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Changelog

Notable changes to this project will be documented in this file. The format is based on Keep a Changelog.

The versioning for this project aligns with that of AMS. The format for this is the original year of the main release as a prefix, and an incremental postfix for each sub-release, starting at 101. In general, subsequent sub-releases after the main release contain only bug fixes. For example, 2024.101 is the major release of 2024, and 2024.102 is the first bugfix release.

This changelog is effective from the 2025 releases.

[Unreleased]

  • New BANDFragment and updated ADFFragment recepis for automatic EDA calculations.

Added

  • AMSAnalysisJobs now have Pisa support, accept multiple AMSJobs as input, and no longer overwrite user supplied input settings.
  • context_config and get_context methods to allow context-based override of global config settings
  • input_to_settings method to convert AMS text input to a settings object
  • get_system_blocks_as_molecules_from_input method to extract molecules from AMS text input
  • JobAnalysis.add_rkf_field method to simplify adding values from an rkf to the analysis
  • JobAnalysis.get_settings_field_key and JobAnalysis.get_rkf_field_key methods to simplify getting the correct keys for analysis fields
  • jobs_in_directory context manager which allows jobs to be run in a subdirectory of the job manager working directory

Changed

  • JobAnalysis returns an updated copy on modification instead of performing the operation in-place
  • packmol can accept a single None value for n_molecules if two of n_atoms, density and box_bounds are specified. The missing value is then auto-calculated.

Fixed

  • Method to guess density in packmol_around changed to resolve large underestimations in molecular volumes

2025.103

Fixed

  • SingleJob.load, JobManager.load_job and load can load jobs from a .dill file from PLAMS<2025

2025.102

2025.101

Added

  • Methods get_system, get_input_system and get_main_system to AMSResults, which return an AMS ChemicalSystem instead of a PLAMS Molecule
  • AMSJob can accept an AMS ChemicalSystem instead of a PLAMS Molecule as an input system
  • Specific ConfigSettings and related settings classes with explicitly defined fields
  • Support for work functions: AMSResults.get_work_function_results and plot_work_function
  • Support for plotting phonons with plot_phonons_band_structure, plot_phonons_dos and plot_phonons_thermodynamic_properties
  • New packmol_around function for packing in non-orthorhombic boxes.
  • New plot_grid_molecules function for plotting with rdkit multiple molecules.
  • Molecule.delete_atoms method to delete multiple atoms with partial success
  • Examples on MoleculeFormats and MoleculeTools
  • Examples on Logging
  • Script generate_example.sh to generate documentation pages from notebook examples
  • GitHub workflows for CI and publishing to PyPI
  • Build using pyproject.toml, addition of extras groups to install optional dependencies
  • Logging of job summaries to CSV logfile
  • Logging of AMS job error messages to stdout and logfile on job failure
  • Method get_errormsg enforced on the Job base class, with a default implementation
  • Added an interface to the Serenity program through methods such as SerenityJob, SerenityResults and SerenitySettings
  • Methods Settings.nested_keys, Settings.block_keys for accessing nested keys and Settings.contains_nested and Settings.pop_nested for checking if nested keys exist in a settings object and popping them
  • Method Settings.compare added to compare and contrast items in two settings objects
  • Method readcoskf added to Molecule class, enabling the reading of COSKF file
  • JobAnalysis tool for extracting job statuses, settings and results
  • Added support for calculating the hydrogen bond center using the Densf calculation in the ADFCOSMORSCompoundJob class
  • Introduced the update_hbc_to_coskf method in ADFCOSMORSCompoundJob class to calculate the hydrogen bond center using an existing COSKF file
  • Added AMSViscosityFromBinLogJob for running the AMS trajectory analysis tool to extract viscosity.

Changed

  • Functions for optional packages (e.g. RDKit, ASE) are available even when these packages are not installed, but will raise an MissingOptionalPackageError when called
  • AMSResults.get_main_ase_atoms also includes atomic charges
  • Global config is initialized with a ConfigSettings instead of loading from the standard plams_defaults file
  • init and finish functions are now optional
  • Job.status is a JobStatus string enum
  • Supercell and RDKit properties are no longer serialized to AMS input
  • Restructuring of examples and conversion of various examples to notebooks
  • Support for networkx>=3 and ase>=3.23
  • Use standard library logger for log function
  • Make Job class inherit from ABC and mark abstract methods
  • Exceptions raised in prerun and postrun will always be caught and populate error message
  • Settings.get_nested takes a default argument which is returned if the nested key is not present in the settings instance
  • JobManager.workdir converted to a readonly property, with the underlying workdir lazily created if it does not exist
  • JobRunner.parallel, JobRunner.maxjobs and JobRunner.maxthreads are properties which can take values of 0 or >1 and JobRunner.semaphore has been moved to a protected attribute JobRunner._job_limit

Fixed

  • Molecule.properties.charge is a numeric instead of string type when loading molecule from a file
  • Molecule.delete_all_bonds removes the reference molecule from the removed bond instances
  • SingleJob.load returns the correctly loaded job
  • AMSJob.check handles a NoneType status, returning False
  • MultiJob.run locking resolved when errors raised within prerun and postrun methods
  • Molecule.add_hatoms to use bonding information if available when adding new hydrogen atoms
  • Changes made to JobRunner.maxjobs after initialization are correctly applied

Deprecated

  • plams launch script is deprecated in favor of simply running with amspython

Removed

  • Legacy BANDJob, DFTBJob, UFFJob, MOPACJob, ReaxFFJob, CSHessianADFJob and ADFJob have been removed
  • Exception classes AMSPipeDecodeError, AMSPipeError, AMSPipeInvalidArgumentError, AMSPipeLogicError, AMSPipeRuntimeError, AMSPipeUnknownArgumentError, AMSPipeUnknownMethodError, AMSPipeUnknownVersionError, were moved from scm.plams to scm.amspipe.