09f3b687f7
new long-rance example with using hybrid/overlay and table only for lj part
2017-05-18 00:31:15 -04:00
436d3fd761
make hybrid example use half the atoms with python, half with lj/cut
2017-05-18 00:30:41 -04:00
9833f38499
change coulomb example to use cutoff coulomb
2017-05-18 00:30:19 -04:00
9725708b90
update pair style python docs
2017-05-18 00:29:02 -04:00
67962b15fc
a bunch refactoring changes in the python pair style and the examples
...
- make all python potential classes derived from LAMMPSPairPotential
which contains shared functionality. We currently don't check
for supported atom types. may want to add that again later.
- keep track of skipped atom types in the C++ code.
- add test against units setting. must set self.units='...' in constructor
- make compute_force method consistent with Pair::single() in LAMMPS and return force/r instead of force.
- rename potentials.py to py_pot.py
- update test runs. some small tweaks.
2017-05-17 20:55:48 -04:00
1d48f287f0
add partial documentation for pair style python
2017-05-17 19:05:18 -04:00
43efe9e417
adding Pair::single() support to python pair style and examples
...
with the single function, python pair styles can be massively
sped up and made compatible to accelerators, as one can translate
the analytic force and energy functions through LAMMPS into suitable
tables and then simply use the on-the-fly tables for production runs
2017-05-17 17:20:56 -04:00
45becfb235
correct author attributions
2017-05-17 09:59:01 -04:00
a34c935e20
update log files in python pair style example
2017-05-17 08:00:21 -04:00
13e16dc3f1
update log files for pair style python examples
2017-05-17 07:52:13 -04:00
96f0a82aa5
simplify class names in pair style python examples. add SPC/E water example
2017-05-17 07:48:15 -04:00
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
a6f0d700f1
Merge branch 'add-pair-python' of github.com:akohlmey/lammps into add-pair-python
2017-05-15 18:44:52 -04:00
14f3deed6b
Minor coefficient lookup improvement
2017-05-15 18:43:46 -04:00
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
69ccbd1562
Extract common wrappers to Python compatibility header
2017-05-15 17:46:57 -04:00
93cc6f4a5d
Use in syntax for key lookup for Python 3 compatibility
2017-05-15 17:34:48 -04:00
6a1f7e61f2
provide reference output for python pair style inputs
2017-05-15 00:25:11 -04:00
d662f5d429
whitspace cleanup and gitignore update
2017-05-15 00:22:22 -04:00
df55a90ef6
some example input file tweaks
2017-05-15 00:22:03 -04:00
6e113c1eaf
basic feature complete version of lj melt example with python interaction function
2017-05-15 00:15:41 -04:00
f484ab6dfb
completed lj parameter set and compute functions for melt example
2017-05-15 00:14:36 -04:00
86283c6309
make melt input consistent with melt example again
2017-05-15 00:13:32 -04:00
34cc3946b8
first few pieces of pair style python
2017-05-14 18:29:06 -04:00
06c151421c
Merge pull request #478 from akohlmey/add-python-source-cmd
...
Add python support features
2017-05-12 13:28:20 -06:00
0008b6fc2d
Merge pull request #477 from lammps/renamings
...
rename some USER/misc dirs
2017-05-12 08:54:12 -06:00
b6a70ec6fd
fixup docs after last change
2017-05-12 00:34:47 -04:00
c4d0f07093
Allow fix python to only execute every N steps
2017-05-12 00:29:58 -04:00
93f6033061
Add documentation about fix python
2017-05-11 23:50:40 -04:00
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
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
27a6371f9b
implement a python source command as suggested in issue #454
2017-05-11 19:18:09 -04:00
7c3b8e014c
rename some USER/misc dirs
2017-05-11 10:15:28 -06:00
a069d21621
Merge pull request #476 from akohlmey/dump_custom_bugfix
...
dump custom memory allocation bugfix
2017-05-11 09:27:08 -06:00
d7f54464c6
Merge pull request #474 from rbberger/dump_vtk_fixes
...
Various dump vtk fixes
2017-05-11 09:25:42 -06:00
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
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
deff6ffaac
Merge pull request #466 from DallasTrinkle/meam-spline-multicomponent
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Meam spline multicomponent
2017-05-11 09:22:25 -06:00
328ef873d8
fix mixed memory alloc bug in dump custom. this closes #475
2017-05-10 22:41:41 -04:00
4ecf876a64
Added two examples of using the VTK dump style
2017-05-10 19:52:00 -04:00
c4ac5773cb
Fix segmentation fault in dump vtk
2017-05-10 19:51:14 -04:00
cac1bf83ef
Work around VTK 7 API change
2017-05-10 19:41:48 -04:00
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
9f7ce39f9f
correct some more omitted updates
2017-05-09 18:14:34 -04:00
29ae8d4ca3
correct broken links and references in documentation
2017-05-09 17:15:07 -04:00
3f4aee1046
implement overlooked changes from 4may2017 patch
2017-05-09 15:57:35 -04:00
d0da0639f0
add a couple of simple example single/multi-elment inputs for meam/spline pair styles
2017-05-09 15:51:59 -04:00
390ceb1475
whitespace cleanup
2017-05-09 15:49:37 -04:00
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
9cd994f57c
fix issues with potential file parser
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- 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
