 Boris Kaminsky
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f8183486c4
Made changes in the part of the code that checks for the overlapped walls by explicitly introducing the accuracy of the comparison. While accuracy is presently set to EPS_C it is now easy to change it by changing MESH_DISTINCTIVE directive all from one place. Added several new tests to the testsuite.
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13 年之前 |
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Boris Kaminsky
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b7dd06aeab
Made changes in the part of the code that checks for the overlapped walls by explicitly introducing the accuracy of the comparison. While accuracy is presently set to EPS_C it is now easy to change it by changing MESH_DISTINCTIVE directive all from one place. Added several new tests to the testsuite.
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13 年之前 |
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Boris Kaminsky
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c6801cddc5
Clarified the description of the units of rate of the reactions that involve surface molecules.
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13 年之前 |
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Boris Kaminsky
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b0e0488460
Clarified the description of the units of rate reactions that involve surface molecules.
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13 年之前 |
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Boris Kaminsky
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367e38b722
Merged with trunk.
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13 年之前 |
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Boris Kaminsky
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c98bdbb2fd
Removed function declaration from '.h' file that is declared static in '.c' file. MCell issued warning during compilation because of the mismatch.
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13 年之前 |
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Boris Kaminsky
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13488603a1
Removed function declaration from '.h' file that is declared static in '.c' file. MCell issued warning during compilation because of the mismatch.
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13 年之前 |
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Boris Kaminsky
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3defedf110
Merged with trunk
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13 年之前 |
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Boris Kaminsky
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ca754766f0
Merged with trunk
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13 年之前 |
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Boris Kaminsky
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202d6fc57b
Fixed syntax error in function's name
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13 年之前 |
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Boris Kaminsky
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25398fe949
Fixed syntax error in function's name
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13 年之前 |
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Boris Kaminsky
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d886b29568
Merged with trunk
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13 年之前 |
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Boris Kaminsky
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2084708108
Merged with trunk
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13 年之前 |
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Boris Kaminsky
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a6b1006be4
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.
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13 年之前 |
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Boris Kaminsky
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eadc07abbd
Added multiple new test cases
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13 年之前 |
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Boris Kaminsky
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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.
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13 年之前 |
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Boris Kaminsky
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bda4a997ee
Merged with trunk
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13 年之前 |
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Boris Kaminsky
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f2d560ffa9
Merged with trunk
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13 年之前 |
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Boris Kaminsky
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4f9c2861c9
Changed the name of the command-line option from 'no_walls_overlap_check' to the more generic 'with_checks=(yes/no)'. The default option is 'yes'. Updated QRG.
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13 年之前 |
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Boris Kaminsky
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d9f2ae880e
Changed the name of the command-line option from 'no_walls_overlap_check' to the more generic 'with_checks=(yes/no)'. The default option is 'yes'. Updated QRG.
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13 年之前 |
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Boris Kaminsky
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f2828acb2f
Merged with trunk
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13 年之前 |
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Boris Kaminsky
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22c1f6b67d
Merged with trunk
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13 年之前 |
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Boris Kaminsky
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a76402bf0f
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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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 |
