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19805 Commits

Author SHA1 Message Date
Vsevak 43a9936241 Fix tagint usage 2020-01-20 03:38:58 +03:00
Vsevak d1f3f659ac Fix GPU package install script to resolve file dependency 
'pair_lj_cut_tip4p_long_gpu' depends on 'pair_lj_cut_tip4p_long' from KSPACE package
 2020-01-20 00:03:04 +03:00
Axel Kohlmeyer 074e18d9cb
fix one more whitespace issue 2020-01-19 13:34:21 -05:00
Axel Kohlmeyer 0471d211a2
remove dead code and silence compiler warnings 2020-01-19 13:33:16 -05:00
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
Axel Kohlmeyer f4d9715cc7
make code follow LAMMPS conventions more closely and do some cleanups 
- remove tabs and trailing whitespace
- remove references to atom style body, since code only works with ellipsoid
- adjust function names and tests for requirements to be more obvious and work correctly in parallel
- remove rather specific debug code
- remove non-essential c++11 features
- refactor, correct, and simplify parsing of types keyword arguments
 2020-01-19 13:07:54 -05:00
Axel Kohlmeyer d739e017ad
tweak examples to be shorter/faster 2020-01-19 12:22:22 -05:00
Vsevak f69a17dd3a Reduce unnecessary data exchanges 2020-01-19 02:05:16 +03:00
Pierre de Buyl 4c8a857960 Merge branch 'master' into fix-active-rebase-5 2020-01-17 22:11:55 +01:00
Axel Kohlmeyer 998b60eabc
restore accidentally renamed keyword 2020-01-17 12:17:47 -05:00
Axel Kohlmeyer 33c846cd5e
guard converting thermo output from other output to the screen and do not crash 
fixes #1844
 2020-01-17 09:48:07 -05:00
Axel Kohlmeyer a53202bad2
removing the time estimate code for create_atoms completely, as we'll have linear scaling soon. 2020-01-16 17:23:57 -05:00
Axel Kohlmeyer dd60bddc33
reset embedding step counter when init_style() is called 2020-01-16 17:14:23 -05:00
Axel Kohlmeyer 868df1f640
Merge pull request #1843 from oywg11/new-ILP-parameters 
New ILP paramters  and pair style improvements
 2020-01-16 16:53:59 -05:00
Axel Kohlmeyer 79f9ede38a
print warning when using pair_write on EAM pair style 2020-01-16 16:51:32 -05:00
Axel Kohlmeyer 070bb8c5cd
change estimate for creating atoms after benchmarking a 440M atom system 2020-01-16 16:46:37 -05:00
Axel Kohlmeyer 93a6d3a1fc
print warning (once) if EAM embedding data is out of sync, error out, if embedding term is not available at all. 2020-01-16 16:35:05 -05:00
Axel Kohlmeyer 96cc098dc1
Merge branch 'new-ILP-parameters' of github.com:oywg11/lammps into new-ILP-parameters 
# Conflicts:
#	doc/txt/pair_ilp_graphene_hbn.txt
#	doc/txt/pair_kolmogorov_crespi_full.txt
 2020-01-16 14:18:42 -05:00
oywg11 8ffe15871a Refine the doc files 2020-01-16 21:12:02 +02:00
Axel Kohlmeyer 4dc37bf56e
replace tabs and remove trailing whitespace 2020-01-16 14:06:15 -05:00
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
Axel Kohlmeyer cf80495a3d
change estimate for time to create an atom from 25ns to 1us 2020-01-16 12:15:42 -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 77a28c404a
Merge pull request #1831 from akohlmey/pair-bop-updates 
Correct some issues with pair style bop and its potential files
 2020-01-15 17:30:07 -05:00
Axel Kohlmeyer 4e32af5d49
Merge branch 'master' into pair-bop-updates 2020-01-15 17:13:22 -05:00
Axel Kohlmeyer 62f0d87e59
update .gitignore for recently added styles 2020-01-15 17:13:14 -05:00
Axel Kohlmeyer df24475ea1
update bop potential files to the latest versions 2020-01-15 16:50:10 -05:00
Axel Kohlmeyer 4801f013a5
correct logic error in reading of bop potential files 2020-01-15 16:49:23 -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
Philipp Kloza cb20d73a82 consistent name for pot file, symbolic link in examples 2020-01-15 20:45:13 +00:00
Axel Kohlmeyer 1ed50bcdde
Merge pull request #1837 from akohlmey/collected-small-changes 
Collected small changes for the next patch release
 2020-01-15 15:34:00 -05:00
Axel Kohlmeyer f888c436c3
use safe fgets version and check sscanf() return value for correct parsion of potential file header 2020-01-15 14:24:02 -05:00
Axel Kohlmeyer 48cdd6c2fb
refactor mesocnt example to be better suited for testing and add logs 2020-01-15 14:23:19 -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
Axel Kohlmeyer 3cb26e576d
make sure communication buffers are fully initialized 2020-01-15 13:47:01 -05:00
Axel Kohlmeyer f05175eb1d
properly initialize eflag/vflag and all related properties 2020-01-15 13:42:50 -05:00
Axel Kohlmeyer 500363ab83
move functions in MathExtra namespace to math_extra.h header file 2020-01-15 13:42:14 -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 a74c3b912b
remove tabs and trailing whitespace, adjust source format to closer match LAMMPS style 2020-01-15 12:54:37 -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 902d772b85 removed harmonic bond and angle from repo 2020-01-15 13:47:51 +00:00
cdt1802 331fff0613 moved files to USER-MISC, added README entry, added examples 2020-01-15 12:07:26 +00:00
cdt1802 198a40ada6 fixed typo in documentation 2020-01-15 11:43:11 +00:00