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12313 Commits

Author SHA1 Message Date
Axel Kohlmeyer 13e16dc3f1 update log files for pair style python examples 2017-05-17 07:52:13 -04:00
Axel Kohlmeyer 96f0a82aa5 simplify class names in pair style python examples. add SPC/E water example 2017-05-17 07:48:15 -04:00
Richard Berger 7caf6cf459 Change how a Python pair style is loaded 
Implements a class loader which takes a fully qualified Python class
name, loads the module and creates an object instance.

To add flexibility, the current working directory and the
directory specified by the LAMMPS_POTENTIALS environment variable are
added to the module search path.
 2017-05-16 23:29:48 -04:00
Richard Berger a6f0d700f1 Merge branch 'add-pair-python' of github.com:akohlmey/lammps into add-pair-python 2017-05-15 18:44:52 -04:00
Richard Berger 14f3deed6b Minor coefficient lookup improvement 2017-05-15 18:43:46 -04:00
Axel Kohlmeyer d66a696a84 avoid preprocessor warnings, by placing Python.h include file on the top, as suggested by python docs 2017-05-15 18:02:02 -04:00
Richard Berger 69ccbd1562 Extract common wrappers to Python compatibility header 2017-05-15 17:46:57 -04:00
Richard Berger 93cc6f4a5d Use in syntax for key lookup for Python 3 compatibility 2017-05-15 17:34:48 -04:00
Axel Kohlmeyer 6a1f7e61f2 provide reference output for python pair style inputs 2017-05-15 00:25:11 -04:00
Axel Kohlmeyer d662f5d429 whitspace cleanup and gitignore update 2017-05-15 00:22:22 -04:00
Axel Kohlmeyer df55a90ef6 some example input file tweaks 2017-05-15 00:22:03 -04:00
Axel Kohlmeyer 6e113c1eaf basic feature complete version of lj melt example with python interaction function 2017-05-15 00:15:41 -04:00
Axel Kohlmeyer f484ab6dfb completed lj parameter set and compute functions for melt example 2017-05-15 00:14:36 -04:00
Axel Kohlmeyer 86283c6309 make melt input consistent with melt example again 2017-05-15 00:13:32 -04:00
Axel Kohlmeyer 34cc3946b8 first few pieces of pair style python 2017-05-14 18:29:06 -04:00
sjplimp 06c151421c Merge pull request #478 from akohlmey/add-python-source-cmd 
Add python support features
 2017-05-12 13:28:20 -06:00
sjplimp 0008b6fc2d Merge pull request #477 from lammps/renamings 
rename some USER/misc dirs
 2017-05-12 08:54:12 -06:00
Richard Berger b6a70ec6fd fixup docs after last change 2017-05-12 00:34:47 -04:00
Richard Berger c4d0f07093 Allow fix python to only execute every N steps 2017-05-12 00:29:58 -04:00
Richard Berger 93f6033061 Add documentation about fix python 2017-05-11 23:50:40 -04:00
Richard Berger 110bb79b14 Implement fix python mentioned in issue #454 
Allows to call a python function at defined points in the integration loop
 2017-05-11 23:50:30 -04:00
Axel Kohlmeyer d84f8898b7 implement functions to execute arbitrary python code from strings or files and recast the python source keyword through using them. 2017-05-11 22:39:08 -04:00
Axel Kohlmeyer 27a6371f9b implement a `python source` command as suggested in issue #454 2017-05-11 19:18:09 -04:00
Steve Plimpton 7c3b8e014c rename some USER/misc dirs 2017-05-11 10:15:28 -06:00
sjplimp a069d21621 Merge pull request #476 from akohlmey/dump_custom_bugfix 
dump custom memory allocation bugfix
 2017-05-11 09:27:08 -06:00
sjplimp d7f54464c6 Merge pull request #474 from rbberger/dump_vtk_fixes 
Various dump vtk fixes
 2017-05-11 09:25:42 -06:00
sjplimp 998eb44e83 Merge pull request #473 from akohlmey/compress-for-reaxc-fixes 
compressed output via gzip for some ReaxFF fixes
 2017-05-11 09:25:18 -06:00
sjplimp 96d1de8575 Merge pull request #471 from akohlmey/fix-4may2017-issues 
Fix a bunch of remaining issues in the 4 may 2017 release
 2017-05-11 09:24:35 -06:00
sjplimp deff6ffaac Merge pull request #466 from DallasTrinkle/meam-spline-multicomponent 
Meam spline multicomponent
 2017-05-11 09:22:25 -06:00
Axel Kohlmeyer 328ef873d8 fix mixed memory alloc bug in dump custom. this closes #475 2017-05-10 22:41:41 -04:00
Richard Berger 4ecf876a64 Added two examples of using the VTK dump style 2017-05-10 19:52:00 -04:00
Richard Berger c4ac5773cb Fix segmentation fault in dump vtk 2017-05-10 19:51:14 -04:00
Richard Berger cac1bf83ef Work around VTK 7 API change 2017-05-10 19:41:48 -04:00
Axel Kohlmeyer abeb1e096a add support for gzip compressed output to fix reax/bonds, reax/c/bonds and reax/c/species 2017-05-10 11:19:18 -04:00
Axel Kohlmeyer 9f7ce39f9f correct some more omitted updates 2017-05-09 18:14:34 -04:00
Axel Kohlmeyer 29ae8d4ca3 correct broken links and references in documentation 2017-05-09 17:15:07 -04:00
Axel Kohlmeyer 3f4aee1046 implement overlooked changes from 4may2017 patch 2017-05-09 15:57:35 -04:00
Axel Kohlmeyer d0da0639f0 add a couple of simple example single/multi-elment inputs for meam/spline pair styles 2017-05-09 15:51:59 -04:00
Axel Kohlmeyer 390ceb1475 whitespace cleanup 2017-05-09 15:49:37 -04:00
Axel Kohlmeyer 6c5edf6c70 performance improvement through avoiding function call and dereference overhead 
- make i_to_potl() and ij_to_potl() functions inline and const
- don't dereference inside the functions, but cache, if possible in external variables
=> up to 15% speedup.
 2017-05-09 15:38:10 -04:00
Axel Kohlmeyer 9cd994f57c fix issues with potential file parser 
- use Force::open_potential()
- replace ftell()/fseek() with rewind()/fgets() which is safer on windows and other platforms with automatic CR/LF to LF conversion on text files
- make parser use properly NULL terminated strings through using strtok()
 2017-05-09 15:35:48 -04:00
sjplimp a6e2d5b5f7 Merge pull request #470 from lammps/integration 
neighbor list bugfix to prevent cycle in copy lists
 2017-05-09 10:32:25 -06:00
Steve Plimpton 08ec55743e neighbor list bugfix to prevent cycle in copy lists 2017-05-09 08:55:18 -06:00
sjplimp c4f90b3841 Merge pull request #449 from rbberger/python_refactoring 
Add Python 3 compatibility and expand Python interface availability
 2017-05-08 08:29:24 -06:00
Richard Berger f8af7edf92 Merge remote-tracking branch 'upstream/master' into python_refactoring 2017-05-06 16:00:22 -04:00
Steve Plimpton a73402ad93 update src/Purge.list with renamed reaxc src files 2017-05-04 14:53:08 -06:00
Steve Plimpton d7dbff0f54 jive Kokkos/reaxc file names with new user-reaxc file names 2017-05-04 14:46:59 -06:00
DallasTrinkle 42531389df Cleanup of style (removing all tabs, shortened long lines). 2017-05-04 15:28:11 -05:00
DallasTrinkle f7230006fe OpenMP version added. 2017-05-04 15:08:04 -05:00
DallasTrinkle 754b40cb31 Removed unused functions. 2017-05-04 13:16:46 -05:00