Diffusion lammps (master) History

History
mastere10ea91c5f42ea64092da70…

Oct 12 2016

add doc file to toctree
e10ea91c5f42
·Axel Kohlmeyer on Oct 12 2016, 05:51.
import dump nc and dump nc/mpiio from lammps-netcdf as USER-NC-DUMP package by…
69cb83170599
·Axel Kohlmeyer on Oct 12 2016, 05:44.
import lammps-netcdf code as USER-NC-DUMP package
ecb03dd2dfda
·Axel Kohlmeyer on Oct 12 2016, 05:03.

Oct 11 2016

tweaks to new USER-DPD docs
0eb7fbf34d23
·Steve Plimpton on Oct 11 2016, 23:43.
Merge pull request #212 from timattox/USER-DPD_fix_eos_atom_style_checks
fbf7df14b55f
·sjplimp / GitHub on Oct 11 2016, 21:40.
Merge pull request #207 from timattox/USER-DPD_new_VV_for_DPD
6f1162927a78
·sjplimp / GitHub on Oct 11 2016, 21:39.
Merge pull request #214 from akohlmey/make-no-lib-no-mpiio
803dc57bfa23
·sjplimp / GitHub on Oct 11 2016, 20:42.
Merge pull request #213 from akohlmey/improper-virial-bugfixes
3e8e2911cc15
·sjplimp / GitHub on Oct 11 2016, 20:42.
added LAST option to dump_modify thresh, more restart info printed out to screen
04f5eadcf14a
·Steve Plimpton on Oct 11 2016, 20:39.
make no-lib should also remove MPIIO and USER-LB packages
b00b40bccdfd
·Axel Kohlmeyer on Oct 11 2016, 14:03.
bugfix for AngleAngle term in CLASS2 impropers by Ivan A. Strelnikov, ICP RAS
ef079ae4eb87
·Axel Kohlmeyer on Oct 11 2016, 05:56.
Merge branch 'master' into improper-virial-bugfixes
bb0bfd508b2f
·Axel Kohlmeyer on Oct 11 2016, 05:55.

Oct 10 2016

Merge pull request #203 from rbberger/txt2rst-external-link-fix
e70d530c46ed
·sjplimp / GitHub on Oct 10 2016, 21:59.
Merge pull request #211 from akohlmey/add-respa-to-fix-flow-gauss
ed8cc827137c
·sjplimp / GitHub on Oct 10 2016, 21:59.
Merge pull request #209 from akohlmey/static-double-deallocation-workaround
27dac0246604
·sjplimp / GitHub on Oct 10 2016, 21:58.
Merge pull request #204 from rbberger/fix-user-omp
467bcad0a04e
·sjplimp / GitHub on Oct 10 2016, 21:57.
USER-DPD: Add atom_style compatibility checks in fix_eos_*.cpp files.
a2b084006467
·Tim Mattox on Oct 10 2016, 19:40.
whitespace cleanup
144e6a809157
·Axel Kohlmeyer on Oct 10 2016, 15:40.
edited documentation
72ac0734123f
·Steven Strong / Axel Kohlmeyer on Oct 10 2016, 15:38.
edited documentation
49c45ab03b6f
·Steven Strong / Axel Kohlmeyer on Oct 10 2016, 15:38.
first draft of documentation for respa
c2cd43994412
·Steven Strong / Axel Kohlmeyer on Oct 10 2016, 15:38.
adjusted default respa level to be outermost
e96ebb29bc59
·Steven Strong / Axel Kohlmeyer on Oct 10 2016, 15:38.
now understand how respa works in lammps
3ce178d43f9d
·Steven Strong / Axel Kohlmeyer on Oct 10 2016, 15:38.
added respa to fix_flow_gauss, not fully understood yet
23781d6ec9a6
·Steven Strong / Axel Kohlmeyer on Oct 10 2016, 15:38.
completed synchronization with non-threaded version
fca6d721c035
·Axel Kohlmeyer on Oct 10 2016, 15:16.
whitespace cleanup
dd192ca7ea15
·Axel Kohlmeyer on Oct 10 2016, 15:15.

Oct 8 2016

revert to previous style conventions for size_t constants
683689c80807
·Axel Kohlmeyer on Oct 8 2016, 17:00.
workaround for double free issue when using USER-COLVARS with lammps code…
e01e90eb965c
·Axel Kohlmeyer on Oct 8 2016, 16:45.

Oct 7 2016

USER-DPD: whitespace and indentation fixes
9507a786f013
·Tim Mattox on Oct 7 2016, 21:59.
USER-DPD: update the USER/dpd examples and their reference outputs
9789f047d78e
·Tim Mattox on Oct 7 2016, 21:55.
USER-DPD: Added support to use VV integrator with USER-DPD if desired. Includes…
e27ed6c94a2e
·Tim Mattox on Oct 7 2016, 21:03.
Migrate changes from GRANULAR to USER-OMP
615a2da044a3
·Richard Berger on Oct 7 2016, 03:48.
Fix broken link
7f3a7c5cbe5e
·Richard Berger on Oct 7 2016, 02:33.
Fix issue with external links containing anchors
e78b4267b7c2
·Richard Berger on Oct 7 2016, 02:29.

Oct 6 2016

Merge pull request #202 from akohlmey/doc-formatting-fixes
e9fed8092893
·sjplimp / GitHub on Oct 6 2016, 23:49.
Merge pull request #199 from akohlmey/small-changes
54fc194e5b33
·sjplimp / GitHub on Oct 6 2016, 23:49.
new fix wall/gran/region command, REBO bug fix, new example log files
b3d2fb91bb6c
·Steve Plimpton on Oct 6 2016, 23:47.
Revert "bugfix for AngleAngle term in CLASS2 impropers by Ivan A. Strelnikov…
19984c9bd17c
·Axel Kohlmeyer on Oct 6 2016, 23:23.
Revert "bugfix for virial tally for improper style umbrella from Steven…
f92618a33b74
·Axel Kohlmeyer on Oct 6 2016, 23:21.
bugfix for virial tally for improper style umbrella from Steven Vandenbrande (U…
887981cfaa29
·Axel Kohlmeyer on Oct 6 2016, 23:20.
collected documentation updates and corrections from LAMMPS-ICMS
0b5d71537a8b
·Axel Kohlmeyer on Oct 6 2016, 21:48.
Merge pull request #197 from giacomofiorin/colvars_2016-10-05
c2134575508a
·sjplimp / GitHub on Oct 6 2016, 21:02.
Merge pull request #196 from akohlmey/charmm-cmap-updates
0f45cd61a542
·sjplimp / GitHub on Oct 6 2016, 21:02.
clean up doc src
493873fb933d
·Steve Plimpton on Oct 6 2016, 21:00.
Merge branch 'USER-DPD_pair_exp6_rx_mathfix' of https://github.
60a031ebacef
·Axel Kohlmeyer on Oct 6 2016, 20:28.
Merge branch 'USER-DPD_hybrid_atom_bugfix' of https://github.
27e76a70b9d7
·Axel Kohlmeyer on Oct 6 2016, 20:27.
USER-DPD: math corrections in pair_exp6_rx.cpp (by Jim Larentzos)
e1e9a5c12604
·Tim Mattox on Oct 6 2016, 19:49.
USER-DPD: bugfix in unpack_comm_hybrid(); now works with hybrid atom style
d31121b18cde
·Tim Mattox on Oct 6 2016, 19:21.
update reference data files for updated/corrected clayff parameters
0853cdbe6f69
·Axel Kohlmeyer on Oct 6 2016, 17:47.
bugfix for AngleAngle term in CLASS2 impropers by Ivan A. Strelnikov, ICP RAS
83bcdb6a5053
·Axel Kohlmeyer on Oct 6 2016, 17:27.
improved whitespace handling in msi2lmp for force fields and topologies
22ce6718048b
·Axel Kohlmeyer on Oct 6 2016, 17:16.
bugfix for virial tally for improper style umbrella from Steven Vandenbrande (U…
4921dc18a058
·Axel Kohlmeyer on Oct 6 2016, 16:47.
Merge branch 'master' of https://github.com/albapa/lammps into small-changes
d133167bf676
·Axel Kohlmeyer on Oct 6 2016, 15:32.
add NETCDF libs (as defined in QUIP) to the linking line if QUIP was built with…
8ea063378eac
·A Bartok-Partay on Oct 6 2016, 13:16.
removed dump_modify command
fd16118cbb22
·A Bartok-Partay on Oct 6 2016, 13:02.
update include statement format
f9f955d5b5d0
·Axel Kohlmeyer on Oct 6 2016, 04:34.
some more updates to the README file to reflect the inclusion of the CMAP…
d7d321a51249
·Axel Kohlmeyer on Oct 6 2016, 00:41.
Colvars update: issue a warning that cannot be ignored regarding total forces
8809a603fb2d
·Giacomo Fiorin on Oct 6 2016, 00:26.
Colvars update: make ABF check that the colvar isn't using already…
969d3cf4b0c4
·Giacomo Fiorin on Oct 6 2016, 00:25.
added 1GB1 example from Robert Latour and update 1AC7 example files
326fdf2cf13a
·Axel Kohlmeyer on Oct 6 2016, 00:20.
added tweak to write out the command line used for the conversion to the…
f32819dd1086
·Axel Kohlmeyer on Oct 6 2016, 00:13.
import updated README file for charmm2lammps.pl with CMAP support
c07a01c661d6
·Axel Kohlmeyer on Oct 6 2016, 00:11.

Oct 5 2016

adjustments to balancing weights and factors, also XOR op for formulas, if…
02bfa898eeb1
·Steve Plimpton on Oct 5 2016, 23:46.
Merge pull request #193 from akohlmey/eam-bugfix
030df745bc57
·sjplimp / GitHub on Oct 5 2016, 18:54.
Merge pull request #192 from rbberger/python-interface-bugfix
6a9721193268
·sjplimp / GitHub on Oct 5 2016, 18:54.
changes to imbalance weight factors
c46be7db625e
·Steve Plimpton on Oct 5 2016, 18:33.

Oct 4 2016

correct the bug discovered by stan due to uninitialized scale factors for…
4381db846bcb
·Axel Kohlmeyer on Oct 4 2016, 20:33.
Fix code path which allows passing a C++ ptr to PyLammps
e2caf5c10577
·Richard Berger on Oct 4 2016, 19:57.
Merge branch 'restrict-weights-and-weight-factors' of https://github.
11c2892e54cf
·Steve Plimpton on Oct 4 2016, 17:49.
Revert type checking commit from July
91be47a0d084
·Richard Berger on Oct 4 2016, 17:43.
Merge pull request #191 from akohlmey/updated-charmm2lammps
ab92529b1953
·sjplimp / GitHub on Oct 4 2016, 01:59.
Merge pull request #190 from akohlmey/small-bufixes-and-enhancements
e07936277635
·sjplimp / GitHub on Oct 4 2016, 01:58.
added XOR operator to variable command
c3ff8812b34d
·Steve Plimpton on Oct 4 2016, 01:57.

Oct 3 2016

apply bugfix for MEAM provided by Wolfgang Verestek on lammps-users
03766dbda76f
·Axel Kohlmeyer on Oct 3 2016, 22:28.
remove trailing whitespace
6e719f2d9469
·Axel Kohlmeyer on Oct 3 2016, 13:07.
permission update for ch2lmp tool folder
45d2cc28951d
·Axel Kohlmeyer on Oct 3 2016, 13:03.
rebuild charmm2lammps example output files with updated tools
690f91300b63
·Axel Kohlmeyer on Oct 3 2016, 12:58.
properly handle -nohints flag, make -cmap flag take version as option. step…
3b94627dfea5
·Axel Kohlmeyer on Oct 3 2016, 12:52.
import updated charmm2lammps.pl script from Rober Latour
c2e11dffa2eb
·Axel Kohlmeyer on Oct 3 2016, 02:33.

Oct 2 2016

correct designation of meam supporting USER-OMP and meam/spline not
1985db4fb152
·Axel Kohlmeyer on Oct 2 2016, 05:05.

Oct 1 2016

permission cleanup
a3e05a2bac7d
·Axel Kohlmeyer on Oct 1 2016, 12:34.
correct logic bug in bufix for fix tmd
035279de8762
·Axel Kohlmeyer on Oct 1 2016, 12:26.

Sep 30 2016

Merge pull request #187 from akohlmey/colvars-update-2016-09-30
e2c7acabac53
·sjplimp / GitHub on Sep 30 2016, 17:21.
Merge pull request #186 from akohlmey/small-bugfixes
91edee25302a
·sjplimp / GitHub on Sep 30 2016, 17:20.
change purge target in Makefile, also fixed one issue with Make.py
b9d0f96a1923
·Steve Plimpton on Sep 30 2016, 17:17.
restrict choice of weight factors and guarantee that weights are >= 0.001
d45e333f7c47
·Axel Kohlmeyer on Sep 30 2016, 17:11.
remove unused variable
5bb85b482d71
·Axel Kohlmeyer on Sep 30 2016, 15:38.
enable dynamic groups for fix dt/reset
d4b074d85b68
·Axel Kohlmeyer on Sep 30 2016, 15:09.
update colvars library to version 2016-09-30
6d200061ca64
·Axel Kohlmeyer on Sep 30 2016, 14:15.
flag header as C++ to emacs
cb7bd2799e7e
·Axel Kohlmeyer on Sep 30 2016, 13:39.
include charmm22 and charmm36 cmap files and include date added signature
4337f2c240d7
·Axel Kohlmeyer on Sep 30 2016, 13:39.
whitespace cleanup, fix bug in looking for empty strings, improve read…
0eeb24073051
·Axel Kohlmeyer on Sep 30 2016, 13:22.
make reader for target geometry file more resilient
c88acc961340
·Axel Kohlmeyer on Sep 30 2016, 04:59.

Sep 29 2016

Merge pull request #184 from akohlmey/dynamic-groups-for-respa
f7b5afee82a1
·sjplimp / GitHub on Sep 29 2016, 23:51.
remove dead code
a315dcda9b84
·Axel Kohlmeyer on Sep 29 2016, 21:13.
support dynamic groups with run style respa
f6c77c3aba63
·Axel Kohlmeyer on Sep 29 2016, 21:13.
Merge branch 'integration' into new-master
5b2becd09b97
·Axel Kohlmeyer on Sep 29 2016, 16:37.
sync Make.py and fix addforce change with GHub
78a22be93ffd
·sjplimp on Sep 29 2016, 00:36.
Merge pull request #45 from akohlmey/small-bugfixes
596b260f5d48
·sjplimp / GitHub on Sep 29 2016, 00:36.
patch for allowing prd command to work with sorted atoms
446e7e736936
·Steve Plimpton on Sep 29 2016, 00:33.

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History
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