Commit Graph

6990 Commits

Author SHA1 Message Date
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
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
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
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
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
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
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