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ef3b90e838
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Merge pull request #70 from jtclemm/create-atoms-mesh
Adding quasirandom mesh option
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2022-05-11 08:12:18 -04:00 |
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c9d350edc2
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Adding quasirandom mesh option
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2022-05-10 18:35:36 -06:00 |
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bdbab77286
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add note about re-generating optimized meshes for STL files
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2022-05-10 15:23:54 -04:00 |
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1220bea011
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Update Colvars to version 2022-05-09
This update includes one new feature (neural-network based collective
variables), several small enhancements (including an automatic definition of
grid boundaries for angle-based CVs, and a normalization option for
eigenvector-based CVs), bugfixes and documentation improvements.
Usage information for specific features included in the Colvars library
(i.e. not just the library as a whole) is now also reported to the screen or
LAMMPS logfile (as is done already in other LAMMPS classes).
Notable to LAMMPS code development are the removals of duplicated code and of
ambiguously-named preprocessor defines in the Colvars headers. Since the
last PR, the existing regression tests have also been running automatically
via GitHub Actions.
The following pull requests in the Colvars repository are relevant to LAMMPS:
- 475 Remove fatal error condition
https://github.com/Colvars/colvars/pull/475 (@jhenin, @giacomofiorin)
- 474 Allow normalizing eigenvector vector components to deal with unit change
https://github.com/Colvars/colvars/pull/474 (@giacomofiorin, @jhenin)
- 470 Better error handling in the initialization of NeuralNetwork CV
https://github.com/Colvars/colvars/pull/470 (@HanatoK)
- 468 Add examples of histogram configuration, with and without explicit grid parameters
https://github.com/Colvars/colvars/pull/468 (@giacomofiorin)
- 464 Fix #463 using more fine-grained features
https://github.com/Colvars/colvars/pull/464 (@jhenin, @giacomofiorin)
- 447 [RFC] New option "scaledBiasingForce" for colvarbias
https://github.com/Colvars/colvars/pull/447 (@HanatoK, @jhenin)
- 444 [RFC] Implementation of dense neural network as CV
https://github.com/Colvars/colvars/pull/444 (@HanatoK, @giacomofiorin, @jhenin)
- 443 Fix explicit gradient dependency of sub-CVs
https://github.com/Colvars/colvars/pull/443 (@HanatoK, @jhenin)
- 442 Persistent bias count
https://github.com/Colvars/colvars/pull/442 (@jhenin, @giacomofiorin)
- 437 Return type of bias from scripting interface
https://github.com/Colvars/colvars/pull/437 (@giacomofiorin)
- 434 More flexible use of boundaries from colvars by grids
https://github.com/Colvars/colvars/pull/434 (@jhenin)
- 433 Prevent double-free in linearCombination
https://github.com/Colvars/colvars/pull/433 (@HanatoK)
- 428 More complete documentation for index file format (NDX)
https://github.com/Colvars/colvars/pull/428 (@giacomofiorin)
- 426 Integrate functional version of backup_file() into base proxy class
https://github.com/Colvars/colvars/pull/426 (@giacomofiorin)
- 424 Track CVC inheritance when documenting feature usage
https://github.com/Colvars/colvars/pull/424 (@giacomofiorin)
- 419 Generate citation report while running computations
https://github.com/Colvars/colvars/pull/419 (@giacomofiorin, @jhenin)
- 415 Rebin metadynamics bias from explicit hills when available
https://github.com/Colvars/colvars/pull/415 (@giacomofiorin)
- 312 Ignore a keyword if it has content to the left of it (regardless of braces)
https://github.com/Colvars/colvars/pull/312 (@giacomofiorin)
Authors: @giacomofiorin, @HanatoK, @jhenin
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2022-05-10 11:24:54 -04:00 |
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5760c59d83
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add a creator: tag to the YAML dump that allows to tell it apart
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2022-05-10 08:31:02 -04:00 |
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b6ee64dc12
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Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
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2022-05-09 21:58:48 -04:00 |
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eb44cbf848
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small updates
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2022-05-09 15:22:48 -04:00 |
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23e17363f9
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Merge remote-tracking branch 'github/doc-variable-extract-settings' into collected-small-changes
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2022-05-09 15:03:13 -04:00 |
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6344c667a0
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more doc info for variable extrat_setting() func
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2022-05-09 09:33:59 -06:00 |
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24ef021fe0
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fix typo
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2022-05-09 10:05:12 -04:00 |
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1660bae22a
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add examples import one image to manual
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2022-05-08 21:15:32 -04:00 |
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9ec35f0235
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update docs to match the latest code
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2022-05-08 19:14:06 -04:00 |
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e0bb27dbb2
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make radscale and radthresh class members
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2022-05-07 23:04:34 -04:00 |
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e9b1ca16a3
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correctly initialize radius and molecule id
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2022-05-07 21:24:08 -04:00 |
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60b9fd2db8
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minor tweaks simplify algorithm
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2022-05-07 17:08:22 -04:00 |
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bcfb6734f3
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use average vertex distance from center as particle radius
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2022-05-07 16:27:03 -04:00 |
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6722d3fb00
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add simple STL binary to ASCII converter (based on Wikipedia specs)
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2022-05-07 16:26:25 -04:00 |
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559dc68197
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implement revised algorithm with recursion
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2022-05-07 15:40:25 -04:00 |
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102b61ae1b
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Merge branch 'develop' into create-atoms-mesh
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2022-05-07 09:33:40 -04:00 |
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5d08b62622
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remove unused class member
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2022-05-07 03:48:54 -04:00 |
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4737b9efb7
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Merge pull request #3250 from akohlmey/collected-small-changes
Collected small changes and bugfixes
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2022-05-07 00:14:32 -04:00 |
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d21d9d95fa
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Merge pull request #3255 from lammps/timer-variable
Add a timer-style variable
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2022-05-06 17:46:22 -04:00 |
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00bb566893
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enforce that the number of neighbors cannot be negative (e.g. w/o neighbor list)
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2022-05-06 17:45:01 -04:00 |
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56e36a5df5
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Merge pull request #2988 from stanmoore1/coo_opt
Add optimized version of compute orientorder/atom from Tomas Oppelstr…
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2022-05-06 17:11:24 -04:00 |
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21d3de65e6
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fix typos
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2022-05-06 17:05:18 -04:00 |
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767f512dcf
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add "make ni" alias to "make no-installed"
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2022-05-06 17:05:03 -04:00 |
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907bc7eaa5
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switch to using wall time
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2022-05-06 16:58:28 -04:00 |
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051c243cfc
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small programming style upgrade, apply clang-format, silence compiler warnings
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2022-05-06 16:44:13 -04:00 |
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905034893c
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finished testing of new delete_atoms options
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2022-05-06 14:15:41 -06:00 |
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6432660bc9
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Merge branch 'develop' of https://github.com/lammps/lammps into coo_opt
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2022-05-06 13:24:14 -06:00 |
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6e78269612
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whitespace
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2022-05-06 15:11:15 -04:00 |
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81a8b0cf85
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Add Kokkos HIP preset
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2022-05-06 12:40:12 -06:00 |
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613ef04357
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Merge branch 'develop' into timer-variable
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2022-05-06 14:27:52 -04:00 |
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5986e11d43
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Merge branch 'develop' of github.com:lammps/lammps into kk_update_3.6.0
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2022-05-06 12:04:00 -06:00 |
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97012f2aaa
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correct classification of electrode package, as it requires BLAS/LAPACK
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2022-05-06 13:57:26 -04:00 |
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62a819d7b6
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Tweak launch bounds to improve GPU performance
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2022-05-06 13:37:05 -04:00 |
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3bb9c64f9e
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update .gitignore and move electrode package for dependency on KSPACE
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2022-05-06 13:35:51 -04:00 |
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78f2907cbb
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implement a "make no-installed" command
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2022-05-06 13:35:21 -04:00 |
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f3fcd16628
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adding of timer-style variables and associated doc pages
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2022-05-06 11:21:36 -06:00 |
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580e01535a
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Update Kokkos AMD Makefiles
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2022-05-06 13:04:58 -04:00 |
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8e423f07c5
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Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
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2022-05-06 12:37:34 -04:00 |
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2549b86d76
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update/correct docs for support of compiling LAMMPS with visual studio on windows
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2022-05-06 12:37:28 -04:00 |
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ae73a9b7f7
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Revert back to original code in npair_ssa_kokkos.h
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2022-05-06 10:05:57 -06:00 |
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73670dafc7
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Merge branch 'develop' into collected-small-changes
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2022-05-06 11:45:51 -04:00 |
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1f4ad99177
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one more virial sign flip in dispersion
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2022-05-06 09:33:55 -06:00 |
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aae44892c0
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consolidate all FFT related redundant defines and typedefs in a single header
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2022-05-06 11:27:17 -04:00 |
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6ec169fa9d
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Fix warnings in Kokkos package
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2022-05-06 08:23:45 -06:00 |
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a35a2441ce
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Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
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2022-05-06 04:48:19 -04:00 |
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abefff828d
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plug memory leak
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2022-05-06 04:39:38 -04:00 |
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71185b9f98
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fix error message
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2022-05-06 01:02:40 -04:00 |
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