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
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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
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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
33a2857b33
Fix whitespace
2020-09-18 17:56:12 -04:00
635b7c04a5
Update docs and docstrings
2020-09-18 14:49:25 -04:00
1afb355d09
Limit int types to LAMMPS_INT and LAMMPS_INT64
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Keep LAMMPS_TAGINT and LAMMPS_BIGINT internal to LAMMPS.
An external caller now only needs to distinguish between 32 and 64bit
integers, doubles and C strings.
2020-09-18 12:05:37 -04:00
42aca25a58
Update docs, fix typos
2020-09-17 18:10:08 -04:00
b4a1c9c24c
Update examples
2020-09-17 17:08:13 -04:00
cf1ae7afa6
Use wrapper lammps.extract_atom_datatype
2020-09-17 17:04:40 -04:00
ab6b69d6bd
Add documentation and better autodetect
2020-09-17 16:39:19 -04:00
b81ad54baa
Simplify extract_atom and extract_global in Python interface
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Both extract methods now can auto-detect the datatype of both global
and per-atom properties. Callers can still enforce different types
if needed by specifying the now optional dtype argument.
The numpy wrapper now has a new extract_atom function method, which
replace the extract_atom_darray and extract_atom_iarray method and
autodetects both type and size. All parameters can still be forced
to use different values if needed.
2020-09-17 16:16:27 -04:00
d88810f13a
Add datatype introspection methods to library
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Adds lammps_extract_atom_datatype and lammps_extract_global_datatype functions
to allow extracting type information of properties.
2020-09-17 13:43:43 -04:00
5dacfc47ca
Change return type of lammps.get_natoms to int
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Closes PR #2370
2020-09-17 10:57:49 -04:00
e6703019bc
Update examples to use Python API constants
2020-09-16 16:10:43 -04:00
2270d8f4ec
Add PyLammps.atoms test and fix bug with -echo screen/both
2020-09-16 12:48:20 -04:00
ca24806f4c
Add tests
2020-09-16 10:11:00 -04:00
38f0a2e24c
Fix doc build errors
2020-09-15 19:50:28 -04:00
7611efeea2
Update python docs
2020-09-15 18:03:26 -04:00
60712e3f90
Add docstrings
2020-09-15 16:22:43 -04:00
556dc67fdc
Correct filename of generated image
2020-09-15 15:20:38 -04:00
6cfad41be4
Add background_color argument to IPyLammps.image
2020-09-15 15:19:39 -04:00
9490370eb0
Use consistent naming in PyLAMMPS classes
2020-09-15 12:22:36 -04:00
2c30de65d2
Fix typos in docstring
2020-09-15 12:16:47 -04:00
b20b234ebe
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-15 10:45:28 -04:00
7b869e8ee8
Start with more detailed description of PyLammps
2020-09-11 17:09:38 -04:00
bd72ef7996
add API to library/python interface to extract the MPI communicator
2020-09-09 22:03:11 -04:00
0541996919
Merge branch 'master' into master
2020-09-01 10:59:03 +02:00
d601acd0ca
merge
2020-09-01 10:57:43 +02:00
2eb6a8a8a4
update python interface
2020-09-01 10:55:45 +02:00
db9de111be
updated python interface
2020-09-01 10:54:18 +02:00
17ec3a4fe8
Fix typo
2020-08-28 15:15:01 -04:00
9412d6f6fc
Add missing argtypes declarations in lammps.py
2020-08-28 15:12:36 -04:00
