43efe9e417
adding Pair::single() support to python pair style and examples
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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
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
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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
14f3deed6b
Minor coefficient lookup improvement
2017-05-15 18:43:46 -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
df55a90ef6
some example input file tweaks
2017-05-15 00:22:03 -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
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Add python support features
2017-05-12 13:28:20 -06:00
c4d0f07093
Allow fix python to only execute every N steps
2017-05-12 00:29:58 -04:00
110bb79b14
Implement fix python mentioned in issue #454
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Allows to call a python function at defined points in the integration loop
2017-05-11 23:50:30 -04:00
7c3b8e014c
rename some USER/misc dirs
2017-05-11 10:15:28 -06:00
d7f54464c6
Merge pull request #474 from rbberger/dump_vtk_fixes
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Various dump vtk fixes
2017-05-11 09:25:42 -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
4ecf876a64
Added two examples of using the VTK dump style
2017-05-10 19:52:00 -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
f8af7edf92
Merge remote-tracking branch 'upstream/master' into python_refactoring
2017-05-06 16:00:22 -04:00
addd87c0f7
new Section package and start doc pages and build scripts
2017-05-04 11:22:20 -06:00
949d61e01e
rename examples folder for USER-CGSDK package
2017-04-26 19:26:27 -04:00
2f32fb7f8b
patch 13Apr17
2017-04-13 11:19:48 -06:00
9a027a01da
Add Python 3 compatibility to PYTHON package
2017-04-11 20:24:42 -04:00
4da8c1c4e2
patch 11Apr17
2017-04-11 09:00:37 -06:00
9f6e126a2f
Merge pull request #437 from ohenrich/user-cgdna
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User cgdna
2017-03-28 12:52:26 -06:00
111d350a22
fix gcmc units change for chemical potential
2017-03-28 12:34:46 -06:00
604afebf6f
Update to oxDNA2
2017-03-28 18:22:02 +01:00
8afed61db1
Upgrade to oxDNA2
2017-03-28 18:16:36 +01:00
394e9b42b0
new CHARMM pair styles with force swithing/shifting
2017-03-24 13:53:07 -06:00
277b93cb89
Merge pull request #417 from tonnamb/add-pair-zhou
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add new pair potential for metal-organic interactions - pair style momb
2017-03-24 09:41:30 -06:00
44841f6891
fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof
2017-03-23 15:31:27 -06:00
568b67eee9
include citation for reference paper into pair style momb
2017-03-23 12:00:53 -04:00
865b41e201
make pair style momb example follow LAMMPS conventions more closely
2017-03-23 11:50:10 -04:00
02e65900e6
add example log file generated from 17Nov16 version of lammps, make minimize and run short in system.in
2017-03-23 11:03:00 -04:00
1075be7eca
rename zhou to momb in examples
2017-03-23 10:18:15 -04:00
43f27250b5
Merge branch 'add-pair-zhou' of https://github.com/tonnamb/lammps into pull-417
2017-03-22 14:05:16 -04:00
7435084375
Verified oxDNA with modified nucleotide layout
2017-03-22 15:59:10 +00:00
5c39dfd740
re-ran example with fixed exchanges
2017-03-20 09:22:09 -04:00
d04ea8653d
add examples for pair_zhou
2017-03-18 21:21:25 -04:00
bed288339e
simplify and shorten examples for fix filter/corotate and combine into a single folder
2017-03-16 15:02:50 -04:00
0d8f74f0c5
Merge branch 'filter_corotate' of https://github.com/lukin17/lammps into pull-416
2017-03-15 18:54:41 -04:00
c3ce3747e0
Added fix filter/corotate.
2017-03-15 11:34:01 +01:00
7a75cd111c
Minor updates in documentation and setup tool, merge before upgrade to oxDNA2
2017-03-14 11:39:09 +00:00
23b8287933
Updated documentation and simple setup tool
2017-03-14 11:36:44 +00:00
920641bbff
Merge pull request #399 from rbberger/docs_spelling_fixes
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Correct spelling errors in documentation
2017-03-07 09:47:22 -07:00
4af6557568
Merge pull request #394 from jaapkroe/kolmogorov-crespi
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Added Kolmogorov-Crespi potential
2017-03-07 09:46:08 -07:00
0798885bdb
Merge pull request #389 from akohlmey/update-agni-potential
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update AGNI potential for Al, reference runs and output and citation
2017-03-07 09:35:31 -07:00
efaa4c6710
new neigh_modify exclude option, other SNAP changes
2017-03-07 09:31:12 -07:00
