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9504 Commits

Author SHA1 Message Date
Axel Kohlmeyer 34a5093229
refactor handling of the python source command. document it and more limits. 2022-11-10 16:03:06 -05:00
Axel Kohlmeyer aa46f5560a
add .. versiondded:: tag to BPM package commands and restrictions text consistent 2022-11-07 22:57:32 -05:00
rohskopf da929b4f7f Fix merge conflicts 2022-11-07 17:37:50 -07:00
rohskopf 1fbd45a05d Format docs 2022-11-07 17:33:00 -07:00
Jacob Gissinger 3b47afa69f Update fix_bond_react.rst 2022-11-05 02:03:02 -04:00
Jacob Gissinger d5929a5cf8 reflect rate_limit restart support in docs 2022-11-04 23:52:13 -04:00
Axel Kohlmeyer 9cbc77f41c
Merge pull request #3511 from akohlmey/next_patch_release 
Step version strings for the next patch release
 2022-11-03 11:53:08 -04:00
Jacob Gissinger 1a271b4870 add mention of Nlimit variable support 2022-11-03 11:21:16 -04:00
Jacob Gissinger eb01f816ec rate_limit docs 2022-11-03 11:09:44 -04:00
Axel Kohlmeyer 292cf5ff09
Merge pull request #3487 from bathmatt/kokkos-mliap-so3 
Created a Kokkos version of the ML-IAP routines.  Completed one model…
 2022-11-02 17:13:16 -04:00
Jacob Gissinger 189f803ef6 correct, simplify rxnbond example 2022-11-01 15:51:37 -04:00
Jacob Gissinger ed6fe96909 simplify, formatting 2022-11-01 15:51:37 -04:00
Jacob Gissinger f0a421eb25 bond:react per-bond custom constraint docs 2022-11-01 15:51:36 -04:00
Stan Moore c6157b51ef Update docs 2022-11-01 07:26:18 -07:00
Axel Kohlmeyer 2d3e5e9930
set pending version info in docs to 3Nov2022 2022-11-01 06:00:05 -04:00
Axel Kohlmeyer 6d7a1e0635
step version strings for the next patch release 2022-11-01 05:59:32 -04:00
Axel Kohlmeyer 05aca2bced
Merge pull request #3507 from hammondkd/thermo_mod_range 
Support thermo_modify format column index ranges
 2022-11-01 05:46:04 -04:00
Axel Kohlmeyer 135c6f24ad
Merge branch 'develop' into fortran-expansion 2022-10-31 17:57:33 -04:00
Axel Kohlmeyer 58c2f25b45
Merge pull request #3504 from akohlmey/library-plugin-update 
Update example for coupling LAMMPS as a dynamically loaded library
 2022-10-31 17:52:34 -04:00
Axel Kohlmeyer 8e6c7fa416
add note about the plugin version of the C library interface 2022-10-31 14:42:12 -04:00
Axel Kohlmeyer 5195a7385c
Merge pull request #3501 from yury-lysogorskiy/bugfix/empty-spatial-domain 
BUGFIX:  fix pair  and empty spatial domains
 2022-10-31 12:23:35 -04:00
Axel Kohlmeyer 7a171ded10
document preference to not use "alternative tokens" 2022-10-30 22:07:43 -04:00
Karl Hammond 00ec3575c4
Fixed typos 2022-10-30 17:04:06 -05:00
Karl Hammond f088fcd949
whitespace 2022-10-30 17:00:16 -05:00
hammondkd 87590ad339
Merge branch 'lammps:develop' into fortran-expansion 2022-10-30 15:30:59 -05:00
Karl Hammond 745f90cb71
merged conflicts in thermo.cpp 2022-10-30 14:34:43 -05:00
Karl Hammond d3ed99c7f8
Optional arguments for find_*_neighlist 2022-10-28 21:01:12 -05:00
Karl Hammond 73bf0334e4
Fixed optional parameters in find_pair_neighlist 2022-10-28 20:53:46 -05:00
Karl Hammond 7a10cf2b53
Missing colon in gather_atoms_subset doc 2022-10-28 07:57:33 -05:00
Karl Hammond dfef232ccb
Fixed omission in gather_bonds example (docs) 2022-10-27 19:09:53 -05:00
Karl Hammond 0b83b8c533
Changed case of intrinsics to match style elsewhere 2022-10-27 18:26:22 -05:00
Karl Hammond 67c165afb2
Fixed typo in gather_bonds example 2022-10-27 18:23:20 -05:00
Axel Kohlmeyer ca091b2e75
update ELECTRODE package instructions for traditional make. fix plural/singular. 2022-10-27 16:23:55 -04:00
hammondkd 3545b491ee
Merge branch 'lammps:develop' into fortran-expansion 2022-10-27 14:15:47 -05:00
Axel Kohlmeyer e6b67683aa
update TIP4P howto 2022-10-27 07:02:16 -04:00
Yury Lysogorskiy 8bb5042a57 small upd to pair/extrapolation docs example 2022-10-27 11:56:12 +02:00
Axel Kohlmeyer 71c8806764
reformat, spelling, whitespace fixes. address minor grammar and content issues 2022-10-26 05:18:06 -04:00
Mehdi Baghaee 371c2d7cbb
Pair ylz docs enhancements 2022-10-26 05:00:25 -04:00
Karl Hammond b8781aca15
Implemented plugin_name and plugin_count and their docs 2022-10-26 00:02:54 -05:00
Karl Hammond 19f93009c1
Implemented and documented has_id, id_count, and id_name 2022-10-25 19:51:08 -05:00
Karl Hammond e68efc039f
Resolved merging conflicts in three files 2022-10-25 14:37:33 -05:00
Karl Hammond dfaff2dc9a
Pre-emptive edits to ease auto-merging 2022-10-25 08:30:21 -05:00
Axel Kohlmeyer 4c176e5afc
whitespace 2022-10-24 19:54:43 -04:00
Axel Kohlmeyer 34d70dd753
Merge branch 'develop' into new-pair_style-ylz 2022-10-24 18:27:24 -04:00
Axel Kohlmeyer 248b7383c7
Merge remote-tracking branch 'github/develop' into collected-small-changes 
# Conflicts:
#	src/DIPOLE/pair_lj_cut_dipole_long.h
#	src/OPENMP/fix_nvt_sllod_omp.h
#	src/PHONON/fix_phonon.h
#	src/SPIN/pair_spin_dipole_cut.h
#	src/SPIN/pair_spin_dipole_long.h
#	src/STUBS/mpi.h
#	src/UEF/fix_nh_uef.h
#	src/fix_nvt_sllod.h
#	tools/coding_standard/homepage.py
 2022-10-24 15:50:50 -04:00
Axel Kohlmeyer 27b37ebad0
Merge pull request #3495 from akohlmey/update-email 
Update contact email address in LAMMPS sources
 2022-10-24 13:49:31 -04:00
Axel Kohlmeyer 3c4b0a0c04
expand homepage checker tool to check a few more folders and apply updates 2022-10-24 10:58:39 -04:00
Karl Hammond 785b46e57b
Implemented lmp_gather_bonds, lmp_find_*_neighlist, lmp_neighlist_num_elements, and their unit tests and documentation 2022-10-24 01:00:48 -05:00
Jacob Gissinger 4f507b36da Update fix_bond_react.rst 2022-10-22 00:25:00 -04:00
Axel Kohlmeyer 165b6b4ba3
add workaround for missing links to fortran functions in sphinx output 2022-10-21 18:55:16 -04:00
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