Diffusion lammps (master) History

History
mastere03cc994673e6b43ef41368…

Jun 2 2017

made the command options more lammps standard style
e03cc994673e
·Emile Maras on Jun 2 2017, 23:42.

May 29 2017

removed a bug in fix_neb.cpp which prevented the freeend to work properly, plus…
c904cfb8bc5f
·Emile Maras on May 29 2017, 15:49.
removed a bug in fix_neb.cpp which prevented the freeend to work properly, plus…
32c87f313180
·Emile Maras on May 29 2017, 14:00.

May 23 2017

restore explicit NAN constants in output
4002dce63984
·Axel Kohlmeyer on May 23 2017, 04:39.
some more formatting cleanup in fix neb
c801cdd81fe0
·Axel Kohlmeyer on May 23 2017, 04:33.
more formatting cleanup
9008a3119009
·Axel Kohlmeyer on May 23 2017, 03:55.

May 22 2017

when growing arrays with reallocate, always check against atom->nmax and not…
62601678cdde
·Axel Kohlmeyer on May 22 2017, 23:16.
do not try to free null communicators
081910adbc41
·Axel Kohlmeyer on May 22 2017, 23:15.
rename nall class member to numall to avoid confusion with the common…
f73fd0625d53
·Axel Kohlmeyer on May 22 2017, 23:14.
NEBLongRange was incorrectly set to false by default. revert to true.
7185db98b4c7
·Axel Kohlmeyer on May 22 2017, 23:13.
avoid use '&&' and '||' instead of 'and' and 'or' for consistency
3fd91a239ff0
·Axel Kohlmeyer on May 22 2017, 20:41.
change example inputs to be backward compatible
8bc829c7f19e
·Axel Kohlmeyer on May 22 2017, 20:40.

May 19 2017

plug some memory leaks
546aed7ccde8
·Axel Kohlmeyer on May 19 2017, 22:14.
silence several compiler warnings
6ef79d371541
·Axel Kohlmeyer on May 19 2017, 21:13.
formatting cleanup. combine 8 MPI_Allreduce() calls into 1
c2bf3269acf4
·Axel Kohlmeyer on May 19 2017, 21:02.
restore spelling fix and semantic fix from upstream
aca16745e4cc
·Axel Kohlmeyer on May 19 2017, 18:17.
correct a bunch of documentation formatting issues for updated neb and fix neb…
a5110d81ea61
·Axel Kohlmeyer on May 19 2017, 18:13.

May 18 2017

changed doc links
d4ee03c778df
·Emile Maras on May 18 2017, 21:31.
small formating changes
069f3e746b46
·Emile Maras on May 18 2017, 21:23.
some small formating change but does not work anymore
8daba0115142
·Emile Maras on May 18 2017, 16:48.
added several features to the NEB
640edbc1d40e
·Emile Maras on May 18 2017, 11:08.

May 12 2017

Merge pull request #478 from akohlmey/add-python-source-cmd
06c151421c4f
·sjplimp / GitHub on May 12 2017, 21:28.
Merge pull request #477 from lammps/renamings
0008b6fc2d18
·sjplimp / GitHub on May 12 2017, 16:54.
fixup docs after last change
b6a70ec6fd74
·Richard Berger on May 12 2017, 06:34.
Allow fix python to only execute every N steps
c4d0f0709331
·Richard Berger on May 12 2017, 06:29.
Add documentation about fix python
93f603306126
·Richard Berger on May 12 2017, 05:50.
Implement fix python mentioned in issue #454
110bb79b14cc
·Richard Berger on May 12 2017, 05:50.
implement functions to execute arbitrary python code from strings or files and…
d84f8898b7b0
·Axel Kohlmeyer on May 12 2017, 04:39.
implement a `python source` command as suggested in issue #454
27a6371f9b52
·Axel Kohlmeyer on May 12 2017, 01:18.

May 11 2017

rename some USER/misc dirs
7c3b8e014c7b
·Steve Plimpton on May 11 2017, 18:15.
Merge pull request #476 from akohlmey/dump_custom_bugfix
a069d21621b0
·sjplimp / GitHub on May 11 2017, 17:27.
Merge pull request #474 from rbberger/dump_vtk_fixes
d7f54464c628
·sjplimp / GitHub on May 11 2017, 17:25.
Merge pull request #473 from akohlmey/compress-for-reaxc-fixes
998eb44e836f
·sjplimp / GitHub on May 11 2017, 17:25.
Merge pull request #471 from akohlmey/fix-4may2017-issues
96d1de857539
·sjplimp / GitHub on May 11 2017, 17:24.
Merge pull request #466 from DallasTrinkle/meam-spline-multicomponent
deff6ffaac3b
·sjplimp / GitHub on May 11 2017, 17:22.
fix mixed memory alloc bug in dump custom. this closes #475
328ef873d838
·Axel Kohlmeyer on May 11 2017, 04:41.
Added two examples of using the VTK dump style
4ecf876a6453
·Richard Berger on May 11 2017, 01:52.
Fix segmentation fault in dump vtk
c4ac5773cb0a
·Richard Berger on May 11 2017, 01:51.
Work around VTK 7 API change
cac1bf83ef42
·Richard Berger on May 11 2017, 01:41.

May 10 2017

add support for gzip compressed output to fix reax/bonds, reax/c/bonds and…
abeb1e096ab6
·Axel Kohlmeyer on May 10 2017, 17:19.
correct some more omitted updates
9f7ce39f9fcb
·Axel Kohlmeyer on May 10 2017, 00:14.

May 9 2017

correct broken links and references in documentation
29ae8d4ca3b9
·Axel Kohlmeyer on May 9 2017, 23:15.
implement overlooked changes from 4may2017 patch
3f4aee1046ab
·Axel Kohlmeyer on May 9 2017, 21:57.
add a couple of simple example single/multi-elment inputs for meam/spline pair…
d0da0639f02b
·Axel Kohlmeyer on May 9 2017, 21:51.
whitespace cleanup
390ceb1475a7
·Axel Kohlmeyer on May 9 2017, 21:49.
performance improvement through avoiding function call and dereference overhead
6c5edf6c709e
·Axel Kohlmeyer on May 9 2017, 21:38.
fix issues with potential file parser
9cd994f57c70
·Axel Kohlmeyer on May 9 2017, 21:35.
Merge pull request #470 from lammps/integration
a6e2d5b5f7fb
·sjplimp / GitHub on May 9 2017, 18:32.
neighbor list bugfix to prevent cycle in copy lists
08ec55743e47
·Steve Plimpton on May 9 2017, 16:55.

May 8 2017

Merge pull request #449 from rbberger/python_refactoring
c4f90b384167
·sjplimp / GitHub on May 8 2017, 16:29.

May 6 2017

Merge remote-tracking branch 'upstream/master' into python_refactoring
f8af7edf927b
·Richard Berger on May 6 2017, 22:00.

May 4 2017

update src/Purge.list with renamed reaxc src files
a73402ad9311
·Steve Plimpton on May 4 2017, 22:53.
jive Kokkos/reaxc file names with new user-reaxc file names
d7dbff0f5441
·Steve Plimpton on May 4 2017, 22:46.
Cleanup of style (removing all tabs, shortened long lines).
42531389df27
·DallasTrinkle on May 4 2017, 22:28.
OpenMP version added.
f7230006fef4
·DallasTrinkle on May 4 2017, 22:08.
Removed unused functions.
754b40cb3100
·DallasTrinkle on May 4 2017, 20:16.
Cleanup.
ffdc8b556d00
·DallasTrinkle on May 4 2017, 20:03.
Cleanup.
5accce976a13
·DallasTrinkle on May 4 2017, 20:02.
Cleanup.
349c1443a1c0
·DallasTrinkle on May 4 2017, 20:01.
Removed extra "helper" functions.
2f71245d8277
·DallasTrinkle on May 4 2017, 20:00.
patch 4May17
51c6d502687b
·Steve Plimpton on May 4 2017, 19:46.
Merge pull request #458 from stanmoore1/kokkos_sync_bugfix
6499cfcf52ae
·sjplimp / GitHub on May 4 2017, 19:24.
Merge pull request #457 from stanmoore1/kokkos_ubuf
f08e2069917d
·sjplimp / GitHub on May 4 2017, 19:23.
Merge pull request #455 from stanmoore1/kokkos_update
fbddfe2729a2
·sjplimp / GitHub on May 4 2017, 19:23.
Merge pull request #452 from akohlmey/small-fixes-and-updates
dcc5472cba99
·sjplimp / GitHub on May 4 2017, 19:23.
new Section package and start doc pages and build scripts
addd87c0f7a4
·Steve Plimpton on May 4 2017, 19:22.
Starting to refactor in preparation to contruct OMP version.
480727815a89
·DallasTrinkle on May 4 2017, 18:27.
Fix system header #include style.
45187a0fc77e
·DallasTrinkle on May 4 2017, 18:05.

May 3 2017

Cleaned up atom->x and atom->f deferences.
7409c6d78132
·DallasTrinkle on May 3 2017, 23:56.
Cleanup: two space indent + no trailing spaces on lines.
11cb0212b7fa
·DallasTrinkle on May 3 2017, 23:49.
print warning about minimization energy with fix box/relax
7f49ee8fd747
·Axel Kohlmeyer on May 3 2017, 21:33.
Merge pull request #464 from akohlmey/rename-cg-cmm-to-cgsdk
f5cf1f1314b0
·sjplimp / GitHub on May 3 2017, 16:37.

May 2 2017

Fix to communication for mpi. Tested, and now working correctly with MPI.
50c7234f2690
·DallasTrinkle on May 2 2017, 16:43.
Fixed neighbor list building that caused error in parallel runs with…
f58fc9488f89
·DallasTrinkle on May 2 2017, 04:56.
Fix for seg fault.
408cc198854c
·DallasTrinkle on May 2 2017, 03:36.
Another fix for seg fault in parallel allocation.
c76d27373ecd
·DallasTrinkle on May 2 2017, 03:33.

May 1 2017

Small error in elements allocation causing seg. fault for parallel runs; fixed.
fb08dc09f3b3
·DallasTrinkle on May 1 2017, 20:38.

Apr 29 2017

Updated version of equations, documentation.
8bddf105bf7a
·DallasTrinkle on Apr 29 2017, 03:22.

Apr 28 2017

Cleanup on equations; JPG to be constructed.
31446e35b9b4
·DallasTrinkle on Apr 28 2017, 22:31.
Updates to pair/meam/spline documentation.
9bdc43bb66ee
·DallasTrinkle on Apr 28 2017, 22:15.
Updates to documentation: equation.
a0b61d17b56a
·DallasTrinkle on Apr 28 2017, 22:08.
Cleanup on pair_meam_spline.cpp
8cc844136709
·DallasTrinkle on Apr 28 2017, 21:53.
Addition of potential, code modifications to incorporate multicomponent spline…
7d9670bc6c48
·DallasTrinkle on Apr 28 2017, 21:48.

Apr 27 2017

rename files in GPU library from cg_cmm to lj_sdk
b8cb80b219b8
·Axel Kohlmeyer on Apr 27 2017, 01:46.
change references from cg_cmm to lj_sdk and from cmm to sdk
cd435c0c58fe
·Axel Kohlmeyer on Apr 27 2017, 01:44.
update the README for USER-CGSDK
548c589f82d3
·Axel Kohlmeyer on Apr 27 2017, 01:35.
rename USER-CG-CMM folder to USER-CGSDK
5c7a63198832
·Axel Kohlmeyer on Apr 27 2017, 01:29.
rename references to USER-CG-CMM to USER-CGSDK
af748745162c
·Axel Kohlmeyer on Apr 27 2017, 01:27.
rename examples folder for USER-CGSDK package
949d61e01eda
·Axel Kohlmeyer on Apr 27 2017, 01:26.

Apr 26 2017

remove cg/cmm style name aliases
3e60f79f1d62
·Axel Kohlmeyer on Apr 26 2017, 23:24.
correct units for some improper force constants in docs
8f9cb3590a32
·Axel Kohlmeyer on Apr 26 2017, 21:34.
Fixing auto_sync logic bug in modify_kokkos
0565b1df5f02
·Stan Moore on Apr 26 2017, 18:49.
Adding ubuf union to Kokkos atom_vec styles
d73d70fa1fdd
·Stan Moore on Apr 26 2017, 16:15.

Apr 25 2017

Merge branch 'master' into kokkos_update
cc6104aeaf32
·Stan Moore on Apr 25 2017, 22:11.
Updating Kokkos lib to 2.03.00
8910ec6e594c
·Stan Moore on Apr 25 2017, 21:48.
detect and refuse to run pair style srp together with fix rigid
ddc1e4e86ea7
·Axel Kohlmeyer on Apr 25 2017, 19:27.
make Python::init() method public and remove the now redundant Python::request…
2e1f8b4aefb7
·Axel Kohlmeyer on Apr 25 2017, 16:21.
Allow requesting Python interpreter without having to define a function just…
958f05a6f384
·Giacomo Fiorin on Apr 25 2017, 07:09.

Apr 23 2017

turn errors from manybody potentials for */tally computes into warnings
0ac22e034c2a
·Axel Kohlmeyer on Apr 23 2017, 03:50.

Apr 21 2017

avoid division by zero also for ewald/disp
197ce4580b29
·Axel Kohlmeyer on Apr 21 2017, 23:27.

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History
mastere03cc994673e6b43ef41368…