2025.105

Full Changelog: 2025.104...2025.105

2025.104

What's Changed

• Fix for loading legacy multi-jobs by @dormrod in #288
• Fix for finalize when job fails during execution and GridRunner regression by @dormrod in #298

Full Changelog: 2025.103...2025.104

2024.107

What's Changed

• Fix NoneType exception in amsjob check SCMSUITE-10161 SO-- by @dormrod in #188

Full Changelog: 2024.106...2024.107

2025.103

What's Changed

• Fix job loading for dill files from PLAMS<2025 by @dormrod in #271
• SO--. Fix bug in PLAMS wrapper for pyCRS example. by @WLChen1118 in #278

Full Changelog: 2025.102...2025.103

PLAMS 2025.102

What's Changed

• Update version to 2025.102 by @robertrueger in #263
• Add plot_phonons* to docs by @dormrod in #266

Full Changelog: 2025.101...2025.102

PLAMS 2025.101

This release corresponds to AMS release 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
• 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.

PLAMS 2024.106

This release corresponds to AMS 2024.106.

Full Changelog: 2024.105...2024.106

PLAMS 2024.105

This release corresponds to AMS 2024.105.

Fixed

• Race-condition in AMSJob.run(watch=True) where final logs may not have been forwarded
• AMSCalculator to work with ase==3.23
• Molecule to work with networkx>=3

PLAMS 2024.104

This release corresponds to AMS 2024.104.

Full Changelog: 2024.103...2024.104

PLAMS 2024.103

Overview

This is the first PLAMS release which uses a new versioning scheme to align with AMS versioning and releases.

Going forwards, there will be a PLAMS release for each main AMS release. This release therefore corresponds to AMS 2024.103.

What's Changed

See release notes