bca99f684f
update list and order of include files from include-what-you-use analysis
2021-09-18 14:16:48 -04:00
7d92d665e8
use explicit scoping when virtual dispatch is not available.
2021-09-15 16:08:17 -04:00
09c19a936b
update URLs in source code and manual
2021-05-24 14:18:20 -04:00
aa6c6169a8
Merge branch 'master' into prepare-clang-format
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# Conflicts:
# src/KOKKOS/nbin_kokkos.h
# src/KOKKOS/nbin_ssa_kokkos.h
# src/MOLECULE/bond_fene_expand.h
# src/USER-DPD/nbin_ssa.h
# src/USER-DPD/nstencil_half_bin_2d_ssa.h
# src/USER-DPD/nstencil_half_bin_3d_ssa.h
# src/USER-INTEL/nbin_intel.h
# src/USER-MISC/fix_propel_self.cpp
# src/USER-OMP/npair_full_multi_old_omp.h
# src/USER-OMP/npair_half_multi_old_newton_omp.h
# src/USER-OMP/npair_half_size_multi_newtoff_omp.h
# src/USER-OMP/npair_halffull_newtoff_omp.h
# src/USER-OMP/npair_halffull_newton_omp.h
# src/USER-OMP/npair_skip_omp.h
# src/main.cpp
# src/nbin_standard.h
# src/npair_full_multi_old.h
# src/npair_halffull_newtoff.h
# src/npair_halffull_newton.h
# src/npair_skip.h
# src/npair_skip_respa.h
# src/npair_skip_size.h
# src/npair_skip_size_off2on.h
# src/npair_skip_size_off2on_oneside.h
# src/nstencil_full_bin_2d.h
# src/nstencil_full_bin_3d.h
# src/nstencil_full_ghost_bin_2d.h
# src/nstencil_full_ghost_bin_3d.h
# src/nstencil_full_multi_2d.h
# src/nstencil_full_multi_3d.h
# src/nstencil_full_multi_old_2d.h
# src/nstencil_full_multi_old_3d.h
# src/nstencil_half_bin_2d_newtoff.cpp
# src/nstencil_half_bin_3d_newtoff.cpp
# src/nstencil_half_bin_3d_newton_tri.h
# src/nstencil_half_ghost_bin_2d_newtoff.cpp
# src/nstencil_half_ghost_bin_2d_newtoff.h
# src/nstencil_half_ghost_bin_3d_newtoff.cpp
# src/nstencil_half_ghost_bin_3d_newtoff.h
# src/nstencil_half_multi_2d.h
# src/nstencil_half_multi_2d_newtoff.h
# src/nstencil_half_multi_2d_newton_tri.h
# src/nstencil_half_multi_2d_tri.h
# src/nstencil_half_multi_3d_newtoff.h
# src/nstencil_half_multi_3d_newton_tri.h
2021-05-14 15:24:02 -04:00
9ef0395313
whitespace fixes
2021-05-12 06:30:52 -04:00
d1941392d3
disable clang-format for all existing .cpp files (for now)
2021-05-05 23:53:38 -04:00
fa386c0e96
Changing how multi/cutoff works, changing collection indexing in user args
2021-05-04 17:12:17 -06:00
bd6dd658d6
Updating to master, misc style changes
2021-04-07 17:21:16 -06:00
58e4938b0f
Updating examples, updating multi in info, fixing memory issues in comm/neighbor
2021-02-08 10:50:57 -07:00
de1205c5a9
Fixing misc valgrind issues, particularly with resizing ncollections
2021-02-07 20:38:24 -07:00
c4ef85ba22
Updating to master
2021-02-05 17:01:32 -07:00
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
852e4efc6f
Updating documentation/examples, patching comm_modify cutoff/multi command
2021-02-02 14:50:30 -07:00
d79a2c3a02
Adding collection array, new user arguments, and multi communication
2021-02-02 09:39:13 -07:00
a25c77e512
Misc comments, typos, and cleanups
2021-01-12 23:04:14 -07:00
2458eaf4f9
Adding custom grouping option
2020-12-26 11:03:29 -07:00
b421c3d676
Adding arguments, initialization, and communication for custom groupings
2020-12-22 10:20:06 -07:00
0a36baf86d
Updating naming in other classes
2020-12-19 17:51:09 -07:00
c1e3bc5794
Updating to master
2020-12-19 15:28:02 -07:00
9b9e5022d6
initializing comm distances, temporarily sorting nlit dumps
2020-11-26 14:57:48 -07:00
00a74558ff
Fixing typos
2020-11-22 20:01:14 -07:00
9a3ece75f2
Batch 1 of typo/bug fixes
2020-11-10 23:30:58 -07:00
943a187be7
Renamed to multi2, initial stencil edits
2020-11-10 16:39:56 -07:00
12288630f5
Fixing comm and renaming bytype
2020-11-09 16:32:11 -07:00
adf74b3a22
use https://lammps.sandia.gov based URLs consistently
2020-10-21 16:45:30 -04:00
b1b014aed3
Fixing merge conflicts
2020-10-02 15:09:47 -06:00
0f6a34775c
Merge branch 'master' into symbolic-atom-constants
2020-09-15 17:44:31 -04:00
cebf6d33ba
Merge pull request #2358 from eagunn/iss2345
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Replace instances of NULL with nullptr
2020-09-15 17:41:24 -04:00
618b08dcfc
Merge branch 'master' into symbolic-atom-constants
2020-09-15 14:58:13 -04:00
0183e999c9
consistently return "memory_usage" as double.
2020-09-15 01:59:58 -04:00
f1ef7d85a8
T2345: Replace instances of NULL with nullptr
...
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
828ce84df5
add check for number of local atom indices overflowing neighbor lists for molecular systems
2020-09-11 22:09:09 -04:00
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
649a8cc01a
Fix typo
2020-03-14 13:57:48 +09:00
11a3fd6ce4
Merge pull request #1556 from lammps/bug-maxexchange
...
more robust version of atom exchange size
2019-07-30 17:09:18 -04:00
2e6850835f
Merge pull request #1542 from akohlmey/improve-include-consistency
...
Improve Consistency of Include Statements (mostly complete)
2019-07-29 20:12:41 -04:00
c098582df8
refactor communication cutoff estimator. move it to Comm class. and adjust heuristics.
2019-07-24 17:27:35 -04:00
be1522d16d
add warning to Comm class against zero communication cutoff
2019-07-24 14:42:17 -04:00
89af88bd10
more changes to robustify comm buf_send length
2019-07-10 08:41:27 -06:00
2fd327d057
more robust version of atom exchange size
2019-07-09 16:17:54 -06:00
7967cb1133
put implementation header first to avoid issues with mpi.h and lmptype.h with OpenMPI
2019-07-03 06:16:16 -04:00
4ec3a508fc
bulk removal of #include <cstdio> from header files
2019-06-27 21:54:07 -04:00
932f052cbf
more header cleanup
2019-06-27 20:52:23 -04:00
ac20d1ab41
fix corner-case issue with hyper communication, also timer
2019-03-18 09:52:16 -06:00
a3c936d283
bug fixes for new local hyperdynamics reduced comm
2019-03-14 15:13:02 -06:00
688945a0ef
silence compiler warnings about initialization order and unused args
2018-10-31 00:34:58 -04:00
3d0722b974
Merge branch 'master' of github.com:lammps/lammps into granular-kokkos
2018-10-10 10:43:54 -06:00
efd81a2854
Merge branch 'master' into bond/react-efficient-competing_reactions
2018-09-04 22:34:04 -06:00
a5f7b418de
bond/react: efficient competing reactions
2018-09-04 22:06:49 -06:00
