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12684 Commits

Author SHA1 Message Date
Richard Berger 06a4f47a4c Merge remote-tracking branch 'upstream/master' into small_updates 2017-05-22 17:14:29 -04:00
Axel Kohlmeyer 7185db98b4 NEBLongRange was incorrectly set to false by default. revert to true. 2017-05-22 17:13:38 -04:00
Axel Kohlmeyer 4780d72809 use '&&' and '||' instead of 'and' and 'or' operators for consistency 2017-05-22 14:42:42 -04:00
Axel Kohlmeyer 3fd91a239f avoid use '&&' and '||' instead of 'and' and 'or' for consistency 2017-05-22 14:41:01 -04:00
Axel Kohlmeyer 8bc829c7f1 change example inputs to be backward compatible 2017-05-22 14:40:01 -04:00
Axel Kohlmeyer 97d3c843c4 small documentation fixes to fix typos and formatting issues 2017-05-21 11:13:47 -04:00
Axel Kohlmeyer 546aed7ccd plug some memory leaks 2017-05-19 16:14:59 -04:00
Axel Kohlmeyer 6ef79d3715 silence several compiler warnings 2017-05-19 15:13:19 -04:00
Axel Kohlmeyer c2bf3269ac formatting cleanup. combine 8 MPI_Allreduce() calls into 1 2017-05-19 15:02:29 -04:00
Axel Kohlmeyer aca16745e4 restore spelling fix and semantic fix from upstream 2017-05-19 12:17:19 -04:00
Axel Kohlmeyer a5110d81ea correct a bunch of documentation formatting issues for updated neb and fix neb commands 2017-05-19 12:13:23 -04:00
Steve Plimpton 2225fce94e patch 19May17 2017-05-19 07:35:36 -06:00
Richard Berger 9593e05c9e Force PDF documentation build to fail on first error 2017-05-18 19:37:08 -04:00
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
Emile Maras d4ee03c778 changed doc links 2017-05-18 21:31:39 +02:00
Emile Maras 069f3e746b small formating changes 2017-05-18 21:23:29 +02:00
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
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