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21335 Commits

Author SHA1 Message Date
Axel Kohlmeyer d382db1c76
Merge pull request #2015 from jvita/fix-spline-meam-binning 
Fix spline meam binning
 2020-04-30 20:55:49 -04:00
Axel Kohlmeyer 25b6d98658
correct references and table format 2020-04-30 20:19:23 -04:00
Axel Kohlmeyer 8689b7a404
Merge branch 'master' into atomvec-custom 2020-04-30 20:09:23 -04:00
Steve Plimpton 5e619b65f6 USER-SPH doc tweak 2020-04-30 17:08:05 -06:00
Steve Plimpton ec9b7c787d more doc changes for USER-SPH 2020-04-30 16:52:32 -06:00
Steve Plimpton 4eb4839f6d renaming of variables and command names in USER-SPH 2020-04-30 16:40:09 -06:00
Richard Berger 814f45d756 Add missing symlink 2020-04-30 18:25:25 -04:00
Steve Plimpton 5ec357adfc spelling errors 2020-04-30 15:06:59 -06:00
Axel Kohlmeyer 6913e3a6a4
Merge pull request #1760 from lammps/fix-dummy 
added internal fix dummy command to enable more control of fix ordering
 2020-04-30 14:46:22 -04:00
Stan Moore 14322a9907 Allow compute_coord_atom to use Kokkos orientorder 2020-04-30 12:37:05 -06:00
Steve Plimpton dda5cb0967 typo in atom_vec.h 2020-04-30 12:02:49 -06:00
Josh Vita ac45befbb6 Pre-compute 1/h and store 2020-04-30 12:57:59 -05:00
Steve Plimpton ecd3652f61 update to current master 2020-04-30 11:57:17 -06:00
Stan Moore 23c5384b47 Merge branch 'master' of https://github.com/lammps/lammps into kk_compute_coord_atom 2020-04-30 11:34:19 -06:00
Axel Kohlmeyer 6b8f26e8ad
Merge pull request #2046 from stanmoore1/kk_cutneighsq 
Fix rare issue in Kokkos neighlist
 2020-04-30 13:00:51 -04:00
Zheng Gong ae3c804cd2 Minor fix in doc 2020-04-30 19:00:37 +02:00
Axel Kohlmeyer 3ecaf0f336
Merge pull request #2047 from lammps/replica-doc-page 
Clarifying AMD quote from review paper for 3 AMD methods in LAMMPS
 2020-04-30 12:50:01 -04:00
Axel Kohlmeyer 0b02108ba1
add add check to refuse running with 2d systems and document it. 2020-04-30 12:46:16 -04:00
Axel Kohlmeyer 859f644481
make spellchecker and sphinx happy 2020-04-30 12:45:36 -04:00
Axel Kohlmeyer 5062d57ccb
Merge branch 'master' into viscosity 2020-04-30 12:32:06 -04:00
Axel Kohlmeyer c39b71cd1b
Merge pull request #2048 from junghans/cmake_disable_static_lib_install 
cmake: disable installing of static libs
 2020-04-30 12:28:41 -04:00
Zheng Gong 26321d49c4 Update How-to viscosity and put the example together with other viscosity examples. 2020-04-30 17:05:01 +02:00
Stan Moore eba1a15616 Port changes to Kokkos package 2020-04-30 08:44:55 -06:00
Stan Moore 88bf503451 Merge from master 2020-04-30 08:17:05 -06:00
Axel Kohlmeyer 002c49737f
update definition for ubuntu20.04 2020-04-29 22:58:08 -04:00
Axel Kohlmeyer 696308a760
set cmake policy to honor HDF5_ROOT and NETCDF_ROOT. search for parallel NetCDF only with parallel builds 2020-04-29 22:39:33 -04:00
Axel Kohlmeyer e97bf005cb
include hdf5 and netcdf in more images 2020-04-29 22:36:33 -04:00
Christoph Junghans 1adda03202 cmake: only install shared lib and friends 2020-04-29 18:06:33 -06:00
Richard Berger aad8659788 Reduce CUDA footprint in containers 2020-04-29 20:02:25 -04:00
Christoph Junghans 600d357155 cmake: disable installing of static libs 2020-04-29 16:26:56 -06:00
Steve Plimpton 18c63ade92 clarified AMD quote from review paper 2020-04-29 16:14:52 -06:00
Richard Berger 633651fa56 Add valgrind, gdb to containers and clean caches 2020-04-29 17:32:19 -04:00
Stan Moore 63a2f17410 Merge branch 'master' of https://github.com/lammps/lammps into kk_compute_coord_atom 2020-04-29 15:16:52 -06:00
Richard Berger 8235c48f49 Avoid errors due to host Lmod in containers 
These changes ensure that environment variables that are automatically passed
to the container don't interfere with Lmod inside of the container. The previous
implementation would not take care of sticky packages from the outside and Lmod
would try to reload them.

Note that Lmod defines the 'module' bash function, which doesn't propagate to
the final shell when using 'singularity shell'. If the 'module' command is needed
a login shell needs to be launched:

$ singularity exec <CONTAINER> bash -l
 2020-04-29 17:01:55 -04:00
Richard Berger 82b1fc717f Add missing python36 and hdf5-devel to CentOS containers 2020-04-29 16:46:22 -04:00
Stan Moore 0588232a34 Fix rare issue in Kokkos neighlist 2020-04-29 14:29:18 -06:00
Axel Kohlmeyer 5c2f0ecc65
Merge pull request #2045 from stanmoore1/kk_team_coul 
Fix issue in Kokkos "team" energy
 2020-04-29 15:32:45 -04:00
Axel Kohlmeyer feed7302d5
Merge pull request #2044 from stanmoore1/kk_reax_full 
Remove full neigh list option in Kokkos ReaxFF
 2020-04-29 14:54:54 -04:00
Stan Moore e10d62c89f Fix energy tally issue 2020-04-29 10:06:09 -06:00
Stan Moore 04388c26f8 Fix Kokkos view runtime issue 2020-04-29 10:05:47 -06:00
Axel Kohlmeyer 7508660d8a
Merge pull request #2036 from stanmoore1/kk_dihedral_charmm 
Fix issues in dihedral_charmm_kokkos
 2020-04-29 10:24:32 -04:00
Stan Moore fe9e6736e1
Merge branch 'master' into kk_dihedral_charmm 2020-04-29 08:00:55 -06:00
Axel Kohlmeyer 910d00f500
Merge pull request #2041 from stanmoore1/kk_team_ev 
Fix Kokkos issue and remove N2 neigh list option
 2020-04-28 19:23:35 -04:00
Axel Kohlmeyer 17f7bf2fb9
Merge pull request #2035 from stanmoore1/kk_uvm 
Fix UVM compile issues
 2020-04-28 19:23:12 -04:00
Axel Kohlmeyer e47dc6fec9
Merge pull request #2043 from ellio167/ubuntu-install-docs 
Update ubuntu ppa install docs
 2020-04-28 19:22:27 -04:00
Stan Moore a88364a2ea Tweak error message 2020-04-28 15:39:01 -06:00
Axel Kohlmeyer 754d9fabc6
Merge branch 'ubuntu-install-docs' of github.com:ellio167/lammps into ubuntu-install-docs 2020-04-28 17:27:49 -04:00
Axel Kohlmeyer b3d8986603
list update kokkos flag 2020-04-28 17:27:23 -04:00
Axel Kohlmeyer 846146c9d4
correct minor formatting and markup issues 2020-04-28 17:23:16 -04:00
Ryan S. Elliott e9a777e63d Add explaination of potenentials directory behavior for `lmp_daily` 2020-04-28 16:16:28 -05:00