Axel Kohlmeyer
4c5aedeaa0
fix typo
2020-09-17 12:50:53 -04:00
Axel Kohlmeyer
91eaaba1be
improve portability of docs makefile
...
- 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
Axel Kohlmeyer
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
Axel Kohlmeyer
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
Axel Kohlmeyer
96f4178d92
add URLs to upstream projects for eigensolvers
2020-09-16 17:53:27 -04:00
Axel Kohlmeyer
bd542efa52
include math_eigen.h, remove it from .gitignore
2020-09-16 14:12:14 -04:00
Axel Kohlmeyer
fd9e39bf1a
update docs
2020-09-16 14:07:06 -04:00
Axel Kohlmeyer
f5998692d0
Merge branch 'master' into math_eigen
2020-09-15 21:37:05 -04:00
Axel Kohlmeyer
3576464268
Merge branch 'master' into consistent-memory-usage
2020-09-15 12:25:16 -04:00
Axel Kohlmeyer
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
Axel Kohlmeyer
c6bc21febf
Merge pull request #2361 from akohlmey/collected-small-changes
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Collected small changes for the next patch release
2020-09-15 11:28:25 -04:00
Axel Kohlmeyer
4b64be77e0
consolidate memory allocation information into a single function (in Info)
2020-09-15 01:59:58 -04:00
Axel Kohlmeyer
df9f0e244b
add false positive
2020-09-14 17:18:14 -04:00
Axel Kohlmeyer
5634dd4394
correct formatting of examples
2020-09-14 17:15:53 -04:00
Axel Kohlmeyer
b1e0990c46
update lammps config settings calls example
2020-09-14 17:11:27 -04:00
Axel Kohlmeyer
f70717710e
fix for zstd support. add styles to list at top and document .zst extension requirement
2020-09-14 17:07:09 -04:00
Axel Kohlmeyer
a1b2f82107
test for exceptions add example
2020-09-14 17:01:28 -04:00
Axel Kohlmeyer
50b80e078d
Merge pull request #2354 from stanmoore1/qeq_refactor
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small fix qeq/reax refactoring for base and accelerated variants
2020-09-14 12:18:32 -04:00
Axel Kohlmeyer
a5740d75cf
add missing option
2020-09-14 09:27:49 -04:00
Axel Kohlmeyer
de49325c0f
add properties example
2020-09-13 17:00:08 -04:00
Axel Kohlmeyer
b702298e83
fix typo
2020-09-12 19:06:58 -04:00
Axel Kohlmeyer
da0cdb0de4
update formatting of keyword summary
2020-09-12 19:06:30 -04:00
Axel Kohlmeyer
eda04dac98
update conventions and guidelines about C++ standard and requirements
2020-09-12 15:13:23 -04:00
Stan Moore
4a8d6016e4
Update docs
2020-09-11 22:49:44 -06:00
Axel Kohlmeyer
612f1d7ce3
fix typo
2020-09-11 17:49:06 -04:00
Axel Kohlmeyer
ded57ba749
move test to avoid issues with indentation from having tabs follow directly a list-table
2020-09-10 16:16:58 -04:00
Axel Kohlmeyer
4452109b60
address spelling issue
2020-09-10 16:15:03 -04:00
Axel Kohlmeyer
0d5f68bc30
make "new in" and "changed in" leads boldface
2020-09-10 16:14:53 -04:00
Axel Kohlmeyer
3d37fd05f4
disable caching - for now - to avoid bad side effects from sphinx-tabs
2020-09-10 16:14:18 -04:00
Axel Kohlmeyer
bd72ef7996
add API to library/python interface to extract the MPI communicator
2020-09-09 22:03:11 -04:00
Giacomo Fiorin
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
Andrew Jewett
ed14793c69
moved eigensolver documentation into pg_dev_utils.rst
2020-09-09 14:59:00 -07:00
Andrew Jewett
3bacf97468
Merge branch 'master' into math_eigen
2020-09-09 14:56:28 -07:00
Axel Kohlmeyer
cdd9d693ad
Merge pull request #2349 from akohlmey/more-progguide-updates
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More Programmer docs updates and related code refactoring
2020-09-09 14:34:41 -04:00
Axel Kohlmeyer
03d43bda3c
make "New in" and "Changed in" statements boldface to stand out more
2020-09-09 09:25:58 -04:00
Axel Kohlmeyer
c818a00523
remove unwanted docs
2020-09-08 16:53:26 -04:00
Axel Kohlmeyer
ea0a9f00e8
swap order of classes in toctree
2020-09-08 16:45:16 -04:00
Axel Kohlmeyer
daf8a2313a
split developer guide into multiple files
2020-09-08 16:38:06 -04:00
Axel Kohlmeyer
9f7e309f07
small updates to MyPage and convert MyPoolChunk similar to MyPage
2020-09-08 15:13:16 -04:00
Christoph Junghans
f72e5b6d13
Typo
2020-09-08 12:52:32 -06:00
Christoph Junghans
b008ba5ecb
Merge remote-tracking branch 'origin/master' into cmake_clean_up
2020-09-08 12:51:49 -06:00
Christoph Junghans
22fac9affc
more doc update
2020-09-08 09:49:07 -06:00
Christoph Junghans
8fb13f4fd1
cmake: make doc more consistent
2020-09-08 09:43:21 -06:00
Axel Kohlmeyer
5df3deb8e6
update/refactor a few more build documentation files for using tabs
2020-09-08 11:40:21 -04:00
Axel Kohlmeyer
88cc673f78
more use of tabs in Build_extras.rst
2020-09-08 10:11:37 -04:00
Axel Kohlmeyer
dd20776915
fix spelling issues
2020-09-07 21:17:56 -04:00
Axel Kohlmeyer
9b01d5bf95
revise and add tabs to some sections
2020-09-07 21:08:47 -04:00
Axel Kohlmeyer
f02db43f63
add discussion and minimal code example for MyPage class.
2020-09-07 16:10:48 -04:00
Axel Kohlmeyer
0447616aaf
address spelling issues
2020-09-07 08:03:41 -04:00
Andrew Jewett
f329d56495
updated pg_developer.rst
2020-09-06 20:12:38 -07:00