 Boris Kaminsky
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43372c58b8
Fixed bugs related to the trimolecular reaction probabilities calculation when one or two reactants are TARGET_ONLY. Made corresponding changes in the testsuite removing artificially big tolerances.
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14 年之前 |
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Boris Kaminsky
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59be74f91c
Fixed bugs related to the trimolecular reaction probabilities calculation when one or two reactanst are TARGET_ONLY. Made corresponding changes in the testsuite removing artificially big tolerances.
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14 年之前 |
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Boris Kaminsky
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d573816fd9
Added docstrings to the utility functions in 'main.py'.
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14 年之前 |
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Boris Kaminsky
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d61f0646e2
Added docstrings to the utility functions in 'main.py'.
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14 年之前 |
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Boris Kaminsky
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979bd5d5b7
Added TARGET_ONLY specifications for selected molecules. Removed statements in multiple tests descriptions that are already present through McellTest constructor.
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14 年之前 |
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Boris Kaminsky
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9ab3b2d1d0
Added TARGET_ONLY specifications for selected molecules. Removed statements in multiple tests descriptions that are already present through McellTest constructor.
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14 年之前 |
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Boris Kaminsky
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725f128849
Merged with trunk
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14 年之前 |
 Markus Dittrich
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913d4dca1f
Added a section explaining the tri-molecular reaction syntax to the QRG.
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14 年之前 |
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Boris Kaminsky
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4fed4053d5
Added three more messages during initialization describing separate sub-stages of the initialization process.
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14 年之前 |
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Boris Kaminsky
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b89283f290
Added three more messages during initialization describing separate sub-stages of the initialization process.
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14 年之前 |
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Boris Kaminsky
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371b8cbde2
Performed multiple changes regarding new representation of vertices through 'world->all_vertices' array and shared walls through 'world->walls_using_vertex' array. Removed references to NORMAL in the parser and testsuite.
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14 年之前 |
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Boris Kaminsky
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8dd6479dde
Performed multiple changes regarding new representation of vertices through 'world->all_vertices' array and shared walls through 'world->walls_using_vertex' array.
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14 年之前 |
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Boris Kaminsky
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08849861c7
Changed the format of the report on the timing of MCell run. Now we report separate times for initialization and simulation (both user and system). Also added message about creating geometry during initialization.
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15 年之前 |
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Boris Kaminsky
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aa111285ec
Changed the format of the report on the timing of MCell run. Added message about creating geometry during initialization.
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15 年之前 |
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Boris Kaminsky
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1d676fadaf
Merged with trunk
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15 年之前 |
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Boris Kaminsky
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26f70ec56f
Testing new version of MCell runtime reporting
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15 年之前 |
 Jed Wing
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8568b476d8
Bugfix: GENERIC_MOLECULE + surface rxns are now correctly added to the rxn hash table.
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15 年之前 |
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Jed Wing
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08c65757ff
Bugfix: surface reversibility now works for volmol + surface rxns.
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15 年之前 |
 Tom Bartol
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19e283f967
Updated value of Avogadro constant to latest recommended value:
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15 年之前 |
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Boris Kaminsky
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60332a2db4
Implemented a global flag that checks whether the shared walls information is necessary to gather during the initialization phase.
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15 年之前 |
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Boris Kaminsky
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8fc48dacee
Implemented a global flag that tells whether the shared walls information is necessary to create during the initialization phase.
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15 年之前 |
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Boris Kaminsky
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f738e709f5
Changed the way how mesh shared vertices are defined that resulted in the significant speedup and improvement in the surface reaction code. Thanks Tom and Jed for the detailed suggestions and thoughtful discussions.
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15 年之前 |
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Boris Kaminsky
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79461f7123
Changed the way how shared mesh vertices are defined that resulted in the significant speedup and improvement in the surface reaction code.
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15 年之前 |
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Boris Kaminsky
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34a6808ec4
Changed code in 'init_sim()' so that we create shared wall vertices information only when surface reactions are present in the simulation.
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15 年之前 |
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Boris Kaminsky
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5f4c3b62a4
Removed temporary commented part of the code in the function 'install_emergency_output_hooks()'.
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15 年之前 |
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Boris Kaminsky
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8cefd9cdb6
Changed code in 'init_sim ( )' so that we create shared wall vertices information only when surface reactions are present in the simulation.
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15 年之前 |
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Boris Kaminsky
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c2345eb861
Fixed bug in setting flags for trimolecular collisions and changed part of the code related to the molecule collision report.
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15 年之前 |
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Boris Kaminsky
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5438d11793
Fixed bug in 'diffuse_3d_big_list()' and changed code related to the molecule collision report.
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15 年之前 |
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Boris Kaminsky
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bb6b3fe720
Merged trunk
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15 年之前 |
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Markus Dittrich
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c5cbca2d2e
Added description for new MOLECULE_COLLISION_REPORT keyword
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15 年之前 |
