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Recent Releases of auto-fox

auto-fox - Auto-FOX 1.0.0b1

What's Changed

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

Full Changelog: https://github.com/nlesc-nano/auto-FOX/compare/0.10.2...1.0.0b1

- Python
Published by BvB93 almost 3 years ago

auto-fox - Auto-FOX 0.10.2

What's Changed

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

Full Changelog: https://github.com/nlesc-nano/auto-FOX/compare/0.10.1...0.10.2

- Python
Published by BvB93 over 3 years ago

auto-fox - 0.10.1

What's Changed

  • TST: Add tests for python 3.10 by @BvB93 in https://github.com/nlesc-nano/auto-FOX/pull/260

Full Changelog: https://github.com/nlesc-nano/auto-FOX/compare/0.10.0...0.10.1

- Python
Published by BvB93 about 4 years ago

auto-fox - Auto-FOX 0.10.0

What's Changed

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

Full Changelog: https://github.com/nlesc-nano/auto-FOX/compare/0.9.1...0.10.0

- Python
Published by BvB93 over 4 years ago

auto-fox - 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.

- Python
Published by BvB93 over 4 years ago

auto-fox - 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.

- Python
Published by BvB93 almost 5 years ago

auto-fox - 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.

- Python
Published by BvB93 almost 5 years ago

auto-fox - 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.

- Python
Published by BvB93 almost 5 years ago

auto-fox - 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.

- Python
Published by BvB93 about 5 years ago

auto-fox - 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.

- Python
Published by BvB93 about 5 years ago

auto-fox - Auto-FOX 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.

- Python
Published by BvB93 about 5 years ago

auto-fox - Auto-FOX 0.8

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

  • Import AbstractFileContainer from Nano-Utils.
  • Removed TypeMapping in favor of TypedDict.
  • Remove travis in favor of GitHub Actions.

0.8.5

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

0.8.4

  • Updated the ARMC documentation.

0.8.3

  • Updated the ARMC tests.
  • Renamed FOX.test_utils to FOX.testing_utils.
  • Added flake8 and pydocstyle to the tests.

0.8.2

  • Fixed and generalized the frocefield parameter guessing procedures (https://github.com/nlesc-nano/auto-FOX/issues/100 and https://github.com/nlesc-nano/auto-FOX/pull/112).
  • Log the optimum ARMC cycle in get_best() and overlay_descriptor() (https://github.com/nlesc-nano/auto-FOX/pull/111).
  • Fixed an issue where certain ADF atom-subset-permutations were ignored (https://github.com/nlesc-nano/auto-FOX/pull/110).
  • Aux error: Ensure that the summation over qm occurs row-wise (https://github.com/nlesc-nano/auto-FOX/pull/108).

0.8.1

  • WiP: Introduction of the ARMCPT class.

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.

- Python
Published by BvB93 over 5 years ago

auto-fox - Auto-FOX 0.7.4

- Python
Published by BvB93 over 5 years ago

auto-fox - Auto-FOX 0.7.4rc

- Python
Published by BvB93 over 5 years ago