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"
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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
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
6e22229424
Merge remote-tracking branch 'github/master' into collected-small-changes
2020-09-17 20:27:55 -04:00
94ad6821f7
Merge pull request #2373 from stanmoore1/kk_wkar
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Add workaround for performance regression in Kokkos Package
2020-09-17 20:24:39 -04:00
d8b6ebdfc8
Add workaround for performance regression
2020-09-17 16:33:48 -06:00
42aca25a58
Update docs, fix typos
2020-09-17 18:10:08 -04:00
b4a1c9c24c
Update examples
2020-09-17 17:08:13 -04:00
cf1ae7afa6
Use wrapper lammps.extract_atom_datatype
2020-09-17 17:04:40 -04:00
6729a42cfa
Merge branch 'master' into collected-small-changes
2020-09-17 17:01:44 -04:00
3b96375888
Merge pull request #2371 from arghdos/kokkos_hip_porting
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Additional Kokkos/HIP porting work
2020-09-17 16:58:46 -04:00
be72ce2534
Simplify Python examples to use numpy.extract_atom
2020-09-17 16:51:46 -04:00
ab6b69d6bd
Add documentation and better autodetect
2020-09-17 16:39:19 -04:00
c06d5f7fb7
Fix type cast
2020-09-17 16:37:25 -04:00
b81ad54baa
Simplify extract_atom and extract_global in Python interface
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Both extract methods now can auto-detect the datatype of both global
and per-atom properties. Callers can still enforce different types
if needed by specifying the now optional dtype argument.
The numpy wrapper now has a new extract_atom function method, which
replace the extract_atom_darray and extract_atom_iarray method and
autodetects both type and size. All parameters can still be forced
to use different values if needed.
2020-09-17 16:16:27 -04:00
3275419872
Allow Colvars to include headers from the LAMMPS source directory
2020-09-17 14:37:26 -04:00
d88810f13a
Add datatype introspection methods to library
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Adds lammps_extract_atom_datatype and lammps_extract_global_datatype functions
to allow extracting type information of properties.
2020-09-17 13:43:43 -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
