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minor cmake fixes #54

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e90d5d7
fix cmake files
Dec 17, 2016
99fb749
rename Doc folder to docs
Dec 17, 2016
7375999
delete non-needed CGAL cmake module
mustafaa2 Jan 21, 2017
a92ae94
compiles with packages available on ubuntu 18
Jan 21, 2017
0e1c635
builds on debian stretch
Dec 14, 2018
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24 changes: 18 additions & 6 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,10 @@ endif()

#
# VTK
find_package(VTK 5.10 REQUIRED NO_MODULE)
find_package(VTK 6 NO_MODULE)
if(NOT VTK_FOUND)
find_package(VTK 5.10 REQUIRED NO_MODULE)
endif()
if(VTK_FOUND)
message(STATUS "VTK found ${VTK_DIR}")
include(${VTK_USE_FILE})
Expand Down Expand Up @@ -135,11 +138,11 @@ endif()

#
# Eigen
find_package(EIGEN 3.0 REQUIRED)
#
if(EIGEN_FOUND)
find_package(Eigen3 REQUIRED)
if(EIGEN3_FOUND)
message(STATUS "eigen found ${EIGEN_DIR} ${EIGEN_INCLUDE_DIR}")
include_directories(${EIGEN_INCLUDE_DIR})
# include_directories(${EIGEN3_INCLUDE_DIR})
# include( ${EIGEN3_USE_FILE} )
else()
message(STATUS "eigen not found")
endif()
Expand Down Expand Up @@ -178,7 +181,7 @@ endif()

#
# CGAL
find_package(CGAL 4.3 REQUIRED)
find_package(CGAL REQUIRED)
#
if(CGAL_FOUND)
message( STATUS "CGAL found ${CGAL_DIR}" )
Expand All @@ -189,6 +192,15 @@ else()
message( STATUS "CGAL not found" )
endif()

#
# GSL
find_package(GSL REQUIRED)
if(GSL_FOUND)
message(STATUS "GSL found ${GSL_DIR}")
else()
message(STATUS "GSL not found")
endif()

#
include_directories( SYSTEM )

Expand Down
2 changes: 1 addition & 1 deletion Fijee/Biophysics/CMakeLists.txt
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Expand Up @@ -25,4 +25,4 @@ add_library( FijeeBiophysics ${Fijee_H} ${HEADERS} ${SOURCES} )
# Add FijeeUtils target libraries
target_link_libraries( FijeeBiophysics ${Fijee_TARGET_LINK_LIBRARIES} )
# Install
install( TARGETS FijeeBiophysics EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib )
install( TARGETS FijeeBiophysics EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib )
2 changes: 1 addition & 1 deletion Fijee/Electrodes/CMakeLists.txt
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Expand Up @@ -25,4 +25,4 @@ add_library( FijeeElectrodes ${Fijee_H} ${HEADERS} ${SOURCES} )
# Add FijeeUtils target libraries
target_link_libraries( FijeeElectrodes ${Fijee_TARGET_LINK_LIBRARIES} )
# Install
install( TARGETS FijeeElectrodes EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib )
install( TARGETS FijeeElectrodes EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib )
2 changes: 1 addition & 1 deletion Fijee/Finite_element_method_models/CMakeLists.txt
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Expand Up @@ -49,4 +49,4 @@ add_library( FijeeFEM ${Fijee_H} ${HEADERS} ${UFL_HEADERS} ${SOURCES} )
# Add FijeeUtils target libraries
target_link_libraries( FijeeFEM ${Fijee_TARGET_LINK_LIBRARIES} ${DOLFIN_LIBRARIES} )
# Install
install( TARGETS FijeeFEM EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib )
install( TARGETS FijeeFEM EXPORT FijeeTargets LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib )
2 changes: 1 addition & 1 deletion Fijee/Finite_element_method_models/Physics.cxx
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Expand Up @@ -81,7 +81,7 @@ Solver::Physics::Physics()
std::string facets_collection_xml = (SDEsp::get_instance())->get_files_path_output_();
facets_collection_xml += "mesh_facets_subdomains.xml";
//
mesh_facets_collection_.reset( new MeshValueCollection< std::size_t > (*mesh_, facets_collection_xml) );
mesh_facets_collection_.reset( new MeshValueCollection< std::size_t > (mesh_, facets_collection_xml) );

//
// MeshDataCollection methode
Expand Down
29 changes: 18 additions & 11 deletions Fijee/Finite_element_method_models/SL_direct.cxx
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Expand Up @@ -36,13 +36,13 @@ Solver::SL_direct::SL_direct():Physics()
{
//
// Define the function space
V_.reset( new SLD_model::FunctionSpace(*mesh_) );
V_.reset( new SLD_model::FunctionSpace(mesh_) );

//
// Define boundary condition
perifery_.reset( new Periphery() );
// Initialize mesh function for boundary domains. We tag the boundaries
boundaries_.reset( new FacetFunction< size_t > (*mesh_) );
boundaries_.reset( new FacetFunction< size_t > (mesh_) );
boundaries_->set_all(0);
perifery_->mark(*boundaries_, 1);

Expand Down Expand Up @@ -155,6 +155,7 @@ Solver::SL_direct::operator () ( /*Solver::Phi& source,
// //
// // Define Dirichlet boundary conditions
// DirichletBC boundary_conditions(*V, source, perifery);
std::vector<std::shared_ptr<const DirichletBC>> bc;


///////////////////////////////////////////////
Expand All @@ -163,26 +164,32 @@ Solver::SL_direct::operator () ( /*Solver::Phi& source,

//
// Define variational forms
SLD_model::BilinearForm a(*V_, *V_);
SLD_model::LinearForm L(*V_);
SLD_model::BilinearForm a(V_, V_);
SLD_model::LinearForm L(V_);

//
// Anisotropy
// Bilinear
a.a_sigma = *sigma_;
a.dx = *domains_;
a.a_sigma = sigma_;
a.dx = domains_;
// Linear
L.J_source = source;
L.J_source = std::make_shared<Current_density>(source);
//
L.dx = *domains_;
L.ds = *boundaries_;
L.dx = domains_;
L.ds = boundaries_;

//
// Compute solution
Function u(V_);
//
LinearVariationalProblem problem(a, L, u);
LinearVariationalSolver solver(problem);
// LinearVariationalProblem problem(a, L, u);
// LinearVariationalSolver solver(problem);
LinearVariationalProblem problem(std::shared_ptr<const dolfin::Form> (&a),
std::shared_ptr<const dolfin::Form> (&L),
std::shared_ptr<dolfin::Function> (&u),
bc);
LinearVariationalSolver solver( (std::shared_ptr<LinearVariationalProblem> (&problem)) );

// krylov
solver.parameters["linear_solver"]
= (SDEsp::get_instance())->get_linear_solver_();
Expand Down
10 changes: 5 additions & 5 deletions Fijee/Finite_element_method_models/SL_subtraction.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ Solver::SL_subtraction::SL_subtraction():Physics()
// Define boundary condition
Periphery perifery;
// Initialize mesh function for boundary domains. We tag the boundaries
boundaries_.reset( new FacetFunction< size_t > (*mesh_) );
boundaries_.reset(new FacetFunction< size_t >(mesh_));
boundaries_->set_all(0);
perifery.mark(*boundaries_, 1);

Expand Down Expand Up @@ -163,7 +163,7 @@ Solver::SL_subtraction::operator () ( /*Solver::Phi& source,
//
// Anisotropy conductivity
// Bilinear form
a_->a_sigma = *sigma_;
a_->a_sigma = sigma_;
// a.dx = *domains_;
//
A_.reset( new Matrix() );
Expand Down Expand Up @@ -202,9 +202,9 @@ Solver::SL_subtraction::operator () ( /*Solver::Phi& source,
Vector L_;

// Linear
L.a_inf = a_inf;
L.a_sigma = *sigma_;
L.Phi_0 = source;
L.a_inf = std::make_shared<Sigma_isotrope>(a_inf);
L.a_sigma = sigma_;
L.Phi_0 = std::make_shared<Phi>(source);
//
// L.dx = *domains_;
// L.ds = *boundaries_;
Expand Down
8 changes: 4 additions & 4 deletions Fijee/Finite_element_method_models/Spheres_electric_monopole.cxx
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Expand Up @@ -295,9 +295,9 @@ Solver::Spheres_electric_monopole::Spheres_electric_monopole(const Spheres_elect
r0_values_ = that.r0_values_;
//
std::copy(that.r_sphere_, that.r_sphere_ + NUM_SPHERES, r_sphere_);
std::copy(that.sigma_, that.sigma_ + NUM_SPHERES, sigma_);
std::copy((double*)that.sigma_, ((double*)that.sigma_) + NUM_SPHERES * 2, (double*)sigma_);
//
std::copy(that.nu_, that.nu_ + NUM_ITERATIONS, nu_);
std::copy((double*)that.nu_, ((double*)that.nu_) + NUM_ITERATIONS * NUM_SPHERES, (double*)nu_);
std::copy(that.R_coeff_, that.R_coeff_ + NUM_ITERATIONS, R_coeff_);
//
for ( int n = 0 ; n < NUM_ITERATIONS ; n++ )
Expand Down Expand Up @@ -531,9 +531,9 @@ Solver::Spheres_electric_monopole::operator =( const Spheres_electric_monopole&
r0_values_ = that.r0_values_;
//
std::copy(that.r_sphere_, that.r_sphere_ + NUM_SPHERES, r_sphere_);
std::copy(that.sigma_, that.sigma_ + NUM_SPHERES, sigma_);
std::copy((double*)that.sigma_, ((double*)that.sigma_) + NUM_SPHERES * 2, (double*)sigma_);
//
std::copy(that.nu_, that.nu_ + NUM_ITERATIONS, nu_);
std::copy((double*)that.nu_, ((double*)that.nu_) + NUM_ITERATIONS * NUM_SPHERES, (double*)nu_);
std::copy(that.R_coeff_, that.R_coeff_ + NUM_ITERATIONS, R_coeff_);
//
for ( int n = 0 ; n < NUM_ITERATIONS ; n++ )
Expand Down
53 changes: 38 additions & 15 deletions Fijee/Finite_element_method_models/tCS_tACS.cxx
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Expand Up @@ -115,6 +115,8 @@ Solver::tCS_tACS::operator () ( /*Solver::Phi& source,
// //
// // PDE boundary conditions
// DirichletBC bc(*V_, *(electrodes_->get_current(0)), *boundaries_, 101);
std::vector<std::shared_ptr<const DirichletBC>> bc;


//
// Define variational forms
Expand All @@ -124,19 +126,25 @@ Solver::tCS_tACS::operator () ( /*Solver::Phi& source,
//
// Anisotropy
// Bilinear
a.a_sigma = *sigma_;
a.a_sigma = sigma_;
// a.dx = *domains_;


// Linear
L.I = *( electrodes_->get_current(local_sample) );
L.ds = *boundaries_;
L.I = electrodes_->get_current(local_sample);
L.ds = boundaries_;

//
// Compute solution
Function u(*V_);
LinearVariationalProblem problem(a, L, u/*, bc*/);
LinearVariationalSolver solver(problem);
Function u(V_);
// LinearVariationalProblem problem(a, L, u, bc);
// LinearVariationalSolver solver(problem);
LinearVariationalProblem problem(std::shared_ptr<const dolfin::Form> (&a),
std::shared_ptr<const dolfin::Form> (&L),
std::shared_ptr<dolfin::Function> (&u),
bc);
LinearVariationalSolver solver( (std::shared_ptr<LinearVariationalProblem> (&problem)) );

// krylov
solver.parameters["linear_solver"]
= (SDEsp::get_instance())->get_linear_solver_();
Expand Down Expand Up @@ -257,15 +265,23 @@ Solver::tCS_tACS::operator () ( /*Solver::Phi& source,


// Linear
L_field.u = u;
L_field.a_sigma = *sigma_;
L_field.u = std::shared_ptr<const GenericFunction> (&u);
L_field.a_sigma = sigma_;
// L.ds = *boundaries_;

//
// Compute solution
Function J(*V_current_density_);
LinearVariationalProblem problem_field(a_field, L_field, J/*, bc*/);
LinearVariationalSolver solver_field(problem_field);
Function J(V_current_density_);
// LinearVariationalProblem problem_field(a_field, L_field, J/*, bc*/);
// LinearVariationalSolver solver_field(problem_field);

LinearVariationalProblem problem_field(std::shared_ptr<const dolfin::Form> (&a_field),
std::shared_ptr<const dolfin::Form> (&L_field),
std::shared_ptr<dolfin::Function> (&J),
bc);
LinearVariationalSolver solver_field( (std::shared_ptr<LinearVariationalProblem> (&problem)) );


// krylov
solver_field.parameters["linear_solver"]
= (SDEsp::get_instance())->get_linear_solver_();
Expand Down Expand Up @@ -334,15 +350,22 @@ Solver::tCS_tACS::operator () ( /*Solver::Phi& source,


// Linear
L_E.u = u;
L_E.u = std::shared_ptr<const GenericFunction> (&u);
// L_Er.a_sigma = *sigma_;
// L.ds = *boundaries_;

//
// Compute solution
Function E(*V_E_);
LinearVariationalProblem problem_E(a_E, L_E, E/*, bc*/);
LinearVariationalSolver solver_E(problem_E);
Function E(V_E_);
// LinearVariationalProblem problem_E(a_E, L_E, E/*, bc*/);
// LinearVariationalSolver solver_E(problem_E);

LinearVariationalProblem problem_E(std::make_shared<const Form> (a_E),
std::make_shared<const Form> (L_E),
std::make_shared<Function> (E),
bc);
LinearVariationalSolver solver_E(std::make_shared<LinearVariationalProblem> (problem_E));

// krylov
solver_E.parameters["linear_solver"]
= (SDEsp::get_instance())->get_linear_solver_();
Expand Down
47 changes: 31 additions & 16 deletions Fijee/Finite_element_method_models/tCS_tDCS.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -108,6 +108,7 @@ Solver::tCS_tDCS::operator () ( /*Solver::Phi& source,
// //
// // PDE boundary conditions
// DirichletBC bc(*V_, *(electrodes_->get_current(0)), *boundaries_, 101);
std::vector<std::shared_ptr<const DirichletBC>> bc;

//
// Define variational forms
Expand All @@ -117,21 +118,24 @@ Solver::tCS_tDCS::operator () ( /*Solver::Phi& source,
//
// Anisotropy
// Bilinear
a.a_sigma = *sigma_;
a.a_sigma = sigma_;
// a.dx = *domains_;
// std::cout << electrodes_->get_current(0)->information("T7").get_I_() << std::endl;

// Linear
L.I = *(electrodes_->get_current( /*local_sample*/ 0));
L.ds = *boundaries_;
L.I = electrodes_->get_current( /*local_sample*/ 0);
L.ds = boundaries_;

//
// Compute solution
Function u(*V_);
LinearVariationalProblem problem(a, L, u/*, bc*/);
LinearVariationalSolver solver(problem);
Function u(V_);
LinearVariationalProblem problem(std::shared_ptr<const dolfin::Form> (&a),
std::shared_ptr<const dolfin::Form> (&L),
std::shared_ptr<dolfin::Function> (&u),
bc);
LinearVariationalSolver solver( (std::shared_ptr<LinearVariationalProblem> (&problem)) );
// krylov
solver.parameters["linear_solver"]
solver.parameters["linear_solver"]
= (SDEsp::get_instance())->get_linear_solver_();
solver.parameters("krylov_solver")["maximum_iterations"]
= (SDEsp::get_instance())->get_maximum_iterations_();
Expand Down Expand Up @@ -225,15 +229,19 @@ Solver::tCS_tDCS::operator () ( /*Solver::Phi& source,


// Linear
L_field.u = u;
L_field.a_sigma = *sigma_;
L_field.u = std::shared_ptr<const GenericFunction> (&u);
L_field.a_sigma = sigma_;
// L.ds = *boundaries_;

//
// Compute solution
Function J(*V_current_density_);
LinearVariationalProblem problem_field(a_field, L_field, J/*, bc*/);
LinearVariationalSolver solver_field(problem_field);
Function J(V_current_density_);
// LinearVariationalProblem problem_field(a_field, L_field, J, bc);
LinearVariationalProblem problem_field(std::make_shared<const Form> (a_field),
std::make_shared<const Form> (L_field),
std::make_shared<Function> (J),
bc);
LinearVariationalSolver solver_field(std::make_shared<LinearVariationalProblem>(problem_field));
// krylov
solver_field.parameters["linear_solver"]
= (SDEsp::get_instance())->get_linear_solver_();
Expand Down Expand Up @@ -277,15 +285,22 @@ Solver::tCS_tDCS::operator () ( /*Solver::Phi& source,


// Linear
L_E.u = u;
L_E.u = std::shared_ptr<const GenericFunction> (&u);
// L_Er.a_sigma = *sigma_;
// L.ds = *boundaries_;

//
// Compute solution
Function E(*V_E_);
LinearVariationalProblem problem_E(a_E, L_E, E/*, bc*/);
LinearVariationalSolver solver_E(problem_E);
Function E(V_E_);
// LinearVariationalProblem problem_E(a_E, L_E, E, bc);
// LinearVariationalSolver solver_E(problem_E);

LinearVariationalProblem problem_E(std::make_shared<const Form> (a_E),
std::make_shared<const Form> (L_E),
std::make_shared<Function> (E),
bc);
LinearVariationalSolver solver_E(std::make_shared<LinearVariationalProblem> (problem_E));

// krylov
solver_E.parameters["linear_solver"]
= (SDEsp::get_instance())->get_linear_solver_();
Expand Down
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