5345ad2da7
merge in the remainder of the USER-REAXC-OMP code. still a lot of work to do. compiles only with -fopenmp active
2017-05-24 16:24:43 -04:00
bb890941ca
first chunk of code from USER-REAXC-OMP imported and adapted into USER-REAXC
2017-05-24 00:19:36 -04:00
4002dce639
restore explicit NAN constants in output
2017-05-22 22:39:52 -04:00
c801cdd81f
some more formatting cleanup in fix neb
2017-05-22 22:33:14 -04:00
9008a31190
more formatting cleanup
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This cleans up and simplifies the neb command code some more
2017-05-22 21:55:55 -04:00
bdfb7c69ea
Remove unused code detected by coverity CID 177700
2017-05-22 17:51:40 -04:00
084626e60b
Fixes coverity issue CID 179426
2017-05-22 17:36:16 -04:00
a7d790a827
Fixes coverity issue CID 179439
2017-05-22 17:33:47 -04:00
8a630ff4ec
Fixes coverity issue CID 179440
2017-05-22 17:32:07 -04:00
617ca4e0c8
Fixes coverity issue CID 179436
2017-05-22 17:30:46 -04:00
62601678cd
when growing arrays with reallocate, always check against atom->nmax and not atom->nlocal or else these arrays may be of inconsistent size and communication can lead to data corruption
2017-05-22 17:16:19 -04:00
081910adbc
do not try to free null communicators
2017-05-22 17:15:14 -04:00
f73fd0625d
rename nall class member to numall to avoid confusion with the common convention nall = atom->nlocal+atom->nghost
2017-05-22 17:14:38 -04:00
7185db98b4
NEBLongRange was incorrectly set to false by default. revert to true.
2017-05-22 17:13:38 -04:00
4780d72809
use '&&' and '||' instead of 'and' and 'or' operators for consistency
2017-05-22 14:42:42 -04:00
3fd91a239f
avoid use '&&' and '||' instead of 'and' and 'or' for consistency
2017-05-22 14:41:01 -04:00
546aed7ccd
plug some memory leaks
2017-05-19 16:14:59 -04:00
6ef79d3715
silence several compiler warnings
2017-05-19 15:13:19 -04:00
c2bf3269ac
formatting cleanup. combine 8 MPI_Allreduce() calls into 1
2017-05-19 15:02:29 -04:00
2225fce94e
patch 19May17
2017-05-19 07:35:36 -06:00
069f3e746b
small formating changes
2017-05-18 21:23:29 +02:00
b28ecd44c2
update docs before patch release
2017-05-18 13:14:47 -06:00
9db9fc9de3
Merge pull request #491 from akohlmey/fix-bigint-thermo-in-variables-bug
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convert bigint values for bonds/angles/dihedrals/impropers to doubles
2017-05-18 13:08:42 -06:00
6ac9b7a1b0
Merge pull request #482 from akohlmey/add-pair-python
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Add python pair style for implementing simple pairwise additive potentials in python
2017-05-18 11:15:58 -06:00
34dbf6b225
do not compute properties twice
2017-05-18 12:45:43 -04:00
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
65eacb6b90
Fix compilation warnings in fix_python
2017-05-18 12:20:39 -04:00
cb3344a337
Merge pull request #489 from akohlmey/thread-safe-biasing
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port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-18 09:15:07 -06:00
5d38cbbce9
Merge pull request #487 from akohlmey/pair_edip_multi_element
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Import multi-element compatible pair style edip as edip/multi
2017-05-18 09:13:30 -06:00
30babd8157
Merge pull request #485 from akohlmey/pair_settings_cut_bugfix
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Bugfix for correct resetting of previously set cutoffs to various Pair::settings() functions
2017-05-18 09:12:47 -06:00
aa09f45b7e
Merge pull request #484 from akohlmey/add-gao-weber-styles
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Add Gao-Weber manybody styles
2017-05-18 09:10:03 -06:00
4b61cf6f52
Merge pull request #483 from akohlmey/airebo-spline-bugfix-refactor
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AIREBO spline code out-of-bounds and bondorder derivative bugfix and refactor
2017-05-18 09:01:33 -06:00
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
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
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
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
45becfb235
correct author attributions
2017-05-17 09:59:01 -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
d2810f9f83
port thread-safe temperature biasing from LAMMPS-ICMS
2017-05-16 18:15:13 -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
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
