Auto-FOX 1.0.0b1

What's Changed

• DEP: Bump qmflows and deal with deprecations by @BvB93 in #280
• ENH: Issue a warning in the psf recipe if the qd or ligands don't have any bonds by @BvB93 in #281
• BUG: Fix an issue with parsing multiple ligands in generate_psf2 by @BvB93 in #282
• MAINT: General maintenance in preperation for Auto-FOX 1.0.0 by @BvB93 in #283

Full Changelog: 0.10.2...1.0.0b1

Auto-FOX 0.10.2

What's Changed

• REL: Update master branch after release (0.10.1) by @BvB93 in #261
• BUG: Fix atom-pairs not being sorted if certain parameters are guessed by @BvB93 in #262
• ENH: Add a workflow for computing Debye scattering by @BvB93 in #263
• BUG: Fix PES-averaged ARMC failing to create multiple ParamMapping columns by @BvB93 in #264
• BUG: Fix PA-ARMC not correctly reshaping the acceptance array by @BvB93 in #265
• BUG: Fix the param columns being incorrectly written to the .hdf5 file by @BvB93 in #266
• BUG: Transpose the axes when returning in get_multi_lig_center by @BvB93 in #267
• ENH: Store the git commit hash of auto-FOX in the ARMC .hdf5 file by @BvB93 in #268
• ENH: Print the offending atoms whenever the ARMC constraint-resolver fails by @BvB93 in #269
• BUG: Fix the ARMC constraints solver falsely rejecting moves due to 0 division by @BvB93 in #270
• ENH: Export warnings to the logger when running ARMC by @BvB93 in #271
• BUG: Fix DataFrame.loc indexing failing when passed a 2-tuple by @BvB93 in #272
• BUG: Fix only settings not being properly updated for PES-averaged ARMC by @BvB93 in #273
• TST: Enable windows tests by @BvB93 in #274
• BUG: Fix improper dihedral-indices being incorrectly sorted by @BvB93 in #275
• ENH: Allow the .xyz parser to handle empty lines by @BvB93 in #277
• ENH: Add special casing for zero-division in the ARMC error func by @BvB93 in #278
• BUG: Do not directly rely on PLAMS for obtaining the Boost ArgumentError type by @BvB93 in #279

Full Changelog: 0.10.1...0.10.2

0.10.1

What's Changed

• TST: Add tests for python 3.10 by @BvB93 in #260

Full Changelog: 0.10.0...0.10.1

Auto-FOX 0.10.0

What's Changed

• ENH: Add a new MultiMolecule method for constructing supercells by @BvB93 in #242
• TST: Refactor the get_non_bonded tests by @BvB93 in #243
• BUG: Fixed an issue wherein init_power_spectrum could raise when the atom subset is specified by @BvB93 in #245
• BLD: Bump the PLAMS minimum version to >= 1.5.1 by @BvB93 in #247
• BUG: Fixed an issue wherein net charges weren't properly conserved in PES-averaged ARMC by @BvB93 in #235
• ENH: Allow users to pass custom error functions by @BvB93 in #249
• ENH: Add a max-based error function by @BvB93 in #250
• BLD: Make rdkit an optional dependency (again) by @BvB93 in #251
• ENH: Add two new error functions by @BvB93 in #252
• MAINT,ENH: Rework the auto-FOX properties system by @BvB93 in #253
• BUG: Fixed an issue wherein auto-FOX would not check the status of jobs by @BvB93 in #254
• BUG: Fixed an issue wherein dataframes were summed along the wrong axis by @BvB93 in #255
• ENH: Add error functions based on non-mse errors by @BvB93 in #256
• ENH: Add the new atom_pairs keyword to init_rdf and init_adf by @BvB93 in #257
• ENH: Round the net charge to the nearest integer by @BvB93 in #258
• REL: Release Auto-FOX 0.10.0 by @BvB93 in #259

Full Changelog: 0.9.1...0.10.0

Auto-FOX 0.9.1

• Added the new segment_dict parameter to the PSFContainer.generate_x() functions.
• Added the new PSFContainer.sort_values method.
• Store metadata and net charges for each individual system in PES-averaged ARMC and ARMCPT.
• Fixed an issue wherein frozen atomic charges were ignored when not explicitly specified.
• Fixed in issue wherein PSFContainer.sort_values did not not update the residue ID.
• Fixed an issue wherein guessed parameters could overwrite ones that were explicitly specified.
• Fixed an issue wherein frozen parameters weren't properly sorted.
• Fixed an issue wherein the mean pair-density was computed using lattice vectors in non-periodic calculations.

Auto-FOX 0.9.0

• Fixed an issue wherein PSFContainer.to_atom_alias_dict would assign incorrect indices to atom aliases.
• Fixed an issue wherein treating an entire ARMC parameter block as frozen could raise.
• Added the FOX.MultiMolecule.lattice property for storing the lattice vectors of periodic systems.
• Added FOX.io.lattice_from_cell, a function for reading lattice vectors from CP2K .cell files.
• Added support for periodic ADF and RDF calculations.
• Added the new job.lattice keyword to the ARMC workflow for specifying lattice vectors of the reference system.
• Lattice vectors are now preserved when interconverting between PLAMS, ASE and Auto-FOX.
• Read the pressure from the CP2K .out file when calculating the bulk modulus, rather than calculating it from scratch.

Auto-FOX 0.9

Auto-FOX 0.9.1

• Added the new segment_dict parameter to the PSFContainer.generate_x() functions.
• Added the new PSFContainer.sort_values method.
• Store metadata and net charges for each individual system in PES-averaged ARMC and ARMCPT.
• Fixed an issue wherein frozen atomic charges were ignored when not explicitly specified.
• Fixed in issue wherein PSFContainer.sort_values did not not update the residue ID.
• Fixed an issue wherein guessed parameters could overwrite ones that were explicitly specified.
• Fixed an issue wherein frozen parameters weren't properly sorted.
• Fixed an issue wherein the mean pair-density was computed using lattice vectors in non-periodic calculations.

Auto-FOX 0.9.0

• Fixed an issue wherein PSFContainer.to_atom_alias_dict would assign incorrect indices to atom aliases.
• Fixed an issue wherein treating an entire ARMC parameter block as frozen could raise.
• Added the FOX.MultiMolecule.lattice property for storing the lattice vectors of periodic systems.
• Added FOX.io.lattice_from_cell, a function for reading lattice vectors from CP2K .cell files.
• Added support for periodic ADF and RDF calculations.
• Added the new job.lattice keyword to the ARMC workflow for specifying lattice vectors of the reference system.
• Lattice vectors are now preserved when interconverting between PLAMS, ASE and Auto-FOX.
• Read the pressure from the CP2K .out file when calculating the bulk modulus, rather than calculating it from scratch.

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.

Auto-FOX 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.

Auto-FOX 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.