Diffusion lammps (master) History

lammps/src
masterc79dc53c6aefbc8e21fd294…

Jun 20 2017

code improvement, less pointer params
c79dc53c6aef
·Sebastian Hütter on Jun 20 2017, 19:36.
Merge branch 'master' into package-meamc
72a1364d854f
·Axel Kohlmeyer / GitHub on Jun 20 2017, 19:21.
fix storing of invalid memory pointer
198fe7ecd7ad
·Sebastian Hütter on Jun 20 2017, 19:00.
minor changes to NEB doc pages and examples
d2610d9e7c0d
·Steve Plimpton on Jun 20 2017, 16:19.
Merge pull request #536 from akohlmey/fix-nvcc-openmp-conflicts
326a8a1289ef
·sjplimp / GitHub on Jun 20 2017, 15:44.
Merge pull request #533 from lammps/user-intel
b5300724bb8b
·sjplimp / GitHub on Jun 20 2017, 15:44.
Merge pull request #530 from akohlmey/no_static_sort_in_dump
e129f18e6f19
·sjplimp / GitHub on Jun 20 2017, 15:43.

Jun 19 2017

cleanup from aidan for fix reax/c/species and its KOKKOS version
8c54fcd1b6c9
·Axel Kohlmeyer on Jun 19 2017, 23:31.
augment fix shardlow check for ordering fixes to be KOKKOS compatible
f5047ac3c7f9
·Axel Kohlmeyer on Jun 19 2017, 23:23.
protect all OpenMP pragmas with ifdefs and add special conditions for nvcc to…
164cedf3539c
·Axel Kohlmeyer on Jun 19 2017, 21:31.
massive whitespace cleanup in USER-INTEL
3c329d170791
·Axel Kohlmeyer on Jun 19 2017, 19:23.
insert C++ file format indicator comments
b687d16177fe
·Axel Kohlmeyer on Jun 19 2017, 19:03.
modified the documentation, first and last freeend can have different spring…
8988b692a392
·Emile Maras on Jun 19 2017, 16:30.
corrected the initial free end
c97415aefab7
·Emile Maras on Jun 19 2017, 14:57.
fix uninitialized members
a9f3f900255e
·Sebastian Hütter on Jun 19 2017, 12:51.

Jun 17 2017

remove ifdefs for selecting between plain and hybrid merge sort. use hybrid…
9b8de3ba2960
·Axel Kohlmeyer on Jun 17 2017, 15:30.
USER-INTEL upgrade from M Brown
9b9f6d6fe2f4
·Steve Plimpton on Jun 17 2017, 00:56.
restore old qsort() based code and add preprocessor directives to switch
c1b0b1b3f9d7
·Axel Kohlmeyer on Jun 17 2017, 00:17.

Jun 16 2017

mergesort performance improvements
2a6f026853e6
·Axel Kohlmeyer on Jun 16 2017, 14:05.

Jun 15 2017

restore heuristics for checking against integrators that broke after PR #499…
8728a8ddae67
·Axel Kohlmeyer on Jun 15 2017, 21:16.
Merge pull request #528 from akohlmey/no_static_in_ring_comm
9aa450b83240
·sjplimp / GitHub on Jun 15 2017, 19:13.
Merge pull request #513 from v0i0/bugfix-airebo-nconj-kronecker
0588c382f0a6
·sjplimp / GitHub on Jun 15 2017, 19:12.
Merge pull request #510 from akohlmey/collected-small-changes
d3c90f3c14dd
·sjplimp / GitHub on Jun 15 2017, 19:12.
Revert "avoid undesired negative forces for high particle velocities in…
b62d526cc98d
·Axel Kohlmeyer on Jun 15 2017, 17:01.
Merge pull request #531 from ohenrich/user-cgdna
1a29048940e9
·sjplimp / GitHub on Jun 15 2017, 16:54.
Merge pull request #527 from dstelter92/master
0a6b3f87901c
·sjplimp / GitHub on Jun 15 2017, 16:54.
Merge pull request #526 from andeplane/vashishta_gpu
7227bc415d00
·sjplimp / GitHub on Jun 15 2017, 16:52.
Merge pull request #525 from akohlmey/user-tally-refactor
a4bc233d8631
·sjplimp / GitHub on Jun 15 2017, 16:51.
Merge pull request #522 from akohlmey/tip4p-cleanup-refactor
5c5b4ffadba9
·sjplimp / GitHub on Jun 15 2017, 16:48.
Merge pull request #521 from pastewka/17_dump_nc
30177c4eaeb0
·sjplimp / GitHub on Jun 15 2017, 16:47.
Merge pull request #519 from Pakketeretet2/USER-MANIFOLD-gaussian-bump
576b7f1d97b7
·sjplimp / GitHub on Jun 15 2017, 16:46.
Merge pull request #517 from akohlmey/select-rigid-reinit-option
86369fec6bab
·sjplimp / GitHub on Jun 15 2017, 16:46.
Merge pull request #516 from akohlmey/check-rigid-overlap
79341ac5d162
·sjplimp / GitHub on Jun 15 2017, 16:44.
Merge pull request #515 from stanmoore1/remove_fences
66945294a9a7
·sjplimp / GitHub on Jun 15 2017, 16:40.
Merge pull request #511 from akohlmey/add-compute-cnp
9a7207e34cb4
·sjplimp / GitHub on Jun 15 2017, 16:38.
Merge pull request #509 from akohlmey/add-atomonly-npair-for-omp
d41c617d1de0
·sjplimp / GitHub on Jun 15 2017, 16:24.
Merge pull request #504 from andeplane/hexorder_fix
1ec9e588fff2
·sjplimp / GitHub on Jun 15 2017, 16:24.
Merge pull request #497 from lammps/add-user-reaxc-omp
3c7417fb598d
·sjplimp / GitHub on Jun 15 2017, 16:24.
Merge pull request #490 from EmileMaras/NEB-Change
34cfc7bd514b
·sjplimp / GitHub on Jun 15 2017, 16:23.
Changed affiliation
77ca68a2b4da
·Oliver Henrich on Jun 15 2017, 13:52.
add missing mergesort header
06fe703eedcb
·Axel Kohlmeyer on Jun 15 2017, 05:22.
whitespace cleanup
8500a197ae13
·Axel Kohlmeyer on Jun 15 2017, 05:13.
remove need for static class member variables in Dump and Irregular
1f17e8ebbbaf
·Axel Kohlmeyer on Jun 15 2017, 05:10.

Jun 14 2017

change ring communication API to no longer require a static variable pointing…
fcc387f23201
·Axel Kohlmeyer on Jun 14 2017, 23:01.
Added compute_scalar to fix_grem for easier output managment, updated example…
0ad66ecb89dc
·dstelter92 on Jun 14 2017, 18:18.
Added vashishta GPU package for NVidia
eeff0b863323
·Anders Hafreager on Jun 14 2017, 10:24.

Jun 13 2017

add rigid body overlap warnings to change_box and delete_atoms
32b967ed9c28
·Axel Kohlmeyer on Jun 13 2017, 22:26.
fix compilation, move meam_cleanup to destructor
3d066283b670
·Sebastian Hütter on Jun 13 2017, 19:41.
Move rho/gamma arrays to fields of MEAM, remove arguments and arrdim macros
29e60fa53a81
·Sebastian Hütter on Jun 13 2017, 18:39.
remove dead code
11751521e788
·Axel Kohlmeyer on Jun 13 2017, 04:49.
refactoring of USER-TALLY computes to handle sparse and hybrid systems
b01143102ddc
·Axel Kohlmeyer on Jun 13 2017, 04:12.
cleanup and bugfix for compute heat/flux/tally
e530ba46f410
·Axel Kohlmeyer on Jun 13 2017, 03:46.
print incompatible pair style warnings in USER-TALLY only on MPI rank 0
420db4459656
·Axel Kohlmeyer on Jun 13 2017, 02:05.

Jun 12 2017

Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into…
cfeb9b5ba544
·Axel Kohlmeyer on Jun 12 2017, 20:20.
correctly skip over point particles and point dipoles when counting extendend…
0c805d0b70ed
·Axel Kohlmeyer on Jun 12 2017, 20:20.
change incorrect EINERTIA constant in rigid body integrators from 4.0 to 2.0…
6b289b07942d
·Axel Kohlmeyer on Jun 12 2017, 20:07.
Convert/Reindex phir* arrays
078f2a0a47f4
·Sebastian Hütter on Jun 12 2017, 17:41.
update documentation for USER-MEAMC package and pair style meam/c
bdd908c30380
·Axel Kohlmeyer on Jun 12 2017, 03:54.
remove ambiguous access conflict to fm_exp() in pair style agni/omp after…
b45a95107d95
·Axel Kohlmeyer on Jun 12 2017, 00:45.

Jun 11 2017

Improve C++-ness, eliminate some macros
9f852f5f5863
·Sebastian Hütter on Jun 11 2017, 16:55.
ensure that allocatable_double_2d types are initialized
fea28d802823
·Axel Kohlmeyer on Jun 11 2017, 13:29.
make changes to pass compilation test
afed8bb97807
·Axel Kohlmeyer on Jun 11 2017, 13:18.
Convert to C++, allow multiple instances
03c93b31d61a
·Sebastian Hütter on Jun 11 2017, 11:29.
Reformat code with clang-format (Mozilla style guide)
d3f31547f945
·Sebastian Hütter on Jun 11 2017, 11:29.
Change c->cpp for better integration with makefile
7c7468ffc218
·Sebastian Hütter on Jun 11 2017, 11:29.
Create package USER-MEAMC
bab292b551ba
·Sebastian Hütter on Jun 11 2017, 11:29.

Jun 10 2017

add restart support to fix deform. only "initial" data is restored and some…
daa77176add6
·Axel Kohlmeyer on Jun 10 2017, 23:28.
add crude check to print warning when using compute cnp/atom on multi-type…
8f18c284d312
·Axel Kohlmeyer on Jun 10 2017, 23:08.
whitespace cleanup
06915162b069
·Axel Kohlmeyer on Jun 10 2017, 22:56.
adjust compute cnp/atom to match the documentation. need to skip atoms not in…
a849f35dcdd3
·Axel Kohlmeyer on Jun 10 2017, 22:55.
apply rigid body check to displace_atoms command
4c69bbcf5c29
·Axel Kohlmeyer on Jun 10 2017, 17:37.
fix bug in compute orientorder/atom argument parsing
dd44189d1ff3
·Axel Kohlmeyer on Jun 10 2017, 10:35.

Jun 9 2017

output detailed multi-thread performance data only with "timer full"
2f6bbcfbbcba
·Axel Kohlmeyer on Jun 9 2017, 21:11.
simplify compatibility check for fix reax/c/bonds with pair styles
2686b7f830f8
·Axel Kohlmeyer on Jun 9 2017, 20:39.
when identifying molecules/clusters fall back to unfiltered coordinates for…
d3a863e7af1c
·Axel Kohlmeyer on Jun 9 2017, 20:35.
expand error message requiring a reax/c derived pair style
64e8000720ec
·Axel Kohlmeyer on Jun 9 2017, 17:42.
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.

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.
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.

lammps/srcmasterc79dc53c6aefbc8e21fd294…

Jun 20 2017

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Jun 17 2017

Jun 16 2017

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Jun 13 2017

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Jun 11 2017

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Jun 6 2017

Jun 5 2017

lammps/src
masterc79dc53c6aefbc8e21fd294…