 Jacob Czech
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872384bede
Bugfix: fix some problems found by coverity.
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7 年之前 |
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Jacob Czech
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0d976434fe
Add unique molecule id to molecule trigger output
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7 年之前 |
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Jacob Czech
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903321422b
Change optimization flag in CMake file.
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7 年之前 |
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Jacob Czech
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e0d6b12bd1
Bugfix: double free introduced during merge.
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7 年之前 |
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Jacob Czech
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33e4e4f818
Merge branch 'master' into dynamic_meshes_pymcell
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7 年之前 |
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Jacob Czech
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39a04baa0d
Merge branch 'mcellNeuronECC' into dynamic_meshes_pymcell
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7 年之前 |
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Jacob Czech
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a9bc5b8842
Merge remote-tracking branch 'origin/dynamic_meshes'
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7 年之前 |
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Jacob Czech
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bc89eb1dea
Fix clang compilation problems.
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7 年之前 |
 Bob Kuczewski
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bae6815842
Moved mcell_logo.gif file for Doxygen and noted errors.
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7 年之前 |
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Bob Kuczewski
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fe7d464417
Added an MCell logo file in the doxygen/html file and ignored others.
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7 年之前 |
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Bob Kuczewski
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e920b89187
Added a doxygen subdirectory containing a Doxyfile for MCell.
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7 年之前 |
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Jacob Czech
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fc1a011d09
Bugfix: all (vol) mol surf class + rxn.
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7 年之前 |
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Jacob Czech
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75af2503ae
Small test to use pyMCell from a Jupyter notebook.
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7 年之前 |
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Jacob Czech
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4446bf8021
Put all python stuff in same subdir.
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7 年之前 |
 Oliver K. Ernst
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2ee6d31a3b
Added function to run multiple iterations at once. This did not improve the simulation speed.
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7 年之前 |
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Jacob Czech
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1130752c89
Finish updating copyright dates.
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7 年之前 |
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Jacob Czech
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0f63b8bc23
Merge branch 'mcellNeuronECC' into dynamic_meshes_pymcell
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7 年之前 |
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Jacob Czech
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d5a8e9031b
Update copyright.
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7 年之前 |
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Jacob Czech
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7ae23f6c76
Use pragma once.
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7 年之前 |
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Jacob Czech
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55c9e8bf3d
Add some arg parsing.
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7 年之前 |
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Oliver K. Ernst
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aa54c625df
Fixed the problem of a slow reaction-rate-update for non-diffusing unimolecular surface reactions. Here, was able to get x10 faster by reorganizing some loops and a little tracking via linked lists. In the future (big note for future pyMCell) this should be done by a hash table of molecule species to reaction that is being updated - should be even more efficient.
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7 年之前 |
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Oliver K. Ernst
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199a5df7d7
Reversed the order of adding to the MCell species list for list releases so it is correct. Really there should also be a typemap involved here
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7 年之前 |
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Oliver K. Ernst
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4e5584c252
Fixed the bug in the fix to the bug for list releases. Also, fixed a bug in the diameter parameter :/
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7 年之前 |
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Oliver K. Ernst
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95fb0e26e9
Fixed a bug in the list release function. Also added a diameter option to specify the diameter to search within to place surface molecules (default is set to 0 = fails almost always)
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7 年之前 |
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Oliver K. Ernst
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0a2e652f9d
Added fix in wrapper function to release surface molecules on surface by list. Also updated example test script.
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7 年之前 |
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Oliver K. Ernst
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aeab5308be
Added list release function called mcell_create_list_release_site in mcell_release.c to create list releases. Also comes with a handy Python wrapper function create_list_release_site.
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7 年之前 |
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Oliver K. Ernst
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0eb087f4c5
First pass at a functnction to update multiple rate constants at once: mcell_modify_multiple_rate_constants in mcell_reactions.c. I get about a factor 10 speedup with this (depends on how many reactions you update at once - here about 2000 reactions took 10 seconds for 2000 separate function calls vs about 0.5 seconds for a single call). Updating the scheduler for unimolecular non-diffusing reactions still takes a while - a real programmer could probably see some efficicent trick in this part of the code, I just copied the for loops from existing code. Also, implemented here are typemaps to automatically convert the lists of strings and doubles from Python (unicode, float) to C (char*,double). This requires Python 3.X > 3.3 (because Python struggles). I think the previous Python limit was >3, but below 3.3 the current typemaps aren't compatible because they use newer C api functions.
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7 年之前 |
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Oliver K. Ernst
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f8dc1deafc
Fixed a major bug in the mcell_modify_rate_constant function in mcell_reactions.c.
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7 年之前 |
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Oliver K. Ernst
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91a17618fa
Minor change to the create_species function in pymcell_helpers.py to allow specification of custom spacetime steps
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7 年之前 |
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Oliver Ernst
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44b743f8c7
Added function in mcell_init for PyMCell to change the seed of the sim.
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7 年之前 |
