Diffusion lammps (master) History

History
masterc2c6dc14588a8aafe95fde7…

Jun 9 2017

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.
DOC: Updated dump_modify and dump netcdf documentation.
c81bc108f9ae
·Lars Pastewka on Jun 8 2017, 23:19.
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.
fix uninitialized data access as reported by @martok in #174
0ecdb998856b
·Axel Kohlmeyer on Jun 8 2017, 19:50.
Remove tpls dir
00ce15d043fa
·Stan Moore on Jun 8 2017, 18:43.
Updating Kokkos lib to v2.03.05
5c1d17d1c031
·Stan Moore on Jun 8 2017, 18:42.

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.
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.
corrected the fix_neb documentation
06c8e95774cc
·Emile Maras on Jun 6 2017, 14:20.
make certain Domain::box_change is initialized before use
d437650c776f
·Axel Kohlmeyer on Jun 6 2017, 14:08.
update rigid fix documentation for added `reinit` keyword
46c5cbae8f3a
·Axel Kohlmeyer on Jun 6 2017, 00:04.

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.
add clarification to impact of special bonds to manybody potentials
ff58ccac2870
·Axel Kohlmeyer on Jun 5 2017, 03:21.

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.

Jun 1 2017

remove no longer correct sentence from set command docs
af5f19604cce
·Axel Kohlmeyer on Jun 1 2017, 05:36.

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.
add example input for compute cnp/atom
2b3c124e61d7
·Axel Kohlmeyer on May 31 2017, 06:43.
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

Merge branch 'fix_adapt_doc_fix' of https://github.com/Pakketeretet2/lammps…
5c6f63d8b4ca
·Axel Kohlmeyer on May 30 2017, 23:06.
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.
Added missing :pre to doc/src/fix_adapt.txt
cace3e3530cb
·Stefan Paquay on May 30 2017, 22:08.
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.
removed a bug in fix_neb.cpp which prevented the freeend to work properly, plus…
32c87f313180
·Emile Maras on May 29 2017, 14:00.
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.
Merge branch 'user-manifold-doc-fix' of https://github.com/Pakketeretet2/lammps…
de446ace2fec
·Axel Kohlmeyer on May 27 2017, 00:44.

May 26 2017

Fixed typo in dox.
2055110e05d0
·Stefan Paquay on May 26 2017, 23:38.
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.
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.
Merge branch 'pair_morse_soft-doc-fix' of https://github.
ead05f81c09c
·Axel Kohlmeyer on May 24 2017, 19:56.
Cleaned up docs for pair_mores, a missing :pre ruined formatting.
4f9e7cbd161f
·Stefan Paquay on May 24 2017, 19:36.
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.
Merge remote-tracking branch 'upstream/master' into small_updates
06a4f47a4c37
·Richard Berger 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.
change example inputs to be backward compatible
8bc829c7f19e
·Axel Kohlmeyer on May 22 2017, 20:40.

May 21 2017

small documentation fixes to fix typos and formatting issues
97d3c843c44a
·Axel Kohlmeyer on May 21 2017, 17:13.

Historymasterc2c6dc14588a8aafe95fde7…

Jun 9 2017

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Jun 2 2017

Jun 1 2017

May 31 2017

May 30 2017

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May 27 2017

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May 21 2017

History
masterc2c6dc14588a8aafe95fde7…