Diffusion lammps (master) History

History
masterb209a4e246b5b6057d95e78…

Aug 11 2017

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

Merge pull request #611 from akohlmey/final-tweaks
f68c6254d48d
·Steve Plimpton / GitHub on Aug 10 2017, 16:02.
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.
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.
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.

Aug 4 2017

Fixed typo in "compute_voronoi_atom.txt"
ca7a3a6316dd
·GarrettTow / GitHub on Aug 4 2017, 23:48.
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.
correct a link and a name for OpenKIM
59ac6ef57357
·Axel Kohlmeyer on Aug 4 2017, 17:19.
make overlapping links to references unique to avoid anchor label errors
2fa16bcd4ca9
·Axel Kohlmeyer on Aug 4 2017, 17:11.
Merge pull request #602 from rbberger/pylammps_fixes
e84b6d806704
·sjplimp / GitHub on Aug 4 2017, 16:35.

Jul 31 2017

Add missing link flag
96d37128170f
·Richard Berger on Jul 31 2017, 23:52.
Update tutorial_pylammps.txt
b395ef00b446
·Richard Berger on Jul 31 2017, 23:50.
Remove Make.py reference in PyLammps examples
d3169eeab3e7
·Richard Berger on Jul 31 2017, 21:56.
Fix PyLammps regression after output.cpp change
71553cf7328e
·Richard Berger on Jul 31 2017, 21:53.

Jul 28 2017

update and automate the QUIP configuration so that no environment variables are…
9bfd9267fabb
·Axel Kohlmeyer on Jul 28 2017, 22:11.
add reference outputs for QUIP/GAP example
7d0d701eaf09
·Axel Kohlmeyer on Jul 28 2017, 22:05.
remove unused variable
841a92c7fada
·Axel Kohlmeyer on Jul 28 2017, 22:03.
update QUIP examples to closer match typical LAMMPS examples
85120842dd84
·Axel Kohlmeyer on Jul 28 2017, 21:20.
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

fix bug in power operator in LAMMPS variable expressions
e3973796bacc
·Axel Kohlmeyer on Jul 27 2017, 21:51.
correct symbolic links to shared Install.py file
c494ec35e242
·Axel Kohlmeyer on Jul 27 2017, 18:48.
Merge pull request #599 from lammps/kim-doc
6d0a2286240a
·sjplimp / GitHub on Jul 27 2017, 18:34.
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 remote-tracking branch 'github/kim-doc' into install-and-docs-reviewed
72419b631313
·Axel Kohlmeyer on Jul 27 2017, 01:35.
Merge branch 'kim-install' into install-and-docs-reviewed
da7a5f55d3e4
·Axel Kohlmeyer on Jul 27 2017, 01:32.
restore lost KIM doc section in Section packages
934cbbbecaff
·Steve Plimpton on Jul 27 2017, 00:07.

Jul 26 2017

Merge pull request #598 from akohlmey/last-minute-changes
2806f070a40f
·sjplimp / GitHub on Jul 26 2017, 23:46.
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.
avoid invalid calls to memcpy(): when ndot == 0, pointers may be NULL
51a06334ad84
·Axel Kohlmeyer on Jul 26 2017, 18:08.
avoid integer overflow and remove unused function argument causing it
aa5ea95a0f34
·Axel Kohlmeyer on Jul 26 2017, 17:55.
import updated fix msst file with some additional cleanup and simplification
60c67b07dc37
·Axel Kohlmeyer on Jul 26 2017, 16:45.

Jul 24 2017

patch 24Jul17
a59b7e4d5647
·Steve Plimpton on Jul 24 2017, 17:09.
Merge pull request #594 from junghans/license
2eaea2d274e5
·sjplimp / GitHub on Jul 24 2017, 16:56.
Merge pull request #595 from libAtoms/idces2quip
1ddace4dba51
·sjplimp / GitHub on Jul 24 2017, 16:55.
Merge pull request #593 from akohlmey/collected-bug-fixes-and-small-updates
af3d0ca381dd
·sjplimp / GitHub on Jul 24 2017, 16:54.

Jul 23 2017

avoid floating point overflows in iterative solvers of fix shake
c24e316baaa6
·Axel Kohlmeyer on Jul 23 2017, 05:15.
avoid reporting negative memory allocation when memory_usage() is called before…
2c6e177d5c55
·Axel Kohlmeyer on Jul 23 2017, 05:14.

Jul 22 2017

disallow binary output with dump style local. fixes #596
7b2182833fea
·Axel Kohlmeyer on Jul 22 2017, 16:35.
Clarified some points in in.molecular example
1afab981b022
·Max Veit on Jul 22 2017, 15:40.
Update in.molecular
1af937e99d71
·Axel Kohlmeyer / GitHub on Jul 22 2017, 04:00.
Add a (contrived) molecular example for USER-QUIP
4e0a249e2779
·Max Veit on Jul 22 2017, 02:33.
LICENSE: update address of Free Software Foundation
edc756a65f76
·Christoph Junghans on Jul 22 2017, 01:13.

Jul 21 2017

add support for trapping floating point exception as an optional compile time…
a477f26477fa
·Axel Kohlmeyer on Jul 21 2017, 21:37.
update readme for examples
b1b399d5c3dd
·Axel Kohlmeyer on Jul 21 2017, 21:06.
handle one more case where allowing shifted potential with cutoff 0.0 would…
00474ab09dcd
·Axel Kohlmeyer on Jul 21 2017, 16:30.
correct typo in USER-REAXC code
733ea61bf107
·Axel Kohlmeyer on Jul 21 2017, 07:15.
Merge pull request #592 from akohlmey/reaxc-bugfix
5c13b087e4a1
·sjplimp / GitHub on Jul 21 2017, 00:26.
fix reaxc division by zero bug also for USER-OMP variant
ec23aef20b22
·Axel Kohlmeyer on Jul 21 2017, 00:19.
avoid division by zero in reaxff bond interaction computations in very rare…
61b1487cbd93
·Axel Kohlmeyer on Jul 21 2017, 00:17.

Jul 20 2017

include pair style kim doc changes that were accidentally included in PR #590
3449d4226701
·Axel Kohlmeyer on Jul 20 2017, 23:58.
Merge pull request #590 from lammps/fortran-dftb
e53583d9c652
·sjplimp / GitHub on Jul 20 2017, 23:30.
revert change, that is part of the kim-install branch and changeset
551001f172a3
·Axel Kohlmeyer on Jul 20 2017, 23:08.
revert change that accidentally undoes part of PRs #583 and #588
5dbe2df85455
·Axel Kohlmeyer on Jul 20 2017, 23:07.
Merge pull request #588 from akohlmey/colvars-quickfix
3f83396837ea
·sjplimp / GitHub on Jul 20 2017, 22:45.
update of Fortran-DFTB interface to be compatible with fix msst
59db5f6a1782
·Steve Plimpton on Jul 20 2017, 22:40.
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.

Historymasterb209a4e246b5b6057d95e78…

Aug 11 2017

Aug 10 2017

Aug 9 2017

Aug 8 2017

Aug 7 2017

Aug 5 2017

Aug 4 2017

Jul 31 2017

Jul 28 2017

Jul 27 2017

Jul 26 2017

Jul 24 2017

Jul 23 2017

Jul 22 2017

Jul 21 2017

Jul 20 2017

History
masterb209a4e246b5b6057d95e78…