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Jintram wants to merge 1730 commits intoecell:masterfrom

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Commits on Dec 21, 2012

More debug output
Thomas Sokolowski
committed
And even more
Thomas Sokolowski
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Convert a boost-python allocated list to Python list instead of bool
Thomas Sokolowski
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Define destructor for pyarray_backed_allocator for completeness
Thomas Sokolowski
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Cleanup
Thomas Sokolowski
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Treat zero-rates properly in load routine
Thomas Sokolowski
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Further cleanup
Thomas Sokolowski
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Merge pull request #104 from YetAnotherTomek/zero-rate-issue
YetAnotherTomek
committed
Increase single shell factor to 3.5 so that it is >= 2* multi shell factor
Thomas Sokolowski
committed

Commits on Jan 15, 2013

Another revision of the rootfinding in EDGE_HITS_EDGE cylinder scaling
Thomas Sokolowski
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Cleanup
Thomas Sokolowski
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Tolerate a certain overlap with overlap_tolerance = TOLERANCE*shell_size
Thomas Sokolowski
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Warn when continuing with overlap within overlap_tolerance
Thomas Sokolowski
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Fix transition pair shell construction problem
Thomas Sokolowski
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One more warn statement
Thomas Sokolowski
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Basic code structure for overlap remover routine
Thomas Sokolowski
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Commits on Jan 16, 2013

Continue
Thomas Sokolowski
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Merge commit 'upstream/develop' into develop
Thomas Sokolowski
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Some cleanup in shells.py
Thomas Sokolowski
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Merge pull request #105 from YetAnotherTomek/develop
YetAnotherTomek
committed

Commits on Feb 13, 2013

Reject single reactions in which a product crosses a plane
Thomas Sokolowski
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Same thing for the BD mode, slightly more effort required
Thomas Sokolowski
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Commits on Feb 14, 2013

Rename crossing_comparison_vector -> side_comparison_vector
Thomas Sokolowski
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Remove comment that is not true any more
Thomas Sokolowski
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Commits on Mar 21, 2013

Merge commit 'upstream/develop' into develop
Thomas Sokolowski
committed

Commits on Aug 16, 2013

Merge pull request #106 from YetAnotherTomek/develop
YetAnotherTomek
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Basic code structure for overlap remover routine
Thomas Sokolowski
committed
Continue
Thomas Sokolowski
committed

Commits on Aug 19, 2013

Merge commit 'origin/overlap_remover' into overlap_remover
Thomas Sokolowski
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WIP + fix weird merge conflict
Thomas Sokolowski
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Finish first version of a working overlap remover
Thomas Sokolowski
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Introduce a function to default-connect one plane in periodic BCs
Thomas Sokolowski
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Use do_back_transform correctly
Thomas Sokolowski
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Include overlap error into print_report
Thomas Sokolowski
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Reconstruct periodic connection correctly upon reloading via the
Thomas Sokolowski
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Commits on Aug 22, 2013

Fix an object creation loop that caused huge memory leaks
Thomas Sokolowski
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WIP - some debug statements
Thomas Sokolowski
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Merge branch 'overlap_remover_fix' into overlap_remover
Thomas Sokolowski
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This is not the right way to treat it...
Thomas Sokolowski
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further WIP
Thomas Sokolowski
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Commits on Aug 23, 2013

Only try to establish connections at loading if such
Thomas Sokolowski
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Avoid applying boundary cond. to self-connected planes + warn
Thomas Sokolowski
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WIP
Thomas Sokolowski
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Some cleanup
Thomas Sokolowski
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Mark a problematic feature in StructureContainer.hpp
Thomas Sokolowski
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Commits on Aug 26, 2013

Temporarily remove debug statement
Thomas Sokolowski
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Commits on Aug 27, 2013

Forgot an important any() in if-statement
Thomas Sokolowski
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Commits on Aug 30, 2013

Merge commit 'upstream/develop' into overlap_remover
Thomas Sokolowski
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Set overlap removing to False as default
Thomas Sokolowski
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Simple on/off functions for overlap remover
Thomas Sokolowski
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Merge branch 'overlap_remover' into develop
Thomas Sokolowski
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Compactify fire_single_reactino() a bit
Thomas Sokolowski
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Allow user to specify custom parent structures for caps
Thomas Sokolowski
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Put dissociating particle on parent structure, not automatically
Thomas Sokolowski
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Commits on Sep 2, 2013

Return structure IDs when creating a box + feed in IDs for
Thomas Sokolowski
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Revise naming convention for planes in box object
Thomas Sokolowski
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Small fix
Thomas Sokolowski
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Allow user to specify more details of the rod
Thomas Sokolowski
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Introduce Cylinder to Plane Interaction Domain
Thomas Sokolowski
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Commits on Sep 3, 2013

Some renaming
Thomas Sokolowski
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Introduce a new ('fake') interaction domain that encloses a particle
Thomas Sokolowski
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Just some useful debugging statements
Thomas Sokolowski
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Commits on Sep 4, 2013

Forgot burst event type in new single class
Thomas Sokolowski
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Just a memo
Thomas Sokolowski
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Basic treatment for the "Interface Pair", i.e. a PlanarSurfacePair
Thomas Sokolowski
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Forgot to rename box planes in connecting routine
Thomas Sokolowski
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Commits on Sep 5, 2013

Fix ignorelists in overlap checking
Thomas Sokolowski
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Basic implementation of PlanarSurfaceCylindricalSurfaceInteraction (testShell)
Thomas Sokolowski
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Basic implementation of PlanarSurfaceCylindricalSurfaceInteraction (domain)
Thomas Sokolowski
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Small fix
Thomas Sokolowski
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Commits on Sep 6, 2013

Always return next-event time = inf for SINGLE_ESCAPE in
Thomas Sokolowski
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Fix domain construction gearbox taking into account the new domain
Thomas Sokolowski
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Introduce a distinction between target and product structure in
Thomas Sokolowski
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Cleanup
Thomas Sokolowski
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Commits on Sep 13, 2013

Check whether static particle is below cylinder in PlanarSurfacePair formation
Thomas Sokolowski
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Some cleanup
Thomas Sokolowski
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Rename 'testMixedPair1DCap' into 'testMixedPair1DStatic' to generalize
Thomas Sokolowski
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Same renaming for the associated pair domain
Thomas Sokolowski
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One more important check
Thomas Sokolowski
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Convert assert statement to exception that can be handled
Thomas Sokolowski
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Generalize construction of MixedPair1DCap to MixedPair1DStatic, i.e.
Thomas Sokolowski
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All interactions need property self.product_structure
Thomas Sokolowski
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Not selfish enough...
Thomas Sokolowski
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Commits on Sep 16, 2013

Fix min-size of plane-cylinder interface shell
Thomas Sokolowski
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WIP on newBDpropagator
Thomas Sokolowski
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Commits on Sep 17, 2013

Better treatment of applying the right rate-modifier function when
Thomas Sokolowski
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Treat case D_2D=0 in MixedPair2D3D
Thomas Sokolowski
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Forgot to save and re-load decay reaction rules in load/save system
Thomas Sokolowski
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Commits on Sep 18, 2013

Some important fixes
Thomas Sokolowski
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Tentative version of Cylinder->Plane Interaction that places the
Thomas Sokolowski
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Some informative commenting
Thomas Sokolowski
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Correctly handle Cylinder->Plane transfer in BD mode structure functions
Thomas Sokolowski
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Small fix
Thomas Sokolowski
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Update shell overlap ignore lists
Thomas Sokolowski
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Make Cyl.SurfacePlanarSurfaceInterfaceSingle an interaction from plane to disk
Thomas Sokolowski
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Commits on Sep 19, 2013

New function that finds the closest structure form a point +
Thomas Sokolowski
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Some consistent renaming and cleanup
Thomas Sokolowski
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Small fixes
Thomas Sokolowski
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Use new search function to find daughter disk
Thomas Sokolowski
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Make sure get_neighbor_surfaces does correctly filter out the
Thomas Sokolowski
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Ignore closest cylinder and check whether it is located correctly
Thomas Sokolowski
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Fix ignore lists in check_domain()
Thomas Sokolowski
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Clean up single_reaction behavior for Cyl.SurfacePlanarSurfaceInterfaceSingle
Thomas Sokolowski
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Put MixedPair1DStatic on correct ignore list in check_domain()
Thomas Sokolowski
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Revise domains for Cyl.Surface->PlanarSurface transfer
Thomas Sokolowski
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Some cleanup of deprecated stuff
Thomas Sokolowski
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Fixes to make MixedPair1DStatic work with the new interface situation
Thomas Sokolowski
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PlanarSurfaceCylindricalSurfaceInteraction -> PlanarSurfaceDiskSurfaceInteraction
Thomas Sokolowski
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New testShell type MixedPair2DStatictestShell, which is for making a
Thomas Sokolowski
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Minor fixes
Thomas Sokolowski
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Commits on Sep 20, 2013

Clean up test pair class definitions a bit
Thomas Sokolowski
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Change order of initialization in MixedPair1DStatictestShell
Thomas Sokolowski
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Same class reorganization for the pair classes
Thomas Sokolowski
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Extend Disk.project_point() method to the case in which the position
Thomas Sokolowski
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Minor fixes
Thomas Sokolowski
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Fix structure functions for Plane->Disk case
Thomas Sokolowski
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Commits on Sep 24, 2013

Useful comments
Thomas Sokolowski
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Fixes in fire_single_reaction() and make_new_domain()
Thomas Sokolowski
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Commits on Sep 25, 2013

New exception 'ShellUpdateError' to be able to catch it specifically
Thomas Sokolowski
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Only add new single to the scheduler after all checks have been made
Thomas Sokolowski
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Replacement '!= None' -> 'is not None'
Thomas Sokolowski
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Commits on Sep 26, 2013

New method dof() which returns degrees of freedom for particle
Thomas Sokolowski
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Make dof() function accessible to Structure etc.
Thomas Sokolowski
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New surface overlap checker method that allows for two ignored structures
Thomas Sokolowski
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Ignore reactant structures when placing product in BD mode
Thomas Sokolowski
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Some cleanup of stuff that did not work
Thomas Sokolowski
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Commits on Sep 30, 2013

New function all_feq to check whether all entries of a difference
Thomas Sokolowski
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Replace '==' by feq() or feq_all() in assert statements
Thomas Sokolowski
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Commits on Oct 1, 2013

Check whether particles are immobile and there is nothing to do
Thomas Sokolowski
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Commits on Oct 2, 2013

Fix unbinding Disk->Plane in BD mode
Thomas Sokolowski
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Introduce MINIMAL_SEPARATION_FACTOR into BD mode (via Defs.hpp)
Thomas Sokolowski
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Ignore structure overlap checks for static particles in BD mode
Thomas Sokolowski
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Minor change
Thomas Sokolowski
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Commits on Oct 3, 2013

More debug info for multis
Thomas Sokolowski
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Ignore surface overlaps for all immobile particles in Multis
Thomas Sokolowski
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Activate hardcore BD limit and overlap remover
Thomas Sokolowski
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Remove costly debug statement
Thomas Sokolowski
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Commits on Oct 11, 2013

Allow user to specify time delay when reloading saved state
Thomas Sokolowski
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Commits on Oct 14, 2013

Some fixes in shellmaking for cylindrical domains
Thomas Sokolowski
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Cleanup
Thomas Sokolowski
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Commits on Oct 17, 2013

Weaken an assert condition in pair.py to allow for formation of
Thomas Sokolowski
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Equalize a_R to zero if it is very close to zero
Thomas Sokolowski
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Allow user to connect edges of parallel structures and treat transitions
Thomas Sokolowski
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Commits on Oct 18, 2013

Some comments and clarifying renamings in distance measurement functions
Thomas Sokolowski
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Change logger name
Thomas Sokolowski
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Check whether particle is in bounds before applying BCs in
Thomas Sokolowski
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small fix
Thomas Sokolowski
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Commits on Oct 21, 2013

Two changes to egfrd.py
Thomas Sokolowski
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Cleanup
Thomas Sokolowski
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Commits on Nov 15, 2013

Improve some simulator consistency checks + increase
Thomas Sokolowski
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Commits on Apr 11, 2014

Examaple script for simple reaction in 2D
Thomas Sokolowski
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Commits on Jun 3, 2014

Include utils.cpp into StructureFunctions.hpp to fix some
Thomas Sokolowski
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Commits on Oct 21, 2014

Commits on Oct 22, 2014

Fix python logger, code from motiyoshi was not correct for old_fashioned case (Py2.6)
Seynen
committed

Commits on Oct 23, 2014

Commits on Oct 27, 2014

Commits on Dec 1, 2014

Added sample unit test files
Luc Blom
committed

Commits on Dec 3, 2014

Merge pull request #107 from Seynen/develop
YetAnotherTomek
committed
Minor cleanup in egfrd.py
Thomas Sokolowski
committed
Replace an assert by raise exception in shells.py
Thomas Sokolowski
committed
Fix a typo
Thomas Sokolowski
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Merge remote-tracking branch 'upstream/develop' into develop
Thomas Sokolowski
committed
Merge pull request #108 from YetAnotherTomek/develop
YetAnotherTomek
committed

Commits on Dec 5, 2014

Removed compiler flag 'no-unused-local-typedefs'.
Seynen
committed

Commits on Dec 8, 2014

Code cleanup, removed 'unused' types/variables/defines. Less warnings (<10).
Seynen
committed

Commits on Dec 9, 2014

Fixed 'narrowing'-warning.
Seynen
committed

Commits on Dec 12, 2014

Merge pull request #109 from Seynen/develop
YetAnotherTomek
committed

Commits on Mar 24, 2015

Commits on Mar 25, 2015

Commits on Aug 30, 2016

Commits on Sep 2, 2016

Commits on Sep 6, 2016

Move info printing in step() to prevent SEGFAULTS
YetAnotherTomek
committed

Commits on Sep 7, 2016

Commits on Sep 8, 2016

Commits on Nov 2, 2016

Commits on Nov 4, 2016

Commits on Nov 7, 2016

Yet more informative debug output in newBDpropagator
YetAnotherTomek
committed

Commits on Nov 8, 2016

Commits on Nov 9, 2016

Commits on Nov 14, 2016

Commits on Mar 3, 2017

Fixes to failing typecast in binding of particle model
YetAnotherTomek
committed

Commits on Mar 6, 2017

Add CPP-flag '-std=gnu++98' as default for compilation
YetAnotherTomek
committed

Commits on Mar 7, 2017

Commits on Mar 8, 2017

Commits on Mar 30, 2017

Small fix
YetAnotherTomek
committed

Commits on Jun 7, 2017

Fix for GCC 4.9 and above (template arg deduction error in range_from_range). (#112)
Seynen
authored

Commits on Jun 8, 2017

Small changes to allow for correct resetting of BD_ONLY_FLAG upon reloading
Thomas Sokolowski
committed

Commits on Aug 31, 2017

Commits on Oct 17, 2017

Commits on Dec 4, 2017

Merge pull request #115 from YetAnotherTomek/develop
YetAnotherTomek
authored