56cd66a6c3
Merge branch 'master' into parse-logical-keyword
...
# Conflicts:
# src/H5MD/dump_h5md.cpp
2021-09-29 23:05:59 -04:00
b3c8f85ff9
make sure the one_coeff flag is applied to sub-styles
...
since the check for Pair::one_coeff was moved to the Input class (to
reduce redundant code), hybrid substyles could "escape" that requirement.
Thus checks have to be added to the hybrid coeff() methods.
2021-09-28 04:39:46 -04:00
41a3eccd1c
apply utils::logical() to more commands
2021-09-21 07:48:50 -04:00
385220fd4b
format changes
2021-09-17 22:50:15 -04:00
8aeaa82909
improve error message
2021-08-19 11:08:04 -04:00
04c7e7543e
use friend statement instead of (incorrect) cast to give access to protected class member
2021-08-02 21:34:30 -04:00
cf3bf374fa
Merge branch 'master' into refactor-reaxff-parser
2021-07-21 00:30:53 -04:00
63794aa698
Merge branch 'master' into track-contacts
...
# Conflicts:
# doc/src/Packages_details.rst
# src/DIELECTRIC/pair_coul_cut_dielectric.h
# src/MISC/fix_pair_tracker.cpp
# src/MISC/fix_pair_tracker.h
# src/MISC/pair_tracker.cpp
# src/MISC/pair_tracker.h
# src/pair_tracker.h
2021-07-20 16:19:38 -04:00
757e2f8cff
Merge branch 'master' into refactor-reaxff-parser
...
# Conflicts:
# doc/src/fix_qeq_reax.rst
# src/OPENMP/reaxc_bond_orders_omp.h
# src/OPENMP/reaxc_bonds_omp.h
# src/OPENMP/reaxc_forces_omp.h
# src/OPENMP/reaxc_hydrogen_bonds_omp.h
# src/OPENMP/reaxc_init_md_omp.cpp
# src/OPENMP/reaxc_init_md_omp.h
# src/OPENMP/reaxc_multi_body_omp.h
# src/OPENMP/reaxc_nonbonded_omp.h
# src/OPENMP/reaxc_torsion_angles_omp.h
# src/OPENMP/reaxc_valence_angles_omp.h
# src/OPENMP/reaxff_omp.h
# src/Purge.list
# src/QEQ/fix_qeq.cpp
# src/QEQ/fix_qeq.h
# src/QEQ/fix_qeq_dynamic.cpp
# src/QEQ/fix_qeq_fire.cpp
# src/REAXFF/fix_qeq_reax.cpp
# src/REAXFF/reaxc_allocate.h
# src/REAXFF/reaxc_bond_orders.h
# src/REAXFF/reaxc_bonds.h
# src/REAXFF/reaxc_control.h
# src/REAXFF/reaxc_defs.h
# src/REAXFF/reaxc_ffield.h
# src/REAXFF/reaxc_forces.h
# src/REAXFF/reaxc_hydrogen_bonds.h
# src/REAXFF/reaxc_init_md.cpp
# src/REAXFF/reaxc_init_md.h
# src/REAXFF/reaxc_io_tools.cpp
# src/REAXFF/reaxc_io_tools.h
# src/REAXFF/reaxc_list.h
# src/REAXFF/reaxc_lookup.h
# src/REAXFF/reaxc_multi_body.h
# src/REAXFF/reaxc_nonbonded.h
# src/REAXFF/reaxc_reset_tools.h
# src/REAXFF/reaxc_system_props.cpp
# src/REAXFF/reaxc_system_props.h
# src/REAXFF/reaxc_tool_box.h
# src/REAXFF/reaxc_torsion_angles.h
# src/REAXFF/reaxc_traj.cpp
# src/REAXFF/reaxc_traj.h
# src/REAXFF/reaxc_types.h
# src/REAXFF/reaxc_valence_angles.h
# src/REAXFF/reaxc_vector.cpp
# src/REAXFF/reaxc_vector.h
# src/REAXFF/reaxff_api.h
# src/REAXFF/reaxff_defs.h
# src/REAXFF/reaxff_inline.h
# src/REAXFF/reaxff_types.h
# src/text_file_reader.cpp
# src/text_file_reader.h
# unittest/force-styles/tests/atomic-pair-reax_c.yaml
# unittest/force-styles/tests/atomic-pair-reax_c_lgvdw.yaml
# unittest/force-styles/tests/atomic-pair-yukawa_colloid.yaml
2021-07-12 14:25:47 -04:00
878795e64a
bulk rename of remaining USER- packages
2021-06-29 20:12:59 -04:00
b8236c6402
improve error messages by printing unrecognized property
2021-06-08 11:19:21 -04:00
2500169193
whitespace
2021-06-04 00:57:26 -04:00
80f28e7fa9
fixing merge conflicts, update to master
2021-06-02 12:33:37 -06:00
09c19a936b
update URLs in source code and manual
2021-05-24 14:18:20 -04:00
a847a7ee9e
print warning when a tip4p pair style may cause incorrect results
2021-05-19 15:33:26 -04:00
d939a16d3b
Completing pair and fix
2021-05-14 17:26:51 -06:00
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
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
f12f9166a5
Resolving merge conflicts, updating URLs
2021-05-05 11:19:44 -06:00
e9e0bb71b6
Use varargs version of Error:all() and Error::one() where applicable
2021-04-25 21:30:51 -04:00
08f4c30051
Merge branch 'master' into refactor-reaxff-parser
2021-04-20 20:52:18 -04:00
fe2efa4cb3
disallow usage of qeq fixes with incompatible GPU and USER-INTEL packages
2021-04-20 14:51:27 -04:00
d60a247138
fix typo
2021-04-19 08:44:46 -04:00
48e9f451f4
disallow using the same GPU pair style multiple times as hybrid sub-style
2021-04-19 01:23:54 -04:00
0496fd27db
reorder include files
2021-04-09 22:49:25 -04:00
a441c7b379
simplify hybrid coeff parsing. check for number is already done with conversion
2021-04-08 17:44:13 -04:00
bd6dd658d6
Updating to master, misc style changes
2021-04-07 17:21:16 -06:00
d54384dd91
Merge branch 'master' into multi_epcc
2021-04-07 16:34:01 -06:00
183b30abd7
use strmatch() consistently to detect respa and verlet runstyles with optional suffix
2021-03-30 18:30:22 -04:00
c4ef85ba22
Updating to master
2021-02-05 17:01:32 -07:00
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
d79a2c3a02
Adding collection array, new user arguments, and multi communication
2021-02-02 09:39:13 -07:00
51a20175c9
more code formatting consistency changes for loops and conditionals
2020-12-30 09:47:45 -05:00
f0e4f9932f
whitespace fixes
2020-11-25 16:51:43 -05:00
6d0c8e71de
Correct assignment of centroidstressflag
2020-11-18 17:51:04 -05:00
5691ec3dfd
insure cvflag is zero, other tweaks
2020-11-18 15:05:11 -07:00
c62c907281
doc string tweak
2020-11-18 13:02:07 -07:00
0876684780
energy/virial flags with CENTROID enum
2020-11-18 12:17:14 -07:00
251dcdf8a2
Make use of ENERGY_ and VIRIAL_ constants
2020-11-16 15:33:15 -05:00
1ba9dd7435
Apply CENTROID_* constants
2020-11-16 11:01:31 -05:00
adf74b3a22
use https://lammps.sandia.gov based URLs consistently
2020-10-21 16:45:30 -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
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()
...
this also removes the now obsolete functions from Force
2020-08-29 20:31:02 -04:00
fcd0b9f78f
move Force::bounds() and Force::boundsbig() to utils.
2020-08-29 18:23:03 -04:00
735f9ad592
address logic error with check for KOKKOS version of hybrid styles
2020-07-03 09:01:59 -04:00
f598ae7ebf
update/add error message for using hybrid pair styles with KOKKOS
2020-07-02 16:40:47 -04:00
06a0b3331a
may only flag having restart info if all substyles support it
2020-06-23 09:25:25 -04:00
