a7c02bb6b8
Update fix_bond_react.cpp
2021-01-15 16:58:18 -05:00
3269f6a2e3
bond/react: reaction constraints bugfix
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bug could occur if subsequent reaction has fewer constraints than previous
2021-01-15 16:52:39 -05:00
b08582de69
fix bond/react buffer overflow: must not use sprintf to write to char variable
2020-12-30 09:55:46 -05:00
51a20175c9
more code formatting consistency changes for loops and conditionals
2020-12-30 09:47:45 -05:00
4f5192fa86
silence compiler warnings
2020-12-30 09:21:11 -05:00
382ade15fe
more consistent formatting of for/while loops and if statements
2020-12-30 09:09:08 -05:00
41d6648ac9
Merge pull request #2504 from jrgissing/bond/react-add-logic-to-constraints
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Bond/react: add logic to constraints
2020-12-23 15:39:30 -05:00
36c2947de7
silence compiler warnings
2020-12-07 01:06:47 -05:00
c332b5ff09
bugfix when no constraints
2020-12-02 13:02:10 -05:00
1e5611f776
finally, add the logic eval
2020-12-02 13:02:09 -05:00
855cf2146f
set for boolean constraint logic
2020-12-02 13:02:09 -05:00
63e8c83599
refactor constraints array into per-rxn
2020-12-02 13:02:09 -05:00
8df26f551e
clean constraints refactor
2020-12-02 13:02:09 -05:00
3a07eef523
refactor dihedral constraint
2020-12-02 13:02:09 -05:00
2af32741fd
refactor angle constraint
2020-12-02 13:02:09 -05:00
04e586c83d
refactor distanace constraint
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NOTE: messes up angle and dihedral constraints!
2020-12-02 13:02:09 -05:00
0de8f829f3
refactor Arrhenius constraint
2020-12-02 13:02:09 -05:00
29667da947
refactor RMSD constraint
2020-12-02 13:02:09 -05:00
206bc93026
bond/react:refactor constraint framework
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constraints are now an array of Contraint structs
2020-12-02 13:02:09 -05:00
8df0ee0dfa
make new warning more gentle
2020-11-27 12:15:31 -05:00
fcf5f34a49
memory fix
2020-11-27 12:08:09 -05:00
f42e907d30
update terminology
2020-11-19 19:06:33 -05:00
2a765efc8c
bond/react: update map file section
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retain old section title for backwards compatibility
2020-11-19 13:50:30 -05:00
348afb6867
correct cutsq check in proper place
2020-11-14 17:27:49 -05:00
c013e6db10
revert cutoff check
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add temporary fix for hybrid pair_style
2020-11-13 00:50:01 -05:00
f6975bf4eb
also add molecule_keyword to close_partner, for consistency
2020-11-09 14:10:41 -05:00
91d9cf97f3
bond/react:add molecule keyword
2020-11-09 13:47:29 -05:00
4d493fd082
relax cutoff checks
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also fixes some issues when using hybrid pair styles
2020-11-09 00:05:20 -05:00
badbb411eb
ringed structures bugfix
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previously, atoms at 'end' of symmetric ring could behave like edge atoms
2020-11-08 22:59:45 -05:00
124feffafa
bond/react: add helpful hint for recurring mistake
2020-11-04 21:35:25 -05:00
cb4549e0f2
bond/react:bugfix for delete atoms feature
2020-11-04 20:31:38 -05:00
adf74b3a22
use https://lammps.sandia.gov based URLs consistently
2020-10-21 16:45:30 -04:00
946a49662f
bond/react: rmsd constraint bugfix
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previously, eligible reactions could have been temporarily prevented, at the edge of the box, in serial
2020-10-02 18:43:35 -04:00
61b83901f5
bond/react: correct new custom_charges logic
2020-09-16 21:28:48 -04:00
55bc1baf97
bond/react: correct recent enum update
2020-09-16 20:33:45 -04:00
6faf436850
bond/react: update all charges by default, even with edge atoms
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custom charges has new keyword, now done with molecule fragments (not backwards compatible)
2020-09-16 17:02:49 -04:00
0f6a34775c
Merge branch 'master' into symbolic-atom-constants
2020-09-15 17:44:31 -04:00
f1ef7d85a8
T2345: Replace instances of NULL with nullptr
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The following changes have been applied to src and lib folders:
regex replace: ([^"_])NULL ⇒ \1nullptr (8968 chgs in src, 1153 in lib)
Manually find/change: (void \*) nullptr ⇒ nullptr (1 case)
regex find: ".*?nullptr.*?"
Manually ~14 cases back to "NULL" in src, ~2 in lib
regex finds a few false positive where nullptr appears between two
strings in a function call
2020-09-12 09:34:38 -06:00
9d0c3bc665
replace some numeric constants in Atom and AtomVec classes with enumerators
2020-09-11 19:07:55 -04:00
91a87b745f
final second round IWYU cleanup
2020-09-04 08:01:11 -04:00
6113169a47
IWYU based include statement cleanup
2020-09-02 17:39:34 -04:00
dd03c7232a
Merge remote-tracking branch 'github/master' into move-convenience-functions
2020-08-31 11:41:18 -04:00
cd0cdf0b74
silence compiler warning
2020-08-30 14:28:29 -04:00
96d8d12a88
replace calls to force->*numeric() with the corresponding utils::*numeric()
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this also removes the now obsolete functions from Force
2020-08-29 20:31:02 -04:00
ef50a67169
bond/react: make rmsd constraint lowercase
2020-08-28 11:06:27 -04:00
ab90493e5b
bond/react: RMSD, remove debugging statements
2020-08-27 14:45:42 -04:00
794e74e064
return of the lost enum
2020-08-27 12:22:48 -04:00
bc49e854ba
bond/react RMSD constraint: manual rebase
2020-08-27 11:53:19 -04:00
6a68715d7b
bond/react:RMSD constraint
2020-06-26 23:33:40 -06:00
db13dff499
minor efficiency correction
2020-05-27 23:32:55 -06:00
