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26497 Commits

Author SHA1 Message Date
Axel Kohlmeyer c311574fe6
add missing fix entry 2021-05-14 23:50:38 -04:00
Axel Kohlmeyer 20de21f8de
Merge branch 'master' into next_patch_release 2021-05-14 23:39:25 -04:00
Axel Kohlmeyer 235e91a337
Merge pull request #2762 from akohlmey/prepare-clang-format 
Prepare LAMMPS to support updating the coding style with clang-format
 2021-05-14 23:23:35 -04:00
Axel Kohlmeyer 1ed75e3db0
fix buffer overflow in writing triclinic headers with MPI-I/O 2021-05-14 22:51:56 -04:00
Axel Kohlmeyer 6b80cb0169
whitespace 2021-05-14 20:47:08 -04:00
Axel Kohlmeyer 07cb55ef7f
Merge branch 'master' into prepare-clang-format 2021-05-14 20:43:51 -04:00
Axel Kohlmeyer 247edbcaa3
Merge pull request #2722 from lammps/kokkos_double_free 
Avoid double free in some Kokkos pair styles destruction
 2021-05-14 20:43:00 -04:00
Axel Kohlmeyer d24d501a4a
Merge branch 'master' into prepare-clang-format 2021-05-14 20:38:54 -04:00
Axel Kohlmeyer b23556e1a8
Merge pull request #2765 from masterleinad/fix_snap_kokkos_sycl 
Fix compiling the SNAP module with Kokkos and SYCL
 2021-05-14 20:31:53 -04:00
Axel Kohlmeyer 06f0a9207e
Merge pull request #2769 from lammps/neigh-copy-bug 
fix bug with mis-indexing of neighbor build copyflag check
 2021-05-14 19:16:56 -04:00
Axel Kohlmeyer 7fcd449864
apply clang-format to all headers with some exceptions 2021-05-14 19:16:07 -04:00
Steve Plimpton 250fbd24a3 neighbor build check on copyflag mis-indexed 2021-05-14 16:06:56 -06:00
Axel Kohlmeyer 60e41a90c2
update new files for clang-format 2021-05-14 17:37:58 -04:00
Axel Kohlmeyer 7284a70900
Merge branch 'master' into prepare-clang-format 2021-05-14 17:25:24 -04:00
Axel Kohlmeyer de025aec47
Merge pull request #2761 from rbberger/collected-small-changes 
Collected small changes and fixes for the next patch release
 2021-05-14 17:24:36 -04:00
Axel Kohlmeyer 79ebf387fe
Merge branch 'prepare-clang-format' of github.com:akohlmey/lammps into prepare-clang-format 2021-05-14 17:22:03 -04:00
Axel Kohlmeyer 9483db9581
Merge branch 'prepare-clang-format' of github.com:akohlmey/lammps into prepare-clang-format 2021-05-14 17:21:18 -04:00
Axel Kohlmeyer 7d44da08ad
Merge branch 'prepare-clang-format' of github.com:akohlmey/lammps into prepare-clang-format 2021-05-14 15:25:05 -04:00
Axel Kohlmeyer aa6c6169a8
Merge branch 'master' into prepare-clang-format 
# 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
Stan Gerald Moore 117b6e2a80 Add copymode flag 2021-05-14 12:43:02 -06:00
Stan Gerald Moore a93ec125a4 Move deep_copy call 2021-05-14 12:24:21 -06:00
Axel Kohlmeyer 6740959c65
Merge pull request #2611 from MolSSI-MDI/mdi 
Add MolSSI Driver Interface Support
 2021-05-14 13:18:52 -04:00
Stan Gerald Moore 6f6adc285a Fix typo 2021-05-14 10:25:32 -06:00
Stan Gerald Moore 5a7e784447 Add missing copymode to parent classes 2021-05-14 10:08:05 -06:00
Stan Gerald Moore eedd726edb Merge branch 'master' of github.com:lammps/lammps into kokkos_double_free 2021-05-14 09:38:21 -06:00
Stan Gerald Moore 7b4fdb92df Use only copymode in Kokkos pair_styles 2021-05-14 09:36:13 -06:00
Axel Kohlmeyer 70ce971d4a
address some warnings from coverity scan 2021-05-14 08:39:47 -04:00
Axel Kohlmeyer ad34953a52
Merge branch 'master' into collected-small-changes 2021-05-14 08:35:49 -04:00
Axel Kohlmeyer e5cc4409a5
Merge pull request #2760 from jrgissing/bond/react-custom_constraint 
Bond/react: custom constraint
 2021-05-13 20:04:48 -04:00
taylor-a-barnes 465cd52707 Fix MDI calls in fix_mdi_engine.cpp 2021-05-13 17:16:07 -04:00
Axel Kohlmeyer 6b275e283c
step version number for the next patch release 2021-05-13 17:14:35 -04:00
Axel Kohlmeyer 242949100a
describe use of clang-format when submitting contributions 2021-05-13 15:01:42 -04:00
taylor-a-barnes d02e09baaa
Merge pull request #17 from akohlmey/mdi_update 
MDI formatting updates and MPI STUBS handling
 2021-05-13 14:41:51 -04:00
Axel Kohlmeyer 44ed6f1896
don't use provided communicator when LAMMPS was compiled with STUBS 2021-05-13 14:21:23 -04:00
Axel Kohlmeyer fa80903ac2
NULL -> nullptr; apply clang-format 2021-05-13 14:20:56 -04:00
Daniel Arndt dc6b8102bc Fix compiling the SNAP module with Kokkos and SYCL 2021-05-13 18:03:22 +00:00
taylor-a-barnes 50de35c41a
Merge pull request #16 from akohlmey/mdi_updates 
USER-MDI updates
 2021-05-13 13:18:16 -04:00
Axel Kohlmeyer 0f7a41590d
fix bug in lammps_reset_box() no-box check and error out when atoms exist 2021-05-13 12:46:43 -04:00
taylor-a-barnes 7c0d632dfb Fix bug in MDI checksums 2021-05-13 12:08:58 -04:00
Axel Kohlmeyer 36de1c4201
remove unused header 2021-05-13 11:49:24 -04:00
Axel Kohlmeyer 8efab68db5
integrate MDI wrapper directly into main.cpp 
we can remove the header, since this dummy interface should not be used elsewhere.
 2021-05-13 11:41:05 -04:00
Axel Kohlmeyer 8d9465ccdb
move MDI C style library calls to separate files 2021-05-13 11:37:05 -04:00
Axel Kohlmeyer 7d7781373c
update gitignore 2021-05-13 11:35:13 -04:00
Axel Kohlmeyer f121ae98d6
forget to update 2021-05-13 11:34:58 -04:00
Axel Kohlmeyer 9cfe665b7a
bugfix 2021-05-13 11:34:28 -04:00
Axel Kohlmeyer 30d2f18ccb
whitespace fixes 2021-05-13 09:57:58 -04:00
Axel Kohlmeyer 33205ed91f
Use "mdi/engine" consistenty, complete integration in manual, spelling 2021-05-13 09:57:08 -04:00
Axel Kohlmeyer f86f182cd3
cosmetic changes 2021-05-13 08:59:02 -04:00
Axel Kohlmeyer 1f7343d60f
format tweaks 2021-05-13 08:57:53 -04:00
Axel Kohlmeyer d9505a4527
cmake tweaks 2021-05-13 08:57:41 -04:00