Diffusion lammps (master) History

History
master93d393aa691a959d6e995f5…

Oct 28 2016

permission cleanup in tools folder
93d393aa691a
·Axel Kohlmeyer on Oct 28 2016, 16:48.
Merge branch 'master' into collected-small-fixes
4216be49f3ce
·Axel Kohlmeyer on Oct 28 2016, 16:46.

Oct 27 2016

new library functions
d9891abdf4d5
·Steve Plimpton on Oct 27 2016, 17:34.

Oct 26 2016

region cylinder is compatible with open_faces[2], so do not disallow it.
f028a9a9678d
·Axel Kohlmeyer on Oct 26 2016, 21:04.

Oct 25 2016

Merge pull request #239 from akohlmey/static-analysis-fixes
efaa8feab591
·sjplimp / GitHub on Oct 25 2016, 18:32.
Merge pull request #238 from giacomofiorin/colvars-2016-10-24
ad5f7c458196
·sjplimp / GitHub on Oct 25 2016, 18:32.
Merge pull request #231 from akohlmey/collected-doc-fixes
6b334991352b
·sjplimp / GitHub on Oct 25 2016, 18:30.
fix issue with docs for orientorder/atom compute reported by @andeplane
63eada242554
·Axel Kohlmeyer on Oct 25 2016, 18:12.
Merge branch 'collected-doc-fixes' of github.com:akohlmey/lammps into collected…
1a436bd7a9bb
·Axel Kohlmeyer on Oct 25 2016, 17:58.
Merge branch 'master' into collected-doc-fixes
52dd9aee5fe6
·Axel Kohlmeyer on Oct 25 2016, 17:55.
Merge branch 'doc'
eca96e21ef25
·Steve Plimpton on Oct 25 2016, 17:46.
doc page changes
9c81ad1ab6e3
·Steve Plimpton on Oct 25 2016, 17:45.

Oct 24 2016

update documentation pdf for updated colvars lib
f8367e3d0fee
·Axel Kohlmeyer on Oct 24 2016, 23:49.
Merge branch 'colvars-2016-10-24' of https://github.com/giacomofiorin/lammps…
ba6d1528bb17
·Axel Kohlmeyer on Oct 24 2016, 23:34.
Make SMP parallelism for Colvars optional
182141b85005
·Giacomo Fiorin on Oct 24 2016, 23:13.
whitespace cleanup
512c413b7ead
·Axel Kohlmeyer on Oct 24 2016, 23:13.
apply corrections to issues reported by static code analysis
7b89e47a38d5
·Axel Kohlmeyer on Oct 24 2016, 23:12.
Add ensemble-biased metadynamics (Fabrizio Marinelli, NIH)
e02505c8cc33
·Giacomo Fiorin on Oct 24 2016, 23:11.
Minor changes and fixes not relevant to LAMMPS
be2d155cef25
·Giacomo Fiorin on Oct 24 2016, 23:10.
Fix wall forces and subtractAppliedForce for extended-Lagrangian ABF
c2430939809e
·Giacomo Fiorin on Oct 24 2016, 23:05.
Add C-linkage wrapper for colvarscript (useful with ctypes)
ad57a17f48c8
·Giacomo Fiorin on Oct 24 2016, 22:48.
Merge pull request #232 from akohlmey/small-bugfixes
477ddaf1125b
·sjplimp / GitHub on Oct 24 2016, 16:15.
Merge pull request #230 from akohlmey/manual-in-ebook-format
4f69d91a99dc
·sjplimp / GitHub on Oct 24 2016, 16:12.

Oct 23 2016

correct typo in write_dump docs
bc4498800319
·Axel Kohlmeyer on Oct 23 2016, 21:18.

Oct 21 2016

stop with error, if molecule command requires special bond auto-generation…
db36c8bcc31e
·Axel Kohlmeyer on Oct 21 2016, 20:51.
have bond style table exit when bond length is outside table range
991034b632c7
·Axel Kohlmeyer on Oct 21 2016, 20:01.
ignore mobi file as well
607246f92310
·Axel Kohlmeyer on Oct 21 2016, 19:25.
remove mobi file format creation from makefile and explain it in README instead
6742fb634aa9
·Axel Kohlmeyer on Oct 21 2016, 18:05.
ignore generated PDF and ePUB files
ed3f02f24944
·Axel Kohlmeyer on Oct 21 2016, 18:04.
make certain, that atom->maxspecial is incremented with extra special space
a2e34aab0a8c
·Axel Kohlmeyer on Oct 21 2016, 17:55.
Merge branch 'collected-small-changes' into collected-doc-fixes
6cd6c106efeb
·Axel Kohlmeyer on Oct 21 2016, 01:27.

Oct 20 2016

Revert "support generation of manual in ePUB format"
a9572275eeb0
·Axel Kohlmeyer on Oct 20 2016, 22:27.
Add support for ebook generation in ePUB and mobi format
2cf77ff778ef
·Axel Kohlmeyer on Oct 20 2016, 22:16.
fix various formatting and broken link issues identified by ebook-convert
f022f6d88ad2
·Axel Kohlmeyer on Oct 20 2016, 20:40.
support generation of manual in ePUB format
8c3f5cb30700
·Axel Kohlmeyer on Oct 20 2016, 15:27.

Oct 19 2016

update packages section in manual with information about USER-NC-DUMP
e8359923f1e4
·Axel Kohlmeyer on Oct 19 2016, 21:58.
forgot pair table change
9954d5d34668
·Steve Plimpton on Oct 19 2016, 18:47.
Merge branch 'master' of github.com:lammps/lammps
3d254780de85
·Steve Plimpton on Oct 19 2016, 16:58.
Merge pull request #229 from akohlmey/small-corrections
b0cf1ded38ab
·sjplimp / GitHub on Oct 19 2016, 16:57.
Merge pull request #228 from akohlmey/correct-prd-for-bigbig
0891ed83a52f
·sjplimp / GitHub on Oct 19 2016, 16:56.
Revert "recognize any word starting with FP as FPRIME style table"
ffb8eb36da4b
·Axel Kohlmeyer on Oct 19 2016, 16:44.
make PRD code compatible with -DLAMMPS_BIGBIG
1a108572441d
·Axel Kohlmeyer on Oct 19 2016, 16:43.
dead code removal
263446867664
·Axel Kohlmeyer on Oct 19 2016, 16:42.
text edit
58141e0559cb
·Steve Plimpton on Oct 19 2016, 16:41.
Merge pull request #226 from akohlmey/pair-gauss-mixing
393337e7cfa2
·sjplimp / GitHub on Oct 19 2016, 16:37.
Merge pull request #224 from akohlmey/get-vars
e0ed218cc496
·sjplimp / GitHub on Oct 19 2016, 16:36.
Merge pull request #216 from akohlmey/user-nc-dump
efc7b23bd863
·sjplimp / GitHub on Oct 19 2016, 16:33.
account for new fix halt properly in PDF and online docs
566effc9c961
·Axel Kohlmeyer on Oct 19 2016, 15:08.
recognize any word starting with FP as FPRIME style table
86f5b5113344
·Axel Kohlmeyer on Oct 19 2016, 15:05.
fix typo
ccca642b3ae6
·Axel Kohlmeyer on Oct 19 2016, 14:08.
fix typos in Makefile.lammps for NetCDF support
019bc0ba0be2
·Axel Kohlmeyer on Oct 19 2016, 13:39.
add mixing for pair styles gauss and gauss/cut contributed by andrew jewett.
7b7cb297e6be
·Axel Kohlmeyer on Oct 19 2016, 04:26.

Oct 18 2016

Merge branch 'master' into user-nc-dump
5a6dea7a2217
·Axel Kohlmeyer on Oct 18 2016, 21:36.
avoid distracting error output
27796b431ee5
·Axel Kohlmeyer on Oct 18 2016, 21:32.
new fix halt command, other sundry small bug fixes
2106dce2b382
·Steve Plimpton on Oct 18 2016, 21:11.
make plain nc dump style a compile time option as well
6e54443d8c19
·Axel Kohlmeyer on Oct 18 2016, 21:11.
update Makefile.lammps and add README according to suggestions by lars pastewka
2b47fa66533e
·Axel Kohlmeyer on Oct 18 2016, 21:05.
Merge pull request #221 from akohlmey/collected-bugfixes
713b2af067cb
·sjplimp / GitHub on Oct 18 2016, 20:58.
forgot to include USER-NC-DUMP in PACKUSER variable
ae77664bddd5
·Axel Kohlmeyer on Oct 18 2016, 20:45.
updated Makefile.lammps for NetCDF support based on suggestions from lars…
4502d3276be4
·Axel Kohlmeyer on Oct 18 2016, 20:45.
Merge branch 'collected-bugfixes' of github.com:akohlmey/lammps into collected…
a752966eefec
·Axel Kohlmeyer on Oct 18 2016, 20:07.
fix typo
1f7693faf289
·Axel Kohlmeyer on Oct 18 2016, 20:06.
reapply changes to the timer class that got lost somehow
2c5ea9fc61e4
·Axel Kohlmeyer on Oct 18 2016, 20:05.
Merge branch 'master' into collected-bugfixes
3e88fb535547
·Axel Kohlmeyer on Oct 18 2016, 19:54.
Merge branch 'halt2'
6eadd45c4567
·Steve Plimpton on Oct 18 2016, 19:16.
final changes to fix halt
003581c6a80c
·Steve Plimpton on Oct 18 2016, 19:16.
add support for "error continue" option, which resets the timer timeout setting…
1f1c87235a07
·Axel Kohlmeyer on Oct 18 2016, 18:21.
add Timer::reset_timeout() API, that allows restoring the previous timeout…
394c3bb50453
·Axel Kohlmeyer on Oct 18 2016, 18:20.
added bondmax method to fix halt
954d536826ee
·Steve Plimpton on Oct 18 2016, 17:27.
provide an accessor for names of LAMMPS variables
c5513c4f7503
·Axel Kohlmeyer on Oct 18 2016, 01:56.

Oct 16 2016

fix typo
e4ff8128f1b2
·Axel Kohlmeyer on Oct 16 2016, 18:29.

Oct 15 2016

import fix halt prototype code with corrections for soft exit
e7825ba21a0b
·Axel Kohlmeyer on Oct 15 2016, 13:30.
replace complex solution to implement a soft exit with simpler one
e77e1f6b8ea6
·Axel Kohlmeyer on Oct 15 2016, 01:40.

Oct 14 2016

remove unused class members
909ec2c09658
·Axel Kohlmeyer on Oct 14 2016, 18:04.
apply proper initialization and remove redundant variable declaration
f67975fd8adf
·Axel Kohlmeyer on Oct 14 2016, 13:37.
remove assignment without effect
deceb9d5c6a4
·Axel Kohlmeyer on Oct 14 2016, 13:31.
replace unsafe code
c9c66ca0bd1a
·Axel Kohlmeyer on Oct 14 2016, 13:28.
re-apply bugfix from two years ago
d07703efff5c
·Axel Kohlmeyer on Oct 14 2016, 13:27.
plug memory leak
411ecca8df96
·Axel Kohlmeyer on Oct 14 2016, 13:27.
Merge pull request #220 from rbberger/fix-doc-makefile
d11363c7eb76
·sjplimp / GitHub on Oct 14 2016, 01:00.
Merge pull request #219 from akohlmey/python-no-double-load
5aefb2a88232
·sjplimp / GitHub on Oct 14 2016, 00:58.
Merge pull request #218 from timattox/USER-DPD_fix_rx_init_bugfix
40f2310a2ab5
·sjplimp / GitHub on Oct 14 2016, 00:56.
bug fix for fix GCMC w/ fix shake, enhance of fix wall/gran/region with…
2c8a7a318a4a
·Steve Plimpton on Oct 14 2016, 00:55.

Oct 13 2016

Allow building other targets without Python3 and virtualenv
95cca1bd9f63
·Richard Berger on Oct 13 2016, 17:40.
do not require the LAMMPS shared library when loading the python wrapper from…
0b426dadc1d1
·Axel Kohlmeyer on Oct 13 2016, 00:36.

Oct 12 2016

USER-DPD: Initialize the dpdThetaLocal array consistently in fix_rx
fcb52710267a
·Tim Mattox on Oct 12 2016, 21:56.
USER-DPD bugfix: Properly initialize the local temperature averaging array.
4958e114bac6
·Tim Mattox on Oct 12 2016, 21:46.
patch to add DPD-VV
63e71cd45b27
·Steve Plimpton on Oct 12 2016, 15:35.
Merge pull request #217 from akohlmey/small-fixes
4a5d9eaae23c
·sjplimp / GitHub on Oct 12 2016, 15:32.
Merge pull request #215 from timattox/USER-DPD_bugfix_for_dtsqrt
4e3a55047f0e
·sjplimp / GitHub on Oct 12 2016, 15:30.
update Timer::force_timeout() to trigger at next loop iteration
f8a26dd158ff
·Axel Kohlmeyer on Oct 12 2016, 13:26.
USER-SMD was missing from PACKLIB variable
2e8edbd2b973
·Axel Kohlmeyer on Oct 12 2016, 12:53.
update #include directives to match current LAMMPS coding conventions
da66c1e649bb
·Axel Kohlmeyer on Oct 12 2016, 06:07.
update #include statements for system includes
c24bf512f31a
·Axel Kohlmeyer on Oct 12 2016, 06:00.
update .gitignore
6b4ab0a39044
·Axel Kohlmeyer on Oct 12 2016, 06:00.
whitespace cleanup in USER-DPD
adc98e07df5d
·Axel Kohlmeyer on Oct 12 2016, 05:58.
correct broken link
39a22039e918
·Axel Kohlmeyer on Oct 12 2016, 05:57.
add doc file to toctree
e10ea91c5f42
·Axel Kohlmeyer on Oct 12 2016, 05:51.
updates for recent changes to the manual
b75860048bd7
·Axel Kohlmeyer on Oct 12 2016, 05:50.
import dump nc and dump nc/mpiio from lammps-netcdf as USER-NC-DUMP package by…
69cb83170599
·Axel Kohlmeyer on Oct 12 2016, 05:44.

Historymaster93d393aa691a959d6e995f5…

Oct 28 2016

Oct 27 2016

Oct 26 2016

Oct 25 2016

Oct 24 2016

Oct 23 2016

Oct 21 2016

Oct 20 2016

Oct 19 2016

Oct 18 2016

Oct 16 2016

Oct 15 2016

Oct 14 2016

Oct 13 2016

Oct 12 2016

History
master93d393aa691a959d6e995f5…