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19503 Commits

Author SHA1 Message Date
Axel Kohlmeyer 72d8bea459
remove backslash escapes for underscore in doc references 2020-01-23 16:52:38 -05:00
Axel Kohlmeyer 958b8d96a9
expand explanations about setting the python version for the python wrapper 2020-01-23 00:14:44 -05:00
Axel Kohlmeyer 204fb6f7ed
fix issue with standalone anchor_check 2020-01-22 23:51:53 -05:00
Axel Kohlmeyer 30444b344b
Merge pull request #1853 from akohlmey/collected-small-changes 
Collected small changes and bugfixes for the next patch release
 2020-01-22 17:25:03 -05:00
Axel Kohlmeyer 8096a78340
Merge pull request #1852 from vklip/bugfix-gjf 
Add unit conversion in setup() in fix_langevin.cpp
 2020-01-22 17:22:01 -05:00
Axel Kohlmeyer 949d7608ba
Merge pull request #1811 from brycelelbach/bug/missing_execution_space_qualifiers 
Fix mismatches in CUDA execution space qualifiers between declarations and definitions.
 2020-01-22 17:10:11 -05:00
Axel Kohlmeyer 5488efbc03
fix typo, update maintainer. 2020-01-22 17:00:10 -05:00
Axel Kohlmeyer 9d06430894
Merge pull request #603 from jrgissing/Ncreate_atoms 
add exactly N particles to available lattice points
 2020-01-22 15:36:54 -05:00
Axel Kohlmeyer 61ddf9bcd8
undo accidental edit of KOKKOS cuda mpi makefile 2020-01-22 15:32:00 -05:00
Axel Kohlmeyer 40e0e78abd
import template atom ID check from PR #1822 2020-01-22 15:02:55 -05:00
Axel Kohlmeyer bb024bc077
add call to KSpace::two_charge() that was overlooked 2020-01-22 14:46:57 -05:00
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