019bc0ba0b
fix typos in Makefile.lammps for NetCDF support
2016-10-19 07:39:03 -04:00
5a6dea7a22
Merge branch 'master' into user-nc-dump
2016-10-18 15:36:18 -04:00
27796b431e
avoid distracting error output
2016-10-18 15:32:20 -04:00
2106dce2b3
new fix halt command, other sundry small bug fixes
2016-10-18 13:11:40 -06:00
6e54443d8c
make plain nc dump style a compile time option as well
...
according to the package author, lars pastewka, some machines
may have only parallel netcdf and not the serial netcdf installed.
hence both netcdf dump styles neet to be optional depending on
the compile time setting in lib/netcdf/Makefile.lammps
The makefile has been set up to auto-detect the necessary flags
for most regular and correct installations.
2016-10-18 15:11:22 -04:00
2b47fa6653
update Makefile.lammps and add README according to suggestions by lars pastewka
2016-10-18 15:05:30 -04:00
713b2af067
Merge pull request #221 from akohlmey/collected-bugfixes
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Collected bugfixes and small changes
2016-10-18 12:58:25 -06:00
ae77664bdd
forgot to include USER-NC-DUMP in PACKUSER variable
2016-10-18 14:45:25 -04:00
4502d3276b
updated Makefile.lammps for NetCDF support based on suggestions from lars pastewka
2016-10-18 14:45:06 -04:00
a752966eef
Merge branch 'collected-bugfixes' of github.com:akohlmey/lammps into collected-bugfixes
2016-10-18 14:07:05 -04:00
1f7693faf2
fix typo
2016-10-18 14:06:43 -04:00
2c5ea9fc61
reapply changes to the timer class that got lost somehow
2016-10-18 14:05:08 -04:00
3e88fb5355
Merge branch 'master' into collected-bugfixes
2016-10-18 13:54:15 -04:00
6eadd45c45
Merge branch 'halt2'
2016-10-18 11:16:44 -06:00
003581c6a8
final changes to fix halt
2016-10-18 11:16:28 -06:00
1f1c87235a
add support for "error continue" option, which resets the timer timeout setting after a soft exit
2016-10-18 12:21:27 -04:00
394c3bb504
add Timer::reset_timeout() API, that allows restoring the previous timeout setting after a forced timeout
2016-10-18 12:20:49 -04:00
954d536826
added bondmax method to fix halt
2016-10-18 09:27:01 -06:00
e4ff8128f1
fix typo
...
(cherry picked from commit c65fb0e311
2016-10-16 12:29:53 -04:00
e7825ba21a
import fix halt prototype code with corrections for soft exit
2016-10-15 07:30:07 -04:00
e77e1f6b8e
replace complex solution to implement a soft exit with simpler one
2016-10-14 19:40:51 -04:00
909ec2c096
remove unused class members
2016-10-14 12:04:32 -04:00
f67975fd8a
apply proper initialization and remove redundant variable declaration
2016-10-14 07:37:06 -04:00
deceb9d5c6
remove assignment without effect
2016-10-14 07:31:52 -04:00
c9c66ca0bd
replace unsafe code
2016-10-14 07:28:25 -04:00
d07703efff
re-apply bugfix from two years ago
2016-10-14 07:27:40 -04:00
411ecca8df
plug memory leak
2016-10-14 07:27:14 -04:00
d11363c7eb
Merge pull request #220 from rbberger/fix-doc-makefile
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Allow building non-html doc targets without Python3 and virtualenv
2016-10-13 17:00:23 -06:00
5aefb2a882
Merge pull request #219 from akohlmey/python-no-double-load
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do not require the LAMMPS shared library when loading the python wrapper from inside LAMMPS
2016-10-13 16:58:35 -06:00
40f2310a2a
Merge pull request #218 from timattox/USER-DPD_fix_rx_init_bugfix
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USER-DPD fix_rx initialization bugfix
2016-10-13 16:56:19 -06:00
2c8a7a318a
bug fix for fix GCMC w/ fix shake, enhance of fix wall/gran/region with restarting
2016-10-13 16:55:53 -06:00
95cca1bd9f
Allow building other targets without Python3 and virtualenv
2016-10-13 11:40:44 -04:00
0b426dadc1
do not require the LAMMPS shared library when loading the python wrapper from inside LAMMPS
...
Thanks to Giacomo Fiorin for figuring this out with NAMD/Colvars.
This requires linking with -Xlinker -export-dynamic or equivalent,
which is the default when using python-config to provide linker flags.
We will fall back to loading the DSO in case the initial load fails.
2016-10-12 18:36:38 -04:00
fcb5271026
USER-DPD: Initialize the dpdThetaLocal array consistently in fix_rx
2016-10-12 15:56:45 -04:00
4958e114ba
USER-DPD bugfix: Properly initialize the local temperature averaging array.
2016-10-12 15:46:46 -04:00
63e71cd45b
patch to add DPD-VV
2016-10-12 07:35:47 -06:00
4a5d9eaae2
Merge pull request #217 from akohlmey/small-fixes
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Collected small changes and bugfixes
2016-10-12 07:32:08 -06:00
4e3a55047f
Merge pull request #215 from timattox/USER-DPD_bugfix_for_dtsqrt
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USER-DPD Bugfix: reset_dt() is not called when I thought it should be called.
2016-10-12 07:30:10 -06:00
f8a26dd158
update Timer::force_timeout() to trigger at next loop iteration
2016-10-12 07:26:03 -04:00
2e8edbd2b9
USER-SMD was missing from PACKLIB variable
2016-10-12 06:53:37 -04:00
da66c1e649
update #include directives to match current LAMMPS coding conventions
2016-10-12 00:07:52 -04:00
c24bf512f3
update #include statements for system includes
2016-10-12 00:00:53 -04:00
6b4ab0a390
update .gitignore
2016-10-12 00:00:21 -04:00
adc98e07df
whitespace cleanup in USER-DPD
2016-10-11 23:58:36 -04:00
39a22039e9
correct broken link
2016-10-11 23:57:40 -04:00
e10ea91c5f
add doc file to toctree
2016-10-11 23:51:42 -04:00
b75860048b
updates for recent changes to the manual
2016-10-11 23:50:45 -04:00
69cb831705
import dump nc and dump nc/mpiio from lammps-netcdf as USER-NC-DUMP package by lars pastewka
2016-10-11 23:44:34 -04:00
ecb03dd2df
import lammps-netcdf code as USER-NC-DUMP package
2016-10-11 23:03:18 -04:00
0eb7fbf34d
tweaks to new USER-DPD docs
2016-10-11 15:43:59 -06:00
