ab6b69d6bd
Add documentation and better autodetect
2020-09-17 16:39:19 -04:00
b81ad54baa
Simplify extract_atom and extract_global in Python interface
...
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
...
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
...
Closes PR #2370
2020-09-17 10:57:49 -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
6bcc263b41
Ensure LAMMPS pointer is of type c_void_p
...
Fixes segfaults caused by API change. The API change in
lammps_open and lammps_open_no_mpi makes them return the LAMMPS pointer
via their return value. However due to how ctypes operates, even
if restype is specified to be c_void_p, the function returns an integer.
Without the proper type of the pointer, calling functions without arglists would default
to using 32bit integers to pass an argument, which cuts away parts of the 64bit pointer.
Subsequently, resolving the truncated pointer in the library causes segfaults.
This commit fixes the root cause. But it also highlights the need of specifying
the arglists of all library functions.
2020-08-28 14:21:03 -04:00
caeb0af0d1
Add missing argtypes for lammps_extract_global
2020-08-28 13:54:06 -04:00
9c84fe8830
Add missing lammps_extract_compute.argtypes
2020-08-27 17:47:49 -04:00
0b8136a38b
Add extract_compute, extract_fix, and extract_variable to lammps.numpy
2020-08-27 17:47:49 -04:00
26d09ea648
Use datatype constants instead of magic numbers
2020-08-27 17:47:49 -04:00
0d8baff7a9
Rename LAMMPS_DBLE2D to LAMMPS_DOUBLE2D
2020-08-27 14:03:17 -04:00
977a89e537
add separators
2020-08-27 12:33:03 -04:00
48d2a48a1f
import updated python module from progguide branch
2020-08-26 09:01:59 -04:00
6f775f6592
fix typo
2020-07-11 13:06:43 -04:00
40e59b27a7
add prototypes for exception handling functions
2020-07-11 13:06:05 -04:00
758c812306
Allow query of available styles from lib interface
...
Adds the following new library functions:
- lammps_has_style()
- lammps_style_count()
- lammps_stlye_name()
The Info class now also has the following member functions:
- Info::has_style()
- Info::get_available_styles()
2020-03-26 22:45:18 -04:00
649a8cc01a
Fix typo
2020-03-14 13:57:48 +09:00
475b7dc4f4
provide access to number of local data rows for fixes
2020-03-07 10:58:35 -05:00
943540b015
bugfix for extracting length of local data through python interface
2020-03-07 10:19:03 -05:00
33c846cd5e
guard converting thermo output from other output to the screen and do not crash
...
fixes #1844
2020-01-17 09:48:07 -05:00
28a9dc40cb
Add docstring to new lammps.py methods
2019-11-13 15:53:25 -05:00
78d5bc3d12
Merge branch 'master' into library_interface_update
2019-11-12 15:17:32 -05:00
9a7caebf57
fix c-syntax in python error.
2019-10-26 05:14:55 -04:00
f21b059cd4
fix another bug in extract_compute() method of LAMMPS python module
2019-10-25 16:16:39 -04:00
8f8bcf5f7b
Fixes bug in extract_compute() python method
2019-10-24 16:17:32 -06:00
8bc54c96b0
Add missing default
2019-09-12 14:44:56 -04:00
fb58eb5f23
Add __len__ implementation for NeighList
2019-09-12 14:37:18 -04:00
fec9817086
Add __getitem__ implementation for NeighList
2019-09-12 14:14:06 -04:00
69854eab42
Expose Neighbor lists via library interface
2019-09-12 13:46:05 -04:00
3353bffb72
Remove magic numbers and additional data types in extract_global
2019-09-12 13:38:04 -04:00
5d7ce839a1
Fix memory leak
2019-09-12 13:37:53 -04:00
2b42428d28
Extend lib interface to set fix external callback
...
This allows creating a callback in Python and attaching it to
a fix external instance.
2019-08-20 14:04:49 -06:00
e582c0d4e5
Update lammps.py
2019-02-12 08:20:54 +01:00
