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19727 Commits

Author SHA1 Message Date
Pierre de Buyl 3ccab876f7 fix string length for strncmp 2020-01-20 18:16:20 +01:00
Axel Kohlmeyer b0ba91d353
add false positive 2020-01-20 11:58:59 -05:00
Pierre de Buyl 8ed271f16f change mode of propel/self to quat instead of quaternion 2020-01-20 17:41:20 +01:00
Podhorszki Norbert 50062d6a44 Added rerun example for ADIOS dump/read_dump to examples/USER/adios/rerun. 
Moved the balance example under examples/USER/adios/balance
 2020-01-20 11:23:18 -05:00
Axel Kohlmeyer 3c55bded69
Merge pull request #1848 from Vsevak/tip4p_gpu_fix 
Fix some issues with lj/cut/tip4p/long/gpu
 2020-01-20 11:17:37 -05:00
Podhorszki Norbert 18c16b4b39 Print lammps style error and abort when adios2_config.xml is not found. Avoid ugly C++ exception stack. 2020-01-20 10:11:57 -05:00
Podhorszki Norbert a1864f8bfd Fix commands table 2020-01-20 10:11:34 -05:00
Podhorszki Norbert fdd330256c update adios example input file to show more read_dump options 2020-01-20 09:23:35 -05:00
Podhorszki Norbert 95b4613e16 Added documentation for 'read_dump ... format adios' command and fixed links and names for 'dump atom/adios' and 'dump custom/adios' commands. 2020-01-20 09:23:35 -05:00
Axel Kohlmeyer 125a82f572 change isReaderParallel flag to parallel and generally adapt more to LAMMPS programming style 2020-01-20 09:20:42 -05:00
Axel Kohlmeyer 76818a47c0 add missing include statement 2020-01-20 09:20:42 -05:00
Axel Kohlmeyer fed1e800a9 revert reformatting of unrelated file 2020-01-20 09:20:42 -05:00
Axel Kohlmeyer 9959997376 change attribution 2020-01-20 09:20:42 -05:00
Podhorszki Norbert 0da85cb2fc update README for USER-ADIOS 2020-01-20 09:20:42 -05:00
Podhorszki N 580909fd47 Implement read_dump with format 'adios'. It modifies read_dump.cpp to support reading from one dataset by all processes. 2020-01-20 09:20:42 -05:00
Axel Kohlmeyer 0bed348073
fix typo 2020-01-20 07:17:39 -05:00
Axel Kohlmeyer 019e269ed9
silence compiler warning 2020-01-20 07:12:22 -05:00
Axel Kohlmeyer 3ff49dfd59
avoid segfault when using per-particle masses 2020-01-20 07:12:12 -05:00
Axel Kohlmeyer c19085dc08
silence compiler warning 2020-01-20 07:06:49 -05:00
Axel Kohlmeyer 926096dc66
silence compiler warning 2020-01-20 07:06:00 -05:00
Pierre de Buyl af1e797271 fix mass and nve/asphere 
1. Set mass to 1. The radius is 1/2, so the density must be
   1/(4/3 pi 1/2^3)
2. Use nve/asphere instead of nve. Else, the particle's orientation are
   not integrated.
 2020-01-20 12:48:26 +01:00
Vsevak 43c184983e Fix lj/cut/tip4p/long/gpu name in docs 2020-01-20 03:39:16 +03:00
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