c6fdd8ddb6
get rid of some non-ASCII characters
2024-09-25 22:01:42 -04:00
5fbdf155e5
remove unused variables
2024-08-27 08:57:42 -04:00
2ebe1f019f
avoid uninitialized data access in case there are no atoms owned by a process
2024-08-26 21:14:44 -04:00
99153f20be
refactor how reactions are skipped
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better treatment of allowing all possible reactions when using 'overlap' keyword of 'create_atoms' feature
2024-08-25 21:55:19 -04:00
a1a72f741a
update docs with recent paper
2024-08-25 14:54:51 -04:00
6514dbb4b6
refactor how to insert atoms
2024-08-25 13:42:51 -04:00
732be489a3
another error check
2024-08-15 19:48:17 -04:00
c68ea4fe1e
better place for error check
2024-08-15 19:09:16 -04:00
27bf4d7974
bond/react: change where to reset mol IDs
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needs to happen after topology changes communicated
2024-08-15 18:15:30 -04:00
445251d569
simplify logic for checking whether occasional neight list needs to be rebuilt
2024-07-22 14:11:04 -06:00
e28f93dca4
programming style updates
2024-01-19 00:03:13 -05:00
4015d1bb39
initialize static string buffers to empty strings
2024-01-19 00:02:50 -05:00
3ae4779c7f
convert defines into static constexpr
2024-01-18 23:59:33 -05:00
0b0b35856c
remove unnecessary newton_bond considerations
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related issue: fix bond/react may need modifications to work as expected when certain special_bond settings are used or when specials are defined explicitly in molecule templates and do not include all neighbors
2024-01-10 19:49:15 -05:00
a6b00a60b2
additional check/warning for valid templates
2024-01-03 20:31:22 -05:00
600eaf837b
update preferred contact info
2024-01-03 16:20:04 -05:00
4d2aed8937
bug fix
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for when reaction site has angles, but post-reaction template has none (same for dihedrals, impropers)
2023-12-18 11:15:56 -05:00
1039f86037
remove unnecessary restriction
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do not check for comm cutoff when initiator atoms are directly bonded
2023-08-26 14:29:07 -04:00
cd5ebb86c8
inserting atoms: correct logic for per-atom mass
2023-08-25 21:37:57 -04:00
564a8e88c1
use blanks on both sides of comparison operators not only one, remove blanks next to parenthesis
2023-07-11 10:31:16 -04:00
900c6cf545
remove unused variable
2023-07-01 18:27:35 -04:00
03b25dcbaa
update error checks
2023-06-13 21:25:58 -04:00
14a27e98c9
fix for when deleting atoms
2023-06-13 21:09:29 -04:00
53f90fff3d
final touch
2023-06-12 21:28:51 -04:00
603e397919
get_totalcharge routine
2023-06-12 20:20:45 -04:00
c214f654b6
update communicated rxn instances to doubles
2023-06-11 19:27:58 -04:00
23552d4b7a
refactor to carry around extra per-reaction values
2023-06-11 17:59:16 -04:00
0d8623c3f2
simplified logic from clang-tidy
2023-03-26 21:33:37 -04:00
ff72268430
rate_limit keyword speedup
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was previously checking for reactions when even one reaction would exceed rate limit
2023-02-18 16:33:57 -05:00
0ead219a8b
backward compatibility with restart
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keep new maxline limit (1024 chars), but old react-ID length limit (256 chars)
2023-02-18 00:37:28 -05:00
eab3c4d382
better map file error handling
2023-02-12 15:08:46 -05:00
b465594aec
bond/react restarts bugfix
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introduced with recent 'rate_limit' keyword
2023-02-12 00:05:07 -05:00
ddc23bb3bf
refactor step 2: reorder when to dedup reactions
2023-02-05 15:14:57 -05:00
162ee16825
refactor step 1: delay check for ghosts
2023-02-05 13:46:29 -05:00
e7fc590f91
simplify and correct dedup routine
2023-02-05 12:00:33 -05:00
843cc98531
Merge pull request #3569 from jrgissing/type-labels-bond/react-examples
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Type labels for bond/react examples
2023-01-05 19:22:43 -05:00
21b14cd7e4
remove now-redundant code
2022-12-20 12:46:59 -05:00
7383a8957b
refactor atom stabilization code
2022-12-20 11:41:11 -05:00
b30ce3ff32
next round of IWYU updates
2022-12-12 01:07:46 -05:00
e0792d3a62
apply code changes suggested by clang-tidy
2022-12-11 18:44:50 -05:00
b0accb4ebf
replace atoi() with suitable utility functions
2022-12-09 16:56:17 -05:00
4ba604fd37
Merge branch 'collected-small-changes' into reset-command
2022-11-23 13:38:40 -05:00
2b9d5c6c9a
rename reset metacommands to use reset_atoms
2022-11-21 17:20:29 -05:00
67c5bb2a0d
small programming style updates
2022-11-15 21:13:22 -05:00
eee6862f25
copy error + other fixes
2022-11-12 02:13:39 -05:00
86172eb75f
bond/react restart revision numbers
2022-11-11 17:16:37 -05:00
0890bc026e
ensure backward compatibility of restarts
2022-11-11 15:28:36 -05:00
aaa8e9d219
populate atoms2bond in bond/react
2022-11-09 17:51:21 -05:00
b2652a4542
fix writing restarts without rate_limit
2022-11-05 01:22:54 -04:00
565853ee07
rescale_charges keyword
2022-11-05 01:05:45 -04:00
