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
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
...
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
0e2b528351
add additional heuristics to prevent python unit tests from failing on MacOS
2021-01-29 18:40:24 -05:00
6e43ccf32b
Fixed bug in get_thermo_data where columns is set to None instead of an empty list
2021-01-27 19:41:24 -05:00
1cdce9233e
identify offloading to Xeon Phi accelerator coprocessors
2021-01-16 01:07:44 -05:00
a647c236d0
make categories contain lists instead of strings as we may have multiple supported settings
2021-01-16 00:56:27 -05:00
a644375afa
make code python2/3 compatible
2021-01-16 00:23:44 -05:00
22bf810b63
recover current package names. this will become simpler once #2525 is implemented
2021-01-12 20:23:57 -05:00
3d3590f02d
add c-library interface and export to python
2021-01-12 20:10:47 -05:00
427d037747
Merge pull request #2508 from athomps/mliappy3
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Add support for Python based models to the MLIAP package
2020-12-29 09:59:43 -05:00
5dc868ec30
whitespace
2020-12-28 09:37:13 -05:00
cf3ae8cdd2
switch setuptools back to distutils
2020-12-22 09:59:50 -07:00
e7fa0a6bac
Changes to MLIAP python
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- update lammps python package to use setuptools
- refactor MLIAP classes into lammps python package
lammps.mliap package
- change TorchWrapper to use dtype and device as arguments
- turn activation of mliappy into functions (was a class)
- add a check to see if python interpreter is compatible
with python lib calls internal to lammps
mliap_model_python_couple.pyx:
- load models ending in '.pt' or '.pth' with pytorch rather than pickle
2020-12-21 11:51:10 -07:00
4c7f71bef3
Merge branch 'master' into mliappy3
2020-12-18 09:16:44 -05:00
de94e28c8b
correct path to find liblammps.dll with Windows installer package
2020-12-17 21:48:04 -05:00
511a1a5395
Update comments mentioning lammps.py
2020-12-17 12:13:06 -05:00
ac203b3683
Keep numpy imports inside of functions
2020-12-15 18:50:38 -05:00
33f9a29639
Split core.py into more files
2020-12-15 16:33:21 -05:00
9e188a3818
Clean up imports
2020-12-15 16:19:23 -05:00
b390c1e3d3
Split lammps.py into core.py and pylammps.py
2020-12-15 16:15:16 -05:00
aca2eefce5
Transform LAMMPS Python module into package
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- Moves lammps.py into its own package
- Imports entire module in __init__.py
- Changes both how legacy and CMake build systems install
- Added traditional setup.py for Python-only installation
Note: the CMake install target runs setup.py build and install
in a way that produces files in CMAKE_BINARY_DIR/python instead
of python/build. This is to maintain out-of-source compilation
support.
2020-12-15 15:11:21 -05:00
3eb22e2406
cleanup and compilation for python off
2020-12-07 17:47:21 -05:00
664ed0f850
Merge remote-tracking branch 'origin/mliappy2' into mliappy3
2020-12-03 17:37:26 -07:00
35f2c9bdf2
Several improvements to capabilities and build.
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- cmake fixed, no longer needs numpy headers.
- models can be loaded from an external interepreter.
2020-11-26 12:40:28 -07:00
875057538f
Fix docstring of extract_variable
2020-11-23 12:45:37 -05:00
08d892d0d9
whitespace
2020-10-15 19:56:31 -04:00
99f9a16a25
Update Python docs
2020-10-15 18:19:57 -04:00
8c5da70823
handle the case where the variable type is invalid and thus a null pointer is returned
2020-10-12 06:16:28 -04:00
bafba4235c
include versionadded tags
2020-10-09 07:26:01 -04:00
471acb2ef8
add unit tests for added APIs
2020-10-09 07:16:34 -04:00
90d511bc86
add wrappers for new library functions
2020-10-08 22:32:33 -04:00
80a054471d
Merge branch 'progguide-updates' into progguide-richard
2020-10-05 19:31:03 -04:00
22cca93603
Add tests for neighbor list API
2020-10-05 17:34:08 -04:00
