Diffusion lammps (master) History

lammps/lib
master60e14f14906c5b2914362c5…

Aug 10 2017

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.
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 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 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

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 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.

Jan 9 2017

add fix mscg command, example, lib
c31f1e9f2252
·Steve Plimpton on Jan 9 2017, 21:36.
Adding enable_lambda to KOKKOS_CUDA_OPTIONS
9250a55923ca
·Stan Moore on Jan 9 2017, 20:24.
Updating Kokkos lib
a9f0b7d523fa
·Stan Moore on Jan 9 2017, 18:39.

Dec 27 2016

Fix missing force with extended-Lagrangian mass
b0263e87bbaa
·Giacomo Fiorin on Dec 27 2016, 23:16.
Update Colvars library to version 2016-12-22
f553e230dbcb
·Giacomo Fiorin on Dec 27 2016, 19:17.
Fix seg fault for gyration collective variable
6ab716164b43
·Giacomo Fiorin on Dec 27 2016, 19:17.
Allow extended Lagrangian on non-scalar collective variables
7a45c72b9735
·Giacomo Fiorin on Dec 27 2016, 18:35.

Oct 24 2016

Make SMP parallelism for Colvars optional
182141b85005
·Giacomo Fiorin on Oct 24 2016, 23:13.
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.

Oct 19 2016

fix typos in Makefile.lammps for NetCDF support
019bc0ba0be2
·Axel Kohlmeyer on Oct 19 2016, 13:39.

Oct 18 2016

avoid distracting error output
27796b431ee5
·Axel Kohlmeyer on Oct 18 2016, 21:32.
update Makefile.lammps and add README according to suggestions by lars pastewka
2b47fa66533e
·Axel Kohlmeyer on Oct 18 2016, 21:05.
updated Makefile.lammps for NetCDF support based on suggestions from lars…
4502d3276be4
·Axel Kohlmeyer on Oct 18 2016, 20:45.

Oct 12 2016

import lammps-netcdf code as USER-NC-DUMP package
ecb03dd2dfda
·Axel Kohlmeyer on Oct 12 2016, 05:03.

Oct 8 2016

revert to previous style conventions for size_t constants
683689c80807
·Axel Kohlmeyer on Oct 8 2016, 17:00.
workaround for double free issue when using USER-COLVARS with lammps code…
e01e90eb965c
·Axel Kohlmeyer on Oct 8 2016, 16:45.

lammps/libmaster60e14f14906c5b2914362c5…

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lammps/lib
master60e14f14906c5b2914362c5…