Changelog

Change Log

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

All asimmodules: calc_id: str parameter replaced by calculator: Dict with keys calc_id (reference into calc_input.yaml) or calc_params (inline calculator specification). Mirrors the existing image/get_atoms pattern.
ase_md.ase_md: calc_spec parameter renamed to calculator
All YAML example files updated to use the new calculator: interface

dry_run option in sim_input.yaml: writes input files to the work directory without submitting the job. Unlike submit: false, the flag is stripped from the written sim_input.yaml so subsequent runs execute normally without manual cleanup.
calc_array: new calculators and template_calculator parameters accepting dicts instead of plain strings. Old calc_ids / template_calc_id string parameters are retained for backward compatibility and auto-converted.

job.py: type annotations modernized to use built-in dict/list/tuple and X | Y union syntax (Python 3.10+) throughout, removing most typing imports

change_dict_value, change_dict_values, expand_wildcards: parameter d renamed to dct
get_str_btn, get_nth_label: parameter s renamed to string
repeat_to_N renamed to repeat_to_n
All call sites in asimmodules/workflows/ updated to use the new parameter names

Pre-commit hooks: pylint (10.00/10 on src/asimtools/ excluding asimmodules) and pytest run on every commit
Tests for previously untested utilities: strip_symbols, get_axis_lims, improve_plot, write_csv_from_dict, new_db, check_if_slurm_job_is_running
Tests for previously untested job functionality: Job getters/updaters, DistributedJob init and inline submit, ChainedJob init and last output, load_job_from_directory, get_subjobs, load_job_tree
Sphinx docs now include all previously missing asimmodule packages: active_learning, ase_md, data, mace, phonopy, vasp
Workflows documentation page with parameter tables and YAML examples for all 7 workflow modules: sim_array, image_array, calc_array, distributed, chained, iterative, update_dependencies
autodoc_mock_imports in Sphinx config for optional heavy dependencies (maml, mace, matgl, chgnet, phonopy, seekpath)

Package moved to src/ layout; pyproject.toml and pytest config updated accordingly
Sphinx docs home page is now the project README
get_sim_input, get_calc_input, get_env_input now return internal references instead of deepcopies
Job.__init__ still deepcopies inputs at construction time to preserve isolation from callers

asim_run.py: precommands were executed twice (once discarding output, once capturing); now runs once
asim_execute.py: calc_input was assigned twice before the conditional read
job.py start() and complete(): two sequential update_output calls (2 reads + 2 writes) collapsed into one
asim_check.py: each job tree node read output.yaml twice per print call; now reads once per node

get_status(): running-job status update no longer triggers a redundant output.yaml re-read
DistributedJob.__init__: use_slurm/use_sh classification reduced from 3 O(n) passes to a single pass with early exit
load_job_from_directory: replaced exists() + read_yaml (2 filesystem calls) with try/except around read_yaml (1 call)

Can now specify an integer N to labels keyword add will use the N-th label for array workflows
Can now use placehodlers in sim_array where the array_values replace part of the string at the given key_sequence
Can now specify whether to write velocities in lammps
Calculator: Now added DFTD3 calculator using the ASE interface, works with any calculator. Two things of note: 1. You need to install DFTD3 from https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3/get_dft-d3. 2. Some calculators which return a 3x3 matrix for stress will break. One can modify ASE source for this as ASIMTools can’t go into the calculator code.
asim_check now also reports the job_ids
get_atoms now allows addition of FixAtoms constraint
output.yaml now includes hostname

VASP interface changed to align more with pymatgen
asimtools.utils.write_yaml now stops sorting keys to help with readability of written yamls
write_atoms now more universally used and recommended in asimmodules
VASP calculation now fails if the max number of iterations is reached for ibrion=1,2,3

ASIMMODULE: vasp/* (For running vasp without ASE calculator and using MP sets)
ASIMMODULE: active_learning/* (Only basic components of the workflow and one step example with MACE. expect major improvements in next release)
ASIMMODULE: benchmarking/distribution
ASIMMODULE: data/collect_images asimmodule
CALCULATOR: OMAT24 calculator
VASP examples
Jobs submitted as an array can now be grouped together in slurm jobs. See distributed examples

We now append rather than rewrite to stderr.txt and stdout.txt
Now forcing natural sorting of files in workflows file-based arrays which were confusing

Bugs in phonopy asimmodule that would give incorrectly sorted EOS energies
If an atoms object had unknown keys, writing the output extxyz file would throw an error, now only the ASE sanctioned properties are written