Diffusion lammps (master) History

History
master14dc1c698c600040c7f7c65…

Oct 9 2017

Merge pull request #683 from wmbrownIntel/pppm_intel_fix
14dc1c698c60
·Steve Plimpton / GitHub on Oct 9 2017, 16:29.
Merge pull request #681 from lammps/dump-modify
a1f5693fe08e
·Steve Plimpton / GitHub on Oct 9 2017, 16:29.
correct handling of "at" keyword for netcdf dumps as suggested by @pastewka in…
02646100e91f
·Axel Kohlmeyer on Oct 9 2017, 13:49.

Oct 8 2017

Fixing bug in pppm/intel for AVX-512 with single precision and ik diff. This…
7e58f084d226
·Michael Brown on Oct 8 2017, 17:33.

Oct 7 2017

Merge pull request #680 from lammps/map-yes
88a33edb5022
·Steve Plimpton / GitHub on Oct 7 2017, 01:43.

Oct 6 2017

avoid merge conflict
6820db99e22f
·Axel Kohlmeyer on Oct 6 2017, 20:41.
rename misleading "CPU time" into "Time spent"
58e1969de241
·Axel Kohlmeyer on Oct 6 2017, 20:34.
remove dependence of dump modify 'at' and 'append'
e91e505fb36e
·Steve Plimpton on Oct 6 2017, 17:44.
Merge pull request #673 from pastewka/17_dump_nc2
f7cbdcf99584
·Steve Plimpton / GitHub on Oct 6 2017, 17:14.
Merge pull request #674 from wmbrownIntel/user-intel-update
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·Steve Plimpton / GitHub on Oct 6 2017, 17:12.
DOC: Updated doc to separate description of 'append' and 'at' keywords.
352a20fc1cb7
·Lars Pastewka on Oct 6 2017, 16:38.
MAINT: Return error when 'at' keyword is used without 'append yes'.
dc0e20947ee7
·Lars Pastewka on Oct 6 2017, 16:37.
Merge branch 'master' into user-intel-update
05847a0e8713
·Axel Kohlmeyer / GitHub on Oct 6 2017, 16:18.
Merge pull request #677 from stanmoore1/kk_update
439c2fd980f8
·Steve Plimpton / GitHub on Oct 6 2017, 01:10.
Merge pull request #676 from stanmoore1/kokkos_reverse_comm
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·Steve Plimpton / GitHub on Oct 6 2017, 01:08.
Merge pull request #675 from wesbarnett/master
bd17ee5df74a
·Steve Plimpton / GitHub on Oct 6 2017, 01:08.
Merge pull request #679 from stanmoore1/kk_reax_comm
a9b7ff1154d3
·Steve Plimpton / GitHub on Oct 6 2017, 01:08.
Merge pull request #672 from akohlmey/phana-w-tricubic
0dd7ba26c080
·Steve Plimpton / GitHub on Oct 6 2017, 01:01.
Merge pull request #668 from ovilab/modify_deallocation_fix
7a90eef527ed
·Steve Plimpton / GitHub on Oct 6 2017, 01:00.
Merge pull request #665 from akohlmey/collected-small-fixes
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·Steve Plimpton / GitHub on Oct 6 2017, 00:58.
Merge pull request #664 from timattox/kokkos_atom2bin
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·Steve Plimpton / GitHub on Oct 6 2017, 00:58.
Merge pull request #663 from jdevemy/master
0ed987dc6186
·Steve Plimpton / GitHub on Oct 6 2017, 00:56.
Merge pull request #660 from junghans/latte_fix
55a3fdca8065
·Steve Plimpton / GitHub on Oct 6 2017, 00:55.
add atom_modify map yes, also timers to create_atoms and replicate
214c0cfb2b7e
·Steve Plimpton on Oct 6 2017, 00:44.

Oct 5 2017

Switch to classic comm if ghost_velocity. The check_forward and check_reverse…
e0efdd50fab3
·Stan Moore on Oct 5 2017, 23:47.
Add pre_reverse to verlet_kokkos and comment out timer
44d2e8ff74d5
·Stan Moore on Oct 5 2017, 23:28.
Fix issues in Kokkos comm
6bf2c60c07ed
·Stan Moore on Oct 5 2017, 22:58.
Remove hardcoded value in fix_qeq_reax
eecd2fbaee77
·Stan Moore on Oct 5 2017, 19:23.
Fix memory leak in pair_reaxc_kokkos
2b0bfcb10f90
·Stan Moore on Oct 5 2017, 18:35.

Oct 4 2017

Reduce unnecessary communication in fix_qeq_reax
3653f4012013
·Stan Moore on Oct 4 2017, 20:10.
Destroy unneeded fix in pair_reaxc_kokkos
bda0ee3aa1eb
·Stan Moore on Oct 4 2017, 20:06.
add call to fftw_cleanup() before exiting to avoid bogus leak reports when…
c522b1b7a974
·Axel Kohlmeyer on Oct 4 2017, 06:22.

Oct 3 2017

Update to Kokkos r2.04.04 and add workaround for performance regression
a55adf4a6848
·Stan Moore on Oct 3 2017, 19:30.
Use -restrict whenever Intel is used, no matter the package
2876baafd07d
·James Barnett on Oct 3 2017, 19:08.
Add Kokkos threaded reverse comm option
ca032f21fbfa
·Stan Moore on Oct 3 2017, 18:14.
cmake: Add -restrict for Intel compilers for some packages
197f08278442
·James Barnett on Oct 3 2017, 17:28.
intel_simd.h is currently also needed by dihedral/charmm, not just sw.
9dc42fd4db71
·Michael Brown on Oct 3 2017, 08:53.
Minor adjustments to intel makefiles and documentation based on the reversed…
5e8926963126
·Michael Brown on Oct 3 2017, 08:41.
update README in USER-INTEL for recent LRT logic reversal
d2aa05cb3661
·Axel Kohlmeyer on Oct 3 2017, 03:24.
update documentation for the reversal in the INTEL_MKL_RNG define
466fde6443bf
·Axel Kohlmeyer on Oct 3 2017, 03:20.
reverse logic for using MKL pRNG: this way, make serial and make mpi will…
2a24cbfe0c2f
·Axel Kohlmeyer on Oct 3 2017, 03:13.

Oct 2 2017

whitespace cleanup
8d384b9149c7
·Axel Kohlmeyer on Oct 2 2017, 21:03.
Reduce GPU data transfer
529eeb603923
·Stan Moore on Oct 2 2017, 17:31.
Adding pair style dpd/intel and dihedral style fourier/intel Adding raw…
cf24dd026520
·Michael Brown on Oct 2 2017, 13:53.

Oct 1 2017

DOC: Corrected syntax for appending at certain frame (NetCDF only)
a7b0d1f521af
·Lars Pastewka on Oct 1 2017, 14:40.
MAINT: Only set append flag when not in multifile mode.
fbe42cda2d24
·Lars Pastewka on Oct 1 2017, 14:31.
DOC: Added multi file example.
da7be99cc4a3
·Lars Pastewka on Oct 1 2017, 14:28.
MAINT: Removed obsolete prmtop writer.
56d21bfb057b
·Lars Pastewka on Oct 1 2017, 14:22.
ENH: Enable multi file writes.
100231bba8f1
·Lars Pastewka on Oct 1 2017, 14:21.
MAINT: Renamed _put_var1_x to _put_var1_bigint
84378f8ae27f
·Lars Pastewka on Oct 1 2017, 14:05.
MAINT: bigint (int64) maps onto either long or long long, depending on platform.
6e342d2e45dc
·Lars Pastewka on Oct 1 2017, 14:03.

Sep 30 2017

Fix typo
091d0580904a
·Richard Berger on Sep 30 2017, 23:44.
cleanup/simplification of compilation for fix phonon analysis tool "phana"
4c71beb02409
·Axel Kohlmeyer on Sep 30 2017, 18:12.
Reduce memory churn in Kokkos package
a86572f4fcb4
·Stan Moore on Sep 30 2017, 00:20.

Sep 29 2017

Partially revert 01d0a5c, avoid atomics, safe because of the while loop. Worst…
9f2740b7f18f
·Stan Moore on Sep 29 2017, 21:41.
Add sync/modify to nbin_kokkos
d7aac2fed53c
·Stan Moore on Sep 29 2017, 21:26.
use <> for system includes not ""
d898afaafb7a
·Axel Kohlmeyer on Sep 29 2017, 15:19.

Sep 27 2017

Fixed proper deletion of fixes if fix is NULL
23e283f13551
·Anders Hafreager on Sep 27 2017, 16:20.
correct bogus links in LATTE docs
de45fa6e7107
·Axel Kohlmeyer on Sep 27 2017, 00:25.

Sep 26 2017

add missing entry for pdf version of manual
bfdc4acb8bbe
·Axel Kohlmeyer on Sep 26 2017, 22:53.
fix typo in formatting
fd3ecd048120
·Axel Kohlmeyer on Sep 26 2017, 22:52.
correct formatting and broken/colliding link issues with LATTE package related…
8bba6d3e8c63
·Axel Kohlmeyer on Sep 26 2017, 22:52.
need to re-init timers after initial setup
53e4ee4f2dc9
·Axel Kohlmeyer on Sep 26 2017, 05:20.
USER-OMP package depends on USER-DRUDE
b60cff7e7773
·Axel Kohlmeyer on Sep 26 2017, 05:15.
-ltbbmalloc is required
38530415c8f0
·Axel Kohlmeyer on Sep 26 2017, 02:03.
update src/.gitignore for LATTE package
0573aaa6da3a
·Axel Kohlmeyer on Sep 26 2017, 01:37.
having plain filelink instead of filelink.o confuses KOKKOS linking with nvcc
e6969002ce55
·Axel Kohlmeyer on Sep 26 2017, 01:37.

Sep 25 2017

whitespace fixes, silence compiler warning about too few format specifiers
836a6d292c10
·Axel Kohlmeyer on Sep 25 2017, 22:31.
first pass at implementing atom2bin for KOKKOS neighbor lists
32e0de7a67a1
·Tim Mattox on Sep 25 2017, 21:06.
KOKKOS: minor typo fix
789812ec3dce
·Tim Mattox on Sep 25 2017, 21:06.
Authorize hybrid/overlay for fix srp
78a486c0fdfe
·Julien Devemy on Sep 25 2017, 16:18.

Sep 22 2017

patch 22Sep17
f2c1172741b5
·Steve Plimpton on Sep 22 2017, 23:46.
cmake: fix build with system latte
d6316c40d94e
·Christoph Junghans on Sep 22 2017, 23:36.
Merge pull request #659 from stanmoore1/kk_border_comm
bcde318ccb0f
·Steve Plimpton / GitHub on Sep 22 2017, 21:47.
Make Kokkos comm give warning and switch to classic comm instead of erroring out
3ed39ca844ba
·Stan Moore on Sep 22 2017, 21:03.
Merge pull request #652 from junghans/latte
ee487ef4aa4f
·Steve Plimpton / GitHub on Sep 22 2017, 18:32.

Sep 21 2017

update fix latte examples and virial
a8ae8866676e
·Steve Plimpton on Sep 21 2017, 18:40.
fixed sucrose
5e35ab251b23
·Christian Negre on Sep 21 2017, 01:11.

Sep 20 2017

cmake: download/build latte if not found
d708e34ba6d4
·Christoph Junghans on Sep 20 2017, 20:01.
Merge pull request #657 from lammps/snap-potentials
638b91bf74c1
·Steve Plimpton / GitHub on Sep 20 2017, 17:34.
whitespace cleanup
ad25a9529758
·Axel Kohlmeyer on Sep 20 2017, 17:13.
convert DOS/Windows CR-LF line endings to native format
e7d042ba1a0e
·Axel Kohlmeyer on Sep 20 2017, 17:12.
new SNAP potentials and examples
dd49d54889a2
·Steve Plimpton on Sep 20 2017, 16:54.
Merge pull request #655 from akohlmey/fixes-for-patch
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·Steve Plimpton / GitHub on Sep 20 2017, 16:51.
Merge pull request #645 from akohlmey/kokkos-makefile-updates
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·Steve Plimpton / GitHub on Sep 20 2017, 16:40.
add .gitignore and add Makefile.lammps.* symlinks to stay consistent with other…
59d2e13d48fe
·Axel Kohlmeyer on Sep 20 2017, 01:06.
add fix latte command to doc pages
76d93f21dd9c
·Steve Plimpton on Sep 20 2017, 00:55.
LATTE package doc update and some small code changes
ac897ea6457c
·Steve Plimpton on Sep 20 2017, 00:27.

Sep 19 2017

correct USER-INTEL installer script for verlet_lrt_intel files
19f1f3a3e063
·Axel Kohlmeyer on Sep 19 2017, 17:48.
compile all objects in the GPU library with -fPIC for building shared object
be96486d6668
·Axel Kohlmeyer on Sep 19 2017, 17:24.
ignore generated header files with OpenCL kernels
48dd824b2601
·Axel Kohlmeyer on Sep 19 2017, 17:24.
reverse the pre-processor logic of the LRT mode define
cdb6ec7419d0
·Axel Kohlmeyer on Sep 19 2017, 17:24.
allow fix viscous to be used with dynamic groups
aad8cd10ffa2
·Axel Kohlmeyer on Sep 19 2017, 00:08.

Sep 18 2017

fix external only needs to collect virial in case it is requested
1ac90815f342
·Axel Kohlmeyer on Sep 18 2017, 05:59.
activate virial contribution in `fix lb/rigid/pc/sphere` by default and protect…
5f1842829e48
·Axel Kohlmeyer on Sep 18 2017, 03:10.
whether virial contributions from fixes are included depend on thermo_virial…
66130f555700
·Axel Kohlmeyer on Sep 18 2017, 02:50.
correctly initialize `thermo_virial` in fix poems and protect access to…
388eab5eebe5
·Axel Kohlmeyer on Sep 18 2017, 02:49.
remove bogus version of temper/npt command
a500048c9c4a
·Axel Kohlmeyer on Sep 18 2017, 01:25.
remove another couple of purge items from long ago
b4ecad7fbf5b
·Axel Kohlmeyer on Sep 18 2017, 01:22.
automatically call 'make purge' before calling 'make package-update' or 'make…
b5894e2190ca
·Axel Kohlmeyer on Sep 18 2017, 01:19.

Historymaster14dc1c698c600040c7f7c65…

Oct 9 2017

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History
master14dc1c698c600040c7f7c65…