hungerzs/mcell: cell modeling for microphysiology @ binary_reaction_output

Markus Dittrich fb19a4d42b Merged in changes from trunk.		11 年之前
..
01-volume_highconc.mdl	d0e42d84d0 Changed reaction rate in the test file for VVV reaction including 2 TARGET_ONLY molecules. Changed equilibrium value and tolerances for this kind of reaction.	14 年之前
02-volume_highconc_noacc3d.mdl	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.	14 年之前
03-surface.mdl	fb19a4d42b Merged in changes from trunk.	11 年之前
04-surface.mdl	43ee6bba5d Added four tests to the testsuite that cover several simultaneously run bimolecular and trimolecular reactions.	12 年之前
06-surface.mdl	5ee0f3fade Cleaned up and commented several of the test files.	16 年之前
07-region_borders.mdl	f2e3005253 Together with Markus wrote a document 'Policy on surface product placement in reactions between surface molecules' and placed document in src/docs. Implemented this new policy. This policy: 1) generalizes how we replace static and non-static surface reactants when we have multiple static and non-static surface products, 2) establishes rules on surface products placement in the presence of restrictive region borders. Fixed bug that allowed duplicate surface classes in the list of wall's surface classes. Fixed bug that allowed multiple SURFACE_CLASS statements inside DEFINE_SURFACE_REGIONS definition. Created multiple new test cases in the testsuite.	13 年之前
08-region_borders.mdl	e6fb22be7c Added tests for several keywords. Clarified QRG regarding use of ALL_ENCLOSED keyword and region element specifier commands. Improved syntax used for multiple region element specifier commands.	13 年之前
09-region_borders.mdl	24939a85ce Removed keyword GENERIC_MOLECULE. Implemented instead three new keywords ALL_MOLECULES, ALL_VOLUME_MOLECULES, ALL_SURFACE_MOLECULES that should be used as part of the surface property command. E.g. ABSORPTIVE=ALL_MOLECULES has the meaning that all volume molecules are absorptive on the region walls and all surface molecules are absorptive on the region borders with declared surface class. The keywords ALL_VOLUME_MOLECULES and ALL_SURFACE_MOLECULES are self-explanatory. Added new tests covering new keywords.	13 年之前
10-surf_properties_all_molecules.mdl	24939a85ce Removed keyword GENERIC_MOLECULE. Implemented instead three new keywords ALL_MOLECULES, ALL_VOLUME_MOLECULES, ALL_SURFACE_MOLECULES that should be used as part of the surface property command. E.g. ABSORPTIVE=ALL_MOLECULES has the meaning that all volume molecules are absorptive on the region walls and all surface molecules are absorptive on the region borders with declared surface class. The keywords ALL_VOLUME_MOLECULES and ALL_SURFACE_MOLECULES are self-explanatory. Added new tests covering new keywords.	13 年之前
11-surf_properties_all_volume_molecules.mdl	e6fb22be7c Added tests for several keywords. Clarified QRG regarding use of ALL_ENCLOSED keyword and region element specifier commands. Improved syntax used for multiple region element specifier commands.	13 年之前
12-all_enclosed_test.mdl	e6fb22be7c Added tests for several keywords. Clarified QRG regarding use of ALL_ENCLOSED keyword and region element specifier commands. Improved syntax used for multiple region element specifier commands.	13 年之前
13-restricted_border_reaction.mdl	f2e3005253 Together with Markus wrote a document 'Policy on surface product placement in reactions between surface molecules' and placed document in src/docs. Implemented this new policy. This policy: 1) generalizes how we replace static and non-static surface reactants when we have multiple static and non-static surface products, 2) establishes rules on surface products placement in the presence of restrictive region borders. Fixed bug that allowed duplicate surface classes in the list of wall's surface classes. Fixed bug that allowed multiple SURFACE_CLASS statements inside DEFINE_SURFACE_REGIONS definition. Created multiple new test cases in the testsuite.	13 年之前
14-restricted_border_product_placement.mdl	f2e3005253 Together with Markus wrote a document 'Policy on surface product placement in reactions between surface molecules' and placed document in src/docs. Implemented this new policy. This policy: 1) generalizes how we replace static and non-static surface reactants when we have multiple static and non-static surface products, 2) establishes rules on surface products placement in the presence of restrictive region borders. Fixed bug that allowed duplicate surface classes in the list of wall's surface classes. Fixed bug that allowed multiple SURFACE_CLASS statements inside DEFINE_SURFACE_REGIONS definition. Created multiple new test cases in the testsuite.	13 年之前
15-overlappingSRs.mdl	eadc07abbd Added multiple new test cases	13 年之前
16-surf_products_replace_reactants.mdl	eadc07abbd Added multiple new test cases	13 年之前
README	0c478854a8 Temporary commit of progress on reactions test suite.	15 年之前
overlappingSRs_Icosphere.mdl	eadc07abbd Added multiple new test cases	13 年之前
sphere_apex_region.mdl	fdf4e51f82 Added a new 'sphere with regions' file that is part of the new test.	14 年之前
surfmols.mdl	edfa497d11 Added surface reactions tests, and an additional version of the volume	16 年之前
test_info.py	548913c174 Removed 'tempsuite'.	15 年之前
test_reactions.py	43ee6bba5d Added four tests to the testsuite that cover several simultaneously run bimolecular and trimolecular reactions.	12 年之前
vizoutput.mdl	5ee0f3fade Cleaned up and commented several of the test files.	16 年之前
volcomplex.mdl	5ee0f3fade Cleaned up and commented several of the test files.	16 年之前
volmols.mdl	9ab3b2d1d0 Added TARGET_ONLY specifications for selected molecules. Removed statements in multiple tests descriptions that are already present through McellTest constructor.	14 年之前

		
				README
			
				The files in this directory test various aspects of reactions.  These are
derived from the tests I used for validation against old mcell behavior, as
well as against Boris' trimolecular code when I merged with macromolecules.
I'll give a summary below of what each file is, with more detailed information
in the header of each MDL file.

Note that most files which use the trimolecular pathway have TIME_STEP_MAX set
to 1.0.  They all should, I think.  The trimolecular code doesn't seem to
safely use safe_diffusion_step, so in order to make fair comparisons for
correctness, I turned off adaptive timesteps.

 * Test 01: All volume rxn types, traditional + trimol. code paths
 * Test 02: Same as test 1, but without ACCURATE_3D_REACTIONS
 * Test 06: All surface rxn types (vol surf, surf surf, vol vol surf, etc.)