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10928 Commits

Author SHA1 Message Date
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
Axel Kohlmeyer 16607a0132 update colvars library to version 2016-08-19 
(cherry picked from commit c67326be6d)
 2016-09-06 21:27:46 -04:00
Axel Kohlmeyer 3b476d914f update colvars to version 2016-08-10 
(cherry picked from commit eba3ad9abb)
 2016-09-06 21:27:46 -04:00
Axel Kohlmeyer 977b9e542f update colvars to another set of changes from the upstream repo 
(cherry picked from commit cb816f8cba)
 2016-09-06 21:27:45 -04:00
Axel Kohlmeyer 1b33d00785 update colvars makefile dependencies 
(cherry picked from commit df99a85930)
 2016-09-06 21:27:45 -04:00
Axel Kohlmeyer 3d2e5d0a50 suppress compiler warning 
(cherry picked from commit 6f227e194e)
 2016-09-06 21:27:45 -04:00
Axel Kohlmeyer ec2a6b9f0d update colvars to version 2016-08-10 
(cherry picked from commit f2ddf828e4)
 2016-09-06 21:27:41 -04:00
Axel Kohlmeyer 77620106a4 update colvars library to version 2016-08-05 
(cherry picked from commit 459db2eb6b)

# Conflicts:
#	doc/src/PDF/colvars-refman-lammps.pdf
 2016-09-06 21:26:50 -04:00
Axel Kohlmeyer f56c41eec0 update with correct error description. sync with manual. 2016-09-06 21:21:28 -04:00
Axel Kohlmeyer fc2d878305 update manual introduction to represent current status. correct some markup to better pass through sphinx 2016-09-06 21:20:47 -04:00
Axel Kohlmeyer 1c17b98500 Merge branch 'integration' into doc-corrections-and-updates 2016-09-06 20:19:02 -04:00
Axel Kohlmeyer 9138152563 Merge branch 'integration' into small-bugfixes 2016-09-06 20:17:07 -04:00
Axel Kohlmeyer ace5dc3c7c Merge remote-tracking branch 'lammps-rw/clean-up-docs-for-sphinx' into clean-up-docs-for-sphinx 2016-09-06 19:54:35 -04:00
Steve Plimpton 0252347d43 sync with 7Sep16 patch 2016-09-06 17:00:32 -06:00
sjplimp c9455c90de Merge pull request #20 from akohlmey/lammps-contribute 
Update description of submitting contributions to LAMMPS
 2016-09-06 16:55:16 -06:00
sjplimp 1e4d6fee93 Merge pull request #19 from akohlmey/clean-up-docs-for-sphinx 
Clean up docs for sphinx (redo)
 2016-09-06 16:54:39 -06:00
Axel Kohlmeyer 42db93e198 one more small correction to document recent fix ave/time changes 2016-09-06 16:10:16 -04:00
Axel Kohlmeyer 906bd24543 fix typos 2016-09-06 16:03:16 -04:00
Axel Kohlmeyer 4f88c75401 update the discussion on how to submit modifications 2016-09-06 16:02:59 -04:00
Axel Kohlmeyer 4314299be9 harden fix shear/history against use-after-delete and from incorrect use of reverse communication 2016-09-06 14:50:04 -04:00
Axel Kohlmeyer 1a7b04e8a6 generate updated html files for corrected .txt files 
(cherry picked from commit 7de57ffd94)
 2016-09-06 13:40:11 -04:00