38075455b6
new keywords for read_data: extra/X/per/atoms + changes to docs
2017-06-28 17:55:30 -07:00
fa30635465
Revert "added feature to write_data.cpp to support "extra bonds" (angles,dihedrals,impropers,special)."
...
This reverts commit 0c2f7c74be
2017-06-28 17:48:32 -07:00
0c2f7c74be
added feature to write_data.cpp to support "extra bonds" (angles,dihedrals,impropers,special).
2017-06-28 14:12:03 -07:00
91bce7ccf9
Replaced std::fabs with fabs.
2017-06-28 09:48:00 -04:00
d0470799ac
consistently check for all per-atom-type masses being set only when per-atom masses are not set
...
rather than placing an if statement around every incidence of calling atom->check_mass() to ensure it is only called when per atom masses are not set, we place that check _inside_ Atom::check_mass(). This avoids unexpected error messages.
2017-06-28 06:26:21 -04:00
076990c28a
Updated Gaussian bump so that it has a better taper function.
2017-06-27 16:48:33 -04:00
9fec8a0470
Remove clean_copy function from pair_vashishta_kokkos
2017-06-26 10:56:03 -06:00
b889776557
Fixing memory leak in Kokkos neighborlist
2017-06-26 10:51:26 -06:00
8fca667e4b
Change indexing of remaining variables and locals
...
- Voigt index tables
- local variables
- remove shims from header
2017-06-26 18:09:11 +02:00
ea4d11fc5e
Merge branch 'master' into USER-DPD_kokkos_testing
2017-06-26 09:36:30 -06:00
f7077d9672
Merge branch 'collected-bugfixes' of github.com:akohlmey/lammps into collected-bugfixes
2017-06-26 11:27:31 -04:00
f89a7266bf
make USER-INTEL compilable again with gcc and without OpenMP active
2017-06-25 23:57:42 -04:00
1370385c8c
patch 23Jun17
2017-06-23 17:10:59 -06:00
c2c6dc1458
remove spurious comment line
2017-06-23 16:24:37 -04:00
18983c307e
fix qeq/reax/omp bugfix from metin
2017-06-23 16:24:00 -04:00
05fbf93455
skip deleting internal data before setup has been run
2017-06-23 10:37:00 -04:00
73b948dcfc
pppm must be fully reinitialized after switching to triclinic box to avoid memory corruption
2017-06-23 10:01:45 -04:00
a714b57741
make neighbor list reset message for minimization more explicit
2017-06-22 19:07:57 -04:00
c5430b0a26
print info messages when changing qqr2e constant in fully CHARMM compatible pair styles
2017-06-22 18:41:44 -04:00
f8364342c2
port corrected triclinic handling from pppm/tip4p to pppm/tip4p/omp
2017-06-22 18:12:28 -04:00
488d1b7a79
correct find_M() function in pppm/tip4p to properly account for ghost atoms not being in lamda space with triclinic cells
2017-06-22 17:36:18 -04:00
dadd1c8b4d
Remove neigh_f2c/c2f, related cleanup
...
- neighbour lists now use C indexing
- removed many arr*v() macros
- removed some unneccessary pointers
- minor reformatting
2017-06-22 19:02:14 +02:00
60c3f3d64c
use CHARMM energy conversion factor with new CHARMM pair styles
2017-06-22 09:15:15 -06:00
7a4a569859
Merge pull request #540 from lammps/neighrespa
...
fix issue with rRESPA inner/middle neighbor lists
2017-06-22 07:54:12 -06:00
4fc3f4f7e5
Merge pull request #538 from akohlmey/collected-small-changes
...
Collected small changes and bugfixes
2017-06-22 07:52:21 -06:00
f092da80a9
Fix some shadowing warnings
2017-06-22 13:28:12 +02:00
b9029ada77
fix bug in incorrect use of O coordinate instead of M coordinate in pppm/tip4p
2017-06-22 00:07:59 -04:00
0c6a751751
may check for 1-4 scaling factors in CHARMM dihedral styles only when "weightflag" is set, since they may be used with amber
2017-06-21 19:29:31 -04:00
612b44a895
enforce using 'special_bonds charmm' for dihedral styles charmm and charmmfsw
2017-06-21 19:15:52 -04:00
684b7334a5
enforce that CHARMM dihedral styles are run at the same r-RESPA level as pair
2017-06-21 19:08:02 -04:00
1fc2eb1e3e
fix issue with rRESPA inner/middle neighbor lists
2017-06-21 15:12:51 -06:00
7dc380b113
insure compute pair/property local will use a copy of granular neigh list
2017-06-21 12:44:35 -06:00
5e165e6782
fix array bounds issue due to typo. spotted by GCC.
2017-06-21 13:33:26 -04:00
02625b2855
fix typos introduced in original translation: results are correct again
2017-06-21 18:54:21 +02:00
0cfe8980d4
dead code removal
2017-06-20 22:07:40 -04:00
2988508cee
correct indexing bug in pair style lj/long/tip4p/long
2017-06-20 17:53:45 -04:00
15c596153a
remove dead code
2017-06-20 17:38:28 -04:00
e13c94ed4f
fix uninitialized variable bug spotted by coverity scan
2017-06-20 17:25:01 -04:00
812f1a8fab
remove local variables shadowing global ones in BondsOMP()
2017-06-20 17:20:57 -04:00
218bc92c82
make pre-processor defines for using libc's qsort() consistent
2017-06-20 17:13:42 -04:00
ffa906de6f
add C++ format identifiers to .h files
2017-06-20 16:18:34 -04:00
cccf72a21d
make certain class member list is initialized to NULL before assigned to a neighbor list
2017-06-20 16:09:11 -04:00
87c028ed02
patch 20Jun17
2017-06-20 12:06:02 -06:00
bb47fa8783
Change indexing of all MEAM element arrays
...
- arrays in MEAM class
- eltind setting
- remove fmap translation
2017-06-20 19:56:14 +02:00
c79dc53c6a
code improvement, less pointer params
2017-06-20 19:36:07 +02:00
72a1364d85
Merge branch 'master' into package-meamc
2017-06-20 13:21:46 -04:00
198fe7ecd7
fix storing of invalid memory pointer
2017-06-20 19:00:57 +02:00
d2610d9e7c
minor changes to NEB doc pages and examples
2017-06-20 08:19:23 -06:00
326a8a1289
Merge pull request #536 from akohlmey/fix-nvcc-openmp-conflicts
...
Implement workaround for NVCC incompatibilities with OpenMP directives
2017-06-20 07:44:40 -06:00
b5300724bb
Merge pull request #533 from lammps/user-intel
...
Updates for USER-INTEL package and NEB command flags/docs updates and issues
2017-06-20 07:44:17 -06:00
