 Jed Wing
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0258a9edb8
Update to handle coincident surfaces. There was a bug in the handling of
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16 年之前 |
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Jed Wing
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2973d40851
Minor efficiency update to count_util.c; wrapped a couple of long lines in count_util.h.
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16 年之前 |
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Jed Wing
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bd4fd8ff81
Updated testsuite to include complete surface macromol numerical validation.
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16 年之前 |
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Jed Wing
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871bebe6ed
A few necessary modifications for the last batch of regression tests added.
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16 年之前 |
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Jed Wing
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3190e4530c
Added a few more regression tests and an automated script to test them.
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16 年之前 |
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Jed Wing
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12867fb934
Fixed incorrect reporting of reaction products in reaction probability report.
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16 年之前 |
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Jed Wing
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ba96114988
Merging across minor bugfixes and the continued expansion of the test suite.
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16 年之前 |
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Jed Wing
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29875c845e
Fixed a bug I introduced when I transplanted code from mdlparse.y to mdlparse_util.c. The bug inverts the orientation of molecules in COUNT statements when they are specified with orientation marks inside quotation marks ("molecule'").
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16 年之前 |
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Jed Wing
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8dc08b2f31
Fixed up articles array to match types array from previous commit.
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16 年之前 |
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Jed Wing
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3cc88249dc
Fixed up type labels which were out-of-sync now that obsolete symbol types have been removed.
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16 年之前 |
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Jed Wing
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2dcfa50048
Updates to macromolecules test suite.
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16 年之前 |
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Jed Wing
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b3d0096fae
Fixing two bugs related to macromolecular reaction parsing.
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16 年之前 |
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Jed Wing
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be1051e2f9
Added non-mixed variant of macromolecules test.
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16 年之前 |
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Jed Wing
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99081511fd
Adding updated test facilities. Fixed a few minor issues found during testing.
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16 年之前 |
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Jed Wing
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c534f094df
Merged across bugfixes from the development tree.
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16 年之前 |
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Jed Wing
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264e8f7eae
Fixed a parser-related bug in the new code for dealing with viz output blocks.
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16 年之前 |
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Jed Wing
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146e9472fd
Fix for hangs I introduced with the output barriers patch. Under certain circumstances, the code would go into an infinite loop...
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16 年之前 |
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Jed Wing
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837ffe8651
Change to prevent output files from including molecules at future locations.
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16 年之前 |
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Jed Wing
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cb865401a4
NOTIFICATIONS { ALL_NOTIFICATIONS = OFF } was not being properly overridden by the -logfreq command-line argument.
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16 年之前 |
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Jed Wing
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b55f885c83
Checkpoint reading was broken -- in particular, the READSTRING macro was broken, and the DATACHECK macro was being misused in 2 places.
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16 年之前 |
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Jed Wing
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830d213b6b
Commented a few new functions, added a little sanity checking, added a const, and gave more default warnings when compiling under GCC.
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16 年之前 |
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Jed Wing
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283ee37110
Final batch of new features/cleanups merged.
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16 年之前 |
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Jed Wing
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25e8d84637
Added ability to set memory partitioning via MEMORY_PARTITION_{X,Y,Z} directives; removed ability to set memory partitioning via environment variable.
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16 年之前 |
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Jed Wing
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aaa94b4e92
Cleaned up some error handling and error messages; renamed some loop variables to make their function clearer.
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16 年之前 |
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Jed Wing
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322ae77cd6
I made an error while transplanting the partition setting code from mdlparse.y to mdlparse_util.c, resulting in incorrect partitioning. This fixes it.
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16 年之前 |
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Jed Wing
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44e4e48a22
Eliminated a number of signed/unsigned inconsistencies to allow (nearly) warning-free compilation with -Wextra -Wshadow.
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16 年之前 |
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Jed Wing
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6cb9814b2b
Simplified mechanism for reconciling ITERATION_REPORT directive in the mdl file with -logfreq on the command line. Also, began reconciling signed/unsigned conflicts.
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16 年之前 |
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Jed Wing
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999dea9fba
Added --enable-unsafe-signals to enable "flush reaction output on signal" behavior. It's not guaranteed to work anywhere, but it generally does work, and allows partial output even if something dire happens.
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16 年之前 |
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Jed Wing
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9ef4cb7592
Switched 'VAR' and 'STR_VALUE' to 'var' and 'str_value' -- non-terminals which reference the old 'VAR' and 'STR_VALUE'. This is for ease of maintenance of a parallel code branch implementing conditionals.
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16 年之前 |
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Jed Wing
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917f49135c
Added new notification types for viz, reaction, and volume data output.
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16 年之前 |
