c80dad0028
new fix flow/gauss command
2016-08-27 16:25:01 -06:00
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
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
74516b571e
port Make.py so it is compatible with python 2.7 *and* python 3.x
2016-08-25 06:30:53 -04:00
b06fa5670a
find functions in atom.cpp checks for id/name being NULL
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(cherry picked from commit f7e741f344
2016-08-25 06:00:58 -04:00
a635c70a26
Fixed so we test for compute,fix and variable id's being NULL in find_ functions
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(cherry picked from commit 12e1857e30
2016-08-25 06:00:58 -04:00
849cec3400
fix memory leak in compute omega/chunk
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(cherry picked from commit e8d0342503
2016-08-24 23:15:08 -04:00
a692398b6c
fix bug in reserving sufficient space for special atoms
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assigning atom->maxspecial will not work, since it will be reset, e.g. when reading from a data file that doesn't have any special neighbors.
instead we need to set force->special_extra so this is going to be preserved.
2016-08-24 23:08:03 -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
e5c37bc7cb
Implemented optional C++ exceptions in Error class
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These can be activated using the -DLAMMPS_EXCEPTIONS compiler flag.
It has no effect for regular execution. However, while using
it as a library, any issued command will capture the exception
and save its error message. This can be queried using the
lammps_has_error() and lammps_get_last_error_message() methods.
The Python wrapper checks these in order to rethrow these errors
as Python exceptions. See issue #146 .
(cherry picked from commit 6c154bb0b67a13d38968bc42d31013b97f87db75)
2016-08-24 15:31:30 -04:00
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
50a82bb345
address uninitialized variable issues pointed out by valgrind/coverity
2016-08-22 15:49:33 -04:00
74b1caf2e6
undo changes that belong to a different branch or are redundant
2016-08-22 15:46:01 -04:00
243137d552
undo obsoleted changes to group command by iain bethune
2016-08-22 15:23:16 -04:00
40fd97bd4c
silence warnings about cases, that cannot happen
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(cherry picked from commit 60bf26bad9
2016-08-22 15:12:24 -04:00
8492212c4b
fix bug found by coverity scan
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(cherry picked from commit 63b41cb139
2016-08-22 15:12:24 -04:00
1976314f40
improve the weight assignment algorithm for compute time based balancing
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(cherry picked from commit 2b052c2a9c
2016-08-22 15:12:23 -04:00
33a98d79fe
remove upper limit for weigh factor on neighbor list and time weights
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(cherry picked from commit 797c6dc2dd
2016-08-22 15:12:23 -04:00
0902b600fb
add new imbalance module store, which allows to store weights in an atom property
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(cherry picked from commit 5405622f3b
2016-08-22 15:12:23 -04:00
7f20afe122
convert from using fix property/atom to using fix store
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(cherry picked from commit 280aef55d2
2016-08-22 15:12:22 -04:00
7e0dc7a74d
whitespace cleanup
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(cherry picked from commit b3bd35c7be
2016-08-22 15:12:22 -04:00
b954283ec2
properly handle the case of neighbor lists never been computed before
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(cherry picked from commit fcba14a0aa
2016-08-22 15:12:22 -04:00
ecc136b6dc
plug small memory leak
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(cherry picked from commit c00aa3c600
2016-08-22 15:12:22 -04:00
4a536d71eb
simplify and correct logic to pass weight to balancer algorithms
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(cherry picked from commit 529417f86c
2016-08-22 15:12:22 -04:00
460bc14822
correct string hanlding with building custom property label
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(cherry picked from commit 6a519e5eef
2016-08-22 15:12:21 -04:00
bb40f63a34
we cannot add a fix while creating a fix. move fix addintion to Fix::init()
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(cherry picked from commit 4c26534245
2016-08-22 15:12:21 -04:00
c6699e19e6
rewrote balancing to use per-atom data stored via fix property/atom
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(cherry picked from commit 1da862b440
2016-08-22 15:12:21 -04:00
2574891160
fix optional argument scanning bug
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(cherry picked from commit 2a90afe7e9
2016-08-22 15:12:21 -04:00
332d6821ca
remove unused class member
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(cherry picked from commit f884bb2c92
2016-08-22 15:12:20 -04:00
b20108bddb
incorporate refactored weighting into fix balance
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(cherry picked from commit 71ef6fb4d9
2016-08-22 15:12:20 -04:00
8d38db07c7
convert weight array from class member to local pointer to temporary storage
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(cherry picked from commit ecbbdc2e7f
2016-08-22 15:12:20 -04:00
4114bafc28
proof-of-concept implementation for neighbor list based balancing with yet unsolved problems
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(cherry picked from commit d40de42af8
2016-08-22 15:12:20 -04:00
23a48916d7
re-factored balance command now works with group and time weights
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(cherry picked from commit 3f674e5062
2016-08-22 15:12:20 -04:00
34b34d8410
complete implementation for group based imbalance class
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(cherry picked from commit 8ff0085cba
2016-08-22 15:12:19 -04:00
a5d38c0875
prototype implementation for extensible imbalance scheme
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(cherry picked from commit 362a26a3de
2016-08-22 15:12:19 -04:00
