jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
20,216 Commits 9 Branches 198 Tags 1.1 GiB
Commit Graph

76 Commits

Author SHA1 Message Date
Eisuke Kawashima 649a8cc01a
Fix typo 2020-03-14 13:57:48 +09:00
Axel Kohlmeyer 475b7dc4f4
provide access to number of local data rows for fixes 2020-03-07 10:58:35 -05:00
Axel Kohlmeyer 943540b015
bugfix for extracting length of local data through python interface 2020-03-07 10:19:03 -05:00
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
Jan Janßen e582c0d4e5
Update lammps.py 2019-02-12 08:20:54 +01:00
Jan Janßen 277f8356b1
Update lammps.py 2019-02-09 08:46:22 +01:00
Jan Janßen b9d8b5f501 lib extension for Mac Os X 2019-02-04 09:23:29 +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
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 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 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
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
sjplimp f718c54430 sync with GH 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15634 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-09-23 21:04:56 +00:00
sjplimp 484122b8b6 sync with GH 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15592 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-09-16 19:21:34 +00:00