SEAMM Util

Utility classes and functions that support other SEAMM tools

• Free software: BSD license

• Documentation: https://seamm-util.readthedocs.io.

History

2026.10.28.1 – Fingerprints of the settings of calculations

• New module seamm_util.fingerprint for telling whether two stored results, such as the energies of the species of a reaction, come from the same kind of calculation. calculation_record() hashes the input a code was given, after the code’s step has removed what does not change the result and what belongs to the species (geometry, charge, multiplicity); basis sets and ECPs written per element are hashed per element, so that species with different elements can be compared. Only the major and minor version of the program are hashed. geometry_fingerprint() identifies a geometry. The steps of the codes use these to store their fingerprints with their results.

2026.10.28 – Bugfix: pint 0.26 broke the chemistry unit conversions

• With pint 0.26 (released 2026-10-19) every conversion between per-molecule and per-mole quantities through SEAMM’s “chemistry” context – eV and kcal/mol or kJ/mol, eV/Å and kcal/mol/Å, molecules and mol – failed with a RecursionError. seamm_util now requires pint < 0.26 until the context is made to work with it.

2026.10.18 – Bugfix: atomic weights from mendeleev

• For the elements whose weight varies in nature, the atomic weights were the midpoints of CIAAW’s intervals rather than the conventional values: Li 6.9675 instead of 6.94 (+0.4%), Ar 39.8775 instead of 39.948 (-0.18%), and B, S, C, O, Mg, Cl and Tl by 0.03% or less. The atomic weights now come from mendeleev: the standard atomic weights at full precision (F 18.998403163 rather than 18.998), the conventional values for those elements, and for elements with no standard atomic weight the mass of the representative isotope (Ra-226 226.025408186). Masses and densities change slightly, by up to 0.01% for most elements; 1000 argon atoms in 47597 Å^3 now have a density of 1.3937 g/mL, not 1.3912.

• This is the one table of element data: molsystem uses it too. devtools/elemental_weights_from_mendeleev.py regenerates the atomic weights and a test checks them against mendeleev.

• LAMMPS takes its masses from this table when the forcefield has none, as for a machine-learned potential, so such MD with lithium ran with Li 0.4% too heavy.

2026.10.2 – Bugfix: the default root for a versioned environment

• seamm-manager now keeps an installation’s Python environment in <root>/venvs/<date and time>, with <root>/venv a link to the current one, and runs everything from the real path. A Python in such an environment now belongs to that installation, so run_flowchart and the apps run by hand from it use its root rather than ~/SEAMM.

2026.9.27.1 – Helpers for finding an installation’s files

• seamm_util.current_root() gives the root of the installation in use: the --root parsed for this run if there is one, otherwise the default root.

• seamm_util.installation_path(*parts) gives a path under that root, falling back to the default installation’s copy in ~/SEAMM when the installation has none. Plug-ins use it for reference data such as the VASP potentials, so a second installation works without copying them but can still have its own.

2026.9.27 – The default root follows the installation

• The default for --root was always ~/SEAMM, so a second installation such as ~/SEAMM_DEV read ~/SEAMM’s configuration and data unless every command was given --root. The default is now the SEAMM_ROOT environment variable if set, otherwise the installation the running Python belongs to (a seamm-manager environment <root>/venv whose root holds Jobs or .ini files), and otherwise ~/SEAMM as before. Existing single installations behave exactly as they did.

• root in the [SEAMM] section of ~/.seamm.d/seamm.ini still works but logs a deprecation warning, since that file is shared by every installation of a user; SEAMM_ROOT takes precedence over it.

• New functions seamm_util.default_root() and seamm_util.installation_root().

2026.9.18 – Bugfix: pip metadata lacked requests

• pip install seamm-util did not install requests, which the Zenodo client imports, so seamm-util failed to import outside a conda-forge environment (whose recipe already listed it). It is now an install requirement.

2026.7.26 – Support anonymous access to public Zenodo records

• Added Zenodo.get_latest_public_record(), which resolves a stable “concept” record id to whichever version of a public record is currently newest, with no authentication – for “always fetch the current data” without hardcoding a version number.

• Fixed Record.download_file(), .get_file(), and .files(), which only recognized the authenticated deposit/edit API’s file-entry shape (filename/links.download). The public records API uses key/links.self instead; these methods now accept either, so a Record from get_latest_public_record() works correctly.

2026.7.20 – Internal: exclude _version.py from black

• Excluded the generated _version.py from the black lint/format targets in the Makefile, matching the other SEAMM packages, so make lint no longer flags it. No effect on the installed package.

2026.7.15 – Added a database-timeout option

• Added the “database-timeout” option (default 20 seconds) that controls how long SEAMM waits for the job database when it is locked by another job before giving up. This helps when many jobs start at the same time, for example a batch of jobs on a cluster.

2025.12.9 – Added transformation for density using g/mol/Å^3

2025.9.10 – Added velocity units for speed of sound

2025.8.27 – Added more pressure units

• Added MPa, GPa, and TPa to the default pressure units.

• Added units for 1/pressure and 1/temperature to support the thermomechanical step.

2025.8.18 – Added ability to output graphs to several formats

• Added graph output to HTML, PNG, JPEG, webp, SVG, and PDF

2024.8.22 – Bugfix: charts with multiple exes, plus units for force constants

• Add units for force constants (kJ/mol/Å^2,…)

• Fixed an issue naming axes in plots with multiple axes

2024.8.1 – Added default units for viscosity and fixed a bug in handling dimensions

• Added more default units: dynamic viscosity (cP, etc) and kinematic viscosity (cSt, etc)

• Fixed a bug handling unit dimensions since the order changed in Pint. Now they are put in a standard alphabetical order.

2024.7.25 – Added configuration file handler

• Added a configuration file handler that preserves comments in the file so that documentation is not stripped.

2024.7.15 – Added temperature-energy conversions

• Added conversions from temeprature units, like K, to energy, like kJ/mol and vice versa.

• Used more of the Pint contexts, which should allow wavenumbers to frequency, etc.

2024.6.27 – Added support for URI’s

• Now recognize URI’s in the form local:path/to/file

• An optional URI handler can be passed in to resolve such URI’s.

2024.6.5 – Bugfix: Handling of duplicates in lists

• Roundoff in floating point numbers caused some duplicates to be missed. The code now checks for duplicates in a more robust way.

2024.4.30 – Added utility for handling list definitions

• Add list_definition.py with parse_list()

• Updated makefile for doctests.

2024.4.26 – Removed debug printing

• Some debug printing was accidentally left in the code.

2024.4.22 – Moving user preferences to ~/.seamm.d

• To better support Docker, moving ~/.seammrc to ~/.seamm.d/seamrc

• Moved seamm.ini from ~/SEAMM to ~/seamm.d since it only contains personal preferences.

2023.11.12 – Internal update

• Versioneer needed to be updated to account for changes in configparser.

2023.11.11 – Updated for changes in Zenodo

• Zenodo updated and made small changes to their API, which required changes in SEAMM.

• Consolidated all private information about the user and their keys for Zenodo in ~/.seammrc

2023.6.4 – Added more unit conversions to support thermochemistry

• added E_h/K –> kJ/mol/K

2023.4.6 – Added more unit conversions to support Buckingham potentials

• added e.g. eV*Å^6 to kcal/mol*Å^6 to support Buckingham pontetials

2023.2.28 – Added a compact JSON encoder

• To make the schema-type JSON more human-readable.

2022.11.3 – More conversions involving substance (mol) to number

• Added energy/mol/Å^2 –> energy/Å^2 for force constants

• Added energy/mol/Å^3 –> energy/Å^3 for stress/pressure/elastic constants

0.1.0 (2017-12-07)

• First release on PyPI.