Diffusion lammps (lammm-master) History

lammps/src
lammm-masterb0ffa46a3bb994e3fe0c157…

Aug 20 2015

Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
e5f316ecf1f8
·Axel Kohlmeyer on Aug 20 2015, 13:42.
Adding optimizations to Kokkos EAM pair style
e4e52616dd89
·stamoor on Aug 20 2015, 00:50.

Aug 19 2015

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13918 f3b2605a-c512-4ea7…
8dae768dcf52
·sjplimp on Aug 19 2015, 18:15.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13910 f3b2605a-c512-4ea7…
cd861535f0d9
·sjplimp on Aug 19 2015, 17:32.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13909 f3b2605a-c512-4ea7…
56d0caefcb66
·sjplimp on Aug 19 2015, 17:23.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13905 f3b2605a-c512-4ea7…
c85a42ab6d62
·sjplimp on Aug 19 2015, 17:11.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13903 f3b2605a-c512-4ea7…
2f55b6da36a3
·sjplimp on Aug 19 2015, 16:55.
remove stray debug printf
2b71bee849ca
·Axel Kohlmeyer on Aug 19 2015, 13:15.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
62b18db5921f
·Axel Kohlmeyer on Aug 19 2015, 13:15.
initialize return value
0c5f1d17b227
·Axel Kohlmeyer on Aug 19 2015, 04:55.
initialize pointer to pRNG.
ff62b51dea76
·Axel Kohlmeyer on Aug 19 2015, 04:53.
fix missing initialization
112568605fcd
·Axel Kohlmeyer on Aug 19 2015, 04:50.
better bugfix for OOB access in fix balance
5a93085e460d
·Axel Kohlmeyer on Aug 19 2015, 04:46.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13895 f3b2605a-c512-4ea7…
4d1904165b04
·sjplimp on Aug 19 2015, 01:22.
avoid segfault when evaporating by molecule id in a non-molecular system
1317dba8a07f
·Axel Kohlmeyer on Aug 19 2015, 01:10.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13892 f3b2605a-c512-4ea7…
dc2ebd0393b3
·sjplimp on Aug 19 2015, 00:59.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13891 f3b2605a-c512-4ea7…
6da9e4c21765
·sjplimp on Aug 19 2015, 00:54.
remove file pointer leak
efff543e9f5d
·Axel Kohlmeyer on Aug 19 2015, 00:20.

Aug 18 2015

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13890 f3b2605a-c512-4ea7…
adabfc38a6b8
·sjplimp on Aug 18 2015, 23:50.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13889 f3b2605a-c512-4ea7…
916fc0f1cb2a
·sjplimp on Aug 18 2015, 23:13.
check for atom->molecule flag if looking for a molecule id
221673e6bf9d
·Axel Kohlmeyer on Aug 18 2015, 17:51.
better handing of exceptional cases for ReaderNative/XYZ::read_lines().
8e8e9de5814c
·Axel Kohlmeyer on Aug 18 2015, 15:00.
better handing of exceptional cases for ReadData::skip_lines().
63f9d4ae31fe
·Axel Kohlmeyer on Aug 18 2015, 14:49.
avoid potential buffer overrun
cde3ef40e1b4
·Axel Kohlmeyer on Aug 18 2015, 14:45.
fix potential out-of-range memory write.
47458f088903
·Axel Kohlmeyer on Aug 18 2015, 14:37.
fix copy-n-paste bugs spotted by coverity: CID 134471, CID 134472
aa73b7899c4f
·Axel Kohlmeyer on Aug 18 2015, 14:01.
avoid insignificant memory leak
498ae98a058b
·Axel Kohlmeyer on Aug 18 2015, 13:50.
initialize did_compute
48cf4d0906fd
·Axel Kohlmeyer on Aug 18 2015, 13:40.
fixed very subtle bug found by coverity
a2f0f9d3cca5
·Axel Kohlmeyer on Aug 18 2015, 12:55.
correct out-of-bounds array access due to one-off error.
79fd06022f33
·Axel Kohlmeyer on Aug 18 2015, 12:52.
fix very subtle possible bug when runstyle respa settings may have changed.
51d724a3a67b
·Axel Kohlmeyer on Aug 18 2015, 05:24.
fixes bug in suffix handling spotted by coverity scan: CID 134474 and CID 134486
b00a3974987a
·Axel Kohlmeyer on Aug 18 2015, 05:16.
fix bug introduced when adding variable cylinder radius region
246d432051bb
·Axel Kohlmeyer on Aug 18 2015, 05:08.
nasty bug when reading data files multiple times.
7575e6a64373
·Axel Kohlmeyer on Aug 18 2015, 04:30.
fix logic issues detected by coverity scan
446427cc8b3e
·Axel Kohlmeyer on Aug 18 2015, 04:28.
silence unitialized variable warning.
185cadc10269
·Axel Kohlmeyer on Aug 18 2015, 03:57.
third in the series of cut-n-paste bugs. CID 134505
0c594f344661
·Axel Kohlmeyer on Aug 18 2015, 03:54.
fix cut-n-paste bug spotted by coverity scan: CID 134509
15448906eb63
·Axel Kohlmeyer on Aug 18 2015, 03:51.
fix cut-n-paste bug spotted by coverity scan: CID 134510
ab69248f2790
·Axel Kohlmeyer on Aug 18 2015, 03:48.
avoid file pointer leak spotted by coverity scan: CID 134485
7a820b818ceb
·Axel Kohlmeyer on Aug 18 2015, 02:33.
fix bug spotted by coverity scan: CID 134484
67960cdad695
·Axel Kohlmeyer on Aug 18 2015, 02:02.
remove dead code spotted by coverity scan. CID 134537
0edf3cbd318f
·Axel Kohlmeyer on Aug 18 2015, 01:44.

Aug 17 2015

update .gitignore
910c9966dd3f
·Axel Kohlmeyer on Aug 17 2015, 02:26.
MPI_Get_library_version() is not portable enough.
e63b4ef359d2
·Axel Kohlmeyer on Aug 17 2015, 00:48.

Aug 16 2015

make info output more consistent and add comm info
66e9f9213034
·Axel Kohlmeyer on Aug 16 2015, 20:55.
add communication output to info command
752ef5d90a56
·Axel Kohlmeyer on Aug 16 2015, 19:00.
add MPI version and level query. correct processor name API C bindings.
eaf74e943fc9
·Axel Kohlmeyer on Aug 16 2015, 18:56.
return 0.0 when querying elapsed time with timers off
1c467528a4f5
·Axel Kohlmeyer on Aug 16 2015, 16:42.
overlooked one tagint to int pointer assignment.
221557d3a9fc
·Axel Kohlmeyer on Aug 16 2015, 04:05.
handle correct compilation problem for 64-bit tags in USER-SMD
3ea04204dc4f
·Axel Kohlmeyer on Aug 16 2015, 03:45.
use zlib.h header instead of a (less portable) forward declaration.
60cdd56380ac
·Axel Kohlmeyer on Aug 16 2015, 03:45.

Aug 15 2015

fix typo
2a9c607da1df
·Axel Kohlmeyer on Aug 15 2015, 04:46.
add proper handling of tags
ffa9ec2c0ab7
·Axel Kohlmeyer on Aug 15 2015, 04:36.
Merge branch 'bugfixes/memory_corruption_and_invalid_reads' of git://github.
b45d4d087336
·Axel Kohlmeyer on Aug 15 2015, 02:32.
basic integration of Travis-CI for build testing
2319e569b5a5
·Axel Kohlmeyer on Aug 15 2015, 00:27.

Aug 14 2015

remove useless neighbor list output from info command.
4bba2484099c
·Axel Kohlmeyer on Aug 14 2015, 21:55.
Avoid access outside of array bounds
bce38482786e
·Richard Berger on Aug 14 2015, 20:51.
Fixes out-of-bounds accesses
8a1bc1088a8d
·Richard Berger on Aug 14 2015, 20:42.
output binning parameters in neighbor list summary
0982c06bf52a
·Axel Kohlmeyer on Aug 14 2015, 15:27.

Aug 13 2015

delete files that have been moved to the COMPRESS package
ccaf2568a852
·Axel Kohlmeyer on Aug 13 2015, 14:24.
make for serial compile with clang++
3e8d242d10e6
·Axel Kohlmeyer on Aug 13 2015, 14:24.
correct PACKLIB list to contain all packages that cannot be built against STUBS
f213cccfb760
·Axel Kohlmeyer on Aug 13 2015, 14:19.

Aug 12 2015

convery library compression styles into "COMPRESS" package
83f21d479ce3
·Axel Kohlmeyer on Aug 12 2015, 14:08.

Aug 11 2015

add compute heat/flux/tally version from loris ercole (@SISSA)
96e92899cceb
·Axel Kohlmeyer on Aug 11 2015, 17:26.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
c020fba2a153
·Axel Kohlmeyer on Aug 11 2015, 16:02.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
68c691f4015e
·Axel Kohlmeyer on Aug 11 2015, 04:33.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13862 f3b2605a-c512-4ea7…
8cc111e8d32f
·sjplimp on Aug 11 2015, 01:53.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13861 f3b2605a-c512-4ea7…
5f76611ecf24
·sjplimp on Aug 11 2015, 01:50.

Aug 10 2015

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13855 f3b2605a-c512-4ea7…
23a8240bfed8
·sjplimp on Aug 10 2015, 22:34.
Fixed molecule mass when gcmc offset applied
4b03a29c04e5
·athomps on Aug 10 2015, 04:57.

Aug 9 2015

must not have "using namespace" in header files
68894871844e
·Axel Kohlmeyer on Aug 9 2015, 19:06.

Aug 8 2015

added dump cfg/gz to the mix
d42409e9b1ed
·Axel Kohlmeyer on Aug 8 2015, 01:37.
add dump styles atom/gz, custom/gz, and xyz/gz using zlib
11f77056a45e
·Axel Kohlmeyer on Aug 8 2015, 01:26.
add code to make it compatible with derived classes holding a custom file…
79cf211c36aa
·Axel Kohlmeyer on Aug 8 2015, 01:25.
fully zlib compatible linker flags
f8b4602f17b9
·Axel Kohlmeyer on Aug 8 2015, 01:24.

Aug 7 2015

fix typo in MPIIO header multiple inclusion guard.
460312f13cb0
·Axel Kohlmeyer on Aug 7 2015, 23:45.
clean up include files and installation script for USER-SMD
ebe0635bf63b
·Axel Kohlmeyer on Aug 7 2015, 06:34.

Aug 6 2015

replace custom data type "real" with standard type "double" to remove namespace…
58a712d3d4fc
·Axel Kohlmeyer on Aug 6 2015, 20:39.
modifications to USER-SMD to reduce namespace pollution.
3276ae3b0a27
·Axel Kohlmeyer on Aug 6 2015, 19:51.
Merge branch 'lammps-icms' of bitbucket.org:akohlmey/lammps-icms into lammps…
4fef3cd9f018
·Axel Kohlmeyer on Aug 6 2015, 06:57.
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
51072805199b
·Axel Kohlmeyer on Aug 6 2015, 06:51.

Aug 5 2015

Kokkos: Pair EAM: remove old code
92f0f87b3629
·crtrott on Aug 5 2015, 19:38.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13840 f3b2605a-c512-4ea7…
cefaee3342f5
·sjplimp on Aug 5 2015, 02:43.

Aug 4 2015

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13832 f3b2605a-c512-4ea7…
318aefa19c70
·sjplimp on Aug 4 2015, 22:56.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13831 f3b2605a-c512-4ea7…
2f7344a02a6b
·sjplimp on Aug 4 2015, 21:55.
Kokkos: Fixing issue in verlet_kokkos.cpp
d0a8cd76e551
·crtrott on Aug 4 2015, 21:31.
Kokkos: Adding support for experimental view implementation
ca954d51819b
·crtrott on Aug 4 2015, 21:30.
Kokkos: EAM Adding option to use FLOAT4 loads for splines
bd44d50ef221
·crtrott on Aug 4 2015, 21:29.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13830 f3b2605a-c512-4ea7…
365d1190a2ca
·sjplimp on Aug 4 2015, 21:26.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13827 f3b2605a-c512-4ea7…
810a13413b28
·sjplimp on Aug 4 2015, 21:08.

Aug 3 2015

manually merged trivial change from lammps github repo from pull request #3
b1baef035448
·Axel Kohlmeyer on Aug 3 2015, 23:58.
integrate USER-H5MD package into package lists.
0b8605a69684
·Axel Kohlmeyer on Aug 3 2015, 23:21.
small adjustments to make USER-H5MD package integration cleaner
c91f33f5b4e5
·Axel Kohlmeyer on Aug 3 2015, 23:21.
Merge branch 'start_dump_h5md' of git://github.com/pdebuyl/lammps into…
c175e7f1805b
·Axel Kohlmeyer on Aug 3 2015, 22:44.
fix dump_charge data name
6873ab71863b
·Pierre de Buyl on Aug 3 2015, 22:03.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13815 f3b2605a-c512-4ea7…
366ae00d2e8b
·athomps / Pierre de Buyl on Aug 3 2015, 21:00.
Added fix gcmc check to init()
51b75f9b859e
·athomps / Pierre de Buyl on Aug 3 2015, 21:00.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13810 f3b2605a-c512-4ea7…
975eb568a669
·sjplimp / Pierre de Buyl on Aug 3 2015, 21:00.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13770 f3b2605a-c512-4ea7…
39d0ff0724f2
·sjplimp / Pierre de Buyl on Aug 3 2015, 21:00.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13768 f3b2605a-c512-4ea7…
edc7e698a50f
·sjplimp / Pierre de Buyl on Aug 3 2015, 21:00.

lammps/srclammm-masterb0ffa46a3bb994e3fe0c157…

Aug 20 2015

Aug 19 2015

Aug 18 2015

Aug 17 2015

Aug 16 2015

Aug 15 2015

Aug 14 2015

Aug 13 2015

Aug 12 2015

Aug 11 2015

Aug 10 2015

Aug 9 2015

Aug 8 2015

Aug 7 2015

Aug 6 2015

Aug 5 2015

Aug 4 2015

Aug 3 2015

lammps/src
lammm-masterb0ffa46a3bb994e3fe0c157…