Diffusion lammps (master) History

History
master4beccf508f9cd072e8ec346…

Sep 25 2017

Move fix to USER-MISH
4beccf508f9c
·Ulf R. Pedersen on Sep 25 2017, 18:35.

Sep 21 2017

Rename fix
fe8244c1c232
·Ulf R. Pedersen on Sep 21 2017, 16:49.
Added readme.m
3381a4337887
·Ulf R. Pedersen on Sep 21 2017, 16:20.
Added readme file, and removed old files
73708b091c42
·Ulf R. Pedersen on Sep 21 2017, 16:17.
Delete README
9a9af2ca5e67
·Ulf R. Pedersen / GitHub on Sep 21 2017, 13:58.
Added USER-PINNING package
491d5f341083
·Ulf R. Pedersen on Sep 21 2017, 11:38.

Sep 20 2017

Merge pull request #657 from lammps/snap-potentials
638b91bf74c1
·Steve Plimpton / GitHub on Sep 20 2017, 17:34.
whitespace cleanup
ad25a9529758
·Axel Kohlmeyer on Sep 20 2017, 17:13.
convert DOS/Windows CR-LF line endings to native format
e7d042ba1a0e
·Axel Kohlmeyer on Sep 20 2017, 17:12.
new SNAP potentials and examples
dd49d54889a2
·Steve Plimpton on Sep 20 2017, 16:54.
Merge pull request #655 from akohlmey/fixes-for-patch
fbaa7ab8fa55
·Steve Plimpton / GitHub on Sep 20 2017, 16:51.
Merge pull request #645 from akohlmey/kokkos-makefile-updates
2e9803efb31d
·Steve Plimpton / GitHub on Sep 20 2017, 16:40.

Sep 19 2017

correct USER-INTEL installer script for verlet_lrt_intel files
19f1f3a3e063
·Axel Kohlmeyer on Sep 19 2017, 17:48.
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.
reverse the pre-processor logic of the LRT mode define
cdb6ec7419d0
·Axel Kohlmeyer on Sep 19 2017, 17:24.
allow fix viscous to be used with dynamic groups
aad8cd10ffa2
·Axel Kohlmeyer on Sep 19 2017, 00:08.

Sep 18 2017

fix external only needs to collect virial in case it is requested
1ac90815f342
·Axel Kohlmeyer on Sep 18 2017, 05:59.
activate virial contribution in `fix lb/rigid/pc/sphere` by default and protect…
5f1842829e48
·Axel Kohlmeyer on Sep 18 2017, 03:10.
whether virial contributions from fixes are included depend on thermo_virial…
66130f555700
·Axel Kohlmeyer on Sep 18 2017, 02:50.
correctly initialize `thermo_virial` in fix poems and protect access to…
388eab5eebe5
·Axel Kohlmeyer on Sep 18 2017, 02:49.
remove bogus version of temper/npt command
a500048c9c4a
·Axel Kohlmeyer on Sep 18 2017, 01:25.
remove another couple of purge items from long ago
b4ecad7fbf5b
·Axel Kohlmeyer on Sep 18 2017, 01:22.
automatically call 'make purge' before calling 'make package-update' or 'make…
b5894e2190ca
·Axel Kohlmeyer on Sep 18 2017, 01:19.

Sep 16 2017

correct embarrassing typo
6f1935ea4058
·Axel Kohlmeyer on Sep 16 2017, 03:58.

Sep 15 2017

Merge pull request #649 from akohlmey/fix-virial-aidan
d101fe3e79fd
·Steve Plimpton / GitHub on Sep 15 2017, 23:25.
Merge pull request #654 from giacomofiorin/colvars-small-fix
27f99534ecc4
·Steve Plimpton / GitHub on Sep 15 2017, 23:22.
Merge pull request #653 from jdevemy/master
5f6937daddcb
·Steve Plimpton / GitHub on Sep 15 2017, 23:21.
Merge pull request #628 from lammps/cmake_improvements
3b39694f2386
·Steve Plimpton / GitHub on Sep 15 2017, 23:19.
add support for fix_modify virial yes to fix smd
99e5dc710461
·Axel Kohlmeyer on Sep 15 2017, 07:21.
correct cut-n-paste errors in the documentation of fix_modify virial
ccb67d8dc511
·Axel Kohlmeyer on Sep 15 2017, 07:20.
correct cut-n-paste error, add docs
2cd7cbd96415
·Axel Kohlmeyer on Sep 15 2017, 06:54.
add virial support to fix addforce
8776b8103337
·Axel Kohlmeyer on Sep 15 2017, 06:46.

Sep 14 2017

Fix small typo to calculation of accumulated work in Colvars
f1fce64ff9df
·Giacomo Fiorin on Sep 14 2017, 18:58.
Bugfix for the limit keyword
da7776f818b8
·Julien Devemy on Sep 14 2017, 11:00.

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 #644 from akohlmey/collected-small-fixes
0cb3a3821ffb
·Steve Plimpton / GitHub on Sep 12 2017, 18:31.
Merge pull request #643 from andeplane/gpu_opencl_compile_fix
e927794696f8
·Steve Plimpton / GitHub on Sep 12 2017, 18:31.
import changes to various fixes by aidan to include virial contributions
e196a2b9e54a
·Axel Kohlmeyer on Sep 12 2017, 04:24.
update src/.gitignore
cb19ef547e0d
·Axel Kohlmeyer on Sep 12 2017, 04:00.
the original fix qeq went away over 7 years ago, we don't need to purge it
95d849285345
·Axel Kohlmeyer on Sep 12 2017, 03:59.

Sep 11 2017

add infrastructure for enabling fixes to contribute to the virial by aidan
b3547a9eca79
·Axel Kohlmeyer on Sep 11 2017, 17:09.

Sep 10 2017

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

Sep 9 2017

cmake: added USER-MESO
0be7f4675083
·Christoph Junghans on Sep 9 2017, 16:25.
Merge remote-tracking branch 'origin/master' into cmake_improvements
4738fedca32f
·Christoph Junghans on Sep 9 2017, 16:22.
cmake: fix lib suffix
1601433ca1e5
·Christoph Junghans on Sep 9 2017, 15:05.
cmake: OpenCL is always found if required
3fdb6f10fac8
·Christoph Junghans on Sep 9 2017, 14:51.
Merge branch 'cmake_pkg_libs' into cmake_improvements
ff18cff46bfe
·Richard Berger on Sep 9 2017, 05:34.
Add OpenCL support to CMake build
8a06a7bc6bfe
·Richard Berger on Sep 9 2017, 04:20.

Sep 6 2017

update docs for changes to makefiles
366d08702780
·Axel Kohlmeyer on Sep 6 2017, 20:20.
have only one common MPI makefile for KOKKOS with CUDA
3a5d8362ffdc
·Axel Kohlmeyer on Sep 6 2017, 20:16.
make kokkos_cuda_mpi compatible with both MPICH and OpenMPI
5089b263b23a
·Axel Kohlmeyer on Sep 6 2017, 20:15.
recover ability to compile USER-INTEL without OpenMP enabled
de8297ea194b
·Axel Kohlmeyer on Sep 6 2017, 18:02.
fix typo in commands table
fe557cb882e2
·Axel Kohlmeyer on Sep 6 2017, 17:35.
Merge pull request #641 from lammps/doc-tweak
c80203cb0115
·Steve Plimpton / GitHub on Sep 6 2017, 16:52.
Merge pull request #640 from ohenrich/user-cgdna
4161868bcf69
·Steve Plimpton / GitHub on Sep 6 2017, 16:52.
Merge pull request #639 from rbberger/python_interface_improvements
9ca39c89a6a3
·Steve Plimpton / GitHub on Sep 6 2017, 16:51.
Merge pull request #632 from timattox/USER-DPD_kokkos_merge
99791ce01c09
·Steve Plimpton / GitHub on Sep 6 2017, 16:50.
remove duplicate listing of deleted USER-DPD files from Purge.list
0248a7b98e9e
·Tim Mattox on Sep 6 2017, 16:24.
Fixed OpenCL compilation issues with __global keywords
dbc60d949f56
·Anders Hafreager on Sep 6 2017, 15:08.

Sep 5 2017

fix syntax error in fix saed/vtk docs example
d886cc91f3b3
·Axel Kohlmeyer on Sep 5 2017, 23:45.
fix stupid typo (too much compiling of fortran codes...)
4c5d901e2b04
·Axel Kohlmeyer on Sep 5 2017, 22:45.
add a couple deleted files from USER-DPD to Purge.list
c8f92c1a617a
·Axel Kohlmeyer on Sep 5 2017, 22:42.
re-indent so that gcc no longer complains about inconsistent indentation
dec1d7b2dc48
·Axel Kohlmeyer on Sep 5 2017, 22:41.
fix another couple of typos
45602e58f99a
·Axel Kohlmeyer / GitHub on Sep 5 2017, 18:48.
fix typo
cd72532fb934
·Axel Kohlmeyer / GitHub on Sep 5 2017, 18:47.
Merge pull request #620 from amilumas/master
b1706060529b
·Steve Plimpton / GitHub on Sep 5 2017, 18:08.
Merge pull request #638 from jdevemy/master
65b295e826aa
·Steve Plimpton / GitHub on Sep 5 2017, 18:05.
small update to docs for new commands
89a0bc947f01
·Steve Plimpton on Sep 5 2017, 18:04.
Included hyperlink to package
c8967a335f26
·Oliver Henrich on Sep 5 2017, 12:45.
More minor changes
2105145f55e6
·Oliver Henrich on Sep 5 2017, 12:40.
Added comment about optimised damping coefficient for BD
f7715ab6ce3c
·Oliver Henrich on Sep 5 2017, 12:35.
Added sequence-dependent stacking and base-pairing strength
12fe614ddf58
·Oliver Henrich on Sep 5 2017, 11:48.
Add way of getting correct ctypes integer type for bigint, tagint, and imageint
0b5a2e199ddb
·Richard Berger on Sep 5 2017, 02:01.
Correct indentation
09bb687918e6
·Richard Berger on Sep 5 2017, 02:01.
Added optional numpy access to atom data
bb3ee752e5e9
·Richard Berger on Sep 5 2017, 01:59.
Add missing globals in library interface
6b2d321d1899
·Richard Berger on Sep 5 2017, 01:57.

Sep 1 2017

Merge branch 'master' of github.com:lammps/lammps
2b9646097c86
·Steve Plimpton on Sep 1 2017, 17:16.
patch 1Sep17
f58088ae619d
·Steve Plimpton on Sep 1 2017, 17:15.

Aug 31 2017

add temper/npt to src/USER-MISC/README
397bc225b27c
·Axel Kohlmeyer on Aug 31 2017, 20:56.
update .gitignore
d9d9ba824474
·Axel Kohlmeyer on Aug 31 2017, 20:52.
adapt formatting and naming conventions to fully match LAMMPS style. allow…
eba4be18c29a
·Axel Kohlmeyer on Aug 31 2017, 20:48.
add reference outputs to temper/npt example
4d2ed30b3526
·Axel Kohlmeyer on Aug 31 2017, 20:13.
fully integrate temper/npt command into manual
f3dda30f8ef3
·Axel Kohlmeyer on Aug 31 2017, 19:53.
Remove all thread fences except one in verlet_kokkos
d95a5f219e69
·Stan Moore on Aug 31 2017, 18:38.
Mods for extra/special/per/atom and add toluene
a5b65c1af48c
·Julien Devemy on Aug 31 2017, 15:03.

Aug 30 2017

USER-DPD: finish renaming #ifdef DEBUG_PAIR_CT to DEBUG_SSA_PAIR_CT
3e6cdd140011
·Tim Mattox on Aug 30 2017, 21:58.
USER-DPD: Kokkos version of Const Temperature DPD isn't implemented yet
dc7f1281b832
·Tim Mattox on Aug 30 2017, 18:01.
link cuda in gpu only, remove duplicated incl. dir
27c962dc3b81
·Christoph Junghans on Aug 30 2017, 17:45.
USER-DPD: remove some out-of-date FIXME comments in fix_shardlow_kokkos.cpp
2dd202cc761d
·Tim Mattox on Aug 30 2017, 17:34.
Rename SSA specific debug #ifdef to DEBUG_SSA_PAIR_CT
f2d8c37f27b1
·Tim Mattox on Aug 30 2017, 17:24.
Remove unnecessary check in npair_kokkos
a4a45f1d9cfb
·Stan Moore on Aug 30 2017, 01:25.

Aug 29 2017

Add files via upload
f57d19492051
·Amulya / GitHub on Aug 29 2017, 16:40.
Fix GPU CMake compilation
34b3fc21572c
·Richard Berger on Aug 29 2017, 07:20.
SOVERSION not needed for STATIC libs
098861375bf0
·Christoph Junghans on Aug 29 2017, 00:18.

Aug 28 2017

fix Fortran flags for MEAM
19b77857dc3e
·Christoph Junghans on Aug 28 2017, 22:59.
cmake: README is markdown
bd9dc4886d89
·Christoph Junghans on Aug 28 2017, 22:27.
fix liblammps install
9207f6540e84
·Christoph Junghans on Aug 28 2017, 22:11.
Merge branch 'master' (21893539cb Aug 25) into USER-DPD_kokkos_merge
736e063971bc
·Tim Mattox on Aug 28 2017, 21:46.
make GPU flags local to libgpu
62928a16377b
·Christoph Junghans on Aug 28 2017, 21:24.

Historymaster4beccf508f9cd072e8ec346…

Sep 25 2017

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Sep 18 2017

Sep 16 2017

Sep 15 2017

Sep 14 2017

Sep 12 2017

Sep 11 2017

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Sep 9 2017

Sep 6 2017

Sep 5 2017

Sep 1 2017

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Aug 28 2017

History
master4beccf508f9cd072e8ec346…