Diffusion lammps (master) History

History
master89a0bc947f01a1abe9d0a49…

Sep 5 2017

small update to docs for new commands
89a0bc947f01
·Steve Plimpton on Sep 5 2017, 18:04.

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 26 2017

Merge pull request #633 from lammps/doc-user-meso
21893539cbca
·Steve Plimpton / GitHub on Aug 26 2017, 01:41.
Merge pull request #582 from stanmoore1/kk_changes
dd101db79ced
·Steve Plimpton / GitHub on Aug 26 2017, 01:06.
tweak an eq in USER-MESO, also allow neigh to be built w/out styles
81ba181349d7
·Steve Plimpton on Aug 26 2017, 01:04.

Aug 24 2017

Merge pull request #631 from akohlmey/small-fixes-and-updates
6195b3c0f6d6
·Steve Plimpton / GitHub on Aug 24 2017, 16:35.
moltemplate bugfix update
de0fdbed6c92
·Axel Kohlmeyer on Aug 24 2017, 13:12.
print write dump systen init warning only on MPI rank 0
dea92fbf5221
·Axel Kohlmeyer on Aug 24 2017, 03:01.

Aug 23 2017

correct typo in header formatting
6db3bd87ee73
·Axel Kohlmeyer on Aug 23 2017, 23:52.
Merge pull request #629 from stanmoore1/kokkos_update
b6c93f96cfe0
·Steve Plimpton / GitHub on Aug 23 2017, 22:39.
Merge pull request #624 from akohlmey/compute-fragment
7b7a5076d00a
·Steve Plimpton / GitHub on Aug 23 2017, 22:14.
Merge pull request #630 from akohlmey/moltemplate-update
1536eb5de549
·Steve Plimpton / GitHub on Aug 23 2017, 22:13.
Merge pull request #622 from akohlmey/collected-small-fixes
f7a0a6eb7069
·Steve Plimpton / GitHub on Aug 23 2017, 22:12.
Merge pull request #621 from lammps/user-meso
d80a6cbd317a
·Steve Plimpton / GitHub on Aug 23 2017, 22:12.
Merge pull request #619 from jrgissing/molecule_maxspecial
c4b37039ab88
·Steve Plimpton / GitHub on Aug 23 2017, 22:11.
add compatibility to NetCDF 4.3.3 as bundled with RHEL 7.x
b52efa28507f
·Axel Kohlmeyer on Aug 23 2017, 21:28.
correct embedded help for GPU lib Install.py
e88ff8d6f932
·Axel Kohlmeyer on Aug 23 2017, 21:20.
update fix qeq docs for the new, more flexible parameter file format
97edf90a7389
·Axel Kohlmeyer on Aug 23 2017, 17:22.
add moltemplate version 2017-8-22
12150ffa7397
·Axel Kohlmeyer on Aug 23 2017, 13:54.
remove old moltemplate version
57aafba7c3bd
·Axel Kohlmeyer on Aug 23 2017, 13:54.
make links unique, fix doc format warnings and add entries to administrative…
cdfb1aa04375
·Axel Kohlmeyer on Aug 23 2017, 06:39.
restore changes to read_data docs, that would have been lost due to merging an…
b80752a40c56
·Axel Kohlmeyer on Aug 23 2017, 06:01.
fix issues indicated by compiler warnings
79d5ca669dcb
·Axel Kohlmeyer on Aug 23 2017, 05:46.
add USER-MESO files to .gitignore
26c15140be20
·Axel Kohlmeyer on Aug 23 2017, 05:46.

Aug 22 2017

Update Kokkos library to v2.04.00
090c792d9070
·Stan Moore on Aug 22 2017, 21:42.

Aug 21 2017

fix typo
24c00b1f7a20
·Axel Kohlmeyer on Aug 21 2017, 19:12.
add a compute aggregate/atom, that combines the rules for compute cluster/atom…
5a0c3aea8ac1
·Axel Kohlmeyer on Aug 21 2017, 19:12.
add initializers for nmatch/nwant variables in molecule file parser
d1a0c040c9f8
·Axel Kohlmeyer on Aug 21 2017, 05:28.

Aug 20 2017

remove non-portable non-ascii blanks from fix wall/ees docs
f5b8f722eee3
·Axel Kohlmeyer on Aug 20 2017, 16:09.
add missing entry in pdf manual
39e51df2c004
·Axel Kohlmeyer on Aug 20 2017, 16:02.
skip over disabled bonds
c895df73d624
·Axel Kohlmeyer on Aug 20 2017, 15:49.
add docs for compute fragment/atom
4dc1195cd851
·Axel Kohlmeyer on Aug 20 2017, 15:41.
trim unneeded includes
35fd82b60282
·Axel Kohlmeyer on Aug 20 2017, 15:19.
use list of bonds per atom instead of bondlist, as that will work with shake as…
c5ce3ffe60e4
·Axel Kohlmeyer on Aug 20 2017, 15:18.

Aug 19 2017

more cleanup, checks and generalization of QEQ parameter file parsing
aa1ce09b1264
·Axel Kohlmeyer on Aug 19 2017, 02:03.
new USER-MESO package
f945d4567d4f
·Steve Plimpton on Aug 19 2017, 01:33.
add checks when reading QEQ parameter file to avoid segfaults and memory…
44ccdb86df24
·Axel Kohlmeyer on Aug 19 2017, 01:24.
ignore file recently added to USER-INTEL
2e6a928aa315
·Axel Kohlmeyer on Aug 19 2017, 01:23.
add new compute fragment/atom
6f66e6c45445
·Axel Kohlmeyer on Aug 19 2017, 01:07.

Aug 18 2017

whitespace cleanup
d671a04274f9
·Axel Kohlmeyer on Aug 18 2017, 20:24.
allocate the temporary special array on the heap and not the stack (it may get…
bf7cff73d42a
·Axel Kohlmeyer on Aug 18 2017, 20:23.
molecule maxspecial value corrected when specials autogenerated
9e85b3178a14
·jrgissing on Aug 18 2017, 05:39.
Merge pull request #573 from junghans/cmake
b11fe2eddb93
·Steve Plimpton / GitHub on Aug 18 2017, 00:06.
patch 17Aug17
7ddcb6812b44
·Steve Plimpton on Aug 18 2017, 00:02.

Aug 17 2017

Merge pull request #613 from akohlmey/collected-small-changes
76cd61350d4c
·Steve Plimpton / GitHub on Aug 17 2017, 19:34.
Merge pull request #618 from lammps/intel
fa3c0c61d6a8
·Steve Plimpton / GitHub on Aug 17 2017, 19:32.
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 16 2017

flag more pair styles as supporting USER-INTEL to match newly added code
7175abcc7170
·Axel Kohlmeyer on Aug 16 2017, 19:58.
Fix a couple of typos in the docs
e34b20405c28
·Axel Kohlmeyer / GitHub on Aug 16 2017, 03:10.
USER-INTEL add-ons from Mike
1d4d2155a23b
·Steve Plimpton on Aug 16 2017, 01:12.

Aug 15 2017

update manual to point to packages.lammps.org instead of rpm.lammps.org
cee87d7a54b5
·Axel Kohlmeyer on Aug 15 2017, 22:19.

Aug 14 2017

add comment to msi2lmp README about symmetry limitations
60e14f14906c
·Axel Kohlmeyer on Aug 14 2017, 14:54.

Aug 12 2017

fix incorrect preprocessor define for windows
81e7d4a94259
·Axel Kohlmeyer on Aug 12 2017, 06:35.

Aug 11 2017

patch 11Aug17
0b3f1b8a156d
·Steve Plimpton on Aug 11 2017, 20:19.
Merge pull request #614 from akohlmey/fixes-for-stable
b209a4e246b5
·Steve Plimpton / GitHub on Aug 11 2017, 16:35.
fix bug with pair_modify <style> compute not triggering the correct global…
27553283c30e
·Axel Kohlmeyer on Aug 11 2017, 14:28.
trigger relink after package library build through updating the time stamp on…
df56b2d6a43a
·Axel Kohlmeyer on Aug 11 2017, 14:16.
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.
patch 10Aug17
52bec0f380dd
·Steve Plimpton on Aug 11 2017, 00:44.

Aug 10 2017

add automatic triggering of review requests with a code owners file
8c16ea1bfca5
·Axel Kohlmeyer on Aug 10 2017, 21:58.
remove special_bonds extra keyword and refer to read_data and create_box instead
c8741f3a01a2
·Axel Kohlmeyer on Aug 10 2017, 21:12.
add more strict checking of data when parsing molecule files to detect format…
2a7d2dee3652
·Axel Kohlmeyer on Aug 10 2017, 20:49.
Merge pull request #611 from akohlmey/final-tweaks
f68c6254d48d
·Steve Plimpton / GitHub on Aug 10 2017, 16:02.
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.
add some remarks about makefile settings on windows
f9a515efd37d
·Axel Kohlmeyer on Aug 10 2017, 13:24.
fix a header line formatting issue
5b557442093c
·Axel Kohlmeyer on Aug 10 2017, 13:21.
Revert "remove -DLAMMPS_MEMALIGN from "make mpi" and "make serial" for…
0dc3cbaa8acc
·Axel Kohlmeyer on Aug 10 2017, 12:51.
when recomputing special bonds, make certain we do not shrink atom->maxspecial…
ce62c41252f6
·Axel Kohlmeyer on Aug 10 2017, 12:47.
remove -DLAMMPS_MEMALIGN from "make mpi" and "make serial" for increased…
4e97b5750873
·Axel Kohlmeyer on Aug 10 2017, 11:46.
Merge pull request #609 from akohlmey/doc-changes-for-stable
7f437d769036
·Steve Plimpton / GitHub on Aug 10 2017, 01:37.
make the deprecation warning nicer looking
77a628e4effe
·Axel Kohlmeyer on Aug 10 2017, 01:13.
correctly use the term CUDA (instead of Cuda) when not referring to the KOKKOS…
f01103dd0885
·Axel Kohlmeyer on Aug 10 2017, 01:08.
rework section 4 (Packages) in the manual to match Install.py scripts
81f4d7ecb535
·Axel Kohlmeyer on Aug 10 2017, 01:07.

Aug 9 2017

add a deprecation warning to pair style meam and make the reax one consistent…
210a77c5a0ea
·Axel Kohlmeyer on Aug 9 2017, 22:36.
Added references to GPU package citations
3e9b41c6b74d
·Trung Nguyen on Aug 9 2017, 17:09.
restore mpic++ makefile to resolve regression test failure
6780c7390736
·Axel Kohlmeyer on Aug 9 2017, 13:10.
updated comment for fix neb by steve
be25a7d9a424
·Axel Kohlmeyer on Aug 9 2017, 02:37.
Merge pull request #607 from akohlmey/final-changes-for-stable
691d1b730dce
·Steve Plimpton / GitHub on Aug 9 2017, 01:26.

Aug 8 2017

consistently use $(PYTHON) in the master makefile (which defaults to "python")
95ece8a6c01c
·Axel Kohlmeyer on Aug 8 2017, 23:03.
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.
do not pollute global namespace by including mscg header in fix header
b7b62f6893c2
·Axel Kohlmeyer on Aug 8 2017, 19:20.
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.
Merge pull request #600 from akohlmey/install-and-docs-reviewed
0a54c34e34c2
·Steve Plimpton / GitHub on Aug 7 2017, 16:02.
Merge pull request #605 from rbberger/bash_on_windows
a8f6a95cba50
·Steve Plimpton / GitHub on Aug 7 2017, 16:00.
Adds BOW tutorial link in main menu
e0f9a7c34c39
·Richard Berger on Aug 7 2017, 06:06.
Added tutorial for using LAMMPS in Bash on Windows
aaf17bde3ff9
·Richard Berger on Aug 7 2017, 06:06.

Aug 5 2017

Merge pull request #55 from GarrettTow/patch-1
5ad8a3332dfc
·Axel Kohlmeyer / GitHub on Aug 5 2017, 01:18.

Historymaster89a0bc947f01a1abe9d0a49…

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Aug 5 2017

History
master89a0bc947f01a1abe9d0a49…