Diffusion lammps (master) History

src
masterf7715ab6ce3c2e943f9f422…

Sep 5 2017

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.

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

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 23 2017

correct typo in header formatting
6db3bd87ee73
·Axel Kohlmeyer on Aug 23 2017, 23:52.
Merge pull request #624 from akohlmey/compute-fragment
7b7a5076d00a
·Steve Plimpton / GitHub on Aug 23 2017, 22:14.
Merge pull request #622 from akohlmey/collected-small-fixes
f7a0a6eb7069
·Steve Plimpton / GitHub on Aug 23 2017, 22:12.
update fix qeq docs for the new, more flexible parameter file format
97edf90a7389
·Axel Kohlmeyer on Aug 23 2017, 17:22.
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.

Aug 21 2017

add a compute aggregate/atom, that combines the rules for compute cluster/atom…
5a0c3aea8ac1
·Axel Kohlmeyer on Aug 21 2017, 19:12.

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.
add docs for compute fragment/atom
4dc1195cd851
·Axel Kohlmeyer on Aug 20 2017, 15:41.

Aug 19 2017

new USER-MESO package
f945d4567d4f
·Steve Plimpton on Aug 19 2017, 01:33.

Aug 18 2017

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.

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 11 2017

patch 11Aug17
0b3f1b8a156d
·Steve Plimpton on Aug 11 2017, 20:19.
patch 10Aug17
52bec0f380dd
·Steve Plimpton on Aug 11 2017, 00:44.

Aug 10 2017

remove special_bonds extra keyword and refer to read_data and create_box instead
c8741f3a01a2
·Axel Kohlmeyer on Aug 10 2017, 21:12.
More robust change from initial to target restraint centers in Colvars
da01be7c1857
·Giacomo Fiorin on Aug 10 2017, 15:22.
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.
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 7 2017

Merge pull request #600 from akohlmey/install-and-docs-reviewed
0a54c34e34c2
·Steve Plimpton / GitHub on Aug 7 2017, 16:02.
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.
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.

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.

Jul 28 2017

Merge branch 'kim-install' into install-and-docs-reviewed
e7d9aabca6ba
·Axel Kohlmeyer on Jul 28 2017, 17:25.

Jul 27 2017

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 24 2017

patch 24Jul17
a59b7e4d5647
·Steve Plimpton on Jul 24 2017, 17:09.

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.
revert change, that is part of the kim-install branch and changeset
551001f172a3
·Axel Kohlmeyer on Jul 20 2017, 23:08.
update of Fortran-DFTB interface to be compatible with fix msst
59db5f6a1782
·Steve Plimpton on Jul 20 2017, 22:40.
Merge pull request #585 from akohlmey/make-py-manual-cleanup
3cd597e948fa
·sjplimp / GitHub on Jul 20 2017, 20:05.
Merge pull request #583 from giacomofiorin/colvars-update-2017-07-19
eca61226c267
·sjplimp / GitHub on Jul 20 2017, 20:04.
Merge pull request #581 from libAtoms/idces2quip
fac3e3daa237
·sjplimp / GitHub on Jul 20 2017, 20:04.
update manual links that got broken when removing and renumbering a section
a351977c5904
·Axel Kohlmeyer on Jul 20 2017, 18:25.

Jul 19 2017

Update Colvars to version 2017-07-15 and support automated builds for it
ee6cac826e65
·Giacomo Fiorin on Jul 19 2017, 20:24.
support QUIP wrapper API version query, relax hybrid restriction to allow…
52a1c54d500e
·Axel Kohlmeyer on Jul 19 2017, 19:17.
Update USER_QUIP docs to clarify use of "special_bonds"
fcf9607a6666
·Max Veit on Jul 19 2017, 18:47.

Jul 18 2017

correct commands table format issue
5cbaf7ca1d32
·Axel Kohlmeyer on Jul 18 2017, 20:47.
remove references to Make.py from the manual and instead refer to section 4
49e6c2eb7d4a
·Axel Kohlmeyer on Jul 18 2017, 19:14.
update manual links that got broken when removing and renumbering a section
a92d79253734
·Axel Kohlmeyer on Jul 18 2017, 18:55.

Jul 15 2017

better Install.py script for KIM from Ryan Elliott
296e572e6998
·Steve Plimpton on Jul 15 2017, 00:25.

Jul 14 2017

correct formatting error in peridynamics pair style docs
3b1134c1649a
·Axel Kohlmeyer on Jul 14 2017, 19:42.

Jul 13 2017

Merge pull request #561 from v0i0/fix-airebo-various
fc36754ca22a
·sjplimp / GitHub on Jul 13 2017, 21:10.
Merge pull request #574 from lammps/snap-virial
3a46c34c2fa3
·sjplimp / GitHub on Jul 13 2017, 21:07.
Merge pull request #570 from akohlmey/collected-small-changes
a3a0c9b144c5
·sjplimp / GitHub on Jul 13 2017, 19:26.
Merge pull request #568 from akohlmey/fix_gcmc_parallel_workaround
e58bcd8b4aa4
·sjplimp / GitHub on Jul 13 2017, 19:23.
Merge pull request #566 from akohlmey/compute_rdf_dynamic
ef2f4980e9dd
·sjplimp / GitHub on Jul 13 2017, 19:23.
Merge pull request #560 from aershadinia/master
d3a45f6d5057
·sjplimp / GitHub on Jul 13 2017, 19:22.
changes to SNAP virial from Aidan
d0cc1dfbb80c
·Steve Plimpton on Jul 13 2017, 19:19.

Jul 11 2017

clarify explanation of body style molecule in rigid fixes
c8939d8df6da
·Axel Kohlmeyer on Jul 11 2017, 15:43.

Jul 10 2017

mention restriction for use with fix shake or fix rigid in fix gcmc docs
c9a0d38a3eff
·Axel Kohlmeyer on Jul 10 2017, 23:34.

Jul 7 2017

add support for recomputing normalization factors and finite size correction…
fe888e462219
·Axel Kohlmeyer on Jul 7 2017, 21:39.

Jul 6 2017

patch 6Jul17
433937994877
·Steve Plimpton on Jul 6 2017, 21:58.
update fix wall/ees and wall/region/ees file to conform more to common…
23925b3a57fc
·Axel Kohlmeyer on Jul 6 2017, 20:47.
integrate fix wall/ees and wall/region/ees into doc system
423e3b6389dc
·Axel Kohlmeyer on Jul 6 2017, 20:45.
Merged two doc files
8be6d5bfd841
·Abdoreza Ershadinia / GitHub on Jul 6 2017, 13:21.
Delete "fix_wall_region_ees.txt"
a62eb43791da
·Abdoreza Ershadinia / GitHub on Jul 6 2017, 13:20.
Deleted "fix wall/region/ees" doc file
33be51af5432
·Abdoreza Ershadinia / GitHub on Jul 6 2017, 13:19.

Jul 5 2017

additional fix external hooks for calling programs
ea4f16bd79df
·Steve Plimpton on Jul 5 2017, 18:01.
Merge branch 'master' of https://github.com/aershadinia/lammps
92831f185b3f
·Abdo on Jul 5 2017, 16:23.
Feature: AIREBO parametrize cutoff switching
7e42af18bc68
·Markus Hoehnerbach on Jul 5 2017, 15:11.

Jul 3 2017

3rd variant of Fortran wrapper for DFTB+ calling LAMMPS
f670dba3d019
·Steve Plimpton on Jul 3 2017, 22:24.
Merge pull request #524 from martok/package-meamc
6fc0a94e8783
·sjplimp / GitHub on Jul 3 2017, 20:30.
memory allocation bugfix for USER-INTEL pppm from M Brown
e634c5a2dec8
·Steve Plimpton on Jul 3 2017, 16:53.

Jun 30 2017

Merge pull request #557 from lammps/create-bonds
883b7aaa0efc
·sjplimp / GitHub on Jun 30 2017, 22:18.
spell-check new additions to create_bonds doc page
b445f8eadf67
·Axel Kohlmeyer on Jun 30 2017, 20:59.
Merge pull request #554 from jewettaij/master
b79044d4f60f
·sjplimp / GitHub on Jun 30 2017, 19:47.
add single options to create_bonds command
711afe5062ff
·Steve Plimpton on Jun 30 2017, 19:30.
Merge pull request #547 from akohlmey/collected-bugfixes
b2b621a2e18b
·sjplimp / GitHub on Jun 30 2017, 19:08.
update documentation for nb3/harmonic pair style according to e-mail to lammps…
f6faad335cf5
·Axel Kohlmeyer on Jun 30 2017, 17:37.

Jun 29 2017

consolidate and update error message and read_data documentation for the…
d5921e9fb9e8
·Axel Kohlmeyer on Jun 29 2017, 22:30.
new keywords for read_data: extra/X/per/atoms + changes to docs
38075455b674
·Andrew Jewett on Jun 29 2017, 02:55.

Jun 24 2017

patch 23Jun17
1370385c8c9f
·Steve Plimpton on Jun 24 2017, 01:10.

Jun 23 2017

doc page clarifications for CHARMM energy and dipole pre-factors
4fcbd58d5a32
·Steve Plimpton on Jun 23 2017, 23:54.
reword the kspace_modify fftbench keyword docs to reflect the current state (i.
feb500b52684
·Axel Kohlmeyer on Jun 23 2017, 01:17.

Jun 22 2017

Merge pull request #540 from lammps/neighrespa
7a4a56985986
·sjplimp / GitHub on Jun 22 2017, 15:54.
document new restrictions to CHARMM compatible dihedral styles
de3157f720b3
·Axel Kohlmeyer on Jun 22 2017, 01:31.

Jun 21 2017

fix issue with rRESPA inner/middle neighbor lists
1fc2eb1e3e4b
·Steve Plimpton on Jun 21 2017, 23:12.
whitespace cleanup in docs
1a77135ed65b
·Axel Kohlmeyer on Jun 21 2017, 15:38.
update fix ti/spring docs to reflect it is part of USER-MISC
f45c7e1fb023
·Axel Kohlmeyer on Jun 21 2017, 15:36.

Jun 20 2017

patch 20Jun17
87c028ed0237
·Steve Plimpton on Jun 20 2017, 20:06.

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lammps/doc/src
masterf7715ab6ce3c2e943f9f422…