Commit Graph

18676 Commits

Author SHA1 Message Date
82ecce8a1a Merge branch 'master' into compute-hma-doc 2019-11-08 09:40:40 -07:00
cbca94e4bf Merge pull request #1765 from rbberger/doc_fixes
Doc Fixes
2019-11-08 11:27:33 -05:00
02a1ef0630 add compute hma to list of computes 2019-11-08 09:25:08 -07:00
81e92de838 Fix doc Makefile 2019-11-07 21:47:29 -05:00
83f0eb0058 Remove unnecessary files 2019-11-07 21:47:02 -05:00
6d7a591dce Merge pull request #1762 from rbberger/doc_lammps_lexer
Add LAMMPSLexer for LAMMPS code-blocks in docs
2019-11-07 16:25:01 -05:00
d2da55f5e3 Update Howto_pylammps.rst and remove Howto_pylammps.txt 2019-11-06 23:52:04 -05:00
3f10c4fcdc Update Manual_build.rst and remove Manual_build.txt 2019-11-06 23:33:14 -05:00
eaef8089a1 Add LAMMPSLexer for LAMMPS code-blocks in docs 2019-11-06 17:40:39 -05:00
bb18adc745 Merge pull request #1761 from rbberger/doc_updates
Update documentation tools and paths
2019-11-06 12:24:03 -05:00
9ac9ba6401 Merge branch 'master' into doc_updates 2019-11-06 11:35:35 -05:00
cf0eac62fa Merge pull request #1745 from yafshar/feature_parameterupdate
New KIM package feature: kim_param command for querying model parameters.
2019-11-06 09:17:07 -05:00
e64f68e73c Merge pull request #1 from akohlmey/kim_update_rst_fixes
Documentation update for your LAMMPS pull request
2019-11-06 07:55:42 -06:00
2fd9a27902 update kim_commands.rst from .txt file 2019-11-06 08:33:05 -05:00
729eabd771 make QUIP_LIBRARY setting consistent and backport change to .rst file only 2019-11-06 08:32:07 -05:00
efcf919ede Merge branch 'master' into feature_parameterupdate 2019-11-06 08:21:33 -05:00
2bbf52073f Merge pull request #1759 from akohlmey/hybrid-exclusion-bugfix
Consistent exclusion settings with multiple kspace-like sub-styles in pair hybrid
2019-11-06 06:24:35 -05:00
ee4e6352c4 Merge pull request #1755 from akohlmey/whitespace-cleanup
Whitespace cleanup
2019-11-06 06:23:16 -05:00
c3e52c3c8c Use globs for style lists 2019-11-05 15:49:09 -05:00
c756e472ae Remove Manual.txt and use variable for version 2019-11-05 15:34:57 -05:00
5e6694f3bc Re-enabled conversion of equations arrays. Disabled works even worse 2019-11-05 15:27:21 -05:00
423a3bb99f Add initial version of updated tools from #1533 2019-11-05 15:27:21 -05:00
74dade3ccb Change doc folder src -> txt, rst -> src 2019-11-05 15:27:21 -05:00
fe91d462db Merge pull request #1758 from marian-code/patch-1
wrong cmake option for QUIP
2019-11-05 12:11:17 -05:00
ae4764e614 address pair match issue with multiple hybrid substyles in exclusion settings 2019-11-05 11:03:25 -05:00
7ec1dccbe0 wrong cmake option for QUIP
QUIP cmake option for specifying library path should be QUIP_LIBRARY not QUIP_LIBRARIES
2019-11-05 14:57:44 +01:00
7bef07e9f7 Merge branch 'master' into HEAD 2019-11-04 16:52:02 -05:00
cf251eb8be Merge pull request #1756 from julient31/correct-minimizer
Correct warning issue in min_cg.cpp
2019-11-04 15:37:32 -05:00
e20439374e Merge pull request #1643 from rbberger/docs_to_rst_migration
Change documentation to use RST directly
2019-11-04 12:15:22 -05:00
1074884f74 Commit JT 110419
- removed fmax uninitialized variable from min_cg.cpp
- removed tabs from comments
- initialized fdotf variables
2019-11-04 09:04:43 -07:00
b6b022b610 whitespace cleanup: remove trailing blanks 2019-11-03 11:03:39 -05:00
9e7ca428aa whitespace cleanup: remove (evil) tabs 2019-11-03 11:01:42 -05:00
12cb19090a Remove txt2html and htmldoc from doc build 2019-11-02 23:07:49 -04:00
8f946b765e Add missing RST files 2019-11-02 23:03:36 -04:00
eac5f6e53e Update RST files 2019-11-02 23:01:18 -04:00
aeaa289d1d Merge branch 'master' into docs_to_rst_migration 2019-11-02 22:57:43 -04:00
9159a43d5d Merge pull request #1737 from akohlmey/next_patch_release
Step version string for next patch release
patch_30Oct2019
2019-10-30 17:47:10 -04:00
fed1a72bb5 Merge pull request #1569 from JunChiehWang/random_deposit
throw away random numbers to avoid unexpected correlations
2019-10-30 16:55:45 -04:00
224ea41838 Merge pull request #1751 from akohlmey/user-vtk-bugfix
USER-VTK bug fix
2019-10-30 16:54:54 -04:00
5b2301c2b5 whitespace cleanup to re-trigger jenkins 2019-10-30 16:28:05 -04:00
28483c085a Merge pull request #1746 from wmbrownIntel/gayberne-fix
Bug fix for gay-berne potential when mu != 1.0.
2019-10-30 14:00:33 -04:00
2f9f4557fe Merge pull request #1750 from rbberger/fix_pour_bugfix
Bugfix for fix pour and PBC
2019-10-30 14:00:22 -04:00
3af7ce17f4 don't segfault if some derived class deletes the list of user format strings 2019-10-30 13:53:09 -04:00
a35279a0cc don't delete arrays the base class expects to be present 2019-10-30 13:52:22 -04:00
3e2b572efd Fix special case for outside check in fix pour
If the range between lo and hi is bigger than the extent in that dimension, in
the periodic case the value will always be inside.
2019-10-30 12:01:38 -04:00
4a0495aefc Fixes issue #1695
There was a logic error in the outside() function used by fix pour.
The previous implementation was essentially doing this:

outside = outside_pbc_range || outside_regular_range

It should have been:

outside = outside_pbc_range && outside_regular_range
2019-10-29 17:09:29 -04:00
63cce391ca Adding the documentation for the new 'kim_param' command
New documnetation is added and the whole document is checked
and partly rewritten for clarity and errors are corrected

Adding the word "Zm" to prevent the spelling error in document
building check.
2019-10-29 11:51:05 -05:00
5ce8860dce Updating the 'kim_query' default behavior and adding the 'list' setting
Adding the 'list' setting of {formatarg} (default behavior or if
{formatarg} is not specified), the result is returned as a
space-separated list of values in {variable}.
2019-10-29 11:51:05 -05:00
c8c92189b4 New capabilities for accessing KIM portable models parameters
Add an ability within LAMMPS for getting/setting KIM
portable models (PM) parameters. The assumption is that
the model is already known (through 'kim_init') when
calling the new command.

'kim_param get' gets the value of PM parameters, where
the command input includes:
parameter name, & location, or indices range, and the
variable(s) name / variable name + split / list /explicit
to return the value(s).

'kim_param get paramname index_range varname [s|split|list|explicit]'

'kim_param set' sets the value(s) of PM parameters, where
the command input includes:
parameter name, & location, or indices range, and the
corresponding variable(s) value(s).

'kim_param set paramname index_range value(s)'

NOTE: The varable_name is the name of the lammps variable in the
lammps input script and can be used in other locations in the
script.
2019-10-29 11:51:05 -05:00
3cca4e0d2d New capabilities for updating KIM portable models parameters
1. Add new capabilities within LAMMPS for setting parameters of
the KIM portable models (PM). The current implementation extends
the 'pair_coeff' command to modify the PM parameters.
A series of additional parameters after the species list is the
input to the modified command. Each set of the other setting
is parameter name, range of array indices, and corresponding
parameter values.

2. Add two getters to the PairKIM class to get the KIM_Model object,
and the atom type list outside the 'pair_kim' command for ease of
use and extension ability of a new 'kim_param' command.
2019-10-29 11:50:28 -05:00