4e03df2d19
Merge branch 'integration' into fix-flow-gauss
2016-08-28 06:55:12 -04:00
e1045851c0
incorporate bugfix and cleanup from lammps-icms and upstream
2016-08-28 06:52:03 -04:00
0192d2e359
Merge pull request #5 from akohlmey/initialize-pointers
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enforce initializing pointers in constructors to NULL
2016-08-27 17:14:27 -06:00
3a1397dc7c
sync with SVN
2016-08-27 17:11:16 -06:00
bb721db8de
Merge branch 'integration' into fix-flow-gauss
2016-08-27 19:02:33 -04:00
0c2e643062
Merge pull request #9 from rbberger/remove_sha1sum_dependency
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Remove sha1sum dependency for doc generation
2016-08-27 17:02:17 -06:00
ef69bf8695
Merge pull request #11 from akohlmey/python3-for-make-py
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Python 3 support for Make.py with Python 2.7 compatibility
2016-08-27 17:01:29 -06:00
6a4633af0a
Merge pull request #12 from akohlmey/shell-script-paranoia
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Disable custom locale and grep options in shell scripts
2016-08-27 16:59:43 -06:00
c80dad0028
new fix flow/gauss command
2016-08-27 16:25:01 -06:00
1c13b30a70
small cleanup and generalization of fix flow/gauss
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- remove unused or unneeded class members
- make the code compatible with per-atom masses
- test for and abend in case of an invalid group mass
(cherry picked from commit e017b33898
2016-08-27 17:33:46 -04:00
c570bf26e0
enforce C or POSIX locale in all shell scripts and turn of enforced global grep options
2016-08-27 01:57:45 -04:00
742c853775
need to ignore src/Make.py.last as well
2016-08-26 17:48:59 -04:00
9932b73227
Merge branch 'integration' into python3-for-make-py
2016-08-26 17:48:06 -04:00
90272f6c71
some more tweaks needed to improve python2/3 compatibility
2016-08-26 17:46:57 -04:00
8dd42789f8
correct for futurize not being able to fully convert functionality of the commands module
2016-08-26 17:15:39 -04:00
a0592d1b64
Merge branch 'gitignore-improvements' into integration
2016-08-26 13:54:29 -06:00
9be235d872
improved .gitignore files to show only changes in relevant folders and files
2016-08-26 14:34:42 -04:00
2beecd1e73
removal of doc/html/_sources and minor sync with SVN
2016-08-26 11:34:37 -06:00
95aabdf51a
Add MacOS X instructions to doc generation README
2016-08-26 10:08:22 -04:00
ea368919f3
Remove sha1sum dependency for doc generation
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On MacOS X there is no sha1sum. So to simplify doc generation on those systems
use a Python script instead to generate a unique string from the repository
path.
2016-08-26 00:01:34 -04:00
74516b571e
port Make.py so it is compatible with python 2.7 *and* python 3.x
2016-08-25 06:30:53 -04:00
7d43f349e6
Fixed initialization of arrays in computes
2016-08-24 17:26:04 -04:00
5e811f16e8
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
fcd54f02e6
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
1f3ef8e0ee
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
3e793d6eb7
Fixed initialization of arrays in computes
2016-08-24 17:26:03 -04:00
95dde5c041
Fixed initialization of arrays in computes
2016-08-24 17:26:02 -04:00
d09a85733b
Fixed initialization of arrays in computes
2016-08-24 17:26:02 -04:00
0e7ce194eb
Fixed initialization of arrays in computes
2016-08-24 17:26:02 -04:00
e27196e91c
doc files
2016-08-23 16:28:36 -06:00
268fdab71b
Merge branch 'small-bugfixes' into integration
2016-08-23 15:39:27 -06:00
8750515cc4
changed dump.cpp back to the way it was
2016-08-23 15:38:38 -06:00
270b07b035
Merge branch 'integration' into small-bugfixes
2016-08-23 15:35:31 -06:00
abc5a32c8a
gpu lib sync
2016-08-23 15:30:01 -06:00
0a3464eb30
test
2016-08-23 15:27:02 -06:00
1ab3891caf
Merge branch 'merge-pull-153' into lammps-icms
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Submitted by Steven E. Strong via github
Contributing authors: Steven E. Strong and Joel D. Eaves Joel.Eaves@Colorado.edu
This branch implements Gaussian dynamics (GD), which is a method to do
nonequilibrium molecular dynamics simulations of steady-state flow. See
http://dx.doi.org/10.1021/acs.jpclett.6b00748 . It is simple to implement
and derives rigorously from Gauss's principle of least constraint.
(cherry picked from commit 75929ee01b
2016-08-23 15:33:16 -04:00
55fe1f6b29
fixed integer division problem in python code snippet
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15486 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-08-22 22:35:23 +00:00
50a82bb345
address uninitialized variable issues pointed out by valgrind/coverity
2016-08-22 15:49:33 -04:00
5909bd5429
correct bug in tracking atom->nlocal vs. atom->nmax when allocating pbc enforcement buffers
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(cherry picked from commit 45a2dd36d0
2016-08-22 14:36:47 -04:00
1383684048
fix bug in recent dump changes for -DLAMMPS_BIGBIG
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(cherry picked from commit a507936878
2016-08-22 14:36:47 -04:00
587bafdf2d
Remove memory leak and unnecessary allocation
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(cherry picked from commit c998f7b81f
2016-08-22 14:36:46 -04:00
c8fe3799ed
Add missing initialization
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(cherry picked from commit 054256cf0a
2016-08-22 14:36:46 -04:00
9babb7a4c2
fix indexing bugs in accessing compute and fix labels in fix ave/histo
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(cherry picked from commit 579c527718
2016-08-22 14:35:32 -04:00
c88e9b46cf
thread timing summare needs to be marked as preformatted
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(cherry picked from commit b745636a67
2016-08-22 14:35:11 -04:00
730e3cb4ac
correct small (but harmless) logic error.
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(cherry picked from commit ac6f4f8a56
2016-08-22 14:34:43 -04:00
2a6561e52a
add run 0 to USER-TALLY examples to enforce shake constraints on step 0
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(cherry picked from commit 433741564d
2016-08-22 14:32:47 -04:00
2fff78a78e
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15484 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-08-20 22:43:04 +00:00
d4891754c8
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15483 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-08-20 22:42:24 +00:00
ccf8cf20b3
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15482 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-08-20 22:42:17 +00:00
6ccf4b4525
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15481 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-08-20 22:41:29 +00:00
