d4cd67ce74
tweak format some more and refactor manual sectioning to be logically correct
...
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
...
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
...
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
42aca25a58
Update docs, fix typos
2020-09-17 18:10:08 -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
...
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
...
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
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
...
Updates to C-Library interface progammer guide and reference
2020-09-15 11:51:02 -04:00
4a48ce76b8
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-15 11:34:16 -04:00
c6bc21febf
Merge pull request #2361 from akohlmey/collected-small-changes
...
Collected small changes for the next patch release
2020-09-15 11:28:25 -04:00
b20b234ebe
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-15 10:45:28 -04:00
4b64be77e0
consolidate memory allocation information into a single function (in Info)
2020-09-15 01:59:58 -04:00
5634dd4394
correct formatting of examples
2020-09-14 17:15:53 -04:00
b1e0990c46
update lammps config settings calls example
2020-09-14 17:11:27 -04:00
f70717710e
fix for zstd support. add styles to list at top and document .zst extension requirement
2020-09-14 17:07:09 -04:00
a1b2f82107
test for exceptions add example
2020-09-14 17:01:28 -04:00
50b80e078d
Merge pull request #2354 from stanmoore1/qeq_refactor
...
small fix qeq/reax refactoring for base and accelerated variants
2020-09-14 12:18:32 -04:00
a5740d75cf
add missing option
2020-09-14 09:27:49 -04:00
de49325c0f
add properties example
2020-09-13 17:00:08 -04:00
b702298e83
fix typo
2020-09-12 19:06:58 -04:00
da0cdb0de4
update formatting of keyword summary
2020-09-12 19:06:30 -04:00
4a8d6016e4
Update docs
2020-09-11 22:49:44 -06:00
612f1d7ce3
fix typo
2020-09-11 17:49:06 -04:00
7b869e8ee8
Start with more detailed description of PyLammps
2020-09-11 17:09:38 -04:00
97000fa016
Merge remote-tracking branch 'origin/master' into python_interface_guide
2020-09-11 09:48:28 -04:00
ded57ba749
move test to avoid issues with indentation from having tabs follow directly a list-table
2020-09-10 16:16:58 -04:00
bd72ef7996
add API to library/python interface to extract the MPI communicator
2020-09-09 22:03:11 -04:00
85c394453c
Update Colvars to version 2020-07-07
...
This update contains several fixes and small new features or usability
improvements. Descriptions and authorship information can be accessed from
the pull requests listed below.
Skip the zero-step also when multiple run commands are executed in sequence (@giacomofiorin)
https://github.com/Colvars/colvars/pull/357
Do not accumulate data at step 0 (@giacomofiorin)
https://github.com/Colvars/colvars/pull/345
Support for symmetry permutations of atoms in RMSD (@jhenin)
https://github.com/Colvars/colvars/pull/344
Detect new grid parameters (@jhenin)
https://github.com/Colvars/colvars/pull/341
Only access the output streams in non-threaded regions (@giacomofiorin)
https://github.com/Colvars/colvars/pull/338
Fix incomplete setting of default colvarsRestartFrequency (@giacomofiorin)
https://github.com/Colvars/colvars/pull/334
Fix typo (@e-kwsm)
https://github.com/Colvars/colvars/pull/333
Convert the input keyword to lowercase in read_state_data_key (@HanatoK)
https://github.com/Colvars/colvars/pull/332
Implement reflecting b.c. for ext Lagrangian (@jhenin)
https://github.com/Colvars/colvars/pull/329
2020-09-09 18:19:21 -04:00
ed14793c69
moved eigensolver documentation into pg_dev_utils.rst
2020-09-09 14:59:00 -07:00
cdd9d693ad
Merge pull request #2349 from akohlmey/more-progguide-updates
...
More Programmer docs updates and related code refactoring
2020-09-09 14:34:41 -04:00
c818a00523
remove unwanted docs
2020-09-08 16:53:26 -04:00
ea0a9f00e8
swap order of classes in toctree
2020-09-08 16:45:16 -04:00
daf8a2313a
split developer guide into multiple files
2020-09-08 16:38:06 -04:00
9f7e309f07
small updates to MyPage and convert MyPoolChunk similar to MyPage
2020-09-08 15:13:16 -04:00
f72e5b6d13
Typo
2020-09-08 12:52:32 -06:00
b008ba5ecb
Merge remote-tracking branch 'origin/master' into cmake_clean_up
2020-09-08 12:51:49 -06:00
22fac9affc
more doc update
2020-09-08 09:49:07 -06:00
