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12556 Commits

Author SHA1 Message Date
sjplimp aa09f45b7e Merge pull request #484 from akohlmey/add-gao-weber-styles 
Add Gao-Weber manybody styles
 2017-05-18 09:10:03 -06:00
sjplimp 4b61cf6f52 Merge pull request #483 from akohlmey/airebo-spline-bugfix-refactor 
AIREBO spline code out-of-bounds and bondorder derivative bugfix and refactor
 2017-05-18 09:01:33 -06:00
sjplimp 683f3d9d2a Merge pull request #481 from akohlmey/collected-small-changes 
Collected small updates and bugfixes
 2017-05-18 09:01:04 -06:00
sjplimp ce18524251 Merge pull request #480 from akohlmey/pair_morse_smooth_linear_bugfix 
corrections to pair style morse/smooth/linear
 2017-05-18 08:57:24 -06:00
sjplimp 95dae9737b Merge pull request #488 from lammps/neigh_occasional_bugfix 
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species update from Stan
 2017-05-18 08:53:54 -06:00
Emile Maras 8daba01151 some small formating change but does not work anymore 2017-05-18 16:48:20 +02:00
Emile Maras 640edbc1d4 added several features to the NEB 2017-05-18 11:08:08 +02:00
Axel Kohlmeyer 4b1914aa1f update citations for multi-element edip potential 2017-05-18 01:07:52 -04:00
Axel Kohlmeyer bd11479a16 lock the sphinx command to version 1.5.6, since version 1.6.x seems to break one of the extensions we use 2017-05-18 00:50:35 -04:00
Axel Kohlmeyer 0208fe9996 update example outputs 2017-05-18 00:46:49 -04:00
Axel Kohlmeyer 24654ad28f small formatting corrections to pair python style 2017-05-18 00:38:36 -04:00
Axel Kohlmeyer 8d46aa6056 add readme file to discuss various python pair style usage examples 2017-05-18 00:31:54 -04:00
Axel Kohlmeyer 09f3b687f7 new long-rance example with using hybrid/overlay and table only for lj part 2017-05-18 00:31:15 -04:00
Axel Kohlmeyer 436d3fd761 make hybrid example use half the atoms with python, half with lj/cut 2017-05-18 00:30:41 -04:00
Axel Kohlmeyer 9833f38499 change coulomb example to use cutoff coulomb 2017-05-18 00:30:19 -04:00
Axel Kohlmeyer 9725708b90 update pair style python docs 2017-05-18 00:29:02 -04:00
Axel Kohlmeyer 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
Axel Kohlmeyer 1d48f287f0 add partial documentation for pair style python 2017-05-17 19:05:18 -04:00
Axel Kohlmeyer 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
Axel Kohlmeyer 278b9f7fba move pair gw and gw/zbl to USER-MISC package 2017-05-17 14:59:46 -04:00
Axel Kohlmeyer 085f3afdfb fix typo in docs 2017-05-17 09:59:30 -04:00
Axel Kohlmeyer 45becfb235 correct author attributions 2017-05-17 09:59:01 -04:00
Axel Kohlmeyer a34c935e20 update log files in python pair style example 2017-05-17 08:00:21 -04:00
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
Axel Kohlmeyer 8936b99e9f add contributed SiC.edip potential file 2017-05-16 18:15:53 -04:00
Axel Kohlmeyer d2810f9f83 port thread-safe temperature biasing from LAMMPS-ICMS 2017-05-16 18:15:13 -04:00
Axel Kohlmeyer 597f95fb1b fix duplicate reference 2017-05-16 17:53:12 -04:00
Steve Plimpton 7f9a331c73 bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue 2017-05-16 15:51:41 -06:00
Axel Kohlmeyer 35e92733e9 import multi-element compatible pair style edip as edip/multi 2017-05-16 17:40:59 -04:00
Axel Kohlmeyer c11e87618b implement second bugfix suggestion from @CF17 on issue #59 2017-05-16 14:18:56 -04:00
Axel Kohlmeyer ca87e57129 improved version of AIREBO splines based on a suggestion by markus hoehnerbach 2017-05-16 11:58:34 -04:00
Axel Kohlmeyer 66084ad1f4 fix typo in rerun docs. closes #486 2017-05-16 04:27:15 -04:00
Axel Kohlmeyer d807ba1974 whitespace cleanup 2017-05-16 00:26:39 -04:00
Axel Kohlmeyer 51fc386e72 correct the inner loop range for resetting cutoffs when redefining a pair style 
this was reported by frank uhlig on lammps-users for lj/cut, but it applies to many more pair styles
 2017-05-16 00:26:18 -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
Axel Kohlmeyer d9d4ef17c8 add gao-weber potentials (regular and with ZBL core) with SiC potential files 
NOTE: documentation is missing
 2017-05-15 17:44:25 -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 0a40a7af7b whitespace cleanup 2017-05-15 17:00:41 -04:00
Axel Kohlmeyer eb6f6a77e5 dead code removal 2017-05-15 16:16:12 -04:00
Axel Kohlmeyer fb7164a811 replace pow(x,-0.5) with 1.0/sqrt(x) 2017-05-15 16:16:01 -04:00
Axel Kohlmeyer 64cf52d3b5 address spline out-of-bounds bug reported in issue #59 and refactor high-level spline code for consistency and efficiency 2017-05-15 15:55:15 -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