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
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
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
3fd91a239f
avoid use '&&' and '||' instead of 'and' and 'or' for consistency
2017-05-22 14:41:01 -04:00
8bc829c7f1
change example inputs to be backward compatible
2017-05-22 14:40:01 -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
aca16745e4
restore spelling fix and semantic fix from upstream
2017-05-19 12:17:19 -04:00
a5110d81ea
correct a bunch of documentation formatting issues for updated neb and fix neb commands
2017-05-19 12:13:23 -04:00
d4ee03c778
changed doc links
2017-05-18 21:31:39 +02:00
069f3e746b
small formating changes
2017-05-18 21:23:29 +02:00
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
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
0008b6fc2d
Merge pull request #477 from lammps/renamings
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rename some USER/misc dirs
2017-05-12 08:54:12 -06:00
b6a70ec6fd
fixup docs after last change
2017-05-12 00:34:47 -04:00
c4d0f07093
Allow fix python to only execute every N steps
2017-05-12 00:29:58 -04:00
93f6033061
Add documentation about fix python
2017-05-11 23:50:40 -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
d84f8898b7
implement functions to execute arbitrary python code from strings or files and recast the python source keyword through using them.
2017-05-11 22:39:08 -04:00
27a6371f9b
implement a python source command as suggested in issue #454
2017-05-11 19:18:09 -04:00
7c3b8e014c
rename some USER/misc dirs
2017-05-11 10:15:28 -06:00
a069d21621
Merge pull request #476 from akohlmey/dump_custom_bugfix
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dump custom memory allocation bugfix
2017-05-11 09:27:08 -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
998eb44e83
Merge pull request #473 from akohlmey/compress-for-reaxc-fixes
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compressed output via gzip for some ReaxFF fixes
2017-05-11 09:25:18 -06:00
96d1de8575
Merge pull request #471 from akohlmey/fix-4may2017-issues
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Fix a bunch of remaining issues in the 4 may 2017 release
2017-05-11 09:24:35 -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
328ef873d8
fix mixed memory alloc bug in dump custom. this closes #475
2017-05-10 22:41:41 -04:00
4ecf876a64
Added two examples of using the VTK dump style
2017-05-10 19:52:00 -04:00
c4ac5773cb
Fix segmentation fault in dump vtk
2017-05-10 19:51:14 -04:00
cac1bf83ef
Work around VTK 7 API change
2017-05-10 19:41:48 -04:00
abeb1e096a
add support for gzip compressed output to fix reax/bonds, reax/c/bonds and reax/c/species
2017-05-10 11:19:18 -04:00
9f7ce39f9f
correct some more omitted updates
2017-05-09 18:14:34 -04:00
29ae8d4ca3
correct broken links and references in documentation
2017-05-09 17:15:07 -04:00
3f4aee1046
implement overlooked changes from 4may2017 patch
2017-05-09 15:57:35 -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
390ceb1475
whitespace cleanup
2017-05-09 15:49:37 -04:00
6c5edf6c70
performance improvement through avoiding function call and dereference overhead
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- make i_to_potl() and ij_to_potl() functions inline and const
- don't dereference inside the functions, but cache, if possible in external variables
=> up to 15% speedup.
2017-05-09 15:38:10 -04:00
9cd994f57c
fix issues with potential file parser
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- use Force::open_potential()
- replace ftell()/fseek() with rewind()/fgets() which is safer on windows and other platforms with automatic CR/LF to LF conversion on text files
- make parser use properly NULL terminated strings through using strtok()
2017-05-09 15:35:48 -04:00
a6e2d5b5f7
Merge pull request #470 from lammps/integration
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neighbor list bugfix to prevent cycle in copy lists
2017-05-09 10:32:25 -06:00
08ec55743e
neighbor list bugfix to prevent cycle in copy lists
2017-05-09 08:55:18 -06:00
c4f90b3841
Merge pull request #449 from rbberger/python_refactoring
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Add Python 3 compatibility and expand Python interface availability
2017-05-08 08:29:24 -06:00
f8af7edf92
Merge remote-tracking branch 'upstream/master' into python_refactoring
2017-05-06 16:00:22 -04:00
a73402ad93
update src/Purge.list with renamed reaxc src files
2017-05-04 14:53:08 -06:00
