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9504 Commits

Author SHA1 Message Date
Axel Kohlmeyer b5cd834c8f
small sphinx tweaks. require sphinx 5.2 or later. 2022-10-21 18:37:16 -04:00
Karl Hammond 2275281c2e
Fixed double-colon "feature" in sphinx documetnation (theme.css) 2022-10-21 15:52:39 -05:00
Karl Hammond a8670f1ce9
Fixed potential inconsistency in lmp_error 2022-10-21 13:44:39 -05:00
Karl Hammond fe09f1209e
Fixed spacing 2022-10-21 12:41:07 -05:00
Karl Hammond 3c936d5a2b
Fixed extract_atom doc 2022-10-21 12:16:57 -05:00
Karl Hammond 3cef658789
Added ":to:" fields to Fortran.rst; edits to :r's for consistency 2022-10-21 12:10:00 -05:00
Karl Hammond 6bb3ae83fd
Fixed typo in Manual.rst 2022-10-21 10:59:48 -05:00
Karl Hammond 337d3f0760
Made module references more uniform 2022-10-21 10:58:05 -05:00
Karl Hammond ed7d608919
Fixed hyperlinks to LIBLAMMPS in Fortran.rst 2022-10-21 09:53:07 -05:00
Axel Kohlmeyer 12baf65d7a
correct implementation of quartic potential in pair style list 2022-10-21 02:25:40 -04:00
Karl Hammond b6287a0fe6
Tweaks to Fortran docs 2022-10-21 00:34:24 -05:00
Karl Hammond 7ce04c8fe1
Fixed spacing on type lammps fields 2022-10-21 00:09:17 -05:00
Karl Hammond 112d616e57
unit tests for has_style, style_count, and style_name; added them to docs 2022-10-20 23:22:43 -05:00
Axel Kohlmeyer b26716c44c
a few more updates 2022-10-20 23:11:45 -04:00
Karl Hammond 60318a5a26
Refactor Fortran properties test into configuration; implemented several configuration functions and wrote unit tests for them; implemented missing unit tests 2022-10-20 20:24:59 -05:00
Karl Hammond 34121e5545
Implemented decode_image_flags and its unit test; updated documentation 2022-10-20 00:27:57 -05:00
Karl Hammond b51c50294e
implemented create_atoms and encode_image_flags and unit tests for them; added IMGMASK and friends to extract_setting and unit tests for them; wrote documentation for them 2022-10-19 18:40:12 -05:00
Mehdi Baghaee 2590f9eea4
Update pair_ylz.rst 
Corrected some typo in formulations
 2022-10-19 18:52:31 +08:00
Axel Kohlmeyer fc5379206f
add versionadded tag 2022-10-19 06:37:45 -04:00
Axel Kohlmeyer d50bb3bffb
minor tweak 2022-10-18 15:45:56 -04:00
Axel Kohlmeyer d3dd394cc5
Merge branch 'develop' into new-pair_style-ylz 2022-10-18 15:43:47 -04:00
Axel Kohlmeyer 450841ca5a
spelling and more whitespace 2022-10-18 15:06:53 -04:00
Axel Kohlmeyer 53c56fdc82
integrate into manual and source distribution 2022-10-18 14:41:46 -04:00
Axel Kohlmeyer 87f316ee72
reformat, remove accelerator info, correct restrictions 2022-10-18 14:35:22 -04:00
Axel Kohlmeyer 39020379da
fix permissions, error docs, URLs, whitespace 2022-10-18 11:53:38 -04:00
Axel Kohlmeyer 78305edf71
delete atomfile style variables with `clear` command 2022-10-18 07:34:06 -04:00
hammondkd 643865221c
Merge branch 'lammps:develop' into thermo_mod_range 2022-10-17 23:05:28 -05:00
Axel Kohlmeyer c10b5b02c0
Merge branch 'develop' into collected-small-changes 2022-10-17 22:40:01 -04:00
Axel Kohlmeyer a746e4f2c0
update dipole pair style examples and docs 2022-10-17 19:05:17 -04:00
Axel Kohlmeyer 74d19b2b6c
update/clarify and make more consistent 2022-10-17 18:45:19 -04:00
Axel Kohlmeyer d8ab00ea78
add CMake check that will refuse compilation of unit tests or skip tests 
This is mainly because the default compilers on RHEL/CentOS 7.x are
not sufficient to compile googletest. Also some Fortran module test
requires a working F90 module and others are more recent Fortran compiler.
 2022-10-17 18:11:30 -04:00
Karl Hammond 637810515a make compute rigid/local consistent with other "possible attributes" docs 2022-10-17 14:51:10 -05:00
Axel Kohlmeyer 677997699d
more consistency 2022-10-15 15:35:29 -04:00
Karl Hammond 9e43e9792c Fixed a couple more mathbf->boldsymbol errors in fix brownian doc 2022-10-15 10:47:33 -05:00
Axel Kohlmeyer 09a14d558d
explicitly select Times New Roman for \textrm, Helvetica for \textsf and Times New Roman for math as well 2022-10-14 21:27:55 -04:00
Axel Kohlmeyer 2b18f6a3d3
replace tab 2022-10-14 21:27:00 -04:00
Karl Hammond b586b72ddd removed an extra space 2022-10-14 18:27:21 -05:00
Karl Hammond 77958b5ef1 Missed one I->i edit 2022-10-14 18:04:49 -05:00
Karl Hammond e346151271 Updated docs for fixes bond/break, bond/create, and bond/react for math/etc. 2022-10-14 17:40:22 -05:00
Karl Hammond 3d0a7d774a Updated docs for fix bocs to match source code and include math 2022-10-14 16:04:07 -05:00
Karl Hammond 7550fdc862 Sphinx conf edit so PDF ToC entries w/ subsections >= 100 work 2022-10-14 15:28:55 -05:00
Axel Kohlmeyer 6087217bd9
update wording and fix typo 2022-10-14 10:21:48 -04:00
Axel Kohlmeyer 9a52019b69
update remarks on neighbor list settings 2022-10-14 09:08:16 -04:00
Axel Kohlmeyer fbc0e02cb2
cosmetic 2022-10-14 04:48:54 -04:00
Axel Kohlmeyer 24379d009c
flag lammps.has_package() python method as new 2022-10-14 04:48:08 -04:00
Axel Kohlmeyer c2e47378b5
fix typo 2022-10-14 04:44:49 -04:00
Axel Kohlmeyer 082defa862
change neighbor list defaults to delay=0, every=1, check=yes 2022-10-14 04:38:30 -04:00
Karl Hammond e3c78b70ed Fixed remaining discrepancies between lists of keywords and doc of them 2022-10-13 23:00:13 -05:00
Karl Hammond edcdedc574 made keyword lists and descriptions consistent for all fix styles 2022-10-13 19:20:08 -05:00
Axel Kohlmeyer 3f215087d2
also print atom-step/s performance metric 2022-10-13 16:32:41 -04:00
Karl Hammond 70fd789b4c missing format keyword in fix ave/time doc 2022-10-13 14:51:30 -05:00
Karl Hammond 3703af9887 Missing keyword in fix_ave_histo doc 2022-10-13 14:48:26 -05:00
Karl Hammond 3607fd766b Missing key word in fix/ave/chunk docs, edits to bond_coeff docs 2022-10-13 14:42:10 -05:00
Axel Kohlmeyer 40d409a8d4
put a few more details on restrictions when parsing types early on. 2022-10-13 15:15:37 -04:00
hammondkd 41c0b39365
Merge branch 'lammps:develop' into thermo_mod_range 2022-10-13 09:01:06 -05:00
hammondkd 8027e02cbb
Merge branch 'lammps:develop' into doc-fixes 2022-10-13 09:00:07 -05:00
Axel Kohlmeyer 6b35251ca2
fix typo and remove correspondign false positive 2022-10-13 05:47:08 -04:00
mehdibghk 0b17654bee New pair-style ylz added to ASPHERE package 2022-10-13 13:45:09 +08:00
Axel Kohlmeyer 7115b890b8
more false positives 2022-10-12 10:27:23 -04:00
Axel Kohlmeyer d499c2f61b
Merge pull request #3474 from stanmoore1/kk_update_3.7 
Update Kokkos library in LAMMPS to v3.7.0
 2022-10-11 16:30:19 -04:00
Stan Gerald Moore 3e1acfc500 Update Kokkos Arch in docs 2022-10-10 16:29:55 -06:00
Axel Kohlmeyer 1bc16d8a78
fix spelling and table format issues. re-wrap paragraphs in doc sources. 2022-10-10 17:26:13 -04:00
ali a38054cf32 change area_per_patch to area/patch 2022-10-10 16:03:09 -05:00
Axel Kohlmeyer aea3421311
whitespace fixes 2022-10-10 15:26:40 -04:00
ali ba45678528 DIELECTRIC package doc and example updates 2022-10-10 11:04:04 -05:00
ali be208f037d quick doc updates 2022-10-10 11:04:04 -05:00
ali b3fa2b7c4f update of DIELECTRIC package documentation and examples 2022-10-10 11:03:52 -05:00
Karl Hammond 2fed3fa003 Minor documentation edits 2022-10-06 22:12:33 -05:00
Karl Hammond 3b292cd50a Fixed bug in thermo_modify and made 2*4 and such work for format fields 2022-10-06 18:08:06 -05:00
hammondkd eca8b77c84
Merge branch 'lammps:develop' into doc-fixes 2022-10-05 22:47:48 -05:00
Axel Kohlmeyer 967c84cb69
Merge pull request #3470 from hammondkd/fortran-further-tinkering 
Further extending the Fortran interface
 2022-10-05 21:20:06 -04:00
Axel Kohlmeyer 7157643fdd
Merge pull request #3315 from yury-lysogorskiy/feature/pace-al 
ML_PACE with extrapolation grade / active learning
 2022-10-05 20:16:13 -04:00
hammondkd 9abc0b6c11
Merge branch 'lammps:develop' into doc-fixes 2022-10-05 14:13:08 -05:00
Axel Kohlmeyer 723255bf7e
Merge remote-tracking branch 'github/develop' into fortran-further-tinkering 2022-10-05 10:52:36 -04:00
Karl Hammond f279b5d042 Math fixes and other edits for fix_brownian.rst 2022-10-04 22:36:30 -05:00
Karl Hammond 3c11fa39b6 Doc edits for mdi.rst 2022-10-04 18:49:35 -05:00
Axel Kohlmeyer 8be7634b5f
Merge branch 'collected-small-changes' into pair-zero-full 2022-10-04 14:36:02 -04:00
Axel Kohlmeyer 90e820e8ec
format mpirun/mpiexec consistently 2022-10-04 08:55:53 -04:00
Axel Kohlmeyer f2b3d8e8c3
use morse interaction energy from bond style morse not pair style morse 2022-10-04 07:02:44 -04:00
Axel Kohlmeyer 4a06559da5
update docs 2022-10-04 05:18:42 -04:00
Terry Suun 5508c7f25e Bug fix for pair_style list quartic. 2022-10-04 13:27:32 +08:00
Terry Suun ed8e317ef6 Added quartic function for explicit pair interaction in pair_style list. 2022-10-04 10:40:32 +08:00
rohskopf 82bf23401f Fix whitespace 2022-10-03 12:45:18 -06:00
rohskopf 981f75d92f Example in docs 2022-10-03 12:40:05 -06:00
rohskopf c82fdd4898 Add docs 2022-10-03 11:57:47 -06:00
Yury Lysogorskiy 94ff9cea4c Revert "update documentation: explain fix_modify pair every N" 
This reverts commit 2f231bcd50.
 2022-10-03 19:43:37 +02:00
Axel Kohlmeyer 6a2023e7df
spelling 2022-10-03 09:55:20 -04:00
Axel Kohlmeyer d711a51657
Merge remote-tracking branch 'github/develop' into fortran-further-tinkering 2022-10-03 09:37:52 -04:00
Karl Hammond dc5324c1db Updated unit tests to use keepstuff; whitespace fixes 2022-10-02 21:26:42 -05:00
Karl Hammond db9b59c269 Implemented scatter_atoms and scatter_atoms_subset + unit tests + documentation + typos/edits 2022-10-02 20:32:42 -05:00
Karl Hammond c5c21bb36c Implemented, tested, and documented gather_atoms and variants; added RST docs for lammps_scatter_atoms and lammps_gather_atoms and variants (library.cpp); checked for missing atom map in lammps_gather_atoms_subset; fixed bug in keepstuff.f90; fixed docs for extract_variable 2022-10-02 15:28:10 -05:00
Axel Kohlmeyer c777434b72
use kcal consistently 2022-10-01 21:05:16 -04:00
Axel Kohlmeyer 39ea6ef30e
make \AA macro available in :math: for HTML and PDF 
use the (newly redefined) \AA macro for Angstrom symbol throughout
instead of either \mathring{A} or AA
 2022-10-01 20:58:48 -04:00
Axel Kohlmeyer 69ca7105ef
provide some more details about typesetting special characters and math 2022-10-01 20:41:48 -04:00
Karl Hammond 9c314966ae More spacing 2022-09-30 19:58:56 -05:00
Karl Hammond eac855343f Spacing 2022-09-30 19:54:58 -05:00
Karl Hammond 6dea4d50d6 Fixed oversight in edits to example in Fortran doc page 2022-09-30 19:51:56 -05:00
hammondkd a323e09822
Merge branch 'lammps:develop' into fortran-further-tinkering 2022-09-30 19:40:32 -05:00
Axel Kohlmeyer bbc08bbf1f
make capitalization consistent 2022-09-30 19:53:11 -04:00
Karl Hammond 953c3d0cad spell check; updated false positives; whitespace 2022-09-30 18:50:16 -05:00
Axel Kohlmeyer c61b356a71
clarify LJ energy function component of the quartic bond style 2022-09-30 19:48:56 -04:00
Axel Kohlmeyer b48868d70b
better document format style variable behavior 2022-09-30 15:05:56 -04:00
Axel Kohlmeyer fce0877cac
update and remove obsolete parts 2022-09-30 09:49:57 -04:00
Karl Hammond a7071fea78 Wrote docs for extract_fix,extract_variable; fixed python so it knows about string variables; doc typo fixes; part of extract_variable unit test 2022-09-29 19:28:15 -05:00
Axel Kohlmeyer 09948f11be
make equation references explicit since .. math:: + 🏷️ does not work with latex 2022-09-29 13:54:09 -04:00
Axel Kohlmeyer c6eb6d858b
implement numbered equations and equation references 2022-09-29 12:04:43 -04:00
Axel Kohlmeyer 96c0d39be2
Merge branch 'develop' into pdlammps-howto 2022-09-29 10:42:34 -04:00
Karl Hammond 3ab8f6ea16 Finished docs for everything currently implemented 2022-09-29 09:14:49 -05:00
Axel Kohlmeyer 8e073c3335
reference the Howto from the rest of the manual. Spelling fixes. 2022-09-29 07:43:01 -04:00
Axel Kohlmeyer 777a074744
Convert PDLAMMPS user doc from latex to sphinx 2022-09-29 06:57:52 -04:00
Karl Hammond 6c0da8cbaf Wrote documentation for extract_fix, extract_variable 2022-09-29 01:07:46 -05:00
hammondkd 6109090d40
Merge branch 'lammps:develop' into fortran-further-tinkering 2022-09-27 20:02:06 -05:00
Axel Kohlmeyer 5da63b1e1d
Merge branch 'develop' into feature/pace-al 2022-09-27 14:01:58 -04:00
Yury Lysogorskiy 2f231bcd50 update documentation: explain fix_modify pair every N 2022-09-27 17:15:20 +02:00
Axel Kohlmeyer 0fe739eb35
Merge branch 'develop' into collected-small-changes 
# Conflicts:
#	doc/utils/sphinx-config/false_positives.txt
 2022-09-26 20:34:37 -04:00
Axel Kohlmeyer be98b5a168
Merge pull request #3458 from Boogie3D/mliappy_unified 
MLIAP Unified Interface
 2022-09-26 20:33:17 -04:00
Axel Kohlmeyer 10068a0fde
Merge pull request #3461 from julient31/llg-correction 
Correction of some LL features in the SPIN package
 2022-09-26 14:56:36 -04:00
Axel Kohlmeyer 5ea37448b6
whitespace 2022-09-26 13:12:04 -04:00
Axel Kohlmeyer a4e92ed4a9
update broken URLs 2022-09-26 12:09:45 -04:00
Axel Kohlmeyer 543e7b8b56
format DOI tags consistently 2022-09-26 11:41:22 -04:00
exapde ee611d8cf7 update pod documentation 2022-09-26 09:55:12 -04:00
Julien Tranchida 30ddb2d4b4 Merge branch 'clean-master2' of github.com:julient31/lammps into llg-correction 2022-09-26 07:53:09 +02:00
Julien Tranchida 90f26f05fc Correcting some aspects of the SPIN package documentation. 2022-09-26 07:43:19 +02:00
Karl Hammond bada1fb348 Finished extract_compute and its unit tests and documentation 2022-09-25 23:54:18 -05:00
Axel Kohlmeyer a6f8ea32a7
reformat docs and fix spelling issues 2022-09-25 17:10:50 -04:00
Yury Lysogorskiy d205d4a6df
remove docs for unexisting command `compute pace/extrapolation` 2022-09-25 17:10:49 -04:00
Axel Kohlmeyer 2e3fc4c054
Merge branch 'develop' into feature/pace-al 2022-09-25 16:01:48 -04:00
Axel Kohlmeyer af3da50bda
add some more versionadded tags, now mostly complete for 2022 2022-09-25 09:41:55 -04:00
Axel Kohlmeyer 3a95a7b973
add utility to detect pending version tags in .. versionadded/changed:: 2022-09-25 03:51:54 -04:00
Axel Kohlmeyer 64b88f2e13
add versionadded/versionchanged markers for features from 15Sep2022 and 3Aug2022 2022-09-25 03:20:29 -04:00
Axel Kohlmeyer ef8090fdd1
flag *unified* keyword as newly added in the next patch release 2022-09-24 15:31:47 -04:00
Karl Hammond 058e49696a Added "New in version TBD" to new functions 2022-09-24 12:12:24 -05:00
Karl Hammond 26e269aacd continued ork on extract_compute unit tests 2022-09-24 12:04:27 -05:00
Axel Kohlmeyer b37c145352
convert URLs to https where possible, check URLs for bit rot and update or remove 2022-09-24 08:02:18 -04:00
Axel Kohlmeyer a0caf34d71
update sjplimp's email and homepage 2022-09-24 05:02:53 -04:00
Axel Kohlmeyer caa80ef344
use upper case LAMMPS as the name of the package consistently 2022-09-24 03:45:23 -04:00
Axel Kohlmeyer 5ddb0aeb16
cosmetic changes 2022-09-24 03:44:19 -04:00
Axel Kohlmeyer c581fca39a
Merge branch 'develop' into mliappy_unified 2022-09-24 03:07:31 -04:00
Axel Kohlmeyer 49a3be17cb
c-library functions should be always present, documented, and lowercase 2022-09-24 03:07:24 -04:00
Karl Hammond 69627eee8d Merged with fortran-tinkering 2022-09-23 22:11:24 -05:00
Steven Ray Anaya 8ad478697e Remove trailing whitespace 2022-09-23 17:20:27 -06:00
Axel Kohlmeyer 86d1aacf7e
add function to dispatch LAMMPS errors to library interfaces 2022-09-23 16:28:15 -04:00
Axel Kohlmeyer 0f2a7d3f33
Merge branch 'develop' into fortran-tinkering 2022-09-23 12:41:39 -04:00
Axel Kohlmeyer d9e2be4b75
updates to the fortran module docs to make it more consistent, fix links, add example similar to C library docs 2022-09-23 12:41:31 -04:00
Axel Kohlmeyer 2a14397318
fix broken link 2022-09-23 11:10:06 -04:00
Axel Kohlmeyer 71c48762fb
correct inconsistent spelling of name 2022-09-23 10:33:44 -04:00
Axel Kohlmeyer 6532640362
spelling 2022-09-23 10:23:32 -04:00
Karl Hammond ac0080f2df Reintroduced some stashed doc edits 2022-09-23 07:20:49 -05:00
Steven Ray Anaya 43aabc7985 Update comments and documentation 2022-09-22 18:29:45 -06:00
Karl Hammond aff5200ded Implemented extract_atom, updated docs, added some unit tests 2022-09-22 19:16:15 -05:00