09c19a936b
update URLs in source code and manual
2021-05-24 14:18:20 -04:00
d8291eea7b
Merge branch 'master' into prepare-clang-format
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# Conflicts:
# src/MOLECULE/bond_fene.h
# src/MOLECULE/bond_fene_expand.h
2021-05-11 21:49:48 -04:00
d1941392d3
disable clang-format for all existing .cpp files (for now)
2021-05-05 23:53:38 -04:00
9f4da1128b
remove optional logflag argument from Error::message() and Error::warning()
2021-05-05 16:02:51 -04:00
e9e0bb71b6
Use varargs version of Error:all() and Error::one() where applicable
2021-04-25 21:30:51 -04:00
d2cdb318ab
apply new logmesg() overload to a bunch of cases.
2021-04-21 23:38:45 -04:00
2d19282961
reorder include statements in RIGID package
2021-04-08 13:45:37 -04:00
183b30abd7
use strmatch() consistently to detect respa and verlet runstyles with optional suffix
2021-03-30 18:30:22 -04:00
33939a0e26
Merge branch 'master' into thermo-energy
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# Conflicts:
# doc/src/fix_ti_spring.rst
# src/RIGID/fix_rigid_small.cpp
# src/fix_langevin.cpp
# src/fix_temp_berendsen.cpp
# src/fix_temp_csld.cpp
# src/fix_temp_csvr.cpp
# src/fix_temp_rescale.cpp
# src/thermo.cpp
2021-02-08 15:24:29 -05:00
95e2214d96
more typecasts to double to avoid 32-bit int overflows when computing memory usage
2021-02-04 14:35:38 -05:00
e2e6639013
add typecast to avoid (unlikely but possible) integer overflows.
...
this will silence a lot of static code analysis warnings
2021-02-02 17:27:04 -05:00
c091515427
changed syntax for virial tallying in standard package fixes
2021-01-21 15:12:16 -07:00
f54fd8fa72
intial refactoring of THERMO_ENERGY mask
2021-01-21 10:31:53 -07:00
8e6b89cc81
fix multiplication issue in shake stats
2020-12-23 15:14:00 -05:00
7507773ead
Merge pull request #2441 from stanmoore1/kk_fix_shake
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Add Kokkos support for fix shake and forward comm on Device for fixes
2020-11-18 11:17:57 -05:00
22a804e634
Fix memory issue
2020-10-27 12:25:27 -06:00
656b7eac8b
correctly report number of constrained bonds and angles
2020-10-26 18:49:09 -04:00
e804235d23
Add Kokkos support for fix shake and forward comm on Device
2020-10-22 11:59:41 -06:00
adf74b3a22
use https://lammps.sandia.gov based URLs consistently
2020-10-21 16:45:30 -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
6113169a47
IWYU based include statement cleanup
2020-09-02 17:39:34 -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
9e1d560fda
refactor using fmtlib and utils::
2020-07-11 21:44:13 -04:00
eafcc06670
secs -> seconds
2020-06-30 13:56:35 -04:00
a8c1ce98cf
remove trailing whitespace
2020-06-11 19:04:15 -04:00
e4d1068c70
flag a couple fixes and their derived clases as incompatible with resetting atom IDs
2020-06-10 16:47:55 -06:00
ca1e1e2dff
Convert British spelling to American
2020-03-18 23:09:23 +09:00
649a8cc01a
Fix typo
2020-03-14 13:57:48 +09:00
dcb1b6500b
allow regexp matches for Modify::find_fix_by_style() and consolidate usage of searching for fixes
2019-10-18 06:59:27 -04:00
416911aa7e
more rearranging of include file order to put implementation headers first
2019-07-03 21:57:39 -04:00
31cbccda85
continue cleaning up include file lists
2019-06-29 09:37:44 -04:00
e56d69a267
silence compiler warnings
2019-04-05 16:52:03 -04:00
8ba1d76055
some dead code removal and more whitespace cleanup
2019-03-27 05:38:41 -04:00
fff28a8666
remove trailing whitespace
2019-03-26 11:17:21 -04:00
1ca0c78a2e
turn off diagnostic output for rendezvous op
2019-03-26 11:01:39 -04:00
62045a9c52
cleanup up rendezvous diagnostic output
2019-03-26 11:01:38 -04:00
bbe6c9bb63
added diagnostic info for memory and balance info
2019-03-26 11:01:38 -04:00
fc002e30d3
added rendezvous via all2all
2019-03-26 11:01:38 -04:00
981f12ebeb
fix a small memory leak in SHAKE setup
2019-03-26 11:01:38 -04:00
b370a61b60
added rendezvous alg to fix shake
2019-03-26 11:01:38 -04:00
71bc72ec13
formatting: add additional space to avoid bad syntax highlights
2018-08-27 22:13:43 -04:00
92a4dc25b1
Fix unused params in packages ( #1076 )
2018-08-24 10:42:08 -06:00
e4071d7f46
replace C-style include files with their C++ equivalents
2018-04-27 18:00:24 -04:00
59dbb49cf9
remove trailing whitespace
2018-03-16 12:37:27 -04:00
e196a2b9e5
import changes to various fixes by aidan to include virial contributions
2017-09-11 22:24:06 -04:00
c24e316baa
avoid floating point overflows in iterative solvers of fix shake
2017-07-22 23:15:01 -04:00
fcc387f232
change ring communication API to no longer require a static variable pointing to 'this' of the caller
2017-06-14 17:01:06 -04:00
addd87c0f7
new Section package and start doc pages and build scripts
2017-05-04 11:22:20 -06:00
