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6990 Commits

Author SHA1 Message Date
Richard Berger 09bc686f71
Avoid extra newline 2020-09-02 10:55:04 -04:00
Axel Kohlmeyer e5e2abe446
update include file policy file and policy for pointers.h special case 2020-09-02 10:51:55 -04:00
Richard Berger e479033109
Avoid breaking already fixed headers 2020-09-02 10:51:47 -04:00
Richard Berger 3c60a9e08e
Update fix_nh.rst 2020-09-02 10:31:21 -04:00
Richard Berger 49a6bf5e30
Update pair_class2.rst 2020-09-02 10:30:31 -04:00
Richard Berger 3a22f26e87
Update pair_cs.rst 2020-09-02 10:29:46 -04:00
Richard Berger 4d6be195ec
Add utility to fixup doc headers 2020-09-02 10:29:29 -04:00
Richard Berger e5f1f58aab
Update pair_born.rst 2020-09-02 10:26:37 -04:00
Richard Berger a6a49d80b2
Update pair_sdk.rst 2020-09-02 10:19:20 -04:00
Richard Berger 7ae98ffae1
Update fix_rigid.rst 2020-09-02 09:50:16 -04:00
Richard Berger dce7a39021
Update pair_buck.rst 2020-09-02 09:47:32 -04:00
Richard Berger 77f803b366
Update pair_charmm.rst 2020-09-02 09:14:20 -04:00
Richard Berger a9cf25db4c
Update pair_eam.rst 2020-09-02 09:13:59 -04:00
Richard Berger 7e733913d7
Update pair_fep_soft.rst 2020-09-02 09:03:00 -04:00
Richard Berger 45100528ad
Update pair_coul.rst 2020-09-02 08:54:53 -04:00
Axel Kohlmeyer 80519cd109
Merge pull request #2331 from rbberger/zstd_support 
Update COMPRESS package
 2020-09-01 15:01:04 -04:00
Richard Berger 31bd76efa5
Merge remote-tracking branch 'origin/master' into zstd_support 2020-09-01 12:58:41 -04:00
Richard Berger 9d3e3526a0
Add false positives and fix spelling in docs 2020-09-01 12:30:35 -04:00
Richard Berger a2b5c379f2
Update docs for COMPRESS styles 2020-09-01 12:17:08 -04:00
tomswinburne fbffcf3321 spelling 2020-09-01 11:34:11 +02:00
tomswinburne c6de769696 Merge branch 'master' of github.com:tomswinburne/lammps 2020-09-01 11:12:29 +02:00
tomswinburne ac080228dc whitespace style fix 2020-09-01 11:12:05 +02:00
TD Swinburne (Tom) 0541996919
Merge branch 'master' into master 2020-09-01 10:59:03 +02:00
Axel Kohlmeyer 675cf20e93
Merge remote-tracking branch 'github/master' into move-convenience-functions 2020-08-31 12:58:21 -04:00
Axel Kohlmeyer 9a4ec23c7f
Merge pull request #2327 from akohlmey/remove-doxygen-tool 
Remove doxygen tool folder and references to it in the manual
 2020-08-31 12:49:24 -04:00
Axel Kohlmeyer 1ff34d4b13
avoid doxygen lookup ambiguity 2020-08-31 12:46:05 -04:00
Axel Kohlmeyer dd03c7232a
Merge remote-tracking branch 'github/master' into move-convenience-functions 2020-08-31 11:41:18 -04:00
Axel Kohlmeyer cf11945e21
get rid of utils::boundsbig() by making it a template function with two specializations 2020-08-31 11:25:43 -04:00
Axel Kohlmeyer 8034a83ee8
Merge pull request #2325 from akohlmey/fortran-interface 
New Fortran interface to LAMMPS
 2020-08-31 10:27:10 -04:00
Axel Kohlmeyer c7360fb808
include example use of PotentialFileReader class 2020-08-31 07:45:52 -04:00
Axel Kohlmeyer c84033677c
add documentation for potential file reader 2020-08-31 07:31:28 -04:00
Axel Kohlmeyer 33f2cbc713
add docs for TextFileReader class to developer guide 2020-08-31 06:57:16 -04:00
Axel Kohlmeyer 39a9974f3d
add ValueTokenizer example and use captions with code-blocks 2020-08-30 23:57:02 -04:00
Axel Kohlmeyer e8e57b0628
remove doxygen tool folder and references to it in the input as it is no longer compatible and needed 2020-08-30 19:59:52 -04:00
Axel Kohlmeyer 4484699ab6
fix spelling 2020-08-30 15:52:42 -04:00
Axel Kohlmeyer 65d2ee7464
add work-in-progress marker to fortran library wrapper 2020-08-30 15:23:02 -04:00
Axel Kohlmeyer 4b0999e167
complete documentation of tokenizer classes 2020-08-30 14:12:21 -04:00
Axel Kohlmeyer 96ee132e85
start documenting tokenizer classes 2020-08-30 01:50:37 -04:00
Axel Kohlmeyer ceeaf1e988
update and correct documentation for utils functions 2020-08-29 23:51:46 -04:00
Axel Kohlmeyer 9c404e02fd
update include file conventions 2020-08-29 22:56:37 -04:00
Axel Kohlmeyer 83a9e5e724
handle spelling issues with new doc text 2020-08-29 22:55:05 -04:00
Axel Kohlmeyer e51a5ad8f4
import doxygen docs for new utils functions 2020-08-29 22:46:25 -04:00
Axel Kohlmeyer 6b7f4c500f
document changes to LAMMPS_POTENTIALS environment variable 2020-08-29 22:22:27 -04:00
Axel Kohlmeyer 31c91a8928
fix typo 2020-08-28 21:22:06 -04:00
Axel Kohlmeyer cec18b6aef
add docs for the new fortran interface 2020-08-28 20:57:19 -04:00
Axel Kohlmeyer 2e1b4498bd
update false positives 2020-08-28 20:30:00 -04:00
Axel Kohlmeyer cb1a2601e1
add more existing programmer guide docs 2020-08-28 20:25:09 -04:00
Axel Kohlmeyer 2a365c17e0
update utils namespace documentation including doxygen parts 2020-08-28 18:21:18 -04:00
Axel Kohlmeyer e64a977ae9
include documentation of utility functions in utils:: to developer guide 2020-08-28 17:14:49 -04:00
Axel Kohlmeyer a1bf772df2
move modifying and extending LAMMPS section to programmer guide 2020-08-28 17:14:29 -04:00
Axel Kohlmeyer 8fcd72405a
port over more of the framework of the programmer guide and remove programming details from user guide 2020-08-28 16:32:23 -04:00
Axel Kohlmeyer ded657120d
Merge pull request #2312 from akohlmey/developer-guide 
Integrate text from developer.tex file to the manual
 2020-08-28 15:01:27 -04:00
Axel Kohlmeyer 899144c0f8
Merge pull request #2314 from jrgissing/bond/react-RMSD_constraint 
Bond/react: add RMSD constraint
 2020-08-28 12:29:11 -04:00
Axel Kohlmeyer 9f2eba981a
a few more tweaks and spellcheck to make this ready for merging 2020-08-28 11:44:31 -04:00
Jacob Gissinger ef50a67169 bond/react: make rmsd constraint lowercase 2020-08-28 11:06:27 -04:00
Axel Kohlmeyer f8495975d3
transfer the rest of the Developer guide and remove the .tex versions and references to it 2020-08-28 10:52:45 -04:00
Axel Kohlmeyer f0788bfe86
transfer of developer.tex almost complete 2020-08-28 09:54:01 -04:00
Axel Kohlmeyer b16746e46e
Merge pull request #2313 from ndtrung81/gpu-bugfix 
Fixed bugs in the CPU kernel for beck, beck/omp and the GPU kernel of gauss/gpu
 2020-08-27 19:56:50 -04:00
Axel Kohlmeyer 463774319e
add missing parenthesis 2020-08-27 17:57:44 -04:00
Axel Kohlmeyer b1fae04751
use consistent style when referencing packages 2020-08-27 17:44:49 -04:00
Axel Kohlmeyer 7b4891a9a3
document the behavior of the gauss pair style to ignore special bond factors 2020-08-27 17:41:43 -04:00
Steve Plimpton de4bf77757 two typos on pair peri doc page 2020-08-27 13:32:27 -06:00
Jacob Gissinger 32aede7769 minor doc clarification 2020-08-27 14:53:09 -04:00
Jacob Gissinger 583a09c808 Merge branch 'master' of https://github.com/lammps/lammps into lammps-master 2020-08-27 12:02:08 -04:00
Axel Kohlmeyer f314b7e54f
update format from enumerate to itemize and start next subsection 2020-08-26 23:05:59 -04:00
Axel Kohlmeyer 6a68743e54
transfer a chunk of text from Developer.tex to the manual. 2020-08-26 22:46:55 -04:00
Axel Kohlmeyer d00807ee9a
Merge pull request #2311 from stanmoore1/kk_update_3.2 
Update Kokkos library in LAMMPS to v3.2
 2020-08-26 15:35:25 -04:00
Axel Kohlmeyer 94db627ba5
fix formatting issue 2020-08-26 12:09:43 -04:00
Axel Kohlmeyer b4403de026
add false positive 2020-08-26 12:09:35 -04:00
Axel Kohlmeyer 8137ada848
Merge branch 'collected-small-changes' into doxygen-integration 2020-08-26 11:51:45 -04:00
Axel Kohlmeyer bdc952ac88
Merge branch 'master' into collected-small-changes 2020-08-26 11:51:05 -04:00
Axel Kohlmeyer c8af729701
Merge branch 'master' into collected-small-changes 2020-08-26 11:49:29 -04:00
Axel Kohlmeyer 4ad68c98a0
Merge pull request #2196 from jibril-b-coulibaly/mindlin_rescale 
Implement force history in Mindlin granular pair styles
 2020-08-26 11:42:06 -04:00
Axel Kohlmeyer e2fd95d8ed
Merge pull request #2240 from jrgissing/bond/react-reset_mol_ids 
support molecule ID resets in fix bond/react
 2020-08-26 10:56:21 -04:00
Axel Kohlmeyer 7ab6def2ca
update list of Kokkos GPU archs in manual as well 2020-08-26 03:49:59 -04:00
Axel Kohlmeyer aa6dec84ed
update list of Kokkos supported architectures 2020-08-26 03:42:42 -04:00
Richard Berger 1c10aa6a4d
GIFs are only supported in HTML 2020-08-25 17:15:34 -04:00
Richard Berger c256f2331f
JPG folder is no longer needed in HTML output 2020-08-25 16:59:39 -04:00
Richard Berger ae5c0bd8d1
Remove targets to JPG images 2020-08-25 16:44:50 -04:00
Axel Kohlmeyer 80e07c69f0
add part of developer guide as to showcase the integration of the programmer guide 2020-08-25 15:07:09 -04:00
Richard Berger df8fb26272
Refactor changes to documentation build 
- Added CMake variables for readability
- Moved Mathjax files to _static to avoid special copy logic
- Moved JPG/lammps-logo.png to _static to avoid special copy logic
- Removed dead CMake code
 2020-08-25 13:41:31 -04:00
Axel Kohlmeyer 3f685c346f
add doxygen integration with conventional and cmake doc build 2020-08-24 17:58:37 -04:00
Axel Kohlmeyer dc241abb85
Merge pull request #2305 from akohlmey/next_patch_version 
Update version strings for updated patch release
 2020-08-24 13:46:50 -04:00
Axel Kohlmeyer 93e4ed9770
Merge pull request #2304 from akohlmey/collected-small-changes 
Collected small changes for the next patch release
 2020-08-24 11:43:42 -04:00
tomswinburne 090ef2d1e8 merge error fix 2020-08-24 17:10:33 +02:00
tomswinburne 28d59ce594 final steps 2020-08-24 17:04:35 +02:00
tomswinburne 2ee6e9077a Merge remote-tracking branch 'upstream/master' into 2020 2020-08-24 17:02:53 +02:00
tomswinburne e8fb7c7ece big update 2020-08-24 16:54:16 +02:00
Axel Kohlmeyer 8f5e8300ea
fix typos in fix restrain docs 2020-08-23 15:29:49 -04:00
Axel Kohlmeyer 2907a10937
update version strings for new attempt for a patch release 2020-08-22 16:42:39 -04:00
Axel Kohlmeyer b776e1ee3c
convert remaining style doc sections to be a logical header 2020-08-21 23:33:41 -04:00
Richard Berger 66438539f2
Avoids HTML doc pages from becoming too large 2020-08-21 19:47:46 -04:00
Axel Kohlmeyer 7f87ccccc8
Merge branch 'collected-small-changes' into next_patch_version 2020-08-21 11:18:10 -04:00
Axel Kohlmeyer ee6ef98b9b
remove trailing whitespace 2020-08-21 00:43:40 -04:00
Axel Kohlmeyer e742ae7475
fix RST syntax and spelling issues in granular pair style docs 2020-08-21 00:31:55 -04:00
Axel Kohlmeyer 900830a4a1
Merge branch 'master' into mindlin_rescale 2020-08-21 00:24:07 -04:00
Axel Kohlmeyer c9773fc288
Merge branch 'master' into bond/react-reset_mol_ids 2020-08-21 00:19:52 -04:00
Axel Kohlmeyer 4c46119a48
Merge pull request #2280 from lammps/gridcomm-tiled 
Support for tiled decompositions in PPPM
 2020-08-21 00:16:20 -04:00
Axel Kohlmeyer 203ab71b62
Merge branch 'master' into gridcomm-tiled 2020-08-20 17:00:55 -04:00
Axel Kohlmeyer cd7ba1d007
Merge branch 'master' into more-fix-tests 2020-08-20 16:41:29 -04:00
Axel Kohlmeyer 92622d9079
add restart support to fix temp/rescale, fix spring/chunk, and fix spring/rg 2020-08-20 15:32:10 -04:00
Axel Kohlmeyer fc9f0dbcbc
correct fix npt/cauchy docs 2020-08-20 11:29:30 -04:00
Axel Kohlmeyer 6bda49e8d8
step version strings for next patch release 2020-08-20 07:46:01 -04:00
Axel Kohlmeyer 729b3d2717
major whitespace cleanup 2020-08-19 18:46:35 -04:00
Axel Kohlmeyer acd0a62de7
add new fix style momentum/chunk 2020-08-19 14:44:18 -04:00
Jacob Gissinger e4ab49c2e5 bond/react: bond-type-checking docs 2020-08-18 18:12:01 -04:00
Thomas Friedrich 23be41a1d3 fix typos and indentations 2020-08-16 04:43:07 +02:00
Axel Kohlmeyer 6d725c9b1c
Merge pull request #2287 from akohlmey/lattice-region-tester 
Add unittest tool for lattice and region (/w create_box/create_atoms)
 2020-08-13 11:47:08 -04:00
Axel Kohlmeyer 33118491a9
update custom lattice example for better syntax highlighting and remove unused lines 2020-08-12 22:16:50 -04:00
Axel Kohlmeyer adf8d638e8
add missing word 2020-08-11 21:23:47 -04:00
Axel Kohlmeyer 99604a6155
Merge branch 'collected-small-fixes' into fix-tester 2020-08-11 20:26:46 -04:00
Axel Kohlmeyer 51a7038dbf
Merge branch 'master' into fix-tester 2020-08-11 16:14:27 -04:00
Axel Kohlmeyer ac43f8f685
Merge pull request #1865 from danicholson/bond-style-special 
Add bond style special
 2020-08-11 16:06:26 -04:00
Axel Kohlmeyer 3cae295f5b
make test for unsupported pair styles more restrictive and improve docs about that 
EAM styles have a single function but are not compatible, so we test for
single_enable == 0 and manybody_flag != 0.
Improve explanation in the documentation about which pair styles are not supported.
 2020-08-11 15:04:14 -04:00
Axel Kohlmeyer 265b7cf11c
use new dependency resolver in pip for the documentation build virtual environment 2020-08-11 14:11:44 -04:00
Axel Kohlmeyer 03ca86ee84
Merge branch 'master' into bond-style-special 2020-08-11 13:55:24 -04:00
David Nicholson 46021a57a6 addressed incompatibility with long range coulombics 2020-08-11 12:22:07 -04:00
abhishandy 5ee4346700 fixed test for tip4p_long_soft, and mentioned the required coefficients for coul/*/soft sub-styles 2020-08-10 17:16:07 -04:00
Jibril B. Coulibaly 2de98999c1 bug fix formula for frame of reference rotation for granular tangential history 2020-08-10 14:51:00 -05:00
Jibril B. Coulibaly bf724332d4 implement tangential force history in mindlin/force and mindlin_rescale/force 2020-08-10 10:53:30 -05:00
Axel Kohlmeyer 869b09a78f
fix typo 2020-08-10 11:08:30 -04:00
Axel Kohlmeyer 4b7356f5af
add support for testing virial contributions from fixes (as an option) 2020-08-09 16:39:31 -04:00
Axel Kohlmeyer f1da1ed180
document restart capability of fix temp/csld and fix temp/csvr 2020-08-09 15:29:12 -04:00
Axel Kohlmeyer 3ebd194090
update documentation for unit testing to include timestepping fix tests 2020-08-09 08:18:35 -04:00
Axel Kohlmeyer 62a501ebda
store cumulative energy change in restart file 2020-08-09 01:27:14 -04:00
Axel Kohlmeyer 15db052c80
Merge branch 'master' into collected-small-changes 2020-08-05 22:10:10 -04:00
Axel Kohlmeyer c3075250ee
Merge pull request #2273 from abhiShandy/pair-tests-aug4 
Bunch of units tests for pair-style, angle-style, bond-style
 2020-08-05 22:09:28 -04:00
Pierre de Buyl 1a642d36ae fix typo in the math of pair style dpd doc 
- missing closing backticks for math
- V fixed to v for relative velocity
 2020-08-04 22:50:26 +02:00
Axel Kohlmeyer f4aede49dc
Merge branch 'master' into multi-comm-tiled 2020-08-03 22:37:23 -04:00
abhishandy 6bc65dc14c reference typos in doc 2020-08-03 20:49:02 -04:00
abhishandy 33aa96b1bf test for buck/mdf, fixed bug in broadcasting inner cutoff, typos in doc 2020-08-03 20:07:24 -04:00
Axel Kohlmeyer 6576c4cbf3
Merge pull request #2260 from akohlmey/collected-small-changes 
Collected small changes
 2020-08-03 18:02:17 -04:00
Axel Kohlmeyer ca7039aa96
Merge pull request #2271 from abhiShandy/pair-tests-Aug3 
Unit tests for born/coul, ufm, yukawa, soft
 2020-08-03 17:23:22 -04:00
Axel Kohlmeyer 8d406403bb
fix typo in manual 2020-08-03 16:07:06 -04:00
Richard Berger d0be219419
Refactor check-styles.py 2020-08-03 14:26:55 -04:00
Richard Berger f9d1a914fb
Update check-packages.py 2020-08-03 13:49:37 -04:00
Richard Berger 4549493145
Refactor check-packages.py 2020-08-03 13:47:40 -04:00
abhishandy 80ceff55d5 failing test for UFM, with cosmetic change in its CPP, and doc correction 2020-08-03 06:01:59 -04:00
Axel Kohlmeyer 74f50ed1bd
Merge branch 'master' into collected-small-changes 2020-07-31 21:51:10 -04:00
Axel Kohlmeyer 1f1263645e
Document warning about short communication cutoff vs. bond length based estimate 2020-07-31 11:03:26 -04:00
Axel Kohlmeyer 7d46aa6185
Merge pull request #2256 from akohlmey/cmake-use-alternate-linker 
Use alternate/faster linker if available
 2020-07-29 21:40:17 -04:00
Axel Kohlmeyer 2fa642d95e
document custom linker choice 2020-07-29 18:01:17 -04:00
Steve Plimpton cb98fa00da enable CommStyle tiled and load-balancing to work for triclinic 2020-07-29 14:30:49 -06:00
Jacob Gissinger cf83ce6745 reset_mol_ids->reset() version 2020-07-25 00:52:39 -06:00
Axel Kohlmeyer 5528d4d18c
trim excessive white from images 2020-07-23 00:36:15 -04:00
Axel Kohlmeyer f60c13c845
fix incorrect link 2020-07-23 00:36:02 -04:00
Axel Kohlmeyer c21ce0b289
make horizontally aligned image formatting consistent and display "click on" message only with html output 2020-07-23 00:35:49 -04:00
Richard Berger b97f2e5b6b
Update compute_saed.rst 2020-07-22 16:48:21 -04:00
Richard Berger bf848c0515
Update compute_xrd.rst 2020-07-22 16:45:56 -04:00
Richard Berger 1123add481
Update create_atoms.rst 2020-07-22 16:44:04 -04:00