28812b1ea7
Merge pull request #2381 from akohlmey/collected-small-changes
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Collected small changes
2020-09-24 16:17:28 -04:00
2f8a5ddd1f
xindy doesn't seem to be required (and is not available on CentOS 8)
2020-09-23 17:13:09 -04:00
b6d98707ec
molecule: revert overzealous error checking
2020-09-23 11:23:10 -04:00
2b30661b07
molecule: correctly update docs
2020-09-23 10:46:23 -04:00
343932f220
document -DLAMMPS_TRAP_FPE
2020-09-23 09:38:07 -04:00
f186eb7005
be more selective about which elements not to display
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we only want to skip the redundant User-Documentation and Programmer-Documentation captions
2020-09-21 22:41:19 -04:00
54aacc47ea
add section about citing LAMMPS
2020-09-21 22:40:36 -04:00
92f8398bed
check more thoroughly for prerequisites to translate the PDF manual. update doc/README
2020-09-19 18:16:52 -04:00
f72fb7290b
fix links
2020-09-19 16:28:20 -04:00
67aeb7a5e5
Merge branch 'move-version-to-lammps' into collected-small-changes
2020-09-19 16:17:01 -04:00
6b0346c299
try use unencrypted download or using wget if normal download of polyfill.js fails
2020-09-19 16:14:08 -04:00
4c51a8ae57
move version and num_ver from Universe to LAMMPS and make num_ver an int
2020-09-19 11:37:08 -04:00
89506efd23
document Pointers class and LAMMPS_NS namespace
2020-09-19 11:16:44 -04:00
73c65d43e1
update list of main folders and descriptions
2020-09-19 02:53:36 -04:00
9030c987e6
tweak formatting and style setting to have the desired structure and layout
2020-09-19 00:54:54 -04:00
f5fda95da6
Merge branch 'master' into next_patch_version
2020-09-18 21:15:12 -04:00
a0afb9b554
Merge branch 'master' into collected-small-changes
2020-09-18 18:38:47 -04:00
7580176020
Merge pull request #2376 from giacomofiorin/colvars-update
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Update Colvars to version 2020-09-17
2020-09-18 18:38:17 -04:00
b520a6287b
Revert parts of "Restore PDF index"
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We need to update the container image(s) for building the
pdf documentation on ci.lammps.org by adding `latexmk`
and `xindy` before we can re-enable this change to the makefile.
This partially reverts commit 3c3b76a781
2020-09-18 18:37:26 -04:00
494498df03
update docs on building the PDF version of the manual
2020-09-18 18:27:23 -04:00
906e000e4c
Merge pull request #2368 from jrgissing/bond/react-update_all_charges_default
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Bond/react update all charges by default
2020-09-18 18:17:54 -04:00
33a2857b33
Fix whitespace
2020-09-18 17:56:12 -04:00
3c3b76a781
Restore PDF index
2020-09-18 17:51:51 -04:00
07c9298558
Fix some broken internal hyperlinks in Colvars PDF
2020-09-18 17:24:12 -04:00
d4cd67ce74
tweak format some more and refactor manual sectioning to be logically correct
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now if only there was a way to make the titles of the parts show in the
navigation sidebar.
2020-09-18 17:15:42 -04:00
7deb773440
Update Colvars to version 2020-09-17
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Small changes
Implement global map of components (@HanatoK)
https://github.com/Colvars/colvars/pull/363
Format code examples with colored background (@giacomofiorin)
https://github.com/Colvars/colvars/pull/361
replaced jacobi() with an open-source version (@jewettaij)
https://github.com/Colvars/colvars/pull/360
2020-09-18 17:09:18 -04:00
e1397b9a88
Merge branch 'master' into collected-small-changes
2020-09-18 16:11:47 -04:00
635b7c04a5
Update docs and docstrings
2020-09-18 14:49:25 -04:00
de811db221
address spelling issues
2020-09-18 14:13:35 -04:00
ae9abf0f7d
correctly update docs
2020-09-18 14:10:32 -04:00
e0b22a51da
Doc updates
2020-09-18 12:35:07 -04:00
1afb355d09
Limit int types to LAMMPS_INT and LAMMPS_INT64
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Keep LAMMPS_TAGINT and LAMMPS_BIGINT internal to LAMMPS.
An external caller now only needs to distinguish between 32 and 64bit
integers, doubles and C strings.
2020-09-18 12:05:37 -04:00
edbfdde372
document ubuf union in developer guide
2020-09-18 11:55:06 -04:00
1264184e7b
tweak some website layout and style settings
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- make previous/next buttoms smaller and show on top and bottom of page
- make tab header items smaller and more rounded
- reduce padding on a few selected items to make pages more compact
remove obsolete lammps.css file variant
2020-09-18 10:55:50 -04:00
1ef36fd20a
step version strings for next patch release
2020-09-17 22:16:42 -04:00
42aca25a58
Update docs, fix typos
2020-09-17 18:10:08 -04:00
4c5aedeaa0
fix typo
2020-09-17 12:50:53 -04:00
91eaaba1be
improve portability of docs makefile
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- detect if /bin/bash is not found and provide a suitable error message
- use $(MAKE) and $(MFLAGS) variables to handle cases where GNU make is not called "make"
2020-09-17 12:40:09 -04:00
706a898163
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-17 12:08:12 -04:00
e924fc6d6e
Merge pull request #2347 from jewettaij/math_eigen
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Replace eigensolver code in LAMMPS with math_eigen.h and updated docs
2020-09-17 00:28:12 -04:00
4e304177a1
Merge pull request #2356 from giacomofiorin/colvars-update
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Update Colvars to version 2020-07-07
2020-09-16 23:37:02 -04:00
96f4178d92
add URLs to upstream projects for eigensolvers
2020-09-16 17:53:27 -04:00
55a054a44a
bond/react: default charge update docs
2020-09-16 17:09:48 -04:00
bd542efa52
include math_eigen.h, remove it from .gitignore
2020-09-16 14:12:14 -04:00
fd9e39bf1a
update docs
2020-09-16 14:07:06 -04:00
f5998692d0
Merge branch 'master' into math_eigen
2020-09-15 21:37:05 -04:00
38f0a2e24c
Fix doc build errors
2020-09-15 19:50:28 -04:00
7611efeea2
Update python docs
2020-09-15 18:03:26 -04:00
3576464268
Merge branch 'master' into consistent-memory-usage
2020-09-15 12:25:16 -04:00
165444004e
Merge pull request #2362 from akohlmey/library-progguide
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Updates to C-Library interface progammer guide and reference
2020-09-15 11:51:02 -04:00
