14dfd3876a
T2345: Walking back nullptr changes to lib/awpmd
2020-09-12 09:34:39 -06:00
05d41cd50d
T2345: Replace instances of NULL with nullptr
...
revert lib/poems to remove nullptr changes.
Walking back changes to lib as needed.
2020-09-12 09:34:39 -06:00
13be8085e5
T2345: Replace instances of NULL with nullptr
...
Per guidance from Axel, revert lib/kokkos and lib/colvars
to remove nullptr changes.
2020-09-12 09:34:39 -06:00
f1ef7d85a8
T2345: Replace instances of NULL with nullptr
...
The following changes have been applied to src and lib folders:
regex replace: ([^"_])NULL ⇒ \1nullptr (8968 chgs in src, 1153 in lib)
Manually find/change: (void \*) nullptr ⇒ nullptr (1 case)
regex find: ".*?nullptr.*?"
Manually ~14 cases back to "NULL" in src, ~2 in lib
regex finds a few false positive where nullptr appears between two
strings in a function call
2020-09-12 09:34:38 -06:00
69962b4de5
add test for MSM kspace without periodic boundaries
2020-09-12 11:10:38 -04:00
3368eb79d8
fix issue with local variable shadowing a global variable
2020-09-12 11:10:12 -04:00
d7500c3e5a
MSM output format tweaks
2020-09-12 11:09:33 -04:00
16d2fef5ad
add check that shrinkwrap boundaries are not use when reading a data file while a MSM kspace style is defined
2020-09-12 11:06:20 -04:00
4a8d6016e4
Update docs
2020-09-11 22:49:44 -06:00
828ce84df5
add check for number of local atom indices overflowing neighbor lists for molecular systems
2020-09-11 22:09:09 -04:00
bc1b876a3d
make fix widom errors and test output consistent with the fix name capitalization
2020-09-11 19:29:17 -04:00
47b3039b28
update unit tests, too
2020-09-11 19:24:32 -04:00
9d0c3bc665
replace some numeric constants in Atom and AtomVec classes with enumerators
2020-09-11 19:07:55 -04:00
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
77d475d121
Add more tests
2020-09-11 15:48:23 -04:00
58833ce11e
Add API tests
2020-09-11 15:21:36 -04:00
cb253b2b1a
Add HTML report option for Python
2020-09-11 14:03:13 -04:00
1855f92694
Use include and omit
2020-09-11 12:44:41 -04:00
377163d940
Add target to generate Python coverage XML
2020-09-11 11:36:22 -04:00
101d39142e
Merge pull request #2357 from akohlmey/lib-get-mpi-comm
...
Add ability to retrieve the MPI communicator from LAMMPS instance via library/python interface
2020-09-11 11:20:12 -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
4452109b60
address spelling issue
2020-09-10 16:15:03 -04:00
0d5f68bc30
make "new in" and "changed in" leads boldface
2020-09-10 16:14:53 -04:00
3d37fd05f4
disable caching - for now - to avoid bad side effects from sphinx-tabs
2020-09-10 16:14:18 -04:00
e813e2d30a
add minimal unit test for lammps_get_mpi_comm() API
2020-09-09 22:12:47 -04:00
bd72ef7996
add API to library/python interface to extract the MPI communicator
2020-09-09 22:03:11 -04:00
b99e005ca1
Update example output files
2020-09-09 18:26:34 -04:00
d43cb34c70
Support debugging flag for Colvars via CMake
2020-09-09 18:19:29 -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
3bacf97468
Merge branch 'master' into math_eigen
2020-09-09 14:56:28 -07:00
2ab0878c9e
remreduced compile time by removing unnecessary instantiations from math_eigen.cpp
2020-09-09 14:43:28 -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
e238201be5
add a couple more versionadded directives
2020-09-09 13:21:19 -04:00
790b2693ba
Merge pull request #2353 from junghans/cmake_clean_up
...
cmake: consistent usage of find variable
2020-09-09 11:04:13 -04:00
a51bebc9e4
Merge pull request #2340 from rbberger/container_update
...
Singularity Container definitions update
2020-09-09 09:53:48 -04:00
f4c4c62349
adjust test to updated API
2020-09-09 09:27:34 -04:00
03d43bda3c
make "New in" and "Changed in" statements boldface to stand out more
2020-09-09 09:25:58 -04:00
2b854ec64f
reformulate
2020-09-09 09:25:34 -04:00
a1cf6c087c
no need to use a deprecated argument in a newly added API
2020-09-09 09:06:28 -04:00
2a42fe66ad
discuss change to get LAMMPS handle as return value instead of argument
2020-09-09 09:06:00 -04:00
56b1300fd3
reverted the default behavior of "jacobi3()". By default it now sorts the eigenvalues again.
2020-09-08 21:58:54 -07:00
dad749b62b
make vget()/vgot() inline functions again for optimal performance.
2020-09-08 20:52:51 -04:00
6ade5dd740
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
2020-09-08 17:05:08 -07:00
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
ca1b5ed936
fix minor issues
2020-09-08 16:43:10 -04:00
daf8a2313a
split developer guide into multiple files
2020-09-08 16:38:06 -04:00
