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
706a898163
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-17 12:08:12 -04:00
9fa43b8b12
Skip Numpy tests if not installed
2020-09-17 12:03:36 -04:00
7bf177a1c7
Fast forward porting work to master
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Change-Id: Ieb428e4a001efadf880dbe2c64c2a685cebdd4ae
2020-09-17 10:45:04 -05:00
0522e3d7b6
a few more unittest tweaks
2020-09-17 11:11:44 -04:00
00641f9f24
relax epsilon a little for passing cross-platform tests
2020-09-17 11:01:59 -04:00
5dacfc47ca
Change return type of lammps.get_natoms to int
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Closes PR #2370
2020-09-17 10:57:49 -04:00
62a63d0cd8
silence compiler warnings
2020-09-17 10:27:06 -04:00
e2fc70da62
Merge branch 'master' into collected-small-changes
2020-09-17 06:51:21 -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
e839fe0d30
Merge branch 'master' into collected-small-changes
2020-09-16 23:53:29 -04:00
b96512171c
set -DCOLVARS_LAMMPS when compiling colvars library
2020-09-16 23:52:06 -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
b9919b72d7
make MSM test w/o PBC run faster
2020-09-16 23:36:17 -04:00
429cc0cacf
add missing updates for symbolic constants in Atom class
2020-09-16 23:19:10 -04:00
