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126 Commits

Author SHA1 Message Date
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
Richard Berger ef940d226c Improve Python 3 compatibility of pizza tools and simplify read_snapshot code 2017-03-16 01:38:05 -04:00
Richard Berger 36da9223ec Fix dump cfg in vizplotgui_atomeye.py example 2017-03-15 22:55:51 -04:00
Richard Berger eb29ef32b1 Fix space/tab error in pizza/gl.py 2017-03-15 22:43:00 -04:00
Richard Berger 29550d472d Fix dump cfg in viz_atomeye.py example 2017-03-15 22:31:14 -04:00
Richard Berger 79cae51156 Document property 'uses_exceptions' of Python interface 2017-03-15 22:20:30 -04:00
Richard Berger a210867025 Fixes lammps_create_atoms library function and its Python interface variant 
The interface of that function has changed and includes two additional
parameters, which haven't been added to the Python interface either.
This showed up by trying to run the simple.py example.
 2017-03-15 22:13:06 -04:00
Richard Berger 0262a54ecf Fix Python 3 compatibility by encoding strings passed as c_char_p 2017-03-15 22:00:43 -04:00
Richard Berger 359af419a7 Fix typo in python README 2017-03-07 00:58:35 -05:00
Richard Berger d6800405a5 Fix more typos in examples 2017-03-07 00:57:23 -05:00
Richard Berger e261bef7bb Spelling fixes in source files 2017-03-05 18:30:39 -05:00
Richard Berger 2383c31f15 Created PyLammps documentation 
Based on material presented during MD Workshop at Temple University in
August 2016.
 2016-11-18 23:58:57 -07:00
Steve Plimpton d9891abdf4 new library functions 2016-10-27 09:34:04 -06:00
Steve Plimpton 2106dce2b3 new fix halt command, other sundry small bug fixes 2016-10-18 13:11:40 -06:00
Axel Kohlmeyer 0b426dadc1 do not require the LAMMPS shared library when loading the python wrapper from inside LAMMPS 
Thanks to Giacomo Fiorin for figuring this out with NAMD/Colvars.
This requires linking with -Xlinker -export-dynamic or equivalent,
which is the default when using python-config to provide linker flags.
We will fall back to loading the DSO in case the initial load fails.
 2016-10-12 18:36:38 -04:00
Richard Berger e2caf5c105 Fix code path which allows passing a C++ ptr to PyLammps 2016-10-04 13:57:21 -04:00
Richard Berger 91be47a0d0 Revert type checking commit from July 
0aebb2eabe
 2016-10-04 11:43:12 -04:00
Richard Berger c87f9aeb9f Merge remote-tracking branch 'akohlmey/integration' into ipython-update-and-cleanup 2016-09-26 11:59:30 -04:00
Richard Berger d3406df6a0 Updated instructions in IPython notebooks 
Make.py is now used to enable exceptions support
 2016-09-21 12:07:59 -04:00