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10928 Commits

Author SHA1 Message Date
Axel Kohlmeyer faa0b401aa fix argument indexing bug in fix ave/atom 
(cherry picked from commit bc11518960)
 2016-09-19 23:24:37 -04:00
sjplimp d17421eb7c Merge pull request #36 from akohlmey/small_bugfixes_and_cleanups 
Small bugfixes and cleanups
 2016-09-16 13:19:39 -06:00
sjplimp 60dfdbc063 Merge pull request #35 from akohlmey/lj_sf_dipole_sf_correction 
corrections for pair style lj/sf/dipole/sf and its /omp variant
 2016-09-16 13:19:23 -06:00
sjplimp e4bd63759b Merge pull request #34 from rbberger/make_py_fixes 
Update Make.py
 2016-09-16 13:19:05 -06:00
sjplimp ca558f6712 Merge pull request #33 from rbberger/pylammps_additions 
PyLammps additions
 2016-09-16 13:18:17 -06:00
Steve Plimpton abf05eed61 comm tiled bug fix 2016-09-16 10:31:52 -06:00
sjplimp 72ce8ff89f Merge pull request #31 from akohlmey/doc-cleanups-and-updates 
More documentation cleanups and updates
 2016-09-16 10:05:53 -06:00
Axel Kohlmeyer 9637a5b530 colvars bugfix. updates colvars library to version 2016-09-14 2016-09-15 19:44:26 -04:00
Axel Kohlmeyer 4149413057 reduce global name space pollution in pair style meam 2016-09-15 16:32:41 -04:00
Axel Kohlmeyer 400ef87c05 make certain, that -log() doesn't overflow and assign a suitable maximum number instead. 2016-09-15 14:55:32 -04:00
Axel Kohlmeyer e9e9790d6e corrections for pair style lj/sf/dipole/sf and its /omp variant 
(cherry picked from commit f0c8b2af28a58485f6795cf85c7d88eaafa3e52a)
 2016-09-15 09:30:40 -04:00
Richard Berger 319b160752 Add exceptions setting to help message of Make.py 2016-09-14 19:26:03 -04:00
Richard Berger cddc1dbb11 Added exceptions flag to Make.py 2016-09-14 19:21:52 -04:00
Axel Kohlmeyer 2831f50790 Merge branch 'integration' into doc-cleanups-and-updates 2016-09-14 19:02:45 -04:00
Richard Berger 62bf307d3c Fix bug introduced into Make.py by latest changes 2016-09-14 18:15:50 -04:00
Richard Berger 5cdc48dd0c Update ipython example to show interface usage 2016-09-14 16:26:19 -04:00
Richard Berger 0ec8fa02e0 Make thermo output accessable through PyLammps 
Thermo data of the last run is now accessable through the `last_run.thermo`
property. This is a dictionary containing the data columns of thermo output.
All run data is kept as list and can be found in the `runs` property.
See issue #144
 2016-09-14 16:14:41 -04:00
Steve Plimpton 2fb666dc69 Merge branch 'doc' into integration 2016-09-14 13:32:39 -06:00
Richard Berger 6e3705f380 Allow writing input script from Python session 
This implements the requested feature in issue #145. The `write_script`
method now gives you a way of dumping out all used commands into a
LAMMPS input script file.

Note: this also dumps all commands which are indirectly issued by PyLammps
 2016-09-14 14:24:19 -04:00
Steve Plimpton 2f298951cf resolved conflicts 2016-09-14 10:22:46 -06:00
Steve Plimpton 717e719b83 HTML update 2016-09-14 09:35:03 -06:00
Axel Kohlmeyer 523c70e0be regenerate html files one more time 2016-09-14 10:01:13 -04:00
Axel Kohlmeyer 77e0a84877 fix an inconsistency and a typo 2016-09-14 09:59:36 -04:00
Axel Kohlmeyer 9779911cea regenerate html files from scratch after merging from upstream and including richard's last updates to the converter tools 2016-09-14 09:54:06 -04:00
Axel Kohlmeyer 1ad15b8711 Merge branch 'integration' into doc-cleanups-and-updates 2016-09-14 09:48:46 -04:00
Axel Kohlmeyer 7025a3f5d1 Merge pull request #32 from rbberger/doc-cleanups-and-updates 
Various updates to tools and some minor documentation fixes
 2016-09-14 09:46:05 -04:00
Richard Berger df304f8ca1 Updated HTML after latest tool changes and corrections 2016-09-13 20:22:17 -04:00
Richard Berger 3c88fa1436 Fix bug introduced in latest changes 2016-09-13 20:18:36 -04:00
Richard Berger b7ddc860c7 Fix error in Manual.txt 2016-09-13 20:00:17 -04:00
Richard Berger c61d5a1a29 Raise exception and output error if ulb,ule and olb,ole are unbalanced 2016-09-13 19:53:57 -04:00
Steve Plimpton 10b4411d5b Merge branch 'integration' of github.com:akohlmey/lammps into integration 2016-09-13 17:22:14 -06:00
Steve Plimpton c744b23c4c doc updates 2016-09-13 17:15:15 -06:00
sjplimp a69e059be3 Merge pull request #27 from akohlmey/small-bugfixes 
Collected small changes and bugfixes
 2016-09-13 17:11:23 -06:00
sjplimp dbc548dd88 Merge pull request #26 from rbberger/is_available_feature 
Extend is_available() function to query optional features
 2016-09-13 17:10:10 -06:00
Richard Berger 1dc19eceb2 Update unit tests to reflect new behavior 2016-09-13 19:03:57 -04:00
Richard Berger ae6b540d3c Add indentation to multi-paragraph entries 2016-09-13 19:03:46 -04:00
Steve Plimpton 25e518a4f4 added options to compute bond/local 2016-09-13 17:03:37 -06:00
Steve Plimpton fe2fca4e9b clean-up of example files 2016-09-13 14:58:02 -06:00
Steve Plimpton ed52f9ea5e pair vashishta/table 2016-09-13 14:54:12 -06:00
Steve Plimpton 944289b018 final version of pair vashishta/table 2016-09-13 14:45:53 -06:00
Axel Kohlmeyer 80c5b01bfc flag 'allocated' must be initialized in constructor 2016-09-13 14:33:00 -04:00
Axel Kohlmeyer 51e4a568c9 Merge branch 'small-bugfixes' of github.com:akohlmey/lammps into small-bugfixes 2016-09-13 14:32:27 -04:00
Richard Berger 300d1ef52e Remove references to former empty file 2016-09-13 14:17:27 -04:00
Richard Berger 633840c876 remove empty file 2016-09-13 13:46:45 -04:00
Richard Berger c44228b0cc Created more complete TOC and indices 
This adds index sections on the main navigation bar and finally silences the
missing TOC warnings.
 2016-09-13 13:40:18 -04:00
Richard Berger 90f6395ddc Filter out more header numbers 2016-09-13 13:31:30 -04:00
Steve Plimpton a8081d4507 fix qeq Kokkos bug fix by Stan 2016-09-13 10:54:04 -06:00
Axel Kohlmeyer 14bed44743 ignore Makefile.lammps in lib tree 2016-09-13 09:36:48 -04:00
Axel Kohlmeyer 18cacb8e1d ignore *.mod generated by fortran compilers 2016-09-13 09:36:19 -04:00
Richard Berger 546582ea02 Escape pipe characters 2016-09-12 23:18:38 -04:00