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
...
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
...
- 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
...
- 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.
...
- 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
02b10380bc
Create ctypes only neighbor list API variant
...
This moves the lammps.get_neighlist() method to lammps.numpy.get_neighlist().
lammps.get_neighlist() now returns a NeighList object, while the NumPy variants
returns a NumPyNeighList object. The main difference between the two is that while
the ctypes variant returns neighlist elements as
atom idx (int), numneighs (int), neighbors (POINTER(c_int))
the NumPy variant returns
atom idx (int), neighbors (numpy.array)
2020-10-05 16:21:37 -04:00
4f1ed775e9
Add missing docstrings
2020-10-05 14:03:19 -04:00
d91d8de76d
Refactor LammpsNumpyWrapper to numpy_wrapper
...
LammpsNumpyWrapper was a class that was defined inside of the
lammps.numpy property when it was first accessed. This made it hard
to document the methods of this class.
This commit extracts this utility class into the lammps module and
renames it to 'numpy_wrapper'.
2020-10-02 17:28:25 -04:00
0089a35d95
Remove dead code
2020-10-02 17:27:08 -04:00
7355977819
Add missing exception handling for functions that could cause errors
2020-10-02 17:26:14 -04:00
d9cbb354d2
Move lammps exception code into its own property
2020-10-02 17:22:01 -04:00
fb33a71720
look for liblammps.dll in windows binary dir only if that directory exists
2020-10-01 00:34:03 -04:00
555fba1e4b
add special case for windows installer package where the .dll file is in the bin folder
2020-09-29 18:46:32 -04:00
5ce6259632
correct reference to function
2020-09-18 22:35:56 -04:00
897a7d0ed4
only try to broadcast if we have a proper communicator
2020-09-18 21:17:31 -04:00
