683f3d9d2a
Merge pull request #481 from akohlmey/collected-small-changes
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Collected small updates and bugfixes
2017-05-18 09:01:04 -06:00
ce18524251
Merge pull request #480 from akohlmey/pair_morse_smooth_linear_bugfix
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corrections to pair style morse/smooth/linear
2017-05-18 08:57:24 -06:00
95dae9737b
Merge pull request #488 from lammps/neigh_occasional_bugfix
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bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species update from Stan
2017-05-18 08:53:54 -06:00
8daba01151
some small formating change but does not work anymore
2017-05-18 16:48:20 +02:00
640edbc1d4
added several features to the NEB
2017-05-18 11:08:08 +02:00
4b1914aa1f
update citations for multi-element edip potential
2017-05-18 01:07:52 -04:00
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
0208fe9996
update example outputs
2017-05-18 00:46:49 -04:00
24654ad28f
small formatting corrections to pair python style
2017-05-18 00:38:36 -04:00
8d46aa6056
add readme file to discuss various python pair style usage examples
2017-05-18 00:31:54 -04:00
09f3b687f7
new long-rance example with using hybrid/overlay and table only for lj part
2017-05-18 00:31:15 -04:00
436d3fd761
make hybrid example use half the atoms with python, half with lj/cut
2017-05-18 00:30:41 -04:00
9833f38499
change coulomb example to use cutoff coulomb
2017-05-18 00:30:19 -04:00
9725708b90
update pair style python docs
2017-05-18 00:29:02 -04:00
67962b15fc
a bunch refactoring changes in the python pair style and the examples
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- 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
1d48f287f0
add partial documentation for pair style python
2017-05-17 19:05:18 -04:00
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
278b9f7fba
move pair gw and gw/zbl to USER-MISC package
2017-05-17 14:59:46 -04:00
6032b8846e
Merge branch 'exaalt' of gitlab.com:exaalt/lammps into exaalt
2017-05-17 11:36:50 -06:00
98713680ec
added alternative linking line for intel mkl
2017-05-17 11:36:31 -06:00
085f3afdfb
fix typo in docs
2017-05-17 09:59:30 -04:00
45becfb235
correct author attributions
2017-05-17 09:59:01 -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
8936b99e9f
add contributed SiC.edip potential file
2017-05-16 18:15:53 -04:00
d2810f9f83
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -04:00
597f95fb1b
fix duplicate reference
2017-05-16 17:53:12 -04:00
7f9a331c73
bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue
2017-05-16 15:51:41 -06:00
35e92733e9
import multi-element compatible pair style edip as edip/multi
2017-05-16 17:40:59 -04:00
c11e87618b
implement second bugfix suggestion from @CF17 on issue #59
2017-05-16 14:18:56 -04:00
ca87e57129
improved version of AIREBO splines based on a suggestion by markus hoehnerbach
2017-05-16 11:58:34 -04:00
66084ad1f4
fix typo in rerun docs. closes #486
2017-05-16 04:27:15 -04:00
d807ba1974
whitespace cleanup
2017-05-16 00:26:39 -04:00
51fc386e72
correct the inner loop range for resetting cutoffs when redefining a pair style
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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
a6f0d700f1
Merge branch 'add-pair-python' of github.com:akohlmey/lammps into add-pair-python
2017-05-15 18:44:52 -04:00
14f3deed6b
Minor coefficient lookup improvement
2017-05-15 18:43:46 -04:00
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
69ccbd1562
Extract common wrappers to Python compatibility header
2017-05-15 17:46:57 -04:00
d9d4ef17c8
add gao-weber potentials (regular and with ZBL core) with SiC potential files
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NOTE: documentation is missing
2017-05-15 17:44:25 -04:00
93cc6f4a5d
Use in syntax for key lookup for Python 3 compatibility
2017-05-15 17:34:48 -04:00
0a40a7af7b
whitespace cleanup
2017-05-15 17:00:41 -04:00
eb6f6a77e5
dead code removal
2017-05-15 16:16:12 -04:00
fb7164a811
replace pow(x,-0.5) with 1.0/sqrt(x)
2017-05-15 16:16:01 -04:00
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
6a1f7e61f2
provide reference output for python pair style inputs
2017-05-15 00:25:11 -04:00
d662f5d429
whitspace cleanup and gitignore update
2017-05-15 00:22:22 -04:00
df55a90ef6
some example input file tweaks
2017-05-15 00:22:03 -04:00
6e113c1eaf
basic feature complete version of lj melt example with python interaction function
2017-05-15 00:15:41 -04:00
