Diffusion lammps (master) History

lammps/src
master

Jun 9 2017

when identifying molecules/clusters fall back to unfiltered coordinates for…
d3a863e7af1c
·Axel Kohlmeyer on Jun 9 2017, 20:35.
Add missing sync/modify to fix_shardlow_kokkos
3c8e75ad590a
·Stan Moore on Jun 9 2017, 18:57.
expand error message requiring a reax/c derived pair style
64e8000720ec
·Axel Kohlmeyer on Jun 9 2017, 17:42.
Fixing CUDA runtime issues in fix_shardlow_kokkos
c51cadcc6c38
·Stan Moore on Jun 9 2017, 17:31.
fix reax/c/species/omp doesn't is not needed anymore
c160d0cd5eec
·Axel Kohlmeyer on Jun 9 2017, 17:04.
match reax/c pair style variants against prefix and not full name
9222278fb5fa
·Axel Kohlmeyer on Jun 9 2017, 17:00.

Jun 8 2017

MAINT: Simplified GPL headers.
bdf03757e686
·Lars Pastewka on Jun 8 2017, 23:20.
MAINT: DumpNetCDF and DumpNetCDFMPIIO need access to thermo output.
10d2e7c380cf
·Lars Pastewka on Jun 8 2017, 23:18.
MAINT: Updated contact data and fixed typos.
bd83c7c7f944
·Lars Pastewka on Jun 8 2017, 23:02.
MAINT: Turned 'global' options into a 'thermo yes'/'thermo no' option that…
d51cee1b821e
·Lars Pastewka on Jun 8 2017, 22:58.
MAINT: Turned 'global' options into a 'thermo yes'/'thermo no' option that…
be476c9e1db2
·Lars Pastewka on Jun 8 2017, 22:43.
Fixing CUDA runtime issues in fix_shardlow_kokkos
86497949f20a
·Stan Moore on Jun 8 2017, 21:40.
Fixing CUDA runtime issues in pair_exp6_rx_kokkos
b4b731088438
·Stan Moore on Jun 8 2017, 21:33.
Reduce memory churn in pair_multi_lucy_rx_kokkos
43cfa10ea48d
·Stan Moore on Jun 8 2017, 17:58.
Reduce memory churn in fix_rx_kokkos
6f24c58c1a31
·Stan Moore on Jun 8 2017, 17:52.
Reduce memory churn in pair_table_rx_kokkos
611bb6f13035
·Stan Moore on Jun 8 2017, 17:31.

Jun 7 2017

Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into…
afd4f5b0a66c
·Axel Kohlmeyer on Jun 7 2017, 23:37.
sbmask function should be flagged as const indicating no side effects
31a734b03d62
·Axel Kohlmeyer on Jun 7 2017, 23:10.
make pair styles lj/cut/tip4p/long/omp, lj/long/tip4p/long and…
2e728972e21e
·Axel Kohlmeyer on Jun 7 2017, 23:09.
Fixing more CUDA runtime issues
520ab26bd966
·Stan Moore on Jun 7 2017, 23:07.
BUG: DumpNCMPIIO is now called DumpNetCDFMPIIO
36c8b26fef94
·Lars Pastewka on Jun 7 2017, 14:01.
MAINT: Switched NetCDF from 64BIT_OFFSET to 64BIT_DATA which can handle frames…
99ef36f44050
·Lars Pastewka on Jun 7 2017, 13:52.
local variable fp in pair style eam/cd was shadowing class member. renamed…
a2edef7c9c3e
·Axel Kohlmeyer on Jun 7 2017, 06:23.

Jun 6 2017

some more bookkeeping updates triggered by the lj/sf style removal
1f9504c54622
·Axel Kohlmeyer on Jun 6 2017, 23:31.
minor whitespace cleanup
04ebd81ac5d0
·Axel Kohlmeyer on Jun 6 2017, 23:26.
alias pair style lj/sf to lj/smooth/linear and remove/update related files
5cb56796a22f
·Axel Kohlmeyer on Jun 6 2017, 23:26.
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into…
0c1b87c8cf67
·Axel Kohlmeyer on Jun 6 2017, 22:27.
update e-mail and affiliation for stefan paquay in USER-MANIFOLD related files
cd67eaa5f42a
·Axel Kohlmeyer on Jun 6 2017, 22:26.
Added Gaussian bump. Updated e-mail address.
18dee3f78ed2
·Stefan Paquay on Jun 6 2017, 22:03.
Fixing more CUDA runtime issues
efe60bf991c6
·Stan Moore on Jun 6 2017, 21:10.
Fixing some CUDA runtime issues in npair_ssa_kokkos
36cbe439780d
·Stan Moore on Jun 6 2017, 18:51.
make certain Domain::box_change is initialized before use
d437650c776f
·Axel Kohlmeyer on Jun 6 2017, 14:08.

Jun 5 2017

add flag "reinit" with args "yes" / "no" to fixes rigid & rigid/small
deff6c666eaf
·Axel Kohlmeyer on Jun 5 2017, 23:31.
simplify code for rigid body overlap checks
3a018363254a
·Axel Kohlmeyer on Jun 5 2017, 22:39.
apply the rigid body checks to some more example codes
0034d2db35b1
·Axel Kohlmeyer on Jun 5 2017, 22:30.
Removing unnecessary fences
ed50bd225494
·Stan Moore on Jun 5 2017, 21:54.
use "body" list via Fix::extract() to correctly identify atoms in bodies
90ca0852c798
·Axel Kohlmeyer on Jun 5 2017, 21:48.
apply test for overlap with rigid bodies to set and velocity command
968de8548c1a
·Axel Kohlmeyer on Jun 5 2017, 19:06.
add 3 APIs to Modify for checking if atoms overlap with any rigid fixes
95d6f05a764e
·Axel Kohlmeyer on Jun 5 2017, 18:41.

Jun 2 2017

made the command options more lammps standard style
e03cc994673e
·Emile Maras on Jun 2 2017, 23:42.
enable support for dynamic groups in fix planeforce and fix lineforce
f59ee5bd62c7
·Axel Kohlmeyer on Jun 2 2017, 14:45.

May 31 2017

Merge branch 'master' into add-user-reaxc-omp
302599640791
·Axel Kohlmeyer on May 31 2017, 18:53.
Fixing issue in fix_qeq_reax
d2b65590392e
·Stan Moore on May 31 2017, 18:52.
Merge branch 'fix_domain_pointer' of https://github.com/andeplane/lammps into…
3c0cef992730
·Axel Kohlmeyer on May 31 2017, 13:10.
Bugfix: Kronecker term ignored in spline forces.
937cf0b996e5
·Markus Hoehnerbach on May 31 2017, 12:20.
Setting lattice to NULL before creating
f57f1efdff0c
·Anders Hafreager on May 31 2017, 09:34.
integrate compute cnp/atom contributed by Paulo Branicio (USC)
85e917ae5200
·Axel Kohlmeyer on May 31 2017, 06:38.
fix bug reported on lammps-users, when not using the first molecule template
0be2cd3d432d
·Axel Kohlmeyer on May 31 2017, 05:58.
avoid undesired negative forces for high particle velocities in granular models
066123007cd9
·Axel Kohlmeyer on May 31 2017, 03:54.
support atom style variables for assigning image flags with the set command
167a51538e16
·Axel Kohlmeyer on May 31 2017, 03:52.

May 30 2017

major neighbor list style whitespace cleanup
03ab8d0f48aa
·Axel Kohlmeyer on May 30 2017, 23:04.
add "atomonly" optimized neighbor list build styles to USER-OMP
75b567a45762
·Axel Kohlmeyer on May 30 2017, 22:50.
Merge pull request #506 from lammps/snap
286d4f2743f8
·sjplimp / GitHub on May 30 2017, 21:32.
Merge pull request #494 from rbberger/small_updates
952b18fc0284
·sjplimp / GitHub on May 30 2017, 18:51.
Merge pull request #499 from akohlmey/add-fix-compute-style-bugfix
816fa934292c
·sjplimp / GitHub on May 30 2017, 18:49.
Merge pull request #495 from akohlmey/doc-fixes
f4f975edd608
·sjplimp / GitHub on May 30 2017, 18:48.
Merge pull request #468 from andeplane/gcmc_fix_nlocal
cff4e4a83744
·sjplimp / GitHub on May 30 2017, 18:45.
Merge pull request #460 from andeplane/gcmc_fix
32db4660bd37
·sjplimp / GitHub on May 30 2017, 18:45.
SNAP changes by Aidan
22fdb1fc1407
·Steve Plimpton on May 30 2017, 18:21.
avoid hang in fix reax/c/species when multiple atoms have the exact same x…
412cb8f089bb
·Axel Kohlmeyer on May 30 2017, 14:15.
no need for special whitespace handling in library interface
092806ad4fe1
·Axel Kohlmeyer on May 30 2017, 13:55.
must not use strtok() in library function as it is not re-entrant and may be…
4ae314731d99
·Axel Kohlmeyer on May 30 2017, 13:42.
triclinic member variable is referenced in destructor and thus must be…
4b8d2e829c24
·Axel Kohlmeyer on May 30 2017, 13:41.

May 29 2017

displace_atom rotate needs to operate on unwrapped coordinates with image flags…
d93938f7e17f
·Axel Kohlmeyer on May 29 2017, 22:57.
removed a bug in fix_neb.cpp which prevented the freeend to work properly, plus…
c904cfb8bc5f
·Emile Maras on May 29 2017, 15:49.
Using correct ndegree instead of nnn
ba0ddea5e1ff
·Anders Hafreager on May 29 2017, 00:44.

May 27 2017

add missing neighbor list class definitions to USER-OMP
c0339120d2a5
·Axel Kohlmeyer on May 27 2017, 03:28.
fix bug in computing mixed EAM potentials introduced by TI modifications
5a23d2d1da75
·Axel Kohlmeyer on May 27 2017, 02:28.

May 26 2017

prevent segfault when defining pair_style comb3 without arguments
5b1e582f0377
·Axel Kohlmeyer on May 26 2017, 16:52.
dead code removal and reformatting
f1ec6dc41aa4
·Axel Kohlmeyer on May 26 2017, 00:55.

May 25 2017

augment documentation for newly added multi-threaded reax/c styles
c3f6e27bfe2e
·Axel Kohlmeyer on May 25 2017, 23:00.
remove redundant code from fix qeq/reax and qeq/reax/omp
0a2fe705114c
·Axel Kohlmeyer on May 25 2017, 22:31.
Updating from master to 19May17
2cf83d9fca6e
·Stan Moore on May 25 2017, 19:21.
Merge branch 'doc-fixes' of github.com:akohlmey/lammps into doc-fixes
53e7fee5b778
·Axel Kohlmeyer on May 25 2017, 16:11.
fix bug in fix shear/history reported by kevin hanley. see #500
5291f2ed6e8d
·Axel Kohlmeyer on May 25 2017, 16:11.
fix suffix style handling bug for adding fixes and computes
99a68e487f07
·Axel Kohlmeyer on May 25 2017, 08:01.

May 24 2017

clean up code so it can be compiled with and without OpenMP enabled regardless…
271431ab1834
·Axel Kohlmeyer on May 24 2017, 23:25.
remove trailing whitespace
88d4150d2bf8
·Axel Kohlmeyer on May 24 2017, 22:29.
remove trailing whitespace
0e3cfbc007c8
·Axel Kohlmeyer on May 24 2017, 22:29.
merge in the remainder of the USER-REAXC-OMP code. still a lot of work to do.
5345ad2da7bd
·Axel Kohlmeyer on May 24 2017, 22:24.
first chunk of code from USER-REAXC-OMP imported and adapted into USER-REAXC
bb890941ca40
·Axel Kohlmeyer on May 24 2017, 06:19.

May 23 2017

restore explicit NAN constants in output
4002dce63984
·Axel Kohlmeyer on May 23 2017, 04:39.
some more formatting cleanup in fix neb
c801cdd81fe0
·Axel Kohlmeyer on May 23 2017, 04:33.
more formatting cleanup
9008a3119009
·Axel Kohlmeyer on May 23 2017, 03:55.

May 22 2017

Remove unused code detected by coverity CID 177700
bdfb7c69ea3f
·Richard Berger on May 22 2017, 23:51.
Fixes coverity issue CID 179426
084626e60b43
·Richard Berger on May 22 2017, 23:36.
Fixes coverity issue CID 179439
a7d790a82778
·Richard Berger on May 22 2017, 23:33.
Fixes coverity issue CID 179440
8a630ff4ec8a
·Richard Berger on May 22 2017, 23:32.
Fixes coverity issue CID 179436
617ca4e0c89b
·Richard Berger on May 22 2017, 23:30.
when growing arrays with reallocate, always check against atom->nmax and not…
62601678cdde
·Axel Kohlmeyer on May 22 2017, 23:16.
do not try to free null communicators
081910adbc41
·Axel Kohlmeyer on May 22 2017, 23:15.
rename nall class member to numall to avoid confusion with the common…
f73fd0625d53
·Axel Kohlmeyer on May 22 2017, 23:14.
NEBLongRange was incorrectly set to false by default. revert to true.
7185db98b4c7
·Axel Kohlmeyer on May 22 2017, 23:13.
use '&&' and '||' instead of 'and' and 'or' operators for consistency
4780d72809c0
·Axel Kohlmeyer on May 22 2017, 20:42.
avoid use '&&' and '||' instead of 'and' and 'or' for consistency
3fd91a239ff0
·Axel Kohlmeyer on May 22 2017, 20:41.

May 19 2017

plug some memory leaks
546aed7ccde8
·Axel Kohlmeyer on May 19 2017, 22:14.
silence several compiler warnings
6ef79d371541
·Axel Kohlmeyer on May 19 2017, 21:13.
formatting cleanup. combine 8 MPI_Allreduce() calls into 1
c2bf3269acf4
·Axel Kohlmeyer on May 19 2017, 21:02.
patch 19May17
2225fce94eee
·Steve Plimpton on May 19 2017, 15:35.

May 18 2017

small formating changes
069f3e746b46
·Emile Maras on May 18 2017, 21:23.

lammps/srcmaster

Jun 9 2017

Jun 8 2017

Jun 7 2017

Jun 6 2017

Jun 5 2017

Jun 2 2017

May 31 2017

May 30 2017

May 29 2017

May 27 2017

May 26 2017

May 25 2017

May 24 2017

May 23 2017

May 22 2017

May 19 2017

May 18 2017

lammps/src
master