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12365 Commits

Author SHA1 Message Date
Steve Plimpton 2225fce94e patch 19May17 2017-05-19 07:35:36 -06:00
sjplimp 941b737319 Merge pull request #493 from akohlmey/doc-and-example-fixes 
Doc and example fixes
 2017-05-18 16:40:46 -06:00
Axel Kohlmeyer 654e09e999 correct input examples affected by the Pair::settings() bugfix 2017-05-18 18:34:27 -04:00
Axel Kohlmeyer 8751850eca a few formatting fixes for pair style python 2017-05-18 18:34:03 -04:00
sjplimp 0f88348917 Merge pull request #492 from lammps/pre-patch 
update docs before patch release
 2017-05-18 13:44:34 -06:00
Steve Plimpton b28ecd44c2 update docs before patch release 2017-05-18 13:14:47 -06:00
sjplimp 9db9fc9de3 Merge pull request #491 from akohlmey/fix-bigint-thermo-in-variables-bug 
convert bigint values for bonds/angles/dihedrals/impropers to doubles
 2017-05-18 13:08:42 -06:00
sjplimp 6ac9b7a1b0 Merge pull request #482 from akohlmey/add-pair-python 
Add python pair style for implementing simple pairwise additive potentials in python
 2017-05-18 11:15:58 -06:00
Axel Kohlmeyer 34dbf6b225 do not compute properties twice 2017-05-18 12:45:43 -04:00
Axel Kohlmeyer 26d71b66e4 convert bigint values for bonds/angles/dihedrals/impropers to doubles when evaluating those keywords in variable expressions 2017-05-18 12:41:48 -04:00
Richard Berger 65eacb6b90 Fix compilation warnings in fix_python 2017-05-18 12:20:39 -04:00
sjplimp cb3344a337 Merge pull request #489 from akohlmey/thread-safe-biasing 
port thread-safe temperature biasing from LAMMPS-ICMS
 2017-05-18 09:15:07 -06:00
sjplimp 5d38cbbce9 Merge pull request #487 from akohlmey/pair_edip_multi_element 
Import multi-element compatible pair style edip as edip/multi
 2017-05-18 09:13:30 -06:00
sjplimp 30babd8157 Merge pull request #485 from akohlmey/pair_settings_cut_bugfix 
Bugfix for correct resetting of previously set cutoffs to various Pair::settings() functions
 2017-05-18 09:12:47 -06:00
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
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