectorsAntiParallel(ofs); + testCompute2Vectors90Degrees(ofs); + testCompute2Vectors45Degrees(ofs); + testCompute4Vectors45Degrees(ofs); + testCompute4VectorsParallel(ofs); + testCompute4VectorsAntiParallel(ofs); + ofs << "float\n"; + testCompute2Vectors90Degrees(ofs); + testCompute2Vectors45Degrees(ofs); + testCompute4Vectors45Degrees(ofs); + testCompute4VectorsParallel(ofs); + testCompute4VectorsAntiParallel(ofs); return 0; } diff --git a/regtest/tools/rt-make-angle/output.reference b/regtest/tools/rt-make-angle/output.reference index 1033f80117..a6959284fa 100644 --- a/regtest/tools/rt-make-angle/output.reference +++ b/regtest/tools/rt-make-angle/output.reference @@ -1,16 +1,23 @@ -testCompute2Vectors90Degrees -1.5708 -testCompute2Vectors45Degrees -0.785398 -testCompute4Vectors45Degrees -0.785398 --0.5 0.5 -0 --0 -1 -0 -testCompute4VectorsParallel -0 -0 0 0 -0 0 0 -testCompute4VectorsAntiParallel -3.14159 -0 0 0 -0 0 0 +testCompute2Vectors90Degrees 1.5708 +testCompute2Vectors45Degrees 0.785398 +testCompute4Vectors45Degrees 0.785398 +testCompute4Vectors45Degrees d1= -0.5 0.5 -0 +testCompute4Vectors45Degrees d2= -0 -1 -0 +testCompute4VectorsParallel 0 +testCompute4VectorsParallel d1= 0 0 0 +testCompute4VectorsParallel d2= 0 0 0 +testCompute4VectorsAntiParallel 3.14159 +testCompute4VectorsAntiParallel d1= 0 0 0 +testCompute4VectorsAntiParallel d2= 0 0 0 +float +testCompute2Vectors90Degrees 1.5708 +testCompute2Vectors45Degrees 0.785398 +testCompute4Vectors45Degrees 0.785398 +testCompute4Vectors45Degrees d1= -0.5 0.5 -0 +testCompute4Vectors45Degrees d2= -0 -1 -0 +testCompute4VectorsParallel 0 +testCompute4VectorsParallel d1= 0 0 0 +testCompute4VectorsParallel d2= 0 0 0 +testCompute4VectorsAntiParallel 3.14159 +testCompute4VectorsAntiParallel d1= 0 0 0 +testCompute4VectorsAntiParallel d2= 0 0 0 diff --git a/src/adjmat/AdjacencyMatrixBase.h b/src/adjmat/AdjacencyMatrixBase.h index 5e08ad57dd..887125eb09 100644 --- a/src/adjmat/AdjacencyMatrixBase.h +++ b/src/adjmat/AdjacencyMatrixBase.h @@ -31,6 +31,8 @@ namespace PLMD { namespace adjmat { +struct ContactMatrix; + template struct AdjacencyMatrixData { T matrixdata; @@ -47,7 +49,7 @@ struct AdjacencyMatrixData { nlist=nlist_v.data(); nlist_three=nlist_three_v.data(); } -#ifdef __PLUMED_USE_OPENACC +#ifdef __PLUMED_HAS_OPENACC void toACCDevice() const { #pragma acc enter data copyin(this[0:1],usepbc,components,nlists, \ natoms_per_list,nlist[0:nlist_v.size()], \ @@ -62,7 +64,7 @@ struct AdjacencyMatrixData { nlist[0:nlist_v.size()], natoms_per_list, \ nlists, components, usepbc, this[0:1]) } -#endif //__PLUMED_USE_OPENACC +#endif //__PLUMED_HAS_OPENACC }; struct AdjacencyMatrixInput { @@ -94,11 +96,13 @@ struct MatrixOutput { } }; -template +template class AdjacencyMatrixBase : public ActionWithMatrix { public: - using input_type = AdjacencyMatrixData; - using PTM = ParallelTaskManager>; + using input_type = AdjacencyMatrixData; + using PTM = ParallelTaskManager>; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: PTM taskmanager; bool nopbc, read_one_group; @@ -116,30 +120,32 @@ class AdjacencyMatrixBase : public ActionWithMatrix { void calculate() override ; void applyNonZeroRankForces( std::vector& outforces ) override ; void getInputData( std::vector& inputdata ) const override; + void getInputData( std::vector& inputdata ) const override; std::string writeInGraph() const override { - if( getName()=="CONTACT_MATRIX_PROPER" ) { + if constexpr ( std::is_same_v ) { + //TODO:this will change to std::is_same_v,CV> when adding the mixed precision to the contact matrix return "CONTACT_MATRIX"; } return getName(); } void setLinkCellCutoff( const bool& symmetric, const double& lcut, double tcut=-1.0 ); static void performTask( std::size_t task_index, - const AdjacencyMatrixData& actiondata, + const AdjacencyMatrixData& actiondata, ParallelActionsInput& input, ParallelActionsOutput output ); static int getNumberOfValuesPerTask( std::size_t task_index, - const AdjacencyMatrixData& actiondata ); + const AdjacencyMatrixData& actiondata ); static void getForceIndices( std::size_t task_index, std::size_t colno, std::size_t ntotal_force, - const AdjacencyMatrixData& actiondata, + const AdjacencyMatrixData& actiondata, const ParallelActionsInput& input, ForceIndexHolder force_indices ); void getMatrixColumnTitles( std::vector& argnames ) const override ; }; -template -void AdjacencyMatrixBase::registerKeywords( Keywords& keys ) { +template +void AdjacencyMatrixBase::registerKeywords( Keywords& keys ) { ActionWithMatrix::registerKeywords( keys ); keys.addInputKeyword("optional","MASK","vector","a vector that is used to used to determine which rows of the adjancency matrix to compute"); keys.add("atoms","GROUP","the atoms for which you would like to calculate the adjacency matrix"); @@ -151,7 +157,7 @@ void AdjacencyMatrixBase::registerKeywords( Keywords& keys ) { keys.addFlag("NOPBC",false,"don't use pbc"); keys.add("compulsory","NL_CUTOFF","0.0","The cutoff for the neighbor list. A value of 0 means we are not using a neighbor list"); keys.add("compulsory","NL_STRIDE","1","The frequency with which we are updating the atoms in the neighbor list"); - T::registerKeywords( keys ); + CV::registerKeywords( keys ); PTM::registerKeywords( keys ); keys.addOutputComponent("w","COMPONENTS","matrix","a matrix containing the weights for the bonds between each pair of atoms"); keys.addOutputComponent("x","COMPONENTS","matrix","the projection of the bond on the x axis"); @@ -161,8 +167,8 @@ void AdjacencyMatrixBase::registerKeywords( Keywords& keys ) { keys.addDOI("10.1021/acs.jctc.6b01073"); } -template -AdjacencyMatrixBase::AdjacencyMatrixBase(const ActionOptions& ao): +template +AdjacencyMatrixBase::AdjacencyMatrixBase(const ActionOptions& ao): Action(ao), ActionWithMatrix(ao), taskmanager(this), @@ -297,7 +303,7 @@ AdjacencyMatrixBase::AdjacencyMatrixBase(const ActionOptions& ao): componentIsNotPeriodic("z"); } log<<" Bibliography "< matdata; + AdjacencyMatrixData matdata; matdata.usepbc = !nopbc; matdata.components = components; matdata.nlists = getPntrToComponent(0)->getShape()[0]; @@ -305,13 +311,13 @@ AdjacencyMatrixBase::AdjacencyMatrixBase(const ActionOptions& ao): taskmanager.setActionInput( matdata ); } -template -unsigned AdjacencyMatrixBase::getNumberOfDerivatives() { +template +unsigned AdjacencyMatrixBase::getNumberOfDerivatives() { return 3*getNumberOfAtoms() + 9; } -template -void AdjacencyMatrixBase::setupThirdAtomBlock( const std::vector& tc, +template +void AdjacencyMatrixBase::setupThirdAtomBlock( const std::vector& tc, std::vector& t ) { threeblocks.resize( tc.size() ); unsigned base=t.size(); @@ -323,8 +329,8 @@ void AdjacencyMatrixBase::setupThirdAtomBlock( const std::vector& log.printf("\n"); } -template -void AdjacencyMatrixBase::setLinkCellCutoff( const bool& symmetric, +template +void AdjacencyMatrixBase::setLinkCellCutoff( const bool& symmetric, const double& lcut, double tcut ) { if( read_one_group && symmetric ) { @@ -348,8 +354,8 @@ void AdjacencyMatrixBase::setLinkCellCutoff( const bool& symmetric, threecells.setCutoff( tcut ); } -template -void AdjacencyMatrixBase::getInputData( std::vector& inputdata ) const { +template +void AdjacencyMatrixBase::getInputData( std::vector& inputdata ) const { if( inputdata.size()!=3*getNumberOfAtoms() ) { inputdata.resize( 3*getNumberOfAtoms() ); } @@ -366,8 +372,26 @@ void AdjacencyMatrixBase::getInputData( std::vector& inputdata ) cons } } -template -void AdjacencyMatrixBase::getMatrixColumnTitles( std::vector& argnames ) const { +template +void AdjacencyMatrixBase::getInputData( std::vector& inputdata ) const { + if( inputdata.size()!=3*getNumberOfAtoms() ) { + inputdata.resize( 3*getNumberOfAtoms() ); + } + + std::size_t k=0; + for(unsigned i=0; i +void AdjacencyMatrixBase::getMatrixColumnTitles( std::vector& argnames ) const { std::string num; for(unsigned i=0; igetShape()[1]; ++i) { Tools::convert( i+1, num ); @@ -375,8 +399,8 @@ void AdjacencyMatrixBase::getMatrixColumnTitles( std::vector& ar } } -template -void AdjacencyMatrixBase::calculate() { +template +void AdjacencyMatrixBase::calculate() { Value* myval = getPntrToComponent(0); // Retrieve the task list std::vector & pTaskList( getListOfActiveTasks(this) ); @@ -481,9 +505,9 @@ void AdjacencyMatrixBase::calculate() { taskmanager.runAllTasks(); } -template -void AdjacencyMatrixBase::performTask( std::size_t task_index, - const AdjacencyMatrixData& actiondata, +template +void AdjacencyMatrixBase::performTask( std::size_t task_index, + const AdjacencyMatrixData& actiondata, ParallelActionsInput& input, ParallelActionsOutput output ) { const unsigned nneigh=actiondata.nlist[task_index]; @@ -545,7 +569,7 @@ void AdjacencyMatrixBase::performTask( std::size_t task_index, const std::size_t valpos = (i-1)*ncomponents; MatrixOutput adjout{View{&output.values[ valpos]}, View{output.derivatives.data() + valpos*nderiv,nderiv}}; - T::calculateWeight( actiondata.matrixdata, adjinp, adjout ); + CV::calculateWeight( actiondata.matrixdata, adjinp, adjout ); if( !actiondata.components ) { continue ; } @@ -557,7 +581,7 @@ void AdjacencyMatrixBase::performTask( std::size_t task_index, } //sugar for not having to repeat [valpos*nderiv+something] for(int ii=1; ii<4; ++ii) { - auto derivs = output.derivatives.subview_n<5>(valpos*nderiv+ii*nderiv); + auto derivs = output.derivatives.template subview_n<5>(valpos*nderiv+ii*nderiv); derivs[0] = -1.0; derivs[1] = 1.0; derivs[2] = -atoms[i][0]; @@ -568,22 +592,22 @@ void AdjacencyMatrixBase::performTask( std::size_t task_index, } } -template -void AdjacencyMatrixBase::applyNonZeroRankForces( std::vector& outforces ) { +template +void AdjacencyMatrixBase::applyNonZeroRankForces( std::vector& outforces ) { taskmanager.applyForces( outforces ); } -template -int AdjacencyMatrixBase::getNumberOfValuesPerTask( std::size_t task_index, - const AdjacencyMatrixData& actiondata ) { +template +int AdjacencyMatrixBase::getNumberOfValuesPerTask( std::size_t task_index, + const AdjacencyMatrixData& actiondata ) { return actiondata.nlist[task_index] - 1; } -template -void AdjacencyMatrixBase::getForceIndices( const std::size_t task_index, +template +void AdjacencyMatrixBase::getForceIndices( const std::size_t task_index, const std::size_t colno, const std::size_t ntotal_force, - const AdjacencyMatrixData& actiondata, + const AdjacencyMatrixData& actiondata, const ParallelActionsInput& /*input*/, ForceIndexHolder force_indices ) { diff --git a/src/adjmat/ContactMatrix.cpp b/src/adjmat/ContactMatrix.cpp index 36afef2fca..633a5ee3b5 100644 --- a/src/adjmat/ContactMatrix.cpp +++ b/src/adjmat/ContactMatrix.cpp @@ -20,6 +20,7 @@ along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ #include "ContactMatrix.h" +#include "ContactMatrixShortcut.h" #include "core/ActionRegister.h" //+PLUMEDOC MATRIX CONTACT_MATRIX_PROPER @@ -55,80 +56,300 @@ PRINT ARG=csums FILE=colvar */ //+ENDPLUMEDOC +//+PLUMEDOC MATRIX CONTACT_MATRIX +/* +Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. + +A useful tool for developing complex collective variables is the notion of the +so called adjacency matrix. An adjacency matrix can be an $N \times N$ matrix in which the $i$th, $j$th element tells you whether +or not the $i$th and $j$th atoms/molecules from a set of $N$ atoms/molecules are adjacent or not. Alternatively, you can calculate +an adjacency matrix between a set of $N$ atoms and a second set of $M$ atoms. For this type of matrix the $i$th, $j$th element tells you +whether the whether the $i$th atom in the first group and the $j$th atom in the second group are adjacent or not. The adjacency matrix in this +case is thus $N \times M$. + +The simplest type of adjacency matrix is a contact matrix. The elements of a contact matrix are calculated using: + +$$ +a_{ij} = \sigma( r_{ij} ) +$$ + +where $r_{ij}$ is the magnitude of the vector connecting atoms $i$ and $j$ and where $\sigma$ is a switching function. If you want to calculate a +contact matrix for one group of atoms the input would look something like this: + +```plumed +c1: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} +``` + +Alternatively, if you want to calculate the contact matrix between two groups of atoms you would use an input like following: + +```plumed +c2: CONTACT_MATRIX GROUPA=1-7 GROUPB=8-20 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} +``` + +Once you have calculated a contact matrix you can perform various matrix operations by using the tools in the matrixtools or clusters modules. + +## Coordination numbers + +If a contact matrix, $\mathbf{C}$, is multiplied from the back by a vector of ones the $i$th element of the resulting matrix tells you the number of atoms that are +within $r_c$ of atom $i$. In other words, the coordination numbers of the atoms can be calculated from the contact matrix by doing matrix vector multiplication. + +This realisation about the relationship between the contact map and the coordination number is heavily used in PLUMED. For example, to calculate +and print the coordination numbers of the first 7 atoms in the system with themselves you would use an input something like this: + +```plumed +c1: CONTACT_MATRIX GROUP=1-7 D_0=0.0 R_0=2.6 NN=6 MM=12 +ones: ONES SIZE=7 +cc: MATRIX_VECTOR_PRODUCT ARG=c1,ones +PRINT ARG=cc FILE=colvar +``` + +This input transforms the distances using the RATIONAL switching function that is discussed in the documentation for [LESS_THAN](LESS_THAN.md) +The parameters for this type of switching function can be specified using `D_0`, `R_0`, `NN` and `MM` keywords as indicated above. However, we would recommend +using the following syntax instead as this allows you to use the full range of switching function types. Most importantly, if you use the following syntax you can +set the D_MAX parameter, as shown below. As discussed in the optimization details section below, __if you want good computational performance on large systems it is essential to set the D_MAX parameter.__ + + +```plumed +c1: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12 D_MAX=5.0} +ones: ONES SIZE=7 +cc: MATRIX_VECTOR_PRODUCT ARG=c1,ones +PRINT ARG=cc FILE=colvar +``` + +Implmenting the coordination number as a product of a matrix and a vector is useful as there are many different ways to define whether two atoms/molecules and to construct a "contact" matrix based on +the result. For example: + +* You could say that two molecules are connected if they are within a certain distance of each other and if they have the same orientation (see [TORSIONS_MATRIX](TORSIONS_MATRIX.md)). +* You could say that two water molecules are connected if they are hydrogen bonded to each other (see [HBOND_MATRIX](HBOND_MATRIX.md)). +* You could say that two atoms are connected if they are within a certain distance of each other and if they have similar values for a CV (see [OUTER_PRODUCT](OUTER_PRODUCT.md)). + +When the coordination numbers is implemented in the way described above (by doing the matrix-vector multiplication) you have the flexibility to define the contact matrix that +is used in the multiplication in whatever way you choose. In other words, this implementation of the coordination number is much more flexible. For example, suppose you want +to calculate the number of atoms that have a coordination is greater than 3.0. You can do this with PLUMED using the following input: + +```plumed +# Calculate the contact matrix for the first seven atoms in the system +c1: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} +# Calculate the coordination numbers for the first seven atoms in the system +ones: ONES SIZE=7 +cc: MATRIX_VECTOR_PRODUCT ARG=c1,ones +# Set the ith element of the vector mtc equal to one if the coordination number of atom i is greater than 3. +mtc: MORE_THAN ARG=cc SWITCH={RATIONAL D_0=3 R_0=1} +# Calculate the number of atoms with a coordination number greater than 3. +s: SUM ARG=mtc PERIODIC=NO +PRINT ARG=s FILE=colvar +``` + +Alternatively, consider the CV that was used to study perovskite nucleation in [this paper](https://pubs.acs.org/doi/abs/10.1021/acs.chemmater.9b04259). The CV here measures the number of +methylamonium molecules that are attached to at least 5 other methylamoniusm molecules, at least 7 lead atoms and at least 11 ionide ions. We can calculate something akin to this +CV and apply a restraint on the resulting quantity by using the following input file: + +```plumed +# Lead ions +Pb: GROUP ATOMS=1-64 +# Iodide atoms +I: GROUP ATOMS=65-256 +# Methylamonium "atoms" -- in the real CV these are centers of mass rather than single atoms +cn: GROUP ATOMS=257-320 + +ones64: ONES SIZE=64 +# Contact matrix that determines if methylamonium molecules are within 8 A of each other +cm_cncn: CONTACT_MATRIX GROUP=cn SWITCH={RATIONAL R_0=0.8} +# Coordination number of methylamounium with methylamonium +cc_cncn: MATRIX_VECTOR_PRODUCT ARG=cm_cncn,ones64 +# Vector with elements that are one if coordiantion of methylamonium with methylamonium >5 +mt_cncn: MORE_THAN ARG=cc_cncn SWITCH={RATIONAL R_0=5 NN=12 MM=24} + +# Contact matrix that determines if methylamoinium moleulcule and Pb atom are within 7.5 A of each other +cm_cnpb: CONTACT_MATRIX GROUPA=cn GROUPB=Pb SWITCH={RATIONAL R_0=0.75} +# Coordination number of methylamonium with Pb +cc_cnpb: MATRIX_VECTOR_PRODUCT ARG=cm_cnpb,ones64 +# Vector with elements that are one if coordination of methylamounium with lead is >7 +mt_cnpb: MORE_THAN ARG=cc_cnpb SWITCH={RATIONAL R_0=7 NN=12 MM=24} + +ones192: ONES SIZE=192 +# Contact matrix that determines if methylamoinium moleulcule and I atom are within 6.5 A of each other +cm_cnI: CONTACT_MATRIX GROUPA=cn GROUPB=I SWITCH={RATIONAL R_0=0.65} +# Coordination number of methylamonium with I +cc_cnI: MATRIX_VECTOR_PRODUCT ARG=cm_cnI,ones192 +# Vector with elements that are one if coordination of methylamounium with lead is >11 +mt_cnI: MORE_THAN ARG=cc_cnI SWITCH={RATIONAL R_0=11 NN=12 MM=24} + +# Element wise product of these three input vectors. +# mm[i]==1 if coordination number of corrsponding methylamounium with methylamonium is >5 +# and if coordination of methylamounium with Pb is >7 and if coordination of methylamounium with I > 11 +mm: CUSTOM ARG=mt_cncn,mt_cnpb,mt_cnI FUNC=x*y*z PERIODIC=NO + +# Sum of coordination numbers and thus equal to number of methylamoniums with desired coordination numbers +ff: SUM ARG=mm PERIODIC=NO + +rr: RESTRAINT ARG=ff AT=62 KAPPA=10 +``` + +## COMPONENTS flag + +If you add the flag COMPONENTS to the input as shown below: + +```plumed +c4: CONTACT_MATRIX GROUP=1-7 COMPONENTS SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} +``` + +then four matrices with the labels `c4.w`, `c4.x`, `c4.y` and `c4.z` are output by the action. The matrix with the label `c4.w` is the adjacency matrix +that would be output if you had not added the COMPONENTS flag. The $i,j$ component of the matrices `c4.x`, `c4.y` and `c4.z` contain the $x$, $y$ and $z$ +components of the vector connecting atoms $i$ and $j$. Importantly, however, the components of these vectors are only stored in `c4.x`, `c4.y` and `c4.z` +if the elements of `c4.w` are non-zero. + +## NOPBC flag + +By default PLUMED calculates the distances that are transformed by the switching function in the CONTACT_MATRIX action in a way that accounts for the periodic boundary +conditions. If for any reason you do not want PLUMED to account for the periodic boundary conditions you can use the NOPBC flag as shown below: + +```plumed +c: CONTACT_MATRIX GROUP=1-7 NOPBC SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} +``` + +If you also add the COMPONENTS flag in this input then the vector connecting each pairs of atoms will also be calculated without taking the periodic boundary conditions into account. + +## Optimisation details + +Adjacency matrices are sparse. Each atom is only be connected to a small number of neighbours and the vast majority of the elements of the contact matrix are thus zero. To reduce +the amount of memory that PLUMED requires PLUMED uses sparse matrix storage. Consequently, whenever you calculate and store a contact matrix only the elements of the matrix that are +non-zero are stored. The same thing holds for the additional values that are created when you use the COMPONENTS flag. The components of the vectors connecting atoms are only stored +when the elements of `c4.w` are non-zero. + +We can also use the sparsity of the adjacency matrix to make the time required to compute a contact matrix scale linearly rather than quadratically with the number of atoms. Element +$i,j$ of the contact matrix is only non-zero if two atoms are within a cutoff, $r_c$. We can determine that many pairs of atoms are further appart than $r_c$ without computing the +distance between these atoms by using divide and conquer strategies such as linked lists and neighbour lists. __To turn on these features you need to set the `D_MAX` parameter in the +switching functions.__ The value you pass to the `D_MAX` keyword is used as the cutoff in the link cell algorithm. + +In theory we could further optimize the implementation of the CONTACT_MATRIX action by exploiting neighbor lists. If we were to do this we would likely add two further keywords as shown +below: + +```plumed +c4: CONTACT_MATRIX GROUP=1-10000 SWITCH={RATIONAL R_0=0.1 NN=6 MM=12 D_MAX=0.5} NL_CUTOFF=0.7 NL_STRIDE=5 +``` + +The `NL_CUTOFF` keyword would be used to specify the cutoff (in nm) to use when constructing neighbor lists. This value would need to be slightly larger than the D_MAX parameter for the switching function. +The `NL_STRIDE` keyword would then be used to specify how frequently the neighbour list should be updated. Thus far we have not found it necessary to implement this algorithm. We have been happy with the +performance even if we use the linked list algorithm to update the neighbors on every step. If you feel that you need this CV to perform better please get in touch as adding a neighbor list for this action +should be relatively straightforward. + +## The MASK keyword + +Suppose that you want to calculate the average coordination number for the atoms that are within a sphere in the center of your simulation box. You can do so by exploiting an input similar to the one shown +below: + +```plumed +# The atoms that are of interest +ow: GROUP ATOMS=1-16500 +# Fixed virtual atom which serves as the probe volume's center (pos. in nm) +center: FIXEDATOM AT=2.5,2.5,2.5 +# Vector in which element i is one if atom i is in sphere of interest and zero otherwise +sphere: INSPHERE ATOMS=ow CENTER=center RADIUS={GAUSSIAN D_0=0.5 R_0=0.01 D_MAX=0.52} +# Calculates cooordination numbers +cmap: CONTACT_MATRIX GROUP=ow SWITCH={GAUSSIAN D_0=0.32 R_0=0.01 D_MAX=0.34} +ones: ONES SIZE=16500 +cc: MATRIX_VECTOR_PRODUCT ARG=cmap,ones +# Multiply coordination numbers by sphere vector +prod: CUSTOM ARG=cc,sphere FUNC=x*y PERIODIC=NO +# Sum of coordination numbers for atoms that are in the sphere of interest +numer: SUM ARG=prod PERIODIC=NO +# Number of atoms that are in sphere of interest +denom: SUM ARG=sphere PERIODIC=NO +# Average coordination number for atoms in sphere of interest +av: CUSTOM ARG=prod,sphere FUNC=x/y PERIODIC=NO +# And print out final CV to a file +PRINT ARG=av FILE=colvar STRIDE=1 +``` + +This calculation is slow because you have to calculate the coordination numbers of all the atoms even though only a small subset of these quanitties are required to compute the average coordination number in the +sphere. To avoid all these unecessary calculations you use the `MASK` keyword as shown below: + +```plumed +# The atoms that are of interest +ow: GROUP ATOMS=1-16500 +# Fixed virtual atom which serves as the probe volume's center (pos. in nm) +center: FIXEDATOM AT=2.5,2.5,2.5 +# Vector in which element i is one if atom i is in sphere of interest and zero otherwise +sphere: INSPHERE ATOMS=ow CENTER=center RADIUS={GAUSSIAN D_0=0.5 R_0=0.01 D_MAX=0.52} +# Calculates cooordination numbers +cmap: CONTACT_MATRIX GROUP=ow SWITCH={GAUSSIAN D_0=0.32 R_0=0.01 D_MAX=0.34} MASK=sphere +ones: ONES SIZE=16500 +cc: MATRIX_VECTOR_PRODUCT ARG=cmap,ones +# Multiply coordination numbers by sphere vector +prod: CUSTOM ARG=cc,sphere FUNC=x*y PERIODIC=NO +# Sum of coordination numbers for atoms that are in the sphere of interest +numer: SUM ARG=prod PERIODIC=NO +# Number of atoms that are in sphere of interest +denom: SUM ARG=sphere PERIODIC=NO +# Average coordination number for atoms in sphere of interest +av: CUSTOM ARG=prod,sphere FUNC=x/y PERIODIC=NO +# And print out final CV to a file +PRINT ARG=av FILE=colvar STRIDE=1 +``` + +Adding the instruction `MASK=sphere` to the CONTACT_MATRIX line in this input tells PLUMED to only calculate the $i$th row in the adjacency matrix if the $i$th element of the vector `sphere` is non-zero. +In other words, by adding this command we have ensured that we are not calculating coordination numbers for atoms that are not in the sphere that is of interest. In this way we can thus reduce the computational +expense of the calculation enormously. + +Notice, that there are other places where we can use this same trick. For example, we could have used MASK as shown below for our calculation of the CV for perovskite nucleation as shown below: + +```plumed +# Lead ions +Pb: GROUP ATOMS=1-64 +# Iodide atoms +I: GROUP ATOMS=65-256 +# Methylamonium "atoms" -- in the real CV these are centers of mass rather than single atoms +cn: GROUP ATOMS=257-320 + +ones192: ONES SIZE=192 +# Contact matrix that determines if methylamoinium moleulcule and I atom are within 6.5 A of each other +cm_cnI: CONTACT_MATRIX GROUPA=cn GROUPB=I SWITCH={RATIONAL R_0=0.65 D_MAX=1.0} +# Coordination number of methylamonium with I +cc_cnI: MATRIX_VECTOR_PRODUCT ARG=cm_cnI,ones192 +# Vector with elements that are one if coordination of methylamounium with lead is >11 +mt_cnI: MORE_THAN ARG=cc_cnI SWITCH={RATIONAL R_0=11 NN=12 MM=24} + +ones64: ONES SIZE=64 +# Contact matrix that determines if methylamoinium moleulcule and Pb atom are within 7.5 A of each other +cm_cnpb: CONTACT_MATRIX GROUPA=cn GROUPB=Pb SWITCH={RATIONAL R_0=0.75 D_MAX=1.5} MASK=mt_cnI +# Coordination number of methylamonium with Pb +cc_cnpb: MATRIX_VECTOR_PRODUCT ARG=cm_cnpb,ones64 +# Vector with elements that are one if coordination of methylamounium with lead is >7 +mt_cnpb: MORE_THAN ARG=cc_cnpb SWITCH={RATIONAL R_0=7 NN=12 MM=24} + +# Contact matrix that determines if methylamonium molecules are within 8 A of each other +cm_cncn: CONTACT_MATRIX GROUP=cn SWITCH={RATIONAL R_0=0.8 D_MAX=1.75} MASK=mt_cnI +# Coordination number of methylamounium with methylamonium +cc_cncn: MATRIX_VECTOR_PRODUCT ARG=cm_cncn,ones64 +# Vector with elements that are one if coordiantion of methylamonium with methylamonium >5 +mt_cncn: MORE_THAN ARG=cc_cncn SWITCH={RATIONAL R_0=5 NN=12 MM=24} + +# Element wise product of these three input vectors. +# mm[i]==1 if coordination number of corrsponding methylamounium with methylamonium is >5 +# and if coordination of methylamounium with Pb is >7 and if coordination of methylamounium with I > 11 +mm: CUSTOM ARG=mt_cncn,mt_cnpb,mt_cnI FUNC=x*y*z PERIODIC=NO + +# Sum of coordination numbers and thus equal to number of methylamoniums with desired coordination numbers +ff: SUM ARG=mm PERIODIC=NO + +rr: RESTRAINT ARG=ff AT=62 KAPPA=10 +``` + +This trick works here because when we find that there are methylamoinium moleulcules with fewer than 11 lead atoms in there first coordination sphere we know that there +is no point calculating the second two coordination numbers. + +*/ +//+ENDPLUMEDOC + namespace PLMD { namespace adjmat { + typedef AdjacencyMatrixBase cmap; PLUMED_REGISTER_ACTION(cmap,"CONTACT_MATRIX_PROPER") - -void ContactMatrix::registerKeywords( Keywords& keys ) { - keys.setDisplayName("CONTACT_MATRIX"); - keys.add("compulsory","NN","6","The n parameter of the switching function "); - keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN"); - keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function"); - keys.add("compulsory","R_0","The r_0 parameter of the switching function"); - keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. " - "The following provides information on the \\ref switchingfunction that are available. " - "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords."); - keys.linkActionInDocs("SWITCH","LESS_THAN"); -} - -void ContactMatrix::parseInput( AdjacencyMatrixBase* action ) { - std::string errors; - std::string swinput; - action->parse("SWITCH",swinput); - if( swinput.length()>0 ) { - switchingFunction.set( swinput, errors ); - if( errors.length()!=0 ) { - action->error("problem reading switching function description " + errors); - } - } else { - int nn=0; - int mm=0; - double r_0=-1.0; - double d_0= 0.0; - action->parse("NN",nn); - action->parse("MM",mm); - action->parse("R_0",r_0); - action->parse("D_0",d_0); - if( r_0<0.0 ) { - action->error("you must set a value for R_0"); - } - switchingFunction.set(nn,mm,r_0,d_0); - } - // And set the link cell cutoff - action->log.printf(" switching function cutoff is %s \n",switchingFunction.description().c_str() ); - action->setLinkCellCutoff( true, switchingFunction.get_dmax() ); -} - -void ContactMatrix::calculateWeight( const ContactMatrix& data, - const AdjacencyMatrixInput& input, - MatrixOutput output ) { - const double mod2 = input.pos.modulo2(); - if( mod2 CMshort; +PLUMED_REGISTER_ACTION(CMshort,"CONTACT_MATRIX") } // namespace adjmat } // namespace PLMD diff --git a/src/adjmat/ContactMatrix.h b/src/adjmat/ContactMatrix.h index 833a5d726e..b63307bd50 100644 --- a/src/adjmat/ContactMatrix.h +++ b/src/adjmat/ContactMatrix.h @@ -22,27 +22,24 @@ #ifndef __PLUMED_adjmat_ContactMatrix_h #define __PLUMED_adjmat_ContactMatrix_h -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC - #include "AdjacencyMatrixBase.h" #include "tools/SwitchingFunction.h" namespace PLMD { namespace adjmat { struct ContactMatrix { -#ifdef __PLUMED_USE_OPENACC +#ifdef __PLUMED_HAS_OPENACC SwitchingFunctionAccelerable switchingFunction; #else SwitchingFunction switchingFunction; #endif static void registerKeywords( Keywords& keys ); - void parseInput( AdjacencyMatrixBase* action ); + template + void parseInput( AdjacencyMatrixBase* action ); static void calculateWeight( const ContactMatrix& data, const AdjacencyMatrixInput& input, MatrixOutput output ); -#ifdef __PLUMED_USE_OPENACC +#ifdef __PLUMED_HAS_OPENACC void toACCDevice() const { #pragma acc enter data copyin(this[0:1]) switchingFunction.toACCDevice(); @@ -51,9 +48,78 @@ struct ContactMatrix { switchingFunction.removeFromACCDevice(); #pragma acc exit data delete(this[0:1]) } -#endif //__PLUMED_USE_OPENACC +#endif //__PLUMED_HAS_OPENACC }; +void ContactMatrix::registerKeywords( Keywords& keys ) { + keys.setDisplayName("CONTACT_MATRIX"); + keys.add("compulsory","NN","6","The n parameter of the switching function "); + keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN"); + keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function"); + keys.add("compulsory","R_0","The r_0 parameter of the switching function"); + keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. " + "The following provides information on the \\ref switchingfunction that are available. " + "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords."); + keys.linkActionInDocs("SWITCH","LESS_THAN"); +} + +template +void ContactMatrix::parseInput( AdjacencyMatrixBase* action ) { + std::string errors; + std::string swinput; + action->parse("SWITCH",swinput); + if( swinput.length()>0 ) { + switchingFunction.set( swinput, errors ); + if( errors.length()!=0 ) { + action->error("problem reading switching function description " + errors); + } + } else { + int nn=0; + int mm=0; + double r_0=-1.0; + double d_0= 0.0; + action->parse("NN",nn); + action->parse("MM",mm); + action->parse("R_0",r_0); + action->parse("D_0",d_0); + if( r_0<0.0 ) { + action->error("you must set a value for R_0"); + } + switchingFunction.set(nn,mm,r_0,d_0); + } + // And set the link cell cutoff + action->log.printf(" switching function cutoff is %s \n",switchingFunction.description().c_str() ); + action->setLinkCellCutoff( true, switchingFunction.get_dmax() ); +} + +void ContactMatrix::calculateWeight( const ContactMatrix& data, + const AdjacencyMatrixInput& input, + MatrixOutput output ) { + const double mod2 = input.pos.modulo2(); + if( mod2. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#include "core/ActionShortcut.h" -#include "core/ActionRegister.h" -#include "core/PlumedMain.h" -#include "core/ActionSet.h" -#include "core/Group.h" -#include "ContactMatrix.h" - -//+PLUMEDOC MATRIX CONTACT_MATRIX -/* -Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff. - -A useful tool for developing complex collective variables is the notion of the -so called adjacency matrix. An adjacency matrix can be an $N \times N$ matrix in which the $i$th, $j$th element tells you whether -or not the $i$th and $j$th atoms/molecules from a set of $N$ atoms/molecules are adjacent or not. Alternatively, you can calculate -an adjacency matrix between a set of $N$ atoms and a second set of $M$ atoms. For this type of matrix the $i$th, $j$th element tells you -whether the whether the $i$th atom in the first group and the $j$th atom in the second group are adjacent or not. The adjacency matrix in this -case is thus $N \times M$. - -The simplest type of adjacency matrix is a contact matrix. The elements of a contact matrix are calculated using: - -$$ -a_{ij} = \sigma( r_{ij} ) -$$ - -where $r_{ij}$ is the magnitude of the vector connecting atoms $i$ and $j$ and where $\sigma$ is a switching function. If you want to calculate a -contact matrix for one group of atoms the input would look something like this: - -```plumed -c1: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} -``` - -Alternatively, if you want to calculate the contact matrix between two groups of atoms you would use an input like following: - -```plumed -c2: CONTACT_MATRIX GROUPA=1-7 GROUPB=8-20 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} -``` - -Once you have calculated a contact matrix you can perform various matrix operations by using the tools in the matrixtools or clusters modules. - -## Coordination numbers - -If a contact matrix, $\mathbf{C}$, is multiplied from the back by a vector of ones the $i$th element of the resulting matrix tells you the number of atoms that are -within $r_c$ of atom $i$. In other words, the coordination numbers of the atoms can be calculated from the contact matrix by doing matrix vector multiplication. - -This realisation about the relationship between the contact map and the coordination number is heavily used in PLUMED. For example, to calculate -and print the coordination numbers of the first 7 atoms in the system with themselves you would use an input something like this: - -```plumed -c1: CONTACT_MATRIX GROUP=1-7 D_0=0.0 R_0=2.6 NN=6 MM=12 -ones: ONES SIZE=7 -cc: MATRIX_VECTOR_PRODUCT ARG=c1,ones -PRINT ARG=cc FILE=colvar -``` - -This input transforms the distances using the RATIONAL switching function that is discussed in the documentation for [LESS_THAN](LESS_THAN.md) -The parameters for this type of switching function can be specified using `D_0`, `R_0`, `NN` and `MM` keywords as indicated above. However, we would recommend -using the following syntax instead as this allows you to use the full range of switching function types. Most importantly, if you use the following syntax you can -set the D_MAX parameter, as shown below. As discussed in the optimization details section below, __if you want good computational performance on large systems it is essential to set the D_MAX parameter.__ - - -```plumed -c1: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12 D_MAX=5.0} -ones: ONES SIZE=7 -cc: MATRIX_VECTOR_PRODUCT ARG=c1,ones -PRINT ARG=cc FILE=colvar -``` - -Implmenting the coordination number as a product of a matrix and a vector is useful as there are many different ways to define whether two atoms/molecules and to construct a "contact" matrix based on -the result. For example: - -* You could say that two molecules are connected if they are within a certain distance of each other and if they have the same orientation (see [TORSIONS_MATRIX](TORSIONS_MATRIX.md)). -* You could say that two water molecules are connected if they are hydrogen bonded to each other (see [HBOND_MATRIX](HBOND_MATRIX.md)). -* You could say that two atoms are connected if they are within a certain distance of each other and if they have similar values for a CV (see [OUTER_PRODUCT](OUTER_PRODUCT.md)). - -When the coordination numbers is implemented in the way described above (by doing the matrix-vector multiplication) you have the flexibility to define the contact matrix that -is used in the multiplication in whatever way you choose. In other words, this implementation of the coordination number is much more flexible. For example, suppose you want -to calculate the number of atoms that have a coordination is greater than 3.0. You can do this with PLUMED using the following input: - -```plumed -# Calculate the contact matrix for the first seven atoms in the system -c1: CONTACT_MATRIX GROUP=1-7 SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} -# Calculate the coordination numbers for the first seven atoms in the system -ones: ONES SIZE=7 -cc: MATRIX_VECTOR_PRODUCT ARG=c1,ones -# Set the ith element of the vector mtc equal to one if the coordination number of atom i is greater than 3. -mtc: MORE_THAN ARG=cc SWITCH={RATIONAL D_0=3 R_0=1} -# Calculate the number of atoms with a coordination number greater than 3. -s: SUM ARG=mtc PERIODIC=NO -PRINT ARG=s FILE=colvar -``` - -Alternatively, consider the CV that was used to study perovskite nucleation in [this paper](https://pubs.acs.org/doi/abs/10.1021/acs.chemmater.9b04259). The CV here measures the number of -methylamonium molecules that are attached to at least 5 other methylamoniusm molecules, at least 7 lead atoms and at least 11 ionide ions. We can calculate something akin to this -CV and apply a restraint on the resulting quantity by using the following input file: - -```plumed -# Lead ions -Pb: GROUP ATOMS=1-64 -# Iodide atoms -I: GROUP ATOMS=65-256 -# Methylamonium "atoms" -- in the real CV these are centers of mass rather than single atoms -cn: GROUP ATOMS=257-320 - -ones64: ONES SIZE=64 -# Contact matrix that determines if methylamonium molecules are within 8 A of each other -cm_cncn: CONTACT_MATRIX GROUP=cn SWITCH={RATIONAL R_0=0.8} -# Coordination number of methylamounium with methylamonium -cc_cncn: MATRIX_VECTOR_PRODUCT ARG=cm_cncn,ones64 -# Vector with elements that are one if coordiantion of methylamonium with methylamonium >5 -mt_cncn: MORE_THAN ARG=cc_cncn SWITCH={RATIONAL R_0=5 NN=12 MM=24} - -# Contact matrix that determines if methylamoinium moleulcule and Pb atom are within 7.5 A of each other -cm_cnpb: CONTACT_MATRIX GROUPA=cn GROUPB=Pb SWITCH={RATIONAL R_0=0.75} -# Coordination number of methylamonium with Pb -cc_cnpb: MATRIX_VECTOR_PRODUCT ARG=cm_cnpb,ones64 -# Vector with elements that are one if coordination of methylamounium with lead is >7 -mt_cnpb: MORE_THAN ARG=cc_cnpb SWITCH={RATIONAL R_0=7 NN=12 MM=24} - -ones192: ONES SIZE=192 -# Contact matrix that determines if methylamoinium moleulcule and I atom are within 6.5 A of each other -cm_cnI: CONTACT_MATRIX GROUPA=cn GROUPB=I SWITCH={RATIONAL R_0=0.65} -# Coordination number of methylamonium with I -cc_cnI: MATRIX_VECTOR_PRODUCT ARG=cm_cnI,ones192 -# Vector with elements that are one if coordination of methylamounium with lead is >11 -mt_cnI: MORE_THAN ARG=cc_cnI SWITCH={RATIONAL R_0=11 NN=12 MM=24} - -# Element wise product of these three input vectors. -# mm[i]==1 if coordination number of corrsponding methylamounium with methylamonium is >5 -# and if coordination of methylamounium with Pb is >7 and if coordination of methylamounium with I > 11 -mm: CUSTOM ARG=mt_cncn,mt_cnpb,mt_cnI FUNC=x*y*z PERIODIC=NO - -# Sum of coordination numbers and thus equal to number of methylamoniums with desired coordination numbers -ff: SUM ARG=mm PERIODIC=NO - -rr: RESTRAINT ARG=ff AT=62 KAPPA=10 -``` - -## COMPONENTS flag - -If you add the flag COMPONENTS to the input as shown below: - -```plumed -c4: CONTACT_MATRIX GROUP=1-7 COMPONENTS SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} -``` - -then four matrices with the labels `c4.w`, `c4.x`, `c4.y` and `c4.z` are output by the action. The matrix with the label `c4.w` is the adjacency matrix -that would be output if you had not added the COMPONENTS flag. The $i,j$ component of the matrices `c4.x`, `c4.y` and `c4.z` contain the $x$, $y$ and $z$ -components of the vector connecting atoms $i$ and $j$. Importantly, however, the components of these vectors are only stored in `c4.x`, `c4.y` and `c4.z` -if the elements of `c4.w` are non-zero. - -## NOPBC flag - -By default PLUMED calculates the distances that are transformed by the switching function in the CONTACT_MATRIX action in a way that accounts for the periodic boundary -conditions. If for any reason you do not want PLUMED to account for the periodic boundary conditions you can use the NOPBC flag as shown below: - -```plumed -c: CONTACT_MATRIX GROUP=1-7 NOPBC SWITCH={RATIONAL R_0=2.6 NN=6 MM=12} -``` - -If you also add the COMPONENTS flag in this input then the vector connecting each pairs of atoms will also be calculated without taking the periodic boundary conditions into account. - -## Optimisation details - -Adjacency matrices are sparse. Each atom is only be connected to a small number of neighbours and the vast majority of the elements of the contact matrix are thus zero. To reduce -the amount of memory that PLUMED requires PLUMED uses sparse matrix storage. Consequently, whenever you calculate and store a contact matrix only the elements of the matrix that are -non-zero are stored. The same thing holds for the additional values that are created when you use the COMPONENTS flag. The components of the vectors connecting atoms are only stored -when the elements of `c4.w` are non-zero. - -We can also use the sparsity of the adjacency matrix to make the time required to compute a contact matrix scale linearly rather than quadratically with the number of atoms. Element -$i,j$ of the contact matrix is only non-zero if two atoms are within a cutoff, $r_c$. We can determine that many pairs of atoms are further appart than $r_c$ without computing the -distance between these atoms by using divide and conquer strategies such as linked lists and neighbour lists. __To turn on these features you need to set the `D_MAX` parameter in the -switching functions.__ The value you pass to the `D_MAX` keyword is used as the cutoff in the link cell algorithm. - -In theory we could further optimize the implementation of the CONTACT_MATRIX action by exploiting neighbor lists. If we were to do this we would likely add two further keywords as shown -below: - -```plumed -c4: CONTACT_MATRIX GROUP=1-10000 SWITCH={RATIONAL R_0=0.1 NN=6 MM=12 D_MAX=0.5} NL_CUTOFF=0.7 NL_STRIDE=5 -``` - -The `NL_CUTOFF` keyword would be used to specify the cutoff (in nm) to use when constructing neighbor lists. This value would need to be slightly larger than the D_MAX parameter for the switching function. -The `NL_STRIDE` keyword would then be used to specify how frequently the neighbour list should be updated. Thus far we have not found it necessary to implement this algorithm. We have been happy with the -performance even if we use the linked list algorithm to update the neighbors on every step. If you feel that you need this CV to perform better please get in touch as adding a neighbor list for this action -should be relatively straightforward. - -## The MASK keyword - -Suppose that you want to calculate the average coordination number for the atoms that are within a sphere in the center of your simulation box. You can do so by exploiting an input similar to the one shown -below: - -```plumed -# The atoms that are of interest -ow: GROUP ATOMS=1-16500 -# Fixed virtual atom which serves as the probe volume's center (pos. in nm) -center: FIXEDATOM AT=2.5,2.5,2.5 -# Vector in which element i is one if atom i is in sphere of interest and zero otherwise -sphere: INSPHERE ATOMS=ow CENTER=center RADIUS={GAUSSIAN D_0=0.5 R_0=0.01 D_MAX=0.52} -# Calculates cooordination numbers -cmap: CONTACT_MATRIX GROUP=ow SWITCH={GAUSSIAN D_0=0.32 R_0=0.01 D_MAX=0.34} -ones: ONES SIZE=16500 -cc: MATRIX_VECTOR_PRODUCT ARG=cmap,ones -# Multiply coordination numbers by sphere vector -prod: CUSTOM ARG=cc,sphere FUNC=x*y PERIODIC=NO -# Sum of coordination numbers for atoms that are in the sphere of interest -numer: SUM ARG=prod PERIODIC=NO -# Number of atoms that are in sphere of interest -denom: SUM ARG=sphere PERIODIC=NO -# Average coordination number for atoms in sphere of interest -av: CUSTOM ARG=prod,sphere FUNC=x/y PERIODIC=NO -# And print out final CV to a file -PRINT ARG=av FILE=colvar STRIDE=1 -``` - -This calculation is slow because you have to calculate the coordination numbers of all the atoms even though only a small subset of these quanitties are required to compute the average coordination number in the -sphere. To avoid all these unecessary calculations you use the `MASK` keyword as shown below: - -```plumed -# The atoms that are of interest -ow: GROUP ATOMS=1-16500 -# Fixed virtual atom which serves as the probe volume's center (pos. in nm) -center: FIXEDATOM AT=2.5,2.5,2.5 -# Vector in which element i is one if atom i is in sphere of interest and zero otherwise -sphere: INSPHERE ATOMS=ow CENTER=center RADIUS={GAUSSIAN D_0=0.5 R_0=0.01 D_MAX=0.52} -# Calculates cooordination numbers -cmap: CONTACT_MATRIX GROUP=ow SWITCH={GAUSSIAN D_0=0.32 R_0=0.01 D_MAX=0.34} MASK=sphere -ones: ONES SIZE=16500 -cc: MATRIX_VECTOR_PRODUCT ARG=cmap,ones -# Multiply coordination numbers by sphere vector -prod: CUSTOM ARG=cc,sphere FUNC=x*y PERIODIC=NO -# Sum of coordination numbers for atoms that are in the sphere of interest -numer: SUM ARG=prod PERIODIC=NO -# Number of atoms that are in sphere of interest -denom: SUM ARG=sphere PERIODIC=NO -# Average coordination number for atoms in sphere of interest -av: CUSTOM ARG=prod,sphere FUNC=x/y PERIODIC=NO -# And print out final CV to a file -PRINT ARG=av FILE=colvar STRIDE=1 -``` - -Adding the instruction `MASK=sphere` to the CONTACT_MATRIX line in this input tells PLUMED to only calculate the $i$th row in the adjacency matrix if the $i$th element of the vector `sphere` is non-zero. -In other words, by adding this command we have ensured that we are not calculating coordination numbers for atoms that are not in the sphere that is of interest. In this way we can thus reduce the computational -expense of the calculation enormously. - -Notice, that there are other places where we can use this same trick. For example, we could have used MASK as shown below for our calculation of the CV for perovskite nucleation as shown below: - -```plumed -# Lead ions -Pb: GROUP ATOMS=1-64 -# Iodide atoms -I: GROUP ATOMS=65-256 -# Methylamonium "atoms" -- in the real CV these are centers of mass rather than single atoms -cn: GROUP ATOMS=257-320 - -ones192: ONES SIZE=192 -# Contact matrix that determines if methylamoinium moleulcule and I atom are within 6.5 A of each other -cm_cnI: CONTACT_MATRIX GROUPA=cn GROUPB=I SWITCH={RATIONAL R_0=0.65 D_MAX=1.0} -# Coordination number of methylamonium with I -cc_cnI: MATRIX_VECTOR_PRODUCT ARG=cm_cnI,ones192 -# Vector with elements that are one if coordination of methylamounium with lead is >11 -mt_cnI: MORE_THAN ARG=cc_cnI SWITCH={RATIONAL R_0=11 NN=12 MM=24} - -ones64: ONES SIZE=64 -# Contact matrix that determines if methylamoinium moleulcule and Pb atom are within 7.5 A of each other -cm_cnpb: CONTACT_MATRIX GROUPA=cn GROUPB=Pb SWITCH={RATIONAL R_0=0.75 D_MAX=1.5} MASK=mt_cnI -# Coordination number of methylamonium with Pb -cc_cnpb: MATRIX_VECTOR_PRODUCT ARG=cm_cnpb,ones64 -# Vector with elements that are one if coordination of methylamounium with lead is >7 -mt_cnpb: MORE_THAN ARG=cc_cnpb SWITCH={RATIONAL R_0=7 NN=12 MM=24} - -# Contact matrix that determines if methylamonium molecules are within 8 A of each other -cm_cncn: CONTACT_MATRIX GROUP=cn SWITCH={RATIONAL R_0=0.8 D_MAX=1.75} MASK=mt_cnI -# Coordination number of methylamounium with methylamonium -cc_cncn: MATRIX_VECTOR_PRODUCT ARG=cm_cncn,ones64 -# Vector with elements that are one if coordiantion of methylamonium with methylamonium >5 -mt_cncn: MORE_THAN ARG=cc_cncn SWITCH={RATIONAL R_0=5 NN=12 MM=24} - -# Element wise product of these three input vectors. -# mm[i]==1 if coordination number of corrsponding methylamounium with methylamonium is >5 -# and if coordination of methylamounium with Pb is >7 and if coordination of methylamounium with I > 11 -mm: CUSTOM ARG=mt_cncn,mt_cnpb,mt_cnI FUNC=x*y*z PERIODIC=NO - -# Sum of coordination numbers and thus equal to number of methylamoniums with desired coordination numbers -ff: SUM ARG=mm PERIODIC=NO - -rr: RESTRAINT ARG=ff AT=62 KAPPA=10 -``` - -This trick works here because when we find that there are methylamoinium moleulcules with fewer than 11 lead atoms in there first coordination sphere we know that there -is no point calculating the second two coordination numbers. - -*/ -//+ENDPLUMEDOC - -namespace PLMD { -namespace adjmat { - -class ContactMatrixShortcut : public ActionShortcut { -public: - static void registerKeywords(Keywords& keys); - explicit ContactMatrixShortcut(const ActionOptions&); -}; - -PLUMED_REGISTER_ACTION(ContactMatrixShortcut,"CONTACT_MATRIX") - -void ContactMatrixShortcut::registerKeywords(Keywords& keys) { - AdjacencyMatrixBase::registerKeywords( keys ); - keys.remove("GROUP"); - keys.remove("SWITCH"); - keys.add("numbered","GROUP","specifies the list of atoms that should be assumed indistinguishable"); - keys.add("numbered","SWITCH","the input for the switching function that acts upon the distance between each pair of atoms"); - keys.linkActionInDocs("SWITCH","LESS_THAN"); - keys.addActionNameSuffix("_PROPER"); - keys.needsAction("TRANSPOSE"); - keys.needsAction("CONCATENATE"); -} - -ContactMatrixShortcut::ContactMatrixShortcut(const ActionOptions& ao): - Action(ao), - ActionShortcut(ao) { - std::vector grp_str; - std::string atomsstr=""; - std::vector atomsvec; - parseVector("ATOMS",atomsvec); - if( atomsvec.size()>0 ) { - for(unsigned i=0; i( atomsvec[i] ); - if( gg ) { - grp_str.push_back( atomsvec[i] ); - } - } - if( grp_str.size()!=atomsvec.size() ) { - grp_str.resize(0); - atomsstr = " ATOMS=" + atomsvec[0]; - for(unsigned i=1; i9 ) { - error("cannot handle more than 9 groups"); - } - if( grp_str.size()==0 ) { - readInputLine( getShortcutLabel() + ": CONTACT_MATRIX_PROPER " + atomsstr + " " + convertInputLineToString() ); - return; - } - - for(unsigned i=0; ij ) { - join_matrices += " MATRIX" + inum + jnum + "=" + getShortcutLabel() + inum + jnum; - } else { - join_matrices += " MATRIX" + inum + jnum + "=" + getShortcutLabel() + inum + jnum; - } - } - } - readInputLine( join_matrices ); -} - -} -} +#include "ContactMatrixShortcut.h" diff --git a/src/adjmat/ContactMatrixShortcut.h b/src/adjmat/ContactMatrixShortcut.h new file mode 100644 index 0000000000..d3ea5a03c9 --- /dev/null +++ b/src/adjmat/ContactMatrixShortcut.h @@ -0,0 +1,145 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2013-2020 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_adjmat_ContactMatrixShortcut_h +#define __PLUMED_adjmat_ContactMatrixShortcut_h +#include "core/ActionShortcut.h" +#include "core/ActionRegister.h" +#include "core/PlumedMain.h" +#include "core/ActionSet.h" +#include "core/Group.h" + +namespace PLMD { +namespace adjmat { + +template +class ContactMatrixShortcut : public ActionShortcut { +public: + static void registerKeywords(Keywords& keys); + explicit ContactMatrixShortcut(const ActionOptions&); +}; + + +template +void ContactMatrixShortcut::registerKeywords(Keywords& keys) { + CM::registerKeywords( keys ); + keys.remove("GROUP"); + keys.remove("SWITCH"); + keys.add("numbered","GROUP","specifies the list of atoms that should be assumed indistinguishable"); + keys.add("numbered","SWITCH","the input for the switching function that acts upon the distance between each pair of atoms"); + keys.linkActionInDocs("SWITCH","LESS_THAN"); + keys.addActionNameSuffix("_PROPER"); + keys.addActionNameSuffix("_PROPERACC"); + if(!keys.exists("USEGPU")) { + keys.addFlag("USEGPU",false,"run this calculation on the GPU"); + keys.addLinkInDocForFlag("USEGPU","gpu.md"); + } + keys.needsAction("TRANSPOSE"); + keys.needsAction("CONCATENATE"); +} + +template +ContactMatrixShortcut::ContactMatrixShortcut(const ActionOptions& ao): + Action(ao), + ActionShortcut(ao) { + std::vector grp_str; + std::string atomsstr=""; + std::vector atomsvec; + parseVector("ATOMS",atomsvec); + bool usegpuFLAG=false; + parseFlag("USEGPU",usegpuFLAG); + const std::string usegpu=(usegpuFLAG)?"ACC " : " "; + if( atomsvec.size()>0 ) { + for(unsigned i=0; i( atomsvec[i] ); + if( gg ) { + grp_str.push_back( atomsvec[i] ); + } + } + if( grp_str.size()!=atomsvec.size() ) { + grp_str.resize(0); + atomsstr = " ATOMS=" + atomsvec[0]; + for(unsigned i=1; i9 ) { + error("cannot handle more than 9 groups"); + } + if( grp_str.size()==0 ) { + readInputLine( getShortcutLabel() + ": CONTACT_MATRIX_PROPER"+usegpu + + atomsstr + " " + convertInputLineToString() ); + return; + } + + for(unsigned i=0; ij ) { + join_matrices += " MATRIX" + inum + jnum + "=" + getShortcutLabel() + inum + jnum; + } else { + join_matrices += " MATRIX" + inum + jnum + "=" + getShortcutLabel() + inum + jnum; + } + } + } + readInputLine( join_matrices ); +} + +} +} +#endif // __PLUMED_adjmat_ContactMatrixShortcut_h diff --git a/src/adjmat/Neighbors.cpp b/src/adjmat/Neighbors.cpp index dd3e980eb3..f73d1238e0 100644 --- a/src/adjmat/Neighbors.cpp +++ b/src/adjmat/Neighbors.cpp @@ -262,6 +262,8 @@ class Neighbors : public ActionWithVector { public: using input_type = T; using PTM = ParallelTaskManager>; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: /// The parallel task manager PTM taskmanager; diff --git a/src/adjmat/TorsionsMatrix.cpp b/src/adjmat/TorsionsMatrix.cpp index 2df2a10bfe..bc646759f0 100644 --- a/src/adjmat/TorsionsMatrix.cpp +++ b/src/adjmat/TorsionsMatrix.cpp @@ -138,6 +138,8 @@ class TorsionsMatrix : public ActionWithMatrix { public: using input_type = TorsionsMatrixInput; using PTM = ParallelTaskManager; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: PTM taskmanager; public: @@ -148,6 +150,7 @@ class TorsionsMatrix : public ActionWithMatrix { void calculate() override ; void applyNonZeroRankForces( std::vector& outforces ) override ; void getInputData( std::vector& inputdata ) const override ; + void getInputData( std::vector& inputdata ) const override ; static void performTask( std::size_t task_index, const TorsionsMatrixInput& actiondata, ParallelActionsInput& input, @@ -302,6 +305,36 @@ void TorsionsMatrix::getInputData( std::vector& inputdata ) const { } +void TorsionsMatrix::getInputData( std::vector& inputdata ) const { + std::size_t total_data = getPntrToArgument(0)->getNumberOfStoredValues() + + getPntrToArgument(1)->getNumberOfStoredValues() + + 3*getNumberOfAtoms(); + + if( inputdata.size()!=total_data ) { + inputdata.resize( total_data ); + } + + total_data = 0; + Value* myarg = getPntrToArgument(0); + for(unsigned j=0; jgetNumberOfStoredValues(); ++j) { + inputdata[total_data] = myarg->get(j,false); + total_data++; + } + myarg = getPntrToArgument(1); + for(unsigned j=0; jgetNumberOfStoredValues(); ++j) { + inputdata[total_data] = myarg->get(j,false); + total_data++; + } + for(unsigned j=0; j. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC -#include "Colvar.h" +#include "Angle.h" #include "ColvarShortcut.h" #include "MultiColvarTemplate.h" #include "core/ActionRegister.h" @@ -100,108 +97,13 @@ PRINT ARG=a4,a5,a6 FILE=colvar */ //+ENDPLUMEDOC -class Angle : public Colvar { - bool pbc; - std::vector value; - std::vector derivs; -public: - explicit Angle(const ActionOptions&); -// active methods: - void calculate() override; - static void registerKeywords( Keywords& keys ); - static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); - static unsigned getModeAndSetupValues( ActionWithValue* av ); - static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); -}; - -typedef ColvarShortcut AngleShortcut; +typedef Angle AngleD; +typedef ColvarShortcut AngleShortcut; PLUMED_REGISTER_ACTION(AngleShortcut,"ANGLE") -PLUMED_REGISTER_ACTION(Angle,"ANGLE_SCALAR") -typedef MultiColvarTemplate AngleMulti; +PLUMED_REGISTER_ACTION(AngleD,"ANGLE_SCALAR") +typedef MultiColvarTemplate AngleMulti; PLUMED_REGISTER_ACTION(AngleMulti,"ANGLE_VECTOR") -void Angle::registerKeywords( Keywords& keys ) { - Colvar::registerKeywords(keys); - keys.setDisplayName("ANGLE"); - keys.add("atoms","ATOMS","the list of atoms involved in this collective variable (either 3 or 4 atoms)"); - keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); - keys.setValueDescription("scalar/vector","the ANGLE involving these atoms"); - keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); -} - -void Angle::parseAtomList( const int& num, std::vector& atoms, ActionAtomistic* aa ) { - aa->parseAtomList("ATOMS",num,atoms); - if(atoms.size()==3) { - aa->log.printf(" between atoms %d %d %d\n",atoms[0].serial(),atoms[1].serial(),atoms[2].serial()); - atoms.resize(4); - atoms[3]=atoms[2]; - atoms[2]=atoms[1]; - } else if(atoms.size()==4) { - aa->log.printf(" between lines %d-%d and %d-%d\n",atoms[0].serial(),atoms[1].serial(),atoms[2].serial(),atoms[3].serial()); - } else if( num<0 || atoms.size()>0 ) { - aa->error("Number of specified atoms should be either 3 or 4"); - } -} - -unsigned Angle::getModeAndSetupValues( ActionWithValue* av ) { - av->addValueWithDerivatives(); - av->setNotPeriodic(); - return 0; -} - -Angle::Angle(const ActionOptions&ao): - PLUMED_COLVAR_INIT(ao), - pbc(true), - value(1) { - std::vector atoms; - parseAtomList( -1, atoms, this ); - bool nopbc=!pbc; - parseFlag("NOPBC",nopbc); - pbc=!nopbc; - - if(pbc) { - log.printf(" using periodic boundary conditions\n"); - } else { - log.printf(" without periodic boundary conditions\n"); - } - - addValueWithDerivatives(); - setNotPeriodic(); - requestAtoms(atoms); - checkRead(); -} - -// calculator -void Angle::calculate() { - - if(pbc) { - makeWhole(); - } - ColvarOutput cvout = ColvarOutput::createColvarOutput(value,derivs,this); - calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), cvout ); - setValue( value[0] ); - for(unsigned i=0; i. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_colvar_Angle_h +#define __PLUMED_colvar_Angle_h +#include "Colvar.h" +#include "ColvarInput.h" +#include "tools/Angle.h" + +namespace PLMD { +namespace colvar { + +template +class Angle : public Colvar { + bool pbc; + std::vector value; + std::vector derivs; +public: + using precision=T; + explicit Angle(const ActionOptions&); +// active methods: + void calculate() override; + static void registerKeywords( Keywords& keys ); + static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); + static unsigned getModeAndSetupValues( ActionWithValue* av ); + static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); +}; + +template +void Angle::registerKeywords( Keywords& keys ) { + Colvar::registerKeywords(keys); + keys.setDisplayName("ANGLE"); + keys.add("atoms","ATOMS","the list of atoms involved in this collective variable (either 3 or 4 atoms)"); + keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); + keys.setValueDescription("scalar/vector","the ANGLE involving these atoms"); + keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); +} + +template +void Angle::parseAtomList( const int& num, std::vector& atoms, ActionAtomistic* aa ) { + aa->parseAtomList("ATOMS",num,atoms); + if(atoms.size()==3) { + aa->log.printf(" between atoms %d %d %d\n",atoms[0].serial(),atoms[1].serial(),atoms[2].serial()); + atoms.resize(4); + atoms[3]=atoms[2]; + atoms[2]=atoms[1]; + } else if(atoms.size()==4) { + aa->log.printf(" between lines %d-%d and %d-%d\n",atoms[0].serial(),atoms[1].serial(),atoms[2].serial(),atoms[3].serial()); + } else if( num<0 || atoms.size()>0 ) { + aa->error("Number of specified atoms should be either 3 or 4"); + } +} + +template +unsigned Angle::getModeAndSetupValues( ActionWithValue* av ) { + av->addValueWithDerivatives(); + av->setNotPeriodic(); + return 0; +} + +template +Angle::Angle(const ActionOptions&ao): + PLUMED_COLVAR_INIT(ao), + pbc(true), + value(1) { + std::vector atoms; + parseAtomList( -1, atoms, this ); + bool nopbc=!pbc; + parseFlag("NOPBC",nopbc); + pbc=!nopbc; + + if(pbc) { + log.printf(" using periodic boundary conditions\n"); + } else { + log.printf(" without periodic boundary conditions\n"); + } + + addValueWithDerivatives(); + setNotPeriodic(); + requestAtoms(atoms); + checkRead(); +} + +// calculator +template +void Angle::calculate() { + + if(pbc) { + makeWhole(); + } + ColvarOutput cvout = ColvarOutput::createColvarOutput(value,derivs,this); + Angle::calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), cvout ); + setValue( value[0] ); + for(unsigned i=0; i +void Angle::calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ) { + auto dij=delta(cvin.pos[2],cvin.pos[3]); + auto dik=delta(cvin.pos[1],cvin.pos[0]); + VectorTyped ddij,ddik; + + cvout.values[0]=PLMD::Angle::compute(dij,dik,ddij,ddik); + cvout.derivs[0][0]=ddik; + cvout.derivs[0][1]=-ddik; + cvout.derivs[0][2]=-ddij; + cvout.derivs[0][3]=ddij; + ColvarInput::setBoxDerivativesNoPbc( cvin, cvout ); +} + +} //namespace colvar +} //namespace PLMD + +#endif //__PLUMED_colvar_Angle_h diff --git a/src/colvar/ColvarInput.cpp b/src/colvar/ColvarInput.cpp index 4eee939115..fc5249b636 100644 --- a/src/colvar/ColvarInput.cpp +++ b/src/colvar/ColvarInput.cpp @@ -25,54 +25,6 @@ namespace PLMD { namespace colvar { -ColvarInput ColvarInput::createColvarInput( unsigned m, - const std::vector& p, - const Colvar* colv ) { - return ColvarInput( m, - p.size(), - &p[0][0], - colv->getMasses().data(), - colv->getCharges(true).data(), - colv->getPbc() ); -} - -void ColvarInput::setBoxDerivativesNoPbc( const ColvarInput& inpt, ColvarOutput& out ) { - //Both version passes the tests, we should discuss wicht onw might be better - - unsigned nat=inpt.pos.size(); - for(unsigned i=0; i::_zero(v.data()); - for(unsigned j=0; j struct ColvarInput { unsigned mode; const Pbc& pbc; - View2D pos; - View mass; - View charges; + View2D pos; + View mass; + View charges; ColvarInput( unsigned m, unsigned natoms, - const double* p, - const double* w, - const double* q, + const T* p, + const T* w, + const T* q, const Pbc& box ) : mode(m), pbc(box), @@ -54,15 +56,64 @@ struct ColvarInput { mass(w,natoms), charges(q,natoms) { } - static ColvarInput createColvarInput( unsigned m, const std::vector& p, const Colvar* colv ); -#pragma acc routine seq - static void setBoxDerivativesNoPbc( const ColvarInput& inpt, ColvarOutput& out ); + static void setBoxDerivativesNoPbc( const ColvarInput& inpt, ColvarOutput& out ); /// same as setBoxDerivativesNoPbc but with no extra memory allocations -#pragma acc routine seq - static void setBoxDerivativesNoPbc_inplace( const ColvarInput& inpt, ColvarOutput& out ); + static void setBoxDerivativesNoPbc_inplace( const ColvarInput& inpt, ColvarOutput& out ); }; +template +ColvarInput ColvarInput::createColvarInput( unsigned m, + const std::vector& p, + const Colvar* colv ) { + //this won't work with floating point + return ColvarInput( m, + p.size(), + &p[0][0], + colv->getMasses().data(), + colv->getCharges(true).data(), + colv->getPbc() ); +} + +template +void ColvarInput::setBoxDerivativesNoPbc( const ColvarInput& inpt, ColvarOutput& out ) { + //Both version passes the tests, we should discuss wicht onw might be better + + unsigned nat=inpt.pos.size(); + for(unsigned i=0; i +void ColvarInput::setBoxDerivativesNoPbc_inplace( const ColvarInput& inpt, ColvarOutput& out ) { + //now with no extra allocated memory: + unsigned nat=inpt.pos.size(); + for(unsigned i=0; i::_zero(v.data()); + for(unsigned j=0; j::registerKeywords(Keywords& keys ) { } keys.addActionNameSuffix("_SCALAR"); keys.addActionNameSuffix("_VECTOR"); + //GPU related settings + keys.addFlag("USEGPU",false,"run this calculation on the GPU"); + keys.addLinkInDocForFlag("USEGPU","gpu.md"); + keys.addActionNameSuffix("_VECTORACC"); } template @@ -64,8 +68,12 @@ ColvarShortcut::ColvarShortcut(const ActionOptions&ao): if( keywords.style( key, "atoms" ) ) { std::string inpt; parseNumbered( key, 1, inpt ); + bool usegpuFLAG=false; + parseFlag("USEGPU",usegpuFLAG); if( inpt.length()>0 ) { - readInputLine( getShortcutLabel() + ": " + getName() + "_VECTOR " + key + "1=" + inpt + " " + convertInputLineToString() ); + readInputLine( getShortcutLabel() + ": " + + getName() + "_VECTOR" + (usegpuFLAG ? "ACC ":" ") + + key + "1=" + inpt + " " + convertInputLineToString() ); scalar=false; break; } diff --git a/src/colvar/DihedralCorrelation.cpp b/src/colvar/DihedralCorrelation.cpp index b5a93ff599..49d08ee6f8 100644 --- a/src/colvar/DihedralCorrelation.cpp +++ b/src/colvar/DihedralCorrelation.cpp @@ -19,18 +19,12 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC -#include "Colvar.h" +#include "DihedralCorrelation.h" #include "ColvarShortcut.h" #include "MultiColvarTemplate.h" #include "tools/Torsion.h" #include "core/ActionRegister.h" -#include -#include - namespace PLMD { namespace colvar { @@ -80,132 +74,13 @@ PRINT ARG=d FILE=colvar */ //+ENDPLUMEDOC -class DihedralCorrelation : public Colvar { -private: - bool pbc; - std::vector value; - std::vector derivs; -public: - static void registerKeywords( Keywords& keys ); - explicit DihedralCorrelation(const ActionOptions&); - static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); - static unsigned getModeAndSetupValues( ActionWithValue* av ); - void calculate() override; - static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); -}; - -typedef ColvarShortcut DihedralCorrelationShortcut; + +typedef DihedralCorrelation DihedralCorrelationD; +typedef ColvarShortcut DihedralCorrelationShortcut; PLUMED_REGISTER_ACTION(DihedralCorrelationShortcut,"DIHEDRAL_CORRELATION") -PLUMED_REGISTER_ACTION(DihedralCorrelation,"DIHEDRAL_CORRELATION_SCALAR") -typedef MultiColvarTemplate DihedralCorrelationMulti; +PLUMED_REGISTER_ACTION(DihedralCorrelationD,"DIHEDRAL_CORRELATION_SCALAR") +typedef MultiColvarTemplate DihedralCorrelationMulti; PLUMED_REGISTER_ACTION(DihedralCorrelationMulti,"DIHEDRAL_CORRELATION_VECTOR") -void DihedralCorrelation::registerKeywords( Keywords& keys ) { - Colvar::registerKeywords( keys ); - keys.setDisplayName("DIHEDRAL_CORRELATION"); - keys.add("atoms","ATOMS","the set of 8 atoms that are being used to calculate this quantity"); - keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); - keys.setValueDescription("scalar/vector","the DIHEDRAL_CORRELATION for these atoms"); - keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); -} - -DihedralCorrelation::DihedralCorrelation(const ActionOptions&ao): - PLUMED_COLVAR_INIT(ao), - pbc(true), - value(1) { - std::vector atoms; - parseAtomList(-1,atoms,this); - if( atoms.size()!=8 ) { - error("Number of specified atoms should be 8"); - } - - bool nopbc=!pbc; - parseFlag("NOPBC",nopbc); - pbc=!nopbc; - - if(pbc) { - log.printf(" using periodic boundary conditions\n"); - } else { - log.printf(" without periodic boundary conditions\n"); - } - addValueWithDerivatives(); - setNotPeriodic(); -} - -void DihedralCorrelation::parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ) { - aa->parseAtomList("ATOMS",num,t); - if( num<0 && t.size()!=8 ) { - aa->error("Number of specified atoms should be 8"); - } - if( t.size()==8 ) { - aa->log.printf(" correlation between dihedral angle for atoms %d %d %d %d and atoms %d %d %d %d\n", - t[0].serial(),t[1].serial(),t[2].serial(),t[3].serial(),t[4].serial(),t[5].serial(),t[6].serial(),t[7].serial()); - } -} - -unsigned DihedralCorrelation::getModeAndSetupValues( ActionWithValue* av ) { - av->addValueWithDerivatives(); - av->setNotPeriodic(); - return 0; -} - -void DihedralCorrelation::calculate() { - - if(pbc) { - makeWhole(); - } - ColvarOutput cvout = ColvarOutput::createColvarOutput(value,derivs,this); - calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), cvout ); - setValue( value[0] ); - for(unsigned i=0; i. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_colvar_DihedralCorrelation_h +#define __PLUMED_colvar_DihedralCorrelation_h +#include "Colvar.h" +#include "ColvarInput.h" +#include "tools/Torsion.h" + +#include +#include + +namespace PLMD { +namespace colvar { + +template +class DihedralCorrelation : public Colvar { +private: + bool pbc; + std::vector value; + std::vector derivs; +public: + using precision=T; + static void registerKeywords( Keywords& keys ); + explicit DihedralCorrelation(const ActionOptions&); + static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); + static unsigned getModeAndSetupValues( ActionWithValue* av ); + void calculate() override; + static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); +}; + +template +void DihedralCorrelation::registerKeywords( Keywords& keys ) { + Colvar::registerKeywords( keys ); + keys.setDisplayName("DIHEDRAL_CORRELATION"); + keys.add("atoms","ATOMS","the set of 8 atoms that are being used to calculate this quantity"); + keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); + keys.setValueDescription("scalar/vector","the DIHEDRAL_CORRELATION for these atoms"); + keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); +} + +template +DihedralCorrelation::DihedralCorrelation(const ActionOptions&ao): + PLUMED_COLVAR_INIT(ao), + pbc(true), + value(1) { + std::vector atoms; + parseAtomList(-1,atoms,this); + if( atoms.size()!=8 ) { + error("Number of specified atoms should be 8"); + } + + bool nopbc=!pbc; + parseFlag("NOPBC",nopbc); + pbc=!nopbc; + + if(pbc) { + log.printf(" using periodic boundary conditions\n"); + } else { + log.printf(" without periodic boundary conditions\n"); + } + addValueWithDerivatives(); + setNotPeriodic(); +} + +template +void DihedralCorrelation::parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ) { + aa->parseAtomList("ATOMS",num,t); + if( num<0 && t.size()!=8 ) { + aa->error("Number of specified atoms should be 8"); + } + if( t.size()==8 ) { + aa->log.printf(" correlation between dihedral angle for atoms %d %d %d %d and atoms %d %d %d %d\n", + t[0].serial(),t[1].serial(),t[2].serial(),t[3].serial(),t[4].serial(),t[5].serial(),t[6].serial(),t[7].serial()); + } +} + +template +unsigned DihedralCorrelation::getModeAndSetupValues( ActionWithValue* av ) { + av->addValueWithDerivatives(); + av->setNotPeriodic(); + return 0; +} + +template +void DihedralCorrelation::calculate() { + + if(pbc) { + makeWhole(); + } + auto cvout = ColvarOutput::createColvarOutput(value,derivs,this); + DihedralCorrelation::calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), cvout ); + setValue( value[0] ); + for(unsigned i=0; i +void DihedralCorrelation::calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ) { + const auto d10=delta(cvin.pos[1],cvin.pos[0]); + const auto d11=delta(cvin.pos[2],cvin.pos[1]); + const auto d12=delta(cvin.pos[3],cvin.pos[2]); + + VectorTyped dd10,dd11,dd12; + const T phi1 = PLMD::Torsion::compute(d10,d11,d12,dd10,dd11,dd12); + + const auto d20=delta(cvin.pos[5],cvin.pos[4]); + const auto d21=delta(cvin.pos[6],cvin.pos[5]); + const auto d22=delta(cvin.pos[7],cvin.pos[6]); + + VectorTyped dd20,dd21,dd22; + const T phi2 = PLMD::Torsion::compute( d20, d21, d22, dd20, dd21, dd22 ); + + // Calculate value + const T diff = phi2 - phi1; + cvout.values[0] = 0.5*(1.+std::cos(diff)); + // Derivatives wrt phi1 + const T dval = 0.5*std::sin(diff); + dd10 *= dval; + dd11 *= dval; + dd12 *= dval; + // And add + cvout.derivs[0][0]=dd10; + cvout.derivs[0][1]=dd11-dd10; + cvout.derivs[0][2]=dd12-dd11; + cvout.derivs[0][3]=-dd12; + // Derivative wrt phi2 + dd20 *= -dval; + dd21 *= -dval; + dd22 *= -dval; + // And add + cvout.derivs[0][4]=dd20; + cvout.derivs[0][5]=dd21-dd20; + cvout.derivs[0][6]=dd22-dd21; + cvout.derivs[0][7]=-dd22; + cvout.virial.set( 0, + -(extProduct(d10,dd10)+extProduct(d11,dd11)+extProduct(d12,dd12)) + -(extProduct(d20,dd20)+extProduct(d21,dd21)+extProduct(d22,dd22)) ); +} + +} // namespace colvar +} // namespace PLMD +#endif //__PLUMED_colvar_DihedralCorrelation_h diff --git a/src/colvar/Dipole.cpp b/src/colvar/Dipole.cpp index f7955b7f46..4cdf0bf7d1 100644 --- a/src/colvar/Dipole.cpp +++ b/src/colvar/Dipole.cpp @@ -19,10 +19,7 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC -#include "Colvar.h" +#include "Dipole.h" #include "ColvarShortcut.h" #include "MultiColvarTemplate.h" #include "core/ActionRegister.h" @@ -91,165 +88,12 @@ PRINT FILE=output STRIDE=5 ARG=d */ //+ENDPLUMEDOC -class Dipole : public Colvar { - std::vector ga_lista; - bool components; - bool nopbc; - std::vector value; - std::vector derivs; - Value* valuex=nullptr; - Value* valuey=nullptr; - Value* valuez=nullptr; -public: - explicit Dipole(const ActionOptions&); - static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); - static unsigned getModeAndSetupValues( ActionWithValue* av ); - void calculate() override; - static void registerKeywords(Keywords& keys); - static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); -}; - -typedef ColvarShortcut DipoleShortcut; +typedef Dipole DipoleD; +typedef ColvarShortcut DipoleShortcut; PLUMED_REGISTER_ACTION(DipoleShortcut,"DIPOLE") -PLUMED_REGISTER_ACTION(Dipole,"DIPOLE_SCALAR") -typedef MultiColvarTemplate DipoleMulti; +PLUMED_REGISTER_ACTION(DipoleD,"DIPOLE_SCALAR") +typedef MultiColvarTemplate DipoleMulti; PLUMED_REGISTER_ACTION(DipoleMulti,"DIPOLE_VECTOR") -void Dipole::registerKeywords(Keywords& keys) { - Colvar::registerKeywords(keys); - keys.setDisplayName("DIPOLE"); - keys.add("atoms","GROUP","the group of atoms we are calculating the dipole moment for"); - keys.addFlag("COMPONENTS",false,"calculate the x, y and z components of the dipole separately and store them as label.x, label.y and label.z"); - keys.addOutputComponent("x","COMPONENTS","scalar/vector","the x-component of the dipole"); - keys.addOutputComponent("y","COMPONENTS","scalar/vector","the y-component of the dipole"); - keys.addOutputComponent("z","COMPONENTS","scalar/vector","the z-component of the dipole"); - keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); - keys.setValueDescription("scalar/vector","the DIPOLE for these atoms"); - keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); -} - -Dipole::Dipole(const ActionOptions&ao): - PLUMED_COLVAR_INIT(ao), - components(false), - value(1) { - parseAtomList(-1,ga_lista,this); - components=(getModeAndSetupValues(this)==1); - if( components ) { - value.resize(3); - valuex=getPntrToComponent("x"); - valuey=getPntrToComponent("y"); - valuez=getPntrToComponent("z"); - } else { - derivs.resize(1,ga_lista.size()); - } - parseFlag("NOPBC",nopbc); - checkRead(); - - if(nopbc) { - log.printf(" without periodic boundary conditions\n"); - } else { - log.printf(" using periodic boundary conditions\n"); - } - - requestAtoms(ga_lista); -} - -void Dipole::parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ) { - aa->parseAtomList("GROUP",num,t); - if( t.size()>0 ) { - aa->log.printf(" of %u atoms\n",static_cast(t.size())); - for(unsigned int i=0; ilog.printf(" %d", t[i].serial()); - } - aa->log.printf(" \n"); - } -} - -unsigned Dipole::getModeAndSetupValues( ActionWithValue* av ) { - bool c; - av->parseFlag("COMPONENTS",c); - if( c ) { - av->addComponentWithDerivatives("x"); - av->componentIsNotPeriodic("x"); - av->addComponentWithDerivatives("y"); - av->componentIsNotPeriodic("y"); - av->addComponentWithDerivatives("z"); - av->componentIsNotPeriodic("z"); - return 1; - } - av->addValueWithDerivatives(); - av->setNotPeriodic(); - return 0; -} - -// calculator -void Dipole::calculate() { - if( !chargesWereSet ) { - error("charges were not set by MD code"); - } - - if(!nopbc) { - makeWhole(); - } - unsigned N=getNumberOfAtoms(); - - if(!components) { - ColvarOutput cvout( ColvarOutput::createColvarOutput(value, derivs, this) ); - calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), cvout ); - for(unsigned i=0; iset(value[0]); - valuey->set(value[1]); - valuez->set(value[2]); - } -} - -void Dipole::calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ) { - unsigned N=cvin.pos.size(); - double ctot=0.; - for(unsigned i=0; i. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_colvar_Dipole_h +#define __PLUMED_colvar_Dipole_h +#include "Colvar.h" +#include "ColvarInput.h" + +namespace PLMD { +namespace colvar { + +template +class Dipole : public Colvar { + std::vector ga_lista; + enum /*class*/ modes:unsigned { + components=1, + scalar=0 + } mode{scalar}; + bool nopbc; + std::vector value; + std::vector derivs; + Value* valuex=nullptr; + Value* valuey=nullptr; + Value* valuez=nullptr; +public: + using precision=T; + explicit Dipole(const ActionOptions&); + static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); + static unsigned getModeAndSetupValues( ActionWithValue* av ); + void calculate() override; + static void registerKeywords(Keywords& keys); + static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); +}; + +template +void Dipole::registerKeywords(Keywords& keys) { + Colvar::registerKeywords(keys); + keys.setDisplayName("DIPOLE"); + keys.add("atoms","GROUP","the group of atoms we are calculating the dipole moment for"); + keys.addFlag("COMPONENTS",false,"calculate the x, y and z components of the dipole separately and store them as label.x, label.y and label.z"); + keys.addOutputComponent("x","COMPONENTS","scalar/vector","the x-component of the dipole"); + keys.addOutputComponent("y","COMPONENTS","scalar/vector","the y-component of the dipole"); + keys.addOutputComponent("z","COMPONENTS","scalar/vector","the z-component of the dipole"); + keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); + keys.setValueDescription("scalar/vector","the DIPOLE for these atoms"); + keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); +} + +template +Dipole::Dipole(const ActionOptions&ao): + PLUMED_COLVAR_INIT(ao) { + parseAtomList(-1,ga_lista,this); + mode=static_cast(getModeAndSetupValues(this)); + if( mode==modes::components ) { + value.resize(3); + valuex=getPntrToComponent("x"); + valuey=getPntrToComponent("y"); + valuez=getPntrToComponent("z"); + } else { + value.resize(1); + derivs.resize(1,ga_lista.size()); + } + parseFlag("NOPBC",nopbc); + checkRead(); + + if(nopbc) { + log.printf(" without periodic boundary conditions\n"); + } else { + log.printf(" using periodic boundary conditions\n"); + } + + requestAtoms(ga_lista); +} + +template +void Dipole::parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ) { + aa->parseAtomList("GROUP",num,t); + if( t.size()>0 ) { + aa->log.printf(" of %u atoms\n",static_cast(t.size())); + for(unsigned int i=0; ilog.printf(" %d", t[i].serial()); + } + aa->log.printf(" \n"); + } +} + +template +unsigned Dipole::getModeAndSetupValues( ActionWithValue* av ) { + bool c; + av->parseFlag("COMPONENTS",c); + if( c ) { + av->addComponentWithDerivatives("x"); + av->componentIsNotPeriodic("x"); + av->addComponentWithDerivatives("y"); + av->componentIsNotPeriodic("y"); + av->addComponentWithDerivatives("z"); + av->componentIsNotPeriodic("z"); + return modes::components; + } + av->addValueWithDerivatives(); + av->setNotPeriodic(); + return modes::scalar; +} + +// calculator +template +void Dipole::calculate() { + if( !chargesWereSet ) { + error("charges were not set by MD code"); + } + + if(!nopbc) { + makeWhole(); + } + const unsigned N=getNumberOfAtoms(); + + auto cvout= ColvarOutput::createColvarOutput(value, derivs, this); + Dipole::calculateCV( ColvarInput::createColvarInput( mode, getPositions(), this ), + cvout ); + if(mode==modes::scalar) { + for(unsigned i=0; iset(value[0]); + valuey->set(value[1]); + valuez->set(value[2]); + } +} + +template +void Dipole::calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ) { + using V3 = VectorTyped; + const unsigned N=cvin.pos.size(); + T ctot=0.; + for(unsigned i=0; i::setBoxDerivativesNoPbc( cvin, cvout ); +} + +} +} +#endif //__PLUMED_colvar_Dipole_h diff --git a/src/colvar/Distance.cpp b/src/colvar/Distance.cpp index 5dad010d39..c2c34ec5af 100644 --- a/src/colvar/Distance.cpp +++ b/src/colvar/Distance.cpp @@ -19,15 +19,10 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -//this is temporary: -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC -#include "Colvar.h" + +#include "Distance.h" #include "ColvarShortcut.h" -#include "MultiColvarTemplate.h" #include "core/ActionRegister.h" -#include "tools/Pbc.h" namespace PLMD { namespace colvar { @@ -141,222 +136,12 @@ with domain (-0.5,+0.5). */ //+ENDPLUMEDOC - -class Distance : public Colvar { - bool components; - bool scaled_components; - bool pbc; - - std::vector value; - std::vector derivs; -public: - static void registerKeywords( Keywords& keys ); - explicit Distance(const ActionOptions&); - static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); - static unsigned getModeAndSetupValues( ActionWithValue* av ); -// active methods: - void calculate() override; - static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); -}; - -typedef ColvarShortcut DistanceShortcut; +typedef Distance DistanceD; +typedef ColvarShortcut DistanceShortcut; PLUMED_REGISTER_ACTION(DistanceShortcut,"DISTANCE") -PLUMED_REGISTER_ACTION(Distance,"DISTANCE_SCALAR") -typedef MultiColvarTemplate DistanceMulti; +PLUMED_REGISTER_ACTION(DistanceD,"DISTANCE_SCALAR") +typedef MultiColvarTemplate DistanceMulti; PLUMED_REGISTER_ACTION(DistanceMulti,"DISTANCE_VECTOR") -void Distance::registerKeywords( Keywords& keys ) { - Colvar::registerKeywords( keys ); - keys.setDisplayName("DISTANCE"); - constexpr auto scalarOrVector = Keywords::componentType::scalar | Keywords::componentType::vector; - keys.add("atoms","ATOMS","the pair of atom that we are calculating the distance between"); - keys.addFlag("COMPONENTS",false,"calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z"); - keys.addFlag("SCALED_COMPONENTS",false,"calculate the a, b and c scaled components of the distance separately and store them as label.a, label.b and label.c"); - keys.addOutputComponent("x","COMPONENTS",scalarOrVector,"the x-component of the vector connecting the two atoms"); - keys.addOutputComponent("y","COMPONENTS",scalarOrVector,"the y-component of the vector connecting the two atoms"); - keys.addOutputComponent("z","COMPONENTS",scalarOrVector,"the z-component of the vector connecting the two atoms"); - keys.addOutputComponent("a","SCALED_COMPONENTS",scalarOrVector,"the normalized projection on the first lattice vector of the vector connecting the two atoms"); - keys.addOutputComponent("b","SCALED_COMPONENTS",scalarOrVector,"the normalized projection on the second lattice vector of the vector connecting the two atoms"); - keys.addOutputComponent("c","SCALED_COMPONENTS",scalarOrVector,"the normalized projection on the third lattice vector of the vector connecting the two atoms"); - keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); - keys.setValueDescription(scalarOrVector,"the DISTANCE between this pair of atoms"); - keys.addDOI("10.1007/978-1-4939-9608-7_21"); - keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); -} - -Distance::Distance(const ActionOptions&ao): - PLUMED_COLVAR_INIT(ao), - components(false), - scaled_components(false), - pbc(true), - value(1) { - std::vector atoms; - parseAtomList(-1,atoms,this); - if(atoms.size()!=2) { - error("Number of specified atoms should be 2"); - } - - bool nopbc=!pbc; - parseFlag("NOPBC",nopbc); - pbc=!nopbc; - - if(pbc) { - log.printf(" using periodic boundary conditions\n"); - } else { - log.printf(" without periodic boundary conditions\n"); - } - - unsigned mode = getModeAndSetupValues( this ); - if(mode==1) { - components=true; - } else if(mode==2) { - scaled_components=true; - } - if( components || scaled_components ) { - value.resize(3); - } - requestAtoms(atoms); -} - -void Distance::parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ) { - aa->parseAtomList("ATOMS",num,t); - if( t.size()==2 ) { - aa->log.printf(" between atoms %d %d\n",t[0].serial(),t[1].serial()); - } -} - -unsigned Distance::getModeAndSetupValues( ActionWithValue* av ) { - bool c; - av->parseFlag("COMPONENTS",c); - bool sc; - av->parseFlag("SCALED_COMPONENTS",sc); - if( c && sc ) { - av->error("COMPONENTS and SCALED_COMPONENTS are not compatible"); - } - - if(c) { - av->addComponentWithDerivatives("x"); - av->componentIsNotPeriodic("x"); - av->addComponentWithDerivatives("y"); - av->componentIsNotPeriodic("y"); - av->addComponentWithDerivatives("z"); - av->componentIsNotPeriodic("z"); - av->log<<" WARNING: components will not have the proper periodicity - see manual\n"; - return 1; - } else if(sc) { - av->addComponentWithDerivatives("a"); - av->componentIsPeriodic("a","-0.5","+0.5"); - av->addComponentWithDerivatives("b"); - av->componentIsPeriodic("b","-0.5","+0.5"); - av->addComponentWithDerivatives("c"); - av->componentIsPeriodic("c","-0.5","+0.5"); - return 2; - } - av->addValueWithDerivatives(); - av->setNotPeriodic(); - return 0; -} - -// calculator -void Distance::calculate() { - - if(pbc) { - makeWhole(); - } - - if( components ) { - ColvarOutput cvout( ColvarOutput::createColvarOutput(value, derivs, this) ); - calculateCV( ColvarInput::createColvarInput( 1, getPositions(), this ), cvout ); - Value* valuex=getPntrToComponent("x"); - Value* valuey=getPntrToComponent("y"); - Value* valuez=getPntrToComponent("z"); - - for(unsigned i=0; i<2; ++i) { - setAtomsDerivatives(valuex,i,cvout.getAtomDerivatives(0,i) ); - } - setBoxDerivatives(valuex,cvout.virial[0]); - valuex->set(value[0]); - - for(unsigned i=0; i<2; ++i) { - setAtomsDerivatives(valuey,i,cvout.getAtomDerivatives(1,i) ); - } - setBoxDerivatives(valuey,cvout.virial[1]); - valuey->set(value[1]); - - for(unsigned i=0; i<2; ++i) { - setAtomsDerivatives(valuez,i,cvout.getAtomDerivatives(2,i) ); - } - setBoxDerivatives(valuez,cvout.virial[2]); - valuez->set(value[2]); - } else if( scaled_components ) { - ColvarOutput cvout( ColvarOutput::createColvarOutput(value, derivs, this) ); - calculateCV( ColvarInput::createColvarInput( 2, getPositions(), this ), cvout ); - - Value* valuea=getPntrToComponent("a"); - Value* valueb=getPntrToComponent("b"); - Value* valuec=getPntrToComponent("c"); - for(unsigned i=0; i<2; ++i) { - setAtomsDerivatives(valuea,i,cvout.getAtomDerivatives(0,i) ); - } - valuea->set(value[0]); - for(unsigned i=0; i<2; ++i) { - setAtomsDerivatives(valueb,i,cvout.getAtomDerivatives(1,i) ); - } - valueb->set(value[1]); - for(unsigned i=0; i<2; ++i) { - setAtomsDerivatives(valuec,i,cvout.getAtomDerivatives(2,i) ); - } - valuec->set(value[2]); - } else { - ColvarOutput cvout( ColvarOutput::createColvarOutput(value, derivs, this) ); - calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), cvout ); - for(unsigned i=0; i<2; ++i) { - setAtomsDerivatives(i,cvout.getAtomDerivatives(0,i) ); - } - setBoxDerivatives(cvout.virial[0]); - setValue (value[0]); - } -} - -void Distance::calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ) { - Vector distance=delta(cvin.pos[0],cvin.pos[1]); - - if(cvin.mode==1) { - cvout.derivs[0][0] = Vector(-1,0,0); - cvout.derivs[0][1] = Vector(+1,0,0); - cvout.values[0] = distance[0]; - - cvout.derivs[1][0] = Vector(0,-1,0); - cvout.derivs[1][1] = Vector(0,+1,0); - cvout.values[1] = distance[1]; - - cvout.derivs[2][0] = Vector(0,0,-1); - cvout.derivs[2][1] = Vector(0,0,+1); - cvout.values[2] = distance[2]; - ColvarInput::setBoxDerivativesNoPbc( cvin, cvout ); - } else if(cvin.mode==2) { - Vector d=cvin.pbc.realToScaled(distance); - cvout.derivs[0][0] = matmul(cvin.pbc.getInvBox(),Vector(-1,0,0)); - cvout.derivs[0][1] = matmul(cvin.pbc.getInvBox(),Vector(+1,0,0)); - cvout.values[0] = Tools::pbc(d[0]); - cvout.derivs[1][0] = matmul(cvin.pbc.getInvBox(),Vector(0,-1,0)); - cvout.derivs[1][1] = matmul(cvin.pbc.getInvBox(),Vector(0,+1,0)); - cvout.values[1] = Tools::pbc(d[1]); - cvout.derivs[2][0] = matmul(cvin.pbc.getInvBox(),Vector(0,0,-1)); - cvout.derivs[2][1] = matmul(cvin.pbc.getInvBox(),Vector(0,0,+1)); - cvout.values[2] = Tools::pbc(d[2]); - } else { - const double value=distance.modulo(); - const double invvalue=1.0/value; - cvout.derivs[0][0] = -invvalue*distance; - cvout.derivs[0][1] = invvalue*distance; - ColvarInput::setBoxDerivativesNoPbc( cvin, cvout ); - cvout.values[0] = value; - } -} - -} -} - - - +} //namespace colvar +} //namespace PLMD diff --git a/src/colvar/Distance.h b/src/colvar/Distance.h new file mode 100644 index 0000000000..8ad3ce1b7d --- /dev/null +++ b/src/colvar/Distance.h @@ -0,0 +1,254 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_colvar_Distance_h +#define __PLUMED_colvar_Distance_h +#include "Colvar.h" +#include "ColvarInput.h" +#include "MultiColvarTemplate.h" +#include "tools/Pbc.h" + +namespace PLMD { +namespace colvar { + +template +class Distance : public Colvar { + enum components:unsigned {scaled=2,standard=1,scalar=0} mode{scalar}; + bool pbc; + + //not Typep, the float version is only used for the PTM + std::vector value; + std::vector derivs; +public: + using precision = T; + static void registerKeywords( Keywords& keys ); + explicit Distance(const ActionOptions&); + static void parseAtomList( const int& num, + std::vector& t, + ActionAtomistic* aa ); + static unsigned getModeAndSetupValues( ActionWithValue* av ); +// active methods: + void calculate() override; + static void calculateCV( const ColvarInput& cvin, + ColvarOutput& cvout ); +}; + +template +void Distance::registerKeywords( Keywords& keys ) { + Colvar::registerKeywords( keys ); + keys.setDisplayName("DISTANCE"); + constexpr auto scalarOrVector = Keywords::componentType::scalar + | Keywords::componentType::vector; + keys.add("atoms","ATOMS","the pair of atom that we are calculating the distance between"); + keys.addFlag("COMPONENTS",false,"calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z"); + keys.addFlag("SCALED_COMPONENTS",false,"calculate the a, b and c scaled components of the distance separately and store them as label.a, label.b and label.c"); + keys.addOutputComponent("x","COMPONENTS",scalarOrVector,"the x-component of the vector connecting the two atoms"); + keys.addOutputComponent("y","COMPONENTS",scalarOrVector,"the y-component of the vector connecting the two atoms"); + keys.addOutputComponent("z","COMPONENTS",scalarOrVector,"the z-component of the vector connecting the two atoms"); + keys.addOutputComponent("a","SCALED_COMPONENTS",scalarOrVector,"the normalized projection on the first lattice vector of the vector connecting the two atoms"); + keys.addOutputComponent("b","SCALED_COMPONENTS",scalarOrVector,"the normalized projection on the second lattice vector of the vector connecting the two atoms"); + keys.addOutputComponent("c","SCALED_COMPONENTS",scalarOrVector,"the normalized projection on the third lattice vector of the vector connecting the two atoms"); + keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); + keys.setValueDescription(scalarOrVector,"the DISTANCE between this pair of atoms"); + keys.addDOI("10.1007/978-1-4939-9608-7_21"); + keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); +} + +template +Distance::Distance(const ActionOptions&ao): + PLUMED_COLVAR_INIT(ao), + pbc(true), + value(1) { + std::vector atoms; + parseAtomList(-1,atoms,this); + if(atoms.size()!=2) { + error("Number of specified atoms should be 2"); + } + + bool nopbc=!pbc; + parseFlag("NOPBC",nopbc); + pbc=!nopbc; + + if(pbc) { + log.printf(" using periodic boundary conditions\n"); + } else { + log.printf(" without periodic boundary conditions\n"); + } + + mode = static_cast(getModeAndSetupValues(this)); + if( mode == components::standard || mode == components::scaled ) { + value.resize(3); + } + requestAtoms(atoms); +} + +template +void Distance::parseAtomList( const int& num, + std::vector& t, + ActionAtomistic* aa ) { + aa->parseAtomList("ATOMS",num,t); + if( t.size()==2 ) { + aa->log.printf(" between atoms %d %d\n",t[0].serial(),t[1].serial()); + } +} + +template +unsigned Distance::getModeAndSetupValues( ActionWithValue* av ) { + bool c; + av->parseFlag("COMPONENTS",c); + bool sc; + av->parseFlag("SCALED_COMPONENTS",sc); + if( c && sc ) { + av->error("COMPONENTS and SCALED_COMPONENTS are not compatible"); + } + if(c) { + av->addComponentWithDerivatives("x"); + av->componentIsNotPeriodic("x"); + av->addComponentWithDerivatives("y"); + av->componentIsNotPeriodic("y"); + av->addComponentWithDerivatives("z"); + av->componentIsNotPeriodic("z"); + av->log<<" WARNING: components will not have the proper periodicity - see manual\n"; + return components::standard; + } else if(sc) { + av->addComponentWithDerivatives("a"); + av->componentIsPeriodic("a","-0.5","+0.5"); + av->addComponentWithDerivatives("b"); + av->componentIsPeriodic("b","-0.5","+0.5"); + av->addComponentWithDerivatives("c"); + av->componentIsPeriodic("c","-0.5","+0.5"); + return components::scaled; + } + av->addValueWithDerivatives(); + av->setNotPeriodic(); + return components::scalar; +} + +// calculator +template +void Distance::calculate() { + + if(pbc) { + makeWhole(); + } + using CVInput= ColvarInput; + using CVOutput=ColvarOutput; + auto cvout = CVOutput::createColvarOutput(value, derivs, this); + Distance::calculateCV( CVInput::createColvarInput( mode, getPositions(), this ), cvout ); + if( mode==components::standard ) { + Value* valuex=getPntrToComponent("x"); + Value* valuey=getPntrToComponent("y"); + Value* valuez=getPntrToComponent("z"); + + for(unsigned i=0; i<2; ++i) { + setAtomsDerivatives(valuex,i,cvout.getAtomDerivatives(0,i) ); + } + setBoxDerivatives(valuex,cvout.virial[0]); + valuex->set(value[0]); + + for(unsigned i=0; i<2; ++i) { + setAtomsDerivatives(valuey,i,cvout.getAtomDerivatives(1,i) ); + } + setBoxDerivatives(valuey,cvout.virial[1]); + valuey->set(value[1]); + + for(unsigned i=0; i<2; ++i) { + setAtomsDerivatives(valuez,i,cvout.getAtomDerivatives(2,i) ); + } + setBoxDerivatives(valuez,cvout.virial[2]); + valuez->set(value[2]); + } else if( mode==components::scaled ) { + + Value* valuea=getPntrToComponent("a"); + Value* valueb=getPntrToComponent("b"); + Value* valuec=getPntrToComponent("c"); + for(unsigned i=0; i<2; ++i) { + setAtomsDerivatives(valuea,i,cvout.getAtomDerivatives(0,i) ); + } + valuea->set(value[0]); + for(unsigned i=0; i<2; ++i) { + setAtomsDerivatives(valueb,i,cvout.getAtomDerivatives(1,i) ); + } + valueb->set(value[1]); + for(unsigned i=0; i<2; ++i) { + setAtomsDerivatives(valuec,i,cvout.getAtomDerivatives(2,i) ); + } + valuec->set(value[2]); + } else { + for(unsigned i=0; i<2; ++i) { + setAtomsDerivatives(i,cvout.getAtomDerivatives(0,i) ); + } + setBoxDerivatives(cvout.virial[0]); + setValue (value[0]); + } +} + +template +void Distance::calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ) { + auto distance=delta(cvin.pos[0],cvin.pos[1]); + //these six can be compacted in a scoped `using namespac3 PLMD::Versors` but plumedcheck won't approve (even in a comment, hence the 3) + using PLMD::Versors::xp; + using PLMD::Versors::xm; + using PLMD::Versors::yp; + using PLMD::Versors::ym; + using PLMD::Versors::zp; + using PLMD::Versors::zm; + if(cvin.mode==components::standard) { + + cvout.derivs[0][0] = xm; + cvout.derivs[0][1] = xp; + cvout.values[0] = distance[0]; + + cvout.derivs[1][0] = ym; + cvout.derivs[1][1] = yp; + cvout.values[1] = distance[1]; + + cvout.derivs[2][0] = zm; + cvout.derivs[2][1] = zp; + cvout.values[2] = distance[2]; + ColvarInput::setBoxDerivativesNoPbc( cvin, cvout ); + } else if(cvin.mode==components::scaled) { + auto d=cvin.pbc.realToScaled(distance); + cvout.derivs[0][0].copyConv(matmul(cvin.pbc.getInvBox(),xm)); + cvout.derivs[0][1].copyConv(matmul(cvin.pbc.getInvBox(),xp)); + cvout.values[0] = Tools::pbc(d[0]); + cvout.derivs[1][0].copyConv(matmul(cvin.pbc.getInvBox(),ym)); + cvout.derivs[1][1].copyConv(matmul(cvin.pbc.getInvBox(),yp)); + cvout.values[1] = Tools::pbc(d[1]); + cvout.derivs[2][0].copyConv(matmul(cvin.pbc.getInvBox(),zm)); + cvout.derivs[2][1].copyConv(matmul(cvin.pbc.getInvBox(),zp)); + cvout.values[2] = Tools::pbc(d[2]); + } else { + const double value=distance.modulo(); + const double invvalue=1.0/value; + cvout.derivs[0][0] = -invvalue*distance; + cvout.derivs[0][1] = invvalue*distance; + ColvarInput::setBoxDerivativesNoPbc( cvin, cvout ); + cvout.values[0] = value; + } +} + +} //namespace colvar +} //namespace PLMD + +#endif //__PLUMED_colvar_Distance_h + + diff --git a/src/colvar/MultiColvarTemplate.h b/src/colvar/MultiColvarTemplate.h index 85b5cd595d..650a1dcece 100644 --- a/src/colvar/MultiColvarTemplate.h +++ b/src/colvar/MultiColvarTemplate.h @@ -47,11 +47,15 @@ struct MultiColvarInput { } }; -template +template class MultiColvarTemplate : public ActionWithVector { public: using input_type = MultiColvarInput; - using PTM = ParallelTaskManager>; + using mytype=MultiColvarTemplate; + using PTM =typename myPTM::template PTM; + using precision = typename cvprecision::type; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; constexpr static size_t virialSize = 9; private: /// The parallel task manager @@ -71,6 +75,7 @@ class MultiColvarTemplate : public ActionWithVector { void addValueWithDerivatives( const std::vector& shape=std::vector() ) override ; void addComponentWithDerivatives( const std::string& name, const std::vector& shape=std::vector() ) override ; void getInputData( std::vector& inputdata ) const override ; + void getInputData( std::vector& inputdata ) const override ; void calculate() override; void applyNonZeroRankForces( std::vector& outforces ) override ; static void performTask( std::size_t task_index, @@ -86,9 +91,9 @@ class MultiColvarTemplate : public ActionWithVector { ForceIndexHolder force_indices ); }; -template -void MultiColvarTemplate::registerKeywords(Keywords& keys ) { - T::registerKeywords( keys ); +template +void MultiColvarTemplate::registerKeywords(Keywords& keys ) { + CV::registerKeywords( keys ); PTM::registerKeywords( keys ); keys.addInputKeyword("optional","MASK","vector","the label for a sparse vector that should be used to determine which elements of the vector should be computed"); unsigned nkeys = keys.size(); @@ -102,8 +107,8 @@ void MultiColvarTemplate::registerKeywords(Keywords& keys ) { } } -template -MultiColvarTemplate::MultiColvarTemplate(const ActionOptions&ao): +template +MultiColvarTemplate::MultiColvarTemplate(const ActionOptions&ao): Action(ao), ActionWithVector(ao), taskmanager(this), @@ -119,7 +124,7 @@ MultiColvarTemplate::MultiColvarTemplate(const ActionOptions&ao): } else { std::vector t; for(int i=1;; ++i ) { - T::parseAtomList( i, t, this ); + CV::parseAtomList( i, t, this ); if( t.empty() ) { break; } @@ -160,47 +165,47 @@ MultiColvarTemplate::MultiColvarTemplate(const ActionOptions&ao): } // Setup the values - mode = T::getModeAndSetupValues( this ); + mode = CV::getModeAndSetupValues( this ); // This sets up an array in the parallel task manager to hold all the indices // Sets up the index list in the task manager taskmanager.setupParallelTaskManager( 3*natoms_per_task + virialSize, virialSize ); taskmanager.setActionInput( MultiColvarInput{ usepbc, mode, natoms_per_task }); } -template -unsigned MultiColvarTemplate::getNumberOfDerivatives() { +template +unsigned MultiColvarTemplate::getNumberOfDerivatives() { return 3*getNumberOfAtoms()+9; } -template -void MultiColvarTemplate::calculate() { +template +void MultiColvarTemplate::calculate() { if( wholemolecules ) { makeWhole(); } taskmanager.runAllTasks(); } -template -void MultiColvarTemplate::applyNonZeroRankForces( std::vector& outforces ) { +template +void MultiColvarTemplate::applyNonZeroRankForces( std::vector& outforces ) { taskmanager.applyForces( outforces ); } -template -void MultiColvarTemplate::addValueWithDerivatives( const std::vector& shape ) { +template +void MultiColvarTemplate::addValueWithDerivatives( const std::vector& shape ) { std::vector s(1); s[0]=getNumberOfAtoms() / natoms_per_task; addValue( s ); } -template -void MultiColvarTemplate::addComponentWithDerivatives( const std::string& compName, const std::vector& shape ) { +template +void MultiColvarTemplate::addComponentWithDerivatives( const std::string& compName, const std::vector& shape ) { std::vector s(1); s[0]=getNumberOfAtoms() / natoms_per_task; addComponent( compName, s ); } -template -void MultiColvarTemplate::getInputData( std::vector& inputdata ) const { +template +void MultiColvarTemplate::getInputData( std::vector& inputdata ) const { std::size_t ntasks = getConstPntrToComponent(0)->getNumberOfStoredValues(); if( inputdata.size()!=5*natoms_per_task*ntasks ) { inputdata.resize( 5*natoms_per_task*ntasks ); @@ -228,19 +233,49 @@ void MultiColvarTemplate::getInputData( std::vector& inputdata ) cons } } -template -void MultiColvarTemplate::performTask( std::size_t task_index, +template +void MultiColvarTemplate::getInputData( std::vector& inputdata ) const { + std::size_t ntasks = getConstPntrToComponent(0)->getNumberOfStoredValues(); + if( inputdata.size()!=5*natoms_per_task*ntasks ) { + inputdata.resize( 5*natoms_per_task*ntasks ); + } + + std::size_t k=0; + for(unsigned i=0; i +void MultiColvarTemplate::performTask( std::size_t task_index, const MultiColvarInput& actiondata, ParallelActionsInput& input, ParallelActionsOutput& output ) { std::size_t pos_start = 5*actiondata.nindices_per_task*task_index; + using V3=VectorT; if( actiondata.usepbc ) { if( actiondata.nindices_per_task==1 ) { //this may be changed to input.pbc.apply() en mass or only on this one - Vector fpos=input.pbc->distance(Vector(0.0,0.0,0.0), - Vector(input.inputdata[pos_start], - input.inputdata[pos_start+1], - input.inputdata[pos_start+2]) ); + V3 fpos=input.pbc->distance(V3(0.0,0.0,0.0), + V3(input.inputdata[pos_start], + input.inputdata[pos_start+1], + input.inputdata[pos_start+2]) ); input.inputdata[pos_start] =fpos[0]; input.inputdata[pos_start+1]=fpos[1]; input.inputdata[pos_start+2]=fpos[2]; @@ -249,12 +284,12 @@ void MultiColvarTemplate::performTask( std::size_t task_index, std::size_t apos_start = pos_start; //if accidentaly nindices_per_task is 0, this will work by looping on all possible unsigned integers!!!! for(unsigned j=0; jdistance(first,second); input.inputdata[apos_start+3]=second[0]; @@ -266,10 +301,10 @@ void MultiColvarTemplate::performTask( std::size_t task_index, } else if( actiondata.nindices_per_task==1 ) { //isn't this equivalent to x = x-0? //why this is needed? - Vector fpos=delta(Vector(0.0,0.0,0.0), - Vector(input.inputdata[pos_start], - input.inputdata[pos_start+1], - input.inputdata[pos_start+2])); + V3 fpos=delta(V3(0.0,0.0,0.0), + V3(input.inputdata[pos_start], + input.inputdata[pos_start+1], + input.inputdata[pos_start+2])); input.inputdata[pos_start]=fpos[0]; input.inputdata[pos_start+1]=fpos[1]; input.inputdata[pos_start+2]=fpos[2]; @@ -281,23 +316,23 @@ void MultiColvarTemplate::performTask( std::size_t task_index, ColvarOutput cvout { output.values, local_ndev, output.derivatives.data() }; - T::calculateCV( ColvarInput{actiondata.mode, - actiondata.nindices_per_task, - input.inputdata+pos_start, - input.inputdata+mass_start, - input.inputdata+charge_start, - *input.pbc}, - cvout ); + CV::calculateCV( ColvarInput{actiondata.mode, + actiondata.nindices_per_task, + input.inputdata+pos_start, + input.inputdata+mass_start, + input.inputdata+charge_start, + *input.pbc}, + cvout ); } -template -int MultiColvarTemplate::getNumberOfValuesPerTask( std::size_t task_index, +template +int MultiColvarTemplate::getNumberOfValuesPerTask( std::size_t task_index, const MultiColvarInput& actiondata ) { return 1; } -template -void MultiColvarTemplate::getForceIndices( std::size_t task_index, +template +void MultiColvarTemplate::getForceIndices( std::size_t task_index, std::size_t colno, std::size_t ntotal_force, const MultiColvarInput& actiondata, diff --git a/src/colvar/Plane.cpp b/src/colvar/Plane.cpp index fa44a3103a..1f0467c6f1 100644 --- a/src/colvar/Plane.cpp +++ b/src/colvar/Plane.cpp @@ -19,18 +19,12 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC -#include "Colvar.h" +#include "Plane.h" #include "ColvarShortcut.h" #include "core/ActionRegister.h" #include "MultiColvarTemplate.h" #include "tools/Pbc.h" -#include -#include - //+PLUMEDOC COLVAR PLANE /* Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule. @@ -78,142 +72,12 @@ nucleation of molecular crystals such as [SMAC](SMAC.md). namespace PLMD { namespace colvar { -class Plane : public Colvar { -private: - bool pbc; - std::vector value; - std::vector derivs; -public: - static void registerKeywords( Keywords& keys ); - explicit Plane(const ActionOptions&); - static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); - static unsigned getModeAndSetupValues( ActionWithValue* av ); -// active methods: - void calculate() override; - static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); -}; - -typedef ColvarShortcut PlaneShortcut; +typedef Plane PlaneD; +typedef ColvarShortcut PlaneShortcut; PLUMED_REGISTER_ACTION(PlaneShortcut,"PLANE") -PLUMED_REGISTER_ACTION(Plane,"PLANE_SCALAR") -typedef MultiColvarTemplate PlaneMulti; +PLUMED_REGISTER_ACTION(PlaneD,"PLANE_SCALAR") +typedef MultiColvarTemplate PlaneMulti; PLUMED_REGISTER_ACTION(PlaneMulti,"PLANE_VECTOR") - -void Plane::registerKeywords( Keywords& keys ) { - Colvar::registerKeywords( keys ); - keys.setDisplayName("PLANE"); - keys.add("atoms","ATOMS","the three or four atoms whose plane we are computing"); - keys.addOutputComponent("x","default","scalar/vector","the x-component of the vector that is normal to the plane containing the atoms"); - keys.addOutputComponent("y","default","scalar/vector","the y-component of the vector that is normal to the plane containing the atoms"); - keys.addOutputComponent("z","default","scalar/vector","the z-component of the vector that is normal to the plane containing the atoms"); - keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); - keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); -} - -void Plane::parseAtomList( const int& num, std::vector& atoms, ActionAtomistic* aa ) { - aa->parseAtomList("ATOMS",num,atoms); - if(atoms.size()==3) { - aa->log.printf(" containing atoms %d %d %d\n",atoms[0].serial(),atoms[1].serial(),atoms[2].serial()); - atoms.resize(4); - atoms[3]=atoms[2]; - atoms[2]=atoms[1]; - } else if(atoms.size()==4) { - aa->log.printf(" containing lines %d-%d and %d-%d\n",atoms[0].serial(),atoms[1].serial(),atoms[2].serial(),atoms[3].serial()); - } else if( num<0 || atoms.size()>0 ) { - aa->error("Number of specified atoms should be either 3 or 4"); - } -} - -unsigned Plane::getModeAndSetupValues( ActionWithValue* av ) { - av->addComponentWithDerivatives("x"); - av->componentIsNotPeriodic("x"); - av->addComponentWithDerivatives("y"); - av->componentIsNotPeriodic("y"); - av->addComponentWithDerivatives("z"); - av->componentIsNotPeriodic("z"); - return 0; -} - -Plane::Plane(const ActionOptions&ao): - PLUMED_COLVAR_INIT(ao), - pbc(true), - value(3) { - std::vector atoms; - parseAtomList(-1,atoms,this); - bool nopbc=!pbc; - parseFlag("NOPBC",nopbc); - pbc=!nopbc; - - if(pbc) { - log.printf(" using periodic boundary conditions\n"); - } else { - log.printf(" without periodic boundary conditions\n"); - } - - getModeAndSetupValues( this ); - requestAtoms(atoms); - checkRead(); -} - -void Plane::calculate() { - - if(pbc) { - makeWhole(); - } - ColvarOutput cvout = ColvarOutput::createColvarOutput(value,derivs,this); - calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), cvout ); - Value* valuex=getPntrToComponent("x"); - Value* valuey=getPntrToComponent("y"); - Value* valuez=getPntrToComponent("z"); - - for(unsigned i=0; iset( value[0] ); - - for(unsigned i=0; iset( value[1] ); - - for(unsigned i=0; iset( value[2] ); -} - -void Plane::calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ) { - Vector d1=delta( cvin.pos[1], cvin.pos[0] ); - Vector d2=delta( cvin.pos[2], cvin.pos[3] ); - Vector cp = crossProduct( d1, d2 ); - - cvout.derivs[0][0] = crossProduct( Vector(-1.0,0,0), d2 ); - cvout.derivs[0][1] = crossProduct( Vector(+1.0,0,0), d2 ); - cvout.derivs[0][2] = crossProduct( Vector(-1.0,0,0), d1 ); - cvout.derivs[0][3] = crossProduct( Vector(+1.0,0,0), d1 ); - cvout.virial.set( 0, Tensor(d1,crossProduct(Vector(+1.0,0,0), d2)) + Tensor( d2, crossProduct(Vector(-1.0,0,0), d1)) ); - cvout.values[0] = cp[0]; - - cvout.derivs[1][0] = crossProduct( Vector(0,-1.0,0), d2 ); - cvout.derivs[1][1] = crossProduct( Vector(0,+1.0,0), d2 ); - cvout.derivs[1][2] = crossProduct( Vector(0,-1.0,0), d1 ); - cvout.derivs[1][3] = crossProduct( Vector(0,+1.0,0), d1 ); - cvout.virial.set(1, Tensor(d1,crossProduct(Vector(0,+1.0,0), d2)) + Tensor( d2, crossProduct(Vector(0,-1.0,0), d1)) ); - cvout.values[1] = cp[1]; - - cvout.derivs[2][0] = crossProduct( Vector(0,0,-1.0), d2 ); - cvout.derivs[2][1] = crossProduct( Vector(0,0,+1.0), d2 ); - cvout.derivs[2][2] = crossProduct( Vector(0,0,-1.0), d1 ); - cvout.derivs[2][3] = crossProduct( Vector(0,0,+1.0), d1 ); - cvout.virial.set(2, Tensor(d1,crossProduct(Vector(0,0,+1.0), d2)) + Tensor( d2, crossProduct(Vector(0,0,-1.0), d1)) ); - cvout.values[2] = cp[2]; -} - } } - - diff --git a/src/colvar/Plane.h b/src/colvar/Plane.h new file mode 100644 index 0000000000..36f69599e7 --- /dev/null +++ b/src/colvar/Plane.h @@ -0,0 +1,176 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_colvar_Plane_h +#define __PLUMED_colvar_Plane_h +#include "Colvar.h" +#include "ColvarInput.h" +#include "tools/Pbc.h" + +#include +#include + +namespace PLMD { +namespace colvar { + +template +class Plane : public Colvar { +private: + bool pbc; + std::vector value; + std::vector derivs; +public: + using precision=T; + static void registerKeywords( Keywords& keys ); + explicit Plane(const ActionOptions&); + static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); + static unsigned getModeAndSetupValues( ActionWithValue* av ); +// active methods: + void calculate() override; + static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); +}; + +template +void Plane::registerKeywords( Keywords& keys ) { + Colvar::registerKeywords( keys ); + keys.setDisplayName("PLANE"); + keys.add("atoms","ATOMS","the three or four atoms whose plane we are computing"); + keys.addOutputComponent("x","default","scalar/vector","the x-component of the vector that is normal to the plane containing the atoms"); + keys.addOutputComponent("y","default","scalar/vector","the y-component of the vector that is normal to the plane containing the atoms"); + keys.addOutputComponent("z","default","scalar/vector","the z-component of the vector that is normal to the plane containing the atoms"); + keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); + keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); +} + +template +void Plane::parseAtomList( const int& num, std::vector& atoms, ActionAtomistic* aa ) { + aa->parseAtomList("ATOMS",num,atoms); + if(atoms.size()==3) { + aa->log.printf(" containing atoms %d %d %d\n",atoms[0].serial(),atoms[1].serial(),atoms[2].serial()); + atoms.resize(4); + atoms[3]=atoms[2]; + atoms[2]=atoms[1]; + } else if(atoms.size()==4) { + aa->log.printf(" containing lines %d-%d and %d-%d\n",atoms[0].serial(),atoms[1].serial(),atoms[2].serial(),atoms[3].serial()); + } else if( num<0 || atoms.size()>0 ) { + aa->error("Number of specified atoms should be either 3 or 4"); + } +} + +template +unsigned Plane::getModeAndSetupValues( ActionWithValue* av ) { + av->addComponentWithDerivatives("x"); + av->componentIsNotPeriodic("x"); + av->addComponentWithDerivatives("y"); + av->componentIsNotPeriodic("y"); + av->addComponentWithDerivatives("z"); + av->componentIsNotPeriodic("z"); + return 0; +} + +template +Plane::Plane(const ActionOptions&ao): + PLUMED_COLVAR_INIT(ao), + pbc(true), + value(3) { + std::vector atoms; + parseAtomList(-1,atoms,this); + bool nopbc=!pbc; + parseFlag("NOPBC",nopbc); + pbc=!nopbc; + + if(pbc) { + log.printf(" using periodic boundary conditions\n"); + } else { + log.printf(" without periodic boundary conditions\n"); + } + + /*auto mode =*/ getModeAndSetupValues( this ); + requestAtoms(atoms); + checkRead(); +} + +template +void Plane::calculate() { + + if(pbc) { + makeWhole(); + } + auto cvout = ColvarOutput::createColvarOutput(value,derivs,this); + Plane::calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), cvout ); + Value* valuex=getPntrToComponent("x"); + Value* valuey=getPntrToComponent("y"); + Value* valuez=getPntrToComponent("z"); + + for(unsigned i=0; iset( value[0] ); + + for(unsigned i=0; iset( value[1] ); + + for(unsigned i=0; iset( value[2] ); +} + +template +void Plane::calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ) { + const auto d1=delta( cvin.pos[1], cvin.pos[0] ); + const auto d2=delta( cvin.pos[2], cvin.pos[3] ); + const auto cp = crossProduct( d1, d2 ); + using T33 = TensorTyped; + cvout.derivs[0][0] = crossProduct( Versors::xm, d2 ); + cvout.derivs[0][1] = crossProduct( Versors::xp, d2 ); + cvout.derivs[0][2] = crossProduct( Versors::xm, d1 ); + cvout.derivs[0][3] = crossProduct( Versors::xp, d1 ); + cvout.virial.set( 0, T33(d1,crossProduct(Versors::xp, d2)) + + T33(d2, crossProduct(Versors::xm, d1))); + cvout.values[0] = cp[0]; + + cvout.derivs[1][0] = crossProduct( Versors::ym, d2 ); + cvout.derivs[1][1] = crossProduct( Versors::yp, d2 ); + cvout.derivs[1][2] = crossProduct( Versors::ym, d1 ); + cvout.derivs[1][3] = crossProduct( Versors::yp, d1 ); + cvout.virial.set(1, T33(d1,crossProduct(Versors::yp, d2)) + + T33(d2, crossProduct(Versors::ym, d1))); + cvout.values[1] = cp[1]; + + cvout.derivs[2][0] = crossProduct( Versors::zm, d2 ); + cvout.derivs[2][1] = crossProduct( Versors::zp, d2 ); + cvout.derivs[2][2] = crossProduct( Versors::zm, d1 ); + cvout.derivs[2][3] = crossProduct( Versors::zp, d1 ); + cvout.virial.set(2, T33(d1,crossProduct(Versors::zp, d2)) + + T33(d2, crossProduct(Versors::zm, d1))); + cvout.values[2] = cp[2]; +} + +} +} + +#endif // __PLUMED_colvar_Plane_h diff --git a/src/colvar/Position.cpp b/src/colvar/Position.cpp index f9e0cd0352..6a76441a07 100644 --- a/src/colvar/Position.cpp +++ b/src/colvar/Position.cpp @@ -19,14 +19,10 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC -#include "Colvar.h" +#include "Position.h" #include "ColvarShortcut.h" #include "MultiColvarTemplate.h" #include "core/ActionRegister.h" -#include "tools/Pbc.h" namespace PLMD { namespace colvar { @@ -106,164 +102,13 @@ PRINT ARG=p.x,p.y,p.z */ //+ENDPLUMEDOC -class Position : public Colvar { - bool scaled_components; - bool pbc; - std::vector value; - std::vector derivs; -public: - static void registerKeywords( Keywords& keys ); - explicit Position(const ActionOptions&); - static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); - static unsigned getModeAndSetupValues( ActionWithValue* av ); -// active methods: - void calculate() override; - static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); -}; - -typedef ColvarShortcut PositionShortcut; +typedef Position PositionD; +typedef ColvarShortcut PositionShortcut; PLUMED_REGISTER_ACTION(PositionShortcut,"POSITION") -PLUMED_REGISTER_ACTION(Position,"POSITION_SCALAR") -typedef MultiColvarTemplate PositionMulti; +PLUMED_REGISTER_ACTION(PositionD,"POSITION_SCALAR") +typedef MultiColvarTemplate PositionMulti; PLUMED_REGISTER_ACTION(PositionMulti,"POSITION_VECTOR") -void Position::registerKeywords( Keywords& keys ) { - Colvar::registerKeywords( keys ); - keys.setDisplayName("POSITION"); - keys.add("atoms","ATOM","the atom number"); - keys.add("atoms","ATOMS","the atom numbers that you would like to use the positions of"); - keys.addFlag("WHOLEMOLECULES",false,"if this is a vector of positions do you want to make the positions into a whole before"); - keys.addFlag("SCALED_COMPONENTS",false,"calculate the a, b and c scaled components of the position separately and store them as label.a, label.b and label.c"); - keys.addOutputComponent("x","default","scalar/vector","the x-component of the atom position"); - keys.addOutputComponent("y","default","scalar/vector","the y-component of the atom position"); - keys.addOutputComponent("z","default","scalar/vector","the z-component of the atom position"); - keys.addOutputComponent("a","SCALED_COMPONENTS","scalar/vector","the normalized projection on the first lattice vector of the atom position"); - keys.addOutputComponent("b","SCALED_COMPONENTS","scalar/vector","the normalized projection on the second lattice vector of the atom position"); - keys.addOutputComponent("c","SCALED_COMPONENTS","scalar/vector","the normalized projection on the third lattice vector of the atom position"); - keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); - keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); -} - -Position::Position(const ActionOptions&ao): - PLUMED_COLVAR_INIT(ao), - scaled_components(false), - pbc(true), - value(3) { - std::vector atoms; - parseAtomList(-1,atoms,this); - unsigned mode=getModeAndSetupValues(this); - if( mode==1 ) { - scaled_components=true; - } - - bool nopbc=!pbc; - parseFlag("NOPBC",nopbc); - pbc=!nopbc; - checkRead(); - - if(pbc) { - log.printf(" using periodic boundary conditions\n"); - } else { - log.printf(" without periodic boundary conditions\n"); - } - - requestAtoms(atoms); -} - -void Position::parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ) { - aa->parseAtomList("ATOM",num,t); - if( t.size()==1 ) { - aa->log.printf(" for atom %d\n",t[0].serial()); - } else if( num<0 || t.size()!=0 ) { - aa->error("Number of specified atoms should be 1"); - } -} - -unsigned Position::getModeAndSetupValues( ActionWithValue* av ) { - bool sc; - av->parseFlag("SCALED_COMPONENTS",sc); - if(sc) { - av->addComponentWithDerivatives("a"); - av->componentIsPeriodic("a","-0.5","+0.5"); - av->addComponentWithDerivatives("b"); - av->componentIsPeriodic("b","-0.5","+0.5"); - av->addComponentWithDerivatives("c"); - av->componentIsPeriodic("c","-0.5","+0.5"); - return 1; - } - av->addComponentWithDerivatives("x"); - av->componentIsNotPeriodic("x"); - av->addComponentWithDerivatives("y"); - av->componentIsNotPeriodic("y"); - av->addComponentWithDerivatives("z"); - av->componentIsNotPeriodic("z"); - av->log<<" WARNING: components will not have the proper periodicity - see manual\n"; - return 0; -} - -// calculator -void Position::calculate() { - - std::vector distance(1); - if(pbc) { - distance[0]=pbcDistance(Vector(0.0,0.0,0.0),getPosition(0)); - } else { - distance[0]=delta(Vector(0.0,0.0,0.0),getPosition(0)); - } - - ColvarOutput cvout = ColvarOutput::createColvarOutput(value,derivs,this); - if(scaled_components) { - calculateCV( ColvarInput::createColvarInput( 1, distance, this ), cvout ); - Value* valuea=getPntrToComponent("a"); - Value* valueb=getPntrToComponent("b"); - Value* valuec=getPntrToComponent("c"); - setAtomsDerivatives (valuea,0,cvout.getAtomDerivatives(0,0)); - valuea->set(value[0]); - setAtomsDerivatives (valueb,0,cvout.getAtomDerivatives(1,0)); - valueb->set(value[1]); - setAtomsDerivatives (valuec,0,cvout.getAtomDerivatives(2,0)); - valuec->set(value[2]); - } else { - calculateCV( ColvarInput::createColvarInput( 0, distance, this ), cvout ); - Value* valuex=getPntrToComponent("x"); - Value* valuey=getPntrToComponent("y"); - Value* valuez=getPntrToComponent("z"); - - setAtomsDerivatives (valuex,0,cvout.getAtomDerivatives(0,0)); - setBoxDerivatives (valuex,cvout.virial[0]); - valuex->set(value[0]); - - setAtomsDerivatives (valuey,0,cvout.getAtomDerivatives(1,0)); - setBoxDerivatives (valuey,cvout.virial[1]); - valuey->set(value[1]); - - setAtomsDerivatives (valuez,0,cvout.getAtomDerivatives(2,0)); - setBoxDerivatives (valuez,cvout.virial[2]); - valuez->set(value[2]); - } -} - -void Position::calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ) { - if( cvin.mode==1 ) { - Vector d=cvin.pbc.realToScaled(Vector(cvin.pos[0][0],cvin.pos[0][1],cvin.pos[0][2])); - cvout.values[0]=Tools::pbc(d[0]); - cvout.values[1]=Tools::pbc(d[1]); - cvout.values[2]=Tools::pbc(d[2]); - cvout.derivs[0][0]=matmul(cvin.pbc.getInvBox(),Vector(+1,0,0)); - cvout.derivs[1][0]=matmul(cvin.pbc.getInvBox(),Vector(0,+1,0)); - cvout.derivs[2][0]=matmul(cvin.pbc.getInvBox(),Vector(0,0,+1)); - } else { - for(unsigned i=0; i<3; ++i) { - cvout.values[i]=cvin.pos[0][i]; - } - cvout.derivs[0][0]=Vector(+1,0,0); - cvout.derivs[1][0]=Vector(0,+1,0); - cvout.derivs[2][0]=Vector(0,0,+1); - cvout.virial.set(0, Tensor(Vector(cvin.pos[0][0],cvin.pos[0][1],cvin.pos[0][2]),Vector(-1,0,0)) ); - cvout.virial.set(1, Tensor(Vector(cvin.pos[0][0],cvin.pos[0][1],cvin.pos[0][2]),Vector(0,-1,0)) ); - cvout.virial.set(2, Tensor(Vector(cvin.pos[0][0],cvin.pos[0][1],cvin.pos[0][2]),Vector(0,0,-1)) ); - } -} } } diff --git a/src/colvar/Position.h b/src/colvar/Position.h new file mode 100644 index 0000000000..2105e0d44e --- /dev/null +++ b/src/colvar/Position.h @@ -0,0 +1,192 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2014-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_colvar_Position_h +#define __PLUMED_colvar_Position_h +#include "Colvar.h" +#include "tools/Pbc.h" +#include "ColvarInput.h" + +namespace PLMD { +namespace colvar { + +template +class Position : public Colvar { + enum components:unsigned {scaled=1,standard=0} mode{standard}; + bool pbc; + std::vector value; + std::vector derivs; +public: + using precision=T; + static void registerKeywords( Keywords& keys ); + explicit Position(const ActionOptions&); + static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); + static unsigned getModeAndSetupValues( ActionWithValue* av ); +// active methods: + void calculate() override; + static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); +}; + +template +void Position::registerKeywords( Keywords& keys ) { + Colvar::registerKeywords( keys ); + keys.setDisplayName("POSITION"); + keys.add("atoms","ATOM","the atom number"); + keys.add("atoms","ATOMS","the atom numbers that you would like to use the positions of"); + keys.addFlag("WHOLEMOLECULES",false,"if this is a vector of positions do you want to make the positions into a whole before"); + keys.addFlag("SCALED_COMPONENTS",false,"calculate the a, b and c scaled components of the position separately and store them as label.a, label.b and label.c"); + keys.addOutputComponent("x","default","scalar/vector","the x-component of the atom position"); + keys.addOutputComponent("y","default","scalar/vector","the y-component of the atom position"); + keys.addOutputComponent("z","default","scalar/vector","the z-component of the atom position"); + keys.addOutputComponent("a","SCALED_COMPONENTS","scalar/vector","the normalized projection on the first lattice vector of the atom position"); + keys.addOutputComponent("b","SCALED_COMPONENTS","scalar/vector","the normalized projection on the second lattice vector of the atom position"); + keys.addOutputComponent("c","SCALED_COMPONENTS","scalar/vector","the normalized projection on the third lattice vector of the atom position"); + keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); + keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); +} + +template +Position::Position(const ActionOptions&ao): + PLUMED_COLVAR_INIT(ao), + pbc(true), + value(3) { + std::vector atoms; + parseAtomList(-1,atoms,this); + mode=static_cast(getModeAndSetupValues(this)); + + bool nopbc=!pbc; + parseFlag("NOPBC",nopbc); + pbc=!nopbc; + checkRead(); + + if(pbc) { + log.printf(" using periodic boundary conditions\n"); + } else { + log.printf(" without periodic boundary conditions\n"); + } + + requestAtoms(atoms); +} + +template +void Position::parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ) { + aa->parseAtomList("ATOM",num,t); + if( t.size()==1 ) { + aa->log.printf(" for atom %d\n",t[0].serial()); + } else if( num<0 || t.size()!=0 ) { + aa->error("Number of specified atoms should be 1"); + } +} + +template +unsigned Position::getModeAndSetupValues( ActionWithValue* av ) { + bool sc; + av->parseFlag("SCALED_COMPONENTS",sc); + if(sc) { + av->addComponentWithDerivatives("a"); + av->componentIsPeriodic("a","-0.5","+0.5"); + av->addComponentWithDerivatives("b"); + av->componentIsPeriodic("b","-0.5","+0.5"); + av->addComponentWithDerivatives("c"); + av->componentIsPeriodic("c","-0.5","+0.5"); + return components::scaled; + } + av->addComponentWithDerivatives("x"); + av->componentIsNotPeriodic("x"); + av->addComponentWithDerivatives("y"); + av->componentIsNotPeriodic("y"); + av->addComponentWithDerivatives("z"); + av->componentIsNotPeriodic("z"); + av->log<<" WARNING: components will not have the proper periodicity - see manual\n"; + return components::standard; +} + +// calculator +template +void Position::calculate() { + + std::vector distance(1); + if(pbc) { + distance[0]=pbcDistance(Vector(0.0,0.0,0.0),getPosition(0)); + } else { + distance[0]=delta(Vector(0.0,0.0,0.0),getPosition(0)); + } + + ColvarOutput cvout = ColvarOutput::createColvarOutput(value,derivs,this); + Position::calculateCV( ColvarInput::createColvarInput( mode, distance, this ), cvout ); + if(mode==components::scaled) { + Value* valuea=getPntrToComponent("a"); + Value* valueb=getPntrToComponent("b"); + Value* valuec=getPntrToComponent("c"); + setAtomsDerivatives (valuea,0,cvout.getAtomDerivatives(0,0)); + valuea->set(value[0]); + setAtomsDerivatives (valueb,0,cvout.getAtomDerivatives(1,0)); + valueb->set(value[1]); + setAtomsDerivatives (valuec,0,cvout.getAtomDerivatives(2,0)); + valuec->set(value[2]); + } else { + Value* valuex=getPntrToComponent("x"); + Value* valuey=getPntrToComponent("y"); + Value* valuez=getPntrToComponent("z"); + + setAtomsDerivatives (valuex,0,cvout.getAtomDerivatives(0,0)); + setBoxDerivatives (valuex,cvout.virial[0]); + valuex->set(value[0]); + + setAtomsDerivatives (valuey,0,cvout.getAtomDerivatives(1,0)); + setBoxDerivatives (valuey,cvout.virial[1]); + valuey->set(value[1]); + + setAtomsDerivatives (valuez,0,cvout.getAtomDerivatives(2,0)); + setBoxDerivatives (valuez,cvout.virial[2]); + valuez->set(value[2]); + } +} + +template +void Position::calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ) { + if( cvin.mode==components::scaled ) { + auto d=cvin.pbc.realToScaled(VectorTyped(cvin.pos[0][0],cvin.pos[0][1],cvin.pos[0][2])); + cvout.values[0]=Tools::pbc(d[0]); + cvout.values[1]=Tools::pbc(d[1]); + cvout.values[2]=Tools::pbc(d[2]); + cvout.derivs[0][0]=matmul(cvin.pbc.getInvBox(),Versors::xp); + cvout.derivs[1][0]=matmul(cvin.pbc.getInvBox(),Versors::yp); + cvout.derivs[2][0]=matmul(cvin.pbc.getInvBox(),Versors::zp); + } else { + for(unsigned i=0; i<3; ++i) { + cvout.values[i]=cvin.pos[0][i]; + } + cvout.derivs[0][0]=Versors::xp; + cvout.derivs[1][0]=Versors::yp; + cvout.derivs[2][0]=Versors::zp; + cvout.virial.set(0, TensorTyped(VectorTyped(cvin.pos[0][0],cvin.pos[0][1],cvin.pos[0][2]), + Versors::xm)); + cvout.virial.set(1, TensorTyped(VectorTyped(cvin.pos[0][0],cvin.pos[0][1],cvin.pos[0][2]), + Versors::ym)); + cvout.virial.set(2, TensorTyped(VectorTyped(cvin.pos[0][0],cvin.pos[0][1],cvin.pos[0][2]), + Versors::zm)); + } +} + +} +} +#endif //__PLUMED_colvar_Position_h diff --git a/src/colvar/RMSDVector.h b/src/colvar/RMSDVector.h index 156576633e..eddc0ad07b 100644 --- a/src/colvar/RMSDVector.h +++ b/src/colvar/RMSDVector.h @@ -42,6 +42,8 @@ class RMSDVector : public ActionWithVector { public: using input_type = RMSDVectorData; using PTM = ParallelTaskManager; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: bool firststep; bool norm_weights; diff --git a/src/colvar/Torsion.cpp b/src/colvar/Torsion.cpp index a55cb3dedb..34ea08d57c 100644 --- a/src/colvar/Torsion.cpp +++ b/src/colvar/Torsion.cpp @@ -19,15 +19,10 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -//this is temporary: -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC -#include "Colvar.h" +#include "Torsion.h" #include "ColvarShortcut.h" #include "MultiColvarTemplate.h" #include "core/ActionRegister.h" -#include "tools/Torsion.h" namespace PLMD { namespace colvar { @@ -114,186 +109,13 @@ PRINT ARG=t FILE=COLVAR */ //+ENDPLUMEDOC - -class Torsion : public Colvar { - bool pbc; - bool do_cosine; - - std::vector value; - std::vector derivs; -public: - explicit Torsion(const ActionOptions&); - static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); - static unsigned getModeAndSetupValues( ActionWithValue* av ); -// active methods: - void calculate() override; - static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); - static void registerKeywords(Keywords& keys); -}; - -typedef ColvarShortcut TorsionShortcut; +typedef Torsion TorsionD; +typedef ColvarShortcut TorsionShortcut; PLUMED_REGISTER_ACTION(TorsionShortcut,"TORSION") -PLUMED_REGISTER_ACTION(Torsion,"TORSION_SCALAR") -typedef MultiColvarTemplate TorsionMulti; +PLUMED_REGISTER_ACTION(TorsionD,"TORSION_SCALAR") +typedef MultiColvarTemplate TorsionMulti; PLUMED_REGISTER_ACTION(TorsionMulti,"TORSION_VECTOR") -void Torsion::registerKeywords(Keywords& keys) { - Colvar::registerKeywords( keys ); - keys.setDisplayName("TORSION"); - keys.add("atoms-1","ATOMS","the four atoms involved in the torsional angle"); - keys.add("atoms-2","AXIS","two atoms that define an axis. You can use this to find the angle in the plane perpendicular to the axis between the vectors specified using the VECTORA and VECTORB keywords."); - keys.add("atoms-2","VECTORA","two atoms that define a vector. You can use this in combination with VECTOR2 and AXIS"); - keys.add("atoms-2","VECTORB","two atoms that define a vector. You can use this in combination with VECTOR1 and AXIS"); - keys.addDeprecatedKeyword("VECTOR1","VECTORA"); - keys.addDeprecatedKeyword("VECTOR2","VECTORB"); - keys.addFlag("COSINE",false,"calculate cosine instead of dihedral"); - keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); - keys.setValueDescription("scalar/vector","the TORSION involving these atoms"); - keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); } - -Torsion::Torsion(const ActionOptions&ao): - PLUMED_COLVAR_INIT(ao), - pbc(true), - do_cosine(false), - value(1) { - std::vector atoms; - std::vector v1; - ActionAtomistic::parseAtomList("VECTOR1",v1); - if( v1.size()>0 ) { - std::vector v2; - ActionAtomistic::parseAtomList("VECTOR2",v2); - std::vector axis; - ActionAtomistic::parseAtomList("AXIS",axis); - if( !(v1.size()==2 && v2.size()==2 && axis.size()==2)) { - error("VECTOR1, VECTOR2 and AXIS should specify 2 atoms each"); - } - atoms.resize(6); - atoms[0]=v1[1]; - atoms[1]=v1[0]; - atoms[2]=axis[0]; - atoms[3]=axis[1]; - atoms[4]=v2[0]; - atoms[5]=v2[1]; - log.printf(" between lines %d-%d and %d-%d, projected on the plane orthogonal to line %d-%d\n", - v1[0].serial(),v1[1].serial(),v2[0].serial(),v2[1].serial(),axis[0].serial(),axis[1].serial()); - } else { - parseAtomList(-1,atoms,this); - } - unsigned mode=getModeAndSetupValues(this); - if( mode==1 ) { - do_cosine=true; - } - - bool nopbc=!pbc; - parseFlag("NOPBC",nopbc); - pbc=!nopbc; - checkRead(); - - if(pbc) { - log.printf(" using periodic boundary conditions\n"); - } else { - log.printf(" without periodic boundary conditions\n"); - } - requestAtoms(atoms); } -void Torsion::parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ) { - std::vector v1,v2,axis; - aa->parseAtomList("ATOMS",num,t); - aa->parseAtomList("VECTORA",num,v1); - aa->parseAtomList("VECTORB",num,v2); - aa->parseAtomList("AXIS",num,axis); - - if(t.size()==4) { - if(!(v1.empty() && v2.empty() && axis.empty())) { - aa->error("ATOMS keyword is not compatible with VECTORA, VECTORB and AXIS keywords"); - } - aa->log.printf(" between atoms %d %d %d %d\n",t[0].serial(),t[1].serial(),t[2].serial(),t[3].serial()); - t.resize(6); - t[5]=t[3]; - t[4]=t[2]; - t[3]=t[2]; - t[2]=t[1]; - } else if(t.empty()) { - if( num>0 && v1.empty() && v2.empty() && axis.empty() ) { - return; - } - if(!(v1.size()==2 && v2.size()==2 && axis.size()==2)) { - aa->error("VECTORA, VECTORB and AXIS should specify 2 atoms each"); - } - aa->log.printf(" between lines %d-%d and %d-%d, projected on the plane orthogonal to line %d-%d\n", - v1[0].serial(),v1[1].serial(),v2[0].serial(),v2[1].serial(),axis[0].serial(),axis[1].serial()); - t.resize(6); - t[0]=v1[1]; - t[1]=v1[0]; - t[2]=axis[0]; - t[3]=axis[1]; - t[4]=v2[0]; - t[5]=v2[1]; - } else if( t.size()!=4 ) { - aa->error("ATOMS should specify 4 atoms"); - } -} - -unsigned Torsion::getModeAndSetupValues( ActionWithValue* av ) { - bool do_cos; - av->parseFlag("COSINE",do_cos); - if(do_cos) { - av->log.printf(" calculating cosine instead of torsion\n"); - } - - av->addValueWithDerivatives(); - if(!do_cos) { - av->setPeriodic("-pi","pi"); - return 0; - } - av->setNotPeriodic(); - return 1; -} - -// calculator -void Torsion::calculate() { - if(pbc) { - makeWhole(); - } - ColvarOutput cvout = ColvarOutput::createColvarOutput(value,derivs,this); - if(do_cosine) { - calculateCV( ColvarInput::createColvarInput( 1, getPositions(), this ), cvout ); - } else { - calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), cvout ); - } - for(unsigned i=0; i<6; ++i) { - setAtomsDerivatives(i,cvout.getAtomDerivatives(0,i) ); - } - setValue(value[0]); - setBoxDerivatives( cvout.virial[0] ); -} - -void Torsion::calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ) { - Vector d0=delta(cvin.pos[1],cvin.pos[0]); - Vector d1=delta(cvin.pos[3],cvin.pos[2]); - Vector d2=delta(cvin.pos[5],cvin.pos[4]); - Vector dd0,dd1,dd2; - PLMD::Torsion t; - cvout.values[0] = t.compute(d0,d1,d2,dd0,dd1,dd2); - if(cvin.mode==1) { - dd0 *= -std::sin(cvout.values[0]); - dd1 *= -std::sin(cvout.values[0]); - dd2 *= -std::sin(cvout.values[0]); - cvout.values[0] = std::cos(cvout.values[0]); - } - cvout.derivs[0][0] = dd0; - cvout.derivs[0][1] = -dd0; - cvout.derivs[0][2] = dd1; - cvout.derivs[0][3] = -dd1; - cvout.derivs[0][4] = dd2; - cvout.derivs[0][5] = -dd2; - ColvarInput::setBoxDerivativesNoPbc( cvin, cvout ); -} - -} -} - - - diff --git a/src/colvar/Torsion.h b/src/colvar/Torsion.h new file mode 100644 index 0000000000..2ecfd72cc6 --- /dev/null +++ b/src/colvar/Torsion.h @@ -0,0 +1,215 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_colvar_Torsion_h +#define __PLUMED_colvar_Torsion_h +#include "Colvar.h" +#include "tools/Torsion.h" +#include "ColvarInput.h" + +namespace PLMD { +namespace colvar { + +template +class Torsion : public Colvar { + bool pbc; + bool do_cosine; + + std::vector value; + std::vector derivs; +public: + using precision=T; + explicit Torsion(const ActionOptions&); + static void parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ); + static unsigned getModeAndSetupValues( ActionWithValue* av ); +// active methods: + void calculate() override; + static void calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ); + static void registerKeywords(Keywords& keys); +}; + +template +void Torsion::registerKeywords(Keywords& keys) { + Colvar::registerKeywords( keys ); + keys.setDisplayName("TORSION"); + keys.add("atoms-1","ATOMS","the four atoms involved in the torsional angle"); + keys.add("atoms-2","AXIS","two atoms that define an axis. You can use this to find the angle in the plane perpendicular to the axis between the vectors specified using the VECTORA and VECTORB keywords."); + keys.add("atoms-2","VECTORA","two atoms that define a vector. You can use this in combination with VECTOR2 and AXIS"); + keys.add("atoms-2","VECTORB","two atoms that define a vector. You can use this in combination with VECTOR1 and AXIS"); + keys.addDeprecatedKeyword("VECTOR1","VECTORA"); + keys.addDeprecatedKeyword("VECTOR2","VECTORB"); + keys.addFlag("COSINE",false,"calculate cosine instead of dihedral"); + keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); + keys.setValueDescription("scalar/vector","the TORSION involving these atoms"); + keys.reset_style("NUMERICAL_DERIVATIVES","hidden"); +} + +template +Torsion::Torsion(const ActionOptions&ao): + PLUMED_COLVAR_INIT(ao), + pbc(true), + do_cosine(false), + value(1) { + std::vector atoms; + std::vector v1; + ActionAtomistic::parseAtomList("VECTOR1",v1); + if( v1.size()>0 ) { + std::vector v2; + ActionAtomistic::parseAtomList("VECTOR2",v2); + std::vector axis; + ActionAtomistic::parseAtomList("AXIS",axis); + if( !(v1.size()==2 && v2.size()==2 && axis.size()==2)) { + error("VECTOR1, VECTOR2 and AXIS should specify 2 atoms each"); + } + atoms.resize(6); + atoms[0]=v1[1]; + atoms[1]=v1[0]; + atoms[2]=axis[0]; + atoms[3]=axis[1]; + atoms[4]=v2[0]; + atoms[5]=v2[1]; + log.printf(" between lines %d-%d and %d-%d, projected on the plane orthogonal to line %d-%d\n", + v1[0].serial(),v1[1].serial(),v2[0].serial(),v2[1].serial(),axis[0].serial(),axis[1].serial()); + } else { + parseAtomList(-1,atoms,this); + } + unsigned mode=getModeAndSetupValues(this); + if( mode==1 ) { + do_cosine=true; + } + + bool nopbc=!pbc; + parseFlag("NOPBC",nopbc); + pbc=!nopbc; + checkRead(); + + if(pbc) { + log.printf(" using periodic boundary conditions\n"); + } else { + log.printf(" without periodic boundary conditions\n"); + } + requestAtoms(atoms); +} + +template +void Torsion::parseAtomList( const int& num, std::vector& t, ActionAtomistic* aa ) { + std::vector v1,v2,axis; + aa->parseAtomList("ATOMS",num,t); + aa->parseAtomList("VECTORA",num,v1); + aa->parseAtomList("VECTORB",num,v2); + aa->parseAtomList("AXIS",num,axis); + + if(t.size()==4) { + if(!(v1.empty() && v2.empty() && axis.empty())) { + aa->error("ATOMS keyword is not compatible with VECTORA, VECTORB and AXIS keywords"); + } + aa->log.printf(" between atoms %d %d %d %d\n",t[0].serial(),t[1].serial(),t[2].serial(),t[3].serial()); + t.resize(6); + t[5]=t[3]; + t[4]=t[2]; + t[3]=t[2]; + t[2]=t[1]; + } else if(t.empty()) { + if( num>0 && v1.empty() && v2.empty() && axis.empty() ) { + return; + } + if(!(v1.size()==2 && v2.size()==2 && axis.size()==2)) { + aa->error("VECTORA, VECTORB and AXIS should specify 2 atoms each"); + } + aa->log.printf(" between lines %d-%d and %d-%d, projected on the plane orthogonal to line %d-%d\n", + v1[0].serial(),v1[1].serial(),v2[0].serial(),v2[1].serial(),axis[0].serial(),axis[1].serial()); + t.resize(6); + t[0]=v1[1]; + t[1]=v1[0]; + t[2]=axis[0]; + t[3]=axis[1]; + t[4]=v2[0]; + t[5]=v2[1]; + } else if( t.size()!=4 ) { + aa->error("ATOMS should specify 4 atoms"); + } +} + +template +unsigned Torsion::getModeAndSetupValues( ActionWithValue* av ) { + bool do_cos; + av->parseFlag("COSINE",do_cos); + if(do_cos) { + av->log.printf(" calculating cosine instead of torsion\n"); + } + + av->addValueWithDerivatives(); + if(!do_cos) { + av->setPeriodic("-pi","pi"); + return 0; + } + av->setNotPeriodic(); + return 1; +} + +// calculator +template +void Torsion::calculate() { + if(pbc) { + makeWhole(); + } + auto cvout = ColvarOutput::createColvarOutput(value,derivs,this); + if(do_cosine) { + Torsion::calculateCV( + ColvarInput::createColvarInput( 1, getPositions(), this ), + cvout ); + } else { + Torsion::calculateCV( + ColvarInput::createColvarInput( 0, getPositions(), this ), + cvout ); + } + for(unsigned i=0; i<6; ++i) { + setAtomsDerivatives(i,cvout.getAtomDerivatives(0,i) ); + } + setValue(value[0]); + setBoxDerivatives( cvout.virial[0] ); +} + +template +void Torsion::calculateCV( const ColvarInput& cvin, ColvarOutput& cvout ) { + auto d0=delta(cvin.pos[1],cvin.pos[0]); + auto d1=delta(cvin.pos[3],cvin.pos[2]); + auto d2=delta(cvin.pos[5],cvin.pos[4]); + VectorTyped dd0,dd1,dd2; + cvout.values[0] = PLMD::Torsion::compute(d0,d1,d2,dd0,dd1,dd2); + if(cvin.mode==1) { + dd0 *= -std::sin(cvout.values[0]); + dd1 *= -std::sin(cvout.values[0]); + dd2 *= -std::sin(cvout.values[0]); + cvout.values[0] = std::cos(cvout.values[0]); + } + cvout.derivs[0][0] = dd0; + cvout.derivs[0][1] = -dd0; + cvout.derivs[0][2] = dd1; + cvout.derivs[0][3] = -dd1; + cvout.derivs[0][4] = dd2; + cvout.derivs[0][5] = -dd2; + ColvarInput::setBoxDerivativesNoPbc( cvin, cvout ); +} + +} +} +#endif // __PLUMED_colvar_Torsion.h diff --git a/src/contour/FindContour.h b/src/contour/FindContour.h index 52ef035158..7bfd26968f 100644 --- a/src/contour/FindContour.h +++ b/src/contour/FindContour.h @@ -35,6 +35,8 @@ class FindContour : public ActionWithVector { public: using input_type = ContourFindingObject; using PTM = ParallelTaskManager; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: bool firststep; /// The parallel task manager diff --git a/src/contour/FindContourSurface.cpp b/src/contour/FindContourSurface.cpp index 9066e3f1d7..1ecf9bf485 100644 --- a/src/contour/FindContourSurface.cpp +++ b/src/contour/FindContourSurface.cpp @@ -155,6 +155,8 @@ class FindContourSurface : public gridtools::ActionWithGrid { public: using input_type = FindContourSurfaceObject; using PTM = ParallelTaskManager; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: bool firststep; /// The parallel task manager diff --git a/src/contour/FindSphericalContour.cpp b/src/contour/FindSphericalContour.cpp index ef5d5b3017..0817eb1523 100644 --- a/src/contour/FindSphericalContour.cpp +++ b/src/contour/FindSphericalContour.cpp @@ -148,6 +148,8 @@ class FindSphericalContour : public gridtools::ActionWithGrid { public: using input_type = FindSphericalContourObject; using PTM = ParallelTaskManager; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: /// The parallel task manager PTM taskmanager; diff --git a/src/core/AccelerableShortcut.cpp b/src/core/AccelerableShortcut.cpp new file mode 100644 index 0000000000..b497020540 --- /dev/null +++ b/src/core/AccelerableShortcut.cpp @@ -0,0 +1,23 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2025 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "AccelerableShortcut.h" + diff --git a/src/core/AccelerableShortcut.h b/src/core/AccelerableShortcut.h new file mode 100644 index 0000000000..33856b10a4 --- /dev/null +++ b/src/core/AccelerableShortcut.h @@ -0,0 +1,59 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2025 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_core_AccelerableShortcut_h +#define __PLUMED_core_AccelerableShortcut_h + +#include "ActionShortcut.h" + +namespace PLMD { + +template +struct AccelerableShortcut : public ActionShortcut { + + static void registerKeywords(Keywords& keys ) { + CV::registerKeywords( keys ); + for (auto& key : keys.getKeys()) { + if( keys.style( key, "atoms" ) ) { + keys.reset_style( key, "numbered" ); + } + } + keys.addActionNameSuffix("_CPU"); + keys.addActionNameSuffix("_ACC"); + //GPU related settings + if (!keys.exists("USEGPU")) { + keys.addFlag("USEGPU",false,"run this calculation on the GPU or the accelerated version, if avaiable"); + keys.addLinkInDocForFlag("USEGPU","gpu.md"); + } + } + + AccelerableShortcut(const ActionOptions&ao): + Action(ao), + ActionShortcut(ao) { + bool usegpuFLAG=false; + parseFlag("USEGPU",usegpuFLAG); + readInputLine( getShortcutLabel() + ": " + + getName() + (usegpuFLAG ? "_ACC ":"_CPU ") + + convertInputLineToString() ); + } +}; +} // namespace PLMD +#endif diff --git a/src/core/ActionShortcut.cpp b/src/core/ActionShortcut.cpp index 62b9ce9bc0..eee1e99762 100644 --- a/src/core/ActionShortcut.cpp +++ b/src/core/ActionShortcut.cpp @@ -147,9 +147,15 @@ void ActionShortcut::readInputLine( const std::string& input, bool saveline ) { error("shortcut is using suffix but action created is not ActionWithValue"); } Keywords thiskeys; + //TODO: check if it is possible to do this: plumed.getKeywordsForAction(av->getName(),thiskeys); actionRegister().getKeywords( av->getName(), thiskeys ); if( thiskeys.getDisplayName()!=getName() ) { - error("mismatch between display name of hidden action " + thiskeys.getDisplayName() + " and shortcut that creates it " + getName() ); + //NOTE: this was an error + // I deactivated it because it clashes with the gpu-openacc-by-LOAD does not load + // at moment of writing this I do not know if there is a way to to the check by passing the + // dlloader object to this function. + // bypassing this check makes my contraption work + warning("mismatch between display name of hidden action " + thiskeys.getDisplayName() + " and shortcut that creates it " + getName() ); } } } else { diff --git a/src/core/ActionWithMatrix.cpp b/src/core/ActionWithMatrix.cpp index 9b4630b872..4a4249bdee 100644 --- a/src/core/ActionWithMatrix.cpp +++ b/src/core/ActionWithMatrix.cpp @@ -116,6 +116,25 @@ void ActionWithMatrix::transferStashToValues( const std::vector& parti } } +void ActionWithMatrix::transferStashToValues( const std::vector& partialTaskList, const std::vector& stash ) { + unsigned ncomp = getNumberOfComponents(); + unsigned ncols = getPntrToComponent(0)->getNumberOfColumns(); + unsigned nrows = partialTaskList.size(); + for(unsigned i=0; igetRowLength(partialTaskList[i]); +#ifndef NDEBUG + for(unsigned k=1; kgetRowLength(partialTaskList[i]) ); + } +#endif + for(unsigned j=0; jset( partialTaskList[i]*ncols+j, stash[ncomp*ncols*partialTaskList[i]+j*ncomp+k] ); + } + } + } +} + void ActionWithMatrix::transferForcesToStash( const std::vector& partialTaskList, std::vector& stash ) const { unsigned ncomp = getNumberOfComponents(); unsigned ncols = getConstPntrToComponent(0)->getNumberOfColumns(); @@ -135,4 +154,23 @@ void ActionWithMatrix::transferForcesToStash( const std::vector& parti } } +void ActionWithMatrix::transferForcesToStash( const std::vector& partialTaskList, std::vector& stash ) const { + unsigned ncomp = getNumberOfComponents(); + unsigned ncols = getConstPntrToComponent(0)->getNumberOfColumns(); + unsigned nrows = partialTaskList.size(); + for(unsigned i=0; igetRowLength(partialTaskList[i]); +#ifndef NDEBUG + for(unsigned k=1; kgetRowLength(partialTaskList[i]) ); + } +#endif + for(unsigned j=0; jgetForce( partialTaskList[i]*ncols+j ); + } + } + } } + +} //namespace PLMD diff --git a/src/core/ActionWithMatrix.h b/src/core/ActionWithMatrix.h index 143469b676..610ed5d458 100644 --- a/src/core/ActionWithMatrix.h +++ b/src/core/ActionWithMatrix.h @@ -79,8 +79,12 @@ class ActionWithMatrix : public ActionWithVector { explicit ActionWithMatrix(const ActionOptions&); /// Get the elements of the matrices into the output values void transferStashToValues( const std::vector& partialTaskList, const std::vector& stash ) override ; +/// Get the elements of the matrices into the output values + void transferStashToValues( const std::vector& partialTaskList, const std::vector& stash ) override ; /// Get the forces from the output values and transfer them to the stash void transferForcesToStash( const std::vector& partialTaskList, std::vector& stash ) const override ; +/// Get the forces from the output values and transfer them to the stash + void transferForcesToStash( const std::vector& partialTaskList, std::vector& stash ) const override ; }; } diff --git a/src/core/ActionWithVector.cpp b/src/core/ActionWithVector.cpp index 9f49e354e3..d861426352 100644 --- a/src/core/ActionWithVector.cpp +++ b/src/core/ActionWithVector.cpp @@ -205,6 +205,33 @@ void ActionWithVector::getInputData( std::vector& inputdata ) const { } } +void ActionWithVector::getInputData( std::vector& inputdata ) const { + plumed_dbg_assert( getNumberOfAtoms()==0 ); + unsigned nargs = getNumberOfArguments(); + int nmasks=getNumberOfMasks(); + if( nargs>=static_cast(nmasks) && nmasks>0 ) { + nargs = nargs - nmasks; + } + + std::size_t total_args = 0; + for(unsigned i=0; igetNumberOfStoredValues(); + } + + if( inputdata.size()!=total_args ) { + inputdata.resize( total_args ); + } + + total_args = 0; + for(unsigned i=0; igetNumberOfStoredValues(); ++j) { + inputdata[total_args] = myarg->get(j,false); + total_args++; + } + } +} + void ActionWithVector::transferStashToValues( const std::vector& partialTaskList, const std::vector& stash ) { unsigned ntask = partialTaskList.size(); unsigned ncomponents = getNumberOfComponents(); @@ -216,6 +243,17 @@ void ActionWithVector::transferStashToValues( const std::vector& parti } } +void ActionWithVector::transferStashToValues( const std::vector& partialTaskList, const std::vector& stash ) { + unsigned ntask = partialTaskList.size(); + unsigned ncomponents = getNumberOfComponents(); + for(unsigned i=0; iset( partialTaskList[j], stash[partialTaskList[j]*ncomponents+i] ); + } + } +} + void ActionWithVector::transferForcesToStash( const std::vector& partialTaskList, std::vector& stash ) const { unsigned ntask = partialTaskList.size(); unsigned ncomponents = getNumberOfComponents(); @@ -227,6 +265,17 @@ void ActionWithVector::transferForcesToStash( const std::vector& parti } } +void ActionWithVector::transferForcesToStash( const std::vector& partialTaskList, std::vector& stash ) const { + unsigned ntask = partialTaskList.size(); + unsigned ncomponents = getNumberOfComponents(); + for(unsigned i=0; igetForce( partialTaskList[j] ); + } + } +} + void ActionWithVector::getNumberOfTasks( unsigned& ntasks ) { if( ntasks==0 ) { if( getNumberOfArguments()==1 && getNumberOfComponents()==1 && getPntrToComponent(0)->getRank()==0 ) { diff --git a/src/core/ActionWithVector.h b/src/core/ActionWithVector.h index a146cc1101..8a0bf6fdce 100644 --- a/src/core/ActionWithVector.h +++ b/src/core/ActionWithVector.h @@ -64,10 +64,15 @@ class ActionWithVector: virtual int checkTaskIsActive( const unsigned& itask ) const ; /// This is so we can parallelize with GPU virtual void getInputData( std::vector& inputdata ) const ; + virtual void getInputData( std::vector& inputdata ) const ; /// This is so we an transfer data gathered in the parallel task manager to the underlying values virtual void transferStashToValues( const std::vector& partialTaskList, const std::vector& stash ); +/// This is so we an transfer data gathered in the parallel task manager to the underlying values + virtual void transferStashToValues( const std::vector& partialTaskList, const std::vector& stash ); /// This is so we can transfer forces from the values to the parallel task manager virtual void transferForcesToStash( const std::vector& partialTaskList, std::vector& stash ) const ; +/// This is so we can transfer forces from the values to the parallel task manager + virtual void transferForcesToStash( const std::vector& partialTaskList, std::vector& stash ) const ; /// Get the number of forces to use unsigned getNumberOfForceDerivatives() const ; /// Apply the forces on this data diff --git a/src/core/ParallelTaskManager.h b/src/core/ParallelTaskManager.h index 30973b55cb..6aa486fc60 100644 --- a/src/core/ParallelTaskManager.h +++ b/src/core/ParallelTaskManager.h @@ -104,7 +104,8 @@ void ArgumentsBookkeeping::setupArguments( const ActionWithArguments* action ) { } } -struct ParallelActionsInput { +template +struct ParActionsInput { /// Do we need to calculate the derivatives bool noderiv{false}; /// Periodic boundary conditions @@ -121,7 +122,7 @@ struct ParallelActionsInput { unsigned threadunsafe_forces_start{0}; /// This holds all the input data that is required to calculate all values for all tasks unsigned dataSize{0}; - double *inputdata{nullptr}; + precision *inputdata{nullptr}; /// Bookeeping stuff for arguments std::size_t nargs{0}; std::size_t ranks_size{0}; @@ -140,8 +141,8 @@ struct ParallelActionsInput { const std::size_t* bookeeping{nullptr}; std::size_t argstarts_size{0}; const std::size_t* argstarts{nullptr}; - static ParallelActionsInput create( const Pbc& box ) { - auto toret=ParallelActionsInput(); + static ParActionsInput create( const Pbc& box ) { + auto toret=ParActionsInput(); toret.pbc=&box; return toret; } @@ -194,7 +195,8 @@ struct ParallelActionsInput { } }; -inline void ParallelActionsInput::setupArguments( const ArgumentsBookkeeping& ab ) { +template +inline void ParActionsInput::setupArguments( const ArgumentsBookkeeping& ab ) { nargs = ab.nargs; ranks = ab.ranks.data(); ranks_size = ab.ranks.size(); @@ -221,7 +223,8 @@ struct ArgumentBookeepingHolder { View shape; View bookeeping; - static ArgumentBookeepingHolder create ( std::size_t argno, const ParallelActionsInput& inp ) { + template + static ArgumentBookeepingHolder create ( std::size_t argno, const ParActionsInput& inp ) { return ArgumentBookeepingHolder{ inp.ranks[argno], // rank inp.ncols[argno], // ncols @@ -232,13 +235,19 @@ struct ArgumentBookeepingHolder { } }; -struct ParallelActionsOutput { - View values; - View derivatives; - View buffer; - - static ParallelActionsOutput create( std::size_t ncomp, double* v, std::size_t ndev, double* d, std::size_t nb, double* b ) { - return ParallelActionsOutput{ +template +struct ParActionsOutput { + View values; + View derivatives; + View buffer; + + static ParActionsOutput create( std::size_t ncomp, + precision* v, + std::size_t ndev, + precision* d, + std::size_t nb, + precision* b ) { + return ParActionsOutput{ View{v,ncomp}, //values View{d,ndev}, // derivatives View{b,nb} // buffer @@ -264,7 +273,9 @@ struct ForceIndexHolder { View2D{ind+2*nc,nc,nd} // indices }; } - static ForceIndexHolder create(const ParallelActionsInput& inp, + + template + static ForceIndexHolder create(const ParActionsInput& inp, std::size_t* ind ) { return create(inp.ncomponents, inp.nderivatives_per_scalar,ind); @@ -283,18 +294,20 @@ struct ForceIndexHolder { + nc // tot_indices + nc*nd; // indices } - static size_t indexesPerScalar(const ParallelActionsInput& inp) { + template + static size_t indexesPerScalar(const ParActionsInput& inp) { return indexesPerScalar(inp.ncomponents, inp.nderivatives_per_scalar); } }; -class ForceInput { +template +class ForcesInput { public: - View force; - View2D deriv; - static ForceInput create( std::size_t nv, double* f, std::size_t nd, double* d ) { - return ForceInput{ + View force; + View2D deriv; + static ForcesInput create( std::size_t nv, precision* f, std::size_t nd, precision* d ) { + return ForcesInput{ View{f,nv}, //force View2D{d,nv,nd} //deriv }; @@ -302,22 +315,23 @@ class ForceInput { }; //There is no need to pass this as reference: -struct ForceOutput { +template +struct ForcesOutput { //I would suggest to invert the name or to be clearer // like something that recalls that "thread_safe" will be need to be reducted (hence it is NOT thread safe) - View thread_safe; + View thread_safe; //these are the forces that we promise will not provoke races - View thread_unsafe; + View thread_unsafe; //const T* is a ptr to const T //T* const is a conts ptr to a modifiable T - static ForceOutput create(std::vector& reduced, std::vector& notReduced) { - return ForceOutput{ + static ForcesOutput create(std::vector& reduced, std::vector& notReduced) { + return ForcesOutput{ View{reduced.data(),reduced.size()}, // thread_safe View{notReduced.data(),notReduced.size()} // thread_unsafe }; } - static ForceOutput create(double* reduced, size_t rs, double* notReduce, size_t nrsz) { - return ForceOutput{ + static ForcesOutput create(precision* reduced, size_t rs, precision* notReduce, size_t nrsz) { + return ForcesOutput{ View{reduced,rs}, // thread_safe View{notReduce,nrsz} // thread_unsafe }; @@ -338,7 +352,7 @@ struct ForceOutput { // std::declval(), // std::declval(), // std::declval(), -// std::declval(), +// std::declval(), // std::declval >(), // std::declval(), // std::declval(), @@ -358,7 +372,7 @@ struct ForceOutput { // decltype(T::gatherForcesGPU( // std::declval(), // std::declval(), -// std::declval(), +// std::declval(), // std::declval(), // std::declval() // )) @@ -377,14 +391,32 @@ struct ForceOutput { // = T::virialSize; // } //namespace PTMUtils +template +struct cvprecision { + typedef double type; +}; + +template +struct cvprecision> { + typedef typename CV::precision type; +}; + +template +using cvprecision_t = typename cvprecision::type; + template class ParallelTaskManager { public: using input_type= typename T::input_type; + using precision = cvprecision_t; + typedef ParActionsInput ParallelActionsInput; + typedef ParActionsOutput ParallelActionsOutput; + typedef ForcesInput ForceInput; + typedef ForcesOutput ForceOutput; // static constexpr bool has_custom_gather=PTMUtils::has_gatherForces_custom; // static constexpr bool has_GPU_gather=PTMUtils::has_gatherForces_GPU; // static constexpr size_t virialSize = PTMUtils::virialSize; -private: +protected: /// The underlying action for which we are managing parallel tasks ActionWithVector* action; /// The MPI communicator @@ -401,14 +433,14 @@ class ParallelTaskManager { /// The number of forces on each thread std::size_t nthreaded_forces; /// This holds the values before we pass them to the value - std::vector value_stash; + std::vector value_stash; /// A tempory set of vectors for holding forces over threads - std::vector > omp_forces; + std::vector > omp_forces; /// This structs is used to pass data between the parallel interface and the function caller ParallelActionsInput myinput; ArgumentsBookkeeping argumentsMap; //this holds the data for myinput that will be passed though myinput - std::vector input_buffer; + std::vector input_buffer; /// This holds tempory data that we use in performTask std::size_t workspace_size; /// This holds data for that the underlying action needs to do the calculation @@ -443,12 +475,17 @@ class ParallelTaskManager { static void gatherThreadSafeForces( const ParallelActionsInput& input, const ForceIndexHolder& force_indices, const ForceInput& fdata, - View forces ); + View forces ); /// This is used to gather forces that are not thread safe static void gatherThreadUnsafeForces( const ParallelActionsInput& input, const ForceIndexHolder& force_indices, const ForceInput& fdata, - View forces ); + View forces ); +}; + +struct defaultPTM { + template + using PTM=ParallelTaskManager; }; template @@ -564,72 +601,6 @@ void ParallelTaskManager::setWorkspaceSize( std::size_t size ) { workspace_size = size; } -#ifdef __PLUMED_USE_OPENACC -//use the __PLUMED_USE_OPENACC_TASKSMINE macro to debug the ptm ins a single file -//so that compiling witha a small modification will be faster (the ptm is included nearly everywhere) -#ifndef __PLUMED_USE_OPENACC_TASKSMINE -template -void runAllTasksACC(typename T::input_type actiondata, - ParallelActionsInput myinput, - std::vector& value_stash, - const std::vector & partialTaskList, - const unsigned nactive_tasks, - const std::size_t nderivatives_per_task, - const std::size_t workspace_size - ) { - auto myinput_acc = OpenACC::fromToDataHelper(myinput); - auto actiondata_acc = OpenACC::fromToDataHelper(actiondata); - - //template type is deduced - OpenACC::memoryManager vs{value_stash}; - auto value_stash_data = vs.devicePtr(); - - OpenACC::memoryManager ptl{partialTaskList}; - auto partialTaskList_data = ptl.devicePtr(); - - OpenACC::memoryManager buff{workspace_size*nactive_tasks}; - - auto buffer = buff.devicePtr(); - OpenACC::memoryManager dev(nderivatives_per_task*nactive_tasks); - auto derivatives = dev.devicePtr(); -#pragma acc parallel loop present(myinput, actiondata) \ - copyin(nactive_tasks, \ - nderivatives_per_task, \ - workspace_size)\ - deviceptr(derivatives, \ - partialTaskList_data, \ - value_stash_data, \ - buffer) \ - default(none) - for(unsigned i=0; i0)? - buffer+workspace_size*i - :nullptr ); - // Calculate the stuff in the loop for this action - T::performTask( task_index, actiondata, myinput, myout ); - } - vs.copyFromDevice(value_stash.data()); -} -#else -template -void runAllTasksACC(typename T::input_type actiondata, - ParallelActionsInput myinput, - std::vector& value_stash, - const std::vector & partialTaskList, - const unsigned nactive_tasks, - const std::size_t nderivatives_per_task, - const std::size_t workspace_size - ) ; -#endif //__PLUMED_USE_OPENACC_TASKSMINE -#endif //__PLUMED_USE_OPENACC - template void ParallelTaskManager::runAllTasks() { // Get the list of active tasks @@ -654,24 +625,10 @@ void ParallelTaskManager::runAllTasks() { if( value_stash.size()!=totalvals ) { value_stash.resize(totalvals); } - std::fill (value_stash.begin(),value_stash.end(), 0.0); + std::fill (value_stash.begin(),value_stash.end(), precision(0.0)); if( useacc ) { -#ifdef __PLUMED_USE_OPENACC - if (comm.Get_rank()== 0) {// no multigpu shenanigans until this works - runAllTasksACC( - actiondata, - myinput, - value_stash, - partialTaskList, - nactive_tasks, - nderivatives_per_task, - workspace_size - ); - } - comm.Bcast( value_stash.data(), value_stash.size(), 0); -#else - plumed_merror("cannot use USEGPU flag if PLUMED has not been compiled with openACC"); -#endif + // there should not be any avaiable path to get here + plumed_merror("to use the USEGPU flag you need to LOAD a plugin like \"openaccPTM\""); } else { // Get the MPI details unsigned stride=comm.Get_size(); @@ -692,8 +649,8 @@ void ParallelTaskManager::runAllTasks() { #pragma omp parallel num_threads(nt) { - std::vector buffer( workspace_size ); - std::vector derivatives( nderivatives_per_task ); + std::vector buffer( workspace_size ); + std::vector derivatives( nderivatives_per_task ); #pragma omp for nowait for(unsigned i=rank; i::runAllTasks() { action->transferStashToValues( partialTaskList, value_stash ); } -#ifdef __PLUMED_USE_OPENACC -//use the __PLUMED_USE_OPENACC_FORCESMINE macro to debug the ptm ins a single file -//so that compiling witha a small modification will be faster (the ptm is included nearly everywhere) -#ifndef __PLUMED_USE_OPENACC_FORCESMINE -template -void applyForcesWithACC(PLMD::View forcesForApply, - typename T::input_type actiondata, - ParallelActionsInput myinput, - const std::vector& value_stash, - const std::vector & partialTaskList, - const unsigned nactive_tasks, - const std::size_t nderivatives_per_task, - const std::size_t workspace_size - ) { - auto myinput_acc = OpenACC::fromToDataHelper(myinput); - auto actiondata_acc = OpenACC::fromToDataHelper(actiondata); - - //template type is deduced - OpenACC::memoryManager vs{value_stash}; - auto value_stash_data = vs.devicePtr(); - - OpenACC::memoryManager ptl{partialTaskList}; - auto partialTaskList_data = ptl.devicePtr(); - - OpenACC::memoryManager ffa {forcesForApply}; - auto forcesForApply_data = ffa.devicePtr(); - const auto forcesForApply_size = ffa.size(); - const auto nind_per_scalar = ForceIndexHolder::indexesPerScalar(myinput); - //nscalars is >=ncomponents (see setupParallelTaskManager ) - const auto nind_per_task = nind_per_scalar*myinput.nscalars; - - OpenACC::memoryManager dev{nderivatives_per_task*nactive_tasks}; - auto derivatives = dev.devicePtr(); - OpenACC::memoryManager ind{nind_per_task*nactive_tasks}; - auto indices = ind.devicePtr(); - OpenACC::memoryManager vtmp{myinput.sizeOfFakeVals()*nactive_tasks}; - auto valstmp = vtmp.devicePtr(); - OpenACC::memoryManager buff{workspace_size*nactive_tasks}; - auto buffer = buff.devicePtr(); - -#define forces_indicesArg(taskID,scalarID) ForceIndexHolder::create(myinput, \ - indices + taskID*nind_per_task + scalarID*nind_per_scalar) -#define derivativeDrift(taskID,scalarID) taskID*nderivatives_per_task \ - + scalarID*myinput.ncomponents*myinput.nderivatives_per_scalar -#define stashDrift(taskID,scalarID) taskID*myinput.nscalars \ - + scalarID*myinput.ncomponents - -#pragma acc data present(myinput,actiondata) \ - copyin(nactive_tasks, \ - forcesForApply_size, \ - nderivatives_per_task, nind_per_task,nind_per_scalar, \ - workspace_size) \ - deviceptr(derivatives, \ - indices, \ - value_stash_data, \ - partialTaskList_data, \ - forcesForApply_data, \ - valstmp, \ - buffer) \ - default(none) - { -#pragma acc parallel loop - for(unsigned t=0; t0)?buffer+workspace_size*t:nullptr); - // Calculate the stuff in the loop for this action - T::performTask( task_index, actiondata, myinput, myout ); - // If this is a matrix this returns a number that isn't one as we have to loop over the columns - const std::size_t nvpt = T::getNumberOfValuesPerTask( task_index, actiondata ); -#pragma acc loop seq - for(unsigned vID=0; vID::gatherThreadSafeForces( myinput, - force_indices, - finput, - View(forcesForApply_data, - forcesForApply_size)); - } - } +template +struct forceData { + std::vector ffa; + forceData( std::vector& forcesForApply ): + ffa(forcesForApply.size()),destination(forcesForApply) {} + void update() { + std::copy(ffa.begin(),ffa.end(),destination.begin()); + } +private: + std::vector& destination; +}; -#pragma acc parallel loop - for(unsigned v=myinput.threadunsafe_forces_start; v +struct forceData { + PLMD::View ffa; + forceData( std::vector& forcesForApply ): + ffa(forcesForApply.data(),forcesForApply.size()) {} + void update() { } -#undef forces_indicesArg -#undef derivativeDrift -#undef stashDrift - ffa.copyFromDevice(forcesForApply.data()); -} -#else -template -void applyForcesWithACC(PLMD::View forcesForApply, - typename T::input_type actiondata, - ParallelActionsInput myinput, - const std::vector& value_stash, - const std::vector & partialTaskList, - const unsigned nactive_tasks, - const std::size_t nderivatives_per_task, - const std::size_t workspace_size - ); -#endif //__PLUMED_USE_OPENACC_FORCESMINE -#endif //__PLUMED_USE_OPENACC +}; template void ParallelTaskManager::applyForces( std::vector& forcesForApply ) { // Get the list of active tasks std::vector & partialTaskList= action->getListOfActiveTasks( action ) ; unsigned nactive_tasks=partialTaskList.size(); + forceData forces(forcesForApply); // Clear force buffer - forcesForApply.assign( forcesForApply.size(), 0.0 ); - //TODO: check if std::fill is faster (i get conflicting answers on the net) - //std::fill (forcesForApply.begin(),forcesForApply.end(), 0.0); + std::fill (forces.ffa.begin(),forces.ffa.end(), precision(0.0)); // Get all the input data so we can broadcast it to the GPU myinput.noderiv = false; // Retrieve the forces from the values action->transferForcesToStash( partialTaskList, value_stash ); if( useacc ) { -#ifdef __PLUMED_USE_OPENACC - std::fill (omp_forces[0].begin(),omp_forces[0].end(), 0.0); - if (comm.Get_rank() == 0) { - applyForcesWithACC( - PLMD::View { forcesForApply.data(), forcesForApply.size() }, - actiondata, - myinput, - value_stash, - partialTaskList, - nactive_tasks, - nderivatives_per_task, - workspace_size - ); - } -#else - plumed_merror("cannot use USEGPU flag if PLUMED has not been compiled with openACC"); -#endif + // there should not be any avaiable path to get here + plumed_merror("to use the USEGPU flag you need to LOAD a plugin like \"openaccPTM\""); } else { // Get the MPI details unsigned stride=comm.Get_size(); @@ -918,9 +731,9 @@ void ParallelTaskManager::applyForces( std::vector& forcesForApply ) { const unsigned t=OpenMP::getThreadNum(); omp_forces[t].assign( omp_forces[t].size(), 0.0 ); - std::vector buffer( workspace_size ); - std::vector fake_vals( myinput.sizeOfFakeVals() ); - std::vector derivatives( nderivatives_per_task ); + std::vector buffer( workspace_size ); + std::vector fake_vals( myinput.sizeOfFakeVals() ); + std::vector derivatives( nderivatives_per_task ); std::vector indices(ForceIndexHolder::indexesPerScalar(myinput)); auto force_indices = ForceIndexHolder::create( myinput,indices.data() ); @@ -942,7 +755,7 @@ void ParallelTaskManager::applyForces( std::vector& forcesForApply ) // Get the force indices T::getForceIndices( task_index, j, - forcesForApply.size(), + forces.ffa.size(), actiondata, myinput, force_indices ); @@ -959,21 +772,22 @@ void ParallelTaskManager::applyForces( std::vector& forcesForApply ) gatherThreadSafeForces( myinput, force_indices, finput, - View(forcesForApply.data(), - forcesForApply.size()) ); + View(forces.ffa.data(), + forces.ffa.size()) ); // Gather forces that are not thread safe gatherThreadUnsafeForces( myinput, force_indices, finput, - View(omp_forces[t].data(), - omp_forces[t].size()) ); + View(omp_forces[t].data(), + omp_forces[t].size()) ); } } #pragma omp critical gatherThreads( ForceOutput::create(omp_forces[t], forcesForApply ) ); } + forces.update(); // MPI Gather everything (this must be extended to the gpu thing, after makning it mpi-aware) if( !serial ) { comm.Sum( forcesForApply ); @@ -985,7 +799,7 @@ template void ParallelTaskManager::gatherThreadSafeForces( const ParallelActionsInput& input, const ForceIndexHolder& force_indices, const ForceInput& fdata, - View forces ) { + View forces ) { for(unsigned i=0; i void ParallelTaskManager::gatherThreadUnsafeForces(const ParallelActionsInput& input, const ForceIndexHolder& force_indices, const ForceInput& fdata, - View forces ) { + View forces ) { for(unsigned i=0; i& cvin, ColvarOutput& cvout ); }; typedef colvar::ColvarShortcut QuaternionShortcut; @@ -178,8 +178,8 @@ void Quaternion::calculate() { makeWhole(); } - ColvarOutput cvout = ColvarOutput::createColvarOutput(value,derivs,this); - calculateCV( colvar::ColvarInput::createColvarInput( 0, getPositions(), this ), cvout ); + auto cvout = ColvarOutput::createColvarOutput(value,derivs,this); + calculateCV( colvar::ColvarInput::createColvarInput( 0, getPositions(), this ), cvout ); for(unsigned j=0; j<4; ++j) { Value* valuej=getPntrToComponent(j); for(unsigned i=0; i<3; ++i) { @@ -191,7 +191,7 @@ void Quaternion::calculate() { } // calculator -void Quaternion::calculateCV( const colvar::ColvarInput& cvin, ColvarOutput& cvout ) { +void Quaternion::calculateCV( const colvar::ColvarInput& cvin, ColvarOutput& cvout ) { //declarations Vector vec1_comp = delta( cvin.pos[0], cvin.pos[1] ); //components between atom 1 and 2 Vector vec2_comp = delta( cvin.pos[0], cvin.pos[2] ); //components between atom 1 and 3 @@ -448,7 +448,7 @@ void Quaternion::calculateCV( const colvar::ColvarInput& cvin, ColvarOutput& cvo cvout.derivs[3][i] =0.25*dS[i]; } } - colvar::ColvarInput::setBoxDerivativesNoPbc( cvin, cvout ); + colvar::ColvarInput::setBoxDerivativesNoPbc( cvin, cvout ); } diff --git a/src/crystdistrib/QuaternionBondProductMatrix.cpp b/src/crystdistrib/QuaternionBondProductMatrix.cpp index 8291ab2cef..6b93ee6186 100644 --- a/src/crystdistrib/QuaternionBondProductMatrix.cpp +++ b/src/crystdistrib/QuaternionBondProductMatrix.cpp @@ -27,9 +27,6 @@ #include "core/ActionRegister.h" #include "tools/Torsion.h" - -#include - namespace PLMD { namespace crystdistrib { @@ -78,6 +75,8 @@ class QuaternionBondProductMatrix : public ActionWithVector { public: using input_type = QuatBondProdMatInput; using PTM = ParallelTaskManager; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: PTM taskmanager; std::vector active_tasks; diff --git a/src/dimred/ProjectPoints.cpp b/src/dimred/ProjectPoints.cpp index 0962ded392..1f639f0f89 100644 --- a/src/dimred/ProjectPoints.cpp +++ b/src/dimred/ProjectPoints.cpp @@ -258,6 +258,8 @@ class ProjectPoints : public ActionWithVector { public: using input_type = ProjectPointsInput; using PTM = ParallelTaskManager; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: unsigned dimout; mutable std::vector rowstart; diff --git a/src/function/Between.cpp b/src/function/Between.cpp index 2be6fe4598..22d06043c7 100644 --- a/src/function/Between.cpp +++ b/src/function/Between.cpp @@ -19,15 +19,11 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC -#include "FunctionSetup.h" +#include "Between.h" #include "FunctionShortcut.h" #include "FunctionOfScalar.h" #include "FunctionOfVector.h" #include "FunctionOfMatrix.h" -#include "tools/HistogramBead.h" #include "core/ActionRegister.h" #include @@ -181,26 +177,6 @@ MASK keyword. PLUMED will use the sparsity pattern for the input matrix to reduc */ //+ENDPLUMEDOC -struct Between { - HistogramBead hist{HistogramBead::KernelType::gaussian,0.0,1.0,0.5}; - static void registerKeywords( Keywords& keys ); - static void read( Between& func, ActionWithArguments* action, - FunctionOptions& options ); - static void calc( const Between& func, - bool noderiv, - const View args, - FunctionOutput& funcout ); -#ifdef __PLUMED_USE_OPENACC - void toACCDevice() const { -#pragma acc enter data copyin(this[0:1]) - hist.toACCDevice(); - } - void removeFromACCDevice() const { - hist.removeFromACCDevice(); -#pragma acc exit data delete(order, this[0:1]) - } -#endif // __PLUMED_USE_OPENACC -}; typedef FunctionShortcut BetweenShortcut; PLUMED_REGISTER_ACTION(BetweenShortcut,"BETWEEN") @@ -210,72 +186,5 @@ typedef FunctionOfVector VectorBetween; PLUMED_REGISTER_ACTION(VectorBetween,"BETWEEN_VECTOR") typedef FunctionOfMatrix MatrixBetween; PLUMED_REGISTER_ACTION(MatrixBetween,"BETWEEN_MATRIX") - -void Between::registerKeywords(Keywords& keys) { - keys.add("compulsory","LOWER","the lower boundary for this particular bin"); - keys.add("compulsory","UPPER","the upper boundary for this particular bin"); - keys.add("compulsory","SMEAR","0.5","the ammount to smear the Gaussian for each value in the distribution"); - keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous function defined above. " - "The following provides information on the \\ref histogrambead that are available. " - "When this keyword is present you no longer need the LOWER, UPPER, SMEAR and KERNEL keywords."); - keys.setValueDescription("scalar/vector/matrix","a function that is one if the input falls within a particular range and zero otherwise"); } - -void Between::read( Between& func, ActionWithArguments* action, FunctionOptions& options ) { - options.derivativeZeroIfValueIsZero = true; - if( action->getNumberOfArguments()!=1 ) { - ActionWithVector* av = dynamic_cast( action ); - if( !av || (av && action->getNumberOfArguments()-av->getNumberOfMasks()!=1) ) { - action->error("should only be one argument to less_than actions"); - } - } - - std::string str_min, str_max; - bool isPeriodic = action->getPntrToArgument(0)->isPeriodic(); - if( isPeriodic ) { - action->getPntrToArgument(0)->getDomain( str_min, str_max ); - } - std::string hinput; - action->parse("SWITCH",hinput); - if(hinput.length()==0) { - std::string low, up, sme; - action->parse("LOWER",low); - action->parse("UPPER",up); - action->parse("SMEAR",sme); - hinput = "GAUSSIAN LOWER=" + low + " UPPER=" + up + " SMEAR=" + sme; - } - std::string errors; - func.hist.set( hinput, errors ); - if( errors.size()!=0 ) { - action->error( errors ); - } - action->log.printf(" %s \n", func.hist.description().c_str() ); - - if( !isPeriodic ) { - func.hist.isNotPeriodic(); - } else { - double min; - double max; - Tools::convert( str_min, min ); - Tools::convert( str_max, max ); - func.hist.isPeriodic( min, max ); - } } - -void Between::calc( const Between& func, - bool noderiv, - const View args, - FunctionOutput& funcout ) { - // the presence of NDEBUG seems to be ignored by nvcc... - // plumed_dbg_assert( args.size()==1 ); - double deriv; - funcout.values[0] = func.hist.calculate( args[0], deriv ); - if( !noderiv ) { - funcout.derivs[0][0] = deriv; - } -} - -} -} - - diff --git a/src/function/Between.h b/src/function/Between.h new file mode 100644 index 0000000000..45b9d04e1e --- /dev/null +++ b/src/function/Between.h @@ -0,0 +1,123 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2017 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_function_Between_h +#define __PLUMED_function_Between_h +#include "FunctionSetup.h" +#include "FunctionShortcut.h" +#include "FunctionOfScalar.h" +#include "FunctionOfVector.h" +#include "FunctionOfMatrix.h" +#include "tools/HistogramBead.h" + +#include + +namespace PLMD { +namespace function { + +struct Between { + HistogramBead hist{HistogramBead::KernelType::gaussian,0.0,1.0,0.5}; + static void registerKeywords( Keywords& keys ); + static void read( Between& func, ActionWithArguments* action, + FunctionOptions& options ); + static void calc( const Between& func, + bool noderiv, + const View args, + FunctionOutput& funcout ); +#ifdef __PLUMED_HAS_OPENACC + void toACCDevice() const { +#pragma acc enter data copyin(this[0:1]) + hist.toACCDevice(); + } + void removeFromACCDevice() const { + hist.removeFromACCDevice(); +#pragma acc exit data delete(order, this[0:1]) + } +#endif // __PLUMED_HAS_OPENACC +}; + +void Between::registerKeywords(Keywords& keys) { + keys.add("compulsory","LOWER","the lower boundary for this particular bin"); + keys.add("compulsory","UPPER","the upper boundary for this particular bin"); + keys.add("compulsory","SMEAR","0.5","the ammount to smear the Gaussian for each value in the distribution"); + keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous function defined above. " + "The following provides information on the \\ref histogrambead that are available. " + "When this keyword is present you no longer need the LOWER, UPPER, SMEAR and KERNEL keywords."); + keys.setValueDescription("scalar/vector/matrix","a function that is one if the input falls within a particular range and zero otherwise"); +} + +void Between::read( Between& func, ActionWithArguments* action, FunctionOptions& options ) { + options.derivativeZeroIfValueIsZero = true; + if( action->getNumberOfArguments()!=1 ) { + ActionWithVector* av = dynamic_cast( action ); + if( !av || (av && action->getNumberOfArguments()-av->getNumberOfMasks()!=1) ) { + action->error("should only be one argument to less_than actions"); + } + } + + std::string str_min, str_max; + bool isPeriodic = action->getPntrToArgument(0)->isPeriodic(); + if( isPeriodic ) { + action->getPntrToArgument(0)->getDomain( str_min, str_max ); + } + std::string hinput; + action->parse("SWITCH",hinput); + if(hinput.length()==0) { + std::string low, up, sme; + action->parse("LOWER",low); + action->parse("UPPER",up); + action->parse("SMEAR",sme); + hinput = "GAUSSIAN LOWER=" + low + " UPPER=" + up + " SMEAR=" + sme; + } + std::string errors; + func.hist.set( hinput, errors ); + if( errors.size()!=0 ) { + action->error( errors ); + } + action->log.printf(" %s \n", func.hist.description().c_str() ); + + if( !isPeriodic ) { + func.hist.isNotPeriodic(); + } else { + double min; + double max; + Tools::convert( str_min, min ); + Tools::convert( str_max, max ); + func.hist.isPeriodic( min, max ); + } +} + +void Between::calc( const Between& func, + bool noderiv, + const View args, + FunctionOutput& funcout ) { + // the presence of NDEBUG seems to be ignored by nvcc... + // plumed_dbg_assert( args.size()==1 ); + double deriv; + funcout.values[0] = func.hist.calculate( args[0], deriv ); + if( !noderiv ) { + funcout.derivs[0][0] = deriv; + } +} + +} +} +#endif //__PLUMED_function_Between_h diff --git a/src/function/Combine.cpp b/src/function/Combine.cpp index b2faffeb0a..da6e96cb2e 100644 --- a/src/function/Combine.cpp +++ b/src/function/Combine.cpp @@ -19,16 +19,13 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC +#include "Combine.h" #include "FunctionShortcut.h" #include "FunctionOfScalar.h" #include "FunctionOfVector.h" #include "FunctionOfMatrix.h" #include "core/ActionRegister.h" -#include namespace PLMD { namespace function { @@ -211,65 +208,6 @@ If the arguments input to the COMBINE action are matrices then the MASK keyword */ //+ENDPLUMEDOC -class Combine { - struct component { - double coefficient{0.0}; - double parameter{0.0}; - double power{0.0}; - double max_minus_min{0.0}; - double inv_max_minus_min{0.0}; - bool periodic{false}; - }; - std::vector components{}; -public: - std::size_t ncomponents{0}; - component * cmps=nullptr; - void update() { - cmps = components.data(); - ncomponents = components.size(); - } - Combine() = default; - ~Combine() = default; - Combine(const Combine&x): - components(x.components) { - update(); - } - Combine(Combine&&x): - components(std::move(x.components)) { - update(); - } - Combine &operator=(const Combine&x) { - if (this!=&x) { - components=x.components; - update(); - } - return *this; - } - Combine &operator=(Combine&&x) { - if (this!=&x) { - components=std::move(x.components); - update(); - } - return *this; - } - static void registerKeywords(Keywords& keys); - static void read( Combine& func, - ActionWithArguments* action, - FunctionOptions& options ); - static void calc( const Combine& func, - bool noderiv, - const View& args, - FunctionOutput& funcout ); -#ifdef __PLUMED_USE_OPENACC - void toACCDevice() const { -#pragma acc enter data copyin(this[0:1], ncomponents, cmps[0:ncomponents]) - } - void removeFromACCDevice() const { -#pragma acc exit data delete(cmps[0:ncomponents], ncomponents, this[0:1]) - } -#endif // __PLUMED_USE_OPENACC -}; - typedef FunctionShortcut CombineShortcut; PLUMED_REGISTER_ACTION(CombineShortcut,"COMBINE") typedef FunctionOfScalar ScalarCombine; @@ -279,100 +217,5 @@ PLUMED_REGISTER_ACTION(VectorCombine,"COMBINE_VECTOR") typedef FunctionOfMatrix MatrixCombine; PLUMED_REGISTER_ACTION(MatrixCombine,"COMBINE_MATRIX") -void Combine::registerKeywords(Keywords& keys) { - keys.use("PERIODIC"); - keys.add("compulsory","COEFFICIENTS","1.0","the coefficients of the arguments in your function"); - keys.add("compulsory","PARAMETERS","0.0","the parameters of the arguments in your function"); - keys.add("compulsory","POWERS","1.0","the powers to which you are raising each of the arguments in your function"); - keys.addFlag("NORMALIZE",false,"normalize all the coefficients so that in total they are equal to one"); - keys.setValueDescription("scalar/vector/matrix","a linear combination"); -} - -void Combine::read( Combine& func, ActionWithArguments* action, - FunctionOptions& options ) { - unsigned nargs = action->getNumberOfArguments(); - ActionWithVector* av=dynamic_cast(action); - if(av && av->getNumberOfMasks()>0) { - nargs = nargs - av->getNumberOfMasks(); - } - std::vector coefficients(nargs); - action->parseVector("COEFFICIENTS",coefficients); - - if(coefficients.size()!=nargs) { - action->error("Size of COEFFICIENTS array should be the same as number for arguments"); - } - std::vector parameters(nargs); - action->parseVector("PARAMETERS",parameters); - if(parameters.size()!=nargs) { - action->error("Size of PARAMETERS array should be the same as number for arguments"); - } - std::vector powers(nargs); - action->parseVector("POWERS",powers); - if(powers.size()!=nargs) { - action->error("Size of POWERS array should be the same as number for arguments"); - } - - bool normalize; - action->parseFlag("NORMALIZE",normalize); - if(normalize) { - double n=std::accumulate(coefficients.begin(),coefficients.end(),0.0); - std::transform(coefficients.begin(),coefficients.end(),coefficients.begin(), - [n](double x) { - return x/n; - }); - } - - action->log.printf(" with coefficients:"); - func.components.resize( nargs ); - func.update(); - for(unsigned i=0; ilog.printf(" %f",func.components[i].coefficient); - } - action->log.printf("\n with parameters:"); - for(unsigned i=0; ilog.printf(" %f",func.components[i].parameter); - } - action->log.printf("\n and powers:"); - for(unsigned i=0; ilog.printf(" %f",func.components[i].power); - } - action->log.printf("\n"); - // Store periodicity stuff - for(unsigned i=0; igetPntrToArgument(i))->isPeriodic() ) { - func.components[i].periodic = true; - std::string min, max; - (action->getPntrToArgument(i))->getDomain( min, max ); - double dmin, dmax; - Tools::convert( min, dmin ); - Tools::convert( max, dmax ); - func.components[i].max_minus_min = dmax - dmin; - func.components[i].inv_max_minus_min = 1.0 / func.components[i].max_minus_min ; - } - } - -} - -void Combine::calc( const Combine& func, - bool noderiv, - const View& args, - FunctionOutput& funcout ) { - funcout.values[0]=0.0; - for(unsigned i=0; i. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_function_Combine_h +#define __PLUMED_function_Combine_h +#include "FunctionSetup.h" +#include "tools/Keywords.h" +#include "tools/View.h" +#include "core/ActionWithArguments.h" + +#include +namespace PLMD { +namespace function { + +class Combine { + struct component { + double coefficient{0.0}; + double parameter{0.0}; + double power{0.0}; + double max_minus_min{0.0}; + double inv_max_minus_min{0.0}; + bool periodic{false}; + }; + std::vector components{}; +public: + std::size_t ncomponents{0}; + component * cmps=nullptr; + void update() { + cmps = components.data(); + ncomponents = components.size(); + } + Combine() = default; + ~Combine() = default; + Combine(const Combine&x): + components(x.components) { + update(); + } + Combine(Combine&&x): + components(std::move(x.components)) { + update(); + } + Combine &operator=(const Combine&x) { + if (this!=&x) { + components=x.components; + update(); + } + return *this; + } + Combine &operator=(Combine&&x) { + if (this!=&x) { + components=std::move(x.components); + update(); + } + return *this; + } + static void registerKeywords(Keywords& keys); + static void read( Combine& func, + ActionWithArguments* action, + FunctionOptions& options ); + static void calc( const Combine& func, + bool noderiv, + const View& args, + FunctionOutput& funcout ); +#ifdef __PLUMED_HAS_OPENACC + void toACCDevice() const { +#pragma acc enter data copyin(this[0:1], ncomponents, cmps[0:ncomponents]) + } + void removeFromACCDevice() const { +#pragma acc exit data delete(cmps[0:ncomponents], ncomponents, this[0:1]) + } +#endif // __PLUMED_HAS_OPENACC +}; + +void Combine::registerKeywords(Keywords& keys) { + keys.use("PERIODIC"); + keys.add("compulsory","COEFFICIENTS","1.0","the coefficients of the arguments in your function"); + keys.add("compulsory","PARAMETERS","0.0","the parameters of the arguments in your function"); + keys.add("compulsory","POWERS","1.0","the powers to which you are raising each of the arguments in your function"); + keys.addFlag("NORMALIZE",false,"normalize all the coefficients so that in total they are equal to one"); + keys.setValueDescription("scalar/vector/matrix","a linear combination"); +} + +void Combine::read( Combine& func, ActionWithArguments* action, + FunctionOptions& options ) { + unsigned nargs = action->getNumberOfArguments(); + ActionWithVector* av=dynamic_cast(action); + if(av && av->getNumberOfMasks()>0) { + nargs = nargs - av->getNumberOfMasks(); + } + std::vector coefficients(nargs); + action->parseVector("COEFFICIENTS",coefficients); + + if(coefficients.size()!=nargs) { + action->error("Size of COEFFICIENTS array should be the same as number for arguments"); + } + std::vector parameters(nargs); + action->parseVector("PARAMETERS",parameters); + if(parameters.size()!=nargs) { + action->error("Size of PARAMETERS array should be the same as number for arguments"); + } + std::vector powers(nargs); + action->parseVector("POWERS",powers); + if(powers.size()!=nargs) { + action->error("Size of POWERS array should be the same as number for arguments"); + } + + bool normalize; + action->parseFlag("NORMALIZE",normalize); + if(normalize) { + double n=std::accumulate(coefficients.begin(),coefficients.end(),0.0); + std::transform(coefficients.begin(),coefficients.end(),coefficients.begin(), + [n](double x) { + return x/n; + }); + } + + action->log.printf(" with coefficients:"); + func.components.resize( nargs ); + func.update(); + for(unsigned i=0; ilog.printf(" %f",func.components[i].coefficient); + } + action->log.printf("\n with parameters:"); + for(unsigned i=0; ilog.printf(" %f",func.components[i].parameter); + } + action->log.printf("\n and powers:"); + for(unsigned i=0; ilog.printf(" %f",func.components[i].power); + } + action->log.printf("\n"); + // Store periodicity stuff + for(unsigned i=0; igetPntrToArgument(i))->isPeriodic() ) { + func.components[i].periodic = true; + std::string min, max; + (action->getPntrToArgument(i))->getDomain( min, max ); + double dmin, dmax; + Tools::convert( min, dmin ); + Tools::convert( max, dmax ); + func.components[i].max_minus_min = dmax - dmin; + func.components[i].inv_max_minus_min = 1.0 / func.components[i].max_minus_min ; + } + } + +} + +void Combine::calc( const Combine& func, + bool noderiv, + const View& args, + FunctionOutput& funcout ) { + funcout.values[0]=0.0; + for(unsigned i=0; i +template class FunctionOfMatrix : public ActionWithVector { public: - using input_type = FunctionData; - using PTM = ParallelTaskManager>; + using input_type = FunctionData; + using mytype = FunctionOfMatrix; + using PTM = typename myPTM::template PTM; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: /// The parallel task manager PTM taskmanager; @@ -60,24 +63,25 @@ class FunctionOfMatrix : public ActionWithVector { void getNumberOfTasks( unsigned& ntasks ) override ; std::vector& getListOfActiveTasks( ActionWithVector* action ) override ; void getInputData( std::vector& inputdata ) const override ; + void getInputData( std::vector& inputdata ) const override ; static void performTask( std::size_t task_index, - const FunctionData& actiondata, + const FunctionData& actiondata, ParallelActionsInput& input, ParallelActionsOutput& output ); /// Add some forces void applyNonZeroRankForces( std::vector& outforces ) override ; /// Get the indices of the forces - static int getNumberOfValuesPerTask( std::size_t task_index, const FunctionData& actiondata ); + static int getNumberOfValuesPerTask( std::size_t task_index, const FunctionData& actiondata ); static void getForceIndices( std::size_t task_index, std::size_t colno, std::size_t ntotal_force, - const FunctionData& actiondata, + const FunctionData& actiondata, const ParallelActionsInput& input, ForceIndexHolder force_indices ); }; -template -void FunctionOfMatrix::registerKeywords(Keywords& keys ) { +template +void FunctionOfMatrix::registerKeywords(Keywords& keys ) { ActionWithVector::registerKeywords(keys); std::string name = keys.getDisplayName(); std::size_t und=name.find("_MATRIX"); @@ -86,7 +90,7 @@ void FunctionOfMatrix::registerKeywords(Keywords& keys ) { keys.addInputKeyword("optional","MASK","matrix","a matrix that is used to used to determine which elements of the output matrix to compute"); keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); keys.reserve("compulsory","PERIODIC","if the output of your function is periodic then you should specify the periodicity of the function. If the output is not periodic you must state this using PERIODIC=NO"); - T::registerKeywords( keys ); + CV::registerKeywords( keys ); if( keys.getDisplayName()=="SUM" ) { keys.setValueDescription("scalar","the sum of all the elements in the input matrix"); } else if( keys.getDisplayName()=="HIGHEST" ) { @@ -99,8 +103,8 @@ void FunctionOfMatrix::registerKeywords(Keywords& keys ) { PTM::registerKeywords( keys ); } -template -unsigned FunctionOfMatrix::getNumberOfFunctionArguments() const { +template +unsigned FunctionOfMatrix::getNumberOfFunctionArguments() const { unsigned nargs=getNumberOfArguments(); if( getNumberOfMasks()>0 ) { return nargs - getNumberOfMasks(); @@ -108,8 +112,8 @@ unsigned FunctionOfMatrix::getNumberOfFunctionArguments() const { return nargs; } -template -FunctionOfMatrix::FunctionOfMatrix(const ActionOptions&ao): +template +FunctionOfMatrix::FunctionOfMatrix(const ActionOptions&ao): Action(ao), ActionWithVector(ao), taskmanager(this), @@ -171,7 +175,7 @@ FunctionOfMatrix::FunctionOfMatrix(const ActionOptions&ao): auto & myfunc = taskmanager.getActionInput(); myfunc.argstart = argstart; myfunc.nscalars = nscalars; - FunctionData::setup( myfunc.f, keywords.getOutputComponents(), shape, false, this ); + FunctionData::setup( myfunc.f, keywords.getOutputComponents(), shape, false, this ); // Copy the fact that this is a symmetric matrix if the input matrices are all symmetric for(unsigned i=0; isetSymmetric( symmetric ); @@ -180,14 +184,14 @@ FunctionOfMatrix::FunctionOfMatrix(const ActionOptions&ao): nscalars ); } -template -std::string FunctionOfMatrix::writeInGraph() const { +template +std::string FunctionOfMatrix::writeInGraph() const { std::size_t und = getName().find_last_of("_"); return getName().substr(0,und); } -template -unsigned FunctionOfMatrix::getNumberOfDerivatives() { +template +unsigned FunctionOfMatrix::getNumberOfDerivatives() { unsigned nder=0; for(unsigned i=argstart; igetNumberOfStoredValues(); @@ -195,8 +199,8 @@ unsigned FunctionOfMatrix::getNumberOfDerivatives() { return nder; } -template -void FunctionOfMatrix::prepare() { +template +void FunctionOfMatrix::prepare() { std::vector shape(getPntrToArgument(argstart)->getShape()); for(unsigned i=0; i::prepare() { active_tasks.resize(0); } -template -void FunctionOfMatrix::getNumberOfTasks( unsigned& ntasks ) { +template +void FunctionOfMatrix::getNumberOfTasks( unsigned& ntasks ) { ntasks=getPntrToComponent(0)->getNumberOfStoredValues(); } -template -std::vector& FunctionOfMatrix::getListOfActiveTasks( ActionWithVector* action ) { +template +std::vector& FunctionOfMatrix::getListOfActiveTasks( ActionWithVector* action ) { if( active_tasks.size()>0 ) { return active_tasks; } @@ -269,8 +273,8 @@ std::vector& FunctionOfMatrix::getListOfActiveTasks( ActionWithVect return active_tasks; } -template -void FunctionOfMatrix::getInputData( std::vector& inputdata ) const { +template +void FunctionOfMatrix::getInputData( std::vector& inputdata ) const { int nmasks = getNumberOfMasks(); unsigned nargs = getNumberOfFunctionArguments(); @@ -310,8 +314,49 @@ void FunctionOfMatrix::getInputData( std::vector& inputdata ) const { } } -template -void FunctionOfMatrix::calculate() { +template +void FunctionOfMatrix::getInputData( std::vector& inputdata ) const { + int nmasks = getNumberOfMasks(); + unsigned nargs = getNumberOfFunctionArguments(); + + const Value* myval = getConstPntrToComponent(0); + std::size_t ntasks = myval->getNumberOfStoredValues(); + std::size_t ndata = static_cast(nargs-argstart)*ntasks; + if( inputdata.size()!=ndata ) { + inputdata.resize( ndata ); + } + + for(unsigned j=argstart; jgetRank()==0 ) { + double val = jarg->get(); + for(unsigned i=0; igetShape()[0]; ++i) { + unsigned colbase=i*myval->getNumberOfColumns(); + for(unsigned k=0; kgetRowLength(i); ++k) { + inputdata[(nargs-argstart)*(colbase+k) + j-argstart] = val; + } + } + } else if( nmasks>0 ) { + for(unsigned i=0; igetShape()[0]; ++i) { + unsigned jcolbase = i*jarg->getShape()[1]; + unsigned vcolbase = i*myval->getNumberOfColumns(); + for(unsigned k=0; kgetRowLength(i); ++k) { + inputdata[(nargs-argstart)*(vcolbase+k) + j-argstart] = jarg->get(jcolbase+myval->getRowIndex(i,k),true); + } + } + } else { + for(unsigned i=0; igetShape()[0]; ++i) { + unsigned colbase=i*jarg->getNumberOfColumns(); + for(unsigned k=0; kgetRowLength(i); ++k) { + inputdata[(nargs-argstart)*(colbase+k) + j-argstart] = jarg->get(colbase+k,false); + } + } + } + } +} + +template +void FunctionOfMatrix::calculate() { Value* myarg = NULL; if( getNumberOfMasks()>0 ) { myarg = getPntrToArgument(getNumberOfArguments()-getNumberOfMasks()); @@ -326,41 +371,41 @@ void FunctionOfMatrix::calculate() { taskmanager.runAllTasks(); } -template -void FunctionOfMatrix::performTask( std::size_t task_index, - const FunctionData& actiondata, - ParallelActionsInput& input, - ParallelActionsOutput& output ) { +template +void FunctionOfMatrix::performTask( std::size_t task_index, + const FunctionData& actiondata, + ParallelActionsInput& input, + ParallelActionsOutput& output ) { auto funcout = FunctionOutput::create( input.ncomponents, output.values.data(), input.nderivatives_per_scalar, output.derivatives.data() ); - T::calc( actiondata.f, - input.noderiv, - View( input.inputdata + task_index*input.nderivatives_per_scalar, - input.nderivatives_per_scalar ), - funcout ); + CV::calc( actiondata.f, + input.noderiv, + View( input.inputdata + task_index*input.nderivatives_per_scalar, + input.nderivatives_per_scalar ), + funcout ); } -template -void FunctionOfMatrix::applyNonZeroRankForces( std::vector& outforces ) { +template +void FunctionOfMatrix::applyNonZeroRankForces( std::vector& outforces ) { taskmanager.applyForces( outforces ); } -template -int FunctionOfMatrix::getNumberOfValuesPerTask( std::size_t task_index, const FunctionData& actiondata ) { +template +int FunctionOfMatrix::getNumberOfValuesPerTask( std::size_t task_index, const FunctionData& actiondata ) { return 1; } -template -void FunctionOfMatrix::getForceIndices( std::size_t task_index, +template +void FunctionOfMatrix::getForceIndices( std::size_t task_index, std::size_t colno, std::size_t ntotal_force, - const FunctionData& actiondata, + const FunctionData& actiondata, const ParallelActionsInput& input, ForceIndexHolder force_indices ) { // The force indices are found in the same way as in FunctionOfVector so we reuse that function here - FunctionOfVector::getForceIndices( task_index, colno, ntotal_force, actiondata, input, force_indices ); + FunctionOfVector::getForceIndices( task_index, colno, ntotal_force, actiondata, input, force_indices ); } } diff --git a/src/function/FunctionOfVector.h b/src/function/FunctionOfVector.h index 7efcd5944d..140db2bb93 100644 --- a/src/function/FunctionOfVector.h +++ b/src/function/FunctionOfVector.h @@ -31,11 +31,14 @@ namespace PLMD { namespace function { -template +template class FunctionOfVector : public ActionWithVector { public: - using input_type = FunctionData; - using PTM = ParallelTaskManager>; + using input_type = FunctionData; + using mytype= FunctionOfVector; + using PTM = typename myPTM::template PTM; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: /// The parallel task manager PTM taskmanager; @@ -45,7 +48,8 @@ class FunctionOfVector : public ActionWithVector { static void registerKeywords(Keywords&); explicit FunctionOfVector(const ActionOptions&); ~FunctionOfVector() {} - std::string getOutputComponentDescription( const std::string& cname, const Keywords& keys ) const override ; + std::string getOutputComponentDescription( const std::string& cname, + const Keywords& keys ) const override ; /// Get the number of derivatives for this action unsigned getNumberOfDerivatives() override ; /// Resize vectors that are the wrong size @@ -58,23 +62,24 @@ class FunctionOfVector : public ActionWithVector { void applyNonZeroRankForces( std::vector& outforces ) override ; /// Get the input data void getInputData( std::vector& inputdata ) const override ; + void getInputData( std::vector& inputdata ) const override ; /// Calculate the function static void performTask( std::size_t task_index, - const FunctionData& actiondata, + const FunctionData& actiondata, ParallelActionsInput& input, ParallelActionsOutput& output ); /// Get the indices of the forces - static int getNumberOfValuesPerTask( std::size_t task_index, const FunctionData& actiondata ); + static int getNumberOfValuesPerTask( std::size_t task_index, const FunctionData& actiondata ); static void getForceIndices( std::size_t task_index, std::size_t colno, std::size_t ntotal_force, - const FunctionData& actiondata, + const FunctionData& actiondata, const ParallelActionsInput& input, ForceIndexHolder force_indices ); }; -template -void FunctionOfVector::registerKeywords(Keywords& keys ) { +template +void FunctionOfVector::registerKeywords(Keywords& keys ) { Action::registerKeywords(keys); ActionWithValue::registerKeywords(keys); ActionWithArguments::registerKeywords(keys); @@ -84,7 +89,7 @@ void FunctionOfVector::registerKeywords(Keywords& keys ) { keys.addInputKeyword("compulsory","ARG","scalar/vector","the labels of the scalar and vector that on which the function is being calculated elementwise"); keys.reserve("compulsory","PERIODIC","if the output of your function is periodic then you should specify the periodicity of the function. If the output is not periodic you must state this using PERIODIC=NO"); keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); - T::registerKeywords( keys ); + CV::registerKeywords( keys ); if( keys.getDisplayName()=="SUM" ) { keys.setValueDescription("scalar","the sum of all the elements in the input vector"); } else if( keys.getDisplayName()=="MEAN" ) { @@ -105,8 +110,8 @@ void FunctionOfVector::registerKeywords(Keywords& keys ) { PTM::registerKeywords( keys ); } -template -FunctionOfVector::FunctionOfVector(const ActionOptions&ao): +template +FunctionOfVector::FunctionOfVector(const ActionOptions&ao): Action(ao), ActionWithVector(ao), taskmanager(this), @@ -156,27 +161,29 @@ FunctionOfVector::FunctionOfVector(const ActionOptions&ao): auto & myfunc = taskmanager.getActionInput(); myfunc.argstart = argstart; myfunc.nscalars = nscalars; - FunctionData::setup( myfunc.f, keywords.getOutputComponents(), shape, false, this ); + FunctionData::setup( myfunc.f, keywords.getOutputComponents(), shape, false, this ); // Setup the parallel task manager taskmanager.setupParallelTaskManager( nargs-argstart, nscalars ); } -template -std::string FunctionOfVector::getOutputComponentDescription( const std::string& cname, const Keywords& keys ) const { +template +std::string FunctionOfVector::getOutputComponentDescription( const std::string& cname, +const Keywords& keys ) const { if( getName().find("SORT")==std::string::npos ) { return ActionWithValue::getOutputComponentDescription( cname, keys ); } return "the " + cname + "th largest element in the input vectors"; } -template -std::string FunctionOfVector::writeInGraph() const { +template +std::string FunctionOfVector::writeInGraph() const { std::size_t und = getName().find_last_of("_"); return getName().substr(0,und); } -template -unsigned FunctionOfVector::getNumberOfDerivatives() { +template +unsigned FunctionOfVector::getNumberOfDerivatives() { unsigned nder = 0; for(unsigned i=argstart; igetNumberOfStoredValues(); @@ -184,8 +191,8 @@ unsigned FunctionOfVector::getNumberOfDerivatives() { return nder; } -template -void FunctionOfVector::prepare() { +template +void FunctionOfVector::prepare() { std::vector shape(1); for(unsigned i=argstart; igetRank()==1 ) { @@ -202,8 +209,8 @@ void FunctionOfVector::prepare() { ActionWithVector::prepare(); } -template -void FunctionOfVector::getInputData( std::vector& inputdata ) const { +template +void FunctionOfVector::getInputData( std::vector& inputdata ) const { unsigned nargs = getNumberOfArguments(); int nmasks = getNumberOfMasks(); if( nargs>=static_cast(nmasks) && nmasks>0 ) { @@ -238,43 +245,81 @@ void FunctionOfVector::getInputData( std::vector& inputdata ) const { } } -template -void FunctionOfVector::calculate() { +template +void FunctionOfVector::getInputData( std::vector& inputdata ) const { + unsigned nargs = getNumberOfArguments(); + int nmasks = getNumberOfMasks(); + if( nargs>=static_cast(nmasks) && nmasks>0 ) { + nargs = nargs - nmasks; + } + + std::size_t ntasks = 0; + for(unsigned i=argstart; igetRank()==1 ) { + ntasks = getPntrToArgument(i)->getShape()[0]; + break; + } + } + + std::size_t ndata = static_cast(nargs-argstart)*ntasks; + if( inputdata.size()!=ndata ) { + inputdata.resize( ndata ); + } + + for(unsigned j=argstart; jgetRank()==0 ) { + double val = myarg->get(); + for(unsigned i=0; iget(i); + } + } + } +} + +template +void FunctionOfVector::calculate() { // This is done if we are calculating a function of multiple cvs taskmanager.runAllTasks(); } -template -void FunctionOfVector::performTask( std::size_t task_index, - const FunctionData& actiondata, - ParallelActionsInput& input, - ParallelActionsOutput& output ) { +template +void FunctionOfVector::performTask( std::size_t task_index, + const FunctionData& actiondata, + ParallelActionsInput& input, + ParallelActionsOutput& output ) { auto funcout = FunctionOutput::create( input.ncomponents, output.values.data(), input.nderivatives_per_scalar, output.derivatives.data() ); - T::calc( actiondata.f, - input.noderiv, - View( input.inputdata + task_index*input.nderivatives_per_scalar, - input.nderivatives_per_scalar ), - funcout ); + CV::calc( actiondata.f, + input.noderiv, + View( input.inputdata + task_index*input.nderivatives_per_scalar, + input.nderivatives_per_scalar ), + funcout ); } -template -void FunctionOfVector::applyNonZeroRankForces( std::vector& outforces ) { +template +void FunctionOfVector::applyNonZeroRankForces( std::vector& outforces ) { taskmanager.applyForces( outforces ); } -template -int FunctionOfVector::getNumberOfValuesPerTask( std::size_t task_index, const FunctionData& actiondata ) { +template +int FunctionOfVector::getNumberOfValuesPerTask( std::size_t task_index, +const FunctionData& actiondata ) { return 1; } -template -void FunctionOfVector::getForceIndices( std::size_t task_index, +template +void FunctionOfVector::getForceIndices( std::size_t task_index, std::size_t colno, std::size_t ntotal_force, - const FunctionData& actiondata, + const FunctionData& actiondata, const ParallelActionsInput& input, ForceIndexHolder force_indices ) { diff --git a/src/function/FunctionSetup.h b/src/function/FunctionSetup.h index 0166403fe5..a2e56987a8 100644 --- a/src/function/FunctionSetup.h +++ b/src/function/FunctionSetup.h @@ -49,7 +49,7 @@ struct FunctionData { const std::vector& shape, bool hasderiv, ActionWithValue* action ); -#ifdef __PLUMED_USE_OPENACC +#ifdef __PLUMED_HAS_OPENACC void toACCDevice() const { #pragma acc enter data copyin(this[0:1], argstart, nscalars) f.toACCDevice(); @@ -58,7 +58,7 @@ struct FunctionData { f.removeFromACCDevice(); #pragma acc exit data delete(nscalars, argstart, this[0:1]) } -#endif //__PLUMED_USE_OPENACC +#endif //__PLUMED_HAS_OPENACC }; template diff --git a/src/function/FunctionShortcut.h b/src/function/FunctionShortcut.h index ea843a3d0b..f3f8c55553 100644 --- a/src/function/FunctionShortcut.h +++ b/src/function/FunctionShortcut.h @@ -40,27 +40,39 @@ class FunctionShortcut : public ActionShortcut { public: static void registerKeywords(Keywords&); explicit FunctionShortcut(const ActionOptions&); - static void createAction( ActionShortcut* action, const std::vector& vals, const std::string& allargs ); + static void createAction( ActionShortcut* action, + const std::vector& vals, + const std::string& allargs, + bool useGPU=false); }; template void FunctionShortcut::registerKeywords(Keywords& keys ) { ActionShortcut::registerKeywords( keys ); - keys.reserve("compulsory","PERIODIC","if the output of your function is periodic then you should specify the periodicity of the function. If the output is not periodic you must state this using PERIODIC=NO"); + keys.reserve("compulsory","PERIODIC", + "if the output of your function is periodic then you should specify " + "the periodicity of the function. " + "If the output is not periodic you must state this using PERIODIC=NO"); keys.addActionNameSuffix("_SCALAR"); keys.addActionNameSuffix("_ONEARG"); keys.addActionNameSuffix("_VECTOR"); + keys.addActionNameSuffix("_VECTORACC"); keys.addActionNameSuffix("_MATRIX"); + keys.addActionNameSuffix("_MATRIXACC"); keys.addActionNameSuffix("_GRID"); - T tfunc; - tfunc.registerKeywords( keys ); + //keys.addActionNameSuffix("_GRIDACC"); + keys.addFlag("USEGPU",false,"run this calculation on the GPU"); + keys.addLinkInDocForFlag("USEGPU","gpu.md"); + T::registerKeywords( keys ); if( keys.getDisplayName()=="SUM" || keys.getDisplayName()=="CUSTOM" || keys.getDisplayName()=="MATHEVAL" ) { keys.addInputKeyword("compulsory","ARG","scalar/vector/matrix/grid","the values input to this function"); } else { keys.addInputKeyword("compulsory","ARG","scalar/vector/matrix","the values input to this function"); } if( keys.outputComponentExists(".#!value") && keys.getDisplayName()!="DIFFERENCE" ) { - keys.addInputKeyword("optional","MASK","vector/matrix","the label for a sparse vector/matrix that should be used to determine which elements of the vector/matrix should be computed"); + keys.addInputKeyword("optional","MASK","vector/matrix", + "the label for a sparse vector/matrix that should be used " + "to determine which elements of the vector/matrix should be computed"); } } @@ -79,13 +91,19 @@ FunctionShortcut::FunctionShortcut(const ActionOptions&ao): if( vals.size()==0 ) { error("found no input arguments to function"); } - createAction( this, vals, allargs ); + bool usegpuFLAG=false; + parseFlag("USEGPU",usegpuFLAG); + createAction( this, vals, allargs,usegpuFLAG); } template -void FunctionShortcut::createAction( ActionShortcut* action, const std::vector& vals, const std::string& allargs ) { +void FunctionShortcut::createAction( ActionShortcut* action, + const std::vector& vals, + const std::string& allargs, + const bool useGPU) { unsigned maxrank=vals[0]->getRank(); bool isgrid=false; + const std::string doUSEGPU = useGPU?"ACC":""; for(unsigned i=0; igetRank()>0 && vals[i]->hasDerivatives() ) { isgrid=true; @@ -95,30 +113,44 @@ void FunctionShortcut::createAction( ActionShortcut* action, const std::vecto } } if( isgrid ) { - if( actionRegister().check( action->getName() + "_GRID") ) { - action->readInputLine( action->getShortcutLabel() + ": " + action->getName() + "_GRID ARG=" + allargs + " " + action->convertInputLineToString() ); + if( action->plumed.checkAction( action->getName() + "_GRID") ) { + action->readInputLine( action->getShortcutLabel() + ": " + + action->getName() + "_GRID ARG=" + allargs + + " " + action->convertInputLineToString() ); } else { - plumed_merror("there is no action registered that allows you to do " + action->getName() + " with functions on a grid"); + plumed_merror("there is no action registered that allows you to do " + + action->getName() + " with functions on a grid"); } } else if( maxrank==0 ) { - if( actionRegister().check( action->getName() + "_SCALAR") ) { - action->readInputLine( action->getShortcutLabel() + ": " + action->getName() + "_SCALAR ARG=" + allargs + " " + action->convertInputLineToString() ); + if( action->plumed.checkAction(action->getName() + "_SCALAR") ) { + action->readInputLine( action->getShortcutLabel() + ": " + + action->getName() + "_SCALAR ARG=" + allargs + + " " + action->convertInputLineToString() ); } else { - plumed_merror("there is no action registered that allows you to do " + action->getName() + " with scalars"); + plumed_merror("there is no action registered that allows you to do " + + action->getName() + " with scalars"); } - } else if( vals.size()==1 && actionRegister().check( action->getName() + "_ONEARG") ) { - action->readInputLine( action->getShortcutLabel() + ": " + action->getName() + "_ONEARG ARG=" + allargs + " " + action->convertInputLineToString() ); + } else if( vals.size()==1 && action->plumed.checkAction(action->getName() + "_ONEARG") ) { + action->readInputLine( action->getShortcutLabel() + ": " + + action->getName() + "_ONEARG ARG=" + allargs + + " " + action->convertInputLineToString() ); } else if( maxrank==1 ) { - if( actionRegister().check( action->getName() + "_VECTOR") ) { - action->readInputLine( action->getShortcutLabel() + ": " + action->getName() + "_VECTOR ARG=" + allargs + " " + action->convertInputLineToString() ); + if( action->plumed.checkAction( action->getName() + "_VECTOR"+doUSEGPU) ) { + action->readInputLine( action->getShortcutLabel() + ": " + + action->getName() + "_VECTOR"+doUSEGPU+" ARG=" + allargs + + " " + action->convertInputLineToString() ); } else { - plumed_merror("there is no action registered that allows you to do " + action->getName() + " with vectors"); + plumed_merror("there is no action registered that allows you to do " + + action->getName() + " with vectors"+ (useGPU?" (with USEGPU)":"")); } } else if( maxrank==2 ) { - if( actionRegister().check( action->getName() + "_MATRIX") ) { - action->readInputLine( action->getShortcutLabel() + ": " + action->getName() + "_MATRIX ARG=" + allargs + " " + action->convertInputLineToString() ); + if( action->plumed.checkAction( action->getName() + "_MATRIX"+doUSEGPU) ) { + action->readInputLine( action->getShortcutLabel() + ": " + + action->getName() + "_MATRIX"+doUSEGPU+" ARG=" + allargs + + " " + action->convertInputLineToString() ); } else { - plumed_merror("there is no action registered that allows you to do " + action->getName() + " with matrices"); + plumed_merror("there is no action registered that allows you to do " + + action->getName() + " with matrices" + (useGPU?" (with USEGPU)":"")); } } else { plumed_error(); diff --git a/src/function/LessThan.cpp b/src/function/LessThan.cpp index 20b686b4e6..f44705d6e7 100644 --- a/src/function/LessThan.cpp +++ b/src/function/LessThan.cpp @@ -19,10 +19,7 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC -#include "FunctionSetup.h" +#include "LessThan.h" #include "FunctionShortcut.h" #include "FunctionOfScalar.h" #include "FunctionOfVector.h" @@ -30,8 +27,6 @@ #include "core/ActionRegister.h" #include "tools/SwitchingFunction.h" -#include - namespace PLMD { namespace function { @@ -452,34 +447,6 @@ was described in the previous section is not performed. */ //+ENDPLUMEDOC -class LessThan { -public: - bool squared; -#ifdef __PLUMED_USE_OPENACC - SwitchingFunctionAccelerable switchingFunction; -#else - SwitchingFunction switchingFunction; -#endif //__PLUMED_USE_OPENACC - static void registerKeywords( Keywords& keys ); - static void read( LessThan& func, - ActionWithArguments* action, - FunctionOptions& options ); - static void calc( const LessThan& func, - bool noderiv, - const View& args, - FunctionOutput& funcout ); -#ifdef __PLUMED_USE_OPENACC - void toACCDevice() const { -#pragma acc enter data copyin(this[0:1],squared) - switchingFunction.toACCDevice(); - } - void removeFromACCDevice() const { - switchingFunction.removeFromACCDevice(); -#pragma acc exit data delete(squared,this[0:1]) - } -#endif //__PLUMED_USE_OPENACC -}; - typedef FunctionShortcut LessThanShortcut; PLUMED_REGISTER_ACTION(LessThanShortcut,"LESS_THAN") typedef FunctionOfScalar ScalarLessThan; @@ -489,76 +456,5 @@ PLUMED_REGISTER_ACTION(VectorLessThan,"LESS_THAN_VECTOR") typedef FunctionOfMatrix MatrixLessThan; PLUMED_REGISTER_ACTION(MatrixLessThan,"LESS_THAN_MATRIX") -void LessThan::registerKeywords(Keywords& keys) { - keys.add("compulsory","NN","6","The n parameter of the switching function "); - keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN"); - keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function"); - keys.add("compulsory","R_0","The r_0 parameter of the switching function"); - keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. " - "The following provides information on the \\ref switchingfunction that are available. " - "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords."); - keys.addFlag("SQUARED",false,"is the input quantity the square of the value that you would like to apply the switching function to"); - keys.setValueDescription("scalar/vector/matrix","a function that is one if the input is less than a threshold"); -} - -void LessThan::read( LessThan& func, ActionWithArguments* action, FunctionOptions& options ) { - options.derivativeZeroIfValueIsZero = true; - if( action->getNumberOfArguments()!=1 ) { - ActionWithVector* av = dynamic_cast( action ); - if( !av || (av && action->getNumberOfArguments()-av->getNumberOfMasks()!=1) ) { - action->error("should only be one argument to less_than actions"); - } - } - if( action->getPntrToArgument(0)->isPeriodic() ) { - action->error("cannot use this function on periodic functions"); - } - - - std::string errors; - std::string sfinput; - action->parse("SWITCH",sfinput); - if(sfinput.length()>0) { - func.switchingFunction.set(sfinput,errors); - if( errors.length()!=0 ) { - action->error("problem reading SWITCH keyword : " + errors ); - } - } else { - int nn=6; - int mm=0; - double d0=0.0; - double r0=0.0; - action->parse("R_0",r0); - if(r0<=0.0) { - action->error("R_0 should be explicitly specified and positive"); - } - action->parse("D_0",d0); - action->parse("NN",nn); - action->parse("MM",mm); - func.switchingFunction.set(nn,mm,r0,d0); - } - action->log<<" using switching function with cutoff "<parseFlag("SQUARED",func.squared); - if( func.squared ) { - action->log<<" input quantity is square of quantity that switching function acts upon\n"; - } -} - -void LessThan::calc( const LessThan& func, - bool noderiv, - const View& args, - FunctionOutput& funcout ) { - double d; - if( func.squared ) { - funcout.values[0] = func.switchingFunction.calculateSqr( args[0], d ); - } else { - funcout.values[0] = func.switchingFunction.calculate( args[0], d ); - } - if( !noderiv ) { - funcout.derivs[0][0] = args[0]*d; - } -} - } } - - diff --git a/src/function/LessThan.h b/src/function/LessThan.h new file mode 100644 index 0000000000..505b951106 --- /dev/null +++ b/src/function/LessThan.h @@ -0,0 +1,133 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2017 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_function_LessThan_h +#define __PLUMED_function_LessThan_h +#include "FunctionSetup.h" +#include "tools/SwitchingFunction.h" + +#include + +namespace PLMD { +namespace function { + +class LessThan { +public: + bool squared; +#ifdef __PLUMED_HAS_OPENACC + SwitchingFunctionAccelerable switchingFunction; +#else + SwitchingFunction switchingFunction; +#endif //__PLUMED_HAS_OPENACC + static void registerKeywords( Keywords& keys ); + static void read( LessThan& func, + ActionWithArguments* action, + FunctionOptions& options ); + static void calc( const LessThan& func, + bool noderiv, + const View& args, + FunctionOutput& funcout ); +#ifdef __PLUMED_HAS_OPENACC + void toACCDevice() const { +#pragma acc enter data copyin(this[0:1],squared) + switchingFunction.toACCDevice(); + } + void removeFromACCDevice() const { + switchingFunction.removeFromACCDevice(); +#pragma acc exit data delete(squared,this[0:1]) + } +#endif //__PLUMED_HAS_OPENACC +}; + +void LessThan::registerKeywords(Keywords& keys) { + keys.add("compulsory","NN","6","The n parameter of the switching function "); + keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN"); + keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function"); + keys.add("compulsory","R_0","The r_0 parameter of the switching function"); + keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. " + "The following provides information on the \\ref switchingfunction that are available. " + "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords."); + keys.addFlag("SQUARED",false,"is the input quantity the square of the value that you would like to apply the switching function to"); + keys.setValueDescription("scalar/vector/matrix","a function that is one if the input is less than a threshold"); +} + +void LessThan::read( LessThan& func, ActionWithArguments* action, FunctionOptions& options ) { + options.derivativeZeroIfValueIsZero = true; + if( action->getNumberOfArguments()!=1 ) { + ActionWithVector* av = dynamic_cast( action ); + if( !av || (av && action->getNumberOfArguments()-av->getNumberOfMasks()!=1) ) { + action->error("should only be one argument to less_than actions"); + } + } + if( action->getPntrToArgument(0)->isPeriodic() ) { + action->error("cannot use this function on periodic functions"); + } + + + std::string errors; + std::string sfinput; + action->parse("SWITCH",sfinput); + if(sfinput.length()>0) { + func.switchingFunction.set(sfinput,errors); + if( errors.length()!=0 ) { + action->error("problem reading SWITCH keyword : " + errors ); + } + } else { + int nn=6; + int mm=0; + double d0=0.0; + double r0=0.0; + action->parse("R_0",r0); + if(r0<=0.0) { + action->error("R_0 should be explicitly specified and positive"); + } + action->parse("D_0",d0); + action->parse("NN",nn); + action->parse("MM",mm); + func.switchingFunction.set(nn,mm,r0,d0); + } + action->log<<" using switching function with cutoff "<parseFlag("SQUARED",func.squared); + if( func.squared ) { + action->log<<" input quantity is square of quantity that switching function acts upon\n"; + } +} + +void LessThan::calc( const LessThan& func, + bool noderiv, + const View& args, + FunctionOutput& funcout ) { + double d; + if( func.squared ) { + funcout.values[0] = func.switchingFunction.calculateSqr( args[0], d ); + } else { + funcout.values[0] = func.switchingFunction.calculate( args[0], d ); + } + if( !noderiv ) { + funcout.derivs[0][0] = args[0]*d; + } +} + +} +} + + +#endif //__PLUMED_function_LessThan_h diff --git a/src/function/MoreThan.cpp b/src/function/MoreThan.cpp index 4b4710f4c9..02b6754093 100644 --- a/src/function/MoreThan.cpp +++ b/src/function/MoreThan.cpp @@ -19,18 +19,13 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC -#include "FunctionSetup.h" +#include "MoreThan.h" #include "FunctionShortcut.h" #include "FunctionOfScalar.h" #include "FunctionOfVector.h" #include "FunctionOfMatrix.h" #include "core/ActionRegister.h" -#include "tools/SwitchingFunction.h" -#include namespace PLMD { namespace function { @@ -158,34 +153,6 @@ MASK keyword. PLUMED will use the sparsity pattern for the input matrix to reduc */ //+ENDPLUMEDOC -class MoreThan { -public: - bool squared; -#ifdef __PLUMED_USE_OPENACC - SwitchingFunctionAccelerable switchingFunction; -#else - SwitchingFunction switchingFunction; -#endif //__PLUMED_USE_OPENACC - static void registerKeywords( Keywords& keys ); - static void read( MoreThan& func, - ActionWithArguments* action, - FunctionOptions& options ); - static void calc( const MoreThan& func, - bool noderiv, - const View& args, - FunctionOutput& funcout ); -#ifdef __PLUMED_USE_OPENACC - void toACCDevice() const { -#pragma acc enter data copyin(this[0:1],squared) - switchingFunction.toACCDevice(); - } - void removeFromACCDevice() const { - switchingFunction.removeFromACCDevice(); -#pragma acc exit data delete(squared,this[0:1]) - } -#endif //__PLUMED_USE_OPENACC -}; - typedef FunctionShortcut MoreThanShortcut; PLUMED_REGISTER_ACTION(MoreThanShortcut,"MORE_THAN") typedef FunctionOfScalar ScalarMoreThan; @@ -195,75 +162,5 @@ PLUMED_REGISTER_ACTION(VectorMoreThan,"MORE_THAN_VECTOR") typedef FunctionOfMatrix MatrixMoreThan; PLUMED_REGISTER_ACTION(MatrixMoreThan,"MORE_THAN_MATRIX") -void MoreThan::registerKeywords(Keywords& keys) { - keys.add("compulsory","NN","6","The n parameter of the switching function "); - keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN"); - keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function"); - keys.add("compulsory","R_0","The r_0 parameter of the switching function"); - keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. " - "The following provides information on the \\ref switchingfunction that are available. " - "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords."); - keys.addFlag("SQUARED",false,"is the input quantity the square of the value that you would like to apply the switching function to"); - keys.setValueDescription("scalar/vector/matrix","a function that is one if the if the input is more than a threshold"); } - -void MoreThan::read( MoreThan& func, ActionWithArguments* action, FunctionOptions& options ) { - options.derivativeZeroIfValueIsZero = true; - if( action->getNumberOfArguments()!=1 ) { - ActionWithVector* av = dynamic_cast( action ); - if( !av || (av && action->getNumberOfArguments()-av->getNumberOfMasks()!=1) ) { - action->error("should only be one argument to less_than actions"); - } - } - if( action->getPntrToArgument(0)->isPeriodic() ) { - action->error("cannot use this function on periodic functions"); - } - - - std::string errors; - std::string sfinput; - action->parse("SWITCH", sfinput); - if(sfinput.length()>0) { - func.switchingFunction.set(sfinput, errors); - if( errors.length()!=0 ) { - action->error("problem reading SWITCH keyword : " + errors ); - } - } else { - int nn=6; - int mm=0; - double d0=0.0; - double r0=0.0; - action->parse("R_0",r0); - if(r0<=0.0) { - action->error("R_0 should be explicitly specified and positive"); - } - action->parse("D_0",d0); - action->parse("NN",nn); - action->parse("MM",mm); - func.switchingFunction.set(nn,mm,r0,d0); - } - action->log<<" using switching function with cutoff "<parseFlag("SQUARED",func.squared); - if( func.squared ) { - action->log<<" input quantity is square of quantity that switching function acts upon\n"; - } } - -void MoreThan::calc( const MoreThan& func, bool noderiv, const View& args, FunctionOutput& funcout ) { - // the presence of NDEBUG seems to be ignored by nvcc... - // plumed_dbg_assert( args.size()==1 ); - double d; - if( func.squared ) { - funcout.values[0] = 1.0 - func.switchingFunction.calculateSqr( args[0], d ); - } else { - funcout.values[0] = 1.0 - func.switchingFunction.calculate( args[0], d ); - } - if( !noderiv ) { - funcout.derivs[0][0] = -args[0]*d; - } -} - -} -} - - diff --git a/src/function/MoreThan.h b/src/function/MoreThan.h new file mode 100644 index 0000000000..1ff0d19664 --- /dev/null +++ b/src/function/MoreThan.h @@ -0,0 +1,135 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2017 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_function_MoreThan_h +#define __PLUMED_function_MoreThan_h +#include "FunctionSetup.h" +#include "FunctionShortcut.h" +#include "FunctionOfScalar.h" +#include "FunctionOfVector.h" +#include "FunctionOfMatrix.h" +#include "core/ActionRegister.h" +#include "tools/SwitchingFunction.h" + +#include + +namespace PLMD { +namespace function { + +class MoreThan { +public: + bool squared; +#ifdef __PLUMED_HAS_OPENACC + SwitchingFunctionAccelerable switchingFunction; +#else + SwitchingFunction switchingFunction; +#endif //__PLUMED_HAS_OPENACC + static void registerKeywords( Keywords& keys ); + static void read( MoreThan& func, + ActionWithArguments* action, + FunctionOptions& options ); + static void calc( const MoreThan& func, + bool noderiv, + const View& args, + FunctionOutput& funcout ); +#ifdef __PLUMED_HAS_OPENACC + void toACCDevice() const { +#pragma acc enter data copyin(this[0:1],squared) + switchingFunction.toACCDevice(); + } + void removeFromACCDevice() const { + switchingFunction.removeFromACCDevice(); +#pragma acc exit data delete(squared,this[0:1]) + } +#endif //__PLUMED_HAS_OPENACC +}; + +void MoreThan::registerKeywords(Keywords& keys) { + keys.add("compulsory","NN","6","The n parameter of the switching function "); + keys.add("compulsory","MM","0","The m parameter of the switching function; 0 implies 2*NN"); + keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function"); + keys.add("compulsory","R_0","The r_0 parameter of the switching function"); + keys.add("optional","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. " + "The following provides information on the \\ref switchingfunction that are available. " + "When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords."); + keys.addFlag("SQUARED",false,"is the input quantity the square of the value that you would like to apply the switching function to"); + keys.setValueDescription("scalar/vector/matrix","a function that is one if the if the input is more than a threshold"); +} + +void MoreThan::read( MoreThan& func, ActionWithArguments* action, FunctionOptions& options ) { + options.derivativeZeroIfValueIsZero = true; + if( action->getNumberOfArguments()!=1 ) { + ActionWithVector* av = dynamic_cast( action ); + if( !av || (av && action->getNumberOfArguments()-av->getNumberOfMasks()!=1) ) { + action->error("should only be one argument to less_than actions"); + } + } + if( action->getPntrToArgument(0)->isPeriodic() ) { + action->error("cannot use this function on periodic functions"); + } + + + std::string errors; + std::string sfinput; + action->parse("SWITCH", sfinput); + if(sfinput.length()>0) { + func.switchingFunction.set(sfinput, errors); + if( errors.length()!=0 ) { + action->error("problem reading SWITCH keyword : " + errors ); + } + } else { + int nn=6; + int mm=0; + double d0=0.0; + double r0=0.0; + action->parse("R_0",r0); + if(r0<=0.0) { + action->error("R_0 should be explicitly specified and positive"); + } + action->parse("D_0",d0); + action->parse("NN",nn); + action->parse("MM",mm); + func.switchingFunction.set(nn,mm,r0,d0); + } + action->log<<" using switching function with cutoff "<parseFlag("SQUARED",func.squared); + if( func.squared ) { + action->log<<" input quantity is square of quantity that switching function acts upon\n"; + } +} + +void MoreThan::calc( const MoreThan& func, bool noderiv, const View& args, FunctionOutput& funcout ) { + // the presence of NDEBUG seems to be ignored by nvcc... + // plumed_dbg_assert( args.size()==1 ); + double d; + if( func.squared ) { + funcout.values[0] = 1.0 - func.switchingFunction.calculateSqr( args[0], d ); + } else { + funcout.values[0] = 1.0 - func.switchingFunction.calculate( args[0], d ); + } + if( !noderiv ) { + funcout.derivs[0][0] = -args[0]*d; + } +} + +} +} +#endif //__PLUMED_function_MoreThan_h diff --git a/src/gridtools/FunctionOfGrid.h b/src/gridtools/FunctionOfGrid.h index 43646fae43..8cbf9b0841 100644 --- a/src/gridtools/FunctionOfGrid.h +++ b/src/gridtools/FunctionOfGrid.h @@ -37,6 +37,8 @@ class FunctionOfGrid : public ActionWithGrid { public: using input_type = function::FunctionData; using PTM = ParallelTaskManager>; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: /// The parallel task manager PTM taskmanager; diff --git a/src/gridtools/InterpolateGrid.cpp b/src/gridtools/InterpolateGrid.cpp index 7e5efee161..a872dacba0 100644 --- a/src/gridtools/InterpolateGrid.cpp +++ b/src/gridtools/InterpolateGrid.cpp @@ -81,6 +81,8 @@ class InterpolateGrid : public ActionWithGrid { public: using input_type = EvaluateGridFunction; using PTM = ParallelTaskManager; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: bool firststep; /// The parallel task manager diff --git a/src/gridtools/KDE.h b/src/gridtools/KDE.h index d28bcaeb63..196d6eb2cc 100644 --- a/src/gridtools/KDE.h +++ b/src/gridtools/KDE.h @@ -268,6 +268,8 @@ class KDE : public ActionWithGrid { public: using input_type = KDEHelper; using PTM = ParallelTaskManager>; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: bool firststep; /// The parallel task manager diff --git a/src/gridtools/Marginal.cpp b/src/gridtools/Marginal.cpp index 8b026895a3..908bf7bab5 100644 --- a/src/gridtools/Marginal.cpp +++ b/src/gridtools/Marginal.cpp @@ -142,6 +142,8 @@ class Marginal : public ActionWithGrid { public: using input_type = MarginalInput; using PTM = ParallelTaskManager; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: bool firststep; /// The parallel task manager diff --git a/src/maketools/makeModuleMap b/src/maketools/makeModuleMap index f5a509e1db..572fc879c8 100755 --- a/src/maketools/makeModuleMap +++ b/src/maketools/makeModuleMap @@ -2,7 +2,7 @@ # shellcheck disable=SC2059 outputfile=$1 -rm -f $outputfile~ +rm -f "$outputfile~" problems="" toPrint=' {"%s", "%s"}' @@ -11,7 +11,7 @@ toPrint=' {"%s", "%s"}' regex='PLUMED_REGISTER_ACTION *\( *[0-9a-zA-Z_]+ *, *"([0-9a-zA-Z_]+)" *\)' regex_cl='PLUMED_REGISTER_CLTOOL *\( *[0-9a-zA-Z_]+ *, *"([0-9a-zA-Z_-]+)" *\)' -for module in ../*/module.type; do +for module in ../*/module.type ../../plugins/*/module.type; do moduledir=${module%%/module.type} modulename=${moduledir##*/} { @@ -41,8 +41,8 @@ for module in ../*/module.type; do # echo $action if [[ $action =~ $regex ]]; then actionName=${BASH_REMATCH[1]} - printf "$toPrint" "$actionName" "$modulename" >> $outputfile~ - + printf "$toPrint" "$actionName" "$modulename" >>"$outputfile~" + toPrint=',\n {"%s", "%s"}' fi done @@ -54,8 +54,8 @@ for module in ../*/module.type; do # echo $action if [[ $cltool =~ $regex_cl ]]; then clName=${BASH_REMATCH[1]} - printf "$toPrint" "$clName" "$modulename" >> $outputfile~ - + printf "$toPrint" "$clName" "$modulename" >>"$outputfile~" + toPrint=',\n {"%s", "%s"}' fi done @@ -67,15 +67,14 @@ for module in ../*/module.type; do done -cmp -s $outputfile~ $outputfile || cp $outputfile~ $outputfile -rm $outputfile~ +cmp -s "$outputfile~" "$outputfile" || cp "$outputfile~" "$outputfile" +rm "$outputfile~" echo -e '\n' if [[ -n $problems ]]; then echo >&2 some problems in the following: for p in $problems; do - echo >&2 $p + echo >&2 "$p" done exit 1 fi - diff --git a/src/matrixtools/MatrixDissimilarities.cpp b/src/matrixtools/MatrixDissimilarities.cpp new file mode 100644 index 0000000000..fbd3a007c0 --- /dev/null +++ b/src/matrixtools/MatrixDissimilarities.cpp @@ -0,0 +1,111 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "MatrixDissimilarities.h" +#include "core/ActionRegister.h" +#include "core/AccelerableShortcut.h" + +//+PLUMEDOC ANALYSIS DISSIMILARITIES +/* +Calculate the matrix of dissimilarities between a trajectory of atomic configurations. + +This action allows you to calculate a dissimilarity matrix, which is a square matrix tht describes the +pairwise distinction between a set of objects. This action is routinely used in dimensionality reduction +calculations. The example shown below shows how we might get a matrix of dissimilarities upon which we can run a +dimensionality reduction calculation. + +```plumed +d1: DISTANCE ATOMS=1,2 +d2: DISTANCE ATOMS=3,4 +# Collect the values of the two distances and store them for later analysis +ff: COLLECT_FRAMES ARG=d1,d2 STRIDE=1 +# Transpose the matrix that is collected above +ff_dataT: TRANSPOSE ARG=ff_data +# Now compute all the dissimilarities between the collected frames +ss1: DISSIMILARITIES ARG=ff_data,ff_dataT +DUMPVECTOR ARG=ss1 FILE=mymatrix.dat +``` + +Some dimensionality reduction algorithms take the squares of the dissimilarities rather than the dissimilarities. +To calculate these quantities using PLUMED you use the SQUARED keyword as shown below: + +```plumed +d1: DISTANCE ATOMS=1,2 +d2: DISTANCE ATOMS=3,4 +# Collect the values of the two distances and store them for later analysis +ff: COLLECT_FRAMES ARG=d1,d2 STRIDE=1 +# Transpose the matrix that is collected above +ff_dataT: TRANSPOSE ARG=ff_data +# Now compute all the dissimilarities between the collected frames +ss1: DISSIMILARITIES ARG=ff_data,ff_dataT SQUARED +DUMPVECTOR ARG=ss1 FILE=mymatrix.dat +``` + +## The MASK keyword + +The MASK keyword for DISSIMILARITIES works in the same way that it does for [MATRIX_PRODUCT](MATRIX_PRODUCT.md). This keyword thus +expects a matrix in input and will only evaluate elements the elements of the dissimilarity matrix whose corresponding elements in +the matrix that was input to MASK are non-zero. The following input shows an example of how this might be used in an example input +that has not been used in any production calculation. + +```plumed +# Calculate and store three vectors connecting three pairs of atoms +d1: DISTANCE COMPONENTS ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 +ff1: VSTACK ARG=d1.x,d1.y,d1.z +# Calculate the magnitude of the vector and transform this magnitude using a +# switching function +d1m: CUSTOM ARG=d1.x,d1.y,d1.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO +sw1: LESS_THAN ARG=d1m SWITCH={RATIONAL R_0=0.2 D_MAX=0.5} +# Now perform the same operations for a different set of three atoms +d2: DISTANCE COMPONENTS ATOMS1=7,8 ATOMS2=9,10 ATOMS3=11,12 +ff2: VSTACK ARG=d2.x,d2.y,d2.z +ff2T: TRANSPOSE ARG=ff2 +d2m: CUSTOM ARG=d2.x,d2.y,d2.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO +sw2: LESS_THAN ARG=d2m SWITCH={RATIONAL R_0=0.2 D_MAX=0.5} +# Use OUTER_PRODUCT to work out which pairs of atoms are less than a certain cutoff +swmat: OUTER_PRODUCT ARG=sw1,sw2 +# Now calculate the dissimilarities between the two sets of vectors for those pairs of atoms that are within a certain cutoff +d: DISSIMILARITIES ARG=ff1,ff2T MASK=swmat +mat: CUSTOM ARG=swmat,d FUNC=x*y PERIODIC=NO +# And compute the average dissimilarity +numer: SUM ARG=mat PERIODIC=NO +denom: SUM ARG=swmat PERIODIC=NO +v: CUSTOM ARG=numer,denom FUNC=x/y PERIODIC=NO +PRINT ARG=v FILE=colvar +``` + +We have not provided a more relevant example because we haven't really used this functionality for anything. If you have a better example +for a way of using this functionality please get in touch so we can update this part of the manual with your example. + +*/ +//+ENDPLUMEDOC + +namespace PLMD { +namespace matrixtools { + +typedef MatrixTimesMatrix dissims; +PLUMED_REGISTER_ACTION(dissims,"DISSIMILARITIES_CPU") +typedef AccelerableShortcut shortcut; +PLUMED_REGISTER_ACTION(shortcut,"DISSIMILARITIES") + + +} +} diff --git a/src/matrixtools/MatrixDissimilarities.h b/src/matrixtools/MatrixDissimilarities.h new file mode 100644 index 0000000000..6f7e2a6b2a --- /dev/null +++ b/src/matrixtools/MatrixDissimilarities.h @@ -0,0 +1,111 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_matrixtools_MatrixDissimilarities_h +#define __PLUMED_matrixtools_MatrixDissimilarities_h +#include "MatrixTimesMatrix.h" + +namespace PLMD { +namespace matrixtools { +struct Dissimilarities { + typedef void isDissimilarities; + bool squared{false}; + bool periodic{false}; + double min{0}; + double max{0}; + double max_minus_min{0}; + double inv_max_minus_min{0}; + static void registerKeywords( Keywords& keys ); + template + void setup( MatrixTimesMatrix* action, + const Value* myval ); + static void calculate( bool noderiv, + const Dissimilarities& actdata, + const InputVectors& vectors, + MatrixElementOutput& output ); +#ifdef __PLUMED_HAS_OPENACC + void toACCDevice() const { +#pragma acc enter data copyin(this[0:1], squared, periodic, min, max, \ + max_minus_min, inv_max_minus_min) + + } + void removeFromACCDevice() const { +#pragma acc exit data delete(inv_max_minus_min, max_minus_min, max, \ + min, periodic, squared, this[0:1]) + } +#endif //__PLUMED_HAS_OPENACC +}; + + +void Dissimilarities::registerKeywords( Keywords& keys ) { + keys.setDisplayName("DISSIMILARITY"); + keys.addFlag("SQUARED",false,"calculate the squares of the dissimilarities (this option cannot be used with MATRIX_PRODUCT)"); + keys.setValueDescription("matrix","the dissimilarity matrix"); +} + +template +void Dissimilarities::setup( MatrixTimesMatrix* action, + const Value* myval ) { + action->parseFlag("SQUARED",squared); + if( squared ) { + action->log.printf(" calculating the squares of the dissimilarities \n"); + } + periodic = myval->isPeriodic(); + if( periodic ) { + std::string strmin, strmax; + myval->getDomain( strmin, strmax ); + Tools::convert( strmin, min ); + Tools::convert( strmax, max ); + max_minus_min = max - min; + plumed_assert( max_minus_min>0 ); + inv_max_minus_min=1.0/max_minus_min; + } +} + +void Dissimilarities::calculate( const bool noderiv, + const Dissimilarities& actdata, + const InputVectors& vectors, + MatrixElementOutput& output ) { + std::size_t pp = vectors.arg1.size(); + for(unsigned i=0; i. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "MatrixProduct.h" +#include "core/ActionRegister.h" +#include "core/AccelerableShortcut.h" + +//+PLUMEDOC MCOLVAR MATRIX_PRODUCT +/* +Calculate the product of two matrices + +This action allows you to [multiply](https://en.wikipedia.org/wiki/Matrix_multiplication) two matrices. The following input shows an +example where two contact matrices are multiplied together. + +```plumed +c1: CONTACT_MATRIX GROUP=1-100 SWITCH={RATIONAL R_0=0.1} +c2: CONTACT_MATRIX GROUP=1-100 SWITCH={RATIONAL R_0=0.2} +m: MATRIX_PRODUCT ARG=c1,c2 +PRINT ARG=m FILE=colvar +``` + +The functionality in this action is useful for claculating the relative orientations of large numbers of molecules. For example in +his input the [DISTANCE](DISTANCE.md) command is used to calculate the orientation of a collection of molecules. We then can then use the [VSTACK](VSTACK.md), [TRANSPOSE](TRANSPOSE.md) and the +MATRIX_PRODUCT commands to calculate the dot products between all these vectors + +```plumed +# Calculate the vectors connecting these three pairs of atoms +d: DISTANCE COMPONENTS ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 +# Construct a matrix that contains all the components of the vectors calculated +v: VSTACK ARG=d.x,d.y,d.z +# Transpose v +vT: TRANSPOSE ARG=v +# And now calculate the 3x3 matrix of dot products +m: MATRIX_PRODUCT ARG=v,vT +# And output the matrix product to a file +PRINT ARG=m FILE=colvar +``` + +## The MASK keyword + +We can use MATRIX_PRODUCT to calculate a measure of local order as shown below: + +```plumed +# Calculate the vectors connecting these three pairs of atoms +d: DISTANCE COMPONENTS ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 +# Normalize the distance vectors +dm: DISTANCE ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 +dx: CUSTOM ARG=d.x,dm FUNC=x/y PERIODIC=NO +dy: CUSTOM ARG=d.y,dm FUNC=x/y PERIODIC=NO +dz: CUSTOM ARG=d.z,dm FUNC=x/y PERIODIC=NO +# Construct a matrix that contains all the directors of the vectors calculated +v: VSTACK ARG=dx,dy,dz +# Transpose v +vT: TRANSPOSE ARG=v +# Calculate a contact matrix between pairs of atoms +cmap: CONTACT_MATRIX GROUP=1,3,5 SWITCH={RATIONAL R_0=0.2 D_MAX=0.5} +# Calculate the matrix of dot products +prod: MATRIX_PRODUCT ARG=v,vT MASK=cmap +# Take the product of the two matrices we computed above +p: CUSTOM ARG=cmap,prod FUNC=x*y PERIODIC=NO +# And compute the average of the dot product for the molecules in the +# first coordination sphere around each of the atoms +ones: ONES SIZE=3 +numer: MATRIX_VECTOR_PRODUCT ARG=p,ones +denom: MATRIX_VECTOR_PRODUCT ARG=cmap,ones +order: CUSTOM ARG=numer,denom FUNC=x/y PERIODIC=NO +# Print the order parameter values +PRINT ARG=order FILE=colvar +``` + +In the above input the [DISTANCE](DISTANCE.md) action is used to calculate the orientations of some molecules (you would normally use more distances than the three +that are used in this input when doing this sort of calculation). We then construct a matrix called `v` that contains the directors of the vectors that define the +orientation of these molecules. The final vector of values `order` that is output here measures the average for the dot product between the orientations of the molecules +and the molecules in their first coordination sphere. + +Ideass similar to this are used in the calculation of [LOCAL_Q3](LOCAL_Q3.md), [LOCAL_Q4](LOCAL_Q4.md) and [LOCAL_Q6](LOCAL_Q6.md). Notice, that it is very important to +use `MASK` keyword in the MATRIX_PRODUCT action when you are doing this type calculation. Using this keyword ensures that PLUMED does not calculate the $(i,j)$ matrix of +the matrix `prod` if the corresponding element in `cmap` is zero. Using this keyword thus ensures that we can avoid a large number of unecessary calculations and improves +the performance of the calculation considerably. + +## Calculating angles + +MATRIX_PRODUCT can also be used to calculate a matrix of angles between bonds as shown below: + +```plumed +# Calculate the directors for a set of vectors +d: DISTANCE COMPONENTS ATOMS1=1,2 ATOMS2=1,3 ATOMS3=1,4 ATOMS4=1,5 ATOMS5=1,6 +dm: DISTANCE ATOMS1=1,2 ATOMS2=1,3 ATOMS3=1,4 ATOMS4=1,5 ATOMS5=1,6 +dx: CUSTOM ARG=d.x,dm FUNC=x/y PERIODIC=NO +dy: CUSTOM ARG=d.y,dm FUNC=x/y PERIODIC=NO +dz: CUSTOM ARG=d.z,dm FUNC=x/y PERIODIC=NO +# Construct a matrix that contains all the directors of the vectors calculated +v: VSTACK ARG=dx,dy,dz +# Transpose v +vT: TRANSPOSE ARG=v +# Calculate the matrix of dot products between the input directors +dpmat: MATRIX_PRODUCT ELEMENTS_ON_DIAGONAL_ARE_ZERO ARG=v,vT +# And calculate the angles +angles: CUSTOM ARG=dpmat FUNC=acos(x) PERIODIC=NO +# Print the matrix of angles +PRINT ARG=angles FILE=colvar +``` + +Notice that we have to use the `ELEMENTS_ON_DIAGONAL_ARE_ZERO` flag here to avoid numerical issues in the calculation. + +*/ +//+ENDPLUMEDOC + +namespace PLMD { +namespace matrixtools { + +typedef MatrixTimesMatrix mtimes; +PLUMED_REGISTER_ACTION(mtimes,"MATRIX_PRODUCT_CPU") +typedef AccelerableShortcut shortcut; +PLUMED_REGISTER_ACTION(shortcut,"MATRIX_PRODUCT") + + +} +} diff --git a/src/matrixtools/MatrixProduct.h b/src/matrixtools/MatrixProduct.h new file mode 100644 index 0000000000..ff605dd1a7 --- /dev/null +++ b/src/matrixtools/MatrixProduct.h @@ -0,0 +1,69 @@ + +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2011-2023 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_matrixtools_MatrixProduct_h +#define __PLUMED_matrixtools_MatrixProduct_h +#include "MatrixTimesMatrix.h" + +namespace PLMD { +namespace matrixtools { + +struct MatrixProduct { + static void registerKeywords( Keywords& keys ); + template + void setup( MatrixTimesMatrix* action, + const Value* myval ) {} + static void calculate( bool noderiv, + const MatrixProduct& actdata, + const InputVectors& vectors, + MatrixElementOutput& output ); +#ifdef __PLUMED_HAS_OPENACC + void toACCDevice() const { +#pragma acc enter data copyin(this[0:1]) + } + void removeFromACCDevice() const { +#pragma acc exit data delete(this[0:1]) + } +#endif //__PLUMED_HAS_OPENACC +}; + + +void MatrixProduct::registerKeywords( Keywords& keys ) { + keys.setDisplayName("MATRIX_PRODUCT"); + keys.setValueDescription("matrix","the product of the two input matrices"); + keys.addFlag("ELEMENTS_ON_DIAGONAL_ARE_ZERO",false,"set all diagonal elements to zero"); +} + +void MatrixProduct::calculate( const bool noderiv, + const MatrixProduct& actdata, + const InputVectors& vectors, + MatrixElementOutput& output ) { + std::size_t pp = vectors.arg1.size(); + for(unsigned i=0; i. +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC #include "MatrixTimesMatrix.h" -#include "core/ActionRegister.h" -//+PLUMEDOC MCOLVAR MATRIX_PRODUCT -/* -Calculate the product of two matrices - -This action allows you to [multiply](https://en.wikipedia.org/wiki/Matrix_multiplication) two matrices. The following input shows an -example where two contact matrices are multiplied together. - -```plumed -c1: CONTACT_MATRIX GROUP=1-100 SWITCH={RATIONAL R_0=0.1} -c2: CONTACT_MATRIX GROUP=1-100 SWITCH={RATIONAL R_0=0.2} -m: MATRIX_PRODUCT ARG=c1,c2 -PRINT ARG=m FILE=colvar -``` - -The functionality in this action is useful for claculating the relative orientations of large numbers of molecules. For example in -his input the [DISTANCE](DISTANCE.md) command is used to calculate the orientation of a collection of molecules. We then can then use the [VSTACK](VSTACK.md), [TRANSPOSE](TRANSPOSE.md) and the -MATRIX_PRODUCT commands to calculate the dot products between all these vectors - -```plumed -# Calculate the vectors connecting these three pairs of atoms -d: DISTANCE COMPONENTS ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 -# Construct a matrix that contains all the components of the vectors calculated -v: VSTACK ARG=d.x,d.y,d.z -# Transpose v -vT: TRANSPOSE ARG=v -# And now calculate the 3x3 matrix of dot products -m: MATRIX_PRODUCT ARG=v,vT -# And output the matrix product to a file -PRINT ARG=m FILE=colvar -``` - -## The MASK keyword - -We can use MATRIX_PRODUCT to calculate a measure of local order as shown below: - -```plumed -# Calculate the vectors connecting these three pairs of atoms -d: DISTANCE COMPONENTS ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 -# Normalize the distance vectors -dm: DISTANCE ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 -dx: CUSTOM ARG=d.x,dm FUNC=x/y PERIODIC=NO -dy: CUSTOM ARG=d.y,dm FUNC=x/y PERIODIC=NO -dz: CUSTOM ARG=d.z,dm FUNC=x/y PERIODIC=NO -# Construct a matrix that contains all the directors of the vectors calculated -v: VSTACK ARG=dx,dy,dz -# Transpose v -vT: TRANSPOSE ARG=v -# Calculate a contact matrix between pairs of atoms -cmap: CONTACT_MATRIX GROUP=1,3,5 SWITCH={RATIONAL R_0=0.2 D_MAX=0.5} -# Calculate the matrix of dot products -prod: MATRIX_PRODUCT ARG=v,vT MASK=cmap -# Take the product of the two matrices we computed above -p: CUSTOM ARG=cmap,prod FUNC=x*y PERIODIC=NO -# And compute the average of the dot product for the molecules in the -# first coordination sphere around each of the atoms -ones: ONES SIZE=3 -numer: MATRIX_VECTOR_PRODUCT ARG=p,ones -denom: MATRIX_VECTOR_PRODUCT ARG=cmap,ones -order: CUSTOM ARG=numer,denom FUNC=x/y PERIODIC=NO -# Print the order parameter values -PRINT ARG=order FILE=colvar -``` - -In the above input the [DISTANCE](DISTANCE.md) action is used to calculate the orientations of some molecules (you would normally use more distances than the three -that are used in this input when doing this sort of calculation). We then construct a matrix called `v` that contains the directors of the vectors that define the -orientation of these molecules. The final vector of values `order` that is output here measures the average for the dot product between the orientations of the molecules -and the molecules in their first coordination sphere. - -Ideass similar to this are used in the calculation of [LOCAL_Q3](LOCAL_Q3.md), [LOCAL_Q4](LOCAL_Q4.md) and [LOCAL_Q6](LOCAL_Q6.md). Notice, that it is very important to -use `MASK` keyword in the MATRIX_PRODUCT action when you are doing this type calculation. Using this keyword ensures that PLUMED does not calculate the $(i,j)$ matrix of -the matrix `prod` if the corresponding element in `cmap` is zero. Using this keyword thus ensures that we can avoid a large number of unecessary calculations and improves -the performance of the calculation considerably. - -## Calculating angles - -MATRIX_PRODUCT can also be used to calculate a matrix of angles between bonds as shown below: - -```plumed -# Calculate the directors for a set of vectors -d: DISTANCE COMPONENTS ATOMS1=1,2 ATOMS2=1,3 ATOMS3=1,4 ATOMS4=1,5 ATOMS5=1,6 -dm: DISTANCE ATOMS1=1,2 ATOMS2=1,3 ATOMS3=1,4 ATOMS4=1,5 ATOMS5=1,6 -dx: CUSTOM ARG=d.x,dm FUNC=x/y PERIODIC=NO -dy: CUSTOM ARG=d.y,dm FUNC=x/y PERIODIC=NO -dz: CUSTOM ARG=d.z,dm FUNC=x/y PERIODIC=NO -# Construct a matrix that contains all the directors of the vectors calculated -v: VSTACK ARG=dx,dy,dz -# Transpose v -vT: TRANSPOSE ARG=v -# Calculate the matrix of dot products between the input directors -dpmat: MATRIX_PRODUCT ELEMENTS_ON_DIAGONAL_ARE_ZERO ARG=v,vT -# And calculate the angles -angles: CUSTOM ARG=dpmat FUNC=acos(x) PERIODIC=NO -# Print the matrix of angles -PRINT ARG=angles FILE=colvar -``` - -Notice that we have to use the `ELEMENTS_ON_DIAGONAL_ARE_ZERO` flag here to avoid numerical issues in the calculation. - -*/ -//+ENDPLUMEDOC - -//+PLUMEDOC ANALYSIS DISSIMILARITIES -/* -Calculate the matrix of dissimilarities between a trajectory of atomic configurations. - -This action allows you to calculate a dissimilarity matrix, which is a square matrix tht describes the -pairwise distinction between a set of objects. This action is routinely used in dimensionality reduction -calculations. The example shown below shows how we might get a matrix of dissimilarities upon which we can run a -dimensionality reduction calculation. - -```plumed -d1: DISTANCE ATOMS=1,2 -d2: DISTANCE ATOMS=3,4 -# Collect the values of the two distances and store them for later analysis -ff: COLLECT_FRAMES ARG=d1,d2 STRIDE=1 -# Transpose the matrix that is collected above -ff_dataT: TRANSPOSE ARG=ff_data -# Now compute all the dissimilarities between the collected frames -ss1: DISSIMILARITIES ARG=ff_data,ff_dataT -DUMPVECTOR ARG=ss1 FILE=mymatrix.dat -``` - -Some dimensionality reduction algorithms take the squares of the dissimilarities rather than the dissimilarities. -To calculate these quantities using PLUMED you use the SQUARED keyword as shown below: - -```plumed -d1: DISTANCE ATOMS=1,2 -d2: DISTANCE ATOMS=3,4 -# Collect the values of the two distances and store them for later analysis -ff: COLLECT_FRAMES ARG=d1,d2 STRIDE=1 -# Transpose the matrix that is collected above -ff_dataT: TRANSPOSE ARG=ff_data -# Now compute all the dissimilarities between the collected frames -ss1: DISSIMILARITIES ARG=ff_data,ff_dataT SQUARED -DUMPVECTOR ARG=ss1 FILE=mymatrix.dat -``` - -## The MASK keyword - -The MASK keyword for DISSIMILARITIES works in the same way that it does for [MATRIX_PRODUCT](MATRIX_PRODUCT.md). This keyword thus -expects a matrix in input and will only evaluate elements the elements of the dissimilarity matrix whose corresponding elements in -the matrix that was input to MASK are non-zero. The following input shows an example of how this might be used in an example input -that has not been used in any production calculation. - -```plumed -# Calculate and store three vectors connecting three pairs of atoms -d1: DISTANCE COMPONENTS ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 -ff1: VSTACK ARG=d1.x,d1.y,d1.z -# Calculate the magnitude of the vector and transform this magnitude using a -# switching function -d1m: CUSTOM ARG=d1.x,d1.y,d1.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO -sw1: LESS_THAN ARG=d1m SWITCH={RATIONAL R_0=0.2 D_MAX=0.5} -# Now perform the same operations for a different set of three atoms -d2: DISTANCE COMPONENTS ATOMS1=7,8 ATOMS2=9,10 ATOMS3=11,12 -ff2: VSTACK ARG=d2.x,d2.y,d2.z -ff2T: TRANSPOSE ARG=ff2 -d2m: CUSTOM ARG=d2.x,d2.y,d2.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO -sw2: LESS_THAN ARG=d2m SWITCH={RATIONAL R_0=0.2 D_MAX=0.5} -# Use OUTER_PRODUCT to work out which pairs of atoms are less than a certain cutoff -swmat: OUTER_PRODUCT ARG=sw1,sw2 -# Now calculate the dissimilarities between the two sets of vectors for those pairs of atoms that are within a certain cutoff -d: DISSIMILARITIES ARG=ff1,ff2T MASK=swmat -mat: CUSTOM ARG=swmat,d FUNC=x*y PERIODIC=NO -# And compute the average dissimilarity -numer: SUM ARG=mat PERIODIC=NO -denom: SUM ARG=swmat PERIODIC=NO -v: CUSTOM ARG=numer,denom FUNC=x/y PERIODIC=NO -PRINT ARG=v FILE=colvar -``` - -We have not provided a more relevant example because we haven't really used this functionality for anything. If you have a better example -for a way of using this functionality please get in touch so we can update this part of the manual with your example. - -*/ -//+ENDPLUMEDOC - -namespace PLMD { -namespace matrixtools { - -struct MatrixProduct { - static void registerKeywords( Keywords& keys ); - void setup( MatrixTimesMatrix* action, const Value* myval ) {} - static void calculate( bool noderiv, - const MatrixProduct& actdata, - const InputVectors& vectors, - MatrixElementOutput& output ); -#ifdef __PLUMED_USE_OPENACC - void toACCDevice() const { -#pragma acc enter data copyin(this[0:1]) - } - void removeFromACCDevice() const { -#pragma acc exit data delete(this[0:1]) - } -#endif //__PLUMED_USE_OPENACC -}; - -typedef MatrixTimesMatrix mtimes; -PLUMED_REGISTER_ACTION(mtimes,"MATRIX_PRODUCT") - -void MatrixProduct::registerKeywords( Keywords& keys ) { - keys.setValueDescription("matrix","the product of the two input matrices"); -} - -void MatrixProduct::calculate( bool noderiv, - const MatrixProduct& actdata, - const InputVectors& vectors, - MatrixElementOutput& output ) { - std::size_t pp = vectors.arg1.size(); - for(unsigned i=0; i* action, - const Value* myval ); - static void calculate( bool noderiv, - const Dissimilarities& actdata, - const InputVectors& vectors, - MatrixElementOutput& output ); -#ifdef __PLUMED_USE_OPENACC - void toACCDevice() const { -#pragma acc enter data copyin(this[0:1], squared, periodic, min, max, \ - max_minus_min, inv_max_minus_min) - - } - void removeFromACCDevice() const { -#pragma acc exit data delete(inv_max_minus_min, max_minus_min, max, \ - min, periodic, squared, this[0:1]) - } -#endif //__PLUMED_USE_OPENACC -}; - -typedef MatrixTimesMatrix dissims; -PLUMED_REGISTER_ACTION(dissims,"DISSIMILARITIES") - -void Dissimilarities::registerKeywords( Keywords& keys ) { - keys.addFlag("SQUARED",false,"calculate the squares of the dissimilarities (this option cannot be used with MATRIX_PRODUCT)"); - keys.setValueDescription("matrix","the dissimilarity matrix"); -} - -void Dissimilarities::setup( MatrixTimesMatrix* action, const Value* myval ) { - action->parseFlag("SQUARED",squared); - if( squared ) { - action->log.printf(" calculating the squares of the dissimilarities \n"); - } - periodic = myval->isPeriodic(); - if( periodic ) { - std::string strmin, strmax; - myval->getDomain( strmin, strmax ); - Tools::convert( strmin, min ); - Tools::convert( strmax, max ); - max_minus_min = max - min; - plumed_assert( max_minus_min>0 ); - inv_max_minus_min=1.0/max_minus_min; - } -} - -void Dissimilarities::calculate( bool noderiv, const Dissimilarities& actdata, const InputVectors& vectors, MatrixElementOutput& output ) { - std::size_t pp = vectors.arg1.size(); - for(unsigned i=0; i +namespace helpers { +template +constexpr bool isDissimilarities=false; +template +constexpr bool isDissimilarities> =true; +} + +template struct MatrixTimesMatrixInput { T funcinput; RequiredMatrixElements outmat; -#ifdef __PLUMED_USE_OPENACC +#ifdef __PLUMED_HAS_OPENACC void toACCDevice() const { #pragma acc enter data copyin(this[0:1]) funcinput.toACCDevice(); @@ -43,7 +50,7 @@ struct MatrixTimesMatrixInput { outmat.removeFromACCDevice(); #pragma acc exit data delete(this[0:1]) } -#endif //__PLUMED_USE_OPENACC +#endif //__PLUMED_HAS_OPENACC }; class InputVectors { @@ -54,11 +61,15 @@ class InputVectors { InputVectors( std::size_t n, double* b ) : nelem(n), arg1(b,n), arg2(b+n,n) {} }; -template +template class MatrixTimesMatrix : public ActionWithMatrix { public: - using input_type = MatrixTimesMatrixInput; - using PTM = ParallelTaskManager>; + using input_type = MatrixTimesMatrixInput; + using mytype = MatrixTimesMatrix; + using PTM = typename myPTM::template PTM; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; + constexpr static bool isDissimilarities=helpers::isDissimilarities; private: PTM taskmanager; public: @@ -68,25 +79,34 @@ class MatrixTimesMatrix : public ActionWithMatrix { unsigned getNumberOfDerivatives() override; void calculate() override ; void applyNonZeroRankForces( std::vector& outforces ) override ; - static void performTask( std::size_t task_index, const MatrixTimesMatrixInput& actiondata, ParallelActionsInput& input, ParallelActionsOutput& output ); - static int getNumberOfValuesPerTask( std::size_t task_index, const MatrixTimesMatrixInput& actiondata ); - static void getForceIndices( std::size_t task_index, std::size_t colno, std::size_t ntotal_force, const MatrixTimesMatrixInput& actiondata, const ParallelActionsInput& input, ForceIndexHolder force_indices ); + static void performTask( std::size_t task_index, + const input_type& actiondata, + ParallelActionsInput& input, + ParallelActionsOutput& output ); + static int getNumberOfValuesPerTask( std::size_t task_index, + const input_type& actiondata ); + static void getForceIndices( std::size_t task_index, + std::size_t colno, + std::size_t ntotal_force, + const input_type& actiondata, + const ParallelActionsInput& input, + ForceIndexHolder force_indices ); }; -template -void MatrixTimesMatrix::registerKeywords( Keywords& keys ) { +template +void MatrixTimesMatrix::registerKeywords( Keywords& keys ) { ActionWithMatrix::registerKeywords(keys); keys.addInputKeyword("optional","MASK","matrix","a matrix that is used to used to determine which elements of the output matrix to compute"); keys.addInputKeyword("compulsory","ARG","matrix","the label of the two matrices from which the product is calculated"); - if( keys.getDisplayName()=="MATRIX_PRODUCT" ) { - keys.addFlag("ELEMENTS_ON_DIAGONAL_ARE_ZERO",false,"set all diagonal elements to zero"); - } - T::registerKeywords( keys ); + //if( keys.getDisplayName()=="MATRIX_PRODUCT" ) { + // keys.addFlag("ELEMENTS_ON_DIAGONAL_ARE_ZERO",false,"set all diagonal elements to zero"); + //} + CV::registerKeywords( keys ); PTM::registerKeywords( keys ); } -template -MatrixTimesMatrix::MatrixTimesMatrix(const ActionOptions&ao): +template +MatrixTimesMatrix::MatrixTimesMatrix(const ActionOptions&ao): Action(ao), ActionWithMatrix(ao), taskmanager(this) { @@ -112,7 +132,7 @@ MatrixTimesMatrix::MatrixTimesMatrix(const ActionOptions&ao): addValue( shape ); setNotPeriodic(); getPntrToComponent(0)->reshapeMatrixStore( shape[1] ); - if( getName()!="DISSIMILARITIES" && getPntrToArgument(0)->isDerivativeZeroWhenValueIsZero() && getPntrToArgument(1)->isDerivativeZeroWhenValueIsZero() ) { + if( !isDissimilarities && getPntrToArgument(0)->isDerivativeZeroWhenValueIsZero() && getPntrToArgument(1)->isDerivativeZeroWhenValueIsZero() ) { getPntrToComponent(0)->setDerivativeIsZeroWhenValueIsZero(); } @@ -125,18 +145,18 @@ MatrixTimesMatrix::MatrixTimesMatrix(const ActionOptions&ao): error("argument passed to MASK keyword has the wrong shape"); } } - MatrixTimesMatrixInput actdata; + input_type actdata; actdata.funcinput.setup( this, getPntrToArgument(0) ); taskmanager.setActionInput( actdata ); } -template -unsigned MatrixTimesMatrix::getNumberOfDerivatives() { +template +unsigned MatrixTimesMatrix::getNumberOfDerivatives() { return getPntrToArgument(0)->getNumberOfStoredValues() + getPntrToArgument(1)->getNumberOfStoredValues(); } -template -void MatrixTimesMatrix::prepare() { +template +void MatrixTimesMatrix::prepare() { ActionWithVector::prepare(); Value* myval = getPntrToComponent(0); if( myval->getShape()[0]==getPntrToArgument(0)->getShape()[0] && myval->getShape()[1]==getPntrToArgument(1)->getShape()[1] ) { @@ -149,35 +169,37 @@ void MatrixTimesMatrix::prepare() { myval->reshapeMatrixStore( shape[1] ); } -template -void MatrixTimesMatrix::calculate() { +template +void MatrixTimesMatrix::calculate() { if( !getPntrToComponent(0)->isDerivativeZeroWhenValueIsZero() ) { if( getPntrToArgument(0)->getNumberOfColumns()getShape()[1] ) { if( !doNotCalculateDerivatives() ) { error("cannot calculate derivatives for this action with sparse matrices"); - } else if( getName()=="DISSIMILARITIES" ) { + } else if(isDissimilarities ) { error("cannot calculate dissimilarities for sparse matrices"); } } if( getPntrToArgument(1)->getNumberOfColumns()getShape()[1] ) { if( !doNotCalculateDerivatives() ) { error("cannot calculate derivatives for this action with sparse matrices"); - } else if( getName()=="DISSIMILARITIES" ) { + } else if( isDissimilarities ) { error("cannot calculate dissimilarities for sparse matrices"); } } } updateBookeepingArrays( taskmanager.getActionInput().outmat ); - taskmanager.setupParallelTaskManager( 2*getPntrToArgument(0)->getNumberOfColumns(), getPntrToArgument(1)->getNumberOfStoredValues() ); + //unsigned nvals = getPntrToComponent(0)->getNumberOfColumns(); + taskmanager.setupParallelTaskManager( 2*getPntrToArgument(0)->getNumberOfColumns(), + getPntrToArgument(1)->getNumberOfStoredValues() ); taskmanager.setWorkspaceSize( 2*getPntrToArgument(0)->getNumberOfColumns() ); taskmanager.runAllTasks(); } -template -void MatrixTimesMatrix::performTask( std::size_t task_index, - const MatrixTimesMatrixInput& actiondata, - ParallelActionsInput& input, - ParallelActionsOutput& output ) { +template +void MatrixTimesMatrix::performTask( std::size_t task_index, + const input_type& actiondata, + ParallelActionsInput& input, + ParallelActionsOutput& output ) { auto arg0=ArgumentBookeepingHolder::create( 0, input ); auto arg1=ArgumentBookeepingHolder::create( 1, input ); std::size_t fpos = task_index*(1+arg0.ncols); @@ -216,7 +238,7 @@ void MatrixTimesMatrix::performTask( std::size_t task_index, } } MatrixElementOutput elem( 1, 2*nmult, output.values.data() + i, output.derivatives.data() + 2*nmult*i ); - T::calculate( input.noderiv, actiondata.funcinput, vectors, elem ); + CV::calculate( input.noderiv, actiondata.funcinput, vectors, elem ); for(unsigned ii=vectors.nelem; ii::performTask( std::size_t task_index, vectors.arg2[j] = input.inputdata[ base + arg1.ncols*arg0.bookeeping[fpos+1+j] ]; } MatrixElementOutput elem( 1, 2*nmult, output.values.data() + i, output.derivatives.data() + 2*nmult*i ); - T::calculate( input.noderiv, actiondata.funcinput, vectors, elem ); + CV::calculate( input.noderiv, actiondata.funcinput, vectors, elem ); } } } -template -void MatrixTimesMatrix::applyNonZeroRankForces( std::vector& outforces ) { +template +void MatrixTimesMatrix::applyNonZeroRankForces( std::vector& outforces ) { taskmanager.applyForces( outforces ); } -template -int MatrixTimesMatrix::getNumberOfValuesPerTask( std::size_t task_index, - const MatrixTimesMatrixInput& actiondata ) { +template +int MatrixTimesMatrix::getNumberOfValuesPerTask( std::size_t task_index, + const input_type& actiondata ) { std::size_t fstart = task_index*(1+actiondata.outmat.ncols); return actiondata.outmat[fstart]; } -template -void MatrixTimesMatrix::getForceIndices( std::size_t task_index, +template +void MatrixTimesMatrix::getForceIndices( std::size_t task_index, std::size_t colno, std::size_t ntotal_force, - const MatrixTimesMatrixInput& actiondata, + const input_type& actiondata, const ParallelActionsInput& input, ForceIndexHolder force_indices ) { auto arg0=ArgumentBookeepingHolder::create( 0, input ); diff --git a/src/matrixtools/MatrixTimesVector.cpp b/src/matrixtools/MatrixTimesVector.cpp index c6c75f3ea1..8f4fefb8ee 100644 --- a/src/matrixtools/MatrixTimesVector.cpp +++ b/src/matrixtools/MatrixTimesVector.cpp @@ -19,10 +19,6 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC - #include "MatrixTimesVectorBase.h" #include "core/ActionRegister.h" #include "core/ActionShortcut.h" @@ -86,7 +82,14 @@ void MatrixTimesVector::registerKeywords( Keywords& keys ) { ActionShortcut::registerKeywords(keys); MatrixTimesVectorBase::registerLocalKeywords( keys ); keys.addActionNameSuffix("_ROWSUMS"); + keys.addActionNameSuffix("_ROWSUMSACC"); keys.addActionNameSuffix("_PROPER"); + keys.addActionNameSuffix("_PROPERACC"); + + if(!keys.exists("USEGPU")) { + keys.addFlag("USEGPU",false,"run this calculation on the GPU"); + keys.addLinkInDocForFlag("USEGPU","gpu.md"); + } } MatrixTimesVector::MatrixTimesVector( const ActionOptions& ao): @@ -96,12 +99,12 @@ MatrixTimesVector::MatrixTimesVector( const ActionOptions& ao): parseVector("ARG",args); std::vector myargs; ActionWithArguments::interpretArgumentList( args, plumed.getActionSet(), this, myargs ); - std::string usegpustr=""; + std::string usegpustr=" "; { bool usegpu; parseFlag("USEGPU",usegpu); if( usegpu ) { - usegpustr = " USEGPU"; + usegpustr = "ACC "; } } unsigned nvectors=0, nmatrices=0; @@ -160,11 +163,11 @@ MatrixTimesVector::MatrixTimesVector( const ActionOptions& ao): } } if( sumrows ) { - readInputLine( getShortcutLabel() + ": MATRIX_VECTOR_PRODUCT_ROWSUMS ARG=" - + argstr + " " + convertInputLineToString() + usegpustr ); + readInputLine( getShortcutLabel() + ": MATRIX_VECTOR_PRODUCT_ROWSUMS"+usegpustr + +"ARG="+ argstr + " " + convertInputLineToString() ); } else { - readInputLine( getShortcutLabel() + ": MATRIX_VECTOR_PRODUCT_PROPER ARG=" - + argstr + " " + convertInputLineToString() + usegpustr ); + readInputLine( getShortcutLabel() + ": MATRIX_VECTOR_PRODUCT_PROPER"+usegpustr + +"ARG="+ argstr + " " + convertInputLineToString() ); } } else if( nmatrices==1 ) { if( myargs[0]->getRank()!=2 || myargs[0]->hasDerivatives() ) { @@ -182,8 +185,8 @@ MatrixTimesVector::MatrixTimesVector( const ActionOptions& ao): error("number of columns in input matrix does not equal number of elements in vector"); } } - readInputLine( getShortcutLabel() + ": MATRIX_VECTOR_PRODUCT_PROPER ARG=" - + argstr + " " + convertInputLineToString() + usegpustr ); + readInputLine( getShortcutLabel() + ": MATRIX_VECTOR_PRODUCT_PROPER"+usegpustr + +"ARG="+ argstr + " " + convertInputLineToString() ); } else { error("You should either have one vector or one matrix in input"); } diff --git a/src/matrixtools/MatrixTimesVectorBase.cpp b/src/matrixtools/MatrixTimesVectorBase.cpp index 9b7aebce7b..7fa872d7ad 100644 --- a/src/matrixtools/MatrixTimesVectorBase.cpp +++ b/src/matrixtools/MatrixTimesVectorBase.cpp @@ -19,75 +19,16 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC #include "MatrixTimesVectorBase.h" #include "core/ActionRegister.h" namespace PLMD { namespace matrixtools { - -class MatrixTimesVectorRowSums { -public: - static void performTask( const MatrixTimesVectorInput& input, - MatrixTimesVectorOutput& output ); - static std::size_t getAdditionalIndices( std::size_t n, - std::size_t vecstart, - const MatrixForceIndexInput& fin, - View indices ) { - return n; - } -}; - -typedef MatrixTimesVectorBase mycr; +typedef MatrixTimesVectorBase> mycr; PLUMED_REGISTER_ACTION(mycr,"MATRIX_VECTOR_PRODUCT_ROWSUMS") - -void MatrixTimesVectorRowSums::performTask( const MatrixTimesVectorInput& input, - MatrixTimesVectorOutput& output ) { - for(unsigned i=0; i indices ); -}; - -typedef MatrixTimesVectorBase mycp; +typedef MatrixTimesVectorBase> mycp; PLUMED_REGISTER_ACTION(mycp,"MATRIX_VECTOR_PRODUCT_PROPER") -void MatrixTimesVectorProper::performTask( const MatrixTimesVectorInput& input, - MatrixTimesVectorOutput& output ) { - for(unsigned i=0; i indices ) { - for(unsigned i=0; i +constexpr bool isRowSum=false; +template +constexpr bool isRowSum> =true; +} + class MatrixTimesVectorData { public: std::size_t fshift; Matrix pairs; -#ifdef __PLUMED_USE_OPENACC +#ifdef __PLUMED_HAS_OPENACC void toACCDevice() const { #pragma acc enter data copyin(this[0:1],fshift) pairs.toACCDevice(); @@ -41,13 +49,15 @@ class MatrixTimesVectorData { pairs.removeFromACCDevice(); #pragma acc exit data delete(fshift,this[0:1]) } -#endif //__PLUMED_USE_OPENACC +#endif //__PLUMED_HAS_OPENACC }; class MatrixForceIndexInput { public: std::size_t rowlen; View indices; +//temporary template for compilation + template MatrixForceIndexInput( std::size_t task_index, std::size_t ipair, const MatrixTimesVectorData& actiondata, @@ -59,18 +69,20 @@ class MatrixForceIndexInput { rowlen) {} }; -class MatrixTimesVectorInput { -public: +template +struct MatrixTimesVectorInput { bool noderiv; std::size_t rowlen; View indices; - View matrow; - View vector; + View matrow; + View vector; +//temporary template for compilation + template MatrixTimesVectorInput( std::size_t task_index, std::size_t ipair, const MatrixTimesVectorData& actiondata, const ParallelActionsInput& input, - double* argdata ): + precision* argdata ): noderiv(input.noderiv), rowlen(input.bookeeping[input.bookstarts[actiondata.pairs[ipair][0]] + (1+input.ncols[actiondata.pairs[ipair][0]])*task_index]), @@ -82,12 +94,15 @@ class MatrixTimesVectorInput { } }; +template class MatrixTimesVectorOutput { public: std::size_t rowlen; - View values; - View matrow_deriv; - View vector_deriv; + View values; + View matrow_deriv; + View vector_deriv; +//temporary template for compilation + template MatrixTimesVectorOutput( std::size_t task_index, std::size_t ipair, std::size_t nder, @@ -102,11 +117,15 @@ class MatrixTimesVectorOutput { } }; -template +template class MatrixTimesVectorBase : public ActionWithVector { public: using input_type = MatrixTimesVectorData; - using PTM = ParallelTaskManager>; + typedef cvprecision_t precision; + typedef MatrixTimesVectorBase mytype; + using PTM = typename myPTM::template PTM; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: /// The parallel task manager PTM taskmanager; @@ -138,8 +157,8 @@ class MatrixTimesVectorBase : public ActionWithVector { ForceIndexHolder force_indices ); }; -template -void MatrixTimesVectorBase::registerKeywords( Keywords& keys ) { +template +void MatrixTimesVectorBase::registerKeywords( Keywords& keys ) { ActionWithVector::registerKeywords(keys); keys.setDisplayName("MATRIX_VECTOR_PRODUCT"); registerLocalKeywords( keys ); @@ -147,8 +166,8 @@ void MatrixTimesVectorBase::registerKeywords( Keywords& keys ) { keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log"); } -template -void MatrixTimesVectorBase::registerLocalKeywords( Keywords& keys ) { +template +void MatrixTimesVectorBase::registerLocalKeywords( Keywords& keys ) { PTM::registerKeywords( keys ); keys.addInputKeyword("compulsory","ARG","matrix/vector/scalar","the label for the matrix and the vector/scalar that are being multiplied. Alternatively, you can provide labels for multiple matrices and a single vector or labels for a single matrix and multiple vectors. In these cases multiple matrix vector products will be computed."); keys.add("hidden","MASKED_INPUT_ALLOWED","turns on that you are allowed to use masked inputs "); @@ -156,8 +175,8 @@ void MatrixTimesVectorBase::registerLocalKeywords( Keywords& keys ) { ActionWithValue::useCustomisableComponents(keys); } -template -std::string MatrixTimesVectorBase::getOutputComponentDescription( const std::string& cname, +template +std::string MatrixTimesVectorBase::getOutputComponentDescription( const std::string& cname, const Keywords& keys ) const { if( getPntrToArgument(1)->getRank()==1 ) { for(unsigned i=1; i::getOutputComponentDescription( const std:: return ""; } -template -MatrixTimesVectorBase::MatrixTimesVectorBase(const ActionOptions&ao): +template +MatrixTimesVectorBase::MatrixTimesVectorBase(const ActionOptions&ao): Action(ao), ActionWithVector(ao), taskmanager(this) { @@ -251,8 +270,8 @@ MatrixTimesVectorBase::MatrixTimesVectorBase(const ActionOptions&ao): taskmanager.setActionInput( input ); } -template -unsigned MatrixTimesVectorBase::getNumberOfDerivatives() { +template +unsigned MatrixTimesVectorBase::getNumberOfDerivatives() { unsigned nderivatives=0; for(unsigned i=0; igetNumberOfStoredValues(); @@ -260,8 +279,8 @@ unsigned MatrixTimesVectorBase::getNumberOfDerivatives() { return nderivatives; } -template -void MatrixTimesVectorBase::prepare() { +template +void MatrixTimesVectorBase::prepare() { ActionWithVector::prepare(); Value* myval = getPntrToComponent(0); if( myval->getShape()[0]==getPntrToArgument(0)->getShape()[0] ) { @@ -272,15 +291,16 @@ void MatrixTimesVectorBase::prepare() { myval->setShape(shape); } -template -void MatrixTimesVectorBase::calculate() { - std::size_t nvectors, nder = getPntrToArgument(getNumberOfArguments()-1)->getNumberOfStoredValues(); +template +void MatrixTimesVectorBase::calculate() { + std::size_t nder = getPntrToArgument(getNumberOfArguments()-1)->getNumberOfStoredValues(); + std::size_t nvectors; if( getPntrToArgument(1)->getRank()==2 ) { nvectors = 1; } else { nvectors = getNumberOfArguments()-1; } - if( getName()=="MATRIX_VECTOR_PRODUCT_ROWSUMS" ) { + if constexpr ( helpers::isRowSum) { //getName()=="MATRIX_VECTOR_PRODUCT_ROWSUMS" ) { taskmanager.setupParallelTaskManager( nder, 0 ); } else { taskmanager.setupParallelTaskManager( 2*nder, nvectors*nder ); @@ -288,8 +308,8 @@ void MatrixTimesVectorBase::calculate() { taskmanager.runAllTasks(); } -template -int MatrixTimesVectorBase::checkTaskIsActive( const unsigned& itask ) const { +template +int MatrixTimesVectorBase::checkTaskIsActive( const unsigned& itask ) const { for(unsigned i=0; igetRank()==1 && !myarg->hasDerivatives() ) { @@ -305,40 +325,40 @@ int MatrixTimesVectorBase::checkTaskIsActive( const unsigned& itask ) const { return 0; } -template -void MatrixTimesVectorBase::performTask( std::size_t task_index, +template +void MatrixTimesVectorBase::performTask( std::size_t task_index, const MatrixTimesVectorData& actiondata, ParallelActionsInput& input, ParallelActionsOutput& output ) { for(unsigned i=0; i doutput( task_index, + i, + input.nderivatives_per_scalar, + actiondata, + input, + output ); + CV::performTask( MatrixTimesVectorInput( task_index, + i, + actiondata, + input, + input.inputdata ), + doutput ); } } -template -void MatrixTimesVectorBase::applyNonZeroRankForces( std::vector& outforces ) { +template +void MatrixTimesVectorBase::applyNonZeroRankForces( std::vector& outforces ) { taskmanager.applyForces( outforces ); } -template -int MatrixTimesVectorBase::getNumberOfValuesPerTask( std::size_t task_index, +template +int MatrixTimesVectorBase::getNumberOfValuesPerTask( std::size_t task_index, const MatrixTimesVectorData& actiondata ) { return 1; } -template -void MatrixTimesVectorBase::getForceIndices( std::size_t task_index, +template +void MatrixTimesVectorBase::getForceIndices( std::size_t task_index, std::size_t colno, std::size_t ntotal_force, const MatrixTimesVectorData& actiondata, @@ -353,13 +373,61 @@ void MatrixTimesVectorBase::getForceIndices( std::size_t task_index, force_indices.indices[i][j] = base + j; } force_indices.threadsafe_derivatives_end[i] = n; - force_indices.tot_indices[i] = T::getAdditionalIndices( n, + force_indices.tot_indices[i] = CV::getAdditionalIndices( n, input.argstarts[actiondata.pairs[i][1]], MatrixForceIndexInput( task_index, i, actiondata, input ), force_indices.indices[i] ); } } +template +struct MatrixTimesVectorRowSums { + typedef void isRowSums; + typedef T precision; + static void performTask( const MatrixTimesVectorInput& input, + MatrixTimesVectorOutput& output ) { + for(unsigned i=0; i indices ) { + return n; + } +}; + + +template +struct MatrixTimesVectorProper { + typedef T precision; + static void performTask( const MatrixTimesVectorInput& input, + MatrixTimesVectorOutput& output ) { + for(unsigned i=0; i indices ) { + for(unsigned i=0; i; using PTM = ParallelTaskManager>; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: bool isproduct; PTM taskmanager; diff --git a/src/refdist/MatrixProductDiagonal.cpp b/src/refdist/MatrixProductDiagonal.cpp index c932d93335..63bfe07dc9 100644 --- a/src/refdist/MatrixProductDiagonal.cpp +++ b/src/refdist/MatrixProductDiagonal.cpp @@ -59,6 +59,8 @@ class MatrixProductDiagonal : public ActionWithVector { public: using input_type = MatrixProductDiagonalInput; using PTM = ParallelTaskManager; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: PTM taskmanager; public: diff --git a/src/secondarystructure/AlphaRMSD.cpp b/src/secondarystructure/AlphaRMSD.cpp index 7b9e8c3090..98eb66c080 100644 --- a/src/secondarystructure/AlphaRMSD.cpp +++ b/src/secondarystructure/AlphaRMSD.cpp @@ -108,7 +108,7 @@ class AlphaRMSD : public ActionShortcut { PLUMED_REGISTER_ACTION(AlphaRMSD,"ALPHARMSD") void AlphaRMSD::registerKeywords( Keywords& keys ) { - SecondaryStructureBase::registerKeywords( keys ); + SecondaryStructureInput::registerKeywords( keys ); keys.remove("ATOMS"); keys.remove("SEGMENT"); keys.remove("STRUCTURE"); @@ -122,11 +122,11 @@ AlphaRMSD::AlphaRMSD(const ActionOptions&ao): ActionShortcut(ao) { // Read in the input and create a string that describes how to compute the less than std::string ltmap; - bool uselessthan=SecondaryStructureBase::readShortcutWords( ltmap, this ); + bool uselessthan=SecondaryStructureInput::readShortcutWords( ltmap, this ); // read in the backbone atoms std::vector chains; std::vector all_atoms; - SecondaryStructureBase::readBackboneAtoms( this, plumed, "protein", chains, all_atoms ); + SecondaryStructureInput::readBackboneAtoms( this, plumed, "protein", chains, all_atoms ); // This constructs all conceivable sections of alpha helix in the backbone of the chains unsigned nprevious=0, segno=1; diff --git a/src/secondarystructure/AntibetaRMSD.cpp b/src/secondarystructure/AntibetaRMSD.cpp index 75e14904d3..d22e76e90d 100644 --- a/src/secondarystructure/AntibetaRMSD.cpp +++ b/src/secondarystructure/AntibetaRMSD.cpp @@ -116,7 +116,7 @@ class AntibetaRMSD : public ActionShortcut { PLUMED_REGISTER_ACTION(AntibetaRMSD,"ANTIBETARMSD") void AntibetaRMSD::registerKeywords( Keywords& keys ) { - SecondaryStructureBase::registerKeywords( keys ); + SecondaryStructureInput::registerKeywords( keys ); keys.remove("ATOMS"); keys.remove("SEGMENT"); keys.remove("STRUCTURE"); @@ -140,11 +140,11 @@ AntibetaRMSD::AntibetaRMSD(const ActionOptions&ao): ActionShortcut(ao) { // Read in the input and create a string that describes how to compute the less than std::string ltmap; - bool uselessthan=SecondaryStructureBase::readShortcutWords( ltmap, this ); + bool uselessthan=SecondaryStructureInput::readShortcutWords( ltmap, this ); // read in the backbone atoms std::vector chains; std::vector all_atoms; - SecondaryStructureBase::readBackboneAtoms( this, plumed, "protein", chains, all_atoms ); + SecondaryStructureInput::readBackboneAtoms( this, plumed, "protein", chains, all_atoms ); bool intra_chain(false), inter_chain(false); std::string style; diff --git a/src/secondarystructure/ParabetaRMSD.cpp b/src/secondarystructure/ParabetaRMSD.cpp index 042c32538a..736dc7e905 100644 --- a/src/secondarystructure/ParabetaRMSD.cpp +++ b/src/secondarystructure/ParabetaRMSD.cpp @@ -116,7 +116,7 @@ class ParabetaRMSD : public ActionShortcut { PLUMED_REGISTER_ACTION(ParabetaRMSD,"PARABETARMSD") void ParabetaRMSD::registerKeywords( Keywords& keys ) { - SecondaryStructureBase::registerKeywords( keys ); + SecondaryStructureInput::registerKeywords( keys ); keys.remove("ATOMS"); keys.remove("SEGMENT"); keys.remove("STRUCTURE"); @@ -141,11 +141,11 @@ ParabetaRMSD::ParabetaRMSD(const ActionOptions&ao): ActionShortcut(ao) { // Read in the input and create a string that describes how to compute the less than std::string ltmap; - bool uselessthan=SecondaryStructureBase::readShortcutWords( ltmap, this ); + bool uselessthan=SecondaryStructureInput::readShortcutWords( ltmap, this ); // read in the backbone atoms std::vector chains; std::vector all_atoms; - SecondaryStructureBase::readBackboneAtoms( this, plumed, "protein", chains, all_atoms ); + SecondaryStructureInput::readBackboneAtoms( this, plumed, "protein", chains, all_atoms ); bool intra_chain(false), inter_chain(false); std::string style; diff --git a/src/secondarystructure/SecondaryStructureBase.h b/src/secondarystructure/SecondaryStructureBase.h index 4c096619b1..f47a173886 100644 --- a/src/secondarystructure/SecondaryStructureBase.h +++ b/src/secondarystructure/SecondaryStructureBase.h @@ -29,23 +29,49 @@ #include "core/GenericMolInfo.h" #include "core/ParallelTaskManager.h" #include "tools/ColvarOutput.h" +#include "tools/TypeUtils.h" #include +#include namespace PLMD { namespace secondarystructure { +namespace helpers { +//this makes the variabe needstype only needed to be declared explicitly +//needsType activate the reading of "TYPE" during the parsing +template +constexpr bool needsType=false; +//specialization to intercept needsType +template +constexpr bool needsType> =T::needsType; + +//this makes the variabe needstype only needed to be declared explicitly +//needsBondLength activate the reading of "TYPE" during the parsing +template +constexpr bool needsBondLength=false; +//specialization to intercept needsBondLength +template +constexpr bool needsBondLength> =T::needsBondLength; +} + /// Base action for calculating things like AlphRMSD, AntibetaRMSD, etc -template +template class SecondaryStructureBase: public ActionWithVector { public: using input_type = T; - using PTM = ParallelTaskManager>; + using mytype=SecondaryStructureBase; + using PTM =typename myPTM::template PTM; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; + using precision = cvprecision_t; static constexpr size_t virialSize=9; static constexpr unsigned customGatherStep=3; static constexpr unsigned customGatherStopBefore=virialSize; private: PTM taskmanager; + static constexpr bool needsType = helpers::needsType; + static constexpr bool needsBondLength = helpers::needsBondLength; public: static void registerKeywords( Keywords& keys ); static void readBackboneAtoms( ActionShortcut* action, PlumedMain& plumed, const std::string& backnames, std::vector& chain_lengths, std::vector& all_atoms ); @@ -54,19 +80,23 @@ class SecondaryStructureBase: public ActionWithVector { unsigned getNumberOfDerivatives() override ; void calculate() override; void getInputData( std::vector& inputdata ) const override ; + void getInputData( std::vector& inputdata ) const override ; void applyNonZeroRankForces( std::vector& outforces ) override ; static void performTask( unsigned task_index, const T& actiondata, ParallelActionsInput& input, ParallelActionsOutput& output ); static int getNumberOfValuesPerTask( std::size_t task_index, const T& actiondata ); static void getForceIndices( std::size_t task_index, std::size_t colno, std::size_t ntotal_force, const T& actiondata, const ParallelActionsInput& input, ForceIndexHolder force_indices ); }; -template -unsigned SecondaryStructureBase::getNumberOfDerivatives() { +//this is used to get some of the static non template dependant functionalities for Secondary structure +using SecondaryStructureInput=SecondaryStructureBase; + +template +unsigned SecondaryStructureBase::getNumberOfDerivatives() { return 3*getNumberOfAtoms()+virialSize; } -template -bool SecondaryStructureBase::readShortcutWords( std::string& ltmap, ActionShortcut* action ) { +template +bool SecondaryStructureBase::readShortcutWords( std::string& ltmap, ActionShortcut* action ) { action->parse("LESS_THAN",ltmap); if( ltmap.length()==0 ) { std::string nn, mm, d_0, r_0; @@ -83,29 +113,31 @@ bool SecondaryStructureBase::readShortcutWords( std::string& ltmap, ActionSho return true; } -template -void SecondaryStructureBase::registerKeywords( Keywords& keys ) { +template +void SecondaryStructureBase::registerKeywords( Keywords& keys ) { ActionWithVector::registerKeywords( keys ); + T::registerKeywords( keys ); PTM::registerKeywords( keys ); keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions"); keys.addInputKeyword("optional","MASK","vector","a vector which is used to determine which elements of the secondary structure variable should be computed"); keys.add("atoms","ATOMS","this is the full list of atoms that we are investigating"); keys.add("numbered","SEGMENT","this is the lists of atoms in the segment that are being considered"); - if( keys.getDisplayName()=="SECONDARY_STRUCTURE_DRMSD" ) { + if constexpr ( needsBondLength /*keys.getDisplayName()=="SECONDARY_STRUCTURE_DRMSD"*/ ) { keys.add("compulsory","BONDLENGTH","0.17","the length to use for bonds"); } keys.add("numbered","STRUCTURE","the reference structure"); - if( keys.getDisplayName()=="SECONDARY_STRUCTURE_RMSD" ) { + if constexpr ( needsType /*keys.getDisplayName()=="SECONDARY_STRUCTURE_RMSD"*/ ) { keys.add("compulsory","TYPE","OPTIMAL","the manner in which RMSD alignment is performed. Should be OPTIMAL or SIMPLE. " "For more details on the OPTIMAL and SIMPLE methods see \\ref RMSD."); - } else if( keys.getDisplayName()!="SECONDARY_STRUCTURE_DRMSD" ) { + } else if constexpr ( !needsBondLength /*keys.getDisplayName()!="SECONDARY_STRUCTURE_DRMSD"*/ ) { keys.add("compulsory","TYPE","DRMSD","the manner in which RMSD alignment is performed. Should be OPTIMAL, SIMPLE or DRMSD. " "For more details on the OPTIMAL and SIMPLE methods see \\ref RMSD. For more details on the " "DRMSD method see \\ref DRMSD."); } keys.addFlag("VERBOSE",false,"write a more detailed output"); keys.reset_style("VERBOSE","hidden"); - if( keys.getDisplayName()!="SECONDARY_STRUCTURE_DRMSD" && keys.getDisplayName()!="SECONDARY_STRUCTURE_RMSD" ) { + //if( keys.getDisplayName()!="SECONDARY_STRUCTURE_DRMSD" && keys.getDisplayName()!="SECONDARY_STRUCTURE_RMSD" ) { + if constexpr ( !needsBondLength && !needsType ) { keys.add("residues","RESIDUES","this command is used to specify the set of residues that could conceivably form part of the secondary structure. " "It is possible to use residues numbers as the various chains and residues should have been identified else using an instance of the " "\\ref MOLINFO action. If you wish to use all the residues from all the chains in your system you can do so by " @@ -130,8 +162,8 @@ void SecondaryStructureBase::registerKeywords( Keywords& keys ) { keys.addDOI("10.1021/ct900202f"); } -template -void SecondaryStructureBase::readBackboneAtoms( ActionShortcut* action, PlumedMain& plumed, const std::string& moltype, std::vector& chain_lengths, std::vector& all_atoms ) { +template +void SecondaryStructureBase::readBackboneAtoms( ActionShortcut* action, PlumedMain& plumed, const std::string& moltype, std::vector& chain_lengths, std::vector& all_atoms ) { auto* moldat=plumed.getActionSet().selectLatest(action); if( ! moldat ) { action->error("Unable to find MOLINFO in input"); @@ -165,8 +197,8 @@ void SecondaryStructureBase::readBackboneAtoms( ActionShortcut* action, Plume } } -template -SecondaryStructureBase::SecondaryStructureBase(const ActionOptions&ao): +template +SecondaryStructureBase::SecondaryStructureBase(const ActionOptions&ao): Action(ao), ActionWithVector(ao), taskmanager(this) { @@ -177,7 +209,7 @@ SecondaryStructureBase::SecondaryStructureBase(const ActionOptions&ao): input_type myinput; parseFlag("NOPBC",myinput.nopbc); std::string alignType=""; - if( getName()=="SECONDARY_STRUCTURE_RMSD" ) { + if constexpr ( needsType ) { parse("TYPE",alignType); } log.printf(" distances from secondary structure elements are calculated using %s algorithm\n", alignType.c_str() ); @@ -223,7 +255,7 @@ SecondaryStructureBase::SecondaryStructureBase(const ActionOptions&ao): } double bondlength=0.0; - if( getName()=="SECONDARY_STRUCTURE_DRMSD" ) { + if constexpr ( needsBondLength ) { parse("BONDLENGTH",bondlength); bondlength=bondlength/getUnits().getLength(); } @@ -266,13 +298,31 @@ SecondaryStructureBase::SecondaryStructureBase(const ActionOptions&ao): taskmanager.setActionInput( myinput ); } -template -void SecondaryStructureBase::calculate() { +template +void SecondaryStructureBase::calculate() { taskmanager.runAllTasks(); } -template -void SecondaryStructureBase::getInputData( std::vector& inputdata ) const { +template +void SecondaryStructureBase::getInputData( std::vector& inputdata ) const { + if( inputdata.size()!=3*getNumberOfAtoms() ) { + inputdata.resize( 3*getNumberOfAtoms() ); + } + + std::size_t k=0; + for(unsigned i=0; i +void SecondaryStructureBase::getInputData( std::vector& inputdata ) const { if( inputdata.size()!=3*getNumberOfAtoms() ) { inputdata.resize( 3*getNumberOfAtoms() ); } @@ -289,8 +339,8 @@ void SecondaryStructureBase::getInputData( std::vector& inputdata ) c } } -template -void SecondaryStructureBase::performTask( unsigned task_index, const T& actiondata, ParallelActionsInput& input, ParallelActionsOutput& output ) { +template +void SecondaryStructureBase::performTask( unsigned task_index, const T& actiondata, ParallelActionsInput& input, ParallelActionsOutput& output ) { // std::vector pos( actiondata.natoms ); std::array pos; @@ -303,11 +353,13 @@ void SecondaryStructureBase::performTask( unsigned task_index, const T& actio // This aligns the two strands if this is required if( actiondata.align_strands ) { Vector distance=input.pbc->distance( pos[6],pos[21] ); - Vector origin_old, origin_new; - origin_old=pos[21]; - origin_new=pos[6]+distance; + distance += pos[6] - pos[21]; + //Vector origin_old, origin_new; + //origin_old=pos[21]; + //origin_new=pos[6]+distance; for(unsigned i=15; i<30; ++i) { - pos[i]+=( origin_new - origin_old ); + //pos[i]+=( origin_new - origin_old ); + pos[i]+=distance; } } else if( !actiondata.nopbc ) { for(unsigned i=0; i::performTask( unsigned task_index, const T& actio } } -template -void SecondaryStructureBase::applyNonZeroRankForces( std::vector& outforces ) { +template +void SecondaryStructureBase::applyNonZeroRankForces( std::vector& outforces ) { taskmanager.applyForces( outforces ); } -template -int SecondaryStructureBase::getNumberOfValuesPerTask( std::size_t task_index, +template +int SecondaryStructureBase::getNumberOfValuesPerTask( std::size_t task_index, const T& actiondata ) { return 1; } -template -void SecondaryStructureBase::getForceIndices( std::size_t task_index, +template +void SecondaryStructureBase::getForceIndices( std::size_t task_index, std::size_t /* colno */, std::size_t ntotal_force, const T& actiondata, diff --git a/src/secondarystructure/SecondaryStructureDRMSD.cpp b/src/secondarystructure/SecondaryStructureDRMSD.cpp index df47a27193..50edf9167f 100644 --- a/src/secondarystructure/SecondaryStructureDRMSD.cpp +++ b/src/secondarystructure/SecondaryStructureDRMSD.cpp @@ -19,14 +19,10 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC -#include "SecondaryStructureBase.h" +#include "SecondaryStructureDRMSD.h" +#include "core/AccelerableShortcut.h" #include "core/ActionRegister.h" -#include "tools/Matrix.h" -#include //+PLUMEDOC MCOLVAR SECONDARY_STRUCTURE_DRMSD /* @@ -124,189 +120,10 @@ values are only computed for parts of the strand that are close together. This a namespace PLMD { namespace secondarystructure { -///This is a sort of compact std::vector> -template -class flexibleMemory { - ///Stores the data - std::vector data{}; - ///Stores the boundaries - std::vector sizes{}; - //helpers for openACC - T* d; - size_t* sz; - void update() { - d=data.data(); - sz=sizes.data(); - } -public: - flexibleMemory() { - update(); - }; - ~flexibleMemory() =default; - flexibleMemory(const flexibleMemory& m) : - data(m.data), - sizes(m.sizes) { - update(); - } - flexibleMemory& operator=(const flexibleMemory& m) { - if (this!=&m) { - data=m.data; - sizes=m.sizes; - update(); - } - return *this; - } - constexpr size_t size() const { - return sizes.size(); - } -//Access the i-th view of the data, use this to access the elements - constexpr View< const T> get(size_t i) const { - //use this at the start of your function, to not calculate again and again the initial index - size_t init=0; - for(size_t j=0; j(d+init,sz[i]); - } - void extend(const std::vector& v) { - data.insert(data.end(),v.begin(),v.end()); - sizes.push_back(v.size()); - update(); - } - void toACCDevice()const { -#pragma acc enter data copyin(this[0:1], d[0:data.size()], sz[0:sizes.size()]) - } - void removeFromACCDevice() const { -#pragma acc exit data delete(sz[0:sizes.size()], d[0:data.size()], this[0:1]) - } -}; - -class SecondaryStructureDRMSDInput { -private: - struct pairDistance { - double distance; - unsigned i; - unsigned j; - }; -/// The list of reference configurations - flexibleMemory drmsd_targets{}; - flexibleMemory drmsd_atoms{}; -/// The general input for the secondary structure variable -public: - size_t natoms{0}; - size_t nstructures{0}; - size_t nindices_per_task{0}; -/// Are we operating without periodic boundary conditions - bool nopbc{false}; -/// Variables for strands cutoff - bool align_strands{false}; -/// The atoms involved in each of the secondary structure segments - Matrix colvar_atoms{}; - static void calculateDistance( unsigned n, - bool noderiv, - const SecondaryStructureDRMSDInput& actiondata, - View pos, - ColvarOutput& output ); - void setReferenceStructure( std::string type, double bondlength, std::vector& structure ); - void toACCDevice()const { -#pragma acc enter data copyin(this[0:1], natoms,nstructures,nindices_per_task,nopbc,align_strands) - drmsd_targets.toACCDevice(); - drmsd_atoms.toACCDevice(); - colvar_atoms.toACCDevice(); - } - void removeFromACCDevice() const { - colvar_atoms.removeFromACCDevice(); - drmsd_atoms.removeFromACCDevice(); - drmsd_targets.removeFromACCDevice(); -#pragma acc exit data delete(align_strands,nopbc,nindices_per_task,nstructures,natoms,this[0:1]) - - } -}; - -typedef SecondaryStructureBase colv; -PLUMED_REGISTER_ACTION(colv,"SECONDARY_STRUCTURE_DRMSD") - -void SecondaryStructureDRMSDInput::setReferenceStructure( - std::string /*type*/, - double bondlength, - std::vector& structure ) { - std::vector targets; - //set is ordered and contains no duplicated data - std::set atoms_targets; - //targets.reserve( (structure.size()*(structure.size()-1))/2 );? - for(unsigned i=0; i bondlength) { - targets.emplace_back(pairDistance{distance,i,j}); - atoms_targets.emplace(i); - atoms_targets.emplace(j); - } - } - } - drmsd_targets.extend( targets ); - - drmsd_atoms.extend(std::vector {atoms_targets.begin(),atoms_targets.end()}); - nstructures = drmsd_targets.size(); - if (natoms==0) { - natoms = structure.size(); - } else if (natoms!=structure.size()) { - plumed_merror("input structures have a different number of atoms"); - } - -} - -void SecondaryStructureDRMSDInput::calculateDistance( - const unsigned n, - const bool noderiv, - const SecondaryStructureDRMSDInput& actiondata, - const View pos, - ColvarOutput& output ) { - { - const auto targetList = actiondata.drmsd_atoms.get(n); - const auto targetAtoms=targetList.size(); - if( !noderiv ) { - output.virial.set( n, Tensor(0,0,0,0,0,0,0,0,0) ); - for(unsigned i=0; i(targetSize); - output.values[n] = sqrt(inpairs*drmsd); - - if( !noderiv ) { - double scalef = inpairs / output.values[n]; - - PLMD::LoopUnroller<9>::_mul(output.virial.getView(n).data(),scalef); - const auto targetList = actiondata.drmsd_atoms.get(n); - for(unsigned i=0; i> colv; +PLUMED_REGISTER_ACTION(colv,"SECONDARY_STRUCTURE_DRMSD_CPU") +typedef AccelerableShortcut shortcut; +PLUMED_REGISTER_ACTION(shortcut,"SECONDARY_STRUCTURE_DRMSD") } } diff --git a/src/secondarystructure/SecondaryStructureDRMSD.h b/src/secondarystructure/SecondaryStructureDRMSD.h new file mode 100644 index 0000000000..d25ee6a222 --- /dev/null +++ b/src/secondarystructure/SecondaryStructureDRMSD.h @@ -0,0 +1,206 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2017-2025 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_secondarystructure_SecondaryStructureDRMSD_h +#define __PLUMED_secondarystructure_SecondaryStructureDRMSD_h +#include "SecondaryStructureBase.h" +#include "tools/Matrix.h" + +#include + +namespace PLMD { +namespace secondarystructure { + +///This is a sort of compact std::vector> +template +class flexibleMemory { + ///Stores the data + std::vector data{}; + ///Stores the boundaries + std::vector sizes{}; + //helpers for openACC + T* d; + size_t* sz; + void update() { + d=data.data(); + sz=sizes.data(); + } +public: + flexibleMemory() { + update(); + }; + ~flexibleMemory() =default; + flexibleMemory(const flexibleMemory& m) : + data(m.data), + sizes(m.sizes) { + update(); + } + flexibleMemory& operator=(const flexibleMemory& m) { + if (this!=&m) { + data=m.data; + sizes=m.sizes; + update(); + } + return *this; + } + constexpr size_t size() const { + return sizes.size(); + } +//Access the i-th view of the data, use this to access the elements + constexpr View< const T> get(size_t i) const { + //use this at the start of your function, to not calculate again and again the initial index + size_t init=0; + for(size_t j=0; j(d+init,sz[i]); + } + void extend(const std::vector& v) { + data.insert(data.end(),v.begin(),v.end()); + sizes.push_back(v.size()); + update(); + } + void toACCDevice()const { +#pragma acc enter data copyin(this[0:1], d[0:data.size()], sz[0:sizes.size()]) + } + void removeFromACCDevice() const { +#pragma acc exit data delete(sz[0:sizes.size()], d[0:data.size()], this[0:1]) + } +}; + +template +class SecondaryStructureDRMSDInput { +private: + struct pairDistance { + T distance; + unsigned i; + unsigned j; + }; +/// The list of reference configurations + flexibleMemory drmsd_targets{}; + flexibleMemory drmsd_atoms{}; +/// The general input for the secondary structure variable +public: + static void registerKeywords( Keywords& keys ) { + keys.setDisplayName("SECONDARY_STRUCTURE_DRMSD"); + } + static constexpr bool needsBondLength=true; + typedef T precision; + size_t natoms{0}; + size_t nstructures{0}; + size_t nindices_per_task{0}; +/// Are we operating without periodic boundary conditions + bool nopbc{false}; +/// Variables for strands cutoff + bool align_strands{false}; +/// The atoms involved in each of the secondary structure segments + Matrix colvar_atoms{}; + static void calculateDistance( const unsigned n, + const bool noderiv, + const SecondaryStructureDRMSDInput& actiondata, + View> pos, + ColvarOutput& output ) { + const auto targetList = actiondata.drmsd_atoms.get(n); + const auto targetAtoms=targetList.size(); + if( !noderiv ) { + output.virial.set( n, TensorT(0,0,0,0,0,0,0,0,0) ); + for(unsigned i=0; i(0.0,0.0,0.0); + } + } + + double drmsd = 0.0; + Vector distance; + Vector dd; + + const auto target = actiondata.drmsd_targets.get(n); + const auto targetSize=target.size(); + + for (unsigned i=0; i(dd,distance) );//-9 mul + } + } + const double inpairs = 1./static_cast(targetSize); + output.values[n] = sqrt(inpairs*drmsd); + + if( !noderiv ) { + double scalef = inpairs / output.values[n]; + + PLMD::LoopUnroller<9>::_mul(output.virial.getView(n).data(),scalef); + for(unsigned i=0; i& structure ) { + std::vector targets; + //set is ordered and contains no duplicated data + std::set atoms_targets; + //targets.reserve( (structure.size()*(structure.size()-1))/2 );? + for(unsigned i=0; i bondlength) { + targets.emplace_back(pairDistance{distance,i,j}); + atoms_targets.emplace(i); + atoms_targets.emplace(j); + } + } + } + drmsd_targets.extend( targets ); + + drmsd_atoms.extend(std::vector {atoms_targets.begin(),atoms_targets.end()}); + nstructures = drmsd_targets.size(); + if (natoms==0) { + natoms = structure.size(); + } else if (natoms!=structure.size()) { + plumed_merror("input structures have a different number of atoms"); + } + + } + void toACCDevice()const { +#pragma acc enter data copyin(this[0:1], natoms,nstructures,nindices_per_task,nopbc,align_strands) + drmsd_targets.toACCDevice(); + drmsd_atoms.toACCDevice(); + colvar_atoms.toACCDevice(); + } + void removeFromACCDevice() const { + colvar_atoms.removeFromACCDevice(); + drmsd_atoms.removeFromACCDevice(); + drmsd_targets.removeFromACCDevice(); +#pragma acc exit data delete(align_strands,nopbc,nindices_per_task,nstructures,natoms,this[0:1]) + + } +}; +} +} +#endif //__PLUMED_secondarystructure_SecondaryStructureDRMSD_h diff --git a/src/secondarystructure/SecondaryStructureRMSD.cpp b/src/secondarystructure/SecondaryStructureRMSD.cpp index ceb826fed8..9a6d8106bd 100644 --- a/src/secondarystructure/SecondaryStructureRMSD.cpp +++ b/src/secondarystructure/SecondaryStructureRMSD.cpp @@ -19,9 +19,6 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -// #ifdef __PLUMED_HAS_OPENACC -// #define __PLUMED_USE_OPENACC 1 -// #endif //__PLUMED_HAS_OPENACC #include "SecondaryStructureBase.h" #include "core/ActionRegister.h" #include "tools/RMSD.h" @@ -128,6 +125,10 @@ class SecondaryStructureRMSDInput { /// The list of reference configurations std::vector myrmsd; public: + static void registerKeywords( Keywords& keys ) { + keys.setDisplayName("SECONDARY_STRUCTURE_RMSD"); + } + static constexpr bool needsType=true; /// The number of atoms std::size_t natoms; /// The number of structures @@ -149,7 +150,7 @@ class SecondaryStructureRMSDInput { // #pragma acc exit data delete(align_strands,nopbc,nstructures,natoms,myrmsd[0:nstructures],this[0:1]) // } - static void calculateDistance( unsigned n, bool noderiv, const SecondaryStructureRMSDInput& actiondata, View pos, ColvarOutput& output ); + static void calculateDistance( unsigned n, bool noderiv, const SecondaryStructureRMSDInput& actiondata, View pos, ColvarOutput& output ); void setReferenceStructure( const std::string& type, double bondlength, std::vector& structure ); SecondaryStructureRMSDInput& operator=( const SecondaryStructureRMSDInput& m ) { natoms = m.natoms; @@ -168,6 +169,9 @@ class SecondaryStructureRMSDInput { typedef SecondaryStructureBase colv; PLUMED_REGISTER_ACTION(colv,"SECONDARY_STRUCTURE_RMSD") +//_REGISTER_ACTION(colv,"SECONDARY_STRUCTURE_RMSD_CPU"); +//typedef AccelerableShortcut shortcut; +//_REGISTER_ACTION(shortcut,"SECONDARY_STRUCTURE_RMSD"); void SecondaryStructureRMSDInput::setReferenceStructure( const std::string& type, double bondlength, std::vector& structure ) { Vector center; @@ -190,7 +194,7 @@ void SecondaryStructureRMSDInput::calculateDistance( unsigned n, bool noderiv, const SecondaryStructureRMSDInput& actiondata, const View pos, - ColvarOutput& output ) { + ColvarOutput& output ) { std::vector myderivs( actiondata.natoms ); output.values[n] = actiondata.myrmsd[n].calculate( pos, myderivs, false ); diff --git a/src/symfunc/Fccubic.cpp b/src/symfunc/Fccubic.cpp index a305fa8cf7..37568a62c7 100644 --- a/src/symfunc/Fccubic.cpp +++ b/src/symfunc/Fccubic.cpp @@ -19,13 +19,12 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "Fccubic.h" #include "function/FunctionSetup.h" #include "function/FunctionShortcut.h" #include "function/FunctionOfMatrix.h" #include "core/ActionRegister.h" -#include -#include namespace PLMD { namespace symfunc { @@ -174,73 +173,12 @@ By using the MASK keyword in the input to FCCUBIC_FUNC we ensure that the [FCCUB */ //+ENDPLUMEDOC -class Fccubic { -public: - double alpha, a1, b1; - static void registerKeywords( Keywords& keys ); - static void read( Fccubic& func, ActionWithArguments* action, function::FunctionOptions& funcout ); - static void calc( const Fccubic& func, bool noderiv, View args, function::FunctionOutput& funcout ); - Fccubic& operator=(const Fccubic& m) { - alpha = m.alpha; - a1 = m.a1; - b1 = m.b1; - return *this; - } -}; - -typedef function::FunctionShortcut FccubicShortcut; + +typedef function::FunctionShortcut> FccubicShortcut; PLUMED_REGISTER_ACTION(FccubicShortcut,"FCCUBIC_FUNC") -typedef function::FunctionOfMatrix MatrixFccubic; +typedef function::FunctionOfMatrix> MatrixFccubic; PLUMED_REGISTER_ACTION(MatrixFccubic,"FCCUBIC_FUNC_MATRIX") -void Fccubic::registerKeywords( Keywords& keys ) { - keys.add("compulsory","ALPHA","3.0","The alpha parameter of the angular function"); - keys.setValueDescription("matrix","a function that measures the similarity with an fcc environment"); -} - -void Fccubic::read( Fccubic& func, ActionWithArguments* action, function::FunctionOptions& funcout ) { - // Scaling factors such that '1' corresponds to fcc lattice - // and '0' corresponds to isotropic (liquid) - action->parse("ALPHA",func.alpha); - func.a1 = 80080. / (2717. + 16*func.alpha); - func.b1 = 16.*(func.alpha-143)/(2717+16*func.alpha); - action->log.printf(" setting alpha paramter equal to %f \n",func.alpha); -} - -void Fccubic::calc( const Fccubic& func, bool noderiv, const View args, function::FunctionOutput& funcout ) { - double x2 = args[0]*args[0]; - double x4 = x2*x2; - - double y2 = args[1]*args[1]; - double y4 = y2*y2; - - double z2 = args[2]*args[2]; - double z4 = z2*z2; - - double d2 = x2 + y2 + z2; - if( d2 < epsilon ) { - d2 = 1; - } - double r8 = pow( d2, 4 ); - double r12 = pow( d2, 6 ); - - double tmp = ((x4*y4)+(x4*z4)+(y4*z4))/r8-func.alpha*x4*y4*z4/r12; - - double t0 = (x2*y4+x2*z4)/r8-func.alpha*x2*y4*z4/r12; - double t1 = (y2*x4+y2*z4)/r8-func.alpha*y2*x4*z4/r12; - double t2 = (z2*x4+z2*y4)/r8-func.alpha*z2*x4*y4/r12; - double t3 = (2*tmp-func.alpha*x4*y4*z4/r12)/d2; - - if( !noderiv ) { - funcout.derivs[0][0]=4*func.a1*args[0]*(t0-t3); - funcout.derivs[0][1]=4*func.a1*args[1]*(t1-t3); - funcout.derivs[0][2]=4*func.a1*args[2]*(t2-t3); - } - - // Set the value and the derivatives - funcout.values[0] = (func.a1*tmp+func.b1); -} - } } diff --git a/src/symfunc/Fccubic.h b/src/symfunc/Fccubic.h new file mode 100644 index 0000000000..6d8052c748 --- /dev/null +++ b/src/symfunc/Fccubic.h @@ -0,0 +1,118 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2014-2020 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_symfunc_Fccubic_h +#define __PLUMED_symfunc_Fccubic_h +#include "function/FunctionSetup.h" + +#include +#include + +namespace PLMD { +namespace symfunc { + +template +struct Fccubic { + using precision=T; + precision alpha; + precision a1; + precision b1; + static void registerKeywords( Keywords& keys ); + static void read( Fccubic& func, + ActionWithArguments* action, + function::FunctionOptions& funcout ); + static void calc( const Fccubic& func, + bool noderiv, + View args, + function::FunctionOutput& funcout ); + +#ifdef __PLUMED_HAS_OPENACC + void toACCDevice() const { +#pragma acc enter data copyin(this[0:1], alpha,a1,b1) + } + void removeFromACCDevice() const { +#pragma acc exit data delete(b1,a1,alpha,this[0:1]) + } +#endif // __PLUMED_HAS_OPENACC +}; + +template +void Fccubic::registerKeywords( Keywords& keys ) { + keys.add("compulsory","ALPHA","3.0", + "The alpha parameter of the angular function"); + keys.setValueDescription("matrix", + "a function that measures the similarity with an fcc environment"); +} + +template +void Fccubic::read( Fccubic& func, + ActionWithArguments* action, + function::FunctionOptions& funcout ) { + // Scaling factors such that '1' corresponds to fcc lattice + // and '0' corresponds to isotropic (liquid) + action->parse("ALPHA",func.alpha); + func.a1 = 80080. / (2717. + 16*func.alpha); + func.b1 = 16.*(func.alpha-143)/(2717+16*func.alpha); + action->log.printf(" setting alpha paramter equal to %f \n",func.alpha); +} + +template +void Fccubic::calc( const Fccubic& func, + bool noderiv, + const View args, + function::FunctionOutput& funcout ) { + precision x2 = args[0]*args[0]; + precision x4 = x2*x2; + + precision y2 = args[1]*args[1]; + precision y4 = y2*y2; + + precision z2 = args[2]*args[2]; + precision z4 = z2*z2; + + precision d2 = x2 + y2 + z2; + if( d2 < epsilon ) { + d2 = 1; + } + precision r8 = pow( d2, 4 ); + precision r12 = pow( d2, 6 ); + + precision tmp = ((x4*y4)+(x4*z4)+(y4*z4))/r8-func.alpha*x4*y4*z4/r12; + + precision t0 = (x2*y4+x2*z4)/r8-func.alpha*x2*y4*z4/r12; + precision t1 = (y2*x4+y2*z4)/r8-func.alpha*y2*x4*z4/r12; + precision t2 = (z2*x4+z2*y4)/r8-func.alpha*z2*x4*y4/r12; + precision t3 = (2*tmp-func.alpha*x4*y4*z4/r12)/d2; + + if( !noderiv ) { + funcout.derivs[0][0]=4*func.a1*args[0]*(t0-t3); + funcout.derivs[0][1]=4*func.a1*args[1]*(t1-t3); + funcout.derivs[0][2]=4*func.a1*args[2]*(t2-t3); + } + + // Set the value and the derivatives + funcout.values[0] = (func.a1*tmp+func.b1); +} + +} +} + +#endif //__PLUMED_symfunc_Fccubic_h diff --git a/src/symfunc/SphericalHarmonic.cpp b/src/symfunc/SphericalHarmonic.cpp index 7ac220dabc..b88bfd6e5a 100644 --- a/src/symfunc/SphericalHarmonic.cpp +++ b/src/symfunc/SphericalHarmonic.cpp @@ -19,15 +19,11 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC -#include "function/FunctionSetup.h" +#include "SphericalHarmonic.h" #include "function/FunctionShortcut.h" #include "function/FunctionOfMatrix.h" #include "core/ActionRegister.h" -#include namespace PLMD { namespace symfunc { @@ -92,336 +88,11 @@ This function is used in the calculation of the Steinhardt order parameters, whi */ //+ENDPLUMEDOC -class SphericalHarmonic { - int tmom=0; - std::vector coeff_poly_v{}; - std::vector normaliz_v{}; - double *coeff_poly=nullptr; - double *normaliz=nullptr; -public: - static void registerKeywords( Keywords& keys ); - static unsigned factorial( unsigned n ); - static void read( SphericalHarmonic& func, - ActionWithArguments* action, - function::FunctionOptions& options ); - static void calc( const SphericalHarmonic& func, - bool noderiv, - View args, - function::FunctionOutput funcout ); - double deriv_poly( unsigned m, - double val, - double& df ) const; - static inline void addVectorDerivatives( unsigned ival, - const Vector& der, - View2D derivatives ); - void update() { - coeff_poly = coeff_poly_v.data(); - normaliz = normaliz_v.data(); - } - SphericalHarmonic() = default; - ~SphericalHarmonic() = default; - SphericalHarmonic(const SphericalHarmonic&x): - tmom(x.tmom), - coeff_poly_v(x.coeff_poly_v), - normaliz_v(x.normaliz_v) { - update(); - } - SphericalHarmonic(SphericalHarmonic&&x): - tmom(x.tmom), - coeff_poly_v(std::move(x.coeff_poly_v)), - normaliz_v(std::move(x.normaliz_v)) { - update(); - } - SphericalHarmonic &operator=(const SphericalHarmonic&x) { - if (this!=&x) { - tmom=x.tmom; - coeff_poly_v=x.coeff_poly_v; - normaliz_v=x.normaliz_v; - update(); - } - return *this; - } - SphericalHarmonic &operator=(SphericalHarmonic&&x) { - if (this!=&x) { - tmom=x.tmom; - coeff_poly_v=std::move(x.coeff_poly_v); - normaliz_v=std::move(x.normaliz_v); - update(); - } - return *this; - } -#ifdef __PLUMED_USE_OPENACC - void toACCDevice() const { - const auto num=tmom+1; -#pragma acc enter data copyin(this[0:1], \ - tmom, coeff_poly[0:num], normaliz[0:num]) - } - void removeFromACCDevice() const { - const auto num=tmom+1; -#pragma acc exit data delete(normaliz[0:num], \ - coeff_poly[0:num], tmom, this[0:1]) - } -#endif // __PLUMED_USE_OPENACC -}; - typedef function::FunctionShortcut SpHarmShortcut; PLUMED_REGISTER_ACTION(SpHarmShortcut,"SPHERICAL_HARMONIC") typedef function::FunctionOfMatrix MatrixSpHarm; PLUMED_REGISTER_ACTION(MatrixSpHarm,"SPHERICAL_HARMONIC_MATRIX") -void SphericalHarmonic::registerKeywords( Keywords& keys ) { - keys.add("compulsory","L","the value of the angular momentum"); - keys.addOutputComponent("rm","default", - "matrix","the real parts of the spherical harmonic values with the m value given"); - keys.addOutputComponent("im","default", - "matrix","the real parts of the spherical harmonic values with the m value given"); - keys.add("hidden","MASKED_INPUT_ALLOWED", - "turns on that you are allowed to use masked inputs"); -} - -unsigned SphericalHarmonic::factorial( unsigned n ) { - return (n == 1 || n == 0) ? 1 : factorial(n - 1) * n; -} - -void SphericalHarmonic::read( SphericalHarmonic& func, - ActionWithArguments* action, - function::FunctionOptions& options ) { - action->parse("L",func.tmom); - action->log.printf(" calculating %dth order spherical harmonic with %s, %s and %s as input \n", - func.tmom, - action->getPntrToArgument(0)->getName().c_str(), - action->getPntrToArgument(1)->getName().c_str(), - action->getPntrToArgument(2)->getName().c_str() ); - if( action->getNumberOfArguments()==4 ) { - action->log.printf(" multiplying cylindrical harmonic by weight from %s \n", - action->getPntrToArgument(3)->getName().c_str() ); - } - - func.normaliz_v.resize( func.tmom+1 ); - func.coeff_poly_v.resize( func.tmom+1 ); - func.update(); - - for(int i=0; i<=func.tmom; ++i) { - func.normaliz[i] = ( i%2==0 ? 1.0 : -1.0 ) - * sqrt( (2*func.tmom+1) - * factorial(func.tmom-i) - /(4*PLMD::pi*factorial(func.tmom+i)) ); - } - - switch (func.tmom) { - case 1: - // Legendre polynomial coefficients of order one - func.coeff_poly[0]=0; - func.coeff_poly[1]=1.0; - break; - case 2: - // Legendre polynomial coefficients of order two - func.coeff_poly[0]=-0.5; - func.coeff_poly[1]=0.0; - func.coeff_poly[2]=1.5; - break; - case 3: - // Legendre polynomial coefficients of order three - func.coeff_poly[0]=0.0; - func.coeff_poly[1]=-1.5; - func.coeff_poly[2]=0.0; - func.coeff_poly[3]=2.5; - break; - case 4: - // Legendre polynomial coefficients of order four - func.coeff_poly[0]=0.375; - func.coeff_poly[1]=0.0; - func.coeff_poly[2]=-3.75; - func.coeff_poly[3]=0.0; - func.coeff_poly[4]=4.375; - break; - case 5: - // Legendre polynomial coefficients of order five - func.coeff_poly[0]=0.0; - func.coeff_poly[1]=1.875; - func.coeff_poly[2]=0.0; - func.coeff_poly[3]=-8.75; - func.coeff_poly[4]=0.0; - func.coeff_poly[5]=7.875; - break; - case 6: - // Legendre polynomial coefficients of order six - func.coeff_poly[0]=-0.3125; - func.coeff_poly[1]=0.0; - func.coeff_poly[2]=6.5625; - func.coeff_poly[3]=0.0; - func.coeff_poly[4]=-19.6875; - func.coeff_poly[5]=0.0; - func.coeff_poly[6]=14.4375; - break; - default: - action->error("Insert Legendre polynomial coefficients into SphericalHarmonics code"); - } - - std::string num; - for(int i=-func.tmom; i<=func.tmom; ++i) { - Tools::convert(std::abs(i),num); - if( i<0 ) { - options.multipleValuesForEachRegisteredComponent.push_back( "-n" + num ); - } else if( i>0 ) { - options.multipleValuesForEachRegisteredComponent.push_back( "-p" + num ); - } else { - options.multipleValuesForEachRegisteredComponent.push_back( "-0"); - } - } - options.derivativeZeroIfValueIsZero = (action->getNumberOfArguments()==4 - && action->getPntrToArgument(3) - ->isDerivativeZeroWhenValueIsZero() ); -} - -void SphericalHarmonic::calc( const SphericalHarmonic& func, - bool noderiv, - const View args, - function::FunctionOutput funcout ) { - double weight=1; - if( args.size()==4 ) { - weight = args[3]; - } - if( weight com1( args[0]*dleninv, args[1]*dleninv ); - std::complex powered(1.0, 0.0); - constexpr std::complex ii(0.0, 1.0); - std::complex dp_x; - std::complex dp_y; - std::complex dp_z; - Vector myrealvec; - Vector myimagvec; - Vector real_dz; - Vector imag_dz; - // Do stuff for all other m values - const unsigned imbase = 3*func.tmom+1; - double pref = -1.0; - for(int m=1; m<=func.tmom; ++m) { - // Calculate Legendre Polynomial - poly_ass=func.deriv_poly( m, args[2]*dleninv, dpoly_ass ); - // Real and imaginary parts of z - double real_z = real(com1*powered); - double imag_z = imag(com1*powered); - - // Calculate steinhardt parameter - double tq6 =poly_ass*real_z; // Real part of steinhardt parameter - double itq6=poly_ass*imag_z; // Imaginary part of steinhardt parameter - - // Real part - funcout.values[func.tmom + m] = weight* tq6; - // Imaginary part - funcout.values[imbase + m] = weight*itq6; - // Store -m part of vector - // -m part of vector is just +m part multiplied by (-1.0)**m and multiplied by complex - // conjugate of Legendre polynomial - // Real part - funcout.values[func.tmom - m] = pref*funcout.values[func.tmom+m]; - // Imaginary part - funcout.values[imbase - m] = -pref*funcout.values[imbase + m]; - if( !noderiv ) { - // Derivatives wrt ( x/r + iy )^m - double md=static_cast(m); - dp_x = md*powered*( (1.0*dleninv)-(args[0]*args[0])*dlen3inv-ii*(args[0]*args[1])*dlen3inv ); - dp_y = md*powered*( ii*(1.0*dleninv)-(args[0]*args[1])*dlen3inv-ii*(args[1]*args[1])*dlen3inv ); - dp_z = md*powered*( -(args[0]*args[2])*dlen3inv-ii*(args[1]*args[2])*dlen3inv ); - // Derivatives of real and imaginary parts of above - real_dz[0] = real( dp_x ); - real_dz[1] = real( dp_y ); - real_dz[2] = real( dp_z ); - imag_dz[0] = imag( dp_x ); - imag_dz[1] = imag( dp_y ); - imag_dz[2] = imag( dp_z ); - // Complete derivative of steinhardt parameter - myrealvec = weight*(dpoly_ass*real_z*dz + poly_ass*real_dz); - myimagvec = weight*(dpoly_ass*imag_z*dz + poly_ass*imag_dz); - funcout.derivs[func.tmom+m] = myrealvec; - funcout.derivs[imbase +m] = myimagvec; - - funcout.derivs[func.tmom-m] = pref*myrealvec; - funcout.derivs[imbase -m] = -pref*myimagvec; - if( args.size()==4 ) { - funcout.derivs[func.tmom + m][3]= tq6; - funcout.derivs[imbase + m][3]= itq6; - funcout.derivs[func.tmom - m][3]= pref* tq6; - funcout.derivs[imbase - m][3]=-pref*itq6; - } - } - // Calculate next power of complex number - powered *= com1; - //hopefully the compiler will optimize with bitflipping the sign here - pref = -pref; - } -} - -double SphericalHarmonic::deriv_poly( const unsigned m, - const double val, - double& df ) const { - double fact=1.0; - for(unsigned j=2; j<=m; ++j) { - fact *= j; - } - double res=coeff_poly[m]*fact; - - double pow=1.0; - double xi=val; - double dxi=1.0; - df=0.0; - for(int i=m+1; i<=tmom; ++i) { - fact = 1.0; - for(int j=i-m+1; j<=i; ++j) { - fact *= j; - } - res += coeff_poly[i]*fact*xi; - df += pow*coeff_poly[i]*fact*dxi; - xi *= val; - dxi *= val; - pow += 1.0; - } - df *= normaliz[m]; - return normaliz[m]*res; -} - } } diff --git a/src/symfunc/SphericalHarmonic.h b/src/symfunc/SphericalHarmonic.h new file mode 100644 index 0000000000..91dcb14ba8 --- /dev/null +++ b/src/symfunc/SphericalHarmonic.h @@ -0,0 +1,360 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2012-2017 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_symfunc_SphericalHarmonic_h +#define __PLUMED_symfunc_SphericalHarmonic_h +#include "function/FunctionSetup.h" +#include "function/FunctionOfMatrix.h" + +#include + +namespace PLMD { +namespace symfunc { + +class SphericalHarmonic { + int tmom=0; + std::vector coeff_poly_v{}; + std::vector normaliz_v{}; + double *coeff_poly=nullptr; + double *normaliz=nullptr; +public: + static void registerKeywords( Keywords& keys ); + static unsigned factorial( unsigned n ); + static void read( SphericalHarmonic& func, + ActionWithArguments* action, + function::FunctionOptions& options ); + static void calc( const SphericalHarmonic& func, + bool noderiv, + View args, + function::FunctionOutput funcout ); + double deriv_poly( unsigned m, + double val, + double& df ) const; + static inline void addVectorDerivatives( unsigned ival, + const Vector& der, + View2D derivatives ); + void update() { + coeff_poly = coeff_poly_v.data(); + normaliz = normaliz_v.data(); + } + SphericalHarmonic() = default; + ~SphericalHarmonic() = default; + SphericalHarmonic(const SphericalHarmonic&x): + tmom(x.tmom), + coeff_poly_v(x.coeff_poly_v), + normaliz_v(x.normaliz_v) { + update(); + } + SphericalHarmonic(SphericalHarmonic&&x): + tmom(x.tmom), + coeff_poly_v(std::move(x.coeff_poly_v)), + normaliz_v(std::move(x.normaliz_v)) { + update(); + } + SphericalHarmonic &operator=(const SphericalHarmonic&x) { + if (this!=&x) { + tmom=x.tmom; + coeff_poly_v=x.coeff_poly_v; + normaliz_v=x.normaliz_v; + update(); + } + return *this; + } + SphericalHarmonic &operator=(SphericalHarmonic&&x) { + if (this!=&x) { + tmom=x.tmom; + coeff_poly_v=std::move(x.coeff_poly_v); + normaliz_v=std::move(x.normaliz_v); + update(); + } + return *this; + } +#ifdef __PLUMED_HAS_OPENACC + void toACCDevice() const { + const auto num=tmom+1; +#pragma acc enter data copyin(this[0:1], \ + tmom, coeff_poly[0:num], normaliz[0:num]) + } + void removeFromACCDevice() const { + const auto num=tmom+1; +#pragma acc exit data delete(normaliz[0:num], \ + coeff_poly[0:num], tmom, this[0:1]) + } +#endif // __PLUMED_HAS_OPENACC +}; + +void SphericalHarmonic::registerKeywords( Keywords& keys ) { + keys.add("compulsory","L","the value of the angular momentum"); + keys.addOutputComponent("rm","default", + "matrix","the real parts of the spherical harmonic values with the m value given"); + keys.addOutputComponent("im","default", + "matrix","the real parts of the spherical harmonic values with the m value given"); + keys.add("hidden","MASKED_INPUT_ALLOWED", + "turns on that you are allowed to use masked inputs"); +} + +unsigned SphericalHarmonic::factorial( unsigned n ) { + return (n == 1 || n == 0) ? 1 : factorial(n - 1) * n; +} + +void SphericalHarmonic::read( SphericalHarmonic& func, + ActionWithArguments* action, + function::FunctionOptions& options ) { + action->parse("L",func.tmom); + action->log.printf(" calculating %dth order spherical harmonic with %s, %s and %s as input \n", + func.tmom, + action->getPntrToArgument(0)->getName().c_str(), + action->getPntrToArgument(1)->getName().c_str(), + action->getPntrToArgument(2)->getName().c_str() ); + if( action->getNumberOfArguments()==4 ) { + action->log.printf(" multiplying cylindrical harmonic by weight from %s \n", + action->getPntrToArgument(3)->getName().c_str() ); + } + + func.normaliz_v.resize( func.tmom+1 ); + func.coeff_poly_v.resize( func.tmom+1 ); + func.update(); + + for(decltype(func.tmom) i=0; i<=func.tmom; ++i) { + func.normaliz[i] = ( i%2==0 ? 1.0 : -1.0 ) + * sqrt( (2*func.tmom+1) + * factorial(func.tmom-i) + /(4*PLMD::pi*factorial(func.tmom+i)) ); + } + + switch (func.tmom) { + case 1: + // Legendre polynomial coefficients of order one + func.coeff_poly[0]=0; + func.coeff_poly[1]=1.0; + break; + case 2: + // Legendre polynomial coefficients of order two + func.coeff_poly[0]=-0.5; + func.coeff_poly[1]=0.0; + func.coeff_poly[2]=1.5; + break; + case 3: + // Legendre polynomial coefficients of order three + func.coeff_poly[0]=0.0; + func.coeff_poly[1]=-1.5; + func.coeff_poly[2]=0.0; + func.coeff_poly[3]=2.5; + break; + case 4: + // Legendre polynomial coefficients of order four + func.coeff_poly[0]=0.375; + func.coeff_poly[1]=0.0; + func.coeff_poly[2]=-3.75; + func.coeff_poly[3]=0.0; + func.coeff_poly[4]=4.375; + break; + case 5: + // Legendre polynomial coefficients of order five + func.coeff_poly[0]=0.0; + func.coeff_poly[1]=1.875; + func.coeff_poly[2]=0.0; + func.coeff_poly[3]=-8.75; + func.coeff_poly[4]=0.0; + func.coeff_poly[5]=7.875; + break; + case 6: + // Legendre polynomial coefficients of order six + func.coeff_poly[0]=-0.3125; + func.coeff_poly[1]=0.0; + func.coeff_poly[2]=6.5625; + func.coeff_poly[3]=0.0; + func.coeff_poly[4]=-19.6875; + func.coeff_poly[5]=0.0; + func.coeff_poly[6]=14.4375; + break; + default: + action->error("Insert Legendre polynomial coefficients into SphericalHarmonics code"); + } + + std::string num; + for(int i=-func.tmom; i<=func.tmom; ++i) { + Tools::convert(abs(i),num); + if( i<0 ) { + options.multipleValuesForEachRegisteredComponent.push_back( "-n" + num ); + } else if( i>0 ) { + options.multipleValuesForEachRegisteredComponent.push_back( "-p" + num ); + } else { + options.multipleValuesForEachRegisteredComponent.push_back( "-0"); + } + } + options.derivativeZeroIfValueIsZero = (action->getNumberOfArguments()==4 + && action->getPntrToArgument(3) + ->isDerivativeZeroWhenValueIsZero() ); +} + +void SphericalHarmonic::calc( const SphericalHarmonic& func, + bool noderiv, + const View args, + function::FunctionOutput funcout ) { + double weight=1; + if( args.size()==4 ) { + weight = args[3]; + } + if( weight com1( args[0]*dleninv, args[1]*dleninv ); + std::complex powered(1.0, 0.0); + constexpr std::complex ii(0.0, 1.0); + std::complex dp_x; + std::complex dp_y; + std::complex dp_z; + Vector myrealvec; + Vector myimagvec; + Vector real_dz; + Vector imag_dz; + // Do stuff for all other m values + const unsigned imbase = 3*func.tmom+1; + double pref = -1.0; + for(decltype(func.tmom) m=1; m<=func.tmom; ++m) { + // Calculate Legendre Polynomial + poly_ass=func.deriv_poly( m, args[2]*dleninv, dpoly_ass ); + // Real and imaginary parts of z + double real_z = real(com1*powered); + double imag_z = imag(com1*powered); + + // Calculate steinhardt parameter + double tq6 =poly_ass*real_z; // Real part of steinhardt parameter + double itq6=poly_ass*imag_z; // Imaginary part of steinhardt parameter + + // Real part + funcout.values[func.tmom + m] = weight* tq6; + // Imaginary part + funcout.values[imbase + m] = weight*itq6; + // Store -m part of vector + // -m part of vector is just +m part multiplied by (-1.0)**m and multiplied by complex + // conjugate of Legendre polynomial + // Real part + funcout.values[func.tmom - m] = pref*funcout.values[func.tmom+m]; + // Imaginary part + funcout.values[imbase - m] = -pref*funcout.values[imbase + m]; + if( !noderiv ) { + // Derivatives wrt ( x/r + iy )^m + double md=static_cast(m); + dp_x = md*powered*( (1.0*dleninv)-(args[0]*args[0])*dlen3inv-ii*(args[0]*args[1])*dlen3inv ); + dp_y = md*powered*( ii*(1.0*dleninv)-(args[0]*args[1])*dlen3inv-ii*(args[1]*args[1])*dlen3inv ); + dp_z = md*powered*( -(args[0]*args[2])*dlen3inv-ii*(args[1]*args[2])*dlen3inv ); + // Derivatives of real and imaginary parts of above + real_dz[0] = real( dp_x ); + real_dz[1] = real( dp_y ); + real_dz[2] = real( dp_z ); + imag_dz[0] = imag( dp_x ); + imag_dz[1] = imag( dp_y ); + imag_dz[2] = imag( dp_z ); + // Complete derivative of steinhardt parameter + myrealvec = weight*(dpoly_ass*real_z*dz + poly_ass*real_dz); + myimagvec = weight*(dpoly_ass*imag_z*dz + poly_ass*imag_dz); + funcout.derivs[func.tmom+m] = myrealvec; + funcout.derivs[imbase +m] = myimagvec; + + funcout.derivs[func.tmom-m] = pref*myrealvec; + funcout.derivs[imbase -m] = -pref*myimagvec; + if( args.size()==4 ) { + funcout.derivs[func.tmom + m][3]= tq6; + funcout.derivs[imbase + m][3]= itq6; + funcout.derivs[func.tmom - m][3]= pref* tq6; + funcout.derivs[imbase - m][3]=-pref*itq6; + } + } + // Calculate next power of complex number + powered *= com1; + //hopefully the compiler will optimize with bitflipping the sign here + pref = -pref; + } +} + +double SphericalHarmonic::deriv_poly( const unsigned m, + const double val, + double& df ) const { + double fact=1.0; + for(unsigned j=2; j<=m; ++j) { + fact *= j; + } + double res=coeff_poly[m]*fact; + + double pow=1.0; + double xi=val; + double dxi=1.0; + df=0.0; + for(int i=m+1; i<=tmom; ++i) { + fact = 1.0; + for(int j=i-m+1; j<=i; ++j) { + fact *= j; + } + res += coeff_poly[i]*fact*xi; + df += pow*coeff_poly[i]*fact*dxi; + xi *= val; + dxi *= val; + pow += 1.0; + } + df *= normaliz[m]; + return normaliz[m]*res; +} + +} +} + +#endif //__PLUMED_symfunc_SphericalHarmonic_h diff --git a/src/symfunc/ThreeBodyGFunctions.cpp b/src/symfunc/ThreeBodyGFunctions.cpp index 8420512df0..43cfedf35b 100644 --- a/src/symfunc/ThreeBodyGFunctions.cpp +++ b/src/symfunc/ThreeBodyGFunctions.cpp @@ -164,6 +164,8 @@ class ThreeBodyGFunctions : public ActionWithVector { public: using input_type = ThreeBodyGFunctionsInput; using PTM = ParallelTaskManager; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; private: PTM taskmanager; public: diff --git a/src/tools/Angle.cpp b/src/tools/Angle.cpp index 466fb25d86..f76000a330 100644 --- a/src/tools/Angle.cpp +++ b/src/tools/Angle.cpp @@ -20,49 +20,3 @@ along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ #include "Angle.h" -#include "Tools.h" -#include - -namespace PLMD { - -double Angle::compute(const Vector& v1,const Vector& v2)const { - return std::acos(dotProduct(v1,v2)/(v1.modulo()*v2.modulo())); -} - -double Angle::compute(const Vector& v1,const Vector& v2,Vector& d1,Vector& d2)const { - const double dp(dotProduct(v1,v2)); - const Vector& dp_dv1(v2); - const Vector& dp_dv2(v1); - const double sv1(v1.modulo2()); - const double sv2(v2.modulo2()); - const Vector dsv1_dv1(2*v1); - const Vector dsv2_dv2(2*v2); - const double nn(1.0/std::sqrt(sv1*sv2)); - const Vector dnn_dv1(-0.5*nn/sv1*dsv1_dv1); - const Vector dnn_dv2(-0.5*nn/sv2*dsv2_dv2); - - const double dpnn(dp*nn); - - if(dpnn>=1.0-epsilon) { - d1=Vector(0.0,0.0,0.0); - d2=Vector(0.0,0.0,0.0); - return 0.0; - } - if(dpnn<=-1.0+epsilon) { - d1=Vector(0.0,0.0,0.0); - d2=Vector(0.0,0.0,0.0); - return pi; - } - const Vector ddpnn_dv1(dp*dnn_dv1+dp_dv1*nn); - const Vector ddpnn_dv2(dp*dnn_dv2+dp_dv2*nn); - - const double x(-1.0/std::sqrt(1-dpnn*dpnn)); - - d1=x*ddpnn_dv1; - d2=x*ddpnn_dv2; - - - return std::acos(dpnn); -} - -} diff --git a/src/tools/Angle.h b/src/tools/Angle.h index a05a53e69c..5e8d8348f5 100644 --- a/src/tools/Angle.h +++ b/src/tools/Angle.h @@ -23,6 +23,8 @@ #define __PLUMED_tools_Angle_h #include "Vector.h" +#include "Tools.h" +#include namespace PLMD { @@ -40,11 +42,51 @@ class Angle { // still empty, but may accommodate some options in the future public: /// Compute the angle between vectors v1 and v2 -#pragma acc routine seq - double compute(const Vector& v1,const Vector& v2)const; + template + static T compute(const VectorTyped v1,const VectorTyped v2) { + return std::acos(dotProduct(v1,v2)/(v1.modulo()*v2.modulo())); + } /// Compute the angle between vectors v1 and v2 and its derivatives wrt v1 and v2 -#pragma acc routine seq - double compute(const Vector& v1,const Vector& v2,Vector& d1,Vector& d2)const; + template + static T compute(const VectorTyped v1, + const VectorTyped v2, + VectorTyped& d1, + VectorTyped& d2) { + using V3=VectorTyped; + const T dp(dotProduct(v1,v2)); + const V3& dp_dv1(v2); + const V3& dp_dv2(v1); + const T sv1(v1.modulo2()); + const T sv2(v2.modulo2()); + const V3 dsv1_dv1(2*v1); + const V3 dsv2_dv2(2*v2); + const T nn(1.0/std::sqrt(sv1*sv2)); + const V3 dnn_dv1(-0.5*nn/sv1*dsv1_dv1); + const V3 dnn_dv2(-0.5*nn/sv2*dsv2_dv2); + + const T dpnn(dp*nn); + if(dpnn>=1.0-epsilon) { + d1=V3(0.0,0.0,0.0); + d2=V3(0.0,0.0,0.0); + return 0.0; + } + if(dpnn<=-1.0+epsilon) { + d1=V3(0.0,0.0,0.0); + d2=V3(0.0,0.0,0.0); + return pi; + } + const V3 ddpnn_dv1(dp*dnn_dv1+dp_dv1*nn); + const V3 ddpnn_dv2(dp*dnn_dv2+dp_dv2*nn); + + const T x(-1.0/std::sqrt(1-dpnn*dpnn)); + + d1=x*ddpnn_dv1; + d2=x*ddpnn_dv2; + + + return std::acos(dpnn); + } + }; } diff --git a/src/tools/ColvarOutput.cpp b/src/tools/ColvarOutput.cpp index e21a82d118..67ae15abd1 100644 --- a/src/tools/ColvarOutput.cpp +++ b/src/tools/ColvarOutput.cpp @@ -20,16 +20,8 @@ along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ #include "ColvarOutput.h" -#include "core/Colvar.h" namespace PLMD { -ColvarOutput ColvarOutput::createColvarOutput( std::vector& v, - std::vector& d, - Colvar* action ) { - View val(v.data(),v.size()); - d.resize( action->getNumberOfComponents()*action->getNumberOfDerivatives() ); - return ColvarOutput( val, action->getNumberOfDerivatives(), d.data() ); -} } // namespace PLMD diff --git a/src/tools/ColvarOutput.h b/src/tools/ColvarOutput.h index 270e112766..4e0d052da2 100644 --- a/src/tools/ColvarOutput.h +++ b/src/tools/ColvarOutput.h @@ -29,20 +29,20 @@ #include "View2D.h" #include "Vector.h" #include "Tensor.h" +#include "core/Colvar.h" namespace PLMD { -class Colvar; - +template class ColvarOutput { private: class DerivHelper { private: std::size_t nderivPerComponent; - double* derivatives; + T* derivatives; public: - DerivHelper(double* d, std::size_t n ) : nderivPerComponent(n), derivatives(d) {} - View2D operator[](std::size_t i) { + DerivHelper(T* d, std::size_t n ) : nderivPerComponent(n), derivatives(d) {} + View2D operator[](std::size_t i) { //the -9 is to "exclude" the virial (even if tecnically is still accessible) return { derivatives + i*nderivPerComponent, nderivPerComponent-9 }; } @@ -52,18 +52,18 @@ class ColvarOutput { return Vector( derivatives[base], derivatives[base+1], derivatives[base+2] ); } - View getView( std::size_t valueID, std::size_t atomID) { + View getView( std::size_t valueID, std::size_t atomID) { std::size_t base = valueID*nderivPerComponent + 3*atomID; - return View { derivatives +base}; + return View { derivatives +base}; } }; public: class VirialHelper { private: std::size_t nderivPerComponent; - double* derivatives; + T* derivatives; public: - VirialHelper(double* d, std::size_t n ) : nderivPerComponent(n), derivatives(d) {} + VirialHelper(T* d, std::size_t n ) : nderivPerComponent(n), derivatives(d) {} Tensor operator[](std::size_t i) const { std::size_t n=(i+1)*nderivPerComponent; return Tensor( derivatives[n-9], @@ -76,9 +76,9 @@ class ColvarOutput { derivatives[n-2], derivatives[n-1] ); } - View getView(std::size_t i) const { + View getView(std::size_t i) const { std::size_t n=(i+1)*nderivPerComponent-9; - return View {derivatives+n}; + return View {derivatives+n}; } void set( std::size_t i, const Tensor& v ) { std::size_t n=(i+1)*nderivPerComponent; @@ -94,18 +94,18 @@ class ColvarOutput { } }; std::size_t ncomponents; - View values; + View values; DerivHelper derivs; VirialHelper virial; - ColvarOutput( View v, std::size_t nderivPerComponent, double *derivatives ): + ColvarOutput( View v, std::size_t nderivPerComponent, T *derivatives ): ncomponents(v.size()), values(v), derivs(derivatives,nderivPerComponent), virial(derivatives,nderivPerComponent) {} - static ColvarOutput createColvarOutput( std::vector& v, - std::vector& d, + static ColvarOutput createColvarOutput( std::vector& v, + std::vector& d, Colvar* action ); Vector getAtomDerivatives( std::size_t i, std::size_t a ) { @@ -113,6 +113,14 @@ class ColvarOutput { } }; +template +ColvarOutput ColvarOutput::createColvarOutput( std::vector& v, + std::vector& d, + Colvar* action ) { + View val(v.data(),v.size()); + d.resize( action->getNumberOfComponents()*action->getNumberOfDerivatives() ); + return ColvarOutput( val, action->getNumberOfDerivatives(), d.data() ); +} } //namespace PLMD #endif // __PLUMED_tools_ColvarOutput_h diff --git a/src/tools/Pbc.cpp b/src/tools/Pbc.cpp index 7f5cd7dc3d..9842d3eefc 100644 --- a/src/tools/Pbc.cpp +++ b/src/tools/Pbc.cpp @@ -414,13 +414,75 @@ Vector Pbc::distance(const Vector&v1,const Vector&v2)const { return d; } +Vector3f Pbc::distance(const Vector3f&v1,const Vector3f&v2)const { + Vector3f d=delta(v1,v2); + if(type==unset) { + // do nothing + } else if(type==orthorombic) { +#ifdef __PLUMED_PBC_WHILE + for(unsigned i=0; i<3; i++) { + while(d[i]>hdiag[i]) { + d[i]-=diag[i]; + } + while(d[i]<=mdiag[i]) { + d[i]+=diag[i]; + } + } +#else + for(int i=0; i<3; i++) { + d[i]=Tools::pbc(d[i]*invBox(i,i))*box(i,i); + } +#endif + } else if(type==generic) { + Vector3f s=matmul(d,invReduced); +// check if images have to be computed: +// if((std::fabs(s[0])+std::fabs(s[1])+std::fabs(s[2])>0.5)){ +// NOTICE: the check in the previous line, albeit correct, is breaking many regtest +// since it does not apply Tools::pbc in many cases. Moreover, it does not +// introduce a significant gain. I thus leave it out for the moment. + if constexpr (true) { +// bring to -0.5,+0.5 region in scaled coordinates: + for(int i=0; i<3; i++) { + s[i]=Tools::pbc(s[i]); + } + d=matmul(s,reduced); +// check if shifts have to be attempted: + if((std::fabs(s[0])+std::fabs(s[1])+std::fabs(s[2])>0.5)) { +// list of shifts is specific for that "octant" (depends on signs of s[i]): + const auto & myshifts(shifts[(s[0]>0?1:0)][(s[1]>0?1:0)][(s[2]>0?1:0)]); + Vector3f best(d); + double lbest(modulo2(best)); +// loop over possible shifts: + for(unsigned i=0; i(); +} + Vector Pbc::scaledToReal(const Vector&d)const { return matmul(box.transpose(),d); } +Vector3f Pbc::scaledToReal(const Vector3f&d)const { + return matmul(box.transpose(),d).convert(); +} bool Pbc::isOrthorombic()const { return type==orthorombic; diff --git a/src/tools/Pbc.h b/src/tools/Pbc.h index 9604235faa..da8cf05c63 100644 --- a/src/tools/Pbc.h +++ b/src/tools/Pbc.h @@ -93,6 +93,8 @@ class Pbc { /// if specified, also returns the number of attempted shifts #pragma acc routine seq Vector distance(const Vector&, const Vector&)const; +#pragma acc routine seq + Vector3f distance(const Vector3f&, const Vector3f&)const; /// Computes v2-v1, using minimal image convention /// if specified, also returns the number of attempted shifts Vector distance(const Vector&, const Vector&,int*nshifts)const; @@ -115,10 +117,14 @@ class Pbc { /// Thus:pbc.realToScaled(v) == matmul(transpose(inverse(pbc.getBox(),v))); #pragma acc routine seq Vector realToScaled(const Vector&)const; +#pragma acc routine seq + Vector3f realToScaled(const Vector3f&)const; /// Transform a vector in scaled coordinates to a vector in real space. /// Thus:pbc.scaledToRead(v) == matmul(transpose(pbc.getBox()),v); #pragma acc routine seq Vector scaledToReal(const Vector&)const; +#pragma acc routine seq + Vector3f scaledToReal(const Vector3f&)const; /// Returns true if the box vectors are orthogonal #pragma acc routine seq bool isOrthorombic()const; diff --git a/src/tools/SwitchingFunction.cpp b/src/tools/SwitchingFunction.cpp index 2c5ae3f6e7..be63c37a1d 100644 --- a/src/tools/SwitchingFunction.cpp +++ b/src/tools/SwitchingFunction.cpp @@ -325,6 +325,7 @@ return std::make_unique>>( \ } #undef FIXEDRATIONALENUM } +#undef FIXEDRATIONALENUM //continue with the 'at runtime implementation' auto data = rational::init(D0,DMAX,R0,N,M); if(2*N==M || M == 0) { @@ -366,6 +367,7 @@ return std::pair {switchType::rationalfix##x,Data::init(D0,DMA } #undef FIXEDRATIONALENUM } +#undef FIXEDRATIONALENUM //continue with the 'at runtime implementation' return rational::init(D0,DMAX,R0,N,M); } diff --git a/src/tools/Tools.h b/src/tools/Tools.h index 2c0ab94555..4f3b3f456e 100644 --- a/src/tools/Tools.h +++ b/src/tools/Tools.h @@ -154,7 +154,8 @@ class Tools { /// Remove trailing comments static void trimComments(std::string & s); /// Apply pbc for a unitary cell - static double pbc(double); + template + static double pbc(T); /// Retrieve a key from a vector of options. /// It finds a key starting with "key=" or equal to "key" and copy the /// part after the = on s. E.g.: @@ -542,8 +543,8 @@ bool Tools::parseFlag(std::vector&line,const std::string&key,bool&v } /// beware: this brings any number into a pbc that ranges from -0.5 to 0.5 -inline -double Tools::pbc(double x) { +template +inline double Tools::pbc(T x) { #ifdef __PLUMED_PBC_WHILE while (x>0.5) { x-=1.0; @@ -554,12 +555,12 @@ double Tools::pbc(double x) { return x; #else if constexpr (std::numeric_limits::round_style == std::round_toward_zero) { - constexpr double offset=100.0; - const double y=x+offset; - if(y>=0) { - return y-int(y+0.5); + constexpr T offset=100.0; + x+=offset; + if(x>=0) { + return x-int(x+0.5); } else { - return y-int(y-0.5); + return x-int(x-0.5); } } else if constexpr (std::numeric_limits::round_style == std::round_to_nearest) { return x-int(x); diff --git a/src/tools/Torsion.cpp b/src/tools/Torsion.cpp index e54f711bea..3d813dffda 100644 --- a/src/tools/Torsion.cpp +++ b/src/tools/Torsion.cpp @@ -20,61 +20,4 @@ along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ #include "Torsion.h" -#include "Tensor.h" - -#include -#include - -namespace PLMD { - -double Torsion::compute(const Vector& v1,const Vector& v2,const Vector& v3)const { - const Vector nv2(v2*(1.0/v2.modulo())); - const Vector a(crossProduct(nv2,v1)); - const Vector b(crossProduct(v3,nv2)); - const double cosangle=dotProduct(a,b); - const double sinangle=dotProduct(crossProduct(a,b),nv2); - return std::atan2(-sinangle,cosangle); -} - -double Torsion::compute(const Vector& v1,const Vector& v2,const Vector& v3,Vector& d1,Vector& d2,Vector& d3)const { - - const double modv2(1./v2.modulo()); - const Vector nv2(v2*modv2); - const Tensor dnv2_v2((Tensor::identity()-extProduct(nv2,nv2))*modv2); - - const Vector a(crossProduct(v2,v1)); - const Tensor da_dv2(dcrossDv1(v2,v1)); - const Tensor da_dv1(dcrossDv2(v2,v1)); - const Vector b(crossProduct(v3,v2)); - const Tensor db_dv3(dcrossDv1(v3,v2)); - const Tensor db_dv2(dcrossDv2(v3,v2)); - const double cosangle=dotProduct(a,b); - const Vector dcosangle_dv1=matmul(b,da_dv1); - const Vector dcosangle_dv2=matmul(b,da_dv2) + matmul(a,db_dv2); - const Vector dcosangle_dv3=matmul(a,db_dv3); - - const Vector cab(crossProduct(a,b)); - const Tensor dcab_dv1(matmul(dcrossDv1(a,b),da_dv1)); - const Tensor dcab_dv2(matmul(dcrossDv1(a,b),da_dv2) + matmul(dcrossDv2(a,b),db_dv2)); - const Tensor dcab_dv3(matmul(dcrossDv2(a,b),db_dv3)); - - const double sinangle=dotProduct(cab,nv2); - const Vector dsinangle_dv1=matmul(nv2,dcab_dv1); - const Vector dsinangle_dv2=matmul(nv2,dcab_dv2)+matmul(cab,dnv2_v2); - const Vector dsinangle_dv3=matmul(nv2,dcab_dv3); - - const double torsion=std::atan2(-sinangle,cosangle); -// this is required since v1 and v3 are not normalized: - const double invR2=1.0/(cosangle*cosangle+sinangle*sinangle); - - d1= ( -dsinangle_dv1*cosangle + sinangle * dcosangle_dv1 ) *invR2; - d2= ( -dsinangle_dv2*cosangle + sinangle * dcosangle_dv2 ) *invR2; - d3= ( -dsinangle_dv3*cosangle + sinangle * dcosangle_dv3 ) *invR2; - - return torsion; -} - -} - - diff --git a/src/tools/Torsion.h b/src/tools/Torsion.h index 167de50092..1937371664 100644 --- a/src/tools/Torsion.h +++ b/src/tools/Torsion.h @@ -22,7 +22,7 @@ #ifndef __PLUMED_tools_Torsion_h #define __PLUMED_tools_Torsion_h -#include "Vector.h" +#include "Tensor.h" namespace PLMD { @@ -32,7 +32,7 @@ namespace PLMD { /// is that in the future I would like to extend it to contain options about /// how the calculation should be done. So, for now use it as /// Torsion t; -/// double angle=t.compute(v1,v2,v3); +/// T angle=t.compute(v1,v2,v3); /// I know it is a bit misleading. If we really do not need to store "options" /// inside the Torsion class, we can remove it later and write compute as /// a static function. @@ -43,11 +43,67 @@ class Torsion { /// to v2. To have a "normal" definition (= plumed1), use it as /// compute(r01,r12,r23); /// See ColvarTorsion for a practical usage... -#pragma acc routine seq - double compute(const Vector& v1,const Vector& v2,const Vector& v3)const; + template + static T compute(const VectorTyped& v1, + const VectorTyped& v2, + const VectorTyped& v3) { + using V3=PLMD::VectorTyped; + + const V3 nv2(v2*(1.0/v2.modulo())); + const V3 a(crossProduct(nv2,v1)); + const V3 b(crossProduct(v3,nv2)); + const T cosangle=dotProduct(a,b); + const T sinangle=dotProduct(crossProduct(a,b),nv2); + return std::atan2(-sinangle,cosangle); + } + /// This is the version which also computes the derivatives wrt the arguments. -#pragma acc routine seq - double compute(const Vector& v1,const Vector& v2,const Vector& v3,Vector& d1,Vector& d2,Vector& d3)const; + template + static T compute(const VectorTyped& v1, + const VectorTyped& v2, + const VectorTyped& v3, + VectorTyped& d1, + VectorTyped& d2, + VectorTyped& d3) { + using V3=PLMD::VectorTyped; + using T33=PLMD::TensorTyped; + + const T modv2(T(1.0)/v2.modulo()); + const V3 nv2(v2*modv2); + const T33 dnv2_v2((T33::identity()-extProduct(nv2,nv2))*modv2); + + const V3 a(crossProduct(v2,v1)); + const T33 da_dv2(dcrossDv1(v2,v1)); + const T33 da_dv1(dcrossDv2(v2,v1)); + const V3 b(crossProduct(v3,v2)); + const T33 db_dv3(dcrossDv1(v3,v2)); + const T33 db_dv2(dcrossDv2(v3,v2)); + const T cosangle=dotProduct(a,b); + const V3 dcosangle_dv1=matmul(b,da_dv1); + const V3 dcosangle_dv2=matmul(b,da_dv2) + matmul(a,db_dv2); + const V3 dcosangle_dv3=matmul(a,db_dv3); + + const V3 cab(crossProduct(a,b)); + const T33 dcab_dv1(matmul(dcrossDv1(a,b),da_dv1)); + const T33 dcab_dv2(matmul(dcrossDv1(a,b),da_dv2) + matmul(dcrossDv2(a,b),db_dv2)); + const T33 dcab_dv3(matmul(dcrossDv2(a,b),db_dv3)); + + const T sinangle=dotProduct(cab,nv2); + const V3 dsinangle_dv1=matmul(nv2,dcab_dv1); + const V3 dsinangle_dv2=matmul(nv2,dcab_dv2)+matmul(cab,dnv2_v2); + const V3 dsinangle_dv3=matmul(nv2,dcab_dv3); + + const T torsion=std::atan2(-sinangle,cosangle); +// this is required since v1 and v3 are not normalized: + const T invR2=T(1.0)/(cosangle*cosangle+sinangle*sinangle); + + d1= ( -dsinangle_dv1*cosangle + sinangle * dcosangle_dv1 ) *invR2; + d2= ( -dsinangle_dv2*cosangle + sinangle * dcosangle_dv2 ) *invR2; + d3= ( -dsinangle_dv3*cosangle + sinangle * dcosangle_dv3 ) *invR2; + + return torsion; + } + }; } diff --git a/src/tools/TypeUtils.cpp b/src/tools/TypeUtils.cpp new file mode 100644 index 0000000000..44d26f2d8f --- /dev/null +++ b/src/tools/TypeUtils.cpp @@ -0,0 +1,22 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2012-2025 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#include "TypeUtils.h" diff --git a/src/tools/TypeUtils.h b/src/tools/TypeUtils.h new file mode 100644 index 0000000000..78d3c4b314 --- /dev/null +++ b/src/tools/TypeUtils.h @@ -0,0 +1,32 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2012-2025 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_tools_TypeUtils_h +#define __PLUMED_tools_TypeUtils_h +namespace PLMD { +class Keywords; +// An empty type witha a empty registerKeywords +// This is useful when setting up certains shortcuts (see ANTIBETARMSD for example) +struct Empty { + static void registerKeywords( Keywords& keys ) {} +}; +} //namespace PLMD +#endif // __PLUMED_tools_TypeUtils_h diff --git a/src/volumes/ActionVolume.h b/src/volumes/ActionVolume.h index 14a95c5c54..debe4575f4 100644 --- a/src/volumes/ActionVolume.h +++ b/src/volumes/ActionVolume.h @@ -29,12 +29,12 @@ namespace PLMD { namespace volumes { -template +template struct VolumeData { bool not_in; std::size_t numberOfNonReferenceAtoms; - T voldata; -#ifdef __PLUMED_USE_OPENACC + CV voldata; +#ifdef __PLUMED_HAS_OPENACC void toACCDevice() const { #pragma acc enter data copyin(this[0:1],not_in,numberOfNonReferenceAtoms) voldata.toACCDevice(); @@ -43,37 +43,39 @@ struct VolumeData { voldata.removeFromACCDevice(); #pragma acc exit data delete(numberOfNonReferenceAtoms,not_in,this[0:1]) } -#endif //__PLUMED_USE_OPENACC +#endif //__PLUMED_HAS_OPENACC }; -struct VolumeInput { +template +struct VolumeIn { std::size_t task_index; const Pbc& pbc; - View cpos; - View2D refpos; - VolumeInput( std::size_t t, unsigned nref, double* p, double* rp, const Pbc& box ) : + View cpos; + View2D refpos; + VolumeIn( std::size_t t, unsigned nref, precision* p, precision* rp, const Pbc& box ) : task_index(t),pbc(box),cpos(p),refpos(rp,nref) { } }; -class VolumeOutput { +template +class VolumeOut { private: class RefderHelper { private: - double* derivatives; + precision* derivatives; public: - RefderHelper( double* d ) : derivatives(d) {} - View operator[](std::size_t i) { - return View( derivatives + 3*(i+1) ); + RefderHelper( precision* d ) : derivatives(d) {} + View operator[](std::size_t i) { + return View( derivatives + 3*(i+1) ); } }; - ColvarOutput fulldata; + ColvarOutput fulldata; public: - View& values; - ColvarOutput::VirialHelper& virial; - View derivatives; + View& values; + typename ColvarOutput::VirialHelper& virial; + View derivatives; RefderHelper refders; - VolumeOutput( View& v, std::size_t nder, double* d ) : + VolumeOut( View& v, std::size_t nder, precision* d ) : fulldata(v, nder, d), values(fulldata.values), virial(fulldata.virial), @@ -88,11 +90,15 @@ box. You can use this to calculate the number of atoms inside that part or the a coordination number inside that part of the cell. */ -template +template class ActionVolume : public ActionWithVector { public: - using input_type = VolumeData; - using PTM = ParallelTaskManager>; + using input_type = VolumeData; + using mytype=ActionVolume; + using PTM =typename myPTM::template PTM; + typedef typename PTM::ParallelActionsInput ParallelActionsInput; + typedef typename PTM::ParallelActionsOutput ParallelActionsOutput; + typedef cvprecision_t precision; private: /// The parallel task manager PTM taskmanager; @@ -101,31 +107,40 @@ class ActionVolume : public ActionWithVector { explicit ActionVolume(const ActionOptions&); unsigned getNumberOfDerivatives() override; void getInputData( std::vector& inputdata ) const override ; + void getInputData( std::vector& inputdata ) const override ; void calculate() override ; void applyNonZeroRankForces( std::vector& outforces ) override ; - static void performTask( std::size_t task_index, const VolumeData& actiondata, ParallelActionsInput& input, ParallelActionsOutput& output ); - static void gatherForces( std::size_t task_index, const VolumeData& actiondata, const ParallelActionsInput& input, const ForceInput& fdata, ForceOutput& forces ); - static int getNumberOfValuesPerTask( std::size_t task_index, const VolumeData& actiondata ); - static void getForceIndices( std::size_t task_index, std::size_t colno, std::size_t ntotal_force, const VolumeData& actiondata, const ParallelActionsInput& input, ForceIndexHolder force_indices ); + static void performTask( std::size_t task_index, + const VolumeData& actiondata, + ParallelActionsInput& input, + ParallelActionsOutput& output ); + static int getNumberOfValuesPerTask( std::size_t task_index, + const VolumeData& actiondata ); + static void getForceIndices( std::size_t task_index, + std::size_t colno, + std::size_t ntotal_force, + const VolumeData& actiondata, + const ParallelActionsInput& input, + ForceIndexHolder force_indices ); }; -template -unsigned ActionVolume::getNumberOfDerivatives() { +template +unsigned ActionVolume::getNumberOfDerivatives() { return 3*getNumberOfAtoms()+9; } -template -void ActionVolume::registerKeywords( Keywords& keys ) { +template +void ActionVolume::registerKeywords( Keywords& keys ) { ActionWithVector::registerKeywords( keys ); PTM::registerKeywords( keys ); keys.add("atoms","ATOMS","the group of atoms that you would like to investigate"); keys.addFlag("OUTSIDE",false,"calculate quantities for colvars that are on atoms outside the region of interest"); keys.setValueDescription("scalar/vector","vector of numbers between 0 and 1 that measure the degree to which each atom is within the volume of interest"); - T::registerKeywords( keys ); + CV::registerKeywords( keys ); } -template -ActionVolume::ActionVolume(const ActionOptions&ao): +template +ActionVolume::ActionVolume(const ActionOptions&ao): Action(ao), ActionWithVector(ao), taskmanager(this) { @@ -143,12 +158,12 @@ ActionVolume::ActionVolume(const ActionOptions&ao): shape[0]=atoms.size(); std::vector refatoms; - T::parseAtoms( this, refatoms ); + CV::parseAtoms( this, refatoms ); for(unsigned i=0; i actioninput; + VolumeData actioninput; actioninput.voldata.parseInput(this); actioninput.numberOfNonReferenceAtoms=shape[0]; @@ -166,8 +181,8 @@ ActionVolume::ActionVolume(const ActionOptions&ao): taskmanager.setActionInput( actioninput ); } -template -void ActionVolume::getInputData( std::vector& inputdata ) const { +template +void ActionVolume::getInputData( std::vector& inputdata ) const { if( inputdata.size()!=3*getNumberOfAtoms() ) { inputdata.resize( 3*getNumberOfAtoms() ); } @@ -180,8 +195,22 @@ void ActionVolume::getInputData( std::vector& inputdata ) const { } } -template -void ActionVolume::calculate() { +template +void ActionVolume::getInputData( std::vector& inputdata ) const { + if( inputdata.size()!=3*getNumberOfAtoms() ) { + inputdata.resize( 3*getNumberOfAtoms() ); + } + + for(unsigned i=0; i +void ActionVolume::calculate() { unsigned k=0; std::vector positions( getNumberOfAtoms()-getPntrToComponent(0)->getNumberOfValues() ); for(unsigned i=getPntrToComponent(0)->getNumberOfValues(); i::calculate() { std::vector deriv( getNumberOfDerivatives() ); std::vector val(1); View valview(val.data(),1); - VolumeOutput output( valview, getNumberOfDerivatives(), deriv.data() ); - T::calculateNumberInside( VolumeInput( 0, nref, posvec.data(), posvec.data()+3, getPbc() ), taskmanager.getActionInput().voldata, output ); + VolumeOut output( valview, getNumberOfDerivatives(), deriv.data() ); + CV::calculateNumberInside( VolumeIn( 0, nref, posvec.data(), posvec.data()+3, getPbc() ), + taskmanager.getActionInput().voldata, + output ); if( taskmanager.getActionInput().not_in ) { val[0] = 1.0 - val[0]; for(unsigned i=0; i::calculate() { } } -template -void ActionVolume::applyNonZeroRankForces( std::vector& outforces ) { +template +void ActionVolume::applyNonZeroRankForces( std::vector& outforces ) { taskmanager.applyForces( outforces ); } -template -void ActionVolume::performTask( std::size_t task_index, const VolumeData& actiondata, ParallelActionsInput& input, ParallelActionsOutput& output ) { +template +void ActionVolume::performTask( std::size_t task_index, + const VolumeData& actiondata, + ParallelActionsInput& input, + ParallelActionsOutput& output ) { std::size_t nref = output.derivatives.size()/3 - 4; // This is the number of reference atoms - VolumeOutput volout( output.values, output.derivatives.size(), output.derivatives.data() ); - T::calculateNumberInside( VolumeInput( task_index, nref, input.inputdata+3*task_index, input.inputdata+3*actiondata.numberOfNonReferenceAtoms, *input.pbc ), actiondata.voldata, volout ); + VolumeOut volout( output.values, output.derivatives.size(), output.derivatives.data() ); + CV::calculateNumberInside( VolumeIn( task_index, nref, input.inputdata+3*task_index, input.inputdata+3*actiondata.numberOfNonReferenceAtoms, *input.pbc ), + actiondata.voldata, + volout ); if( actiondata.not_in ) { output.values[0] = 1.0 - output.values[0]; @@ -237,19 +273,19 @@ void ActionVolume::performTask( std::size_t task_index, const VolumeData& } } -template -int ActionVolume::getNumberOfValuesPerTask( std::size_t task_index, - const VolumeData& actiondata ) { +template +int ActionVolume::getNumberOfValuesPerTask( std::size_t task_index, + const VolumeData& actiondata ) { return 1; } -template -void ActionVolume::getForceIndices( std::size_t task_index, - std::size_t colno, - std::size_t ntotal_force, - const VolumeData& actiondata, - const ParallelActionsInput& input, - ForceIndexHolder force_indices ) { +template +void ActionVolume::getForceIndices( std::size_t task_index, + std::size_t colno, + std::size_t ntotal_force, + const VolumeData& actiondata, + const ParallelActionsInput& input, + ForceIndexHolder force_indices ) { std::size_t base = 3*task_index; force_indices.indices[0][0] = base; force_indices.indices[0][1] = base + 1; diff --git a/src/volumes/VolumeAround.cpp b/src/volumes/VolumeAround.cpp index 3a7e65385e..2ef762efe6 100644 --- a/src/volumes/VolumeAround.cpp +++ b/src/volumes/VolumeAround.cpp @@ -19,13 +19,10 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC +#include "VolumeAround.h" #include "core/ActionRegister.h" #include "tools/Pbc.h" #include "tools/HistogramBead.h" -#include "ActionVolume.h" #include "VolumeShortcut.h" //+PLUMEDOC VOLUMES AROUND @@ -251,137 +248,10 @@ PRINT ARG=lessthan,between,morethan FILE=colvar namespace PLMD { namespace volumes { - -class VolumeAround { -public: - bool dox{true}, doy{true}, doz{true}; - double sigma; - double xlow{0.0}, xhigh{0.0}; - double ylow{0.0}, yhigh{0.0}; - double zlow{0.0}, zhigh{0.0}; - HistogramBead::KernelType kerneltype; - static void registerKeywords( Keywords& keys ); - void parseInput( ActionVolume* action ); - void setupRegions( ActionVolume* action, - const Pbc& pbc, - const std::vector& positions ) {} - static void parseAtoms( ActionVolume* action, - std::vector& atom ); - static void calculateNumberInside( const VolumeInput& input, - const VolumeAround& actioninput, - VolumeOutput& output ); -#ifdef __PLUMED_USE_OPENACC - void toACCDevice() const { -#pragma acc enter data copyin(this[0:1],dox,doy,doz,sigma,\ - xlow,xhigh,ylow,yhigh,zlow,zhigh,kerneltype) - } - void removeFromACCDevice() const { -#pragma acc exit data delete(kerneltype,zhigh,zlow,yhigh,ylow,xhigh,xlow,\ - sigma,doz,doy,dox,this[0:1]) - } -#endif //__PLUMED_USE_OPENACC -}; - typedef ActionVolume Vola; PLUMED_REGISTER_ACTION(Vola,"AROUND_CALC") char glob_around[] = "AROUND"; typedef VolumeShortcut VolumeAroundShortcut; PLUMED_REGISTER_ACTION(VolumeAroundShortcut,"AROUND") - -void VolumeAround::registerKeywords( Keywords& keys ) { - keys.setDisplayName("AROUND"); - keys.add("atoms","ORIGIN","the atom whose vicinity we are interested in examining"); - keys.addDeprecatedKeyword("ATOM","ORIGIN"); - keys.add("compulsory","SIGMA","the width of the function to be used for kernel density estimation"); - keys.add("compulsory","KERNEL","gaussian","the type of kernel function to be used"); - keys.add("compulsory","XLOWER","0.0","the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)."); - keys.add("compulsory","XUPPER","0.0","the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)."); - keys.add("compulsory","YLOWER","0.0","the lower boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box)."); - keys.add("compulsory","YUPPER","0.0","the upper boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box)."); - keys.add("compulsory","ZLOWER","0.0","the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)."); - keys.add("compulsory","ZUPPER","0.0","the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)."); -} - -void VolumeAround::parseAtoms( ActionVolume* action, std::vector& atom ) { - action->parseAtomList("ORIGIN",atom); - if( atom.size()==0 ) { - action->parseAtomList("ATOM",atom); - } - if( atom.size()!=1 ) { - action->error("should only be one atom specified"); - } - action->log.printf(" boundaries for region are calculated based on positions of atom : %d\n",atom[0].serial() ); -} - -void VolumeAround::parseInput( ActionVolume* action ) { - action->parse("SIGMA",sigma); - std::string mykerneltype; - action->parse("KERNEL",mykerneltype); - kerneltype=HistogramBead::getKernelType(mykerneltype); - dox=true; - action->parse("XLOWER",xlow); - action->parse("XUPPER",xhigh); - doy=true; - action->parse("YLOWER",ylow); - action->parse("YUPPER",yhigh); - doz=true; - action->parse("ZLOWER",zlow); - action->parse("ZUPPER",zhigh); - if( xlow==0.0 && xhigh==0.0 ) { - dox=false; - } - if( ylow==0.0 && yhigh==0.0 ) { - doy=false; - } - if( zlow==0.0 && zhigh==0.0 ) { - doz=false; - } - if( !dox && !doy && !doz ) { - action->error("no subregion defined use XLOWER, XUPPER, YLOWER, YUPPER, ZLOWER, ZUPPER"); - } - action->log.printf(" boundaries for region (region of interest about atom) : x %f %f, y %f %f, z %f %f \n",xlow,xhigh,ylow,yhigh,zlow,zhigh); -} - -void VolumeAround::calculateNumberInside( const VolumeInput& input, - const VolumeAround& actioninput, - VolumeOutput& output ) { - // Setup the histogram bead - HistogramBead bead(actioninput.kerneltype, actioninput.xlow, actioninput.xhigh, actioninput.sigma ); - - // Calculate position of atom wrt to origin - Vector fpos=input.pbc.distance( Vector(input.refpos[0][0],input.refpos[0][1],input.refpos[0][2]), - Vector(input.cpos[0],input.cpos[1],input.cpos[2]) ); - double xcontr=1.0; - double xder=0.0; - if( actioninput.dox ) { - //bead parameters set in the constructor - xcontr=bead.calculate( fpos[0], xder ); - } - double ycontr=1.0; - double yder=0.0; - if( actioninput.doy ) { - bead.set( actioninput.ylow, actioninput.yhigh, actioninput.sigma ); - ycontr=bead.calculate( fpos[1], yder ); - } - double zcontr=1.0; - double zder=0.0; - if( actioninput.doz ) { - bead.set( actioninput.zlow, actioninput.zhigh, actioninput.sigma ); - zcontr=bead.calculate( fpos[2], zder ); - } - - output.derivatives[0]=xder*ycontr*zcontr; - output.derivatives[1]=xcontr*yder*zcontr; - output.derivatives[2]=xcontr*ycontr*zder; - // Add derivatives wrt to position of origin atom - output.refders[0][0] = -output.derivatives[0]; - output.refders[0][1] = -output.derivatives[1]; - output.refders[0][2] = -output.derivatives[2]; - // Add virial contribution - output.virial.set( 0, -Tensor(fpos, - Vector(output.derivatives[0], output.derivatives[1], output.derivatives[2])) ); - output.values[0] = xcontr*ycontr*zcontr; -} - } } diff --git a/src/volumes/VolumeAround.h b/src/volumes/VolumeAround.h new file mode 100644 index 0000000000..9c12c09990 --- /dev/null +++ b/src/volumes/VolumeAround.h @@ -0,0 +1,167 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2013-2020 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_volumes_VolumeAround_h +#define __PLUMED_volumes_VolumeAround_h +#include "tools/Pbc.h" +#include "tools/HistogramBead.h" +#include "ActionVolume.h" + + +namespace PLMD { +namespace volumes { + +class VolumeAround { +public: + using precision=double; + typedef VolumeIn VolumeInput; + typedef VolumeOut VolumeOutput; + bool dox{true}, doy{true}, doz{true}; + double sigma; + double xlow{0.0}, xhigh{0.0}; + double ylow{0.0}, yhigh{0.0}; + double zlow{0.0}, zhigh{0.0}; + HistogramBead::KernelType kerneltype; + static void registerKeywords( Keywords& keys ); + template + void parseInput( ActionVolume* action ); + template + void setupRegions( ActionVolume* action, + const Pbc& pbc, + const std::vector& positions ) {} + template + static void parseAtoms( ActionVolume* action, + std::vector& atom ); + static void calculateNumberInside( const VolumeInput& input, + const VolumeAround& actioninput, + VolumeOutput& output ); +#ifdef __PLUMED_HAS_OPENACC + void toACCDevice() const { +#pragma acc enter data copyin(this[0:1],dox,doy,doz,sigma,\ + xlow,xhigh,ylow,yhigh,zlow,zhigh,kerneltype) + } + void removeFromACCDevice() const { +#pragma acc exit data delete(kerneltype,zhigh,zlow,yhigh,ylow,xhigh,xlow,\ + sigma,doz,doy,dox,this[0:1]) + } +#endif //__PLUMED_HAS_OPENACC +}; + +void VolumeAround::registerKeywords( Keywords& keys ) { + keys.setDisplayName("AROUND"); + keys.add("atoms","ORIGIN","the atom whose vicinity we are interested in examining"); + keys.addDeprecatedKeyword("ATOM","ORIGIN"); + keys.add("compulsory","SIGMA","the width of the function to be used for kernel density estimation"); + keys.add("compulsory","KERNEL","gaussian","the type of kernel function to be used"); + keys.add("compulsory","XLOWER","0.0","the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)."); + keys.add("compulsory","XUPPER","0.0","the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box)."); + keys.add("compulsory","YLOWER","0.0","the lower boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box)."); + keys.add("compulsory","YUPPER","0.0","the upper boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box)."); + keys.add("compulsory","ZLOWER","0.0","the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)."); + keys.add("compulsory","ZUPPER","0.0","the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box)."); +} + +template +void VolumeAround::parseAtoms( ActionVolume* action, std::vector& atom ) { + action->parseAtomList("ORIGIN",atom); + if( atom.size()==0 ) { + action->parseAtomList("ATOM",atom); + } + if( atom.size()!=1 ) { + action->error("should only be one atom specified"); + } + action->log.printf(" boundaries for region are calculated based on positions of atom : %d\n",atom[0].serial() ); +} + +template +void VolumeAround::parseInput( ActionVolume* action ) { + action->parse("SIGMA",sigma); + std::string mykerneltype; + action->parse("KERNEL",mykerneltype); + kerneltype=HistogramBead::getKernelType(mykerneltype); + dox=true; + action->parse("XLOWER",xlow); + action->parse("XUPPER",xhigh); + doy=true; + action->parse("YLOWER",ylow); + action->parse("YUPPER",yhigh); + doz=true; + action->parse("ZLOWER",zlow); + action->parse("ZUPPER",zhigh); + if( xlow==0.0 && xhigh==0.0 ) { + dox=false; + } + if( ylow==0.0 && yhigh==0.0 ) { + doy=false; + } + if( zlow==0.0 && zhigh==0.0 ) { + doz=false; + } + if( !dox && !doy && !doz ) { + action->error("no subregion defined use XLOWER, XUPPER, YLOWER, YUPPER, ZLOWER, ZUPPER"); + } + action->log.printf(" boundaries for region (region of interest about atom) : x %f %f, y %f %f, z %f %f \n",xlow,xhigh,ylow,yhigh,zlow,zhigh); +} + +void VolumeAround::calculateNumberInside( const VolumeInput& input, + const VolumeAround& actioninput, + VolumeOutput& output ) { + // Setup the histogram bead + HistogramBead bead(actioninput.kerneltype, actioninput.xlow, actioninput.xhigh, actioninput.sigma ); + + // Calculate position of atom wrt to origin + Vector fpos=input.pbc.distance( Vector(input.refpos[0][0],input.refpos[0][1],input.refpos[0][2]), + Vector(input.cpos[0],input.cpos[1],input.cpos[2]) ); + double xcontr=1.0; + double xder=0.0; + if( actioninput.dox ) { + //bead parameters set in the constructor + xcontr=bead.calculate( fpos[0], xder ); + } + double ycontr=1.0; + double yder=0.0; + if( actioninput.doy ) { + bead.set( actioninput.ylow, actioninput.yhigh, actioninput.sigma ); + ycontr=bead.calculate( fpos[1], yder ); + } + double zcontr=1.0; + double zder=0.0; + if( actioninput.doz ) { + bead.set( actioninput.zlow, actioninput.zhigh, actioninput.sigma ); + zcontr=bead.calculate( fpos[2], zder ); + } + + output.derivatives[0]=xder*ycontr*zcontr; + output.derivatives[1]=xcontr*yder*zcontr; + output.derivatives[2]=xcontr*ycontr*zder; + // Add derivatives wrt to position of origin atom + output.refders[0][0] = -output.derivatives[0]; + output.refders[0][1] = -output.derivatives[1]; + output.refders[0][2] = -output.derivatives[2]; + // Add virial contribution + output.virial.set( 0, -Tensor(fpos, + Vector(output.derivatives[0], output.derivatives[1], output.derivatives[2])) ); + output.values[0] = xcontr*ycontr*zcontr; +} + +} +} +#endif //__PLUMED_volumes_VolumeAround_h diff --git a/src/volumes/VolumeBetweenContours.cpp b/src/volumes/VolumeBetweenContours.cpp index a0225d1fe3..4530223f7d 100644 --- a/src/volumes/VolumeBetweenContours.cpp +++ b/src/volumes/VolumeBetweenContours.cpp @@ -90,6 +90,9 @@ namespace volumes { class VolumeInEnvelope { public: + using precision=double; + typedef VolumeIn VolumeInput; + typedef VolumeOut VolumeOutput; double gvol, maxs; std::string kerneltype; std::vector bandwidth; diff --git a/src/volumes/VolumeCavity.cpp b/src/volumes/VolumeCavity.cpp index 44cf14a2bf..55ac034751 100644 --- a/src/volumes/VolumeCavity.cpp +++ b/src/volumes/VolumeCavity.cpp @@ -131,6 +131,9 @@ namespace volumes { class VolumeCavity { public: + using precision=double; + typedef VolumeIn VolumeInput; + typedef VolumeOut VolumeOutput; double jacob_det; double len_bi, len_cross, len_perp, sigma; Vector bi, cross, perp; diff --git a/src/volumes/VolumeInCylinder.cpp b/src/volumes/VolumeInCylinder.cpp index aca9e1aafa..de54b62379 100644 --- a/src/volumes/VolumeInCylinder.cpp +++ b/src/volumes/VolumeInCylinder.cpp @@ -19,9 +19,7 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC +#include "VolumeInCylinder.h" #include "core/ActionRegister.h" #include "tools/Pbc.h" #include "tools/SwitchingFunction.h" @@ -108,35 +106,6 @@ Notice that now the cylinder is centered on the `x` axis rather than the `z` axi namespace PLMD { namespace volumes { -class VolumeInCylinder { -public: - bool docylinder; - double min, max, sigma; - HistogramBead::KernelType kerneltype; - std::array dir; -#ifdef __PLUMED_USE_OPENACC - SwitchingFunctionAccelerable switchingFunction; -#else - SwitchingFunction switchingFunction; -#endif //__PLUMED_USE_OPENACC - static void registerKeywords( Keywords& keys ); - void parseInput( ActionVolume* action ); - void setupRegions( ActionVolume* action, const Pbc& pbc, const std::vector& positions ) {} - static void parseAtoms( ActionVolume* action, std::vector& atom ); - static void calculateNumberInside( const VolumeInput& input, const VolumeInCylinder& actioninput, VolumeOutput& output ); -#ifdef __PLUMED_USE_OPENACC - void toACCDevice() const { -#pragma acc enter data copyin(this[0:1], \ -docylinder, min, max, sigma, kerneltype, dir[0:3]) - switchingFunction.toACCDevice(); - } - void removeFromACCDevice() const { - switchingFunction.removeFromACCDevice(); -#pragma acc exit data delete(dir[0:3], kerneltype, sigma, max, min, \ - docylinder, this[0:1]) - } -#endif //__PLUMED_USE_OPENACC -}; typedef ActionVolume Volc; PLUMED_REGISTER_ACTION(Volc,"INCYLINDER_CALC") @@ -144,102 +113,5 @@ char glob_cylinder[] = "INCYLINDER"; typedef VolumeShortcut VolumeInCylinderShortcut; PLUMED_REGISTER_ACTION(VolumeInCylinderShortcut,"INCYLINDER") -void VolumeInCylinder::registerKeywords( Keywords& keys ) { - keys.setDisplayName("INCYLINDER"); - keys.add("atoms","CENTER","the atom whose vicinity we are interested in examining"); - keys.add("optional","SIGMA","the width of the function to be used for kernel density estimation"); - keys.add("compulsory","KERNEL","gaussian","the type of kernel function to be used"); - keys.add("compulsory","DIRECTION","the direction of the long axis of the cylinder. Must be x, y or z"); - keys.add("compulsory","RADIUS","a switching function that gives the extent of the cylinder in the plane perpendicular to the direction"); - keys.add("compulsory","LOWER","0.0","the lower boundary on the direction parallel to the long axis of the cylinder"); - keys.add("compulsory","UPPER","0.0","the upper boundary on the direction parallel to the long axis of the cylinder"); - keys.linkActionInDocs("RADIUS","LESS_THAN"); -} - -void VolumeInCylinder::parseInput( ActionVolume* action ) { - action->parse("SIGMA",sigma); - std::string mykerneltype; - action->parse("KERNEL",mykerneltype); - kerneltype=HistogramBead::getKernelType(mykerneltype); - std::string sdir; - action->parse("DIRECTION",sdir); - if( sdir=="X") { - dir[0]=1; - dir[1]=2; - dir[2]=0; - } else if( sdir=="Y") { - dir[0]=0; - dir[1]=2; - dir[2]=1; - } else if( sdir=="Z") { - dir[0]=0; - dir[1]=1; - dir[2]=2; - } else { - action->error(sdir + "is not a valid direction. Should be X, Y or Z"); - } - action->log.printf(" cylinder's long axis is along %s axis\n",sdir.c_str() ); - - std::string errors; - std::string swinput; - action->parse("RADIUS",swinput); - if(swinput.length()==0) { - action->error("missing RADIUS keyword"); - } - switchingFunction.set(swinput,errors); - if( errors.length()!=0 ) { - action->error("problem reading RADIUS keyword : " + errors ); - } - action->log.printf(" radius of cylinder is given by %s \n", ( switchingFunction.description() ).c_str() ); - - docylinder=false; - action->parse("LOWER",min); - action->parse("UPPER",max); - if( min!=0.0 || max!=0.0 ) { - if( min>max ) { - action->error("minimum of cylinder should be less than maximum"); - } - docylinder=true; - action->log.printf(" cylinder extends from %f to %f along the %s axis\n",min,max,sdir.c_str() ); - } -} - -void VolumeInCylinder::parseAtoms( ActionVolume* action, std::vector& atom ) { - action->parseAtomList("CENTER",atom); - if( atom.size()!=1 ) { - action->error("should only be one atom specified"); - } - action->log.printf(" center of cylinder is at position of atom : %d\n",atom[0].serial() ); -} - -void VolumeInCylinder::calculateNumberInside( const VolumeInput& input, const VolumeInCylinder& actioninput, VolumeOutput& output ) { - // Calculate position of atom wrt to origin - Vector fpos=input.pbc.distance( Vector(input.refpos[0][0],input.refpos[0][1],input.refpos[0][2]), Vector(input.cpos[0],input.cpos[1],input.cpos[2]) ); - - double vcylinder, dcylinder; - if( actioninput.docylinder ) { - HistogramBead bead( actioninput.kerneltype, - actioninput.min, actioninput.max, actioninput.sigma ); - vcylinder=bead.calculate( fpos[actioninput.dir[2]], dcylinder ); - } else { - vcylinder=1.0; - dcylinder=0.0; - } - - const double dd = fpos[actioninput.dir[0]]*fpos[actioninput.dir[0]] + fpos[actioninput.dir[1]]*fpos[actioninput.dir[1]]; - double dfunc; - double vswitch = actioninput.switchingFunction.calculateSqr( dd, dfunc ); - output.values[0]=vswitch*vcylinder; - output.derivatives[actioninput.dir[0]]=vcylinder*dfunc*fpos[actioninput.dir[0]]; - output.derivatives[actioninput.dir[1]]=vcylinder*dfunc*fpos[actioninput.dir[1]]; - output.derivatives[actioninput.dir[2]]=vswitch*dcylinder; - // Add derivatives wrt to position of origin atom - output.refders[0][0] = -output.derivatives[0]; - output.refders[0][1] = -output.derivatives[1]; - output.refders[0][2] = -output.derivatives[2]; - // Add virial contribution - output.virial.set( 0, -Tensor(fpos,Vector(output.derivatives[0], output.derivatives[1], output.derivatives[2])) ); -} - } } diff --git a/src/volumes/VolumeInCylinder.h b/src/volumes/VolumeInCylinder.h new file mode 100644 index 0000000000..7666830ff4 --- /dev/null +++ b/src/volumes/VolumeInCylinder.h @@ -0,0 +1,178 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2015-2020 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_volumes_VolumeInCylinder_h +#define __PLUMED_volumes_VolumeInCylinder_h +#include "tools/Pbc.h" +#include "tools/SwitchingFunction.h" +#include "ActionVolume.h" +#include "tools/HistogramBead.h" + + +namespace PLMD { +namespace volumes { + +class VolumeInCylinder { +public: + using precision=double; + typedef VolumeIn VolumeInput; + typedef VolumeOut VolumeOutput; + bool docylinder; + double min, max, sigma; + HistogramBead::KernelType kerneltype; + std::array dir; +#ifdef __PLUMED_HAS_OPENACC + SwitchingFunctionAccelerable switchingFunction; +#else + SwitchingFunction switchingFunction; +#endif //__PLUMED_HAS_OPENACC + static void registerKeywords( Keywords& keys ); + template + void parseInput( ActionVolume* action ); + template + void setupRegions( ActionVolume* action, + const Pbc& pbc, + const std::vector& positions ) {} + template + static void parseAtoms( ActionVolume* action, + std::vector& atom ); + static void calculateNumberInside( const VolumeInput& input, + const VolumeInCylinder& actioninput, + VolumeOutput& output ); +#ifdef __PLUMED_HAS_OPENACC + void toACCDevice() const { +#pragma acc enter data copyin(this[0:1], \ +docylinder, min, max, sigma, kerneltype, dir[0:3]) + switchingFunction.toACCDevice(); + } + void removeFromACCDevice() const { + switchingFunction.removeFromACCDevice(); +#pragma acc exit data delete(dir[0:3], kerneltype, sigma, max, min, \ + docylinder, this[0:1]) + } +#endif //__PLUMED_HAS_OPENACC +}; + +void VolumeInCylinder::registerKeywords( Keywords& keys ) { + keys.setDisplayName("INCYLINDER"); + keys.add("atoms","CENTER","the atom whose vicinity we are interested in examining"); + keys.add("optional","SIGMA","the width of the function to be used for kernel density estimation"); + keys.add("compulsory","KERNEL","gaussian","the type of kernel function to be used"); + keys.add("compulsory","DIRECTION","the direction of the long axis of the cylinder. Must be x, y or z"); + keys.add("compulsory","RADIUS","a switching function that gives the extent of the cylinder in the plane perpendicular to the direction"); + keys.add("compulsory","LOWER","0.0","the lower boundary on the direction parallel to the long axis of the cylinder"); + keys.add("compulsory","UPPER","0.0","the upper boundary on the direction parallel to the long axis of the cylinder"); + keys.linkActionInDocs("RADIUS","LESS_THAN"); +} + +template +void VolumeInCylinder::parseInput( ActionVolume* action ) { + action->parse("SIGMA",sigma); + std::string mykerneltype; + action->parse("KERNEL",mykerneltype); + kerneltype=HistogramBead::getKernelType(mykerneltype); + std::string sdir; + action->parse("DIRECTION",sdir); + if( sdir=="X") { + dir[0]=1; + dir[1]=2; + dir[2]=0; + } else if( sdir=="Y") { + dir[0]=0; + dir[1]=2; + dir[2]=1; + } else if( sdir=="Z") { + dir[0]=0; + dir[1]=1; + dir[2]=2; + } else { + action->error(sdir + "is not a valid direction. Should be X, Y or Z"); + } + action->log.printf(" cylinder's long axis is along %s axis\n",sdir.c_str() ); + + std::string errors; + std::string swinput; + action->parse("RADIUS",swinput); + if(swinput.length()==0) { + action->error("missing RADIUS keyword"); + } + switchingFunction.set(swinput,errors); + if( errors.length()!=0 ) { + action->error("problem reading RADIUS keyword : " + errors ); + } + action->log.printf(" radius of cylinder is given by %s \n", ( switchingFunction.description() ).c_str() ); + + docylinder=false; + action->parse("LOWER",min); + action->parse("UPPER",max); + if( min!=0.0 || max!=0.0 ) { + if( min>max ) { + action->error("minimum of cylinder should be less than maximum"); + } + docylinder=true; + action->log.printf(" cylinder extends from %f to %f along the %s axis\n",min,max,sdir.c_str() ); + } +} + +template +void VolumeInCylinder::parseAtoms( ActionVolume* action, + std::vector& atom ) { + action->parseAtomList("CENTER",atom); + if( atom.size()!=1 ) { + action->error("should only be one atom specified"); + } + action->log.printf(" center of cylinder is at position of atom : %d\n",atom[0].serial() ); +} + +void VolumeInCylinder::calculateNumberInside( const VolumeInput& input, + const VolumeInCylinder& actioninput, + VolumeOutput& output ) { + // Calculate position of atom wrt to origin + Vector fpos=input.pbc.distance( Vector(input.refpos[0][0],input.refpos[0][1],input.refpos[0][2]), Vector(input.cpos[0],input.cpos[1],input.cpos[2]) ); + + double vcylinder, dcylinder; + if( actioninput.docylinder ) { + HistogramBead bead( actioninput.kerneltype, + actioninput.min, actioninput.max, actioninput.sigma ); + vcylinder=bead.calculate( fpos[actioninput.dir[2]], dcylinder ); + } else { + vcylinder=1.0; + dcylinder=0.0; + } + + const double dd = fpos[actioninput.dir[0]]*fpos[actioninput.dir[0]] + fpos[actioninput.dir[1]]*fpos[actioninput.dir[1]]; + double dfunc; + double vswitch = actioninput.switchingFunction.calculateSqr( dd, dfunc ); + output.values[0]=vswitch*vcylinder; + output.derivatives[actioninput.dir[0]]=vcylinder*dfunc*fpos[actioninput.dir[0]]; + output.derivatives[actioninput.dir[1]]=vcylinder*dfunc*fpos[actioninput.dir[1]]; + output.derivatives[actioninput.dir[2]]=vswitch*dcylinder; + // Add derivatives wrt to position of origin atom + output.refders[0][0] = -output.derivatives[0]; + output.refders[0][1] = -output.derivatives[1]; + output.refders[0][2] = -output.derivatives[2]; + // Add virial contribution + output.virial.set( 0, -Tensor(fpos,Vector(output.derivatives[0], output.derivatives[1], output.derivatives[2])) ); +} + +} +} +#endif //__PLUMED_volumes_VolumeInCylinder_h diff --git a/src/volumes/VolumeInSphere.cpp b/src/volumes/VolumeInSphere.cpp index 17996d2acf..6fa54a5741 100644 --- a/src/volumes/VolumeInSphere.cpp +++ b/src/volumes/VolumeInSphere.cpp @@ -19,13 +19,8 @@ You should have received a copy of the GNU Lesser General Public License along with plumed. If not, see . +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ -#ifdef __PLUMED_HAS_OPENACC -#define __PLUMED_USE_OPENACC 1 -#endif //__PLUMED_HAS_OPENACC +#include "VolumeInSphere.h" #include "core/ActionRegister.h" -#include "tools/Pbc.h" -#include "tools/SwitchingFunction.h" -#include "ActionVolume.h" #include "VolumeShortcut.h" //+PLUMEDOC VOLUMES INSPHERE @@ -86,85 +81,10 @@ PRINT ARG=s FILE=colvar namespace PLMD { namespace volumes { -struct VolumeInSphere { -#ifdef __PLUMED_USE_OPENACC - SwitchingFunctionAccelerable switchingFunction; -#else - SwitchingFunction switchingFunction; -#endif //__PLUMED_USE_OPENACC - static void registerKeywords( Keywords& keys ); - void parseInput( ActionVolume* action ); - void setupRegions( ActionVolume* action, const Pbc& pbc, const std::vector& positions ) {} - static void parseAtoms( ActionVolume* action, std::vector& atom ); - static void calculateNumberInside( const VolumeInput& input, const VolumeInSphere& actioninput, VolumeOutput& output ); -#ifdef __PLUMED_USE_OPENACC - void toACCDevice() const { -#pragma acc enter data copyin(this[0:1]) - switchingFunction.toACCDevice(); - } - void removeFromACCDevice() const { - switchingFunction.removeFromACCDevice(); -#pragma acc exit data delete(this[0:1]) - } -#endif //__PLUMED_USE_OPENACC -}; - typedef ActionVolume Vols; PLUMED_REGISTER_ACTION(Vols,"INSPHERE_CALC") char glob_sphere[] = "INSPHERE"; typedef VolumeShortcut VolumeInSphereShortcut; PLUMED_REGISTER_ACTION(VolumeInSphereShortcut,"INSPHERE") - -void VolumeInSphere::registerKeywords( Keywords& keys ) { - keys.setDisplayName("INSPHERE"); - keys.add("atoms","CENTER","the atom whose vicinity we are interested in examining"); - keys.addDeprecatedKeyword("ATOM","CENTER"); - keys.add("compulsory","RADIUS","the switching function that tells us the extent of the sphereical region of interest"); - keys.linkActionInDocs("RADIUS","LESS_THAN"); -} - -void VolumeInSphere::parseInput( ActionVolume* action ) { - std::string errors; - std::string swinput; - action->parse("RADIUS",swinput); - if(swinput.length()==0) { - action->error("missing RADIUS keyword"); - } - - switchingFunction.set(swinput,errors); - if( errors.length()!=0 ) { - action->error("problem reading RADIUS keyword : " + errors ); - } - - action->log.printf(" radius of sphere is given by %s \n", - switchingFunction.description().c_str() ); -} - -void VolumeInSphere::parseAtoms( ActionVolume* action, std::vector& atom ) { - action->parseAtomList("CENTER",atom); - if( atom.size()==0 ) { - action->parseAtomList("ATOM",atom); - } - if( atom.size()!=1 ) { - action->error("should only be one atom specified"); - } - action->log.printf(" center of sphere is at position of atom : %d\n",atom[0].serial() ); -} - -void VolumeInSphere::calculateNumberInside( const VolumeInput& input, - const VolumeInSphere& actioninput, - VolumeOutput& output ) { - // Calculate position of atom wrt to origin - Vector fpos=input.pbc.distance( Vector(input.refpos[0][0],input.refpos[0][1],input.refpos[0][2]), Vector(input.cpos[0],input.cpos[1],input.cpos[2]) ); - double dfunc; - output.values[0] = actioninput.switchingFunction.calculateSqr( fpos.modulo2(), dfunc ); - output.derivatives = dfunc*fpos; - output.refders[0][0] = -output.derivatives[0]; - output.refders[0][1] = -output.derivatives[1]; - output.refders[0][2] = -output.derivatives[2]; - // Add a virial contribution - output.virial.set( 0, -Tensor(fpos,Vector(output.derivatives[0], output.derivatives[1], output.derivatives[2])) ); -} - -} -} +} // namespace PLMD +} // namespace volumes diff --git a/src/volumes/VolumeInSphere.h b/src/volumes/VolumeInSphere.h new file mode 100644 index 0000000000..f8efc2ccc6 --- /dev/null +++ b/src/volumes/VolumeInSphere.h @@ -0,0 +1,121 @@ +/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Copyright (c) 2015-2020 The plumed team + (see the PEOPLE file at the root of the distribution for a list of names) + + See http://www.plumed.org for more information. + + This file is part of plumed, version 2. + + plumed is free software: you can redistribute it and/or modify + it under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + plumed is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public License + along with plumed. If not, see . ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */ +#ifndef __PLUMED_volumes_VolumeInSphere_h +#define __PLUMED_volumes_VolumeInSphere_h +#include "tools/Pbc.h" +#include "tools/SwitchingFunction.h" +#include "ActionVolume.h" + +namespace PLMD { +namespace volumes { + +struct VolumeInSphere { + using precision=double; + typedef VolumeIn VolumeInput; + typedef VolumeOut VolumeOutput; +#ifdef __PLUMED_HAS_OPENACC + SwitchingFunctionAccelerable switchingFunction; +#else + SwitchingFunction switchingFunction; +#endif //__PLUMED_HAS_OPENACC + static void registerKeywords( Keywords& keys ); + template + void parseInput( ActionVolume* action ); + template + void setupRegions( ActionVolume* action, + const Pbc& pbc, + const std::vector& positions ) {} + template + static void parseAtoms( ActionVolume* action, + std::vector& atom ); + static void calculateNumberInside( const VolumeInput& input, + const VolumeInSphere& actioninput, + VolumeOutput& output ); +#ifdef __PLUMED_HAS_OPENACC + void toACCDevice() const { +#pragma acc enter data copyin(this[0:1]) + switchingFunction.toACCDevice(); + } + void removeFromACCDevice() const { + switchingFunction.removeFromACCDevice(); +#pragma acc exit data delete(this[0:1]) + } +#endif //__PLUMED_HAS_OPENACC +}; + +void VolumeInSphere::registerKeywords( Keywords& keys ) { + keys.setDisplayName("INSPHERE"); + keys.add("atoms","CENTER","the atom whose vicinity we are interested in examining"); + keys.addDeprecatedKeyword("ATOM","CENTER"); + keys.add("compulsory","RADIUS","the switching function that tells us the extent of the sphereical region of interest"); + keys.linkActionInDocs("RADIUS","LESS_THAN"); +} + +template +void VolumeInSphere::parseInput( ActionVolume* action ) { + std::string errors; + std::string swinput; + action->parse("RADIUS",swinput); + if(swinput.length()==0) { + action->error("missing RADIUS keyword"); + } + + switchingFunction.set(swinput,errors); + if( errors.length()!=0 ) { + action->error("problem reading RADIUS keyword : " + errors ); + } + + action->log.printf(" radius of sphere is given by %s \n", + switchingFunction.description().c_str() ); +} + +template +void VolumeInSphere::parseAtoms( ActionVolume* action, + std::vector& atom ) { + action->parseAtomList("CENTER",atom); + if( atom.size()==0 ) { + action->parseAtomList("ATOM",atom); + } + if( atom.size()!=1 ) { + action->error("should only be one atom specified"); + } + action->log.printf(" center of sphere is at position of atom : %d\n",atom[0].serial() ); +} + +void VolumeInSphere::calculateNumberInside( const VolumeInput& input, + const VolumeInSphere& actioninput, + VolumeOutput& output ) { + // Calculate position of atom wrt to origin + Vector fpos=input.pbc.distance( Vector(input.refpos[0][0],input.refpos[0][1],input.refpos[0][2]), Vector(input.cpos[0],input.cpos[1],input.cpos[2]) ); + double dfunc; + output.values[0] = actioninput.switchingFunction.calculateSqr( fpos.modulo2(), dfunc ); + output.derivatives = dfunc*fpos; + output.refders[0][0] = -output.derivatives[0]; + output.refders[0][1] = -output.derivatives[1]; + output.refders[0][2] = -output.derivatives[2]; + // Add a virial contribution + output.virial.set( 0, -Tensor(fpos,Vector(output.derivatives[0], output.derivatives[1], output.derivatives[2])) ); +} + +} +} +#endif //__PLUMED_volumes_VolumeInSphere_h diff --git a/src/volumes/VolumeShortcut.h b/src/volumes/VolumeShortcut.h index 60106b3987..d40f478f91 100644 --- a/src/volumes/VolumeShortcut.h +++ b/src/volumes/VolumeShortcut.h @@ -54,6 +54,7 @@ void VolumeShortcut::registerKeywords( Keywords& keys ) { keys.addDeprecatedFlag("MEAN",""); keys.addOutputComponent("mean","MEAN","scalar","the average values of the colvar in the region of interest"); keys.addActionNameSuffix("_CALC"); + keys.addActionNameSuffix("_ACC"); keys.needsAction("LESS_THAN"); keys.needsAction("MORE_THAN"); keys.needsAction("GROUP"); @@ -72,6 +73,14 @@ VolumeShortcut::VolumeShortcut(const ActionOptions&ao): parse("DATA",mc_lab); bool dosum; parseFlag("SUM",dosum); + std::string shortcutType="_CALC "; + { + bool usegpu; + parseFlag("USEGPU",usegpu); + if (usegpu) { + shortcutType="_ACC "; + } + } if( mc_lab.length()>0 ) { Group* mygrp = plumed.getActionSet().template selectWithLabel(mc_lab); Group* mygrp2 = plumed.getActionSet().template selectWithLabel(mc_lab + "_grp"); @@ -90,7 +99,7 @@ VolumeShortcut::VolumeShortcut(const ActionOptions&ao): atomsd=mc_lab; } // Create the apprpriate volume object - readInputLine( getShortcutLabel() + ": " + voltype + "_CALC " + convertInputLineToString() + " ATOMS=" + atomsd ); + readInputLine( getShortcutLabel() + ": " + voltype + shortcutType + convertInputLineToString() + " ATOMS=" + atomsd ); // Now create input for sums if( dosum || domean ) { readInputLine( getShortcutLabel() + "_prod: CUSTOM ARG=" + mc_lab + "," + getShortcutLabel() + " FUNC=x*y PERIODIC=NO"); @@ -135,10 +144,10 @@ VolumeShortcut::VolumeShortcut(const ActionOptions&ao): readInputLine( getShortcutLabel() + "_between: SUM ARG=" + getShortcutLabel() + "_bt PERIODIC=NO"); } } else if( dosum ) { - readInputLine( getShortcutLabel() + "_vols: " + voltype + "_CALC " + convertInputLineToString() ); + readInputLine( getShortcutLabel() + "_vols: " + voltype + shortcutType + convertInputLineToString() ); readInputLine( getShortcutLabel() + ": SUM ARG=" + getShortcutLabel() + "_vols PERIODIC=NO"); } else { - readInputLine( getShortcutLabel() + ": " + voltype + "_CALC " + convertInputLineToString() ); + readInputLine( getShortcutLabel() + ": " + voltype + shortcutType + convertInputLineToString() ); } } diff --git a/src/volumes/VolumeTetrapore.cpp b/src/volumes/VolumeTetrapore.cpp index c13fe4b0f4..3db7aee61b 100644 --- a/src/volumes/VolumeTetrapore.cpp +++ b/src/volumes/VolumeTetrapore.cpp @@ -137,6 +137,9 @@ namespace volumes { class VolumeTetrapore { public: + using precision=double; + typedef VolumeIn VolumeInput; + typedef VolumeOut VolumeOutput; double jacob_det{0.0}; double len_bi{0.0}, len_cross{0.0}, len_perp{0.0}, sigma{0.0}; Vector bi, cross, perp; From 7d6e556735d07eea154cb6b020f130f463bb205e Mon Sep 17 00:00:00 2001 From: Daniele Rapetti <5535617+Iximiel@users.noreply.github.com> Date: Mon, 15 Sep 2025 14:45:40 +0200 Subject: [PATCH 2/2] Updating the workflow for compiling the PTM plugin in the CI check if linuxWF can be run with nvhpc --- .github/workflows/linuxWF.yml | 63 +++++++++++++++++++++++++++-------- 1 file changed, 49 insertions(+), 14 deletions(-) diff --git a/.github/workflows/linuxWF.yml b/.github/workflows/linuxWF.yml index f6da5db42d..9a141d7233 100644 --- a/.github/workflows/linuxWF.yml +++ b/.github/workflows/linuxWF.yml @@ -146,18 +146,6 @@ jobs: echo "CXX=icpx" >> $GITHUB_ENV echo "CC=icx" >> $GITHUB_ENV echo "FC=ifx" >> $GITHUB_ENV - - name: Install NVHPC compiler - if: contains( matrix.variant, '-nvhpc-' ) - # use this if it does not work - # wget https://developer.download.nvidia.com/hpc-sdk/24.3/nvhpc_2024_243_Linux_x86_64_cuda_12.3.tar.gz - # tar xpzf nvhpc_2024_243_Linux_x86_64_cuda_12.3.tar.gz - # nvhpc_2024_243_Linux_x86_64_cuda_12.3/install - run: | - curl https://developer.download.nvidia.com/hpc-sdk/ubuntu/DEB-GPG-KEY-NVIDIA-HPC-SDK | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg - echo 'deb [signed-by=/usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg] https://developer.download.nvidia.com/hpc-sdk/ubuntu/amd64 /' | sudo tee /etc/apt/sources.list.d/nvhpc.list - sudo apt-get update -y - sudo apt-get install -y nvhpc-24-3 - # nvhpcinstalls his own mpi compilers - name: Install MPI # install MPI at last since it modifies CC and CXX if: contains( matrix.variant, '-mpi-' ) @@ -172,18 +160,65 @@ jobs: echo "OMPI_MCA_rmaps_base_oversubscribe=yes" >> $GITHUB_ENV pip install --user mpi4py python -c "import mpi4py" + - name: Configure PLUMED + id: config + run: | + ccache -s -M 100M + #removed LDFLAGS=-Wl,-rpath,$LD_LIBRARY_PATH + ./configure CXX="ccache $CXX" --enable-boost_serialization --disable-dependency-tracking --enable-modules=all $PLUMED_CONFIG --prefix="$HOME/opt" + ccache -s -M 100M + - name: Config Log + if: failure() && steps.config.outcome == 'failure' + run: cat config.log + - name: Build PLUMED run: | ccache -s -M 100M - ./configure CXX="ccache $CXX" --enable-boost_serialization --disable-dependency-tracking --enable-modules=all $PLUMED_CONFIG --prefix=$HOME/opt make -j 4 make install # check for global symbols, see https://github.com/plumed/plumed2/issues/549 make nmcheck ccache -s -M 100M + - name: Install NVHPC compiler + if: contains( matrix.variant, '-nvhpc-' ) + # use this if it does not work + # wget https://developer.download.nvidia.com/hpc-sdk/24.3/nvhpc_2024_243_Linux_x86_64_cuda_12.3.tar.gz + # tar xpzf nvhpc_2024_243_Linux_x86_64_cuda_12.3.tar.gz + # nvhpc_2024_243_Linux_x86_64_cuda_12.3/install + run: | + curl https://developer.download.nvidia.com/hpc-sdk/ubuntu/DEB-GPG-KEY-NVIDIA-HPC-SDK | sudo gpg --dearmor -o /usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg + echo 'deb [signed-by=/usr/share/keyrings/nvidia-hpcsdk-archive-keyring.gpg] https://developer.download.nvidia.com/hpc-sdk/ubuntu/amd64 /' | sudo tee /etc/apt/sources.list.d/nvhpc.list + sudo apt-get update -y + sudo apt-get install -y nvhpc-24-3 + NVHOME=/opt/nvidia/hpc_sdk + NVARCH=`uname -s`_`uname -m` + # echo "NVHPC=$NVHOME" >> $GITHUB_ENV + # echo "NVHPC_ROOT=$NVHOME/$NVARCH/24.3" >> $GITHUB_ENV + nvcudadir=$NVHOME/$NVARCH/24.3/cuda + nvcompdir=$NVHOME/$NVARCH/24.3/compilers + nvmathdir=$NVHOME/$NVARCH/24.3/math_libs + nvcommdir=$NVHOME/$NVARCH/24.3/comm_libs + + echo "PATH=$nvcudadir/bin:$nvcompdir/bin:$nvcommdir/mpi/bin:$nvcompdir/extras/qd/bin:$PATH" >> $GITHUB_ENV + # echo "LD_LIBRARY_PATH=$nvcudadir/lib64:$nvcudadir/12.3/targets/x86_64-linux/lib/stubs/:$nvcudadir/extras/CUPTI/lib64:$nvcompdir/extras/qd/lib:$nvcompdir/lib:$nvmathdir/lib64:$nvcommdir/nccl/lib:$nvcommdir/nvshmem/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV + # echo "CPATH=$nvmathdir/include:$nvcommdir/nccl/include:$nvcommdir/nvshmem/include:$nvcompdir/extras/qd/include/qd:$CPATH" >> $GITHUB_ENV + # echo "NVHPC_CUDA_HOME=$nvcudadir/12.3" >> $GITHUB_ENV + + $nvcompdir/bin/nvc++ -help -gpu + echo "NVCXX=$nvcommdir/mpi/bin/mpic++" >> $GITHUB_ENV + echo "NVCC=$nvcommdir/mpi/bin/mpicc" >> $GITHUB_ENV + echo "NVFC=$nvcompdir/bin/nvfortran" >> $GITHUB_ENV + - name: check if the openacc module can be compiled + if: contains( matrix.variant, '-nvhpc-' ) + run: | + source sourceme.sh + cd plugins/openaccPTM/ + ./configure.sh + NVCXX=$NVCXX make + - name: Run tests - if: ${{ ! contains( matrix.variant, '-doc-mpi-' ) && ! contains( matrix.variant, '-pycv-mpi-' ) }} + if: ${{ ! contains( matrix.variant, '-doc-mpi-' ) && ! contains( matrix.variant, '-pycv-mpi-' ) && ! contains( matrix.variant, '-nvhpc-' ) }} run: | (while true; do # see https://github.com/actions/virtual-environments/issues/1860 df -h