 Bob Kuczewski
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8e25df058d
Only output the molecule-location data when dump_level > 0
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6 年之前 |
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Bob Kuczewski
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3919a2e349
Added dump option to mcell to allow additional (non-debug) output.
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6 年之前 |
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Bob Kuczewski
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5550e871e9
Unwrapped help lines in preparation for adding a "verbose" or "dump" flag.
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6 年之前 |
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Bob Kuczewski
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a9cd2360c0
Merge branch 'spatially_structured_mol_viz' of https://github.com/mcellteam/mcell into spatially_structured_mol_viz
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6 年之前 |
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Bob Kuczewski
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f5f5831895
Added some output statements to viz_output.c to allow importing into Java
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6 年之前 |
 Tom Bartol
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9483704c59
Change define of the constant called "NONSPATIAL" to be called "COINCIDENT" instead
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6 年之前 |
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Bob Kuczewski
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9ae2bd1dd0
Commented out a lot of the debug statements in viz_output.c.
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6 年之前 |
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Bob Kuczewski
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3f9312c34b
Implemented at least the "XYZ" (2D) option for spatial component positioning.
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6 年之前 |
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Bob Kuczewski
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5aae43bcc8
Corrected the paths in mdlr2mdl.py
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6 年之前 |
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Tom Bartol
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3dbea93aaf
Add flag to bngl component data structure to indicate desired type of spatial structure to use
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6 年之前 |
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Bob Kuczewski
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ca7b67616d
Merge branch 'spatially_structured_mol_viz' of https://github.com/mcellteam/mcell into spatially_structured_mol_viz
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6 年之前 |
 Tom Bartol
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5f5a30abab
Merge branch 'spatially_structured_mol_viz' of http://github.com/mcellteam/mcell into spatially_structured_mol_viz
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6 年之前 |
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Bob Kuczewski
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bfdf49457b
Pulled out the ugly "reference" code in set_component_positions_by_table
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6 年之前 |
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Tom Bartol
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4e316d321c
Add loc_x,y,z rot_axis_x,y,z and rot_angle to struct mol_comp_ss, as alternative to the t_matrix
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6 年之前 |
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Bob Kuczewski
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daa47e19b2
Merge branch 'spatially_structured_mol_viz' of https://github.com/mcellteam/mcell into spatially_structured_mol_viz
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6 年之前 |
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Bob Kuczewski
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b83afdcb5f
Added viz_output code to try to dump the mol_ss tables.
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6 年之前 |
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Tom Bartol
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2693280c3c
Initialize bngl molecule spatial structure to the identity matrix for molecules with no specified structure
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6 年之前 |
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Bob Kuczewski
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2f594a9243
Modified rules_py/mdlr2mdl.py to look in extensions/mcell for files.
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6 年之前 |
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Tom Bartol
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fe44ff9764
Merge branch 'spatially_structured_mol_viz' of http://github.com/mcellteam/mcell into spatially_structured_mol_viz
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6 年之前 |
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Bob Kuczewski
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aff7ac0b73
Restored the original write function while preserving the debug version.
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6 年之前 |
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Tom Bartol
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6f4920b611
Merge branch 'spatially_structured_mol_viz' of http://github.com/mcellteam/mcell into spatially_structured_mol_viz
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6 年之前 |
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Tom Bartol
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56e7dacdc6
bngl molecule spatial structure spec is optional, and should not include a diffusion constant block
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6 年之前 |
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Bob Kuczewski
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d5f36d3d24
Added forced file flush for testing, also print "=#= New Graph Pattern"
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6 年之前 |
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Bob Kuczewski
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54cc2e34bc
Merge branch 'spatially_structured_mol_viz' of https://github.com/mcellteam/mcell into spatially_structured_mol_viz
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6 年之前 |
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Bob Kuczewski
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e3a767925d
Remove diffusion constant definition from DEFINE_MOLECULE_STRUCTURES
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6 年之前 |
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Tom Bartol
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36b85a840f
Modify parser and helper functions to handle BNGL molecules with multiple components having the same name
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6 年之前 |
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Bob Kuczewski
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0cb3c2f0a9
Merge branch 'spatially_structured_mol_viz' of https://github.com/mcellteam/mcell into spatially_structured_mol_viz
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6 年之前 |
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Bob Kuczewski
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4f186f6c7a
Removed debug output to speed up simulation. Maybe a flag would be good!
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6 年之前 |
 Jacob Czech
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45244c5e2d
Python parsing of component loc and rot in MDLR.
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6 年之前 |
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Bob Kuczewski
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14461ce701
Initialized the spatial molecules properly and improved debug output
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6 年之前 |
