Diffusion lammps (lammm-master) History

lammps/tools
lammm-master429d56e3a3801c99b750dbb…

Aug 23 2013

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10662 f3b2605a-c512-4ea7…
f143f1a5465d
·sjplimp on Aug 23 2013, 16:31.

Aug 13 2013

use parallel compile throughout and include AtC examples
98608c6e434b
·Axel Kohlmeyer on Aug 13 2013, 06:00.

Aug 5 2013

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10534 f3b2605a-c512-4ea7…
ebe6ead34839
·sjplimp on Aug 5 2013, 16:11.

Aug 3 2013

build in parallel. add msi2lmp proper readme.
9a97db1f954f
·Axel Kohlmeyer on Aug 3 2013, 15:01.
adjust for additional README file
70aa47a8e237
·Axel Kohlmeyer on Aug 3 2013, 14:57.
Merge remote branch 'lammps-ro/master' into lammps-icms
addeed415a25
·Axel Kohlmeyer on Aug 3 2013, 14:20.

Aug 2 2013

fix typo
c07625e15b3c
·Axel Kohlmeyer on Aug 2 2013, 19:43.
step version number of data file comparison tool
d4c0bcecdc66
·Axel Kohlmeyer on Aug 2 2013, 19:19.
rename $BIOSYM_LIBRARY to $MSI2LMP_LIBRARY and biosym_frc_files for frc_files
60ac646a0ce3
·Axel Kohlmeyer on Aug 2 2013, 19:17.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10524 f3b2605a-c512-4ea7…
7b1a0c4b1f70
·sjplimp on Aug 2 2013, 17:06.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10523 f3b2605a-c512-4ea7…
0ce4185a7cbd
·sjplimp on Aug 2 2013, 17:06.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10522 f3b2605a-c512-4ea7…
69d7e0a82341
·sjplimp on Aug 2 2013, 17:05.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10521 f3b2605a-c512-4ea7…
e3300dd7b36a
·sjplimp on Aug 2 2013, 17:05.
include msi2lmp test examples and data file in common package as example
431a1b68a2fd
·Axel Kohlmeyer on Aug 2 2013, 14:15.
import and adapt changes from jeff greathouse to support opls-aa
dbae00bfce44
·Axel Kohlmeyer on Aug 2 2013, 13:13.

Jul 28 2013

add likely installation dir for MPICH2 to %PATH
7d838f00b7ca
·Axel Kohlmeyer on Jul 28 2013, 23:18.

Jul 26 2013

Merge remote branch 'lammps-ro/master' into lammps-icms
60e58c44cf1f
·Axel Kohlmeyer on Jul 26 2013, 13:15.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10391 f3b2605a-c512-4ea7…
6cc90ecca273
·sjplimp on Jul 26 2013, 01:51.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10378 f3b2605a-c512-4ea7…
d348e525e8ef
·sjplimp on Jul 26 2013, 00:59.

Jul 25 2013

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10359 f3b2605a-c512-4ea7…
fadc25d704ef
·sjplimp on Jul 25 2013, 23:54.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10358 f3b2605a-c512-4ea7…
9f07d255bf46
·sjplimp on Jul 25 2013, 23:53.

Jul 24 2013

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10317 f3b2605a-c512-4ea7…
4746837b5e25
·sjplimp on Jul 24 2013, 15:58.
Merge remote branch 'lammps-ro/master' into lammps-icms
f6484736ec08
·Axel Kohlmeyer on Jul 24 2013, 13:33.

Jul 23 2013

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10288 f3b2605a-c512-4ea7…
fd39535f88d7
·sjplimp on Jul 23 2013, 17:16.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10287 f3b2605a-c512-4ea7…
1d95bd961d33
·sjplimp on Jul 23 2013, 17:14.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10286 f3b2605a-c512-4ea7…
8f9c6b5a0214
·sjplimp on Jul 23 2013, 17:13.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10276 f3b2605a-c512-4ea7…
bec0c049d838
·sjplimp on Jul 23 2013, 00:49.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10275 f3b2605a-c512-4ea7…
268c782771f1
·sjplimp on Jul 23 2013, 00:49.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10274 f3b2605a-c512-4ea7…
9034be4e5e43
·sjplimp on Jul 23 2013, 00:49.

Jul 22 2013

adjust for change in charmm dihedral style restart format
619c914ee553
·Axel Kohlmeyer on Jul 22 2013, 11:04.

Jul 20 2013

enable deltarpm metadata generation in repository
f20a3088396f
·Axel Kohlmeyer on Jul 20 2013, 13:50.

Jul 19 2013

next attempt to fix the deltarpm generation
1c5f43a1f25f
·Axel Kohlmeyer on Jul 19 2013, 19:53.
add support for building deltarpms
b4239022c5c1
·Axel Kohlmeyer on Jul 19 2013, 17:19.

Jul 18 2013

update readme
e8f6cfdc1a78
·Axel Kohlmeyer on Jul 18 2013, 22:16.
add contributed test for triclinic and clayff
8e6777342774
·Axel Kohlmeyer on Jul 18 2013, 22:12.
store mass and charge in double variables to reduce truncation errors
ff0f7a0659b7
·Axel Kohlmeyer on Jul 18 2013, 21:56.
write out coordinates with correct image flags. various cleanups. bugfixes.
2e202dc7bfdf
·Axel Kohlmeyer on Jul 18 2013, 21:31.

Jul 13 2013

handle the case that there may be nothing to symlink to for the "latest" entry
1ce7d8240b2e
·Axel Kohlmeyer on Jul 13 2013, 13:47.
use margin and padding style properties instead of page breaks for formatting
56f37f264195
·Axel Kohlmeyer on Jul 13 2013, 13:46.
Merge branch 'lammps-icms' of git://git.icms.temple.edu/lammps-icms into lammps…
fbbb5498e3d8
·Axel Kohlmeyer on Jul 13 2013, 13:45.
apply inexact floating point comparison where needed and lower threshold
6c44d993b769
·Axel Kohlmeyer on Jul 13 2013, 13:44.

Jul 12 2013

port fix to overzealous deleting bug from rpm sync script
a2b86fa7de52
·Axel Kohlmeyer on Jul 12 2013, 18:58.
add name and crank version
19d2d19f2762
·Axel Kohlmeyer on Jul 12 2013, 18:18.
add name/email
445566acb191
·Axel Kohlmeyer on Jul 12 2013, 18:14.
remove old references and add input files
31c545fc4f89
·Axel Kohlmeyer on Jul 12 2013, 17:52.
remove c++ style comments. do not recenter for non-periodic, add a buffer.
eda8e60d1540
·Axel Kohlmeyer on Jul 12 2013, 17:49.
finish conversion of original reference inputs to new scheme
2c0fe147e574
·Axel Kohlmeyer on Jul 12 2013, 17:49.
fix some bug in data file validator
50902731f2ce
·Axel Kohlmeyer on Jul 12 2013, 17:32.
added nylon and crambin examples with support for regtester
7872de697b4f
·Axel Kohlmeyer on Jul 12 2013, 17:31.
small tweak, test for multi-molecule
fd864ba269da
·Axel Kohlmeyer on Jul 12 2013, 16:09.
new test added naphthalene
47fd071935cc
·Axel Kohlmeyer on Jul 12 2013, 16:09.
make script less verbose, but make verbosity easily configurable
1af8f60a4206
·Axel Kohlmeyer on Jul 12 2013, 15:18.
update class2 reference output for ethane after bugfix
8521abad583a
·Axel Kohlmeyer on Jul 12 2013, 15:18.
minor formatting improvement
23f84861a11c
·Axel Kohlmeyer on Jul 12 2013, 15:17.
add set of benzene molecule tests
024a29e6ed8d
·Axel Kohlmeyer on Jul 12 2013, 15:08.
replace needless use of fprintf with fputs
6ceff875f44f
·Axel Kohlmeyer on Jul 12 2013, 14:58.
made the code for writing dihedrals coeffs more readable.
d16f8fd229f7
·Axel Kohlmeyer on Jul 12 2013, 14:54.
we need to output cvff style imporpers for class1 not harmonic
f19c7987eeef
·Axel Kohlmeyer on Jul 12 2013, 14:29.
update reference data after implementing write_data into class2 impropers
12c77237fb00
·Axel Kohlmeyer on Jul 12 2013, 13:44.
include ethane test for class 1 force field
185666821f53
·Axel Kohlmeyer on Jul 12 2013, 11:35.
support more types of comparison.
0cbd052c81b3
·Axel Kohlmeyer on Jul 12 2013, 11:34.
update reference data for shifted boxes
a52044609033
·Axel Kohlmeyer on Jul 12 2013, 09:29.
add support for dihedrals and impropers and more class2 coeff sections
454636a783ca
·Axel Kohlmeyer on Jul 12 2013, 09:28.
update readme
245f3d4a1e5c
·Axel Kohlmeyer on Jul 12 2013, 08:32.
add flag to make recentering optional
4f7adaca2cf1
·Axel Kohlmeyer on Jul 12 2013, 07:33.
clean up box handling by using a separate storage for LAMMPS data shift box to…
0db8b7e21633
·Axel Kohlmeyer on Jul 12 2013, 01:07.
rename class2 reference files, too
af632edbf7fc
·Axel Kohlmeyer on Jul 12 2013, 00:06.

Jul 11 2013

fix typos
cf323341576d
·Axel Kohlmeyer on Jul 11 2013, 23:57.
split class two tests into two variants 2a and 2b with pcff and compass
503bf92a95da
·Axel Kohlmeyer on Jul 11 2013, 23:56.
fix longstanding improper/OOP bug in msi2lmp
1adad55790f7
·Axel Kohlmeyer on Jul 11 2013, 23:53.
update reference data files with corrected versions
87579249082c
·Axel Kohlmeyer on Jul 11 2013, 21:41.
update reference data files to corrected versions
7d9e834df16f
·Axel Kohlmeyer on Jul 11 2013, 21:34.
count tests and errors and report both
894cd7edb0e7
·Axel Kohlmeyer on Jul 11 2013, 21:05.
next test example: one hydrogen and one water
4de9ded00908
·Axel Kohlmeyer on Jul 11 2013, 20:59.
add second test example: water
a47b17026742
·Axel Kohlmeyer on Jul 11 2013, 20:33.
add support for angles
583b59c0a1c3
·Axel Kohlmeyer on Jul 11 2013, 20:33.
add new regression test suite for msi2lmp and one pair of tests
e99ae55b6908
·Axel Kohlmeyer on Jul 11 2013, 19:47.

Jul 10 2013

remove support for older versions of LAMMPS
4d937a0e319a
·Axel Kohlmeyer on Jul 10 2013, 14:31.

Jul 9 2013

we cannot have hyphens in varible names. ugh.
2375bf2da541
·Axel Kohlmeyer on Jul 9 2013, 16:15.
another try to fix this annoying pruning thing.
90560d223445
·Axel Kohlmeyer on Jul 9 2013, 16:00.
differentiate between subpackages when pruning
62d8484b85ea
·Axel Kohlmeyer on Jul 9 2013, 15:53.
exclude "latest" entries from repomd
8a2c6dbcd5ac
·Axel Kohlmeyer on Jul 9 2013, 14:50.
include date selection logic from rpm sync script
7eb24e316dd6
·Axel Kohlmeyer on Jul 9 2013, 14:32.
fix typo in sync script
010ea8f925b2
·Axel Kohlmeyer on Jul 9 2013, 14:31.
fix build issue with msi2lmp potentials
d7fedb825e1f
·Axel Kohlmeyer on Jul 9 2013, 13:47.
improve file delete logic
5984a300898d
·Axel Kohlmeyer on Jul 9 2013, 13:41.

Jul 7 2013

mention fedora 19 as available repository
15c36924d889
·Axel Kohlmeyer on Jul 7 2013, 21:25.
update webpage for bundling msi2lmp
66e3a739323a
·Axel Kohlmeyer on Jul 7 2013, 15:20.
support potential/forcefield environment variables and include msi2lmp
cbd640ab048c
·Axel Kohlmeyer on Jul 7 2013, 15:16.
make location of potential/forcefield files depend on the RPM variables
c1db4de795ce
·Axel Kohlmeyer on Jul 7 2013, 15:04.

Jul 6 2013

make pruning more verbose
d8023fecd5dd
·Axel Kohlmeyer on Jul 6 2013, 20:22.
fix typo
1075cecaf47c
·Axel Kohlmeyer on Jul 6 2013, 14:31.

Jul 5 2013

correct CMAKE toolchain file references
72318ae605a0
·Axel Kohlmeyer on Jul 5 2013, 22:43.
include pruning and symlinking into windows package sync
cd88b73edded
·Axel Kohlmeyer on Jul 5 2013, 17:11.
fix quoted filename bug
3f395044fa55
·Axel Kohlmeyer on Jul 5 2013, 16:18.
do not delete the directory where we collect the packages
e44be7e44e95
·Axel Kohlmeyer on Jul 5 2013, 15:00.
shell script bug fix on conditional
65c114233bf6
·Axel Kohlmeyer on Jul 5 2013, 14:49.
apply pruning scheme to windows packages. reorganize directories
32fb8c114953
·Axel Kohlmeyer on Jul 5 2013, 14:49.
apply bugfixes and let go life with pruning
eddb08b90a38
·Axel Kohlmeyer on Jul 5 2013, 14:15.
reverse sort order of files
105720427be1
·Axel Kohlmeyer on Jul 5 2013, 14:15.

lammps/toolslammm-master429d56e3a3801c99b750dbb…

Aug 23 2013

Aug 13 2013

Aug 5 2013

Aug 3 2013

Aug 2 2013

Jul 28 2013

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Jul 25 2013

Jul 24 2013

Jul 23 2013

Jul 22 2013

Jul 20 2013

Jul 19 2013

Jul 18 2013

Jul 13 2013

Jul 12 2013

Jul 11 2013

Jul 10 2013

Jul 9 2013

Jul 7 2013

Jul 6 2013

Jul 5 2013

lammps/tools
lammm-master429d56e3a3801c99b750dbb…