 borisk
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7d79bf11aa
Added test case in the testsuite that covers the bug with checkpointing and unimoleclar reaction with variable rates.
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12 年之前 |
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borisk
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7681677079
Added test case in the testsuite that covers the bug with checkpointing and unimoleclar reaction with variable rates.
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12 年之前 |
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borisk
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08a9cfbae5
Removed some leftover debugging messages - thanks Markus for pointing.
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12 年之前 |
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borisk
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6baf3d441f
Removed some leftover debugging messages - thanks Markus for pointing.
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12 年之前 |
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borisk
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c5e36be693
Jun Ma recently reported a bug in the code that represents itself as molecule's negative lifetime. He developed a very complex model and checkpointed at 174115 and later ran 1000 iterations more. That's where the negative lifetimes appear. After careful study of the model and the code I realized that the bug showed up under the combination of two simultaneous conditions: 1) checkpointing, 2) unimolecular reactions with variable rates. It appeared that variable rates files were not properly read and molecule's scheduling times were not properly set up. Applied code changes fix the problem.
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12 年之前 |
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borisk
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b7730d4b87
Jun Ma recently reported a bug in the code that represents itself as molecule's negative lifetime. He developed a very complex model and checkpointed at 174115 and later ran 1000 iterations more. That's where the negative lifetimes appear. After careful study of the model and the code I realized that the bug showed up under the combination of two simultaneous conditions: 1) checkpointing, 2) unimolecular reactions with variable rates. It appeared that variable rates files were not properly read and molecule's scheduling times were not properly set up. Applied code changes fix the problem.
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12 年之前 |
 Boris Kaminsky
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6f842a7d08
Merged with trunk
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13 年之前 |
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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 |
