feb0a49f2f
Python: Make NeighList a subclass of object
2021-05-10 18:42:27 -04:00
de3a49ac4f
silence codeql warnings
2021-05-10 03:48:55 -04:00
54b7baea7b
more codeql recommendations
2021-05-09 20:25:20 -04:00
92fe1373a5
fix bug
2021-05-09 20:24:22 -04:00
69a92a3e00
apply some codeql recommendations
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- remove unused imports
- avoid overlaps of variable names with keywords
- make some exception processing more explicit
2021-05-09 19:52:31 -04:00
c1891dca82
explicitly set vstring to None in case of exceptions
2021-05-09 05:58:20 -04:00
51200de45d
Use correct shape for 1d numpy arrays
2021-05-07 12:51:49 -04:00
bddc6d5820
make installation procedure consistent with install.py
2021-04-13 09:58:19 -04:00
c324d754a0
when installing the LAMMPS python package create a valid version id
2021-04-12 10:51:44 -04:00
38d5798223
must not look for package metadata when using python module from source tree
2021-04-11 21:36:18 -04:00
17355f967a
address spelling and manual processing issues
2021-04-03 11:11:18 -04:00
50b789cc36
Merge branch 'master' into neighlist-interface-updates
2021-04-03 10:18:28 -04:00
85a5698c1b
add find method to neighbor list wrapper classes
2021-04-02 21:41:08 -04:00
51212e62d9
correct/update docs and parameter names for finding neighbor lists
2021-04-02 19:55:53 -04:00
e613da98d6
Merge pull request #2650 from akohlmey/plugin-loader
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New PLUGIN package with a LAMMPS plugin loader command
2021-04-02 15:08:44 -04:00
c9652f3aa6
update documentation for the extract_global() method of the lammps.lammps class
2021-04-01 09:31:54 -04:00
a193d9d429
fix several issues when using extract_global() from python exposed by tests
2021-03-25 20:34:25 -04:00
b8f02d759a
add support for extracting respa levels and timestep values
2021-03-25 20:34:25 -04:00
e0fdd2ad89
correct lammps.extract_global() method for returned arrays which are returned as list
2021-03-25 20:34:24 -04:00
b0bc0b9a2f
Use time.strptime instead of datetime.strptime
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Embedding the Python interpreter multiple times in the same process can
cause this issue due to import caching. https://bugs.python.org/issue27400
This seems to be avoidable by using the time module instead.
2021-03-24 17:54:13 -04:00
772d270974
Merge pull request #2662 from evoyiatzis/master
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Addition of a PyLammps script to compute elastic constants using OpenKIM
2021-03-19 13:43:19 -04:00
945ecd1f1c
Update kim commands
2021-03-19 13:23:15 -04:00
64ba2f4ee2
Add missing checks for C++ exceptions
2021-03-18 14:26:18 -04:00
ecbb75ff3c
removing parentheses from mass dictionary
2021-03-17 12:30:02 +01:00
05d6c1e757
Update python/examples/pylammps/elastic/elastic.py
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Co-authored-by: Richard Berger <richard.berger@temple.edu >
2021-03-17 10:37:39 +01:00
611eb306be
Update python/examples/pylammps/elastic/elastic.py
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Co-authored-by: Richard Berger <richard.berger@temple.edu >
2021-03-17 10:37:24 +01:00
28e986c266
add python module support for plugins
2021-03-16 23:25:46 -04:00
5e3ddb6986
Use stable branch for checkout
2021-03-16 16:36:34 -04:00
45b01aba0c
Update Jupyter notebooks
2021-03-16 15:18:07 -04:00
32a2ee6dc2
Update mc.ipynb
2021-03-16 14:38:26 -04:00
e9e1a96335
Update simply.ipynb
2021-03-16 14:22:26 -04:00
644b61cd1f
Add __dir__() to Atom class
2021-03-16 14:21:19 -04:00
a8597de4be
Add __dir__() to variable_set
2021-03-16 14:04:24 -04:00
b4633bc2b2
Update PyLammps examples README
2021-03-16 11:49:24 -04:00
a1d8e21b04
Add files via upload
2021-03-16 13:14:20 +01:00
6f07564a92
Create README
2021-03-16 13:13:45 +01:00
76ef7a9081
safer detection and load of lammps shared library
2021-02-27 15:50:58 -05:00
f92089298d
Fix bug in AvgChunkReader and add docs
2021-02-25 16:56:19 -05:00
977ba9ff66
Add LogFile and AvgChunkFile readers
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Implements changes proposed in #144
2021-02-25 15:32:53 -05:00
f467832e0f
Make PyLammps command history feature optional
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PyLammps so far has been saving a history for every executed command. This was
originally added to allow writing out the commands of interactive PyLammps
sessions as regular input scripts.
This commit disables this history by default, which avoids the small, but
rising memory consumption over time. It can be enabled and disabled with the
enable_cmd_history property. There is also now a method to clear the history
at any time.
2021-02-22 01:29:50 -05:00
742eebec2d
support checking the size of MPI communicators and fail if LAMMPS and mpi4py have a mismatch
2021-02-16 20:22:18 -05:00
f929e57261
avoid loading mpi4py if the LAMMPS executable has been built without MPI
2021-02-16 14:38:03 -05:00
d256614c9f
Fix docs after PR #2592
2021-02-15 13:19:25 -05:00
2dd3b368cd
do not install mliap python support for python 2.x
2021-02-09 20:57:08 -05:00
fff1c0c9a7
rename numpy.py to numpy_wrapper.py to avoid lookup conflicts with python2.7
2021-02-09 20:56:33 -05:00
903433d9dd
use datetime module to convert string date to numeric date
2021-02-09 14:22:37 -05:00
62a152e4a2
get version number from package version instead of rewriting the __init__.py file
2021-02-09 14:13:18 -05:00
653c296246
document __version__ module member and version check
2021-02-09 12:29:14 -05:00
b53b993c68
recover in-place usage by defaulting to version 0 and changing it back after installation
2021-02-09 02:12:37 -05:00
7826b58f73
add check to lammps python module to check consistent versions between module and shared library
2021-02-09 00:38:17 -05:00
