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cba479bf6e
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Update Colvars library to version 2025-04-18
The following is a list of pull requests relevant to LAMMPS in the Colvars repository since 2024-08-06:
- 752 New tool poisson_integrator_conv
https://github.com/Colvars/colvars/pull/752 (@jhenin)
- 733 Custom grids for all biases
https://github.com/Colvars/colvars/pull/733 (@giacomofiorin, @jhenin)
- 776 Avoid error in acos and asin with fast-math
https://github.com/Colvars/colvars/pull/776 (@jhenin)
- 773 fix: fix the clang build test failure of OPES
https://github.com/Colvars/colvars/pull/773 (@HanatoK)
- 768 fix: clamp the input values of asin and acos in case of fast math on aarch64
https://github.com/Colvars/colvars/pull/768 (@HanatoK)
- 761 Add debug code for the Jacobi failure
https://github.com/Colvars/colvars/pull/761 (@HanatoK)
- 759 min_image fix; Saves long runs from crashes;
https://github.com/Colvars/colvars/pull/759 (@PolyachenkoYA)
- 757 Fix MSVC OpenMP issue
https://github.com/Colvars/colvars/pull/757 (@HanatoK)
- 755 Fix indentation of 'Init CVC' message in standard output
https://github.com/Colvars/colvars/pull/755 (@jhenin)
- 750 Optimize and simplify the calculation of dihedral gradients
https://github.com/Colvars/colvars/pull/750 (@HanatoK)
- 749 Add references to new Colvars paper
https://github.com/Colvars/colvars/pull/749 (@jhenin, @giacomofiorin)
- 740 Report the specific C++ standard at init time, stop warning about C++97/03
https://github.com/Colvars/colvars/pull/740 (@giacomofiorin)
- 731 Improve detection of hard/mathematical boundaries
https://github.com/Colvars/colvars/pull/731 (@giacomofiorin)
- 729 Optimize the fit gradients
https://github.com/Colvars/colvars/pull/729 (@HanatoK, @jhenin)
- 728 Fix undefined behavior when getting the current working directory from std::filesystem
https://github.com/Colvars/colvars/pull/728 (@giacomofiorin)
- 727 Add patchversion scripting command
https://github.com/Colvars/colvars/pull/727 (@giacomofiorin)
- 724 Fix gradients and metric functions of distanceDir
https://github.com/Colvars/colvars/pull/724 (@giacomofiorin)
- 715 Add missing rotation in orientation component
https://github.com/Colvars/colvars/pull/715 (@giacomofiorin)
- 713 fix: try to solve #87 for non-scala components
https://github.com/Colvars/colvars/pull/713 (@HanatoK)
- 709 Implementation of OPES in Colvars
https://github.com/Colvars/colvars/pull/709 (@HanatoK, @giacomofiorin, @jhenin)
- 706 BUGFIX for Segmentation fault in colvarbias_meta::calc_energy() with useGrids off
https://github.com/Colvars/colvars/pull/706 (@alphataubio)
- 570 enable use of CVs defined by PyTorch neural network models
https://github.com/Colvars/colvars/pull/570 (@zwpku, @giacomofiorin, @HanatoK, @jhenin)
Authors: @alphataubio, @EzryStIago, @giacomofiorin, @HanatoK, @jhenin, @PolyachenkoYA, @zwpku
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2025-04-30 15:32:30 -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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