Diffusion lammps (lammm-master) History

lammps/src
lammm-mastera362ece3e7e195f14535393…

Oct 17 2011

bug fix for angle pressure and energy accounting
d25353a56b39
·Axel Kohlmeyer on Oct 17 2011, 18:57.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7098 f3b2605a-c512-4ea7…
df52f93e5ebf
·sjplimp on Oct 17 2011, 17:22.
register the individual per-atom energy and virial arrays separately
892ae7b30bb5
·Axel Kohlmeyer on Oct 17 2011, 14:16.
added basic openmp support for angles and bonds
824031fdaf17
·Axel Kohlmeyer on Oct 17 2011, 01:53.

Oct 16 2011

Merge branch 'openmp-step5' into openmp-master
14e85af66bea
·Axel Kohlmeyer on Oct 16 2011, 19:03.
complete port of dihedral styles
5a28241e6757
·Axel Kohlmeyer on Oct 16 2011, 07:08.
make -suffix omp imply using package omp with default settings
c11cd8e8d233
·Axel Kohlmeyer on Oct 16 2011, 04:31.
port CHARMM dihedrals to new threading
79dbd4f7c9ad
·Axel Kohlmeyer on Oct 16 2011, 04:02.
ported first dihedral
d2c033d96362
·Axel Kohlmeyer on Oct 16 2011, 03:27.
ported the final pair styles
1ab5bcfc20c5
·Axel Kohlmeyer on Oct 16 2011, 03:27.
bugfix for resquared potential
745ed99913df
·Axel Kohlmeyer on Oct 16 2011, 02:47.
ported resquared
b40688c17306
·Axel Kohlmeyer on Oct 16 2011, 02:45.
fix bug in openmp neighbor list selection logic and port morse and peridynamics
92cd5bf435b5
·Axel Kohlmeyer on Oct 16 2011, 02:37.
ported final lj styles and lubricate
94fafdcaf965
·Axel Kohlmeyer on Oct 16 2011, 00:53.
ported a first chunk of lj pair potentials
56994681f764
·Axel Kohlmeyer on Oct 16 2011, 00:35.
use const where possible to help the compiler to do a better job
c0b7289780e0
·Axel Kohlmeyer on Oct 16 2011, 00:34.

Oct 15 2011

port dreiding hbond potentials
0d37279e8539
·Axel Kohlmeyer on Oct 15 2011, 23:49.
ported granular pair styles
fbf9c8970b6d
·Axel Kohlmeyer on Oct 15 2011, 23:35.
performance optimization for gay-berne
4d1a17cea3df
·Axel Kohlmeyer on Oct 15 2011, 23:16.
prot gauss and gay-berne
4d68dfabd93b
·Axel Kohlmeyer on Oct 15 2011, 23:11.
port over eam and eim
f379e385d12a
·Axel Kohlmeyer on Oct 15 2011, 22:33.
port pair styles using name starting with c or d
5547df4854e9
·Axel Kohlmeyer on Oct 15 2011, 22:09.
reformulate text one more time
aac322c77131
·Axel Kohlmeyer on Oct 15 2011, 19:06.
fix compilation issues without OpenMP active clarify message about threaded…
669b4e628ade
·Axel Kohlmeyer on Oct 15 2011, 17:31.
hook omp neighbor list build versions into list selection
80cea44a3d04
·Axel Kohlmeyer on Oct 15 2011, 14:57.
reinstate non-openmp versions of the neighbor list builds
72c850ce8b32
·Axel Kohlmeyer on Oct 15 2011, 14:36.
move OpenMP parallel neighbor list builds to separate files
7b7a041ff257
·Axel Kohlmeyer on Oct 15 2011, 13:58.
reinstate special neighbors handling for local atoms
8972490ff755
·Axel Kohlmeyer on Oct 15 2011, 07:33.
add code to support switching neighbor list flags with package omp
8591189ea09b
·Axel Kohlmeyer on Oct 15 2011, 07:32.
we cannot look for special atoms when building a full neighborlist with ghosts
e2b5a643f766
·Axel Kohlmeyer on Oct 15 2011, 04:53.
coefficient shadowing bugfix
ef4a84321910
·Axel Kohlmeyer on Oct 15 2011, 01:10.

Oct 14 2011

REBO neighbor list allocation bugfix
60e04bfead26
·Axel Kohlmeyer on Oct 14 2011, 23:51.
fix PI vs MY_PI issue
afab10eedbe5
·Axel Kohlmeyer on Oct 14 2011, 23:33.
complete support for airebo
8fa59cc88e2f
·Axel Kohlmeyer on Oct 14 2011, 23:32.
remove remaining race conditions in neighbor list builds
8ff73df6d742
·Axel Kohlmeyer on Oct 14 2011, 23:32.
more scripted changes to prepare for conversion
a055c0dfc4ac
·Axel Kohlmeyer on Oct 14 2011, 06:52.
convert all b*/omp pair styles
8416aba5cf39
·Axel Kohlmeyer on Oct 14 2011, 06:50.
change ThrOMP initializer through sed script
5344894becf0
·Axel Kohlmeyer on Oct 14 2011, 04:40.
convert two more pair styles
9fe212d8e68e
·Axel Kohlmeyer on Oct 14 2011, 04:38.
zeroing out arrays is no longer needed in eval()
06a02ca6750a
·Axel Kohlmeyer on Oct 14 2011, 04:22.
convert all pair header files to new thread infrastructure
cb230b449486
·Axel Kohlmeyer on Oct 14 2011, 04:09.
more cleanup and rewrites in thread support. port adp/omp.
c43abbce7f76
·Axel Kohlmeyer on Oct 14 2011, 04:07.
correct calculation of memory usage
f4de9d0c42c0
·Axel Kohlmeyer on Oct 14 2011, 04:05.

Oct 13 2011

refactor argument parsing for "package omp" handle selection of OpenMP or…
f5424c6f3a4c
·Axel Kohlmeyer on Oct 13 2011, 22:09.
fix API for rRESPA fix methods silence warnings in loop setup helper function
236f48fc0471
·Axel Kohlmeyer on Oct 13 2011, 17:55.
rename API for more clarity
111bc088b957
·Axel Kohlmeyer on Oct 13 2011, 06:50.
whitespace cleanup
1f21b4e693e0
·Axel Kohlmeyer on Oct 13 2011, 06:45.
simplified loop setup and access to force
c36e9214f346
·Axel Kohlmeyer on Oct 13 2011, 06:39.
some more cleanups and simplifications
17ff605492f5
·Axel Kohlmeyer on Oct 13 2011, 04:41.
another massive overhaul. now all stress calculations are working well. false…
d94fbfa39c21
·Axel Kohlmeyer on Oct 13 2011, 04:23.
force arrays and alike are cleared in parallel when the omp package command is…
747ea7246185
·Axel Kohlmeyer on Oct 13 2011, 04:20.

Oct 12 2011

another step toward proper thread data handling
c9ca5dad3787
·Axel Kohlmeyer on Oct 12 2011, 18:21.
code works for "newton off"
e180f2168c9a
·Axel Kohlmeyer on Oct 12 2011, 04:40.
manage per thread data similar to force and torque
a1d85e42fa68
·Axel Kohlmeyer on Oct 12 2011, 02:36.

Oct 11 2011

start integrating new thread infrastructure
a8e368e7ac06
·Axel Kohlmeyer on Oct 11 2011, 15:48.
start of new ev_tally infrastructure
593987561e89
·Axel Kohlmeyer on Oct 11 2011, 15:47.
give access to ThrData object
cbc1feeb19e8
·Axel Kohlmeyer on Oct 11 2011, 15:46.
update to make it compile without any /omp styles.
ae9b92b7ad87
·Axel Kohlmeyer on Oct 11 2011, 00:26.

Oct 10 2011

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7071 f3b2605a-c512-4ea7…
d2a730bc4031
·sjplimp on Oct 10 2011, 19:29.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7069 f3b2605a-c512-4ea7…
850a3cf8a4de
·sjplimp on Oct 10 2011, 19:22.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7068 f3b2605a-c512-4ea7…
49573998e714
·sjplimp on Oct 10 2011, 19:15.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7067 f3b2605a-c512-4ea7…
855e2aa3538e
·sjplimp on Oct 10 2011, 19:13.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7066 f3b2605a-c512-4ea7…
90a5d2b322bf
·sjplimp on Oct 10 2011, 19:11.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7065 f3b2605a-c512-4ea7…
e6a0e39b5070
·sjplimp on Oct 10 2011, 19:03.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7063 f3b2605a-c512-4ea7…
2e2abb3a7271
·sjplimp on Oct 10 2011, 18:36.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7061 f3b2605a-c512-4ea7…
6d849fea0e36
·sjplimp on Oct 10 2011, 18:26.
more improvements.
b9daeed889a6
·Axel Kohlmeyer on Oct 10 2011, 17:11.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7059 f3b2605a-c512-4ea7…
76da1a753ba1
·sjplimp on Oct 10 2011, 17:03.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7057 f3b2605a-c512-4ea7…
c1bfbd8e6165
·sjplimp on Oct 10 2011, 16:58.
incomplete rewrite of thread data handling
ca14e5bb83d1
·Axel Kohlmeyer on Oct 10 2011, 01:57.
create fix omp instance with package omp command
af967c6070ec
·Axel Kohlmeyer on Oct 10 2011, 01:54.
fix omp needs access to eflag/vflag
c57b98d77e33
·Axel Kohlmeyer on Oct 10 2011, 01:40.

Oct 9 2011

added class for per-thread data
caeabdc854d9
·Axel Kohlmeyer on Oct 9 2011, 20:39.
avoid race condition in REBO neighbor list
27c6af21d264
·Axel Kohlmeyer on Oct 9 2011, 19:43.
OpenMP support for COMB neighbor list
f4e72661d836
·Axel Kohlmeyer on Oct 9 2011, 19:42.

Oct 8 2011

include COMB changes from patch file
8d8f81627ca1
·Axel Kohlmeyer on Oct 8 2011, 21:55.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7049 f3b2605a-c512-4ea7…
2182b0443bba
·sjplimp on Oct 8 2011, 01:52.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7047 f3b2605a-c512-4ea7…
c8fa1bd5df84
·sjplimp on Oct 8 2011, 01:50.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7045 f3b2605a-c512-4ea7…
3e908537397e
·sjplimp on Oct 8 2011, 01:40.

Oct 7 2011

more obsolete code removed
a5ab1198ad4a
·Axel Kohlmeyer on Oct 7 2011, 15:26.
remove last traces of obsolete suffix handling
646b58958d02
·Axel Kohlmeyer on Oct 7 2011, 15:17.
fix compilation errors.
9741650e162d
·Axel Kohlmeyer on Oct 7 2011, 15:06.
silence warnings from (unused) MPI c++ bindings
43d4df434d1e
·Axel Kohlmeyer on Oct 7 2011, 15:05.
one more
de71bdbcb7aa
·Axel Kohlmeyer on Oct 7 2011, 14:55.
hybrid/omp styles no longer needed. removed.
db0954bbeec0
·Axel Kohlmeyer on Oct 7 2011, 14:54.
Merge branch 'openmp-step4' into openmp-master
280a43d68507
·Axel Kohlmeyer on Oct 7 2011, 14:51.
Merge branch 'master' into openmp-step4
a35cb79bc19c
·Axel Kohlmeyer on Oct 7 2011, 14:51.

Oct 6 2011

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7042 f3b2605a-c512-4ea7…
1579654c97b0
·sjplimp on Oct 6 2011, 20:36.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7040 f3b2605a-c512-4ea7…
0974524f0f9c
·sjplimp on Oct 6 2011, 19:55.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7039 f3b2605a-c512-4ea7…
15203cb79244
·sjplimp on Oct 6 2011, 19:55.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7036 f3b2605a-c512-4ea7…
8f91d37efdc8
·sjplimp on Oct 6 2011, 16:47.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7035 f3b2605a-c512-4ea7…
a7d891fbf02c
·sjplimp on Oct 6 2011, 16:46.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7033 f3b2605a-c512-4ea7…
6afceab52050
·sjplimp on Oct 6 2011, 16:32.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7031 f3b2605a-c512-4ea7…
2e32772d1da9
·sjplimp on Oct 6 2011, 16:25.
Remove MAX parentheses again
77371a142fc4
·athomps on Oct 6 2011, 16:25.

Oct 5 2011

Added brackets around MAX macro.
dab569f8cc70
·athomps on Oct 5 2011, 22:48.

Oct 4 2011

used typename instead of class for templated MIN/MAX inline functions
6b4e8e1d6250
·Axel Kohlmeyer on Oct 4 2011, 18:38.
prep work for future ev_tally changes.
c1a4462acb4e
·Axel Kohlmeyer on Oct 4 2011, 05:15.
silence warnings about redefined macros
5012cb4662df
·Axel Kohlmeyer on Oct 4 2011, 04:37.
fix bug that was interfering with suffix handling
6e5fd08ec5a0
·Axel Kohlmeyer on Oct 4 2011, 04:32.

lammps/srclammm-mastera362ece3e7e195f14535393…

Oct 17 2011

Oct 16 2011

Oct 15 2011

Oct 14 2011

Oct 13 2011

Oct 12 2011

Oct 11 2011

Oct 10 2011

Oct 9 2011

Oct 8 2011

Oct 7 2011

Oct 6 2011

Oct 5 2011

Oct 4 2011

lammps/src
lammm-mastera362ece3e7e195f14535393…