Diffusion lammps (master) History

History
masterbf7cff73d42a2fc446942be…

Aug 18 2017

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.

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.
Merge branch 'cmake' of github.com:junghans/lammps into cmake
93190a548a4a
·Richard Berger on Jul 31 2017, 19:48.
Add -DLAMMPS_EXCEPTIONS flag
72f50c91ee01
·Richard Berger on Jul 31 2017, 19:48.
cmake: improve some error messages
408d9d99a946
·Christoph Junghans on Jul 31 2017, 19:35.
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.
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.
cmake: some more typo fixes
0231cc38a35e
·Christoph Junghans on Jul 26 2017, 03:09.

Jul 25 2017

allow user to override PYTHON_INSTDIR
6716de532073
·Christoph Junghans on Jul 25 2017, 04:17.

Historymasterbf7cff73d42a2fc446942be…

Aug 18 2017

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Aug 9 2017

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History
masterbf7cff73d42a2fc446942be…