Diffusion lammps (master) History

History
masterb1b4a52b14e255597d8af22…

Oct 18 2017

Merge pull request #695 from timattox/USER-DPD_small_updates
b1b4a52b14e2
·Steve Plimpton / GitHub on Oct 18 2017, 21:25.
Merge pull request #696 from wmbrownIntel/intel-update-oct17
382de5034188
·Steve Plimpton / GitHub on Oct 18 2017, 21:25.
Merge pull request #688 from lammps/history
7dfc6b7eab71
·Steve Plimpton / GitHub on Oct 18 2017, 21:24.
update multi-threaded neighbor list build for neighbor list refactor
17c17ac40996
·Axel Kohlmeyer on Oct 18 2017, 17:25.
update respa/omp integrator style for neighbor list refactor
39ededd46cf7
·Axel Kohlmeyer on Oct 18 2017, 17:24.
update several pair styles to be compliant with refactored respa lists data…
2c7528811d7f
·Axel Kohlmeyer on Oct 18 2017, 17:24.
more changes to rRESPA neighbor lists
0966e14e73a7
·Steve Plimpton on Oct 18 2017, 01:33.

Oct 17 2017

USER-INTEL: Bug fix for case where a bond/angle/dihedral/improper style is…
bb141aaae04f
·Michael Brown on Oct 17 2017, 07:51.

Oct 16 2017

Merge branch 'history' of github.com:lammps/lammps into history
59de1a71c8cd
·Axel Kohlmeyer on Oct 16 2017, 20:37.
USER-DPD Kokkos: propagate the new neigh_modify options from efaa4c67
4c6779cb0d61
·Tim Mattox on Oct 16 2017, 20:37.
update USER-OMP code for shear history neighbor refactoring
5fb5f70ec684
·Axel Kohlmeyer on Oct 16 2017, 20:37.
USER-DPD: remove unused coord2bin() variants, and add ISFINITE checks
b0bba1976b33
·Tim Mattox on Oct 16 2017, 20:36.

Oct 14 2017

Merge pull request #693 from giacomofiorin/colvars-update
f8f13d929fad
·Steve Plimpton / GitHub on Oct 14 2017, 01:25.

Oct 13 2017

Update Colvars to version 2017-10-11
3e89b270fdf8
·Giacomo Fiorin on Oct 13 2017, 19:45.
Fix compile errors from neigh history refactor
f6ddc8c7c9ba
·Stan Moore on Oct 13 2017, 18:49.
Merge pull request #691 from akohlmey/collected-fixes
a973c65d67cf
·Steve Plimpton / GitHub on Oct 13 2017, 17:50.
Merge pull request #689 from rbberger/pylammps_autocomplete_fix
1a200588bd4b
·Steve Plimpton / GitHub on Oct 13 2017, 17:49.
Merge pull request #686 from giacomofiorin/lepton-library
18ca2292c28f
·Steve Plimpton / GitHub on Oct 13 2017, 17:48.
Merge pull request #685 from ellio167/kim-api-v1.9.2
d3ef4bd59414
·Steve Plimpton / GitHub on Oct 13 2017, 17:48.
drop const qualifier to allow bracketing of lookup index
3df9caf43533
·Axel Kohlmeyer on Oct 13 2017, 16:29.
handle lookup exceptions consistently across energy and energy+force lookup in…
fa2e5ac2d902
·Axel Kohlmeyer on Oct 13 2017, 16:13.
handle invalid lookup for bond/angle tabulation
b7c749260885
·Axel Kohlmeyer on Oct 13 2017, 15:50.
bugfix. avoiding operating on uninitialize data. closes #690
cee94da85e16
·Axel Kohlmeyer on Oct 13 2017, 06:15.

Oct 12 2017

Limit IPython autocomplete to known commands and properties
45aa7de171dd
·Richard Berger on Oct 12 2017, 20:43.

Oct 11 2017

add support for neighbor list history refactoring in USER-OMP part 2
53aa92cfafd1
·Axel Kohlmeyer on Oct 11 2017, 16:30.
add support for neighbor list history refactoring in USER-OMP part 1
7e35042c42e9
·Axel Kohlmeyer on Oct 11 2017, 16:29.
refactoring of neighbor history
01051e4cb13c
·Steve Plimpton on Oct 11 2017, 00:53.

Oct 9 2017

Add Lepton library within lib/colvars
d90aad887eb6
·Giacomo Fiorin on Oct 9 2017, 21:25.
Update lib/kim for kim-api-v1.9.2
775a15b9da58
·Ryan S. Elliott on Oct 9 2017, 21:06.
Merge pull request #684 from irisTa56/bugfix-in-domain.cpp
93c9a9274319
·Steve Plimpton / GitHub on Oct 9 2017, 16:30.
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.
Bugfix for checking image flags
534b7adde4b3
·irisTa56 on Oct 9 2017, 14:29.
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
4cfa88b70f90
·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
15853a0e38dc
·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
5d0626e50e30
·Steve Plimpton / GitHub on Oct 6 2017, 00:58.
Merge pull request #664 from timattox/kokkos_atom2bin
4b7ca0383aac
·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.

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History
masterb1b4a52b14e255597d8af22…