Releases · nlesc-nano/auto-FOX

0.8.12

Added a recipe for calculating the similarity between 2 MD trajectories.
Added improved support for custom atom types.
Made the ligand optional in the FOX.recipes.generate_psf() recipe.
Fixed an issue where non-absolute distances were used when calculating the pressure.
Fixed an issue where non-charge parameters were updated incorrectly.
Fixed an issue where parameter guessing could fail if no .prm file was provided.

0.8.11

Fixed an issue where the .hdf5 status would not be properly cleared (if necessary).
Grab the cell parameters from previous jobs if applicable.
More thoroughly check the qmflows.Result status before accessing it.
Automatically determine appropriate chunk sizes when calculating the RDF.
Added a new sub-module dedicated to the calculation of properties: FOX.properties.
Fixed an issue where parsing the unit would fail when parameter guessing.
Fixed an issue where writing nan to armc.xyz.hdf5 would fail.

0.8.10

Reorganized the dataframes in FOX.armc.ParamMapping.
Added the pes_validation keyword. Used for constructing a set of PES descriptors for the purpose of validation.
Dissallow the specification of duplicate .yaml keys.
Allow users to provide unique settings for each molecule in PES-averaged ARMC.
Added tests using CP2K, python 3.9, pre-releases and the minimum supported version of dependencies.
Removed the plotting and .csv-related entry points.
Added the param.validation.enforce_constraints keyword; used for checking whether or not initially supplied parameters satisfy all user-provided constraints.
Added the unit field to the param_metadata dataset.
Added the new pes.block.ref keyword; used for constructing PES descriptors from qmflows.Result objects rather than the FOX.MultiMolecule instances constructed therefrom.

0.8.9

Fixed an issue where frozen parameters were not respected when performing constrained parameter updates.
Fixed an issue where the ARMCPT parameters weren't properly swapped.
Added two new ARMC options: param.validation.allow_non_existent and param.validation.charge_tolerance.
Updated the type hints within Auto-FOX.
Allow the ARMC(PT) input to, once again, be dumped to a .yaml file via the armc2yaml command.
Dump more information into the ARMC logger.
Re-enabled the ARMC restart option.

0.8.8

Added recipes for calculating time-resolved angular/radial distribution functions.
Various documentation-related updates.
The order in wich atom-pair/-triplet based parameters are provided is now irrelevant.
For example Cd Se and Se Cd are now treated as equivalent, as well as O C H and H C O (but not O H C).
Fixed an issue where guessed parameters were not properly parsed.
Relaxed the PLAMS version requirement.
Log all local variables whenever an exception is encountered.
Move the ARMC test files to their own repo.
Export parameter metadata to the .hdf5 file.

0.8.7

Moved from PRMContainer.__dict__ to a PRMContainer.__slots__ based class structure.
Cleaned up the PRMContainer code; updated annotations, etc..
Removed assertionlib.AbstractDataClass as base class from PRMContainer.
Do not read or write comments to and from a .prm file.
Upped the minimum Sphinx version to 2.1.
Removed sphinx-autodoc-typehints.

0.8.6

0.8.5

Moved a number of functions to the Nano-Utils <https://github.com/nlesc-nano/Nano-Utils>_ Package.

0.8.4

0.8.3

0.8.2

Fixed and generalized the frocefield parameter guessing procedures
(#100 and #112).
Log the optimum ARMC cycle in get_best() and overlay_descriptor()
(#111).
Fixed an issue where certain ADF atom-subset-permutations were ignored
(#110).
Aux error: Ensure that the summation over qm occurs row-wise
(#108).

0.8.1

0.8.0

Move all ARMC related modules to the new FOX.armc module.
Switched from plams.Job to qmflows.Package runners.
Introduced the PhiUpdater class for handling and updating the phi parameter.
Introduced the ParamMapping class for handling and updating the forcefield parameters.
Introduced the PackageManager class for handling the and managing the qmflows.Package
instances, including the running of jobs.
Store the Auto-FOX __version__ in the .hdf5 file.
Changed the .yaml input to closer resemble the actual class structure.
Overhauled the .yaml input parsing.
Bumped the minimum Python version to 3.7.
Marked Auto-FOX as a typed package.
Added qmflows and noodles as new dependencies.
Added typing_extensions as a new dependency for Python < 3.8.

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