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
cc81dc2046
remove redundant initializers
2020-01-22 14:32:34 -05:00
8a1f893b43
repair incorrect conversions on [*] expressions by txt2rst
2020-01-22 13:20:04 -05:00
37e8195b01
fix whitespace issue
2020-01-22 12:44:24 -05:00
a87c7a4a53
avoid segfault
2020-01-22 12:41:59 -05:00
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
0623859f36
fix small bug in pair style extep
2020-01-22 11:25:13 -05:00
0ae40c5967
Add unit conversion in setup()
2020-01-22 17:13:10 +01:00
ac143dbdb7
capitalize comment
2020-01-21 17:57:12 -07:00
11f687c1fb
make comment string consistent
2020-01-21 17:56:00 -07:00
b29ffabe56
move two_charge_force calc to occur at init, not constructor
2020-01-21 14:24:55 -07:00
f7dc70a986
add new error/warning messages to documentation
2020-01-21 16:05:55 -05:00
a6f59a8607
Merge remote-tracking branch 'github/master' into Ncreate_atoms
...
# Conflicts:
# src/create_atoms.cpp
2020-01-21 15:52:01 -05:00
646dc83394
remove trailing whitespace
2020-01-21 15:46:28 -05:00
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
d83cf8e4b0
add Jake's name as contributor
2020-01-21 13:36:36 -07:00
90ff2eb6c9
modified versions of creating atoms on subset of lattice, ditto for set type/fraction
2020-01-21 13:31:47 -07:00
4ea679dd54
Merge branch 'master' into nparticles
2020-01-21 13:26:03 -07:00
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
3db920b8a6
fix minor issues with docs
2020-01-20 17:03:54 -05:00
12de17621f
Merge branch 'master' into collected-small-changes
...
# Conflicts:
# doc/src/Commands_fix.rst
2020-01-20 16:59:42 -05:00
795a872bf3
Merge pull request #1847 from pdebuyl/fix-active
...
Add fix propel/self
2020-01-20 16:57:04 -05:00
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
946bd8f3c0
print warning about adjusting the communication cutoff only during integrator or minimizer setup phase
2020-01-20 16:23:26 -05:00
41cfb91d7d
Reformat README and mention about the timeout option
2020-01-20 15:55:31 -05:00
7766b29c97
replace strncmp by strcmp
2020-01-20 21:54:29 +01:00
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
95d3b9e708
Change BPFile to BP4 in adios config so that streaming through files is enabled
2020-01-20 14:35:51 -05:00
3ccab876f7
fix string length for strncmp
2020-01-20 18:16:20 +01:00
b0ba91d353
add false positive
2020-01-20 11:58:59 -05:00
8ed271f16f
change mode of propel/self to quat instead of quaternion
2020-01-20 17:41:20 +01:00
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
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
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
a1864f8bfd
Fix commands table
2020-01-20 10:11:34 -05:00
fdd330256c
update adios example input file to show more read_dump options
2020-01-20 09:23:35 -05:00
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
125a82f572
change isReaderParallel flag to parallel and generally adapt more to LAMMPS programming style
2020-01-20 09:20:42 -05:00
76818a47c0
add missing include statement
2020-01-20 09:20:42 -05:00
fed1e800a9
revert reformatting of unrelated file
2020-01-20 09:20:42 -05:00
9959997376
change attribution
2020-01-20 09:20:42 -05:00
0da85cb2fc
update README for USER-ADIOS
2020-01-20 09:20:42 -05:00
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
0bed348073
fix typo
2020-01-20 07:17:39 -05:00
019e269ed9
silence compiler warning
2020-01-20 07:12:22 -05:00
3ff49dfd59
avoid segfault when using per-particle masses
2020-01-20 07:12:12 -05:00
c19085dc08
silence compiler warning
2020-01-20 07:06:49 -05:00
926096dc66
silence compiler warning
2020-01-20 07:06:00 -05:00
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
43c184983e
Fix lj/cut/tip4p/long/gpu name in docs
2020-01-20 03:39:16 +03:00
