Diffusion lammps (master) History

lammps/lib
masterd1bbe9546c026d1aea600e7…

Oct 20 2017

Merge branch 'master' into lammm-devel
d1bbe9546c02
·branch: lammm-devel
·junge on Oct 20 2017, 11:52.
final state cneuronet
1ebe65076d3b
·junge on Oct 20 2017, 11:33.
First time functional looking
eb9ef2452b83
·junge on Oct 20 2017, 11:30.
mostly tested, ready to go main
0683d7d23ba0
·junge on Oct 20 2017, 11:07.
Verified, yields identical results to pmd
a87e5f381f0d
·junge on Oct 20 2017, 11:03.

Oct 19 2017

Ryo's neuronet without Memory issues, not tested yet
545da2f40cea
·junge on Oct 19 2017, 17:46.
Import segfault fix in Colvars module
6e7504f15328
·Giacomo Fiorin on Oct 19 2017, 14:09.

Oct 13 2017

Update Colvars to version 2017-10-11
3e89b270fdf8
·Giacomo Fiorin on Oct 13 2017, 19:45.
Merge pull request #686 from giacomofiorin/lepton-library
18ca2292c28f
·Steve Plimpton / GitHub on Oct 13 2017, 17:48.

Oct 9 2017

Add Lepton library within lib/colvars
d90aad887eb6
·Giacomo Fiorin on Oct 9 2017, 21:25.
Update lib/kim for kim-api-v1.9.2
775a15b9da58
·Ryan S. Elliott on Oct 9 2017, 21:06.

Oct 6 2017

Merge pull request #677 from stanmoore1/kk_update
439c2fd980f8
·Steve Plimpton / GitHub on Oct 6 2017, 01:10.

Oct 3 2017

Update to Kokkos r2.04.04 and add workaround for performance regression
a55adf4a6848
·Stan Moore on Oct 3 2017, 19:30.

Sep 26 2017

having plain filelink instead of filelink.o confuses KOKKOS linking with nvcc
e6969002ce55
·Axel Kohlmeyer on Sep 26 2017, 01:37.

Sep 22 2017

Merge pull request #652 from junghans/latte
ee487ef4aa4f
·Steve Plimpton / GitHub on Sep 22 2017, 18:32.

Sep 21 2017

update fix latte examples and virial
a8ae8866676e
·Steve Plimpton on Sep 21 2017, 18:40.

Sep 20 2017

new SNAP potentials and examples
dd49d54889a2
·Steve Plimpton on Sep 20 2017, 16:54.
add .gitignore and add Makefile.lammps.* symlinks to stay consistent with other…
59d2e13d48fe
·Axel Kohlmeyer on Sep 20 2017, 01:06.
LATTE package doc update and some small code changes
ac897ea6457c
·Steve Plimpton on Sep 20 2017, 00:27.

Sep 19 2017

compile all objects in the GPU library with -fPIC for building shared object
be96486d6668
·Axel Kohlmeyer on Sep 19 2017, 17:24.
ignore generated header files with OpenCL kernels
48dd824b2601
·Axel Kohlmeyer on Sep 19 2017, 17:24.

Sep 16 2017

fix doc in lib/latte/Makefile.lammps.*
02665e45a400
·Christoph Junghans on Sep 16 2017, 01:52.
Merge remote-tracking branch 'origin/master' into latte
17aeccf19f3f
·Christoph Junghans on Sep 16 2017, 00:18.

Sep 14 2017

Fix small typo to calculation of accumulated work in Colvars
f1fce64ff9df
·Giacomo Fiorin on Sep 14 2017, 18:58.

Sep 12 2017

Merge pull request #647 from rbberger/gpu_opencl_2
f971cd6e4510
·Steve Plimpton / GitHub on Sep 12 2017, 18:56.
Merge pull request #643 from andeplane/gpu_opencl_compile_fix
e927794696f8
·Steve Plimpton / GitHub on Sep 12 2017, 18:31.

Sep 10 2017

Use OpenCL 2.x API in GPU package when supported
84b84c10db1b
·Richard Berger on Sep 10 2017, 01:53.

Sep 8 2017

Merge remote-tracking branch 'origin/master' into exaalt
2f6be88c4a4b
·Christoph Junghans on Sep 8 2017, 15:04.
merging stable and exaalt branches into exaaltstable
7b1542a0ba2b
·Richard Zamora on Sep 8 2017, 00:31.

Sep 6 2017

Fixed OpenCL compilation issues with __global keywords
dbc60d949f56
·Anders Hafreager on Sep 6 2017, 15:08.

Aug 23 2017

Merge branch 'master' into USER-DPD_kokkos
cbf3646806f9
·Stan Moore on Aug 23 2017, 23:20.
Merge pull request #629 from stanmoore1/kokkos_update
b6c93f96cfe0
·Steve Plimpton / GitHub on Aug 23 2017, 22:39.
correct embedded help for GPU lib Install.py
e88ff8d6f932
·Axel Kohlmeyer on Aug 23 2017, 21:20.

Aug 22 2017

Merge branch 'master' into USER-DPD_kokkos
5c985946d58f
·Stan Moore on Aug 22 2017, 21:50.
Update Kokkos library to v2.04.00
090c792d9070
·Stan Moore on Aug 22 2017, 21:42.

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

Merge branch 'master' into USER-DPD_kokkos as of patch 10Aug17
4041db8d1a74
·Tim Mattox on Aug 11 2017, 19:25.
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

Merge branch 'master' into USER-DPD_kokkos_testing
9695aa60925d
·Stan Moore on Jul 27 2017, 23:51.
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 25 2017

Merge branch 'master' into USER-DPD_kokkos_testing
bc446bb8b01b
·Stan Moore on Jul 25 2017, 20:12.

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.

lammps/libmasterd1bbe9546c026d1aea600e7…

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lammps/lib
masterd1bbe9546c026d1aea600e7…