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6011 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 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 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 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 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 6424883daf
apply revisions suggested by @sjplimp 2020-01-31 10:52:31 -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 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 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 5962e880d4
remove some unneeded backslash escapes 2020-01-29 14:33:36 -05:00
Axel Kohlmeyer c855bbb6bf
Merge branch 'master' into adaptglok 2020-01-29 11:42:25 -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
Axel Kohlmeyer ec381964e4
Merge branch 'master' into remove-txt-files 
# Conflicts:
#	doc/src/Build_settings.rst
 2020-01-24 21:32:24 -05:00
Axel Kohlmeyer 4134d7fddd
Merge pull request #1854 from akohlmey/next_patch_release 
Update version string for the next patch release
 2020-01-24 20:58:03 -05:00
Stan Moore 9d333c351a Small clarification to kspace_style.rst 2020-01-24 14:42:40 -07:00
Axel Kohlmeyer 0302c0ba24
correct malformed tables 2020-01-24 12:30:15 -05:00
Axel Kohlmeyer c9cc13c2a6
add mpi4py url and expand/update the python with MPI introduction 2020-01-24 11:27:43 -05:00
Axel Kohlmeyer fa4d9ff0d8
remove automatic translation of .txt to .rst and references to txt folder 2020-01-23 16:56:41 -05:00
Axel Kohlmeyer daa5efe1fd
remove .txt doc sources 2020-01-23 16:53:11 -05:00
Axel Kohlmeyer 72d8bea459
remove backslash escapes for underscore in doc references 2020-01-23 16:52:38 -05:00
Axel Kohlmeyer cb5138a335
update version string for the next patch release 2020-01-23 12:00:33 -05:00
Axel Kohlmeyer df23460e18
Merge branch 'master' into fft 
# Conflicts:
#	src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
 2020-01-23 00:22:38 -05:00
Axel Kohlmeyer 958b8d96a9
expand explanations about setting the python version for the python wrapper 2020-01-23 00:14:44 -05:00
Axel Kohlmeyer 204fb6f7ed
fix issue with standalone anchor_check 2020-01-22 23:51:53 -05:00
Axel Kohlmeyer 30444b344b
Merge pull request #1853 from akohlmey/collected-small-changes 
Collected small changes and bugfixes for the next patch release
 2020-01-22 17:25:03 -05:00
Axel Kohlmeyer 9a27aa4e9e
Merge branch 'master' into fft 
# Conflicts:
#	src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
 2020-01-22 15:21:08 -05:00
Axel Kohlmeyer 40e0e78abd
import template atom ID check from PR #1822 2020-01-22 15:02:55 -05:00
Axel Kohlmeyer 8a1f893b43
repair incorrect conversions on [*] expressions by txt2rst 2020-01-22 13:20:04 -05:00
Axel Kohlmeyer f7dc70a986
add new error/warning messages to documentation 2020-01-21 16:05:55 -05:00
Axel Kohlmeyer a6f59a8607
Merge remote-tracking branch 'github/master' into Ncreate_atoms 
# Conflicts:
#	src/create_atoms.cpp
 2020-01-21 15:52:01 -05:00
Steve Plimpton 90ff2eb6c9 modified versions of creating atoms on subset of lattice, ditto for set type/fraction 2020-01-21 13:31:47 -07:00
Steve Plimpton 4ea679dd54 Merge branch 'master' into nparticles 2020-01-21 13:26:03 -07:00
Axel Kohlmeyer 405eb63a51
update sphinx extension to automatically pad lists to fill tables and avoid errors processing the documentation 2020-01-21 11:39:29 -05:00
Axel Kohlmeyer 3db920b8a6
fix minor issues with docs 2020-01-20 17:03:54 -05:00
Axel Kohlmeyer 12de17621f
Merge branch 'master' into collected-small-changes 
# Conflicts:
#	doc/src/Commands_fix.rst
 2020-01-20 16:59:42 -05:00
Axel Kohlmeyer 795a872bf3
Merge pull request #1847 from pdebuyl/fix-active 
Add fix propel/self
 2020-01-20 16:57:04 -05:00