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144 Commits

Author SHA1 Message Date
Axel Kohlmeyer 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
Richard Berger 28a9dc40cb Add docstring to new lammps.py methods 2019-11-13 15:53:25 -05:00
Richard Berger 78d5bc3d12 Merge branch 'master' into library_interface_update 2019-11-12 15:17:32 -05:00
Axel Kohlmeyer 9a7caebf57
fix c-syntax in python error. 2019-10-26 05:14:55 -04:00
Axel Kohlmeyer f21b059cd4
fix another bug in extract_compute() method of LAMMPS python module 2019-10-25 16:16:39 -04:00
Aidan Thompson 8f8bcf5f7b Fixes bug in extract_compute() python method 2019-10-24 16:17:32 -06:00
Richard Berger 8bc54c96b0 Add missing default 2019-09-12 14:44:56 -04:00
Richard Berger fb58eb5f23 Add __len__ implementation for NeighList 2019-09-12 14:37:18 -04:00
Richard Berger fec9817086 Add __getitem__ implementation for NeighList 2019-09-12 14:14:06 -04:00
Richard Berger 69854eab42 Expose Neighbor lists via library interface 2019-09-12 13:46:05 -04:00
Richard Berger 3353bffb72 Remove magic numbers and additional data types in extract_global 2019-09-12 13:38:04 -04:00
Richard Berger 5d7ce839a1 Fix memory leak 2019-09-12 13:37:53 -04:00
Richard Berger 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
Axel Kohlmeyer 77e323d28c
prefix option in install.py not needed 2019-03-26 21:55:07 -04:00
Axel Kohlmeyer 0edb82eb5e
update format 2019-03-25 17:14:58 -04:00
Axel Kohlmeyer b0a741fc58
add support for --prefix to python module installer 2019-03-25 16:51:35 -04:00
Axel Kohlmeyer f69173f410
partial documentation update 2019-03-22 17:25:03 -04:00
Axel Kohlmeyer 0f030acc59
refactoring python module installer script to be (more) platform neutral and compatible with conventional make and CMake builds 2019-03-22 11:59:15 -04:00
Jan Janßen e582c0d4e5
Update lammps.py 2019-02-12 08:20:54 +01:00
Jan Janßen f5e3c53880
Update install.py 2019-02-12 08:08:22 +01:00
Jan Janßen e7c1ca1fca
Revert changes 2019-02-12 08:07:28 +01:00
Jan Janßen 277f8356b1
Update lammps.py 2019-02-09 08:46:22 +01:00
Jan Janßen 0fade44b43
Update install.py 2019-02-09 08:45:03 +01:00
Jan Janßen b9d8b5f501 lib extension for Mac Os X 2019-02-04 09:23:29 +01:00
Jan Janßen 7c2a61ad4c
Define lib_ext 2019-02-02 17:55:09 +01:00
Jan Janßen 562bc4e584
Update install.py 2019-02-02 13:05:26 +01:00
Axel Kohlmeyer 1927659fb1 fix cut-n-paste bug in extract_setting() method 2019-01-24 17:55:37 +01:00
Axel Kohlmeyer 49da946398 fix bug reported in https://github.com/lammps/lammps/issues/1294 2019-01-21 05:52:28 -05:00
Richard Berger 4b0382cadd Fixes issue #1069 2018-08-21 14:45:01 -04:00
Richard Berger d00eaef070 Allow 'set' command to change atom velocities 2018-07-13 23:05:44 -04:00
Axel Kohlmeyer 43ffee980d fix typo in python module 2018-06-29 19:07:14 -04:00
Richard Berger 19f81e0802 Add library functions for accessing LAMMPS configuration 2018-06-25 23:56:18 -04:00
Axel Kohlmeyer 5bf8e1bc5b add ability to retrieve the number of local rows for computes returning local data 
this is done supporting the combination of type == 2 with style == 0,
i.e. a local scalar, which is not available in C++ (but there one can
access the compute style data member directly. for the python interface,
the pointer is automatically dereferenced and returned as a c_int.
 2018-04-19 18:37:15 -04:00
Axel Kohlmeyer 164537cf37 whitespace cleanup 2018-04-19 18:30:51 -04:00
Steven J. Plimpton d14c16a47c a few new lib interface methods 2018-03-23 13:34:22 -06:00
Christoph Junghans 62d446668c lammps.py: inconsistent use of tabs and spaces in indentation 2018-03-08 16:23:44 -07:00
Axel Kohlmeyer a1bb877d55 correct commented out MPI examples 2018-03-07 11:17:03 -05:00
Steven J. Plimpton fd1edaf04f allow for mpi4py version 2 or 3 in Python wrapper 2018-03-07 08:52:46 -07:00
Axel Kohlmeyer f914da62e0 fix typo 2018-02-06 16:57:27 +01:00
Richard Berger 2a131d1416 Merge remote-tracking branch 'upstream/master' into fix_python_move 2017-12-15 13:56:54 -05:00
Richard Berger 93be2d264e Detect correct integer type in lammps python interface 2017-12-02 00:39:15 -05:00
Richard Berger 6f7bd78ea2 Fixes issue #701 
PyLammps now supports thermo_style entries such as c_msd[4]
 2017-11-29 01:06:44 -05:00
Richard Berger 45aa7de171 Limit IPython autocomplete to known commands and properties 2017-10-12 14:43:17 -04:00
Richard Berger 0b5a2e199d Add way of getting correct ctypes integer type for bigint, tagint, and imageint 2017-09-04 20:01:31 -04:00
Richard Berger 09bb687918 Correct indentation 2017-09-04 20:01:04 -04:00
Richard Berger bb3ee752e5 Added optional numpy access to atom data 
The library interface was extended to provide direct access to atom data using
numpy arrays. No data copies are made and numpy operations directly manipulate
memory of the native code.

To keep this numpy dependency optional, all functions are wrapped into the
lammps.numpy sub-object which is only loaded when accessed.
 2017-09-04 19:59:50 -04:00
Richard Berger d3169eeab3 Remove Make.py reference in PyLammps examples 
Also fixes some regressions due to command syntax changes
 2017-07-31 13:56:20 -06:00
Richard Berger 71553cf732 Fix PyLammps regression after output.cpp change 2017-07-31 13:53:41 -06:00
Richard Berger 9a027a01da Add Python 3 compatibility to PYTHON package 2017-04-11 20:24:42 -04:00
Richard Berger cda8213892 Added Python matplotlib plot example 2017-03-16 01:41:28 -04:00