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6315 Commits

Author SHA1 Message Date
Axel Kohlmeyer 9955c8f94b
convert pair styles gauss to gromacs 2020-02-24 13:30:58 -05:00
Axel Kohlmeyer 8774ec04a9
convert pair styles hbond to lebedeva 2020-02-24 12:01:22 -05:00
Axel Kohlmeyer 6139617458
convert remaining lj pair styles 2020-02-24 10:50:31 -05:00
Axel Kohlmeyer d00f8fcd0a
convert pair styles local/density to meam/c 2020-02-24 09:21:08 -05:00
Axel Kohlmeyer 0b10c0ac60
convert math in more pair styles 2020-02-24 07:46:51 -05:00
Axel Kohlmeyer 54b7480478
convert pair styles sdk to soft 2020-02-23 16:33:37 -05:00
Axel Kohlmeyer eaeb9cad33
trim the lammps logo a little bit 2020-02-23 15:01:10 -05:00
Axel Kohlmeyer 0cc3f234dc
convert math in spin and sph pair styles 2020-02-23 15:00:43 -05:00
Axel Kohlmeyer d9a7edcf1a
Merge commit 'refs/pull/1893/head' of github.com:lammps/lammps into release-preparation 2020-02-23 13:38:26 -05:00
Oliver Henrich 607604d38c Added oxrna2 information 2020-02-23 17:36:57 +00:00
Axel Kohlmeyer 31165082c1
change pseudo external link to internal link. provide links to the command subpages 2020-02-22 18:41:36 -05:00
Axel Kohlmeyer ac639fe629
replace parsed-literal with code-block where applicable. improve typesetting 2020-02-22 13:50:35 -05:00
Axel Kohlmeyer cdf795652a
fix typesetting issues 2020-02-22 13:50:15 -05:00
Axel Kohlmeyer ca650ba43f
add some missing dependencies 2020-02-22 13:49:57 -05:00
Axel Kohlmeyer 6b79b1f978
use table_from_list in Packages_details and check for completenes there, too 2020-02-22 13:25:21 -05:00
Axel Kohlmeyer b1757bb26c
make names/lables more consistent and avoid reference errors in sphinx 2020-02-22 13:24:23 -05:00
Axel Kohlmeyer e8d1288527
added script to check for missing packages in package tables in manual 2020-02-22 11:46:31 -05:00
Axel Kohlmeyer ffabee6ae5
move logo symlink 2020-02-22 10:43:58 -05:00
Axel Kohlmeyer 57711f0dcb
improve layout and logical structure. add references 2020-02-22 10:39:15 -05:00
Axel Kohlmeyer 44a54324c1
more typesetting updates 2020-02-22 07:40:31 -05:00
Axel Kohlmeyer a915397668
more code-blocks 2020-02-22 06:14:52 -05:00
Axel Kohlmeyer 09ef55ac26
include small logo image in navigation bar. update copyright date 2020-02-22 06:14:39 -05:00
Axel Kohlmeyer 4ff0279bde
remove references and docs about using subversion to download LAMMPS 2020-02-22 05:49:30 -05:00
Axel Kohlmeyer ff316aa4d0
replace more parsed-literal with code-block sections 2020-02-22 05:42:05 -05:00
Axel Kohlmeyer f9b451de32
fix spell check 2020-02-22 04:32:26 -05:00
Axel Kohlmeyer 60cb4416f0
add ability to build an offline viewable html format manual in html-offline 2020-02-22 02:27:18 -05:00
Axel Kohlmeyer 59ed320bef
more small improvements and additions 2020-02-21 16:52:44 -05:00
Axel Kohlmeyer 6b96dedf75
fix grammar issue 2020-02-21 16:04:00 -05:00
Axel Kohlmeyer 926dbed70a
fix spelling issue 2020-02-21 15:25:55 -05:00
Axel Kohlmeyer b4c65a645e
fix some minor style issues 2020-02-21 15:12:53 -05:00
Axel Kohlmeyer bf3e7237c3
replace dir with directory where appropriate 2020-02-21 15:08:18 -05:00
Axel Kohlmeyer c144918441
fix typo in markup resulting in broken link 2020-02-21 13:39:31 -05:00
Axel Kohlmeyer f0e8e3aab8
small cleanup 2020-02-21 13:36:15 -05:00
Axel Kohlmeyer 7186b4795b
remove \begin{equation} \end{equation} which are not needed and break epub 2020-02-21 13:21:59 -05:00
Axel Kohlmeyer 0ede04be6c
more build docs refactoring, correcting, and expanding 2020-02-21 10:40:18 -05:00
Axel Kohlmeyer 404b4cf299
update and expand the description of building the LAMMPS documentation 2020-02-21 08:10:30 -05:00
Axel Kohlmeyer e2f2ec3031
fix minor grammar issues in colomb pair style docs 2020-02-20 18:37:29 -05:00
Axel Kohlmeyer c6b5606c24
more cosmetic changes and replacing "dirs" with "directories" 2020-02-20 18:20:00 +01:00
Axel Kohlmeyer 1c8b7022a3
update documentation for the conventional build 2020-02-20 17:33:57 +01:00
Axel Kohlmeyer febb381880
updates and corrections to building LAMMPS as a library and using the USER-QMMM package 2020-02-20 14:58:02 +01:00
Axel Kohlmeyer dcd9b7c891
replace two tables with code-block sections 2020-02-20 02:12:32 -05:00
Axel Kohlmeyer a5ab3b13c5
cleaner typesetting 2020-02-19 16:15:35 -05:00
Axel Kohlmeyer 75a43398d9
replace more "parsed-literal" with "code-block" in build docs 2020-02-19 16:11:42 -05:00
Axel Kohlmeyer a9dc629489
replace non-printable ASCII characters 2020-02-19 15:34:58 -05:00
Axel Kohlmeyer aa5b870f7e
use "code-block" instead of "parsed-literal" 2020-02-19 15:32:58 -05:00
Axel Kohlmeyer 91ad19754c
correct, expand, and clarify documentation for linking with LAMMPS as a library 2020-02-19 18:14:57 +01:00
Axel Kohlmeyer 012dce93a0
Update package build docs for building the USER-QMMM package 2020-02-18 15:12:31 +01:00
jrgissing 9c507e6b81 Update Packages_details.rst 2020-02-17 21:53:14 -07:00
jrgissing 49e82e738d Update false_positives.txt 2020-02-17 21:50:54 -07:00
jrgissing ec887b37da Merge branch 'master' of https://github.com/lammps/lammps into bond/react-new-examples-and-package 2020-02-17 21:34:20 -07:00
Axel Kohlmeyer ad125bf36a
Merge pull request #1881 from akohlmey/next_lammps_version 
Update version string for next patch release
 2020-02-17 14:53:17 -05:00
Axel Kohlmeyer fe6f6b3002
Merge pull request #1869 from akohlmey/doc-continued-refactoring 
More documentation refactoring for embedding math expressions
 2020-02-17 13:06:07 -05:00
Axel Kohlmeyer f9bee338dd
Merge pull request #1875 from akohlmey/collected-small-fixes 
Collected small bug fixes and updates
 2020-02-17 11:40:27 -05:00
Axel Kohlmeyer f69c6196a0
Merge branch 'master' into doc-continued-refactoring 
# Conflicts:
#	doc/src/compute_fep.rst
 2020-02-17 17:37:10 +01:00
Axel Kohlmeyer c8561ecef0
Merge pull request #1879 from akohlmey/user-plumed-update 
Update USER-PLUMED to include support for version 2.6.0. Fix bug in API check
 2020-02-17 11:32:10 -05:00
Axel Kohlmeyer b30670d405
correct some grammar and style issues in describing using/building LAMMPS on windows 2020-02-17 10:27:57 +01:00
Axel Kohlmeyer 4a2f05d333
convert pair styles srp to tersoff 2020-02-16 13:42:37 -05:00
Axel Kohlmeyer 3f5bb96aed
pair ufm to pair zbl 2020-02-15 16:47:32 -05:00
Axel Kohlmeyer a508138510
convert wall fixes to embedded math 2020-02-15 12:13:32 -05:00
Axel Kohlmeyer b25f781071
convert docs for more fixes 2020-02-15 11:35:21 -05:00
Agilio Padua 0e2604fc80 Convert documentation of compute_fep and pair_fep_soft to mathjax 2020-02-15 16:19:39 +01:00
Axel Kohlmeyer fd8cd6faa5
typeset hyperdynamics fix docs with embedded math 2020-02-15 06:50:04 -05:00
Axel Kohlmeyer b0de48e47f
convert some more fixes 2020-02-15 02:31:50 -05:00
Axel Kohlmeyer 2de515c671
improve layout 2020-02-14 12:31:55 +01:00
Axel Kohlmeyer 74a2fd973b
convert docs for fixes eos/cv, eos/table/rx, gcmc, grem, langevin/spin, lb/fluid 2020-02-14 12:27:55 +01:00
Axel Kohlmeyer c47245c629
update/correct lammps executable manpage 2020-02-14 10:33:08 +01:00
Axel Kohlmeyer d7a7c103ca
Update version string for next patch release 2020-02-14 09:55:56 +01:00
Richard Berger 7b32b1e595 Update pair_body_rounded_polyhedron docs 2020-02-14 09:52:06 +01:00
Richard Berger b1493d651f Update pair_body_rounded_polygon docs 2020-02-14 09:44:03 +01:00
Axel Kohlmeyer f70e39c366
update fix ave/correlate/long docs to include info about limitations in output options vs. ave/correlate 2020-02-14 09:30:06 +01:00
Richard Berger 147d430a6d Update pair_body_nparticle docs 2020-02-14 09:27:55 +01:00
Richard Berger e339e1735d Update pair_beck docs 2020-02-14 09:19:32 +01:00
Axel Kohlmeyer 4cacc4701d
update plumed support to include version 2.6.0. Fix bug in API check 2020-02-13 16:03:58 +01:00
Ryan S. Elliott cf67c16fcb Add openkim-models install instructions 2020-02-11 22:33:56 -06:00
Axel Kohlmeyer bfaae6860e
fix controller 2020-02-11 16:28:45 +01:00
Axel Kohlmeyer e4a730d57a
fix bond/react, box/relax, ehex 2020-02-11 16:14:00 +01:00
Axel Kohlmeyer 6d5c001b61
delete no longer used equations 2020-02-11 14:57:31 +01:00
Axel Kohlmeyer 440f3b9492
correct for typo in txt style markup 2020-02-11 14:54:54 +01:00
Axel Kohlmeyer 3314b4853e
convert compute xrd to use embedded math 2020-02-11 11:26:29 +01:00
Axel Kohlmeyer 002fff95c6
copy large target image files only once 2020-02-11 11:07:55 +01:00
Axel Kohlmeyer c8034d19c4
fix up remaining computes for embedded math and a few other issues 2020-02-10 16:21:19 -05:00
Richard Berger e952bcb5ac Fix pdf build of pair_atm docs 2020-02-08 20:09:40 +01:00
Richard Berger 86ebc8260e Update pair_atm docs 2020-02-08 19:24:27 +01:00
Richard Berger 712dbe6acc Update pair_airebo docs 2020-02-08 19:07:54 +01:00
Richard Berger 5bb28e9e84 Update pair_agni docs 2020-02-08 18:36:34 +01:00
Richard Berger 01805cf6ce Update pair_adp 2020-02-08 18:09:19 +01:00
Axel Kohlmeyer db805bc009
first chunk of compute commands to be converted to use embedded math 2020-02-04 17:05:23 -05:00
Axel Kohlmeyer 301a662a1d
cosmetic corrections 2020-02-03 13:41:50 -05:00
Axel Kohlmeyer f0935feabe
Merge pull request #1868 from akohlmey/next_patch_version 
Step version strings for next patch release
 2020-02-03 11:50:12 -05:00
Axel Kohlmeyer 966bc626fc
Merge pull request #1858 from akohlmey/fft-consistency 
Improved consistency and thread support in FFTs
 2020-02-03 11:14:16 -05:00
Axel Kohlmeyer b71e41dc8a
minor fixes 2020-02-03 10:48:04 -05:00
Axel Kohlmeyer 1827ce1d32
update dynamical_matrix docs 2020-02-03 09:01:31 -05:00
Axel Kohlmeyer 73364404a1
Step version strings for next patch release 2020-02-03 07:18:31 -05:00
Axel Kohlmeyer ecf30b47a0
Convert and revise a few more files (minimize, neb, tricilinic) 2020-02-02 22:35:39 -05:00
Axel Kohlmeyer fde2a59b0e
update documentation for contributing files and building the manual to using rst files 2020-02-02 19:05:35 -05:00
Axel Kohlmeyer 5b557ca4c8
remove references to .txt files for building the documentation 2020-02-02 18:50:49 -05:00
Axel Kohlmeyer 8ef3d77724
Convert documentation of improper styles from images to mathjax 2020-02-02 18:22:40 -05:00
Axel Kohlmeyer 949f88eb65
Convert documentation of dihedral styles from images to mathjax 2020-02-02 17:22:54 -05:00
Axel Kohlmeyer 2b6a022309
Merge branch 'master' into fft-consistency 2020-01-31 20:51:58 -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
jrgissing a35dc180bd bond/react: dihedral reaction constraint 2020-01-30 00:28:59 -07:00
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 99cfc9e668
small documentation tweak 2020-01-27 11:17:08 -05:00
Axel Kohlmeyer 795f2fd894
properly support threaded FFTs with MKL and document it. remove commented out FFTW2 code 2020-01-27 11:00:57 -05:00
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
Axel Kohlmeyer f03cfba029
Merge pull request #1820 from ornladios/adios_read_dump 
Support read_dump with dump style 'adios'
 2020-01-20 16:27:09 -05:00
Podhorszki Norbert 44a814ec1d Added 'timeout <value>' option to the adios reader, so that a rerun can concurrently run with the first simulation 2020-01-20 15:52:21 -05:00
Axel Kohlmeyer b0ba91d353
add false positive 2020-01-20 11:58:59 -05:00
Pierre de Buyl 8ed271f16f change mode of propel/self to quat instead of quaternion 2020-01-20 17:41:20 +01:00
Podhorszki Norbert a1864f8bfd Fix commands table 2020-01-20 10:11:34 -05:00
Podhorszki Norbert 95b4613e16 Added documentation for 'read_dump ... format adios' command and fixed links and names for 'dump atom/adios' and 'dump custom/adios' commands. 2020-01-20 09:23:35 -05:00
Vsevak 43c184983e Fix lj/cut/tip4p/long/gpu name in docs 2020-01-20 03:39:16 +03:00
Axel Kohlmeyer 5e740c9cc5
documentation and examples cleanup for fix propel/self 
- rename example folder
- remove .txt format docs
- remove obsolete fix active sources
- update readme in src/USER-MISC
- replace non-ASCII characters and fix spelling issues
 2020-01-19 13:29:52 -05:00
Pierre de Buyl 4c8a857960 Merge branch 'master' into fix-active-rebase-5 2020-01-17 22:11:55 +01:00
Axel Kohlmeyer 2c86c79dbb
correct issue with command table for fix styles 2020-01-16 14:04:48 -05:00
Axel Kohlmeyer ef2ac8aa26
convert updated docs to rst and remove .txt sources 2020-01-16 14:04:14 -05:00
oywg11 b2b28015c4 New ILP paramters 2020-01-16 16:46:04 +02:00
Axel Kohlmeyer 9f018b9aa2
make list of fixes have a multiple of 6 number of entries 2020-01-15 17:40:51 -05:00
Axel Kohlmeyer f1c79fb914
Merge pull request #1096 from ProfessorMiller/master 
Changes to the NH fix enabling Cauchy stress control (Cauhchystat) du…
 2020-01-15 17:35:03 -05:00
Axel Kohlmeyer 3efc5b0b64
Merge pull request #1841 from phankl/stable 
Mesoscopic potential for carbon nanotubes
 2020-01-15 16:31:40 -05:00
Axel Kohlmeyer 90d5f7be01
Merge remote-tracking branch 'cntmeso/stable' into ph-cntmeso 
# Conflicts:
#	doc/src/pair_mesocnt.rst
 2020-01-15 13:54:37 -05:00
Philipp Kloza 34bc3b1b2e changed documentation format to .rst 2020-01-15 18:23:45 +00:00
Axel Kohlmeyer 51f41d4559
add missing rst format doc file 2020-01-15 13:05:28 -05:00
Axel Kohlmeyer 4d20f1623c
remove outdated .txt versions of documentation 2020-01-15 11:53:21 -05:00
Axel Kohlmeyer 97bcce77d3
update documentation to rst format and integrate into lists/tables 2020-01-15 11:52:49 -05:00
Axel Kohlmeyer 2f1e3d8490
Merge branch 'master' into ph-cntmeso 
# Conflicts:
#	doc/src/pairs.txt
 2020-01-15 11:45:14 -05:00
cdt1802 a8d27efbe7 fixed typos in documenation, added words to false positives for spell check 2020-01-15 14:33:52 +00:00
cdt1802 198a40ada6 fixed typo in documentation 2020-01-15 11:43:11 +00:00
cdt1802 9ef984daaa added documentation 2020-01-15 11:04:43 +00:00
Axel Kohlmeyer 93b6d5312d
update the github workflow document for recent changes 2020-01-14 15:42:55 -05:00
Axel Kohlmeyer ded3354fa9
add comments about thread safety to the library howto 2020-01-14 15:04:17 -05:00
Axel Kohlmeyer 7f0373afa3
fix typo 2020-01-14 14:51:00 -05:00
Steve Plimpton be8832be99 Merge branch 'master' into nparticles 2020-01-14 12:36:02 -07:00
Axel Kohlmeyer b9c6e0f700
Merge pull request #1691 from toquydong/stochasticwall 
Implementation of statistical gas wall boundary conditions
 2020-01-14 14:11:16 -05:00
Axel Kohlmeyer 75b2066506
correct spelling issues 2020-01-14 13:34:19 -05:00
Axel Kohlmeyer 660264855a
update rst documentation for fix hyper/local 2020-01-14 13:27:35 -05:00
Steve Plimpton 628dc6dd2a sync with master 2020-01-14 10:40:05 -07:00
Steve Plimpton 07e58fd681 document latest fix hyper/local diagnostics 2020-01-14 10:36:19 -07:00
Steve Plimpton ea24ec8d6a minor formatting edits 2020-01-14 09:15:05 -07:00
Steve Plimpton 95a3abc74e Merge branch 'master' into fire 2020-01-14 08:53:40 -07:00
Axel Kohlmeyer 02c99d1554
convert documentation to rst format and remove corresponding txt files 2020-01-14 10:14:39 -05:00
Axel Kohlmeyer e03b7c5441
Merge branch 'master' into message-iterate 2020-01-14 10:10:08 -05:00
Axel Kohlmeyer 6c851f6db0
remove outdated .txt file 2020-01-13 23:15:20 -05:00
Axel Kohlmeyer f095aacad7
remove outdated .txt files 2020-01-13 23:08:20 -05:00
Axel Kohlmeyer 6fa02ea3e0
update spelling false positives list 2020-01-13 23:03:37 -05:00
Axel Kohlmeyer 7c591b9b62
list new fix in overview lists and tables 2020-01-13 23:03:24 -05:00
Axel Kohlmeyer 146e6faad4
add rst version of doc file 2020-01-13 22:58:56 -05:00
Axel Kohlmeyer d35b15525b
remove obsolete .txt files 2020-01-13 22:58:35 -05:00
Axel Kohlmeyer bd5a97e07e
add false positives 2020-01-13 22:41:08 -05:00
Axel Kohlmeyer 8258d0cb59
remove obsolete .txt file 2020-01-13 22:28:02 -05:00
Steve Plimpton d3348371e1 refactoring of code and doc files 2020-01-13 15:22:02 -07:00
Steve Plimpton 51efee43be sync to master 2020-01-13 13:42:05 -07:00
Steve Plimpton 9ed987c255 minor changes to syntax and documentation of fix deposit orient 2020-01-13 13:15:17 -07:00
Steve Plimpton e8d11931ec merged in current master 2020-01-13 10:34:31 -07:00
Steve Plimpton 99dc283f82 Merge branch 'master' into message-iterate 2020-01-13 09:30:51 -07:00
Axel Kohlmeyer 88448ef950
update rst docs since .txt file is gone 2020-01-13 10:57:36 -05:00
Axel Kohlmeyer 2834965e98
Merge branch 'master' into fft 
# Conflicts:
#	doc/txt/kspace_style.txt
 2020-01-13 10:53:26 -05:00
Axel Kohlmeyer 6813ab4c9c
Merge pull request #1832 from akohlmey/doc-styles-check 
Check style command lists against existing styles in sources
 2020-01-13 10:38:26 -05:00
Axel Kohlmeyer eed85bb676
Merge pull request #1834 from akohlmey/suffix-flag-refactor 
Small Suffix flag refactoring and disallow per substyle special overrides for USER-INTEL and GPU
 2020-01-13 10:37:35 -05:00
Axel Kohlmeyer bfaea66e66
update documentation 2020-01-12 23:03:45 -05:00
Axel Kohlmeyer 15603e0ff7
add documentation for including cufft with KOKKOS+CUDA (for conventional build, CMake is automatic) 2020-01-12 21:46:02 -05:00
Axel Kohlmeyer 3784df23f0
use FFT_FFTW_THREADS consistently, add CUFFT to CMake, minor improvements 2020-01-12 21:32:07 -05:00
Axel Kohlmeyer 7cb36d1705
Merge branch 'master' into fft 2020-01-12 20:22:15 -05:00
Axel Kohlmeyer a88e6494cf
address documentation spelling issues and remove obsolete file 2020-01-12 15:11:45 -05:00
Axel Kohlmeyer 0d6ec02d5a
small corrections and more cleanup 2020-01-12 14:31:05 -05:00
Axel Kohlmeyer 57f4b06db5
integrate RST version of npt/cauchy documentation 2020-01-12 14:06:12 -05:00
Axel Kohlmeyer 107c5bbced
Merge branch 'master' into cauchystat and resolve conflicts 
# Conflicts:
#	cmake/CMakeLists.txt
#	doc/src/Commands_fix.txt
#	doc/src/Packages_details.txt
#	doc/src/Packages_user.txt
#	doc/src/fix_nh.txt
#	doc/src/fixes.txt
#	doc/src/lammps.book
#	src/Makefile
 2020-01-12 13:58:41 -05:00
Axel Kohlmeyer 2231feaf9b
some corrections to the documentation 2020-01-12 13:55:39 -05:00
Axel Kohlmeyer b6d86e3c91
merge fix sources and move into USER-MISC package. clean up docs 2020-01-12 13:45:22 -05:00
Axel Kohlmeyer 755620acb7
correct documentation link 2020-01-12 13:10:37 -05:00
Axel Kohlmeyer 7cdd39b894
remove references to fix npt/cauchy which has its own doc file now 2020-01-12 13:10:26 -05:00
Axel Kohlmeyer 64e72b1cd5
indent consistently with tabs only 2020-01-12 12:34:54 -05:00
Axel Kohlmeyer 4a5511d00a
Merge branch 'collected-small-changes' into doc-styles-check 2020-01-12 10:19:22 -05:00
Axel Kohlmeyer 81c9b0b12e
small update to kspace overview 2020-01-12 10:17:56 -05:00
Axel Kohlmeyer 7b9abda6c4
refactor to use a function to process files with lists of styles 2020-01-12 10:17:14 -05:00
Axel Kohlmeyer c93ee1045c
Merge branch 'collected-small-changes' into doc-styles-check 2020-01-12 10:13:34 -05:00
Axel Kohlmeyer a0ecf539f6
clean up and correct some documentation link issues 2020-01-12 10:08:14 -05:00
Axel Kohlmeyer 675bd26085
Merge branch 'master' into doc-styles-check 2020-01-11 21:00:49 -05:00
Axel Kohlmeyer 587fc9d962
Merge pull request #1828 from lammps/post-patch-tweaks 
minor omissions in recent patch release
 2020-01-11 21:00:09 -05:00
Axel Kohlmeyer 3b32141330
update documentation for style check 2020-01-11 20:47:10 -05:00
Axel Kohlmeyer d7242eaa6a
print total styles and count/report the number of issues 2020-01-11 20:41:14 -05:00
Axel Kohlmeyer 26830d09f8
hook style check into makefile 2020-01-11 20:39:58 -05:00
Axel Kohlmeyer 1d7b554e9a
Merge branch 'post-patch-tweaks' into doc-styles-check 2020-01-11 20:08:03 -05:00
Axel Kohlmeyer b2c4385661
clean up and correct fix style command overview 2020-01-11 20:02:23 -05:00
Axel Kohlmeyer b4a87d79a0
make anchors and file names for lj/switch3/coulgauss/long consistent 2020-01-11 20:02:04 -05:00
Axel Kohlmeyer bc9436a04f
add support for computes and fixes 2020-01-11 19:58:31 -05:00
Axel Kohlmeyer 4a58d356b0
Merge branch 'post-patch-tweaks' into doc-styles-check 2020-01-11 19:43:42 -05:00
Axel Kohlmeyer 05b68d9e0d
add missing pair style entries 2020-01-11 19:43:29 -05:00
Axel Kohlmeyer 019c70140f
add and correct kspace style entries 2020-01-11 19:43:18 -05:00
Axel Kohlmeyer 7ea366b3ce
fix formatting issue 2020-01-11 19:42:40 -05:00
Axel Kohlmeyer 1d838dad19
add checking of kspace styles 2020-01-11 19:41:59 -05:00
Axel Kohlmeyer 555f9b3450
Merge branch 'post-patch-tweaks' into doc-styles-check 2020-01-11 19:16:44 -05:00
Axel Kohlmeyer ff7110028b
make doc of pair style mm3/switch3/coulgauss/long consistent and complete 2020-01-11 19:16:34 -05:00
Axel Kohlmeyer 66296616ae
handle removed styles on bonded command table 2020-01-11 19:10:21 -05:00
Axel Kohlmeyer 8f9c3a3a9c
Merge branch 'post-patch-tweaks' into doc-styles-check 2020-01-11 19:04:38 -05:00
Axel Kohlmeyer 84a975439a
clean up pair style command overview some 2020-01-11 19:04:02 -05:00
Axel Kohlmeyer f713e9acc3
add missing bond style 2020-01-11 19:03:20 -05:00
Axel Kohlmeyer 297d31ab8f
clean up and update general command overview 2020-01-11 19:02:49 -05:00
Axel Kohlmeyer a38cf075db
add checks for global commands, pair and bonded styles 2020-01-11 18:53:09 -05:00
Axel Kohlmeyer 7ebddb6088
Merge pull request #1829 from lammps/rerun-example 
added rerun example dir
 2020-01-11 18:49:40 -05:00
Axel Kohlmeyer 00a31f6637
Merge branch 'master' into doc-styles-check 2020-01-11 17:05:16 -05:00
Axel Kohlmeyer d7d1d57170
remove outdated txt files 2020-01-11 16:35:27 -05:00
Axel Kohlmeyer e1849232b8
remove redundant lj/cut/tip4p/long/gpu entry and correct underline length 2020-01-11 16:21:42 -05:00
Axel Kohlmeyer 9c207bb751
remove outdated .txt file for pair style meam/c 2020-01-11 16:20:13 -05:00