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19688 Commits

Author SHA1 Message Date
Axel Kohlmeyer 73364404a1
Step version strings for next patch release 2020-02-03 07:18:31 -05:00
Axel Kohlmeyer bbf229e8cc
Merge pull request #1866 from YunxingZuo/master 
add SNAP and quadratic SNAP potentials for six elemental systems
 2020-02-02 06:55:09 -05:00
YunxingZuo 0a10f5567a correct potential file format to be compatible with latest lammps 2020-01-31 21:04:03 -08:00
YunxingZuo 01a6608fb6 add SNAP and quadratic SNAP potentials for six elemental systems 2020-01-31 19:30:02 -08:00
Axel Kohlmeyer dd91d519e1
Merge pull request #1703 from jboschen/nwchem 
add NWChem wrapper to client/server mode for AIMD
 2020-01-31 20:50:51 -05:00
Axel Kohlmeyer 5983c2a87d
Merge pull request #1864 from akohlmey/doc-remove-redundant-links 
More documentation ReStructuredText cleanup
 2020-01-31 17:32:51 -05:00
Axel Kohlmeyer 472fe8216f
address spelling errors 2020-01-31 16:54:27 -05:00
Axel Kohlmeyer b66717d8cb
add one more missing link 2020-01-31 16:40:41 -05:00
Axel Kohlmeyer a9a2a9fef9
provide updated information on how to report bugs on github or via e-mail 2020-01-31 16:39:34 -05:00
Axel Kohlmeyer f386598c54
restore missing links 2020-01-31 16:39:09 -05:00
Axel Kohlmeyer 1a4e6228a2
add false positive 2020-01-31 15:59:26 -05:00
Axel Kohlmeyer 21a80e9b50
fix typo 2020-01-31 15:57:52 -05:00
Axel Kohlmeyer 8fd2ab78f1
Merge branch 'master' into nwchem 
# Conflicts:
#	doc/src/Howto_client_server.rst
#	doc/src/server_md.txt
 2020-01-31 15:56:25 -05:00
Axel Kohlmeyer 97addd2bee
Merge branch 'master' into doc-remove-redundant-links 
# Conflicts:
#	doc/src/min_modify.rst
#	doc/src/min_style.rst
#	doc/src/minimize.rst
 2020-01-31 15:39:25 -05:00
Axel Kohlmeyer 947827fe1f
Merge pull request #1052 from jguenole/adaptglok 
Optimized implementation of FIRE
 2020-01-31 15:24:00 -05:00
Axel Kohlmeyer 0f37e641eb
restore one global definition of previously removed links, that are still in use 2020-01-31 14:09:12 -05:00
Axel Kohlmeyer 3169ef772b
delete superfluous horizontal line plus preceding empty lines at the end of doc files 2020-01-31 14:06:14 -05:00
Axel Kohlmeyer cdf2f66c0a
delete empty lines at the end of files 2020-01-31 14:03:52 -05:00
Axel Kohlmeyer ce10fd01a8
remove redundant/obsolete link definitions 2020-01-31 14:00:53 -05:00
Axel Kohlmeyer b524db88a3
Merge remote-tracking branch 'github/master' into adaptglok 
# Conflicts:
#	doc/src/min_modify.rst
 2020-01-31 12:24:59 -05:00
Axel Kohlmeyer 56ff70de70
Merge pull request #1860 from akohlmey/collected-small-changes 
Collected small changes for next patch release
 2020-01-31 12:21:17 -05:00
Axel Kohlmeyer 39188da85b
Merge pull request #1857 from ohenrich/user-cgdna 
USER-CGDNA: Increased tolerance for fatal error in FENE bond
 2020-01-31 12:20:57 -05:00
Axel Kohlmeyer 710929da1d
Merge pull request #1861 from akohlmey/doc-link-escape-removal 
Documentation link formatting cleanup and fixup
 2020-01-31 11:00:27 -05:00
Axel Kohlmeyer 6424883daf
apply revisions suggested by @sjplimp 2020-01-31 10:52:31 -05:00
Axel Kohlmeyer 82aab36898
reset array size since we don't use the last element anymore 2020-01-31 09:59:35 -05:00
Axel Kohlmeyer 2069c7a5fd
correct incorrect bugfix 2020-01-31 09:58:04 -05:00
Axel Kohlmeyer 31c4833707
correct out-of-bounds array access in RanMars::select_subset() 2020-01-31 09:51:23 -05:00
Axel Kohlmeyer ed628a2de7
remove some more unneeded backslash escapes and fix up a few more doc links 2020-01-31 09:01:26 -05:00
Axel Kohlmeyer 82286702cb
switch OpenMP pragma to default(shared), so it is compatible with all OpenMP standard versions 2020-01-31 08:32:14 -05:00
jboschen bc3807aa4b Fix sign of forces in AO mode, update h2o examples 2020-01-31 00:42:00 -06:00
Axel Kohlmeyer e4cf0a07a0
remove more `\_` escapes from doc anchors and a bunch of other issues found in the process 2020-01-31 00:45:13 -05:00
Axel Kohlmeyer bb94303e73
remove backslash escapes from link anchors 2020-01-30 17:04:09 -05:00
Axel Kohlmeyer c732ccc0f8
remove trailing whitespace 2020-01-30 17:02:06 -05:00
Axel Kohlmeyer f872d374a0
Merge branch 'adaptglok' of github.com:jguenole/lammps into adaptglok 2020-01-30 17:00:10 -05:00
Axel Kohlmeyer 292fc77dce
correct broken links to commands 2020-01-30 12:55:59 -05:00
Axel Kohlmeyer eb7958d04c
update documentation for pair_modify to reflect code changes and clarify the use of special 2020-01-30 12:55:25 -05:00
Axel Kohlmeyer 0613790b6b
support having the keyword special multiple times after pair in pair_modify 2020-01-29 17:23:11 -05:00
Axel Kohlmeyer ccd395fdd8
remove dead code 2020-01-29 14:34:03 -05:00
Axel Kohlmeyer 5962e880d4
remove some unneeded backslash escapes 2020-01-29 14:33:36 -05:00
Julien Guénolé 426ca97aa6 correct bug introduced in previous commit 2020-01-29 17:53:10 +01:00
Julien Guénolé 1e7f09bded removing deprecated functions in log comment 2020-01-29 17:50:56 +01:00
Julien Guénolé 60b9627657 one missing example 2020-01-29 17:48:58 +01:00
Axel Kohlmeyer c855bbb6bf
Merge branch 'master' into adaptglok 2020-01-29 11:42:25 -05:00
Julien Guénolé 6bd23f4909 New example folder for fire 2020-01-29 17:31:20 +01:00
Axel Kohlmeyer 668feb22b5
Merge pull request #1859 from giacomofiorin/colvars-update 
Update Colvars library to version 2020-01-27
 2020-01-28 16:01:59 -05:00
Giacomo Fiorin 9427fc50a5 Update Colvars library to version 2020-01-27 
One new feature (arithmetic path variables) and several smaller enhancements
or bugfixes.

    Fix error check when loading an old state file
    https://github.com/Colvars/colvars/pull/317

    Get default values for grid boundaries when available
    https://github.com/Colvars/colvars/pull/310

    Allow redefining existing index groups (warn when this happens)
    https://github.com/Colvars/colvars/pull/302

    Simplified replica communication syntax in metadynamics
    https://github.com/Colvars/colvars/pull/301

    Obtain the bias_energy for ABF biases
    https://github.com/Colvars/colvars/pull/294

    Fix reading path file with vector CVCs
    https://github.com/Colvars/colvars/pull/288

    Fix segfault at deleting CVBasedPath
    https://github.com/Colvars/colvars/pull/286

    Parrinello's (arithmetic) pathCV in CV space
    https://github.com/Colvars/colvars/pull/274

    Fix race condition when starting a bundle of walkers
    https://github.com/Colvars/colvars/pull/279
 2020-01-28 14:15:05 -05:00
Julien Guénolé e9b6824e11 correct spelling 2020-01-28 16:27:19 +01:00
Julien Guénolé a3d10d537c Updated documentation 2020-01-28 16:03:49 +01:00
Julien Guénolé 197ba62cd9 Change fire to fire/old and fire2 to fire. Implement normstyle in fire. Update author affiliation. 2020-01-28 14:51:23 +01:00
Axel Kohlmeyer 5eef3b1828
Merge pull request #1855 from akohlmey/remove-txt-files 
Remove txt sources of rst files from doc folder
 2020-01-27 12:04:37 -05:00