Diffusion lammps (master) History

lammps/lib
master1f4c550f9fab00198f687af…

Aug 17 2017

Merge pull request #612 from giacomofiorin/colvars-update-2017-08-10
c46d5ff422c2
·Steve Plimpton / GitHub on Aug 17 2017, 19:32.
Merge pull request #601 from stanmoore1/kokkos_update
dd67989c7675
·Steve Plimpton / GitHub on Aug 17 2017, 19:32.
Merge pull request #597 from ndtrung81/three-body-short-nlist
00aafef1a851
·Steve Plimpton / GitHub on Aug 17 2017, 19:31.

Aug 11 2017

make download function more resilient by also catching failed execution
c6d923b6c889
·Axel Kohlmeyer on Aug 11 2017, 03:15.
whitespace cleanup
6d24be8bb70f
·Axel Kohlmeyer on Aug 11 2017, 03:14.

Aug 10 2017

More robust change from initial to target restraint centers in Colvars
da01be7c1857
·Giacomo Fiorin on Aug 10 2017, 15:22.
fall back to wget when curl is not available
146aa4cdbdd3
·Axel Kohlmeyer on Aug 10 2017, 15:05.
we need to override compiler flags in lib/voronoi/Install.py
2f3747eb6e6c
·Axel Kohlmeyer on Aug 10 2017, 14:34.
avoid writable string and deprecated implicit conversion warning
2bc6ad80d404
·Axel Kohlmeyer on Aug 10 2017, 13:45.

Aug 9 2017

restore mpic++ makefile to resolve regression test failure
6780c7390736
·Axel Kohlmeyer on Aug 9 2017, 13:10.

Aug 8 2017

remove attempts to use urllib and use curl for all downloading. restore…
b7b1257b0146
·Axel Kohlmeyer on Aug 8 2017, 23:00.
rework Install.py for gpu library. make it consistent with other lib folders…
30431d4edb77
·Axel Kohlmeyer on Aug 8 2017, 22:57.
Remove redundant check in Makefile.kokkos
8a7a831bd6c0
·Stan Moore on Aug 8 2017, 20:57.
update README file for lib/mscg
c53a84a967c0
·Axel Kohlmeyer on Aug 8 2017, 19:55.
add local makefile overrides to be compatible with standard suffixes
d2b0c287d26e
·Axel Kohlmeyer on Aug 8 2017, 19:19.
more lib compilation updates
b3244f9c9807
·Axel Kohlmeyer on Aug 8 2017, 13:20.

Aug 7 2017

more lib installation cleanup
8bba29d91e11
·Axel Kohlmeyer on Aug 7 2017, 23:21.
revamp of library builds
135b1650f11c
·Axel Kohlmeyer on Aug 7 2017, 23:13.

Aug 4 2017

update .gitignore
163ed276181a
·Axel Kohlmeyer on Aug 4 2017, 22:10.
more updates to kim/Install.py to restore missing functionality and align with…
23ca0099f7ab
·Axel Kohlmeyer on Aug 4 2017, 20:47.

Jul 31 2017

Remove tpls directory
8431ca5fecbc
·Stan Moore on Jul 31 2017, 18:54.
Update Kokkos library to v2.03.13
13f2d39f55b1
·Stan Moore on Jul 31 2017, 18:34.

Jul 28 2017

update and automate the QUIP configuration so that no environment variables are…
9bfd9267fabb
·Axel Kohlmeyer on Jul 28 2017, 22:11.
remove tarball after unpacking
3ebf561e0dea
·Axel Kohlmeyer on Jul 28 2017, 20:25.
make Install.py for lib/smd and lib/voronoi consistent
ffb778cf9b25
·Axel Kohlmeyer on Jul 28 2017, 20:03.
clean up makefiles provide "serial" and "mpi" targets for atc and awpmd
f3850da9fe9d
·Axel Kohlmeyer on Jul 28 2017, 19:36.
Merge branch 'kim-install' into install-and-docs-reviewed
e7d9aabca6ba
·Axel Kohlmeyer on Jul 28 2017, 17:25.

Jul 27 2017

correct symbolic links to shared Install.py file
c494ec35e242
·Axel Kohlmeyer on Jul 27 2017, 18:48.
python3 port, yet untested
acf6d54ec170
·Axel Kohlmeyer on Jul 27 2017, 15:25.
fix typo
0427f6205ec5
·Axel Kohlmeyer on Jul 27 2017, 15:25.
Merge branch 'kim-install' into install-and-docs-reviewed
da7a5f55d3e4
·Axel Kohlmeyer on Jul 27 2017, 01:32.

Jul 26 2017

simplify Install.py for voronoi
715c797df051
·Axel Kohlmeyer on Jul 26 2017, 21:14.
convert copies of Install.py files to symlinks
fd6e11f8217a
·Axel Kohlmeyer on Jul 26 2017, 20:29.
convert explicit copies back into symbolic links
f7a243a4d9ee
·Axel Kohlmeyer on Jul 26 2017, 20:20.
must not include system headers within 'extern "C"' blocks. breaks with MPICH
f0d286358ea0
·Axel Kohlmeyer on Jul 26 2017, 20:02.

Jul 23 2017

Cleaned up 3-body kernels, reverted some mistaken changes to vashishta
aa60ef6ed8cf
·Trung Nguyen on Jul 23 2017, 07:08.
Enabled again neigh no with tpa > 1 for 3-body gpu styles for backward…
a71f5a0c20f7
·Trung Nguyen on Jul 23 2017, 05:57.

Jul 21 2017

Cleaned up 3-body gpu styles, and fixed a bug for tersoff/zbl/gpu. There is a…
3d1d0c58c732
·Trung Nguyen on Jul 21 2017, 19:08.

Jul 20 2017

Merge branch 'colvars-safer-makefiles' of https://github.
1b704bab18ba
·Axel Kohlmeyer on Jul 20 2017, 21:59.
Change order of targets in Makefiles for Colvars
c98f6140e755
·Giacomo Fiorin on Jul 20 2017, 21:49.
Comment out use by Colvars of Makefile.lammps from other packages
5031f5b8079c
·Giacomo Fiorin on Jul 20 2017, 21:48.
README clarification from giacomo
9d0d90c03860
·Axel Kohlmeyer on Jul 20 2017, 21:25.
avoid makefile failure, if LAMMPS has not been configured yet
66154e8a8b31
·Axel Kohlmeyer on Jul 20 2017, 21:05.
Refactor lib/kim/Install.py; works with phtyon 3 2.7
84065dde2112
·Ryan S. Elliott on Jul 20 2017, 19:02.
Detect number of processors for make
ef9fb944c727
·Giacomo Fiorin on Jul 20 2017, 16:53.
Add forgotten decode() in Install.py
187a80be7738
·Giacomo Fiorin on Jul 20 2017, 04:21.

Jul 19 2017

restore python3 support. this now can run with python 2.7.13 and 3.5.3.
355aad969166
·Axel Kohlmeyer on Jul 19 2017, 23:19.
Update Colvars to version 2017-07-15 and support automated builds for it
ee6cac826e65
·Giacomo Fiorin on Jul 19 2017, 20:24.
Update lib/kim/Install.py for phthon 2.7 conversion
f181a0bfabbb
·Ryan S. Elliott on Jul 19 2017, 19:54.
fix variable name bug and synchronize with other ported Install.py files
81f342aafa23
·Axel Kohlmeyer on Jul 19 2017, 00:06.

Jul 18 2017

port USER-SMD folder. make voronoi consistent with it
7ccb0d37cdd6
·Axel Kohlmeyer on Jul 18 2017, 23:37.
ported lib/voronoi/Install.py to python 3.x and tested with 2.7
03cd4c525557
·Axel Kohlmeyer on Jul 18 2017, 23:16.

Jul 15 2017

Make KIM Install.py Python 3 compatible
d7355801dff5
·Richard Berger on Jul 15 2017, 19:03.
better Install.py script for KIM from Ryan Elliott
296e572e6998
·Steve Plimpton on Jul 15 2017, 00:25.

Jul 11 2017

Built 3-body short neighbor list for the 3-body kernels using per-pair cutoffs…
cdac5f496c53
·Trung Nguyen on Jul 11 2017, 07:13.
Built 2-body short neighbor list and used for 2-body kernels in tersoff gpu…
8c9db3ea0010
·Trung Nguyen on Jul 11 2017, 06:50.
Fixed shebang and renamed to lib/kim/Install.py
e30c5fc9560c
·Ryan S. Elliott on Jul 11 2017, 04:05.
Updated lib/kim/README file to go along with new install.py
c29e8fba9bd0
·Ryan S. Elliott on Jul 11 2017, 00:00.

Jul 10 2017

Finalized code for lib/kim/install.py
8d592f4b9e43
·Ryan S. Elliott on Jul 10 2017, 23:43.

Jul 9 2017

Refactored 3-body gpu styles to remove code duplication
ea2b01e83b91
·Trung Nguyen on Jul 9 2017, 03:17.

Jul 8 2017

Added short neighbor list implementation for tersoff/zbl/gpu and tersoff/mod/gpu
34fe2273f64b
·Trung Nguyen on Jul 8 2017, 21:59.
Minor cleanups for tersoff/gpu
77c60189b8cd
·Trung Nguyen on Jul 8 2017, 21:43.
Working on short neighbor list for tersoff/gpu
1c6533e53df2
·Trung Nguyen on Jul 8 2017, 21:15.

Jul 7 2017

Supported short neighbor lists for 3-body kernels in sw/gpu and vashishta/gpu
68206079da39
·Trung Nguyen on Jul 7 2017, 23:47.

Jul 6 2017

Further work on lib/kim/install.py
b0be8b24eac9
·Ryan S. Elliott on Jul 6 2017, 22:50.
Add install.py and update config for kim lib
16fc2d6fe179
·Ryan S. Elliott on Jul 6 2017, 22:49.

Jun 15 2017

Merge pull request #510 from akohlmey/collected-small-changes
d3c90f3c14dd
·sjplimp / GitHub on Jun 15 2017, 19:12.
Merge pull request #526 from andeplane/vashishta_gpu
7227bc415d00
·sjplimp / GitHub on Jun 15 2017, 16:52.

Jun 14 2017

Fixed opencl error
d7646aeeed78
·Anders Hafreager on Jun 14 2017, 12:03.
Removed debug output
5f9341813ddf
·Anders Hafreager on Jun 14 2017, 10:57.
Removed non-general CUDA-dir in makefile
8441307185f1
·Anders Hafreager on Jun 14 2017, 10:28.
Added vashishta to OpenCL makefile
720af5c3607f
·Anders Hafreager on Jun 14 2017, 10:27.
Added vashishta GPU package for NVidia
eeff0b863323
·Anders Hafreager on Jun 14 2017, 10:24.

Jun 8 2017

fix uninitialized data access as reported by @martok in #174
0ecdb998856b
·Axel Kohlmeyer on Jun 8 2017, 19:50.
Remove tpls dir
00ce15d043fa
·Stan Moore on Jun 8 2017, 18:43.
Updating Kokkos lib to v2.03.05
5c1d17d1c031
·Stan Moore on Jun 8 2017, 18:42.

May 6 2017

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

May 4 2017

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.

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.

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.

Apr 18 2017

whitespace cleanup in VMD plugin headers
25e8ed63a236
·Axel Kohlmeyer on Apr 18 2017, 17:46.
update VMD molfile plugin headers and move them to lib/molfile (where they…
dee353614420
·Axel Kohlmeyer on Apr 18 2017, 17:42.

Apr 14 2017

correct logic bug in else branch of the conditional
3cbf4f3b5812
·Axel Kohlmeyer on Apr 14 2017, 17:57.
pass the name of the python interpreter compatible with the python package to…
6c2dd7ebb17c
·Axel Kohlmeyer on Apr 14 2017, 17:44.

Apr 12 2017

Add Python 3 compatibility to PYTHON package
9a027a01daf8
·Richard Berger on Apr 12 2017, 02:24.

Apr 11 2017

fix gcmc updates from Aidan, trimming of output for replica commands
49dd9449b875
·Steve Plimpton on Apr 11 2017, 16:35.

Mar 10 2017

Update Colvars module to version 2017-03-10
5fe620663813
·Giacomo Fiorin on Mar 10 2017, 15:16.

Mar 6 2017

Spelling fixes in source files
e261bef7bba7
·Richard Berger on Mar 6 2017, 00:30.

Feb 13 2017

Add missing flags to Kokkos Makefile
90e5ae965d7f
·Stan Moore on Feb 13 2017, 19:19.
Remove merge line
33af7ab24874
·Stan Moore on Feb 13 2017, 18:59.
Removing unused files in Kokkos lib
8f9b2aca06e7
·Stan Moore on Feb 13 2017, 18:53.
Updating Kokkos lib
383da816c221
·Stan Moore on Feb 13 2017, 18:50.

Jan 17 2017

Merge pull request #327 from stanmoore1/kokkos_lib_update
d8bc590aaf1f
·sjplimp / GitHub on Jan 17 2017, 17:04.

Jan 10 2017

Squelching output from Makefile
7162cafdf5a5
·Stan Moore on Jan 10 2017, 22:46.
Fixing Kokkos CUDA Makefile issue
ee9e7cfbd5e3
·Stan Moore on Jan 10 2017, 21:22.
Fixing compile error with Kokkos CUDA Makefiles
7839c335da14
·Stan Moore on Jan 10 2017, 21:05.

lammps/libmaster1f4c550f9fab00198f687af…

Aug 17 2017

Aug 11 2017

Aug 10 2017

Aug 9 2017

Aug 8 2017

Aug 7 2017

Aug 4 2017

Jul 31 2017

Jul 28 2017

Jul 27 2017

Jul 26 2017

Jul 23 2017

Jul 21 2017

Jul 20 2017

Jul 19 2017

Jul 18 2017

Jul 15 2017

Jul 11 2017

Jul 10 2017

Jul 9 2017

Jul 8 2017

Jul 7 2017

Jul 6 2017

Jun 15 2017

Jun 14 2017

Jun 8 2017

May 6 2017

May 4 2017

Apr 27 2017

Apr 25 2017

Apr 18 2017

Apr 14 2017

Apr 12 2017

Apr 11 2017

Mar 10 2017

Mar 6 2017

Feb 13 2017

Jan 17 2017

Jan 10 2017

lammps/lib
master1f4c550f9fab00198f687af…