jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
19,805 Commits 9 Branches 198 Tags 1.1 GiB
Commit Graph

19805 Commits

Author SHA1 Message Date
Axel Kohlmeyer 48cae2703b
move memory allocation for atom style variable data where it belongs and cannot be skipped 
this fixes the bug reported on lammps-users on 2020-01-22 by Olivier Politano
 2020-01-22 14:34:12 -05:00
Axel Kohlmeyer cc81dc2046
remove redundant initializers 2020-01-22 14:32:34 -05:00
Axel Kohlmeyer 8a1f893b43
repair incorrect conversions on [*] expressions by txt2rst 2020-01-22 13:20:04 -05:00
Axel Kohlmeyer 37e8195b01
fix whitespace issue 2020-01-22 12:44:24 -05:00
Axel Kohlmeyer a87c7a4a53
avoid segfault 2020-01-22 12:41:59 -05:00
Axel Kohlmeyer 64a4bf6a42
Merge pull request #1850 from lammps/kspace-bugfix 
move two_charge_force calc to occur at init, not constructor, fix small bug in pair style extep
 2020-01-22 12:38:33 -05:00
Axel Kohlmeyer 0623859f36
fix small bug in pair style extep 2020-01-22 11:25:13 -05:00
Viktor Klippenstein 0ae40c5967 Add unit conversion in setup() 2020-01-22 17:13:10 +01:00
Steve Plimpton ac143dbdb7 capitalize comment 2020-01-21 17:57:12 -07:00
Steve Plimpton 11f687c1fb make comment string consistent 2020-01-21 17:56:00 -07:00
Steve Plimpton b29ffabe56 move two_charge_force calc to occur at init, not constructor 2020-01-21 14:24:55 -07:00
Axel Kohlmeyer f7dc70a986
add new error/warning messages to documentation 2020-01-21 16:05:55 -05:00
Axel Kohlmeyer a6f59a8607
Merge remote-tracking branch 'github/master' into Ncreate_atoms 
# Conflicts:
#	src/create_atoms.cpp
 2020-01-21 15:52:01 -05:00
Axel Kohlmeyer 646dc83394
remove trailing whitespace 2020-01-21 15:46:28 -05:00
Axel Kohlmeyer 7728c5069f
Merge pull request #1845 from akohlmey/collected-small-changes 
Collected small changes for next patch release
 2020-01-21 15:45:41 -05:00
Steve Plimpton d83cf8e4b0 add Jake's name as contributor 2020-01-21 13:36:36 -07:00
Steve Plimpton 90ff2eb6c9 modified versions of creating atoms on subset of lattice, ditto for set type/fraction 2020-01-21 13:31:47 -07:00
Steve Plimpton 4ea679dd54 Merge branch 'master' into nparticles 2020-01-21 13:26:03 -07:00
Axel Kohlmeyer 405eb63a51
update sphinx extension to automatically pad lists to fill tables and avoid errors processing the documentation 2020-01-21 11:39:29 -05:00
Axel Kohlmeyer 3db920b8a6
fix minor issues with docs 2020-01-20 17:03:54 -05:00
Axel Kohlmeyer 12de17621f
Merge branch 'master' into collected-small-changes 
# Conflicts:
#	doc/src/Commands_fix.rst
 2020-01-20 16:59:42 -05:00
Axel Kohlmeyer 795a872bf3
Merge pull request #1847 from pdebuyl/fix-active 
Add fix propel/self
 2020-01-20 16:57:04 -05:00
Axel Kohlmeyer f03cfba029
Merge pull request #1820 from ornladios/adios_read_dump 
Support read_dump with dump style 'adios'
 2020-01-20 16:27:09 -05:00
Axel Kohlmeyer 946bd8f3c0
print warning about adjusting the communication cutoff only during integrator or minimizer setup phase 2020-01-20 16:23:26 -05:00
Podhorszki Norbert 41cfb91d7d Reformat README and mention about the timeout option 2020-01-20 15:55:31 -05:00
Pierre de Buyl 7766b29c97 replace strncmp by strcmp 2020-01-20 21:54:29 +01:00
Podhorszki Norbert 44a814ec1d Added 'timeout <value>' option to the adios reader, so that a rerun can concurrently run with the first simulation 2020-01-20 15:52:21 -05:00
Podhorszki Norbert 95d3b9e708 Change BPFile to BP4 in adios config so that streaming through files is enabled 2020-01-20 14:35:51 -05:00
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