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5608f87c15
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bond/react:unfix_deletes_internal_groups
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2019-03-13 21:55:17 -06:00 |
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d08979737c
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bond/react:partially_revert_bonding_atom_choice
choose closest eligible bonding partner, unless directly bonded (in which case we assume a bond-breaking reaction)
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2019-02-13 22:56:56 -07:00 |
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13f1c7d2d7
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bond/react_VLA_compliance
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2019-02-13 20:42:52 -07:00 |
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7a10ac2019
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bond/react:reaction_constraints
introduce a distance constraint between any two reaction-site atoms, in order for reaction to occur
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2019-01-22 23:14:58 -07:00 |
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94dc5e1133
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bond/react: strict reaction limit
also, fixes a bug in the 'serial' build introduced in #1099, wherein no reactions could occur in some cases
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2019-01-17 23:13:21 -07:00 |
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b0af54ac37
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bond/react:limit reaction occurrences
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2019-01-13 00:07:03 -07:00 |
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8387b2953b
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bond_react:correctly delete internally-created fixes
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2019-01-09 23:14:24 -07:00 |
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9ae84bc367
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bond/react: check template for topology overflow
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2019-01-06 17:07:35 -07:00 |
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6e866f82a7
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correct typo (missing increment operator) in fix bond/react
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2018-12-29 16:31:44 -05:00 |
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afaaf442d3
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bond/react doc tweaks 2
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2018-12-06 21:32:10 -07:00 |
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d14404254e
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check for illegally deleted atoms
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2018-12-01 15:18:11 -07:00 |
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53e66dcd15
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bond/react: delete atoms
allows deleting of a user-specified set of atoms, based on topology
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2018-11-30 22:35:10 -07:00 |
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84fcf01bed
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bond/react: allow custom update of charges near template edges
also, fixes a bug introduced in PR #1189, when not using stabilization
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2018-11-06 19:59:22 -07:00 |
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6d1ea2d0b1
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broke smooth restarts at some point. fixed
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2018-11-05 00:46:53 -07:00 |
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f7aa01d74a
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bond/react: convert group-ID to group-ID-prefix
enables consistent syntax when using custom groups
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2018-11-03 11:57:46 -06:00 |
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0c7c344e19
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additional molecule templates sanity-check
thanks to Sagar Patil for report
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2018-11-01 01:26:12 -06:00 |
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5821a5ecc8
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bond/react: custom group with stabilization option
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2018-11-01 01:04:45 -06:00 |
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3faecc4d28
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add option to update all atoms' atomic charges
option to update all atomic charges, even when edge atoms are defined
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2018-10-30 22:11:52 -06:00 |
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e9ed95c2db
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Merge pull request #1108 from akohlmey/fix-sprintf-buffer-overflows
Avoid more buffer overflows due to using snprintf() on fixed size buffers
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2018-09-18 16:57:10 -04:00 |
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9c27548a5c
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more replacing of sprintf() with snprintf()
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2018-09-06 10:45:48 -04:00 |
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ae7b18fb77
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only one call to extract needed
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2018-09-05 00:11:50 -06:00 |
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efd81a2854
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Merge branch 'master' into bond/react-efficient-competing_reactions
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2018-09-04 22:34:04 -06:00 |
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a5f7b418de
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bond/react: efficient competing reactions
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2018-09-04 22:06:49 -06:00 |
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40e7ea83a3
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Merge pull request #1084 from rbberger/cmake-and-warning-suppression-bugs
Fixes various compilation issues
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2018-08-29 07:49:52 -06:00 |
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ed61ed5b56
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Merge pull request #1082 from jrgissing/bond/react-competing-reactions
Bond/react: treatment of simultaneous competing reactions
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2018-08-29 07:49:25 -06:00 |
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71bc72ec13
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formatting: add additional space to avoid bad syntax highlights
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2018-08-27 22:13:43 -04:00 |
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b05aa62c49
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correctly exclude atoms from simultaneous competing reactions
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2018-08-25 15:46:48 -06:00 |
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38a998c03c
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Fix misc. warnings (#1076)
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2018-08-24 14:58:28 -06:00 |
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92a4dc25b1
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Fix unused params in packages (#1076)
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2018-08-24 10:42:08 -06:00 |
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2baa0b3452
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nasty little bug
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2018-08-22 03:32:17 -06:00 |
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fd0b041e0e
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remove debugging comments
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2018-08-21 21:10:34 -06:00 |
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95d462e5d3
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bond/react: better template validity check
now always throws error if a bond type changes, but both of of the involved atoms are too close to edge of template
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2018-08-21 02:28:53 -06:00 |
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5c4bf8ac47
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bond/react: optional EdgeIDs take2
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2018-06-26 20:40:02 -06:00 |
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ebe622ff7d
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make edge atoms optional
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2018-06-26 09:35:38 -06:00 |
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3750e0a427
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resolve newton setting and parallel disparities, improve syntax error catching
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2018-06-16 11:13:52 -06:00 |
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8303d1a375
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allow smooth restarts
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2018-05-13 22:49:54 -06:00 |
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f864584bce
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correct small bugs found by coverity scan static code analysis
- in fix rigid, rigid/small, and poems, a string argument was
incorrectly assigned to a %d format
- plug two small memory leaks in fix bond/react
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2018-05-11 00:43:09 -04:00 |
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863a85353a
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type reassignment bugfix for edge atoms
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2018-05-09 23:55:04 -06:00 |
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941d289a69
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cosmetic changes to avoid compiler warnings
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2018-05-06 10:54:34 -04:00 |
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e1f9ee1347
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fix1
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2018-05-06 01:04:23 -06:00 |
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916ed71760
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fix bond/react final touches
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2018-05-06 00:34:03 -06:00 |
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c8a0689d78
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correct typo in converting c-library header includes to c++ styles
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2018-05-03 15:44:17 -04:00 |
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28786ef99b
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tweak to header file names
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2018-05-03 11:49:27 -06:00 |
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caa990746e
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bugfix
fixes crash e.g. when building on Ubuntu for Windows
thanks to Márk Jenei (University of Cambridge) for submitting error report
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2018-04-18 22:27:12 -06:00 |
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e8eeb52636
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fix memory leaks detected by valgrind
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2018-03-03 19:31:53 -05:00 |
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21364f38b0
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gatherv fix, take 2
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2018-03-01 23:11:46 -07:00 |
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51b19dfd1a
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plug memory leak in fix bond/react
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2018-02-25 14:10:28 +01:00 |
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7d1de34533
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gatherv fix, doc updates
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2018-02-24 22:49:28 -07:00 |
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d5e43a9ab1
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whitespace cleanup and reindent
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2018-02-23 10:20:29 +01:00 |
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8fef7880e7
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dead code removal and loop construct fixes to silence compiler warnings.
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2018-02-22 02:23:57 -05:00 |
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