54b9e60dd0
reformat
2020-09-20 14:06:40 -04:00
4cbf821af3
modernize example
2020-09-20 14:03:13 -04:00
774bffe623
relax result precision requirement somewhat
2020-09-20 13:57:04 -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
c91ee210e4
simplify variable lookup in set command
2020-09-19 16:04:09 -04:00
9c0808e95a
update unit tests for move of version string location
2020-09-19 15:00:03 -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
6dda562501
skip over uninitialized and internal variables. correctly identify all kinds of boolean values
2020-09-18 23:40:31 -04:00
9cdde97863
correct test logic
2020-09-18 22:37:54 -04:00
5ce6259632
correct reference to function
2020-09-18 22:35:56 -04:00
56d9222156
Merge pull request #2374 from akohlmey/next_patch_version
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Step version strings for the next patch release
2020-09-18 21:45:34 -04:00
897a7d0ed4
only try to broadcast if we have a proper communicator
2020-09-18 21:17:31 -04:00
f5fda95da6
Merge branch 'master' into next_patch_version
2020-09-18 21:15:12 -04:00
094a1bea91
Merge pull request #2369 from akohlmey/collected-small-changes
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Collected small changes and fixes for the next patch release
2020-09-18 20:20:41 -04:00
51957a6219
fix merge conflict
2020-09-18 19:49:36 -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"
...
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
34ba8ec83c
Merge pull request #2359 from rbberger/python_interface_guide
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Library interface updates and Python documentation
2020-09-18 16:11:08 -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
9a6dfbc0ee
add some cross referencing
2020-09-18 13:45:33 -04:00
449513703b
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-18 12:35:17 -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
df4ab6c39e
Merge pull request #2375 from akohlmey/fmtlib-update
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Update bundled fmtlib to version 7.0.3
2020-09-18 10:30:18 -04:00
dc89f0879c
update specific pull request templates as they are available through the github cli now
2020-09-18 06:54:31 -04:00
3a2457bb3d
update bundled fmtlib to version 7.0.3
2020-09-18 06:14:46 -04:00
2b1e249483
add comments to mark LAMMPS specific customizations
2020-09-18 06:12:42 -04:00
1ef36fd20a
step version strings for next patch release
2020-09-17 22:16:42 -04:00
0e81803c8b
some embedded documentation tweaks
2020-09-17 22:00:58 -04:00
90abe12a3e
update LAMMPS version reference
2020-09-17 21:04:43 -04:00
445e57923f
add one-time deprecation warning to lammps_open() and lammps_open_no_mpi()
2020-09-17 21:01:38 -04:00
