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47b3039b28
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update unit tests, too
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2020-09-11 19:24:32 -04:00 |
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9d0c3bc665
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replace some numeric constants in Atom and AtomVec classes with enumerators
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2020-09-11 19:07:55 -04:00 |
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612f1d7ce3
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fix typo
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2020-09-11 17:49:06 -04:00 |
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7b869e8ee8
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Start with more detailed description of PyLammps
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2020-09-11 17:09:38 -04:00 |
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77d475d121
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Add more tests
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2020-09-11 15:48:23 -04:00 |
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58833ce11e
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Add API tests
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2020-09-11 15:21:36 -04:00 |
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cb253b2b1a
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Add HTML report option for Python
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2020-09-11 14:03:13 -04:00 |
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1855f92694
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Use include and omit
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2020-09-11 12:44:41 -04:00 |
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377163d940
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Add target to generate Python coverage XML
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2020-09-11 11:36:22 -04:00 |
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101d39142e
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Merge pull request #2357 from akohlmey/lib-get-mpi-comm
Add ability to retrieve the MPI communicator from LAMMPS instance via library/python interface
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2020-09-11 11:20:12 -04:00 |
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97000fa016
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Merge remote-tracking branch 'origin/master' into python_interface_guide
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2020-09-11 09:48:28 -04:00 |
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ded57ba749
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move test to avoid issues with indentation from having tabs follow directly a list-table
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2020-09-10 16:16:58 -04:00 |
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4452109b60
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address spelling issue
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2020-09-10 16:15:03 -04:00 |
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0d5f68bc30
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make "new in" and "changed in" leads boldface
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2020-09-10 16:14:53 -04:00 |
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3d37fd05f4
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disable caching - for now - to avoid bad side effects from sphinx-tabs
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2020-09-10 16:14:18 -04:00 |
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e813e2d30a
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add minimal unit test for lammps_get_mpi_comm() API
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2020-09-09 22:12:47 -04:00 |
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bd72ef7996
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add API to library/python interface to extract the MPI communicator
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2020-09-09 22:03:11 -04:00 |
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b99e005ca1
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Update example output files
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2020-09-09 18:26:34 -04:00 |
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d43cb34c70
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Support debugging flag for Colvars via CMake
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2020-09-09 18:19:29 -04:00 |
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85c394453c
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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
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2020-09-09 18:19:21 -04:00 |
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ed14793c69
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moved eigensolver documentation into pg_dev_utils.rst
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2020-09-09 14:59:00 -07:00 |
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3bacf97468
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Merge branch 'master' into math_eigen
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2020-09-09 14:56:28 -07:00 |
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2ab0878c9e
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remreduced compile time by removing unnecessary instantiations from math_eigen.cpp
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2020-09-09 14:43:28 -07:00 |
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cdd9d693ad
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Merge pull request #2349 from akohlmey/more-progguide-updates
More Programmer docs updates and related code refactoring
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2020-09-09 14:34:41 -04:00 |
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e238201be5
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add a couple more versionadded directives
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2020-09-09 13:21:19 -04:00 |
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790b2693ba
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Merge pull request #2353 from junghans/cmake_clean_up
cmake: consistent usage of find variable
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2020-09-09 11:04:13 -04:00 |
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a51bebc9e4
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Merge pull request #2340 from rbberger/container_update
Singularity Container definitions update
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2020-09-09 09:53:48 -04:00 |
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f4c4c62349
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adjust test to updated API
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2020-09-09 09:27:34 -04:00 |
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03d43bda3c
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make "New in" and "Changed in" statements boldface to stand out more
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2020-09-09 09:25:58 -04:00 |
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2b854ec64f
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reformulate
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2020-09-09 09:25:34 -04:00 |
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a1cf6c087c
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no need to use a deprecated argument in a newly added API
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2020-09-09 09:06:28 -04:00 |
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2a42fe66ad
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discuss change to get LAMMPS handle as return value instead of argument
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2020-09-09 09:06:00 -04:00 |
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56b1300fd3
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reverted the default behavior of "jacobi3()". By default it now sorts the eigenvalues again.
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2020-09-08 21:58:54 -07:00 |
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dad749b62b
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make vget()/vgot() inline functions again for optimal performance.
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2020-09-08 20:52:51 -04:00 |
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6ade5dd740
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changed the default sorting options in "jacobi3()" to be more similar to the original "jacobi()" function from "math_extra.h". This should not have any effect on LAMMPS behavior
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2020-09-08 17:05:08 -07:00 |
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c818a00523
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remove unwanted docs
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2020-09-08 16:53:26 -04:00 |
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ea0a9f00e8
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swap order of classes in toctree
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2020-09-08 16:45:16 -04:00 |
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ca1b5ed936
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fix minor issues
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2020-09-08 16:43:10 -04:00 |
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daf8a2313a
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split developer guide into multiple files
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2020-09-08 16:38:06 -04:00 |
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ee25ed3897
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update/correct documentation for memory pool classes
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2020-09-08 16:36:48 -04:00 |
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9f4a991fc5
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move over doxygen comments for a few LAMMPS classes
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2020-09-08 16:36:29 -04:00 |
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1273179d03
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Fix compile error
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2020-09-08 13:42:25 -06:00 |
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9e47452382
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recover compilation for platforms using malloc() instead of posix_memalign()
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2020-09-08 15:36:21 -04:00 |
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7a9d31328e
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remove obsolete comment
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2020-09-08 15:29:42 -04:00 |
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4f8e627479
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QEq refactor
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2020-09-08 13:16:45 -06:00 |
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9f7e309f07
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small updates to MyPage and convert MyPoolChunk similar to MyPage
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2020-09-08 15:13:16 -04:00 |
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a3cc7581b1
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rename test for memory pools
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2020-09-08 15:12:08 -04:00 |
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f72e5b6d13
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Typo
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2020-09-08 12:52:32 -06:00 |
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b008ba5ecb
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Merge remote-tracking branch 'origin/master' into cmake_clean_up
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2020-09-08 12:51:49 -06:00 |
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9f8b8529b1
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Merge pull request #2348 from akohlmey/use-tabs-with-html
Enable sphinx-tabs extension with the html version of the documentation
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2020-09-08 12:02:43 -04:00 |
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