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641 Commits

Author SHA1 Message Date
sjplimp 1a29048940 Merge pull request #531 from ohenrich/user-cgdna 
Affiliation Update for USER-CGDNA
 2017-06-15 08:54:52 -06:00
sjplimp 0a6b3f8790 Merge pull request #527 from dstelter92/master 
Added compute_scalar to fix_grem
 2017-06-15 08:54:22 -06:00
sjplimp a4bc233d86 Merge pull request #525 from akohlmey/user-tally-refactor 
Refactoring of USER-TALLY computes to handle sparse/hybrid system for many processors plus bugfixes
 2017-06-15 08:51:24 -06:00
sjplimp 9a7207e34c Merge pull request #511 from akohlmey/add-compute-cnp 
Integrate compute cnp/atom contributed by Paulo Branicio (USC)
 2017-06-15 08:38:05 -06:00
sjplimp 34cfc7bd51 Merge pull request #490 from EmileMaras/NEB-Change 
added several features to the NEB
 2017-06-15 08:23:04 -06:00
Oliver Henrich c98bb7fa5f Corrected minor bug in utility script 2017-06-15 12:57:44 +01:00
Oliver Henrich 77ca68a2b4 Changed affiliation 2017-06-15 12:52:19 +01:00
dstelter92 e7634a44f4 updated thermo_modify in example 2017-06-14 13:11:54 -04:00
dstelter92 3214d639aa removed unneeded .gitignore 2017-06-14 12:26:52 -04:00
dstelter92 0ad66ecb89 Added compute_scalar to fix_grem for easier output managment, updated example to show use 2017-06-14 12:18:22 -04:00
Axel Kohlmeyer 7a05d87f7c update USER-TALLY examples 2017-06-12 22:20:36 -04:00
Emile Maras e03cc99467 made the command options more lammps standard style 2017-06-02 23:42:16 +02:00
Axel Kohlmeyer 2b3c124e61 add example input for compute cnp/atom 2017-05-31 00:43:53 -04:00
Steve Plimpton 22fdb1fc14 SNAP changes by Aidan 2017-05-30 10:21:07 -06:00
Emile Maras c904cfb8bc removed a bug in fix_neb.cpp which prevented the freeend to work properly, plus added an example for the neb freeend 2017-05-29 15:49:04 +02:00
Emile Maras 32c87f3131 removed a bug in fix_neb.cpp which prevented the freeend to work properly, plus added an example for the neb freeend 2017-05-29 14:00:13 +02:00
Axel Kohlmeyer 8bc829c7f1 change example inputs to be backward compatible 2017-05-22 14:40:01 -04:00
Axel Kohlmeyer 654e09e999 correct input examples affected by the Pair::settings() bugfix 2017-05-18 18:34:27 -04:00
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 0208fe9996 update example outputs 2017-05-18 00:46:49 -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 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 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 35e92733e9 import multi-element compatible pair style edip as edip/multi 2017-05-16 17:40:59 -04:00
Richard Berger 14f3deed6b Minor coefficient lookup improvement 2017-05-15 18:43:46 -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 df55a90ef6 some example input file tweaks 2017-05-15 00:22:03 -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
Richard Berger c4d0f07093 Allow fix python to only execute every N steps 2017-05-12 00:29:58 -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
Steve Plimpton 7c3b8e014c rename some USER/misc dirs 2017-05-11 10:15:28 -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 deff6ffaac Merge pull request #466 from DallasTrinkle/meam-spline-multicomponent 
Meam spline multicomponent
 2017-05-11 09:22:25 -06:00
Richard Berger 4ecf876a64 Added two examples of using the VTK dump style 2017-05-10 19:52:00 -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
Richard Berger f8af7edf92 Merge remote-tracking branch 'upstream/master' into python_refactoring 2017-05-06 16:00:22 -04:00
Steve Plimpton addd87c0f7 new Section package and start doc pages and build scripts 2017-05-04 11:22:20 -06:00
Axel Kohlmeyer 949d61e01e rename examples folder for USER-CGSDK package 2017-04-26 19:26:27 -04:00