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10848 Commits

Author SHA1 Message Date
Axel Kohlmeyer 5c927ca839 Merge remote-tracking branch 'lammps-rw/integration' into vashishta-tabulation 2016-09-08 17:22:21 -04:00
Axel Kohlmeyer 4bb42be3cc implement vashishta/table/omp in USER-OMP 2016-09-08 17:22:03 -04:00
Axel Kohlmeyer 7de5143050 update vashishta pair style example 2016-09-08 17:21:14 -04:00
Axel Kohlmeyer 71eed1d612 update documentation for vashishta pair style 2016-09-08 17:20:52 -04:00
Steve Plimpton dd34feb2bd Merge branch 'small' into integration 2016-09-08 14:35:36 -06:00
Steve Plimpton 2524c5b526 Merge branch 'small-bugfixes' of https://github.com/akohlmey/lammps into small 2016-09-08 14:31:27 -06:00
Axel Kohlmeyer fe581e8ced Merge remote-tracking branch 'lammps-rw/integration' into vashishta-tabulation 2016-09-08 16:21:05 -04:00
sjplimp b866e0663b Merge pull request #24 from rbberger/info_command_styles 
Info command extensions
 2016-09-08 14:16:41 -06:00
sjplimp 5d0da95a0b Merge pull request #23 from akohlmey/doc-corrections-and-updates 
Doc corrections and updates
 2016-09-08 14:15:56 -06:00
sjplimp 07e55ef61e Merge pull request #22 from akohlmey/colvars-update 
accumulated colvars library update and lib "make clean" improvement
 2016-09-08 14:14:49 -06:00
Steve Plimpton 236ebf7fab Kokkos lib update 2016-09-08 13:56:18 -06:00
Axel Kohlmeyer a6df1e53b4 ignore all variants of the vashishta pair styles in src/ 2016-09-08 14:46:09 -04:00
Axel Kohlmeyer 9b2d5ff3e7 remove executable permissions on non-executables and non-scripts 2016-09-08 14:45:07 -04:00
Axel Kohlmeyer c33e1049d8 delete duplicate fclose() in fix ttm/mod constructor 2016-09-08 11:51:22 -04:00
Richard Berger 1f901c9b2d Update generated HTML docs of info command 2016-09-08 09:53:57 -04:00
Richard Berger 79b8f6320d Update docs of info command 2016-09-08 09:53:14 -04:00
Richard Berger 2dcfb51d18 Change info command styles syntax 
Change to `info styles [all|atom|pair|compute|...]`.
By default, `info styles` will print all styles.
 2016-09-08 09:38:52 -04:00
Richard Berger ba2b523bf4 Use factory for region style creation 2016-09-08 09:38:51 -04:00
Richard Berger fd2b886422 Use factory for dump style creation 2016-09-08 09:38:51 -04:00
Richard Berger 9952d8a210 Use factory for minimize style creation 2016-09-08 09:38:51 -04:00
Richard Berger 85c132943e Use factory for integrate style creation 2016-09-08 09:38:48 -04:00
Richard Berger 55260ad53e Add missing delete in destructor 2016-09-08 09:32:48 -04:00
Richard Berger a1e5fc0fca Use factory for AtomVec style creation 2016-09-08 09:32:48 -04:00
Richard Berger 88e10b401d Cleanup force.h after refactoring 2016-09-08 09:32:48 -04:00
Richard Berger 1d03913aa3 Use factory for kspace style creation 2016-09-08 09:32:48 -04:00
Richard Berger 0745a9f33f Use factory for improper style creation 2016-09-08 09:32:48 -04:00
Richard Berger 906c50223a Use factory for dihedral style creation 2016-09-08 09:32:47 -04:00
Richard Berger 35bdeb63e2 Use factory for angle style creation 2016-09-08 09:32:47 -04:00
Richard Berger 69c58ef0d5 Use factory for bond style creation 2016-09-08 09:32:47 -04:00
Richard Berger 95ee6440ad Use pair_map to list pair styles 2016-09-08 09:32:47 -04:00
Richard Berger 00b08bb5e1 Use compute_map and fix_map to list compute and fix styles 2016-09-08 09:32:47 -04:00
Richard Berger e483cb9ef9 Use command_map to list command styles 2016-09-08 09:32:47 -04:00
Richard Berger 06e3a11c2d Add styles output to info command 
Adds the ability to list all available styles in LAMMPS with:

```
info styles
```

Each style can also be printed separately using one of the following:

```
info atom_styles
info integrate_styles
info minimize_styles
info pair_styles
info bond_styles
info angle_styles
info dihedral_styles
info improper_styles
info kspace_styles
info fix_styles
info compute_styles
info region_styles
info dump_styles
```
 2016-09-08 09:32:46 -04:00
Steve Plimpton 7e8440cbab undo changes to vashishita/omp 2016-09-07 12:02:38 -06:00
Steve Plimpton 43b05a60c7 created vashishta/table variant 2016-09-07 11:56:38 -06:00
Axel Kohlmeyer 0fe7d1d361 correct internal links for Modify LAMMPS section 2016-09-07 10:13:34 -04:00
Axel Kohlmeyer 346ff42498 correct reference in modify section 2016-09-07 10:10:12 -04:00
Axel Kohlmeyer 5feedbd829 regenerate html pages with new txt2rst tool 2016-09-07 10:09:53 -04:00
Axel Kohlmeyer 44ce6fac4b replace backquote with regular quote and `` + '' with double quote. 2016-09-07 08:29:16 -04:00
Axel Kohlmeyer 70d6718aa3 Update discussion on parallel python packages. There seem to be only two left. 2016-09-07 07:42:06 -04:00
Axel Kohlmeyer 348b677148 Make formatting and links more consistent and unique 2016-09-07 07:41:17 -04:00
Richard Berger 4c783ea3b7 Enforce l,ule or l,ole command order for RST 
(cherry picked from commit 79e867c213)
 2016-09-07 02:16:55 -04:00
Richard Berger 9e8256aeb0 Refactored code and escape RST special character '_' 
(cherry picked from commit 4629a464f7)
 2016-09-07 02:16:55 -04:00
Richard Berger 925f1bfb6f Escape RST special character '^' and take care of special math cases 
(cherry picked from commit 453521c8e6)
 2016-09-07 02:16:55 -04:00
Richard Berger 3f312244a0 Escape RST special character '*' in final output 
(cherry picked from commit 7cb39811d4)
 2016-09-07 02:16:54 -04:00
Axel Kohlmeyer 55022d1263 replace :l,ule and :l,ole with :l :ule or :l :ole 2016-09-07 02:11:59 -04:00
Axel Kohlmeyer 0d491d483c avoid Inline substitution_reference start-string without end-string 2016-09-07 02:10:49 -04:00
Axel Kohlmeyer a31c507370 correct error message text, sync with source 2016-09-06 22:15:49 -04:00
Axel Kohlmeyer 3a74ccffa2 update colvars library to version 2016-09-03 
(cherry picked from commit 4181f5ac9d)
 2016-09-06 21:28:59 -04:00
Axel Kohlmeyer c8cfd53c1b adjust makefiles in lib tree, so they don't return an error exit code on "make clean" targets. 
(cherry picked from commit 4117218ca3)
 2016-09-06 21:28:55 -04:00