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5738 Commits

Author SHA1 Message Date
Yaser Afshar 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
julient31 4743c0004f Commit JT 102819 
- corrected issue in Zeeman precession
- improved documentation of Zeeman interaction
 2019-10-28 15:34:52 -06:00
Michael Brown a0d74ca2ae Bug fix for gay-berne potential when mu != 1.0. 2019-10-27 22:31:00 -07:00
Evangelos Voyiatzis 050a0d4f5c fixing link issues 2019-10-27 12:15:50 +01:00
Evangelos Voyiatzis e263890a6b inclusion of reference links in the text 2019-10-26 18:09:11 +02:00
Axel Kohlmeyer b3dbf7925a
print warning when GPU pair style increases the communication cutoff 2019-10-26 05:15:58 -04:00
Axel Kohlmeyer 22288e06b7
Merge branch 'master' into fix-compiler-warnings 2019-10-25 14:07:50 -04:00
Axel Kohlmeyer 33b14891ab
Merge pull request #1730 from ohenrich/user-cgdna 
USER-CGDNA quasi-unique base pairing
 2019-10-25 13:45:29 -04:00
Axel Kohlmeyer 9ecbaf0407
Merge pull request #1732 from wmbrownIntel/doc-gayberne-update 
Fixing Gay-Berne "extra" documentation to define epsilon parameters c…
 2019-10-25 13:43:40 -04:00
Axel Kohlmeyer b7fbb36b81
one more missing entry to required files 2019-10-23 12:10:20 -04:00
Axel Kohlmeyer fad4cecc20
no need to define link targets that are not pointed to 2019-10-23 12:10:03 -04:00
Evangelos Voyiatzis 22b9cce436 Update lammps.book 2019-10-22 20:44:06 +02:00
Evangelos Voyiatzis a8501f922c Computing the eigenvalues of the gyration tensor and shape parameters per chunk 2019-10-22 20:35:54 +02:00
Axel Kohlmeyer cac57ec7e0
Move release date ahead by another week to 30 October 2019 2019-10-22 16:48:39 +02:00
Axel Kohlmeyer 57da9d177f
step version string for next patch release 2019-10-21 04:02:08 -04:00
jrgissing e44402326f doc typo 2019-10-20 13:21:20 -06:00
jrgissing a69bd0405a add lowercase 'arrhenius' keyword to spellcheck 2019-10-19 23:09:10 -06:00
jrgissing d429143589 bond/react: Arrhenius constraint 2019-10-19 22:15:52 -06:00
Michael Brown 30cff3faf3 Fixing Gay-Berne "extra" documentation to define epsilon parameters consistent with LAMMPS input. 2019-10-18 03:10:31 -07:00
Axel Kohlmeyer bb21847f8a
have sphinx configuration switch math formula renderer for epub 
this still needs work, that has to be done after we switched to RST
 2019-10-18 04:47:18 -04:00
Giacomo Fiorin c578e4e7fc Enable COLVARS_LEPTON for make, update build doc for USER-COLVARS 2019-10-17 22:48:57 -04:00
Oliver Henrich c6f637f78f Merge branch 'master' into user-cgdna 2019-10-17 18:40:50 +01:00
Oliver Henrich 68dc2a7966 Added description of quasi-unique base pairing 2019-10-17 16:06:06 +01:00
Axel Kohlmeyer 68adc56e93
Merge branch 'master' into fix-compiler-warnings 2019-10-17 06:03:59 -04:00
Axel Kohlmeyer e4c77f047f
document COLVARS_LEPTON flag to CMake configuration 2019-10-16 16:19:12 -04:00
Axel Kohlmeyer 4e6f83ced2
Merge pull request #1726 from akohlmey/singularity 
Add Singularity definition files suitable for compiling and debugging LAMMPS
 2019-10-16 21:12:22 +02:00
Evangelos Voyiatzis 10031e91bd
Update false_positives.txt 
Added the name of Mattice in the list
 2019-10-16 20:25:53 +02:00
Evangelos Voyiatzis 38c819c281
Update compute_gyration_shape.txt 
Addition of a textbook where the computed quantities are presented in more detail
 2019-10-16 20:12:46 +02:00
Axel Kohlmeyer 45e8a41704
document support for r-RESPA in pair style zero 2019-10-15 17:34:37 -04:00
Axel Kohlmeyer f3b2ec80af
add false positives and correct spelling to have a clean spellcheck run on centos 7 2019-10-15 16:56:23 +02:00
Axel Kohlmeyer faf5ded721
fix formatting and include example for setting compiler flags to enable C++11 2019-10-15 16:55:51 +02:00
Axel Kohlmeyer e4bbfc992b
Singularity definition files for compiling LAMMPS 2019-10-15 16:22:08 +02:00
Axel Kohlmeyer 29574eaa45
added "likewise" as suggested by @sjplimp 2019-10-11 17:19:47 +02:00
Axel Kohlmeyer da56c7fc66
document freshly added warnings in header and manual 2019-10-11 16:47:35 +02:00
Axel Kohlmeyer 6e244bc8dc
Merge pull request #1631 from jibril-b-coulibaly/patch-2 
Bug fixes for pair style granular
 2019-10-09 14:14:48 +02:00
Steve Plimpton 945f903683 added an examples/UNITS dir 2019-10-08 18:02:21 -06:00
Axel Kohlmeyer e77e286d95
Merge pull request #1707 from charlessievers/lammps_gjf 
Lammps gjf small updates
 2019-10-08 23:06:36 +02:00
Axel Kohlmeyer 0e10fbb133
Merge pull request #1690 from charlessievers/third_order 
Added third order, added documentation, took out extraneous lines, ad…
 2019-10-08 21:57:15 +02:00
charlie sievers 9b15f4e2dc Added the change to langevin gjf documentation 2019-10-08 12:47:30 -07:00
Axel Kohlmeyer 4f57332a89
Merge pull request #1706 from TOFarmer/create_bonds_improper 
Add single/improper to create_bonds
 2019-10-08 21:40:31 +02:00
Axel Kohlmeyer ac8f2e431e
fix a few cut-n-paste issues 2019-10-08 14:49:20 +02:00
TOFarmer cf11e4be3c Added documentation for single/improper 2019-10-08 11:51:19 +01:00
Axel Kohlmeyer 8c063343a1 Merge branch 'master' into collected-small-changes 2019-10-07 18:54:33 +02:00
julient31 ed467d8867 Merge branch 'master' of github.com:alxvov/lammps into OSO 
- solved conflict in doc/src/fix_nve_spin.txt
 2019-10-04 08:56:49 -06:00
Axel Kohlmeyer ed5678d646
Merge pull request #1673 from charlessievers/lammps_gjf 
Lammps fix langevin updates for gjf option
 2019-10-04 10:02:46 +02:00
Axel Kohlmeyer a102d2343e
Merge pull request #1692 from julient31/restart-correction 
Bug correction in the SPIN package, and fix nve/spin option modification
 2019-10-04 09:55:40 +02:00
Axel Kohlmeyer 747bfa31f2 apply changes suggested by Andrew Santos 2019-10-03 18:31:42 +02:00
Axel Kohlmeyer bb4dc59803
fix typo 2019-09-30 16:33:07 -04:00
Axel Kohlmeyer 6cd460072b
add docs for dump_modify time yes. consolidate keywords 2019-09-30 11:01:41 -04:00
alxvov fc10817950 Merge remote-tracking branch 'origin/OSO' into OSO 2019-09-30 14:55:45 +00:00
alxvov 14933958f7 change units 2019-09-30 14:55:33 +00:00
jrgissing 23040a98f8 adds an angle constraint option for reacting molecules 
also, previously, reaction templates had to contain more than two atoms
 2019-09-28 23:10:34 -06:00
charlie sievers 5927f056c5 Removed redundant and out of scope gjf info from fix_langevin.txt 2019-09-25 17:22:15 -07:00
charlie sievers b771225f3d Edit gjf option syntax within fix_langevin.txt 2019-09-25 17:19:27 -07:00
Axel Kohlmeyer a5db0463ec
list lines in doc source files with non-ASCII characters 2019-09-25 13:36:57 -04:00
Axel Kohlmeyer 107369518e
replace non-ASCII characters with their ASCII equivalents 
# Conflicts:
#	doc/src/fix_wall_stochastic.txt
 2019-09-25 13:36:18 -04:00
julient31 a6a78208aa Commit3 JT 092419 
- modified other doc files
 2019-09-24 16:01:37 -06:00
julient31 a0974bc09d Commit JT 092419 
- changed the nve/spin lattice option
- from (yes/no) to (moving/frozen)
- changed the doc and all examples
 2019-09-24 15:58:22 -06:00
julient31 d9306a5865 Commit JT 092419 
- added inf norm option
 2019-09-24 13:58:56 -06:00
julient31 a31aa5debc Merge branch 'master' of github.com:alxvov/lammps into OSO 2019-09-23 14:22:26 -06:00
julient31 34f8104146 Commit3 JT 092319 
- corrected a typo in doc/src/min_modify.txt
 2019-09-23 13:52:48 -06:00
julient31 bc0ff0db61 Commit2 JT 092319 
- added enum to min.h (for norm choice)
- completed doc min_modify
- corrected torque tol issue in spin/min
 2019-09-23 13:48:33 -06:00
julient31 56e1a05287 Commit JT 092319 
- modified norm input in min_modify
- corrected doc/src/min_modify.txt
- added expression of the norms
- added a min max method in src/min.h
 2019-09-23 11:12:31 -06:00
Axel Kohlmeyer fddc164d5b
register a couple more false positives to clear doc test 2019-09-23 11:54:46 -04:00
Axel Kohlmeyer 03de73f66f
rename "ballistico" keyword to "eskm" to match dynamical_matrix 2019-09-23 11:54:26 -04:00
Axel Kohlmeyer 2da6083df2
fully integrate third_order command into manual and READMEs 2019-09-23 11:53:37 -04:00
Axel Kohlmeyer 804a49c3ea
Merge branch 'master' into third_order 2019-09-23 11:39:01 -04:00
charlie sievers cf1c31cd3d Added third order, added documentation, took out extraneous lines, added documentation figures. 2019-09-20 14:42:04 -07:00
Axel Kohlmeyer aa2b885783
Merge pull request #1687 from akohlmey/next_patch_release 
Step version string for next patch release
 2019-09-19 17:18:12 -04:00
Axel Kohlmeyer 6f06b3ecf1
Merge pull request #1645 from jrgissing/bond/react-max_rxn-bug 
Bond/react: max_rxn bugfix + restart reaction counts
 2019-09-19 15:21:40 -04:00
Axel Kohlmeyer b7d9337da4
remove a tab 2019-09-19 15:13:53 -04:00
Axel Kohlmeyer 077647b4e2
whitespace cleanup 2019-09-19 14:54:48 -04:00
Axel Kohlmeyer 95f59f5bf1
cosmetic changes 2019-09-19 13:58:30 -04:00
Axel Kohlmeyer 5c74782c84
step version for next patch release 2019-09-19 11:54:24 -04:00
Axel Kohlmeyer b0b340051c
Merge pull request #1684 from akohlmey/cxx-11-test 
Implement test for C++11 and document it
 2019-09-19 11:46:08 -04:00
Axel Kohlmeyer ed6dd1a632
Merge pull request #1666 from tanmoy7989/local_density 
added LD potential and wrote html-style doc
 2019-09-19 11:45:46 -04:00
Axel Kohlmeyer d4dbc32ba2
Merge pull request #1672 from akohlmey/dump-with-unit 
Add ITEM: UNITS line to native text format dumps
 2019-09-19 10:31:13 -04:00
Axel Kohlmeyer eab66f27fd
Merge pull request #1681 from akohlmey/collected-small-fixes 
Collected small changes for next patch release
 2019-09-19 10:27:54 -04:00
tanmoy.7989 b049b59015 revised documentation and added a citation trigger in .cpp file 2019-09-19 00:25:22 -07:00
Axel Kohlmeyer 5dba4b66c8
add warning banner to the LAMMPS output and refer to the C++11 issue on github 2019-09-18 16:56:14 -04:00
Axel Kohlmeyer 2ea11b3195
implement test for C++11 and document it 2019-09-18 15:50:26 -04:00
Axel Kohlmeyer 572235e66a
Merge pull request #1660 from tanmoy7989/reorder_remd_traj 
python tool to reorder replica traj
 2019-09-17 17:29:50 -04:00
charlie sievers aba472df3b removed excess line in langevin docs 2019-09-17 12:25:07 -07:00
charlie sievers eba10b10e8 Merge remote-tracking branch 'origin/master' into lammps_gjf 2019-09-17 12:08:12 -07:00
Axel Kohlmeyer 8ff6122560
correct documentation of improper style fourier 2019-09-17 14:48:11 -04:00
Axel Kohlmeyer 0c9697a685
documentation whitespace cleanup 2019-09-17 08:35:20 -04:00
Axel Kohlmeyer 3e4f1d1cb8
replace tabs 2019-09-17 08:02:30 -04:00
Axel Kohlmeyer f81c1aae26
Merge branch 'master' into hybrid-svector-fix 2019-09-16 22:28:48 -04:00
charlie sievers 971f4763e3 removed text referencing removed graphs 2019-09-16 16:36:50 -07:00
charlie sievers 0366a5aae9 Fix langevin changed <utils.h> to utils.h 2019-09-14 00:13:05 -07:00
charlie sievers 09b6794631 Updated fix langevin errors and warnings as well as associated doc files. Updated fix langevin kokkos errors and warnings as well as associated doc files 2019-09-13 23:25:48 -07:00
Axel Kohlmeyer c37d001178
fix stupid typo 2019-09-13 16:13:16 -04:00
Axel Kohlmeyer c1e7294b42
Merge branch 'master' into kk_ports 2019-09-13 12:30:53 -04:00
Axel Kohlmeyer e8f94447f7
Merge branch 'master' into hybrid-svector-fix 2019-09-13 12:28:45 -04:00
Axel Kohlmeyer 4593e159ef
update docs to indicate KOKKOS support for dihedral style harmonic 2019-09-13 12:25:23 -04:00
Axel Kohlmeyer 5a07db8465
tweak docs for dump_modify units command some more 2019-09-13 12:07:39 -04:00
Axel Kohlmeyer 0a176d48d8
clarify that each created file will have the ITEM: UNITS lines 2019-09-13 11:59:55 -04:00
Axel Kohlmeyer 7386956dc5
remove misspelled word from false positives list 2019-09-13 08:52:09 -04:00
Axel Kohlmeyer 1f9decadf8
fix typo 2019-09-13 08:03:02 -04:00
charlie sievers a948a34f8a added false positive, removed graphs from examples, updated langevin kokkos, improved diff readability in langevin 2019-09-12 16:34:15 -07:00
Axel Kohlmeyer 0c52a7ed70
update documentation 2019-09-12 15:23:15 -04:00
Axel Kohlmeyer fa164fffba
explain new semantics for accessing pN for hybrid styles 2019-09-12 13:59:05 -04:00
Axel Kohlmeyer 1631ecb3fe
integrate pair style local density into manual builds 2019-09-11 14:18:27 -04:00
Axel Kohlmeyer ae1054a243
change formatting so that sphinx is happier 2019-09-11 14:17:53 -04:00
Axel Kohlmeyer ce7c3e6864
Merge pull request #1648 from athomps/add_w_l_orientorder 
Add w l orientorder
 2019-09-11 14:08:33 -04:00
Axel Kohlmeyer df63a53788
Merge pull request #1650 from stanmoore1/kk_minimize 
Add Kokkos version of minimize
 2019-09-11 14:04:47 -04:00
Axel Kohlmeyer 102db258bc
Merge pull request #1667 from edwardsmith999/master 
Adjusted compute_bond_local to allow components of force to be obtained.
 2019-09-11 14:02:09 -04:00
Axel Kohlmeyer 07cda306a6
Merge pull request #1668 from stanmoore1/kk_hpe 
Add support for HPE MPI to Kokkos package
 2019-09-11 14:00:24 -04:00
charlie sievers 1e8e34f33d appended fix_langevin.txt documentation 2019-09-10 17:34:49 -07:00
charlie sievers 3df5321e00 Fixed extraneous paragraph in doc/src/fix_langevin.tct 2019-09-10 16:56:31 -07:00
charlie sievers e34b7840d5 Updated documentation and added MD results 2019-09-10 15:53:32 -07:00
tanmoy.7989 cde16580c0 fixed alphabetical ordering in Tools.txt and added a line highlighting the tool in temper.txt 2019-09-09 14:15:05 -07:00
Stan Moore 51786a459f Add support for HPE MPI to Kokkos package 2019-09-09 10:14:30 -06:00
Ed b08b3b90da Adjusted compute_bond_local to allow components of force to be obtained 2019-09-09 14:43:34 +01:00
tanmoy.7989 22fde86fd0 possible spelling mistake report from Sphinx for unidentified word ccache; added this to the false_positives.txt file 2019-09-09 02:27:54 -07:00
tanmoy.7989 e7d8165a46 fixed spelling mistakes reported by sphix 2019-09-09 02:16:30 -07:00
tanmoy.7989 91a1971977 added a line to tools/README and fixed the alphabetical ordering in docs 2019-09-09 02:04:59 -07:00
tanmoy.7989 8c113f5fdb added LD potential and wrote html-style doc 2019-09-09 01:51:04 -07:00
jrgissing 450f437d9f bond/react:another edge atom clarification 2019-09-08 22:59:59 -06:00
jrgissing e40a710f04 comm_modify docs tweak 
comm_modify cutoff usage clarification, when using restart files
 2019-09-06 01:38:17 -06:00
jrgissing 49b5825e8d bond/react docs tweak: address a common mistake 
no atom of a small molecule should be specified as an edge atom
 2019-09-05 23:50:57 -06:00
Axel Kohlmeyer bb0225c02e
clear svector for every invocation. document changes 2019-09-05 14:29:10 -04:00
tanmoy.7989 96c21bec98 added new valid words to doc/utils/sphinx-config/false_positives.txt 2019-09-04 23:16:19 -07:00
tanmoy.7989 21699b89e0 python tool to reorder replica traj 2019-09-04 15:26:10 -07:00
jrgissing 50af20d194 bond/react: remember reaction counts 
allow restart files to restore cumutative reaction counts
 2019-09-01 23:31:31 -06:00
Stan Moore 9961229226 Update docs 2019-08-28 10:01:00 -06:00
julient31 f1563ed988 Commit JT 082719 
- correcting min_modify.txt
 2019-08-27 17:44:04 -06:00
Aidan Thompson 3ec9317d03 Modified documentation 2019-08-26 14:28:09 -06:00
Aidan Thompson 07fceec1ee Tweaked doc page 2019-08-25 23:26:42 -06:00
Aidan Thompson fb702fa9d6 Added FCC, BCC, and ICOS examples 2019-08-25 23:02:41 -06:00
Axel Kohlmeyer 0b34db7881
Merge pull request #1642 from lammps/chunk-doc 
add another example to Howto chunk doc page
 2019-08-25 20:16:35 -04:00
Aidan Thompson f44470fe63 Added fcc and bcc examples for the Steinhardt-Nelson parameters 2019-08-23 16:28:13 -06:00
Richard Berger ddab4eeb1a Remove SHA1 utility used in doc Makefile 2019-08-22 14:11:32 -06:00
Richard Berger 574e4067dc Add documentation files in RST format 
This is the first step for moving the documentation format from *.txt to the
*.rst format.

In the last years we've been automatically converting txt files from Steve's
markup into RST to generate the documentation pages via Sphinx. The decision
has now been made to fully migrate to RST and avoid the conversion in the
future.

This will enable us to fully use RST and Sphinx to improve the documentation.

For the intermediate period, while there are still pending PRs with
documentation changes, we will keep both source files and update the RST files
accordingly.
 2019-08-22 14:11:32 -06:00
Axel Kohlmeyer cb999ad65f
fix typo 2019-08-22 13:46:24 -04:00
Steve Plimpton c74f5ae416 add another example to Howto chunk doc page 2019-08-22 11:37:21 -06:00
julient31 8ec4e3fc91 Commit JT 082219 
- modified min spin names (removed oso from spin/cg and spin/lbfgs)
- modified associated option name (from spin_oso_cg to spin/cg, same for
lbfgs)
- modified .gitignore, doc pages, and examples accordingly
 2019-08-22 10:48:58 -06:00
Axel Kohlmeyer ad83f0e2e3
update docs to add morse in a similar style to fix wall/region 2019-08-21 17:12:04 -04:00
Axel Kohlmeyer aac557a98f
integrate fix wall/morse docs properly into manual 2019-08-21 16:00:14 -04:00
Axel Kohlmeyer 6a584672e8
implement fix wall/morse based on fix wall/region and fix wall/harmonic 2019-08-21 16:00:14 -04:00
Axel Kohlmeyer 82b3fad152
Merge pull request #1628 from erozic/feature-wall-region-morse 
Added "morse" style to the "wall/region" fix
 2019-08-21 11:47:43 -04:00
alxvov 12c73e7a61 Merge branch 'upstream-master' into OSO 2019-08-21 14:03:42 +00:00
Axel Kohlmeyer cfa9179b28
Merge pull request #1503 from etomica/master 
Implement HMA compute in LAMMPS
 2019-08-21 00:12:16 -04:00
Axel Kohlmeyer b5a79f9616
update fix wall/region docs as requested by @sjplimp (i hope) 2019-08-20 16:50:49 -04:00
Axel Kohlmeyer 3d9e737a19
change order of morse style wall potential parameters to be consistent with pair morse and bond morse 2019-08-20 11:27:29 -04:00
Andrew Schultz a0f49f27d9 Final tweaks to HMA documentation 2019-08-19 18:15:19 -04:00
Stan Moore 9a849a4d4f
Merge branch 'master' into master 2019-08-19 15:55:39 -06:00
Axel Kohlmeyer a5acf1655b
resolve small formatting glitch 
Text blocks must all be flush on the left side or else sphinx gets confused since indenting is part of the syntax.
 2019-08-16 17:30:37 -04:00
Jibril B. Coulibaly cc14103f28 Bug fixes in granular pair style: 
- correct formula for tangent forces in style with no history in compute() and in single() functions
- remove tangent history update in the single() function
- implement correct output for tangent, normal and rolling forces in single() function
- correct typos in documentation
 2019-08-16 15:28:36 -05:00
Eugen Rožić 47533bc526
Update fix_wall_region.txt 2019-08-13 00:31:03 +02:00
Eugen Rožić ff09c19149 documentation for fix_wall_region morse 2019-08-13 00:10:50 +02:00
Axel Kohlmeyer 18725ce060
reformat documentation to match typical LAMMPS conventions, change links 2019-08-09 15:42:32 -04:00
Axel Kohlmeyer 5f442d7b64
add a couple of false positives 2019-08-09 15:31:22 -04:00
Axel Kohlmeyer 11f1ba220b
fix typo 2019-08-09 15:30:55 -04:00
Eugen Rožić 838238b1ca documentation 2019-08-08 00:38:41 +02:00
Axel Kohlmeyer d08d6b5fb0
Merge pull request #1623 from akohlmey/next-version 
Step version string for stable release
 2019-08-06 11:17:40 -04:00
Axel Kohlmeyer 59046e7444
step version number for stable release 2019-08-06 08:52:54 -04:00
Steve Plimpton 2d64323354 fix formatting and augment explanation for bbox option 2019-08-05 17:21:11 -06:00
Axel Kohlmeyer 25b504d4fd
Merge pull request #1615 from akohlmey/next_version 
Step version string for stable release
 2019-08-05 19:13:17 -04:00
Axel Kohlmeyer 34cc7ed5b1
Merge pull request #1619 from ellio167/kim-doc-update 
Update kim query url in docs
 2019-08-05 17:39:40 -04:00
Axel Kohlmeyer 2092b2c010
Step version string for stable release 2019-08-05 16:58:26 -04:00
Ryan S. Elliott e39b85b62f Update kim query url in docs 2019-08-05 15:23:57 -05:00
Richard Berger f2757eaf41 Mention LAMMPS_LIB_SUFFIX in docs 2019-08-05 14:00:56 -04:00
Axel Kohlmeyer 096c225594
Merge pull request #1613 from rbberger/cmake_docs_update 
Update CMake documentation
 2019-08-04 18:32:11 -04:00
Richard Berger b65ae605e5 Added one-liner for HTML-only docs in Build.txt 2019-08-03 15:17:18 -04:00
Axel Kohlmeyer 91fdd98fbc
restore accidentally deleted text 2019-08-02 18:44:40 -04:00
Richard Berger bd87b67232
Update false_positives.txt 2019-08-02 17:35:26 -04:00
Richard Berger eb7fa1b6cb Update CMake documentation 2019-08-02 17:04:59 -04:00
Axel Kohlmeyer aff5f06e8f
Merge pull request #1612 from akohlmey/new_version 
Step version string for next patch release
 2019-08-02 14:27:13 -04:00
Axel Kohlmeyer bd3ffe1321
Merge pull request #1603 from eagunn/iss1572clean 
Iss1572clean: Clean fix for error handling, clarify data requirements for fix bocs input
 2019-08-02 10:43:30 -04:00
Axel Kohlmeyer 11198e9d29
Merge pull request #1607 from giacomofiorin/colvars-update 
Update Colvars to version 2019-08-01
 2019-08-02 10:43:13 -04:00
Anne Gunn d750cc02c0
Changed the code in the read_F_table function to conform to the "expected behavior" description in #1572. Adopted a best-of-both-worlds approach, though, and processed the whole input file all the way through, emitting a message for each problem found, before issuing a final error message to stop processing. Updated doc to clarify requirement for uniform spacing of pressure correction points. 2019-08-02 08:46:04 -04:00
Axel Kohlmeyer 9ed43e55f0
add some more descriptions for fixes to list of style in fix command docs 2019-08-02 08:41:34 -04:00
Axel Kohlmeyer 8fd28cd78d
fix typo 2019-08-02 08:40:59 -04:00
Axel Kohlmeyer b5f19b93c2
Step version string for next patch release 2019-08-02 05:15:29 -04:00
Evangelos Voyiatzis 5076f1a36c
small clean-up of fix.txt 2019-08-02 10:55:18 +02:00
Giacomo Fiorin 52e2db44a1 Update Colvars to version 2019-08-01 
One new feature (geometric path variables) and bugfixes.

Minimize occurrence of file-read errors in multiple-walker metadynamics
https://github.com/Colvars/colvars/pull/276

Better error messages for RMSD
https://github.com/Colvars/colvars/pull/272

Ensemble-biased metadynamics documentation
https://github.com/Colvars/colvars/pull/261

Fix bug on multiple walkers metadynamics, pmf included twice
https://github.com/Colvars/colvars/pull/259

Implementation of the geometric path collective variables (C++11-only feature)
https://github.com/Colvars/colvars/pull/249
 2019-08-01 15:15:58 -04:00
Axel Kohlmeyer 5fe457667e
restore showing references to potential files without pathnames 2019-08-01 11:19:39 -04:00
oywg11 8f5cd8661f Fix communication bug of ILP 2019-08-01 16:38:19 +03:00
Axel Kohlmeyer 8803183b8b
Merge pull request #1593 from akohlmey/next_version 
Step version string for next patch release
 2019-07-30 22:25:26 -04:00
julient31 f4e3186abf Commit JT 073019 
- modified the false_positive file to correct errors
- improved the doc page of fix nve/spin
 2019-07-30 13:10:27 -06:00
Axel Kohlmeyer d4503a05a4
mention that cstdlib is included in lmptype.h now, too. 2019-07-30 14:22:33 -04:00
Axel Kohlmeyer 2d93a713e2
Merge branch 'master' into collected-small-changes 2019-07-30 14:14:11 -04:00
julient31 b5621b2c90 Merge branch 'master' of github.com:alxvov/lammps into OSO 
Conflicts:
	src/SPIN/neb_spin.cpp
 2019-07-30 09:14:49 -06:00
julient31 74fa4f7415 Commit JT 073019 
- modified doc doc/src/min_modify.txt
- tested lattice minimizers with norm styles
 2019-07-30 08:58:12 -06:00
Axel Kohlmeyer 8fa4efa08e
Merge pull request #1440 from ellio167/kim-simulator-models 
Develop native support for KIM simulator models
 2019-07-30 10:53:58 -04:00
Axel Kohlmeyer 3eadfa15ef
Merge pull request #1512 from mkanski/rotate_molecules 
Extend support of "rotate" keyword to all styles of "create_atoms"
 2019-07-30 10:53:37 -04:00
Axel Kohlmeyer d1e8d7cbf8
Step version string for next patch release 2019-07-30 08:26:11 -04:00
alxvov aa3c44ad4a modify documentation a bit 2019-07-30 12:02:10 +00:00
Axel Kohlmeyer 3ee86470bb
correct documentation URL for PLUMED 2019-07-30 05:53:28 -04:00
mkanski d201d6c2d1 fix grammar error 2019-07-30 10:18:53 +02:00
Axel Kohlmeyer 88523fdd6e
Merge pull request #1529 from rupertnash/compute_momentum 
add compute momentum command
 2019-07-29 22:51:29 -04:00
Axel Kohlmeyer d2c4989dbf
Merge pull request #1583 from evoyiatzis/gyration_shape 
computing the eigenvalues of gyration tensor & shape parameters
 2019-07-29 22:16:13 -04:00
Axel Kohlmeyer edf64ed16c
Merge pull request #1511 from jdevemy/master 
Add keyword hybrid/pair for compute_pressure
 2019-07-29 22:15:20 -04:00
Axel Kohlmeyer 9004ebc3fe
one more fixup for compatibility for old PDF build scheme 2019-07-29 21:11:13 -04:00
Axel Kohlmeyer 90c678849a
replace non-ascii characters with ASCII equivalents 2019-07-29 21:10:49 -04:00
Axel Kohlmeyer 9f276be0e5
fix up legacy doc building for final kim doc files 2019-07-29 20:48:47 -04:00
Axel Kohlmeyer 6833d6def6
Merge branch 'master' into kim-simulator-models 
# Resolved Conflicts:
#	src/KIM/kim_query.cpp
#	src/KIM/pair_kim.cpp
 2019-07-29 20:43:10 -04:00
Axel Kohlmeyer 2e6850835f
Merge pull request #1542 from akohlmey/improve-include-consistency 
Improve Consistency of Include Statements (mostly complete)
 2019-07-29 20:12:41 -04:00
Axel Kohlmeyer 7043b9f620
Merge pull request #1548 from jrgissing/bond/react-clarify-how-stabilization-works 
Bond/react clarify how stabilization works
 2019-07-29 19:55:24 -04:00