 Boris Kaminsky
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178760881c
Improved surface reactions code. Now surface reactants cannot look across restrictive (REFLECTIVE/ABSORPTIVE) region boundaries when searching for reaction partners. Implemented policy on the surface products placement that takes into account whether they have restrictive region boundary properties. Added corresponding tests to the testsuite.
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13 年之前 |
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Boris Kaminsky
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8dc7d5b7d6
Merged with trunk.
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13 年之前 |
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Boris Kaminsky
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1d3472b768
Implemented several changes in the code related to the surface molecules reactions and product placement. Initiator molecule should not look across the restrictive region border (REFLECTIVE/ABSORPTIVE) in search for reaction partners. Also when all reactants are behind restrictive region border, the reaction products that are surface molecules, are placed inside restrictive region border.
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13 年之前 |
 Tom Bartol
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e53f117d70
During calculation of binding probability in prepare_reactions(), set
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13 年之前 |
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Boris Kaminsky
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3e25d25972
Added check for the overlapped walls during initialization. Command-line option '-no_walls_overlap_check' will skip this procedure.
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13 年之前 |
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Boris Kaminsky
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0597ef2cd9
Added check for the overlapped walls during initialization. Command-line option '-no_walls_overlap_check' will skip this procedure.
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13 年之前 |
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Boris Kaminsky
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4e51fe856d
Merged with a trunk
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13 年之前 |
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Boris Kaminsky
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21fa1f150f
Merged with a trunk
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13 年之前 |
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Tom Bartol
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d2c1a84cec
Fix segfault bug in counting macromolecules caused by not setting flag
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13 年之前 |
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Boris Kaminsky
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cb85267211
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.
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13 年之前 |
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Boris Kaminsky
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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.
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13 年之前 |
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Boris Kaminsky
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1487b6df93
Merged with trunk.
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13 年之前 |
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Boris Kaminsky
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31e7d3efe4
Merged with trunk.
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13 年之前 |
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Boris Kaminsky
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1f17310e52
Changed QRG to reflect new keywords ALL_MOLECULES, ALL_VOLUME_MOLECULES and ALL_SURFACE_MOLECULES in the context of surface properties.
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13 年之前 |
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Boris Kaminsky
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59e8ee43dc
Changed QRG to reflect new keywords ALL_MOLECULES, ALL_VOLUME_MOLECULES and ALL_SURFACE_MOLECULES in the context of surface properties.
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13 年之前 |
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Boris Kaminsky
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91841ff1ac
Merged with trunk.
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13 年之前 |
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Boris Kaminsky
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b015e854df
Merged with trunk.
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13 年之前 |
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Boris Kaminsky
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cbc19179f6
Removed GENERAL_SURFACE and associated species. This species was practically used only in the part of the code related to wall's multiple surface classes. But we checked for this species in multiple functions increasing overhead. The wall's multiple classes code was rewritten so that this species is not used anymore.
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13 年之前 |
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Boris Kaminsky
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4cdc23ff7e
Removed GENERAL_SURFACE and associated species. This species was practically used only in the part of the code related to wall's multiple surface classes. But we checked for this species in multiple functions increasing overhead. The wall's multiple classes code was rewritten so that this species is not used anymore.
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13 年之前 |
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Boris Kaminsky
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93338c5a17
Merged with trunk.
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13 年之前 |
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Boris Kaminsky
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02a6f09a20
Merged with trunk.
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13 年之前 |
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Boris Kaminsky
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9c891ce5e2
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.
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13 年之前 |
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Boris Kaminsky
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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.
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13 年之前 |
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Boris Kaminsky
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224ba51d46
Merged with trunk.
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13 年之前 |
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Boris Kaminsky
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e41a8d8f25
Merged with trunk.
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13 年之前 |
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Boris Kaminsky
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e8ee2ca7ab
Made two enhancements. First, the message 'Reaction probabilities generated for following reactions' is printed only if there are any reactions declared. Second, added a warning at the very end of the simulation if any reaction probabilities, including ones originated from the variable reaction rates, were greater than 1.
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13 年之前 |
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Boris Kaminsky
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d9aec0de14
Removed a comment.
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13 年之前 |
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Boris Kaminsky
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4fc11925ba
Made two enhancements. First, the message 'Reaction probabilities generated for following reactions' is printed only if there are any reactions declared. Second, added a warning at the very end of the simulation if any reaction probabilities, including ones originated from the variable reaction rates, were greater than 1.
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13 年之前 |
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Boris Kaminsky
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56ea5d8038
Merged with trunk
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13 年之前 |
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Boris Kaminsky
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3c88e5287e
Commit some trial changes.
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13 年之前 |
