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18923 Commits

Author SHA1 Message Date
Axel Kohlmeyer 5d042cf629
Merge pull request #1740 from cabb99/master 
Fix print patch to allow print on rerun
 2019-11-14 09:25:50 -05:00
Axel Kohlmeyer 60fe0c0b86
Silence compiler warning 2019-11-14 09:24:56 -05:00
julient31 93bd2f4ab0 Commit JT 111319 
- addind 4 first benchmark examples (in examples/SPIN/benchmark)
- corrected typo in examples (in dump commands)
 2019-11-13 20:46:28 -07:00
Richard Berger 62b3e79022 Add autodoc for lammps.lammps and lammps.NeighList 2019-11-13 15:54:22 -05:00
Richard Berger 28a9dc40cb Add docstring to new lammps.py methods 2019-11-13 15:53:25 -05:00
Richard Berger 7e92c2e0ee Add more detailed code documentation 2019-11-13 14:30:13 -05:00
Donatas Surblys f18cb83def fix spelling: dihedras -> dihedrals 2019-11-14 01:07:30 +09:00
Donatas Surblys 28269c4a21 change wording to be more in line with LAMMPS terminology and current state of implementation 2019-11-13 22:19:34 +09:00
Donatas Surblys 85e96bf31c fix broken italization 2019-11-13 22:02:10 +09:00
Donatas Surblys e44c394680 pairwise -> two-body for clarity in appropriate comments 2019-11-13 19:48:52 +09:00
Donatas Surblys b80e5d3d11 fix spelling: forth -> fourth 2019-11-13 18:45:49 +09:00
Donatas Surblys b5c6647992 prevent pair hybrid from needlessly allocating vatom when only cvatom is needed 2019-11-13 18:42:34 +09:00
Donatas Surblys 6b94126f67 change flag name in pair.h: cntratmstressflag -> centroidstressflag 2019-11-13 18:37:48 +09:00
Axel Kohlmeyer e0646b73e3
revised implementation of inclusion of embedding energy in PairEAM::single() 
this variant is also ported to USER-OMP and OPT
 2019-11-13 01:46:00 -05:00
Axel Kohlmeyer f1e4f98364
include embedding energy term in PairEAM::single() 2019-11-13 01:04:39 -05:00
Axel Kohlmeyer f704079fb7
remove trailing whitespace 2019-11-12 16:13:01 -05:00
Richard Berger 78d5bc3d12 Merge branch 'master' into library_interface_update 2019-11-12 15:17:32 -05:00
Axel Kohlmeyer 25e2a7a37f
update bond style table docs about out-of-range errors 2019-11-12 14:25:45 -05:00
Steve Plimpton 1955c57791 make fix print work the same for run, multiple runs, rerun 2019-11-12 10:16:50 -07:00
Donatas Surblys 2d75e6b167 Add author name to false positives for citation "Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579–5587 (2019)." 2019-11-12 23:37:14 +09:00
Donatas Surblys b6930cbc8d Add author names to false positives for citation "Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019)." 2019-11-12 23:34:03 +09:00
Donatas Surblys b65a3e94a7 update compute heat/flux documentation 2019-11-12 22:43:52 +09:00
Axel Kohlmeyer de7a8c6559
Merge pull request #1768 from ellio167/doc-conda 
Add Install_conda doc
 2019-11-11 17:11:22 -05:00
Axel Kohlmeyer 5289417e9c
Merge pull request #1739 from evoyiatzis/shape_chunk 
Computing the eigenvalues of the gyration tensor and shape parameters…
 2019-11-11 17:10:52 -05:00
Evangelos Voyiatzis 06fdaa04b3
Merge pull request #2 from rbberger/shape_chunk 
Fix documentation
 2019-11-11 21:46:44 +01:00
Richard Berger 0018a88f45 Only keep RST version of compute_gyration_shape_chunk 2019-11-11 15:32:48 -05:00
Richard Berger 22a033f5d4 Move compute_gyration_shape_chunk.txt into txt/ folder 2019-11-11 15:32:09 -05:00
Richard Berger 16f67ee56a Add new words to false-positives.txt 2019-11-11 15:26:48 -05:00
Donatas Surblys 5ba7686939 add documentation about centroid/stress/atom compute 2019-11-12 01:40:59 +09:00
Axel Kohlmeyer 9e2129b676
Merge pull request #1767 from LucienPan0903/p_class2 
Patch of class2 dihedral
 2019-11-11 10:44:37 -05:00
Donatas Surblys 7db3d7b5c0 setting cntatmstressflag = 1 for true pariwise styles 2019-11-12 00:02:50 +09:00
Donatas Surblys 0a64dff132 add initial support to centroid virial in USER-OMP pair styles 2019-11-11 23:27:10 +09:00
Donatas Surblys 7937bec396 add pair style compatibility check to compute centroid/stress/atom 2019-11-11 22:45:59 +09:00
Donatas Surblys a782245179 support for par-atom centroid virial in pair hybrid 2019-11-11 19:39:01 +09:00
Donatas Surblys 61a286a0da compute centroid/atom/stress will use cvatom from pair styles when available 2019-11-11 19:16:21 +09:00
Donatas Surblys 3258a14923 initial support for par-atom centroid virial in pair styles 2019-11-11 18:46:59 +09:00
Ryan S. Elliott 02791e0b4d Add Install_conda doc 2019-11-10 17:49:15 -06:00
Evangelos Voyiatzis 93b03aa82c
Merge pull request #1 from akohlmey/shape_chunk 
Documentation update
 2019-11-10 21:35:30 +01:00
lucienPan 599a189545 Patch of class2 dihedral 2019-11-08 17:28:49 -05:00
lucienPan 59b5ef8fb0 Patch of Dihedral class2 2019-11-08 17:17:01 -05:00
lucienPan cb30ab7556 Merge branch 'p_class2' of github.com:LucienPan0903/lammps into p_class2 2019-11-08 16:28:49 -05:00
lucienPan 4baa665a80 Patch of class2 dihedral 
Fix the NAN problem when any two bonds are nearly parallel
 2019-11-08 16:26:54 -05:00
lucienPan e5933ecc4a Fix previous submission of nan problem 2019-11-08 16:22:57 -05:00
lucienPan 29b2dc7043 Patch of class2 dihedral 
Fix the nan problem when any two bonds are nearly parallel
 2019-11-08 16:11:34 -05:00
Richard Berger b9648884bb Add rst versions of new documentation 2019-11-08 15:28:12 -05:00
Richard Berger 07a34382ae Magic 
Merge branch 'master' into shape_chunk
 2019-11-08 15:25:47 -05:00
Axel Kohlmeyer 90729ebe25
Merge pull request #1764 from jwood13/stable 
Add a max and min option to fix_gcmc
 2019-11-08 15:01:51 -05:00
Axel Kohlmeyer 6623169d97
Delete example file on request of @athomps 2019-11-08 15:00:26 -05:00
Axel Kohlmeyer 95a6498569
Merge pull request #1766 from lammps/compute-hma-doc 
Link compute hma docs
 2019-11-08 14:51:32 -05:00
Axel Kohlmeyer 8778ec9dde
Merge pull request #1763 from lammps/fix-pour-doc 
add documention to FixPour::outside(), simplify logic a bit
 2019-11-08 12:09:19 -05:00