diff -pruN 3.24.0-1/.gitlab/issue_templates/Default.md 3.26.0-1/.gitlab/issue_templates/Default.md --- 3.24.0-1/.gitlab/issue_templates/Default.md 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/.gitlab/issue_templates/Default.md 2025-08-12 11:26:23.000000000 +0000 @@ -1,6 +1,6 @@ # Checklist -- [ ] The issue remains in the [development version of ASE](https://wiki.fysik.dtu.dk/ase/install.html#installation-from-source). +- [ ] The issue remains in the [development version of ASE](https://ase-lib.org/install.html#installation-from-source). - [ ] An minimal example is provided to reproduce the issue. # Summary diff -pruN 3.24.0-1/.gitlab/merge_request_templates/Default.md 3.26.0-1/.gitlab/merge_request_templates/Default.md --- 3.24.0-1/.gitlab/merge_request_templates/Default.md 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/.gitlab/merge_request_templates/Default.md 2025-08-12 11:26:23.000000000 +0000 @@ -1,8 +1,9 @@ Here: Your concise description of the content of this merge request. -# Checklist +# Checklist: `x` (done) or `~` (irrelevant) -- [ ] I am familiar with [ASE's contribution guidelines](https://wiki.fysik.dtu.dk/ase/development/contribute.html). -- [ ] [**Doc strings**](https://wiki.fysik.dtu.dk/ase/development/python_codingstandard.html#writing-documentation-in-the-code) in code changed in this MR are up to date. -- [ ] [**Unit tests** have been added for new or changed code.](https://wiki.fysik.dtu.dk/ase/development/tests.html) +- [ ] [I am familiar with **ASE's contribution guidelines.**](https://ase-lib.org/development/contribute.html) +- [ ] [**Doc strings** in code changed in this MR are up to date.](https://ase-lib.org/development/python_codingstandard.html#writing-documentation-in-the-code) +- [ ] [**Unit tests** have been added for new or changed code.](https://ase-lib.org/development/tests.html) +- [ ] [**Changes** have been added in `changelog.d` using `scriv`.](https://ase-lib.org/development/writing_changelog.html) - [ ] [**Issue is resolved** via "closes #XXXX" if applicable.](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically) diff -pruN 3.24.0-1/.gitlab-ci.yml 3.26.0-1/.gitlab-ci.yml --- 3.24.0-1/.gitlab-ci.yml 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/.gitlab-ci.yml 2025-08-12 11:26:23.000000000 +0000 @@ -2,57 +2,55 @@ variables: OMP_NUM_THREADS: "1" + PIP_CACHE_DIR: "$CI_PROJECT_DIR/pip-cache" + PYTEST_ADDOPTS: "--color=yes --durations=20 -r s" stages: - test - paperwork - deploy -# Test a non-standard port (default is 3306) to prevent bugs like -# https://gitlab.com/ase/ase/-/merge_requests/2789 from reoccuring -# UPDATE: MYSQL_TCP_PORT does not work at all with gitlab-runner. -# No matter what the variable is set to, it errors out. -# Thus (temporarily?) disabled as of April 2023. -.database-configuration: - variables: - POSTGRES_DB: testase - POSTGRES_USER: ase - POSTGRES_PASSWORD: "ase" - MYSQL_DATABASE: testase_mysql - MYSQL_ROOT_PASSWORD: ase - # MYSQL_TCP_PORT: 3306 - - services: - - postgres:latest - - mysql:latest - - mariadb:latest +# This will ensure that only pipelines in master get to update the cache, +# see https://docs.gitlab.com/ci/caching/ +# conditional-policy: +# rules: +# - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH +# variables: +# POLICY: pull-push +# - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH +# variables: +# POLICY: pull # Check oldest supported Python with oldest supported libraries. # Does not install any optional libraries except matplotlib. -# -# With older python, pytest-xdist jumbles the tests differently -# on different codes, then complains. So we use -j 0. oldlibs: image: registry.gitlab.com/ase/ase:ase-oldlibs - extends: .database-configuration - script: - - pip install --no-deps . + before_script: + - pwd + - whoami - > - ase test -j0 --pytest --color=yes - -W "ignore:can't resolve package" - -W ignore::PendingDeprecationWarning + pip install + numpy==1.19.5 scipy==1.6.0 matplotlib==3.3.4 + pytest==7.0.0 attrs==20.3.0 pluggy==1.0.0 py==1.11.0 six==1.15.0 + pytest-xdist==2.1.0 execnet==1.8.1 pytest-forked==1.4.0 + - pip install --no-deps . + script: + - ase test + cache: + key: oldlibs + paths: + - $PIP_CACHE_DIR # For testing newest versions of libraries against standard images # on dockerhub. pipinstall: image: python:3.11 - extends: .database-configuration - script: + before_script: - python --version - - pip install psycopg2-binary pymysql cryptography - pip install .[test] - - ase test --pytest --color=yes + script: + - ase test when: manual # This is the main test job using new versions of libraries. @@ -63,39 +61,18 @@ pipinstall: # It would be better to install it for real, and for things to just work. main: image: registry.gitlab.com/ase/ase:ase-main - extends: .database-configuration - # Inheriting variables from the database-configuration job - # seems to be broken all of a sudden (gitlab-runner 13.0.1 and 13.3.1) - # We need to redefine them here then, otherwise gitlab-runner will fail - # those tests when run locally. Meanwhile everything works on gitlab.com. - # Strange! - variables: - POSTGRES_DB: testase - POSTGRES_USER: ase - POSTGRES_PASSWORD: "ase" - MYSQL_DATABASE: testase_mysql - MYSQL_ROOT_PASSWORD: ase - # MYSQL_TCP_PORT: 3306 - - services: - - postgres:latest - - mysql:latest - - mariadb:latest - - # We ignore a DeprecationWarning about --rsyncdir from pytest-xdist. - # This seems to be internal between pytest libs. - script: + before_script: - python --version - pip install --no-deps --editable . - ase info --calculators - cd $CI_PROJECT_DIR + script: - > ase test --calculators asap,ff,lj,morse,tip3p,tip4p - --coverage --pytest --color=yes --durations 20 -v -r s + --coverage --pytest --junit-xml=report.xml - -W "ignore:The --rsyncdir command line argument" - -W "ignore:NumPy will stop allowing conversion of out-of-bound Python integers" + after_script: - coverage xml --data-file ase/test/.coverage - mv ase/test/coverage-html coverage-main - mv ase/test/.coverage coverage-main/coverage.dat @@ -108,21 +85,26 @@ main: path: coverage.xml junit: ase/test/report.xml expire_in: 1 week + cache: + key: main + paths: + - $PIP_CACHE_DIR # Calculator integration tests which always run. # Encompasses those tests marked as @pytest.mark.calculator_lite. # Please make sure these tests are cheap. calculators-lite: image: registry.gitlab.com/ase/ase:ase-full-monty - script: + before_script: - pip install --no-deps --editable . - export ASE_CONFIG_PATH=/home/ase/aseconfig.ini - sed 's/binary = /command = /' -i /home/ase/aseconfig.ini + script: - > ase test calculator --calculators=auto --coverage - --pytest -m calculator_lite --color=yes --durations=20 -v - --junit-xml=report.xml -r s - -W "ignore:The --rsyncdir command line argument" + --pytest -m calculator_lite + --junit-xml=report.xml + after_script: - coverage xml --data-file ase/test/.coverage - mv ase/test/coverage-html coverage-calculators-lite - mv ase/test/.coverage coverage-calculators-lite/coverage.dat @@ -135,6 +117,10 @@ calculators-lite: path: coverage.xml junit: ase/test/report.xml expire_in: 1 week + cache: + key: calculators + paths: + - $PIP_CACHE_DIR # Plan: Test as many calculators as possible as well as possible. # Obviously this is kind of expensive so the job is manually activated. @@ -144,15 +130,16 @@ calculators-lite: # It would be great if someone could enable more calculators with this. calculators: image: registry.gitlab.com/ase/ase:ase-full-monty - script: + before_script: - pip install --no-deps --editable . - export ASE_CONFIG_PATH=/home/ase/aseconfig.ini - sed 's/binary = /command = /' -i /home/ase/aseconfig.ini - ase info --calculators + script: - > ase test calculator --calculators abinit,asap,cp2k,dftb,espresso,gpaw,kim,lammpslib,lammpsrun,mopac,nwchem,octopus,siesta - --coverage --pytest --color=yes --durations 20 --junit-xml=report.xml - -W "ignore:The --rsyncdir command line argument" + --coverage --pytest --junit-xml=report.xml + after_script: - coverage xml --data-file ase/test/.coverage - mv ase/test/coverage-html coverage-calculators - mv ase/test/.coverage coverage-calculators/coverage.dat @@ -170,58 +157,74 @@ calculators: path: coverage.xml junit: ase/test/report.xml expire_in: 1 week + cache: + key: calculators + policy: pull + paths: + - $PIP_CACHE_DIR bleeding-edge: - image: python:3.12.4-alpine + image: python:3-alpine variables: PIP_CACHE_DIR: "$CI_PROJECT_DIR/pip-cache" before_script: + - pip install --upgrade numpy scipy matplotlib - pip install --editable .[test] - pip freeze script: - - > - ase test -j0 --pytest --color=yes -m 'not slow' - --ignore gui/ --ignore test_imports.py - --durations 20 + - ase test --pytest --ignore gui/ --ignore test_imports.py cache: paths: - $PIP_CACHE_DIR - key: $CI_PROJECT_ID + key: bleeding-edge doc: image: registry.gitlab.com/ase/ase:ase-main - script: + variables: + PIP_CACHE_DIR: "$CI_PROJECT_DIR/pip-cache-doc" + before_script: + - pip install scriv sphinx_book_theme - pip install --no-deps .[docs] - ase info - which sphinx-build - - cd $CI_PROJECT_DIR/doc + script: + - scriv collect --keep || echo Not compiling changelog then # Avoid error - python -m ase.utils.sphinx run # test scripts - - sphinx-build -W . build + - sphinx-build -W doc doc/build + - mv doc/build web-html + cache: + paths: + - $PIP_CACHE_DIR + key: doc artifacts: paths: - - $CI_PROJECT_DIR/doc/build/ + - web-html expire_in: 1 week distribution-package: image: registry.gitlab.com/ase/ase:ase-main - extends: .database-configuration before_script: - mkdir dist - - pip install setuptools + - pip install setuptools build script: - - python setup.py sdist | tee dist/setup_sdist.log - - python setup.py bdist_wheel | tee dist/setup_bdist_wheel.log + - python -m build + - ls dist/* - pip install dist/ase-*.tar.gz - - ase test --pytest --color=yes + - ase test - pip uninstall --yes ase - pip install dist/ase-*-py3-none-any.whl - - ase test --pytest --color=yes + - ase test artifacts: paths: - dist expire_in: 1 week - when: manual + rules: + - if: $CI_COMMIT_TAG + - if: $CI_PIPELINE_SOURCE == "schedule" + - if: $CI_PIPELINE_SOURCE == "push" + when: manual + # Publish code coverage data on web. # * The deploy stage is specially recognized by gitlab @@ -232,8 +235,13 @@ pages: stage: deploy dependencies: - coverage-combine + - doc script: - - mv coverage-html public + - mkdir public + - mv coverage-html public/ + - pwd + - ls + - mv web-html/* public/ artifacts: paths: - public @@ -242,13 +250,22 @@ pages: - master lint: - image: registry.gitlab.com/ase/ase:ase-paperwork + image: python:3.12.4-alpine + before_script: + - pip install .[lint] + - pip freeze script: - - cd $CI_PROJECT_DIR - mypy --version - mypy --color-output -p ase - python -We:invalid -m compileall -f -q ase/ - ruff check + - ruff format --check + variables: + PIP_CACHE_DIR: "$CI_PROJECT_DIR/pip-cache" + cache: + paths: + - $PIP_CACHE_DIR + key: lint coverage-combine: image: registry.gitlab.com/ase/ase:ase-paperwork @@ -281,13 +298,13 @@ coverage-combine: - refreshenv - python --version - python -m pip install --upgrade pip - - python -m pip install pytest pytest-mock + - python -m pip install pytest - python -m pip install . script: - > ase test --calculators eam,ff,lj,morse,tip3p,tip4p - --pytest --color=yes --durations 20 + --pytest -W "ignore:The --rsyncdir command line argument" -W "ignore:NumPy will stop allowing conversion of out-of-bound Python integers" rules: diff -pruN 3.24.0-1/CHANGELOG.rst 3.26.0-1/CHANGELOG.rst --- 3.24.0-1/CHANGELOG.rst 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/CHANGELOG.rst 2025-08-12 11:26:23.000000000 +0000 @@ -3,4 +3,4 @@ Changelog See what's new in ASE here: - https://wiki.fysik.dtu.dk/ase/releasenotes.html + https://ase-lib.org/releasenotes.html diff -pruN 3.24.0-1/CONTRIBUTING.rst 3.26.0-1/CONTRIBUTING.rst --- 3.24.0-1/CONTRIBUTING.rst 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/CONTRIBUTING.rst 2025-08-12 11:26:23.000000000 +0000 @@ -3,4 +3,4 @@ Contributing See how to contribute here: - https://wiki.fysik.dtu.dk/ase/development/contribute.html + https://ase-lib.org/development/contribute.html diff -pruN 3.24.0-1/README.rst 3.26.0-1/README.rst --- 3.24.0-1/README.rst 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/README.rst 2025-08-12 11:26:23.000000000 +0000 @@ -4,7 +4,7 @@ Atomic Simulation Environment ASE is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations. -Webpage: http://wiki.fysik.dtu.dk/ase +Webpage: https://ase-lib.org/ Requirements diff -pruN 3.24.0-1/appveyor.yml 3.26.0-1/appveyor.yml --- 3.24.0-1/appveyor.yml 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/appveyor.yml 1970-01-01 00:00:00.000000000 +0000 @@ -1,63 +0,0 @@ -environment: - matrix: - # For Python versions available on Appveyor, see - # http://www.appveyor.com/docs/installed-software#python - # # Python 3.9 - #- PYTHON: "C:\\Python39" - # Python 3.9 - 64-bit - - PYTHON: "C:\\Python39-x64" - # # Conda 3.9 - #- PYTHON: "C:\\Miniconda39" - # # Conda 3.9 64-bit - #- PYTHON: "C:\\Miniconda39-x64" - -install: - # Prepend chosen Python to the PATH of this build - - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%" - # Check that we have the expected version and architecture for Python - - "python --version" - - "python -c \"import struct; print(struct.calcsize('P') * 8)\"" - # Install the conda supplied packages if using conda, otherwise use pip - # The wheel package is needed for 'pip wheel' - # Turn off progressbars '-q' otherwise PowerShell thinks there are errors - - "echo %PYTHON%" - - ps: | - if($env:PYTHON -match "conda") - { - echo "install with conda" - conda update -yq conda - conda install -yq pip=21.0.1 wheel numpy scipy pyflakes matplotlib flask pytest pytest-mock - } - else - { - echo "install with pip" - #pip install --upgrade pip - python.exe -m pip install --upgrade pip==21.0.1 - pip install wheel pytest --disable-pip-version-check - } - # install ase into the current python - - "echo %cd%" - - "where pip" - - "pip install .[test] --disable-pip-version-check" - -build: off - -test_script: - # run tests from temp dir so source tree doesn't interfere - - "cd %TEMP%" - - "ase info" - - "ase -T test" - -after_test: - # This step builds distribution. - - "cd %APPVEYOR_BUILD_FOLDER%" - - "pip wheel -w dist --no-deps ." - -artifacts: - # bdist_wheel puts your built wheel in the dist directory - - path: dist\* - -#on_success: -# You can use this step to upload your artifacts to a public website. -# See Appveyor's documentation for more details. Or you can simply -# access your wheels from the Appveyor "artifacts" tab for your build. diff -pruN 3.24.0-1/ase/_4/__init__.py 3.26.0-1/ase/_4/__init__.py --- 3.24.0-1/ase/_4/__init__.py 1970-01-01 00:00:00.000000000 +0000 +++ 3.26.0-1/ase/_4/__init__.py 2025-08-12 11:26:23.000000000 +0000 @@ -0,0 +1,3 @@ +"""This package holds temporary developments for ASE 4. + +Things in ase._4 are likely to change without warning.""" diff -pruN 3.24.0-1/ase/__init__.py 3.26.0-1/ase/__init__.py --- 3.24.0-1/ase/__init__.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/__init__.py 2025-08-12 11:26:23.000000000 +0000 @@ -10,6 +10,6 @@ from ase.atom import Atom from ase.atoms import Atoms __all__ = ['Atoms', 'Atom'] -__version__ = '3.24.0' +__version__ = '3.26.0' ase.parallel # silence pyflakes diff -pruN 3.24.0-1/ase/atom.py 3.26.0-1/ase/atom.py --- 3.24.0-1/ase/atom.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/atom.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """This module defines the Atom object.""" import numpy as np diff -pruN 3.24.0-1/ase/atoms.py 3.26.0-1/ase/atoms.py --- 3.24.0-1/ase/atoms.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/atoms.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Copyright 2008, 2009 CAMd # (see accompanying license files for details). @@ -6,13 +8,16 @@ This module defines the central object in the ASE package: the Atoms object. """ +from __future__ import annotations + import copy import numbers from math import cos, pi, sin +from typing import Sequence, Union, overload import numpy as np -import ase.units as units +from ase import units from ase.atom import Atom from ase.cell import Cell from ase.data import atomic_masses, atomic_masses_common @@ -200,7 +205,7 @@ class Atoms: if info is None: info = copy.deepcopy(atoms.info) - self.arrays = {} + self.arrays: dict[str, np.ndarray] = {} if symbols is not None and numbers is not None: raise TypeError('Use only one of "symbols" and "numbers".') @@ -266,10 +271,28 @@ class Atoms: @property def symbols(self): - """Get chemical symbols as a :class:`ase.symbols.Symbols` object. + """Get chemical symbols as a :class:`~ase.symbols.Symbols` object. + + The object works like ``atoms.numbers`` except its values are strings. + It supports in-place editing. - The object works like ``atoms.numbers`` except its values - are strings. It supports in-place editing.""" + Examples + -------- + >>> from ase.build import molecule + >>> atoms = molecule('CH3CH2OH') + >>> atoms.symbols + Symbols('C2OH6') + >>> list(atoms.symbols) + ['C', 'C', 'O', 'H', 'H', 'H', 'H', 'H', 'H'] + >>> atoms.symbols == 'C' # doctest: +ELLIPSIS + array([ True, True, False, False, False, False, False, False, False]...) + >>> atoms.symbols.indices() + {'C': array([0, 1]), 'O': array([2]), 'H': array([3, 4, 5, 6, 7, 8])} + >>> list(atoms.symbols.indices()) # unique elements + ['C', 'O', 'H'] + >>> atoms.symbols.species() # doctest: +SKIP + {'C', 'O', 'H'} + """ # noqa return Symbols(self.numbers) @symbols.setter @@ -277,6 +300,71 @@ class Atoms: new_symbols = Symbols.fromsymbols(obj) self.numbers[:] = new_symbols.numbers + def get_chemical_symbols(self): + """Get list of chemical symbol strings. + + Equivalent to ``list(atoms.symbols)``.""" + return list(self.symbols) + + def set_chemical_symbols(self, symbols): + """Set chemical symbols.""" + self.set_array('numbers', symbols2numbers(symbols), int, ()) + + @property + def numbers(self): + """Attribute for direct manipulation of the atomic numbers.""" + return self.arrays['numbers'] + + @numbers.setter + def numbers(self, numbers): + self.set_atomic_numbers(numbers) + + def set_atomic_numbers(self, numbers): + """Set atomic numbers.""" + self.set_array('numbers', numbers, int, ()) + + def get_atomic_numbers(self): + """Get integer array of atomic numbers.""" + return self.arrays['numbers'].copy() + + @property + def positions(self): + """Attribute for direct manipulation of the positions.""" + return self.arrays['positions'] + + @positions.setter + def positions(self, pos): + self.arrays['positions'][:] = pos + + def set_positions(self, newpositions, apply_constraint=True): + """Set positions, honoring any constraints. To ignore constraints, + use *apply_constraint=False*.""" + if self.constraints and apply_constraint: + newpositions = np.array(newpositions, float) + for constraint in self.constraints: + constraint.adjust_positions(self, newpositions) + + self.set_array('positions', newpositions, shape=(3,)) + + def get_positions(self, wrap=False, **wrap_kw): + """Get array of positions. + + Parameters: + + wrap: bool + wrap atoms back to the cell before returning positions + wrap_kw: (keyword=value) pairs + optional keywords `pbc`, `center`, `pretty_translation`, `eps`, + see :func:`ase.geometry.wrap_positions` + """ + from ase.geometry import wrap_positions + if wrap: + if 'pbc' not in wrap_kw: + wrap_kw['pbc'] = self.pbc + return wrap_positions(self.positions, self.cell, **wrap_kw) + else: + return self.arrays['positions'].copy() + @deprecated("Please use atoms.calc = calc", FutureWarning) def set_calculator(self, calc=None): """Attach calculator object. @@ -330,6 +418,18 @@ class Atoms: """ return self.cell.rank + @property + def constraints(self): + return self._constraints + + @constraints.setter + def constraints(self, constraint): + self.set_constraint(constraint) + + @constraints.deleter + def constraints(self): + self._constraints = [] + def set_constraint(self, constraint=None): """Apply one or more constrains. @@ -345,15 +445,6 @@ class Atoms: else: self._constraints = [constraint] - def _get_constraints(self): - return self._constraints - - def _del_constraints(self): - self._constraints = [] - - constraints = property(_get_constraints, set_constraint, _del_constraints, - 'Constraints of the atoms.') - def get_number_of_degrees_of_freedom(self): """Calculate the number of degrees of freedom in the system.""" return len(self) * 3 - sum( @@ -553,24 +644,6 @@ class Atoms: # XXX extend has to calculator properties return name in self.arrays - def set_atomic_numbers(self, numbers): - """Set atomic numbers.""" - self.set_array('numbers', numbers, int, ()) - - def get_atomic_numbers(self): - """Get integer array of atomic numbers.""" - return self.arrays['numbers'].copy() - - def get_chemical_symbols(self): - """Get list of chemical symbol strings. - - Equivalent to ``list(atoms.symbols)``.""" - return list(self.symbols) - - def set_chemical_symbols(self, symbols): - """Set chemical symbols.""" - self.set_array('numbers', symbols2numbers(symbols), int, ()) - def get_chemical_formula(self, mode='hill', empirical=False): """Get the chemical formula as a string based on the chemical symbols. @@ -624,10 +697,6 @@ class Atoms: constraint.adjust_momenta(self, momenta) self.set_array('momenta', momenta, float, (3,)) - def set_velocities(self, velocities): - """Set the momenta by specifying the velocities.""" - self.set_momenta(self.get_masses()[:, np.newaxis] * velocities) - def get_momenta(self): """Get array of momenta.""" if 'momenta' in self.arrays: @@ -635,6 +704,16 @@ class Atoms: else: return np.zeros((len(self), 3)) + def get_velocities(self): + """Get array of velocities.""" + momenta = self.get_momenta() + masses = self.get_masses() + return momenta / masses[:, np.newaxis] + + def set_velocities(self, velocities): + """Set the momenta by specifying the velocities.""" + self.set_momenta(self.get_masses()[:, np.newaxis] * velocities) + def set_masses(self, masses='defaults'): """Set atomic masses in atomic mass units. @@ -656,12 +735,27 @@ class Atoms: masses[i] = atomic_masses[self.numbers[i]] self.set_array('masses', masses, float, ()) - def get_masses(self): - """Get array of masses in atomic mass units.""" + def get_masses(self) -> np.ndarray: + """Get masses of atoms. + + Returns + ------- + masses : np.ndarray + Atomic masses in dalton (unified atomic mass units). + + Examples + -------- + >>> from ase.build import molecule + >>> atoms = molecule('CH4') + >>> atoms.get_masses() + array([ 12.011, 1.008, 1.008, 1.008, 1.008]) + >>> total_mass = atoms.get_masses().sum() + >>> print(f'{total_mass:f}') + 16.043000 + """ if 'masses' in self.arrays: return self.arrays['masses'].copy() - else: - return atomic_masses[self.arrays['numbers']] + return atomic_masses[self.arrays['numbers']] def set_initial_magnetic_moments(self, magmoms=None): """Set the initial magnetic moments. @@ -720,35 +814,6 @@ class Atoms: from ase.calculators.calculator import PropertyNotImplementedError raise PropertyNotImplementedError - def set_positions(self, newpositions, apply_constraint=True): - """Set positions, honoring any constraints. To ignore constraints, - use *apply_constraint=False*.""" - if self.constraints and apply_constraint: - newpositions = np.array(newpositions, float) - for constraint in self.constraints: - constraint.adjust_positions(self, newpositions) - - self.set_array('positions', newpositions, shape=(3,)) - - def get_positions(self, wrap=False, **wrap_kw): - """Get array of positions. - - Parameters: - - wrap: bool - wrap atoms back to the cell before returning positions - wrap_kw: (keyword=value) pairs - optional keywords `pbc`, `center`, `pretty_translation`, `eps`, - see :func:`ase.geometry.wrap_positions` - """ - from ase.geometry import wrap_positions - if wrap: - if 'pbc' not in wrap_kw: - wrap_kw['pbc'] = self.pbc - return wrap_positions(self.positions, self.cell, **wrap_kw) - else: - return self.arrays['positions'].copy() - def get_potential_energy(self, force_consistent=False, apply_constraint=True): """Calculate potential energy. @@ -798,12 +863,6 @@ class Atoms: return 0.0 return 0.5 * np.vdot(momenta, self.get_velocities()) - def get_velocities(self): - """Get array of velocities.""" - momenta = self.get_momenta() - masses = self.get_masses() - return momenta / masses[:, np.newaxis] - def get_total_energy(self): """Get the total energy - potential plus kinetic energy.""" return self.get_potential_energy() + self.get_kinetic_energy() @@ -1134,6 +1193,12 @@ class Atoms: for i in range(len(self)): yield self[i] + @overload + def __getitem__(self, i: Union[int, np.integer]) -> Atom: ... + + @overload + def __getitem__(self, i: Union[Sequence, slice, np.ndarray]) -> Atoms: ... + def __getitem__(self, i): """Return a subset of the atoms. @@ -1539,53 +1604,42 @@ class Atoms: center = np.array(center, float) return center - def euler_rotate(self, phi=0.0, theta=0.0, psi=0.0, center=(0, 0, 0)): + def euler_rotate( + self, + phi: float = 0.0, + theta: float = 0.0, + psi: float = 0.0, + center: Sequence[float] = (0.0, 0.0, 0.0), + ) -> None: """Rotate atoms via Euler angles (in degrees). See e.g http://mathworld.wolfram.com/EulerAngles.html for explanation. - Parameters: + Note that the rotations in this method are passive and applied **not** + to the atomic coordinates in the present frame **but** the frame itself. - center : - The point to rotate about. A sequence of length 3 with the - coordinates, or 'COM' to select the center of mass, 'COP' to - select center of positions or 'COU' to select center of cell. - phi : + Parameters + ---------- + phi : float The 1st rotation angle around the z axis. - theta : + theta : float Rotation around the x axis. - psi : + psi : float 2nd rotation around the z axis. + center : Sequence[float], default = (0.0, 0.0, 0.0) + The point to rotate about. A sequence of length 3 with the + coordinates, or 'COM' to select the center of mass, 'COP' to + select center of positions or 'COU' to select center of cell. """ + from scipy.spatial.transform import Rotation as R + center = self._centering_as_array(center) - phi *= pi / 180 - theta *= pi / 180 - psi *= pi / 180 - - # First move the molecule to the origin In contrast to MATLAB, - # numpy broadcasts the smaller array to the larger row-wise, - # so there is no need to play with the Kronecker product. - rcoords = self.positions - center - # First Euler rotation about z in matrix form - D = np.array(((cos(phi), sin(phi), 0.), - (-sin(phi), cos(phi), 0.), - (0., 0., 1.))) - # Second Euler rotation about x: - C = np.array(((1., 0., 0.), - (0., cos(theta), sin(theta)), - (0., -sin(theta), cos(theta)))) - # Third Euler rotation, 2nd rotation about z: - B = np.array(((cos(psi), sin(psi), 0.), - (-sin(psi), cos(psi), 0.), - (0., 0., 1.))) - # Total Euler rotation - A = np.dot(B, np.dot(C, D)) - # Do the rotation - rcoords = np.dot(A, np.transpose(rcoords)) - # Move back to the rotation point - self.positions = np.transpose(rcoords) + center + # passive rotations (negative angles) for backward compatibility + rotation = R.from_euler('zxz', (-phi, -theta, -psi), degrees=True) + + self.positions = rotation.apply(self.positions - center) + center def get_dihedral(self, a0, a1, a2, a3, mic=False): """Calculate dihedral angle. @@ -2005,27 +2059,6 @@ class Atoms: .format(self.cell.rank)) return self.cell.volume - def _get_positions(self): - """Return reference to positions-array for in-place manipulations.""" - return self.arrays['positions'] - - def _set_positions(self, pos): - """Set positions directly, bypassing constraints.""" - self.arrays['positions'][:] = pos - - positions = property(_get_positions, _set_positions, - doc='Attribute for direct ' + - 'manipulation of the positions.') - - def _get_atomic_numbers(self): - """Return reference to atomic numbers for in-place - manipulations.""" - return self.arrays['numbers'] - - numbers = property(_get_atomic_numbers, set_atomic_numbers, - doc='Attribute for direct ' + - 'manipulation of the atomic numbers.') - @property def cell(self): """The :class:`ase.cell.Cell` for direct manipulation.""" diff -pruN 3.24.0-1/ase/build/__init__.py 3.26.0-1/ase/build/__init__.py --- 3.24.0-1/ase/build/__init__.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/__init__.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from ase.build.bulk import bulk from ase.build.connected import ( connected_atoms, diff -pruN 3.24.0-1/ase/build/attach.py 3.26.0-1/ase/build/attach.py --- 3.24.0-1/ase/build/attach.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/attach.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase.geometry import get_distances diff -pruN 3.24.0-1/ase/build/bulk.py 3.26.0-1/ase/build/bulk.py --- 3.24.0-1/ase/build/bulk.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/bulk.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Build crystalline systems""" from math import sqrt from typing import Any diff -pruN 3.24.0-1/ase/build/general_surface.py 3.26.0-1/ase/build/general_surface.py --- 3.24.0-1/ase/build/general_surface.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/general_surface.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from math import gcd import numpy as np diff -pruN 3.24.0-1/ase/build/molecule.py 3.26.0-1/ase/build/molecule.py --- 3.24.0-1/ase/build/molecule.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/molecule.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from ase.atoms import Atoms from ase.collections import g2 diff -pruN 3.24.0-1/ase/build/niggli.py 3.26.0-1/ase/build/niggli.py --- 3.24.0-1/ase/build/niggli.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/niggli.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np diff -pruN 3.24.0-1/ase/build/ribbon.py 3.26.0-1/ase/build/ribbon.py --- 3.24.0-1/ase/build/ribbon.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/ribbon.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from math import sqrt import numpy as np diff -pruN 3.24.0-1/ase/build/root.py 3.26.0-1/ase/build/root.py --- 3.24.0-1/ase/build/root.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/root.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from math import atan2, cos, log10, sin import numpy as np diff -pruN 3.24.0-1/ase/build/rotate.py 3.26.0-1/ase/build/rotate.py --- 3.24.0-1/ase/build/rotate.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/rotate.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase.geometry import find_mic diff -pruN 3.24.0-1/ase/build/supercells.py 3.26.0-1/ase/build/supercells.py --- 3.24.0-1/ase/build/supercells.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/supercells.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,17 +1,72 @@ -"""Helper functions for creating supercells.""" +# fmt: off -import warnings +"""Helper functions for creating supercells.""" import numpy as np from ase import Atoms +from ase.utils import deprecated class SupercellError(Exception): """Use if construction of supercell fails""" -def get_deviation_from_optimal_cell_shape(cell, target_shape="sc", norm=None): +@deprecated('use `eval_length_deviation` instead.') +def get_deviation_from_optimal_cell_shape(*args, **kwargs): + return eval_length_deviation(*args, **kwargs) + + +def eval_shape_deviation(cell, target_shape="sc"): + r""" + Calculates the deviation of the given cell from the target cell metric. + + Parameters + ---------- + cell : (..., 3, 3) array_like + Metric given as a 3x3 matrix of the input structure. + Multiple cells can also be given as a higher-dimensional array. + target_shape : {'sc', 'fcc'} + Desired supercell shape. + + Returns + ------- + float or ndarray + Cell metric(s) (0 is perfect score) + + """ + + cell = np.asarray(cell) + + eff_cubic_length = np.cbrt(np.abs(np.linalg.det(cell))) # 'a_0' + + if target_shape == 'sc': + target_len = eff_cubic_length + target_cos = 0.0 # cos(+-pi/2) = 0.0 + target_metric = np.eye(3) + elif target_shape == 'fcc': + # FCC is characterised by 60 degree angles & lattice vectors = 2**(1/6) + # times the eff cubic length: + target_len = eff_cubic_length * 2 ** (1 / 6) + target_cos = 0.5 # cos(+-pi/3) = 0.5 + target_metric = np.eye(3) + target_cos * (np.ones((3, 3)) - np.eye(3)) + else: + raise ValueError(target_shape) + + # calculate cell @ cell.T for (... , 3, 3) + # with cell -> C_mij + # and metric -> M_mkl + # M_mkl = (sum_j C_mkj * C_mlj) / leff**2 + metric = cell @ np.swapaxes(cell, -2, -1) + normed = metric / target_len[..., None, None] ** 2 + + # offdiagonal ~ cos angle -> score = np.abs(cos angle - cos target_angle) + scores = np.add.reduce((normed - target_metric) ** 2, axis=(-2, -1)) + + return scores + + +def eval_length_deviation(cell, target_shape="sc"): r"""Calculate the deviation from the target cell shape. Calculates the deviation of the given cell metric from the ideal @@ -35,10 +90,6 @@ def get_deviation_from_optimal_cell_shap target_shape : {'sc', 'fcc'} Desired supercell shape. Can be 'sc' for simple cubic or 'fcc' for face-centered cubic. - norm : float - Specify the normalization factor. This is useful to avoid - recomputing the normalization factor when computing the - deviation for a series of P matrices. Returns ------- @@ -49,76 +100,34 @@ def get_deviation_from_optimal_cell_shap `norm` is unused in ASE 3.24.0 and removed in ASE 3.25.0. """ - if norm is not None: - warnings.warn( - '`norm` is unused in ASE 3.24.0 and removed in ASE 3.25.0', - FutureWarning, - ) cell = np.asarray(cell) cell_lengths = np.sqrt(np.add.reduce(cell**2, axis=-1)) + eff_cubic_length = np.cbrt(np.abs(np.linalg.det(cell))) # 'a_0' if target_shape == 'sc': - target_length = eff_cubic_length + target_len = eff_cubic_length elif target_shape == 'fcc': # FCC is characterised by 60 degree angles & lattice vectors = 2**(1/6) # times the eff cubic length: - target_length = eff_cubic_length * 2 ** (1 / 6) + target_len = eff_cubic_length * 2 ** (1 / 6) else: raise ValueError(target_shape) - inv_target_length = 1.0 / target_length + inv_target_len = 1.0 / target_len # rms difference to eff cubic/FCC length: - diffs = cell_lengths * inv_target_length[..., None] - 1.0 - return np.sqrt(np.add.reduce(diffs**2, axis=-1)) - + diffs = cell_lengths * inv_target_len[..., None] - 1.0 + scores = np.sqrt(np.add.reduce(diffs**2, axis=-1)) -def find_optimal_cell_shape( - cell, - target_size, - target_shape, - lower_limit=-2, - upper_limit=2, - verbose=False, -): - """Obtain the optimal transformation matrix for a supercell of target size - and shape. + return scores - Returns the transformation matrix that produces a supercell - corresponding to *target_size* unit cells with metric *cell* that - most closely approximates the shape defined by *target_shape*. - Updated with code from the `doped` defect simulation package - (https://doped.readthedocs.io) to be rotationally invariant and - allow transformation matrices with negative determinants, boosting - performance. - - Parameters: - - cell: 2D array of floats - Metric given as a (3x3 matrix) of the input structure. - target_size: integer - Size of desired supercell in number of unit cells. - target_shape: str - Desired supercell shape. Can be 'sc' for simple cubic or - 'fcc' for face-centered cubic. - lower_limit: int - Lower limit of search range. - upper_limit: int - Upper limit of search range. - verbose: bool - Set to True to obtain additional information regarding - construction of transformation matrix. - - Returns: - 2D array of integers: Transformation matrix that produces the - optimal supercell. - """ - cell = np.asarray(cell) +def _guess_initial_transformation(cell, target_shape, + target_size, verbose=False): # Set up target metric if target_shape == 'sc': @@ -150,41 +159,140 @@ def find_optimal_cell_shape( print("closest integer transformation matrix (P_0):") print(starting_P) + return ideal_P, starting_P + + +def _build_matrix_operations(starting_P, lower_limit, upper_limit): + mat_dim = starting_P.shape[0] + + if not mat_dim == starting_P.shape[1]: + raise ValueError('Cell matrix should be quadratic.') + # Build a big matrix of all admissible integer matrix operations. # (If this takes too much memory we could do blocking but there are # too many for looping one by one.) - dimensions = [(upper_limit + 1) - lower_limit] * 9 - operations = np.moveaxis(np.indices(dimensions), 0, -1).reshape(-1, 3, 3) + dimensions = [(upper_limit + 1) - lower_limit] * mat_dim**2 + operations = np.moveaxis(np.indices(dimensions), 0, -1) + operations = operations.reshape(-1, mat_dim, mat_dim) operations += lower_limit # Each element runs from lower to upper limits. operations += starting_P - determinants = np.linalg.det(operations) + + return operations + + +def _screen_supercell_size(operations, target_size): # screen supercells with the target size - good_indices = np.where(abs(determinants - target_size) < 1e-12)[0] + determinants = np.round(np.linalg.det(operations), 0).astype(int) + good_indices = np.where(np.abs(determinants) == target_size)[0] + if not good_indices.size: print("Failed to find a transformation matrix.") return None operations = operations[good_indices] - # evaluate derivations of the screened supercells - scores = get_deviation_from_optimal_cell_shape( - operations @ cell, - target_shape, - ) + return operations + + +def _optimal_transformation(operations, scores, ideal_P): + imin = np.argmin(scores) best_score = scores[imin] - # screen candidates with the same best score operations = operations[np.abs(scores - best_score) < 1e-6] # select the one whose cell orientation is the closest to the target # https://gitlab.com/ase/ase/-/merge_requests/3522 imin = np.argmin(np.add.reduce((operations - ideal_P)**2, axis=(-2, -1))) + optimal_P = operations[imin] if np.linalg.det(optimal_P) <= 0: optimal_P *= -1 # flip signs if negative determinant + return optimal_P, best_score + + +all_score_funcs = {"length": eval_length_deviation, + "metric": eval_shape_deviation} + + +def find_optimal_cell_shape( + cell, + target_size, + target_shape, + lower_limit=-2, + upper_limit=2, + verbose=False, + score_key='length' +): + """Obtain the optimal transformation matrix for a supercell of target size + and shape. + + Returns the transformation matrix that produces a supercell + corresponding to *target_size* unit cells with metric *cell* that + most closely approximates the shape defined by *target_shape*. + + Updated with code from the `doped` defect simulation package + (https://doped.readthedocs.io) to be rotationally invariant and + allow transformation matrices with negative determinants, boosting + performance. + + Parameters: + + cell: 2D array of floats + Metric given as a (3x3 matrix) of the input structure. + target_size: integer + Size of desired supercell in number of unit cells. + target_shape: str + Desired supercell shape. Can be 'sc' for simple cubic or + 'fcc' for face-centered cubic. + lower_limit: int + Lower limit of search range. + upper_limit: int + Upper limit of search range. + verbose: bool + Set to True to obtain additional information regarding + construction of transformation matrix. + score_key: str + key from all_score_funcs to select score function. + + Returns: + 2D array of integers: Transformation matrix that produces the + optimal supercell. + """ + + # transform to np.array + cell = np.asarray(cell) + + # get starting transformation + # ideal_P ... transformation: target_cell = ideal_P @ cell + # starting_P ... integer rounded (ideal_P) + ideal_P, starting_P = _guess_initial_transformation(cell, target_shape, + target_size, + verbose=verbose) + + # build all admissible matrix operations 'centered' at starting_P + operations = _build_matrix_operations(starting_P, + lower_limit, upper_limit) + + # pre-screen operations based on target_size + operations = _screen_supercell_size(operations, target_size) + + # evaluate derivations of the screened supercells + if score_key in all_score_funcs: + get_deviation_score = all_score_funcs[score_key] + else: + msg = (f'Score func key {score_key} not implemented.' + + f'Please select from {all_score_funcs}.') + raise SupercellError(msg) + + scores = get_deviation_score(operations @ cell, + target_shape) + + # obtain optimal transformation from scores + optimal_P, best_score = _optimal_transformation(operations, scores, ideal_P) + # Finalize. if verbose: print(f"smallest score (|Q P h_p - h_target|_2): {best_score:f}") @@ -194,6 +302,7 @@ def find_optimal_cell_shape( print(np.round(np.dot(optimal_P, cell), 4)) det = np.linalg.det(optimal_P) print(f"determinant of optimal transformation matrix: {det:g}") + return optimal_P diff -pruN 3.24.0-1/ase/build/surface.py 3.26.0-1/ase/build/surface.py --- 3.24.0-1/ase/build/surface.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/surface.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Helper functions for creating the most common surfaces and related tasks. The helper functions can create the most common low-index surfaces, diff -pruN 3.24.0-1/ase/build/surfaces_with_termination.py 3.26.0-1/ase/build/surfaces_with_termination.py --- 3.24.0-1/ase/build/surfaces_with_termination.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/surfaces_with_termination.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase.build.general_surface import surface diff -pruN 3.24.0-1/ase/build/tools.py 3.26.0-1/ase/build/tools.py --- 3.24.0-1/ase/build/tools.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/tools.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase.build.niggli import niggli_reduce_cell diff -pruN 3.24.0-1/ase/build/tube.py 3.26.0-1/ase/build/tube.py --- 3.24.0-1/ase/build/tube.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/build/tube.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from math import gcd, sqrt import numpy as np diff -pruN 3.24.0-1/ase/calculators/abc.py 3.26.0-1/ase/calculators/abc.py --- 3.24.0-1/ase/calculators/abc.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/abc.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ This module defines abstract helper classes with the objective of reducing boilerplace method definitions (i.e. duplication) in calculators. diff -pruN 3.24.0-1/ase/calculators/abinit.py 3.26.0-1/ase/calculators/abinit.py --- 3.24.0-1/ase/calculators/abinit.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/abinit.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """This module defines an ASE interface to ABINIT. http://www.abinit.org/ diff -pruN 3.24.0-1/ase/calculators/acemolecule.py 3.26.0-1/ase/calculators/acemolecule.py --- 3.24.0-1/ase/calculators/acemolecule.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/acemolecule.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import os from copy import deepcopy diff -pruN 3.24.0-1/ase/calculators/acn.py 3.26.0-1/ase/calculators/acn.py --- 3.24.0-1/ase/calculators/acn.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/acn.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np import ase.units as units diff -pruN 3.24.0-1/ase/calculators/aims.py 3.26.0-1/ase/calculators/aims.py --- 3.24.0-1/ase/calculators/aims.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/aims.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """This module defines an ASE interface to FHI-aims. Felix Hanke hanke@liverpool.ac.uk @@ -158,8 +160,7 @@ class AimsTemplate(CalculatorTemplate): write_control(control, atoms, parameters) def execute(self, directory, profile): - profile.run(directory, None, self.outputname, - errorfile=self.errorname) + profile.run(directory, None, self.outputname, errorfile=self.errorname) def read_results(self, directory): from ase.io.aims import read_aims_results @@ -171,7 +172,7 @@ class AimsTemplate(CalculatorTemplate): return AimsProfile.from_config(cfg, self.name, **kwargs) def socketio_argv(self, profile, unixsocket, port): - return [profile.command] + return profile._split_command def socketio_parameters(self, unixsocket, port): if port: diff -pruN 3.24.0-1/ase/calculators/amber.py 3.26.0-1/ase/calculators/amber.py --- 3.24.0-1/ase/calculators/amber.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/amber.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """This module defines an ASE interface to Amber16. Usage: (Tested only with Amber16, http://ambermd.org/) diff -pruN 3.24.0-1/ase/calculators/bond_polarizability.py 3.26.0-1/ase/calculators/bond_polarizability.py --- 3.24.0-1/ase/calculators/bond_polarizability.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/bond_polarizability.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from typing import Tuple import numpy as np diff -pruN 3.24.0-1/ase/calculators/calculator.py 3.26.0-1/ase/calculators/calculator.py --- 3.24.0-1/ase/calculators/calculator.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/calculator.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import copy import os import shlex @@ -203,6 +205,10 @@ def get_calculator_class(name): from ase.calculators.acemolecule import ACE as Calculator elif name == 'Psi4': from ase.calculators.psi4 import Psi4 as Calculator + elif name == 'mattersim': + from mattersim.forcefield import MatterSimCalculator as Calculator + elif name == 'mace_mp': + from mace.calculators import mace_mp as Calculator elif name in external_calculators: Calculator = external_calculators[name] else: @@ -387,31 +393,6 @@ def kpts2ndarray(kpts, atoms=None): return kpts2kpts(kpts, atoms=atoms).kpts -class EigenvalOccupationMixin: - """Define 'eigenvalues' and 'occupations' properties on class. - - eigenvalues and occupations will be arrays of shape (spin, kpts, nbands). - - Classes must implement the old-fashioned get_eigenvalues and - get_occupations methods.""" - - # We should maybe deprecate this and rely on the new - # Properties object for eigenvalues/occupations. - - @property - def eigenvalues(self): - return self._propwrapper().eigenvalues - - @property - def occupations(self): - return self._propwrapper().occupations - - def _propwrapper(self): - from ase.calculator.singlepoint import OutputPropertyWrapper - - return OutputPropertyWrapper(self) - - class Parameters(dict): """Dictionary for parameters. @@ -569,6 +550,10 @@ class BaseCalculator(GetPropertiesMixin) def name(self) -> str: return self._get_name() + def todict(self) -> dict[str, Any]: + """Obtain a dictionary of parameter information""" + return {} + class Calculator(BaseCalculator): """Base-class for all ASE calculators. diff -pruN 3.24.0-1/ase/calculators/castep.py 3.26.0-1/ase/calculators/castep.py --- 3.24.0-1/ase/calculators/castep.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/castep.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,5 +1,7 @@ +# fmt: off + """This module defines an interface to CASTEP for - use by the ASE (Webpage: http://wiki.fysik.dtu.dk/ase) + use by the ASE (Webpage: https://ase-lib.org/) Authors: Max Hoffmann, max.hoffmann@ch.tum.de diff -pruN 3.24.0-1/ase/calculators/checkpoint.py 3.26.0-1/ase/calculators/checkpoint.py --- 3.24.0-1/ase/calculators/checkpoint.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/checkpoint.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Checkpointing and restart functionality for scripts using ASE Atoms objects. Initialize checkpoint object: @@ -268,11 +270,9 @@ class CheckpointCalculator(Calculator): try: results = self.checkpoint.load(atoms) prev_atoms, results = results[0], results[1:] - try: - assert atoms_almost_equal(atoms, prev_atoms) - except AssertionError: - raise AssertionError('mismatch between current atoms and ' - 'those read from checkpoint file') + if not atoms_almost_equal(atoms, prev_atoms): + raise RuntimeError('mismatch between current atoms and ' + 'those read from checkpoint file') self.logfile.write('retrieved results for {} from checkpoint\n' .format(properties)) # save results in calculator for next time diff -pruN 3.24.0-1/ase/calculators/combine_mm.py 3.26.0-1/ase/calculators/combine_mm.py --- 3.24.0-1/ase/calculators/combine_mm.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/combine_mm.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import copy import numpy as np diff -pruN 3.24.0-1/ase/calculators/counterions.py 3.26.0-1/ase/calculators/counterions.py --- 3.24.0-1/ase/calculators/counterions.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/counterions.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase import units diff -pruN 3.24.0-1/ase/calculators/cp2k.py 3.26.0-1/ase/calculators/cp2k.py --- 3.24.0-1/ase/calculators/cp2k.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/cp2k.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """This module defines an ASE interface to CP2K. https://www.cp2k.org/ diff -pruN 3.24.0-1/ase/calculators/crystal.py 3.26.0-1/ase/calculators/crystal.py --- 3.24.0-1/ase/calculators/crystal.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/crystal.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """This module defines an ASE interface to CRYSTAL14/CRYSTAL17 http://www.crystal.unito.it/ diff -pruN 3.24.0-1/ase/calculators/demon/demon.py 3.26.0-1/ase/calculators/demon/demon.py --- 3.24.0-1/ase/calculators/demon/demon.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/demon/demon.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """This module defines an ASE interface to deMon. http://www.demon-software.com diff -pruN 3.24.0-1/ase/calculators/demon/demon_io.py 3.26.0-1/ase/calculators/demon/demon_io.py --- 3.24.0-1/ase/calculators/demon/demon_io.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/demon/demon_io.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import os.path as op import numpy as np diff -pruN 3.24.0-1/ase/calculators/demonnano.py 3.26.0-1/ase/calculators/demonnano.py --- 3.24.0-1/ase/calculators/demonnano.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/demonnano.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # flake8: noqa """This module defines an ASE interface to deMon-nano. diff -pruN 3.24.0-1/ase/calculators/dftb.py 3.26.0-1/ase/calculators/dftb.py --- 3.24.0-1/ase/calculators/dftb.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/dftb.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ This module defines a FileIOCalculator for DFTB+ http://www.dftbplus.org/ diff -pruN 3.24.0-1/ase/calculators/dftd3.py 3.26.0-1/ase/calculators/dftd3.py --- 3.24.0-1/ase/calculators/dftd3.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/dftd3.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import os import subprocess from pathlib import Path @@ -313,20 +315,14 @@ class PureDFTD3(FileIOCalculator): else: damppars = None - pbc = any(atoms.pbc) - if pbc and not all(atoms.pbc): - warn('WARNING! dftd3 can only calculate the dispersion energy ' - 'of non-periodic or 3D-periodic systems. We will treat ' - 'this system as 3D-periodic!') - if self.comm.rank == 0: self._actually_write_input( directory=Path(self.directory), atoms=atoms, properties=properties, prefix=self.label, - damppars=damppars, pbc=pbc) + damppars=damppars, pbc=any(atoms.pbc)) def _actually_write_input(self, directory, prefix, atoms, properties, - damppars, pbc): + damppars, pbc: bool): if pbc: fname = directory / f'{prefix}.POSCAR' # We sort the atoms so that the atomtypes list becomes as diff -pruN 3.24.0-1/ase/calculators/dmol.py 3.26.0-1/ase/calculators/dmol.py --- 3.24.0-1/ase/calculators/dmol.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/dmol.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """This module defines an ASE interface to DMol3. Contacts diff -pruN 3.24.0-1/ase/calculators/eam.py 3.26.0-1/ase/calculators/eam.py --- 3.24.0-1/ase/calculators/eam.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/eam.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # flake8: noqa """Calculator for the Embedded Atom Method Potential""" @@ -17,6 +19,7 @@ from ase.calculators.calculator import C from ase.data import chemical_symbols from ase.neighborlist import NeighborList from ase.units import Bohr, Hartree +from ase.stress import full_3x3_to_voigt_6_stress class EAM(Calculator): @@ -95,7 +98,7 @@ by element types. Running the Calculator ====================== -EAM calculates the cohesive atom energy and forces. Internally the +EAM calculates the cohesive atom energy, forces and stress. Internally the potential functions are defined by splines which may be directly supplied or created by reading the spline points from a data file from which a spline function is created. The LAMMPS compatible ``.alloy``, ``.fs`` @@ -114,6 +117,7 @@ For example:: slab.calc = mishin slab.get_potential_energy() slab.get_forces() + slab.get_stress() The breakdown of energy contribution from the indvidual components are stored in the calculator instance ``.results['energy_components']`` @@ -232,7 +236,7 @@ Notes/Issues End EAM Interface Documentation """ - implemented_properties = ['energy', 'forces'] + implemented_properties = ['energy', 'free_energy', 'forces', 'stress'] default_parameters = dict( skin=1.0, @@ -680,7 +684,7 @@ End EAM Interface Documentation self.update(self.atoms) self.calculate_energy(self.atoms) - if 'forces' in properties: + if 'forces' in properties or 'stress' in properties: self.calculate_forces(self.atoms) # check we have all the properties requested @@ -689,7 +693,7 @@ End EAM Interface Documentation if property == 'energy': self.calculate_energy(self.atoms) - if property == 'forces': + if property in ['forces', 'stress']: self.calculate_forces(self.atoms) # we need to remember the previous state of parameters @@ -783,12 +787,14 @@ End EAM Interface Documentation self.results['energy_components'] = components self.results['energy'] = energy + self.results['free_energy'] = energy def calculate_forces(self, atoms): # calculate the forces based on derivatives of the three EAM functions self.update(atoms) self.results['forces'] = np.zeros((len(atoms), 3)) + stresses = np.zeros((len(atoms), 3, 3)) for i in range(len(atoms)): # this is the atom to be embedded neighbors, offsets = self.neighbors.get_neighbors(i) @@ -827,9 +833,12 @@ End EAM Interface Documentation self.d_electron_density[self.index[i]](rnuse))) self.results['forces'][i] += np.dot(scale, urvec[nearest][use]) + stresses[i] += np.dot( + (scale[:,np.newaxis] * urvec[nearest][use]).T, + rvec[nearest][use]) if self.form == 'adp': - adp_forces = self.angular_forces( + adp_forces, adp_stresses = self.angular_forces( self.mu[i], self.mu[neighbors[nearest][use]], self.lam[i], @@ -840,6 +849,11 @@ End EAM Interface Documentation j_index) self.results['forces'][i] += adp_forces + stresses[i] += adp_stresses + + if self.atoms.cell.rank == 3: + stress = 0.5 * np.sum(stresses, axis=0) / self.atoms.get_volume() + self.results['stress'] = full_3x3_to_voigt_6_stress(stress) def angular_forces(self, mu_i, mu, lam_i, lam, r, rvec, form1, form2): # calculate the extra components for the adp forces @@ -872,7 +886,7 @@ End EAM Interface Documentation # on the NIST website with the AlH potential psi[:, gamma] = term1 + term2 + term3 + term4 - term5 - return np.sum(psi, axis=0) + return np.sum(psi, axis=0), np.dot(psi.T, rvec) def adp_dipole(self, r, rvec, d): # calculate the dipole contribution diff -pruN 3.24.0-1/ase/calculators/elk.py 3.26.0-1/ase/calculators/elk.py --- 3.24.0-1/ase/calculators/elk.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/elk.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,44 +1,102 @@ -from pathlib import Path +""" +`Elk `_ is an all-electron full-potential linearised +augmented-plane wave (LAPW) code. -from ase.calculators.abc import GetOutputsMixin -from ase.calculators.calculator import FileIOCalculator -from ase.io import write -from ase.io.elk import ElkReader - - -class ELK(FileIOCalculator, GetOutputsMixin): - _legacy_default_command = 'elk > elk.out' - implemented_properties = ['energy', 'forces'] - ignored_changes = {'pbc'} - discard_results_on_any_change = True - - fileio_rules = FileIOCalculator.ruleset( - stdout_name='elk.out') - - def __init__(self, **kwargs): - """Construct ELK calculator. - - The keyword arguments (kwargs) can be one of the ASE standard - keywords: 'xc', 'kpts' and 'smearing' or any of ELK' - native keywords. - """ +.. versionchanged:: 3.26.0 + :class:`ELK` is now a subclass of :class:`GenericFileIOCalculator`. + +.. |config| replace:: ``config.ini`` +.. _config: calculators.html#calculator-configuration + +:class:`ELK` can be configured with |config|_. + +.. code-block:: ini + + [elk] + command = /path/to/elk + sppath = /path/to/species + +If you need to override it for programmatic control of the ``elk`` command, +use :class:`ElkProfile`. + +.. code-block:: python + + from ase.calculators.elk import ELK, ElkProfile + + profile = ElkProfile(command='/path/to/elk') + calc = ELK(profile=profile) - super().__init__(**kwargs) +""" - def write_input(self, atoms, properties=None, system_changes=None): - FileIOCalculator.write_input(self, atoms, properties, system_changes) +import os +import re +import warnings +from pathlib import Path +from typing import Optional - parameters = dict(self.parameters) +from ase.calculators.genericfileio import ( + BaseProfile, + CalculatorTemplate, + GenericFileIOCalculator, + read_stdout, +) +from ase.io.elk import ElkReader, write_elk_in + +COMPATIBILITY_MSG = ( + '`ELK` has been restructured. ' + 'Please use `ELK(profile=ElkProfile(command))` instead.' +) + + +class ElkProfile(BaseProfile): + """Profile for :class:`ELK`.""" + + configvars = {'sppath'} + + def __init__(self, command, sppath: Optional[str] = None, **kwargs) -> None: + super().__init__(command, **kwargs) + self.sppath = sppath + + def get_calculator_command(self, inputfile): + return [] + + def version(self): + output = read_stdout(self._split_command) + match = re.search(r'Elk code version (\S+)', output, re.M) + return match.group(1) + + +class ElkTemplate(CalculatorTemplate): + """Template for :class:`ELK`.""" + + def __init__(self): + super().__init__('elk', ['energy', 'forces']) + self.inputname = 'elk.in' + self.outputname = 'elk.out' + + def write_input( + self, + profile: ElkProfile, + directory, + atoms, + parameters, + properties, + ): + directory = Path(directory) + parameters = dict(parameters) if 'forces' in properties: parameters['tforce'] = True + if 'sppath' not in parameters and profile.sppath: + parameters['sppath'] = profile.sppath + write_elk_in(directory / self.inputname, atoms, parameters=parameters) - directory = Path(self.directory) - write(directory / 'elk.in', atoms, parameters=parameters, - format='elk-in') + def execute(self, directory, profile: ElkProfile) -> None: + profile.run(directory, self.inputname, self.outputname) - def read_results(self): + def read_results(self, directory): from ase.outputs import Properties - reader = ElkReader(self.directory) + + reader = ElkReader(directory) dct = dict(reader.read_everything()) converged = dct.pop('converged') @@ -47,7 +105,50 @@ class ELK(FileIOCalculator, GetOutputsMi # (Filter results thorugh Properties for error detection) props = Properties(dct) - self.results = dict(props) + return dict(props) + + def load_profile(self, cfg, **kwargs): + return ElkProfile.from_config(cfg, self.name, **kwargs) + + +class ELK(GenericFileIOCalculator): + """Elk calculator.""" + + def __init__( + self, + *, + profile=None, + command=GenericFileIOCalculator._deprecated, + label=GenericFileIOCalculator._deprecated, + directory='.', + **kwargs, + ) -> None: + """ + + Parameters + ---------- + **kwargs : dict, optional + ASE standard keywords like ``xc``, ``kpts`` and ``smearing`` or any + Elk-native keywords. + + Examples + -------- + >>> calc = ELK(tasks=0, ngridk=(3, 3, 3)) + + """ + if command is not self._deprecated: + raise RuntimeError(COMPATIBILITY_MSG) - def _outputmixin_get_results(self): - return self.results + if label is not self._deprecated: + msg = 'Ignoring label, please use directory instead' + warnings.warn(msg, FutureWarning) + + if 'ASE_ELK_COMMAND' in os.environ and profile is None: + warnings.warn(COMPATIBILITY_MSG, FutureWarning) + + super().__init__( + template=ElkTemplate(), + profile=profile, + directory=directory, + parameters=kwargs, + ) diff -pruN 3.24.0-1/ase/calculators/emt.py 3.26.0-1/ase/calculators/emt.py --- 3.24.0-1/ase/calculators/emt.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/emt.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Effective medium theory potential.""" from collections import defaultdict from math import log, sqrt diff -pruN 3.24.0-1/ase/calculators/espresso.py 3.26.0-1/ase/calculators/espresso.py --- 3.24.0-1/ase/calculators/espresso.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/espresso.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Quantum ESPRESSO Calculator Run pw.x jobs. diff -pruN 3.24.0-1/ase/calculators/excitation_list.py 3.26.0-1/ase/calculators/excitation_list.py --- 3.24.0-1/ase/calculators/excitation_list.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/excitation_list.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase.units import Bohr, Hartree diff -pruN 3.24.0-1/ase/calculators/exciting/__init__.py 3.26.0-1/ase/calculators/exciting/__init__.py --- 3.24.0-1/ase/calculators/exciting/__init__.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/exciting/__init__.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from .exciting import ExcitingGroundStateCalculator __all__ = ["ExcitingGroundStateCalculator"] diff -pruN 3.24.0-1/ase/calculators/exciting/exciting.py 3.26.0-1/ase/calculators/exciting/exciting.py --- 3.24.0-1/ase/calculators/exciting/exciting.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/exciting/exciting.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ASE Calculator for the ground state exciting DFT code. Exciting calculator class in this file allow for writing exciting input diff -pruN 3.24.0-1/ase/calculators/exciting/runner.py 3.26.0-1/ase/calculators/exciting/runner.py --- 3.24.0-1/ase/calculators/exciting/runner.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/exciting/runner.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Binary runner and results class.""" import os import subprocess diff -pruN 3.24.0-1/ase/calculators/fd.py 3.26.0-1/ase/calculators/fd.py --- 3.24.0-1/ase/calculators/fd.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/fd.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,4 +1,7 @@ +"""Module for `FiniteDifferenceCalculator`.""" + from collections.abc import Iterable +from functools import partial from typing import Optional import numpy as np @@ -20,8 +23,10 @@ class FiniteDifferenceCalculator(BaseCal def __init__( self, calc: BaseCalculator, - eps_disp: float = 1e-6, - eps_strain: float = 1e-6, + eps_disp: Optional[float] = 1e-6, + eps_strain: Optional[float] = 1e-6, + *, + force_consistent: bool = True, ) -> None: """ @@ -29,26 +34,47 @@ class FiniteDifferenceCalculator(BaseCal ---------- calc : :class:`~ase.calculators.calculator.BaseCalculator` ASE Calculator object to be wrapped. - eps_disp : float, default 1e-6 + eps_disp : Optional[float], default 1e-6 Displacement used for computing forces. - eps_strain : float, default 1e-6 + If :py:obj:`None`, analytical forces are computed. + eps_strain : Optional[float], default 1e-6 Strain used for computing stress. + If :py:obj:`None`, analytical stress is computed. + force_consistent : bool, default :py:obj:`True` + If :py:obj:`True`, the energies consistent with the forces are used + for finite-difference calculations. """ super().__init__() self.calc = calc self.eps_disp = eps_disp self.eps_strain = eps_strain + self.force_consistent = force_consistent def calculate(self, atoms: Atoms, properties, system_changes) -> None: atoms = atoms.copy() # copy to not mess up original `atoms` atoms.calc = self.calc - self.results = { - 'energy': atoms.get_potential_energy(), - 'forces': calculate_numerical_forces(atoms, eps=self.eps_disp), - 'stress': calculate_numerical_stress(atoms, eps=self.eps_strain), - } - self.results['free_energy'] = self.results['energy'] + self.results = {} + self.results['energy'] = self.calc.get_potential_energy(atoms) + for key in ['free_energy']: + if key in self.calc.results: + self.results[key] = self.calc.results[key] + if self.eps_disp is None: + self.results['forces'] = self.calc.get_forces(atoms) + else: + self.results['forces'] = calculate_numerical_forces( + atoms, + eps=self.eps_disp, + force_consistent=self.force_consistent, + ) + if self.eps_strain is None: + self.results['stress'] = self.calc.get_stress(atoms) + else: + self.results['stress'] = calculate_numerical_stress( + atoms, + eps=self.eps_strain, + force_consistent=self.force_consistent, + ) def _numeric_force( @@ -56,6 +82,8 @@ def _numeric_force( iatom: int, icart: int, eps: float = 1e-6, + *, + force_consistent: bool = False, ) -> float: """Calculate numerical force on a specific atom along a specific direction. @@ -69,16 +97,19 @@ def _numeric_force( Index of Cartesian component. eps : float, default 1e-6 Displacement. + force_consistent : bool, default :py:obj:`False` + If :py:obj:`True`, the energies consistent with the forces are used for + finite-difference calculations. """ p0 = atoms.get_positions() p = p0.copy() p[iatom, icart] = p0[iatom, icart] + eps atoms.set_positions(p, apply_constraint=False) - eplus = atoms.get_potential_energy() + eplus = atoms.get_potential_energy(force_consistent=force_consistent) p[iatom, icart] = p0[iatom, icart] - eps atoms.set_positions(p, apply_constraint=False) - eminus = atoms.get_potential_energy() + eminus = atoms.get_potential_energy(force_consistent=force_consistent) atoms.set_positions(p0, apply_constraint=False) return (eminus - eplus) / (2 * eps) @@ -88,6 +119,8 @@ def calculate_numerical_forces( eps: float = 1e-6, iatoms: Optional[Iterable[int]] = None, icarts: Optional[Iterable[int]] = None, + *, + force_consistent: bool = False, ) -> np.ndarray: """Calculate forces numerically based on the finite-difference method. @@ -103,6 +136,9 @@ def calculate_numerical_forces( icarts : Optional[Iterable[int]] Indices of Cartesian coordinates for which forces are computed. By default, all three coordinates are considered. + force_consistent : bool, default :py:obj:`False` + If :py:obj:`True`, the energies consistent with the forces are used for + finite-difference calculations. Returns ------- @@ -114,18 +150,17 @@ def calculate_numerical_forces( iatoms = range(len(atoms)) if icarts is None: icarts = [0, 1, 2] - return np.array( - [ - [_numeric_force(atoms, iatom, icart, eps) for icart in icarts] - for iatom in iatoms - ] - ) + f = partial(_numeric_force, eps=eps, force_consistent=force_consistent) + forces = [[f(atoms, iatom, icart) for icart in icarts] for iatom in iatoms] + return np.array(forces) def calculate_numerical_stress( atoms: Atoms, eps: float = 1e-6, voigt: bool = True, + *, + force_consistent: bool = True, ) -> np.ndarray: """Calculate stress numerically based on the finite-difference method. @@ -135,8 +170,11 @@ def calculate_numerical_stress( ASE :class:`~ase.Atoms` object. eps : float, default 1e-6 Strain in the Voigt notation. - voigt : bool, default True - If True, the stress is returned in the Voigt notation. + voigt : bool, default :py:obj:`True` + If :py:obj:`True`, the stress is returned in the Voigt notation. + force_consistent : bool, default :py:obj:`True` + If :py:obj:`True`, the energies consistent with the forces are used for + finite-difference calculations. Returns ------- @@ -152,11 +190,11 @@ def calculate_numerical_stress( x = np.eye(3) x[i, i] = 1.0 + eps atoms.set_cell(cell @ x, scale_atoms=True) - eplus = atoms.get_potential_energy(force_consistent=True) + eplus = atoms.get_potential_energy(force_consistent=force_consistent) x[i, i] = 1.0 - eps atoms.set_cell(cell @ x, scale_atoms=True) - eminus = atoms.get_potential_energy(force_consistent=True) + eminus = atoms.get_potential_energy(force_consistent=force_consistent) stress[i, i] = (eplus - eminus) / (2 * eps * volume) x[i, i] = 1.0 @@ -164,11 +202,11 @@ def calculate_numerical_stress( j = i - 2 x[i, j] = x[j, i] = +0.5 * eps atoms.set_cell(cell @ x, scale_atoms=True) - eplus = atoms.get_potential_energy(force_consistent=True) + eplus = atoms.get_potential_energy(force_consistent=force_consistent) x[i, j] = x[j, i] = -0.5 * eps atoms.set_cell(cell @ x, scale_atoms=True) - eminus = atoms.get_potential_energy(force_consistent=True) + eminus = atoms.get_potential_energy(force_consistent=force_consistent) stress[i, j] = stress[j, i] = (eplus - eminus) / (2 * eps * volume) diff -pruN 3.24.0-1/ase/calculators/ff.py 3.26.0-1/ase/calculators/ff.py --- 3.24.0-1/ase/calculators/ff.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/ff.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase.calculators.calculator import Calculator diff -pruN 3.24.0-1/ase/calculators/fleur.py 3.26.0-1/ase/calculators/fleur.py --- 3.24.0-1/ase/calculators/fleur.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/fleur.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + def FLEUR(*args, **kwargs): raise RuntimeError( 'Please refer to the python package ase-fleur for ' diff -pruN 3.24.0-1/ase/calculators/gamess_us.py 3.26.0-1/ase/calculators/gamess_us.py --- 3.24.0-1/ase/calculators/gamess_us.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/gamess_us.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import warnings from ase.calculators.calculator import FileIOCalculator diff -pruN 3.24.0-1/ase/calculators/gaussian.py 3.26.0-1/ase/calculators/gaussian.py --- 3.24.0-1/ase/calculators/gaussian.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/gaussian.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import copy import os from collections.abc import Iterable diff -pruN 3.24.0-1/ase/calculators/genericfileio.py 3.26.0-1/ase/calculators/genericfileio.py --- 3.24.0-1/ase/calculators/genericfileio.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/genericfileio.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import shlex from abc import ABC, abstractmethod from contextlib import ExitStack @@ -14,7 +16,7 @@ from ase.calculators.calculator import ( from ase.config import cfg as _cfg link_calculator_docs = ( - "https://wiki.fysik.dtu.dk/ase/ase/calculators/" + "https://ase-lib.org/ase/calculators/" "calculators.html#calculator-configuration" ) diff -pruN 3.24.0-1/ase/calculators/gromacs.py 3.26.0-1/ase/calculators/gromacs.py --- 3.24.0-1/ase/calculators/gromacs.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/gromacs.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """This module defines an ASE interface to GROMACS. http://www.gromacs.org/ diff -pruN 3.24.0-1/ase/calculators/gulp.py 3.26.0-1/ase/calculators/gulp.py --- 3.24.0-1/ase/calculators/gulp.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/gulp.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """This module defines an ASE interface to GULP. Written by: diff -pruN 3.24.0-1/ase/calculators/h2morse.py 3.26.0-1/ase/calculators/h2morse.py --- 3.24.0-1/ase/calculators/h2morse.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/h2morse.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from itertools import count import numpy as np diff -pruN 3.24.0-1/ase/calculators/harmonic.py 3.26.0-1/ase/calculators/harmonic.py --- 3.24.0-1/ase/calculators/harmonic.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/harmonic.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from numpy.linalg import eigh, norm, pinv from scipy.linalg import lstsq # performs better than numpy.linalg.lstsq diff -pruN 3.24.0-1/ase/calculators/idealgas.py 3.26.0-1/ase/calculators/idealgas.py --- 3.24.0-1/ase/calculators/idealgas.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/idealgas.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Ideal gas calculator - the potential energy is always zero.""" import numpy as np diff -pruN 3.24.0-1/ase/calculators/kim/__init__.py 3.26.0-1/ase/calculators/kim/__init__.py --- 3.24.0-1/ase/calculators/kim/__init__.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/kim/__init__.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from .kim import KIM, get_model_supported_species from .kimpy_wrappers import kimpy diff -pruN 3.24.0-1/ase/calculators/kim/calculators.py 3.26.0-1/ase/calculators/kim/calculators.py --- 3.24.0-1/ase/calculators/kim/calculators.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/kim/calculators.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import os import re diff -pruN 3.24.0-1/ase/calculators/kim/exceptions.py 3.26.0-1/ase/calculators/kim/exceptions.py --- 3.24.0-1/ase/calculators/kim/exceptions.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/kim/exceptions.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ Exceptions for the general error types that can occur either while setting up the calculator, which requires constructing KIM API C++ diff -pruN 3.24.0-1/ase/calculators/kim/kim.py 3.26.0-1/ase/calculators/kim/kim.py --- 3.24.0-1/ase/calculators/kim/kim.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/kim/kim.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ Knowledgebase of Interatomic Models (KIM) Calculator for ASE written by: @@ -86,7 +88,7 @@ def KIM(model_name, simulator=None, opti model to run with multiple concurrent threads. (Default: False) See the ASE LAMMPS calculators doc page - (https://wiki.fysik.dtu.dk/ase/ase/calculators/lammps.html) for + (https://ase-lib.org/ase/calculators/lammps.html) for available options for the lammpslib and lammpsrun calculators. debug : bool, optional diff -pruN 3.24.0-1/ase/calculators/kim/kimmodel.py 3.26.0-1/ase/calculators/kim/kimmodel.py --- 3.24.0-1/ase/calculators/kim/kimmodel.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/kim/kimmodel.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ ASE Calculator for interatomic models compatible with the Knowledgebase of Interatomic Models (KIM) application programming interface (API). diff -pruN 3.24.0-1/ase/calculators/kim/kimpy_wrappers.py 3.26.0-1/ase/calculators/kim/kimpy_wrappers.py --- 3.24.0-1/ase/calculators/kim/kimpy_wrappers.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/kim/kimpy_wrappers.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ Wrappers that provide a minimal interface to kimpy methods and objects diff -pruN 3.24.0-1/ase/calculators/kim/neighborlist.py 3.26.0-1/ase/calculators/kim/neighborlist.py --- 3.24.0-1/ase/calculators/kim/neighborlist.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/kim/neighborlist.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from collections import defaultdict import numpy as np diff -pruN 3.24.0-1/ase/calculators/lammps/__init__.py 3.26.0-1/ase/calculators/lammps/__init__.py --- 3.24.0-1/ase/calculators/lammps/__init__.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/lammps/__init__.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Collection of helper function for LAMMPS* calculator """ from .coordinatetransform import Prism diff -pruN 3.24.0-1/ase/calculators/lammps/coordinatetransform.py 3.26.0-1/ase/calculators/lammps/coordinatetransform.py --- 3.24.0-1/ase/calculators/lammps/coordinatetransform.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/lammps/coordinatetransform.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,6 +1,8 @@ +# fmt: off + """Prism""" import warnings -from typing import Sequence +from typing import Sequence, Union import numpy as np @@ -38,7 +40,10 @@ def calc_rotated_cell(cell: np.ndarray) return np.array(((ax, 0.0, 0.0), (bx, by, 0.0), (cx, cy, cz))) -def calc_reduced_cell(cell: np.ndarray, pbc: Sequence[bool]) -> np.ndarray: +def calc_reduced_cell( + cell: np.ndarray, + pbc: Union[np.ndarray, Sequence[bool]], +) -> np.ndarray: """Calculate LAMMPS cell with short lattice basis vectors The lengths of the second and the third lattice basis vectors, b and c, are @@ -137,7 +142,7 @@ class Prism: def __init__( self, cell: np.ndarray, - pbc: bool = True, + pbc: Union[bool, np.ndarray] = True, reduce_cell: bool = False, tolerance: float = 1.0e-8, ): diff -pruN 3.24.0-1/ase/calculators/lammps/inputwriter.py 3.26.0-1/ase/calculators/lammps/inputwriter.py --- 3.24.0-1/ase/calculators/lammps/inputwriter.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/lammps/inputwriter.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ Stream input commands to lammps to perform desired simulations """ diff -pruN 3.24.0-1/ase/calculators/lammps/unitconvert.py 3.26.0-1/ase/calculators/lammps/unitconvert.py --- 3.24.0-1/ase/calculators/lammps/unitconvert.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/lammps/unitconvert.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """LAMMPS has the options to use several internal units (which can be different from the ones used in ase). Mapping is therefore necessary. diff -pruN 3.24.0-1/ase/calculators/lammps/unitconvert_constants.py 3.26.0-1/ase/calculators/lammps/unitconvert_constants.py --- 3.24.0-1/ase/calculators/lammps/unitconvert_constants.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/lammps/unitconvert_constants.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # The following definitions are all given in SI and are excerpted from the # kim_units.cpp file created by Prof. Ellad B. Tadmor (UMinn) distributed with # LAMMPS. Note that these values do not correspond to any official CODATA set diff -pruN 3.24.0-1/ase/calculators/lammpslib.py 3.26.0-1/ase/calculators/lammpslib.py --- 3.24.0-1/ase/calculators/lammpslib.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/lammpslib.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ASE LAMMPS Calculator Library Version""" @@ -495,10 +497,13 @@ xz and yz are the tilt of the lattice ve ) self.results['free_energy'] = self.results['energy'] - ids = self.lmp.numpy.extract_atom("id") - # if ids doesn't match atoms then data is MPI distributed, which - # we can't handle - assert len(ids) == len(atoms) + # check for MPI active as per https://matsci.org/t/lammps-ids-in-python/60509/5 + world_size = self.lmp.extract_setting('world_size') + if world_size != 1: + raise RuntimeError('Unsupported MPI active as indicated by ' + f'world_size == {world_size} != 1') + # select just n_local which we assume is equal to len(atoms) + ids = self.lmp.numpy.extract_atom("id")[0:len(atoms)] self.results["energies"] = convert( self.lmp.numpy.extract_compute('pe_peratom', self.LMP_STYLE_ATOM, diff -pruN 3.24.0-1/ase/calculators/lammpsrun.py 3.26.0-1/ase/calculators/lammpsrun.py --- 3.24.0-1/ase/calculators/lammpsrun.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/lammpsrun.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ASE calculator for the LAMMPS classical MD code""" # lammps.py (2011/03/29) # diff -pruN 3.24.0-1/ase/calculators/lj.py 3.26.0-1/ase/calculators/lj.py --- 3.24.0-1/ase/calculators/lj.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/lj.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase.calculators.calculator import Calculator, all_changes diff -pruN 3.24.0-1/ase/calculators/loggingcalc.py 3.26.0-1/ase/calculators/loggingcalc.py --- 3.24.0-1/ase/calculators/loggingcalc.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/loggingcalc.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ Provides LoggingCalculator class to wrap a Calculator and record number of enery and force calls diff -pruN 3.24.0-1/ase/calculators/mixing.py 3.26.0-1/ase/calculators/mixing.py --- 3.24.0-1/ase/calculators/mixing.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/mixing.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from ase.calculators.calculator import ( BaseCalculator, CalculatorSetupError, diff -pruN 3.24.0-1/ase/calculators/mopac.py 3.26.0-1/ase/calculators/mopac.py --- 3.24.0-1/ase/calculators/mopac.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/mopac.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """This module defines an ASE interface to MOPAC. Set $ASE_MOPAC_COMMAND to something like:: diff -pruN 3.24.0-1/ase/calculators/morse.py 3.26.0-1/ase/calculators/morse.py --- 3.24.0-1/ase/calculators/morse.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/morse.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,7 +1,9 @@ +# fmt: off + import numpy as np from ase.calculators.calculator import Calculator, all_changes -from ase.neighborlist import neighbor_list +from ase.neighborlist import neighbor_list as ase_neighbor_list from ase.stress import full_3x3_to_voigt_6_stress @@ -58,7 +60,7 @@ class MorsePotential(Calculator): 'rcut2': 2.7} nolabel = True - def __init__(self, **kwargs): + def __init__(self, neighbor_list=ase_neighbor_list, **kwargs): r""" The pairwise energy between atoms *i* and *j* is given by @@ -88,12 +90,16 @@ class MorsePotential(Calculator): Distance starting a smooth cutoff normalized by ``r0``. rcut2 : float, default 2.7 Distance ending a smooth cutoff normalized by ``r0``. + neighbor_list : callable, optional + neighbor_list function compatible with + ase.neighborlist.neighbor_list Notes ----- The default values are chosen to be similar as Lennard-Jones. """ + self.neighbor_list = neighbor_list Calculator.__init__(self, **kwargs) def calculate(self, atoms=None, properties=['energy'], @@ -109,7 +115,7 @@ class MorsePotential(Calculator): forces = np.zeros((number_of_atoms, 3)) - i, _j, d, D = neighbor_list('ijdD', atoms, rcut2) + i, _j, d, D = self.neighbor_list('ijdD', atoms, rcut2) dhat = (D / d[:, None]).T expf = np.exp(rho0 * (1.0 - d / r0)) diff -pruN 3.24.0-1/ase/calculators/names.py 3.26.0-1/ase/calculators/names.py --- 3.24.0-1/ase/calculators/names.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/names.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import importlib from collections.abc import Mapping @@ -8,11 +10,11 @@ names = ['abinit', 'ace', 'aims', 'amber 'gaussian', 'gpaw', 'gromacs', 'gulp', 'hotbit', 'kim', 'lammpslib', 'lammpsrun', 'lj', 'mopac', 'morse', 'nwchem', 'octopus', 'onetep', 'openmx', 'orca', - 'plumed', 'psi4', 'qchem', 'siesta', + 'plumed', 'psi4', 'qchem', 'siesta', 'tersoff', 'tip3p', 'tip4p', 'turbomole', 'vasp'] -builtin = {'eam', 'emt', 'ff', 'lj', 'morse', 'tip3p', 'tip4p'} +builtin = {'eam', 'emt', 'ff', 'lj', 'morse', 'tersoff', 'tip3p', 'tip4p'} class Templates(Mapping): diff -pruN 3.24.0-1/ase/calculators/nwchem.py 3.26.0-1/ase/calculators/nwchem.py --- 3.24.0-1/ase/calculators/nwchem.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/nwchem.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """This module defines an ASE interface to NWchem https://nwchemgit.github.io diff -pruN 3.24.0-1/ase/calculators/octopus.py 3.26.0-1/ase/calculators/octopus.py --- 3.24.0-1/ase/calculators/octopus.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/octopus.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ASE-interface to Octopus. Ask Hjorth Larsen diff -pruN 3.24.0-1/ase/calculators/onetep.py 3.26.0-1/ase/calculators/onetep.py --- 3.24.0-1/ase/calculators/onetep.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/onetep.py 2025-08-12 11:26:23.000000000 +0000 @@ -29,8 +29,7 @@ class OnetepProfile(BaseProfile): command: str The onetep command (not including inputfile). **kwargs: dict - Additional kwargs are passed to the BaseProfile - class. + Additional kwargs are passed to the BaseProfile class. """ super().__init__(command, **kwargs) self.pseudo_path = pseudo_path @@ -56,15 +55,22 @@ class OnetepTemplate(CalculatorTemplate) 'energy', 'free_energy', 'forces', - 'stress']) + 'stress', + ], + ) self.inputname = f'{self._label}.dat' self.outputname = f'{self._label}.out' self.errorname = f'{self._label}.err' self.append = append def execute(self, directory, profile): - profile.run(directory, self.inputname, self.outputname, - self.errorname, append=self.append) + profile.run( + directory, + self.inputname, + self.outputname, + self.errorname, + append=self.append, + ) def read_results(self, directory): output_path = directory / self.outputname @@ -80,8 +86,13 @@ class OnetepTemplate(CalculatorTemplate) keywords.setdefault('pseudo_path', profile.pseudo_path) parameters['keywords'] = keywords - write(input_path, atoms, format='onetep-in', - properties=properties, **parameters) + write( + input_path, + atoms, + format='onetep-in', + properties=properties, + **parameters, + ) def load_profile(self, cfg, **kwargs): return OnetepProfile.from_config(cfg, self.name, **kwargs) @@ -90,8 +101,6 @@ class OnetepTemplate(CalculatorTemplate) class Onetep(GenericFileIOCalculator): """ Class for the ONETEP calculator, uses ase/io/onetep.py. - Need the env variable "ASE_ONETEP_COMMAND" defined to - properly work. All other options are passed in kwargs. Parameters ---------- @@ -147,18 +156,13 @@ class Onetep(GenericFileIOCalculator): are valid ONETEP keywords. """ - def __init__( - self, - *, - profile=None, - directory='.', - **kwargs): - + def __init__(self, *, profile=None, directory='.', **kwargs): self.keywords = kwargs.get('keywords', None) - self.template = OnetepTemplate( - append=kwargs.pop('append', False) - ) + self.template = OnetepTemplate(append=kwargs.pop('append', False)) - super().__init__(profile=profile, template=self.template, - directory=directory, - parameters=kwargs) + super().__init__( + profile=profile, + template=self.template, + directory=directory, + parameters=kwargs, + ) diff -pruN 3.24.0-1/ase/calculators/openmx/default_settings.py 3.26.0-1/ase/calculators/openmx/default_settings.py --- 3.24.0-1/ase/calculators/openmx/default_settings.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/openmx/default_settings.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ The ASE Calculator for OpenMX : Python interface to the software package for nano-scale material simulations based on density diff -pruN 3.24.0-1/ase/calculators/openmx/dos.py 3.26.0-1/ase/calculators/openmx/dos.py --- 3.24.0-1/ase/calculators/openmx/dos.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/openmx/dos.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ The ASE Calculator for OpenMX : Python interface to the software package for nano-scale material simulations based on density diff -pruN 3.24.0-1/ase/calculators/openmx/openmx.py 3.26.0-1/ase/calculators/openmx/openmx.py --- 3.24.0-1/ase/calculators/openmx/openmx.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/openmx/openmx.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ The ASE Calculator for OpenMX A Python interface to the software package for nano-scale diff -pruN 3.24.0-1/ase/calculators/openmx/parameters.py 3.26.0-1/ase/calculators/openmx/parameters.py --- 3.24.0-1/ase/calculators/openmx/parameters.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/openmx/parameters.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ The ASE Calculator for OpenMX : Python interface to the software package for nano-scale material simulations based on density diff -pruN 3.24.0-1/ase/calculators/openmx/reader.py 3.26.0-1/ase/calculators/openmx/reader.py --- 3.24.0-1/ase/calculators/openmx/reader.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/openmx/reader.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # flake8: noqa """ The ASE Calculator for OpenMX : Python interface diff -pruN 3.24.0-1/ase/calculators/openmx/writer.py 3.26.0-1/ase/calculators/openmx/writer.py --- 3.24.0-1/ase/calculators/openmx/writer.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/openmx/writer.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ The ASE Calculator for OpenMX : Python interface to the software package for nano-scale material simulations based on density diff -pruN 3.24.0-1/ase/calculators/orca.py 3.26.0-1/ase/calculators/orca.py --- 3.24.0-1/ase/calculators/orca.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/orca.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import re import ase.io.orca as io diff -pruN 3.24.0-1/ase/calculators/plumed.py 3.26.0-1/ase/calculators/plumed.py --- 3.24.0-1/ase/calculators/plumed.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/plumed.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from os.path import exists import numpy as np diff -pruN 3.24.0-1/ase/calculators/psi4.py 3.26.0-1/ase/calculators/psi4.py --- 3.24.0-1/ase/calculators/psi4.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/psi4.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ authors: Ben Comer (Georgia Tech), Xiangyun (Ray) Lei (Georgia Tech) diff -pruN 3.24.0-1/ase/calculators/qchem.py 3.26.0-1/ase/calculators/qchem.py --- 3.24.0-1/ase/calculators/qchem.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/qchem.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np import ase.units diff -pruN 3.24.0-1/ase/calculators/qmmm.py 3.26.0-1/ase/calculators/qmmm.py --- 3.24.0-1/ase/calculators/qmmm.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/qmmm.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from typing import Sequence import numpy as np diff -pruN 3.24.0-1/ase/calculators/siesta/import_ion_xml.py 3.26.0-1/ase/calculators/siesta/import_ion_xml.py --- 3.24.0-1/ase/calculators/siesta/import_ion_xml.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/siesta/import_ion_xml.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import re from xml.dom import minidom diff -pruN 3.24.0-1/ase/calculators/siesta/parameters.py 3.26.0-1/ase/calculators/siesta/parameters.py --- 3.24.0-1/ase/calculators/siesta/parameters.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/siesta/parameters.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from ase.calculators.calculator import Parameters """ diff -pruN 3.24.0-1/ase/calculators/siesta/siesta.py 3.26.0-1/ase/calculators/siesta/siesta.py --- 3.24.0-1/ase/calculators/siesta/siesta.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/siesta/siesta.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ This module defines the ASE interface to SIESTA. diff -pruN 3.24.0-1/ase/calculators/siesta/siesta_lrtddft.py 3.26.0-1/ase/calculators/siesta/siesta_lrtddft.py --- 3.24.0-1/ase/calculators/siesta/siesta_lrtddft.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/siesta/siesta_lrtddft.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np import ase.units as un diff -pruN 3.24.0-1/ase/calculators/singlepoint.py 3.26.0-1/ase/calculators/singlepoint.py --- 3.24.0-1/ase/calculators/singlepoint.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/singlepoint.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,7 @@ +# fmt: off + +from functools import cached_property + import numpy as np from ase.calculators.calculator import ( @@ -7,7 +11,6 @@ from ase.calculators.calculator import ( all_properties, ) from ase.outputs import Properties -from ase.utils import lazyproperty class SinglePointCalculator(Calculator): @@ -227,7 +230,7 @@ def propertygetter(func): if value is None: raise PropertyNotPresent(func.__name__) return value - return lazyproperty(getter) + return cached_property(getter) class OutputPropertyWrapper: diff -pruN 3.24.0-1/ase/calculators/socketio.py 3.26.0-1/ase/calculators/socketio.py --- 3.24.0-1/ase/calculators/socketio.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/socketio.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,6 +1,8 @@ +# fmt: off + import os import socket -from contextlib import contextmanager +from contextlib import ExitStack, contextmanager from subprocess import PIPE, Popen import numpy as np @@ -245,6 +247,13 @@ class FileIOSocketClientLauncher: argv = template.socketio_argv( profile, unixsocket=None, port=port ) + + if hasattr(self.calc.template, "outputname"): + with ExitStack() as stack: + output_path = self.calc.template.outputname + fd_out = stack.enter_context(open(output_path, "w")) + return Popen(argv, cwd=cwd, env=os.environ, stdout=fd_out) + return Popen(argv, cwd=cwd, env=os.environ) else: # Old FileIOCalculator: diff -pruN 3.24.0-1/ase/calculators/subprocesscalculator.py 3.26.0-1/ase/calculators/subprocesscalculator.py --- 3.24.0-1/ase/calculators/subprocesscalculator.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/subprocesscalculator.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import os import pickle import sys diff -pruN 3.24.0-1/ase/calculators/tersoff.py 3.26.0-1/ase/calculators/tersoff.py --- 3.24.0-1/ase/calculators/tersoff.py 1970-01-01 00:00:00.000000000 +0000 +++ 3.26.0-1/ase/calculators/tersoff.py 2025-08-12 11:26:23.000000000 +0000 @@ -0,0 +1,576 @@ +from dataclasses import dataclass +from pathlib import Path +from typing import Dict, List, Tuple, Type, Union + +import numpy as np + +from ase.calculators.calculator import Calculator, all_changes +from ase.neighborlist import NeighborList +from ase.stress import full_3x3_to_voigt_6_stress + +__author__ = 'Stefan Bringuier ' +__description__ = 'LAMMPS-style native Tersoff potential for ASE' + +# Maximum/minimum exponents for numerical stability +# in bond order calculation +_MAX_EXP_ARG = 69.0776e0 +_MIN_EXP_ARG = -69.0776e0 + + +@dataclass +class TersoffParameters: + """Parameters for 3 element Tersoff potential interaction. + + Can be instantiated with either positional or keyword arguments: + TersoffParameters(1.0, 2.0, ...) or + TersoffParameters(m=1.0, gamma=2.0, ...) + """ + + m: float + gamma: float + lambda3: float + c: float + d: float + h: float + n: float + beta: float + lambda2: float + B: float + R: float + D: float + lambda1: float + A: float + + @classmethod + def from_list(cls, params: List[float]) -> 'TersoffParameters': + """Create TersoffParameters from a list of 14 parameter values.""" + if len(params) != 14: + raise ValueError(f'Expected 14 parameters, got {len(params)}') + return cls(*map(float, params)) + + +class Tersoff(Calculator): + """ASE Calculator for Tersoff interatomic potential. + + .. versionadded:: 3.25.0 + """ + + implemented_properties = [ + 'free_energy', + 'energy', + 'energies', + 'forces', + 'stress', + ] + + def __init__( + self, + parameters: Dict[Tuple[str, str, str], TersoffParameters], + skin: float = 0.3, + **kwargs, + ) -> None: + """ + Parameters + ---------- + parameters : dict + Mapping element combinations to TersoffParameters objects:: + + { + ('A', 'B', 'C'): TersoffParameters( + m, gamma, lambda3, c, d, h, n, + beta, lambda2, B, R, D, lambda1, A), + ... + } + + where ('A', 'B', 'C') are the elements involved in the interaction. + skin : float, default 0.3 + The skin distance for neighbor list calculations. + **kwargs : dict + Additional parameters to be passed to + :class:`~ase.calculators.Calculator`. + + """ + Calculator.__init__(self, **kwargs) + self.cutoff_skin = skin + self.parameters = parameters + + @classmethod + def from_lammps( + cls: Type['Tersoff'], + potential_file: Union[str, Path], + skin: float = 0.3, + **kwargs, + ) -> 'Tersoff': + """Make :class:`Tersoff` from a LAMMPS-style Tersoff potential file. + + Parameters + ---------- + potential_file : str or Path + The path to a LAMMPS-style Tersoff potential file. + skin : float, default 0.3 + The skin distance for neighbor list calculations. + **kwargs : dict + Additional parameters to be passed to the + ASE Calculator constructor. + + Returns + ------- + :class:`Tersoff` + Initialized Tersoff calculator with parameters from the file. + + """ + parameters = cls.read_lammps_format(potential_file) + return cls(parameters=parameters, skin=skin, **kwargs) + + @staticmethod + def read_lammps_format( + potential_file: Union[str, Path], + ) -> Dict[Tuple[str, str, str], TersoffParameters]: + """Read the Tersoff potential parameters from a LAMMPS-style file. + + Parameters + ---------- + potential_file : str or Path + Path to the LAMMPS-style Tersoff potential file + + Returns + ------- + dict + Dictionary mapping element combinations to TersoffParameters objects + + """ + block_size = 17 + with Path(potential_file).open('r', encoding='utf-8') as fd: + content = ( + ''.join( + [line for line in fd if not line.strip().startswith('#')] + ) + .replace('\n', ' ') + .split() + ) + + if len(content) % block_size != 0: + raise ValueError( + 'The potential file does not have the correct LAMMPS format.' + ) + + parameters: Dict[Tuple[str, str, str], TersoffParameters] = {} + for i in range(0, len(content), block_size): + block = content[i : i + block_size] + e1, e2, e3 = block[0], block[1], block[2] + current_elements = (e1, e2, e3) + params = map(float, block[3:]) + parameters[current_elements] = TersoffParameters(*params) + + return parameters + + def set_parameters( + self, + key: Tuple[str, str, str], + params: TersoffParameters = None, + **kwargs, + ) -> None: + """Update parameters for a specific element combination. + + Parameters + ---------- + key: Tuple[str, str, str] + The element combination key of the parameters to be updated + params: TersoffParameters, optional + A TersoffParameters instance to completely replace the parameters + **kwargs: + Individual parameter values to update, e.g. R=2.9 + + """ + if key not in self.parameters: + raise KeyError(f"Key '{key}' not found in parameters.") + + if params is not None: + if kwargs: + raise ValueError('Cannot provide both params and kwargs.') + self.parameters[key] = params + else: + for name, value in kwargs.items(): + if not hasattr(self.parameters[key], name): + raise ValueError(f'Invalid parameter name: {name}') + setattr(self.parameters[key], name, value) + + def _update_nl(self, atoms) -> None: + """Update the neighbor list with the parameter R+D cutoffs. + + Parameters + ---------- + atoms: ase.Atoms + The atoms to calculate the neighbor list for. + + Notes + ----- + The cutoffs are determined by the parameters of the Tersoff potential. + Each atom's cutoff is based on the R+D values from the parameter set + where that atom's element appears first in the key tuple. + + """ + # Get cutoff for each atom based on its element type + cutoffs = [] + + for symbol in atoms.symbols: + # Find first parameter set, element is the first slot + param_key = next( + key for key in self.parameters.keys() if key[0] == symbol + ) + params = self.parameters[param_key] + cutoffs.append(params.R + params.D) + + self.nl = NeighborList( + cutoffs, + skin=self.cutoff_skin, + self_interaction=False, + bothways=True, + ) + + self.nl.update(atoms) + + def calculate( + self, + atoms=None, + properties=None, + system_changes=all_changes, + ) -> None: + """Calculate energy, forces, and stress. + + Notes + ----- + The force and stress are calculated regardless if they are + requested, despite some additional overhead cost, + therefore they are always stored in the results dict. + + """ + Calculator.calculate(self, atoms, properties, system_changes) + + # Rebuild neighbor list when any relevant system changes occur + checks = {'positions', 'numbers', 'cell', 'pbc'} + if any(change in checks for change in system_changes) or not hasattr( + self, 'nl' + ): + self._update_nl(atoms) + + self.results = {} + energies = np.zeros(len(atoms)) + forces = np.zeros((len(atoms), 3)) + virial = np.zeros((3, 3)) + + # Duplicates atoms.get_distances() functionality, but uses + # neighbor list's pre-computed offsets for efficiency in a + # tight force-calculation loop rather than recompute MIC + for i in range(len(atoms)): + self._calc_atom_contribution(i, energies, forces, virial) + + self.results['energies'] = energies + self.results['energy'] = self.results['free_energy'] = energies.sum() + self.results['forces'] = forces + # Virial to stress (i.e., eV/A^3) + if self.atoms.cell.rank == 3: + stress = virial / self.atoms.get_volume() + self.results['stress'] = full_3x3_to_voigt_6_stress(stress) + + def _calc_atom_contribution( + self, + idx_i: int, + energies: np.ndarray, + forces: np.ndarray, + virial: np.ndarray, + ) -> None: + """Calculate the contributions of a single atom to the properties. + + This function calculates the energy, force, and stress on atom i + by looking at i-j pair interactions and the modification made by + the bond order term bij with includes 3-body interaction i-j-k. + + Parameters + ---------- + idx_i: int + Index of atom i + energies: array_like + Site energies to be updated. + forces: array_like + Forces to be updated. + virial: array_like + Virial tensor to be updated. + + """ + indices, offsets = self.nl.get_neighbors(idx_i) + vectors = self.atoms.positions[indices] + vectors += offsets @ self.atoms.cell + vectors -= self.atoms.positions[idx_i] + distances = np.sqrt(np.add.reduce(vectors**2, axis=1)) + + type_i = self.atoms.symbols[idx_i] + for j, (idx_j, abs_rij, rij) in enumerate( + zip(indices, distances, vectors) + ): + type_j = self.atoms.symbols[idx_j] + key = (type_i, type_j, type_j) + params = self.parameters[key] + + rij_hat = rij / abs_rij + + fc = self._calc_fc(abs_rij, params.R, params.D) + if fc == 0.0: + continue + + zeta = self._calc_zeta(type_i, j, indices, distances, vectors) + bij = self._calc_bij(zeta, params.beta, params.n) + bij_d = self._calc_bij_d(zeta, params.beta, params.n) + + repulsive = params.A * np.exp(-params.lambda1 * abs_rij) + attractive = -params.B * np.exp(-params.lambda2 * abs_rij) + + # distribute the pair energy evenly to be consistent with LAMMPS + energies[idx_i] += 0.25 * fc * (repulsive + bij * attractive) + energies[idx_j] += 0.25 * fc * (repulsive + bij * attractive) + + dfc = self._calc_fc_d(abs_rij, params.R, params.D) + rep_deriv = -params.lambda1 * repulsive + att_deriv = -params.lambda2 * attractive + + tmp = dfc * (repulsive + bij * attractive) + tmp += fc * (rep_deriv + bij * att_deriv) + + # derivative with respect to the position of atom j + grad = 0.5 * tmp * rij_hat + + forces[idx_i] += grad + forces[idx_j] -= grad + + virial += np.outer(grad, rij) + + for k, idx_k in enumerate(indices): + if k == j: + continue + + type_k = self.atoms.symbols[idx_k] + key = (type_i, type_j, type_k) + params = self.parameters[key] + + if distances[k] > params.R + params.D: + continue + + rik = vectors[k] + + dztdri, dztdrj, dztdrk = self._calc_zeta_d(rij, rik, params) + + gradi = 0.5 * fc * bij_d * dztdri * attractive + gradj = 0.5 * fc * bij_d * dztdrj * attractive + gradk = 0.5 * fc * bij_d * dztdrk * attractive + + forces[idx_i] -= gradi + forces[idx_j] -= gradj + forces[idx_k] -= gradk + + virial += np.outer(gradj, rij) + virial += np.outer(gradk, rik) + + def _calc_bij(self, zeta: float, beta: float, n: float) -> float: + """Calculate the bond order ``bij`` between atoms ``i`` and ``j``.""" + tmp = beta * zeta + return (1.0 + tmp**n) ** (-1.0 / (2.0 * n)) + + def _calc_bij_d(self, zeta: float, beta: float, n: float) -> float: + """Calculate the derivative of ``bij`` with respect to ``zeta``.""" + tmp = beta * zeta + return ( + -0.5 + * (1.0 + tmp**n) ** (-1.0 - (1.0 / (2.0 * n))) + * (beta * tmp ** (n - 1.0)) + ) + + def _calc_zeta( + self, + type_i: str, + j: int, + neighbors: np.ndarray, + distances: np.ndarray, + vectors: np.ndarray, + ) -> float: + """Calculate ``zeta_ij``.""" + idx_j = neighbors[j] + type_j = self.atoms.symbols[idx_j] + abs_rij = distances[j] + + zeta = 0.0 + + for k, idx_k in enumerate(neighbors): + if k == j: + continue + + type_k = self.atoms.symbols[idx_k] + key = (type_i, type_j, type_k) + params = self.parameters[key] + + abs_rik = distances[k] + if abs_rik > params.R + params.D: + continue + + costheta = np.dot(vectors[j], vectors[k]) / (abs_rij * abs_rik) + fc_ik = self._calc_fc(abs_rik, params.R, params.D) + + g_theta = self._calc_gijk(costheta, params) + + # Calculate the exponential for the bond order zeta term + # This is the term that modifies the bond order based + # on the distance between atoms i-j and i-k. Tresholds are + # used to prevent overflow/underflow. + arg = (params.lambda3 * (abs_rij - abs_rik)) ** params.m + if arg > _MAX_EXP_ARG: + ex_delr = 1.0e30 + elif arg < _MIN_EXP_ARG: + ex_delr = 0.0 + else: + ex_delr = np.exp(arg) + + zeta += fc_ik * g_theta * ex_delr + + return zeta + + def _calc_gijk(self, costheta: float, params: TersoffParameters) -> float: + r"""Calculate the angular function ``g`` for the Tersoff potential. + + .. math:: + g(\theta) = \gamma \left( 1 + \frac{c^2}{d^2} + - \frac{c^2}{d^2 + (h - \cos \theta)^2} \right) + + where :math:`\theta` is the angle between the bond vector + and the vector of atom i and its neighbors j-k. + """ + c2 = params.c * params.c + d2 = params.d * params.d + hcth = params.h - costheta + return params.gamma * (1.0 + c2 / d2 - c2 / (d2 + hcth**2)) + + def _calc_gijk_d(self, costheta: float, params: TersoffParameters) -> float: + """Calculate the derivative of ``g`` with respect to ``costheta``.""" + c2 = params.c * params.c + d2 = params.d * params.d + hcth = params.h - costheta + numerator = -2.0 * params.gamma * c2 * hcth + denominator = (d2 + hcth**2) ** 2 + return numerator / denominator + + def _calc_fc(self, r: np.floating, R: float, D: float) -> float: + """Calculate the cutoff function.""" + if r > R + D: + return 0.0 + if r < R - D: + return 1.0 + return 0.5 * (1.0 - np.sin(np.pi * (r - R) / (2.0 * D))) + + def _calc_fc_d(self, r: np.floating, R: float, D: float) -> float: + """Calculate cutoff function derivative with respect to ``r``.""" + if r > R + D or r < R - D: + return 0.0 + return -0.25 * np.pi / D * np.cos(np.pi * (r - R) / (2.0 * D)) + + def _calc_zeta_d( + self, + rij: np.ndarray, + rik: np.ndarray, + params: TersoffParameters, + ) -> tuple[np.ndarray, np.ndarray, np.ndarray]: + """Calculate the derivatives of ``zeta``. + + Returns + ------- + dri : ndarray of shape (3,), dtype float + Derivative with respect to the position of atom ``i``. + drj : ndarray of shape (3,), dtype float + Derivative with respect to the position of atom ``j``. + drk : ndarray of shape (3,), dtype float + Derivative with respect to the position of atom ``k``. + + """ + lam3 = params.lambda3 + m = params.m + + abs_rij = np.linalg.norm(rij) + abs_rik = np.linalg.norm(rik) + + rij_hat = rij / abs_rij + rik_hat = rik / abs_rik + + fcik = self._calc_fc(abs_rik, params.R, params.D) + dfcik = self._calc_fc_d(abs_rik, params.R, params.D) + + tmp = (lam3 * (abs_rij - abs_rik)) ** m + if tmp > _MAX_EXP_ARG: + ex_delr = 1.0e30 + elif tmp < _MIN_EXP_ARG: + ex_delr = 0.0 + else: + ex_delr = np.exp(tmp) + + ex_delr_d = m * lam3**m * (abs_rij - abs_rik) ** (m - 1) * ex_delr + + costheta = rij_hat @ rik_hat + gijk = self._calc_gijk(costheta, params) + gijk_d = self._calc_gijk_d(costheta, params) + + dcosdri, dcosdrj, dcosdrk = self._calc_costheta_d(rij, rik) + + dri = -dfcik * gijk * ex_delr * rik_hat + dri += fcik * gijk_d * ex_delr * dcosdri + dri += fcik * gijk * ex_delr_d * rik_hat + dri -= fcik * gijk * ex_delr_d * rij_hat + + drj = fcik * gijk_d * ex_delr * dcosdrj + drj += fcik * gijk * ex_delr_d * rij_hat + + drk = dfcik * gijk * ex_delr * rik_hat + drk += fcik * gijk_d * ex_delr * dcosdrk + drk -= fcik * gijk * ex_delr_d * rik_hat + + return dri, drj, drk + + def _calc_costheta_d( + self, + rij: np.ndarray, + rik: np.ndarray, + ) -> tuple[np.ndarray, np.ndarray, np.ndarray]: + r"""Calculate the derivatives of ``costheta``. + + If + + .. math:: + \cos \theta = \frac{\mathbf{u} \cdot \mathbf{v}}{u v} + + Then + + .. math:: + \frac{\partial \cos \theta}{\partial \mathbf{u}} + = \frac{\mathbf{v}}{u v} + - \frac{\mathbf{u} \cdot \mathbf{v}}{v} \cdot \frac{\mathbf{u}}{u^3} + = \frac{\mathbf{v}}{u v} - \frac{\cos \theta}{u^2} \mathbf{u} + + Parameters + ---------- + rij : ndarray of shape (3,), dtype float + Vector from atoms ``i`` to ``j``. + rik : ndarray of shape (3,), dtype float + Vector from atoms ``i`` to ``k``. + + Returns + ------- + dri : ndarray of shape (3,), dtype float + Derivative with respect to the position of atom ``i``. + drj : ndarray of shape (3,), dtype float + Derivative with respect to the position of atom ``j``. + drk : ndarray of shape (3,), dtype float + Derivative with respect to the position of atom ``k``. + + """ + abs_rij = np.linalg.norm(rij) + abs_rik = np.linalg.norm(rik) + costheta = (rij @ rik) / (abs_rij * abs_rik) + drj = (rik / abs_rik - costheta * rij / abs_rij) / abs_rij + drk = (rij / abs_rij - costheta * rik / abs_rik) / abs_rik + dri = -(drj + drk) + return dri, drj, drk diff -pruN 3.24.0-1/ase/calculators/test.py 3.26.0-1/ase/calculators/test.py --- 3.24.0-1/ase/calculators/test.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/test.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from math import pi import numpy as np diff -pruN 3.24.0-1/ase/calculators/tip3p.py 3.26.0-1/ase/calculators/tip3p.py --- 3.24.0-1/ase/calculators/tip3p.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/tip3p.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """TIP3P potential.""" import numpy as np diff -pruN 3.24.0-1/ase/calculators/tip4p.py 3.26.0-1/ase/calculators/tip4p.py --- 3.24.0-1/ase/calculators/tip4p.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/tip4p.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase import units diff -pruN 3.24.0-1/ase/calculators/turbomole/executor.py 3.26.0-1/ase/calculators/turbomole/executor.py --- 3.24.0-1/ase/calculators/turbomole/executor.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/turbomole/executor.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ Execution of turbomole binaries and scripts: define, dscf, grad, ridft, rdgrad, aoforce, jobex, NumForce diff -pruN 3.24.0-1/ase/calculators/turbomole/parameters.py 3.26.0-1/ase/calculators/turbomole/parameters.py --- 3.24.0-1/ase/calculators/turbomole/parameters.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/turbomole/parameters.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # type: ignore """turbomole parameters management classes and functions""" diff -pruN 3.24.0-1/ase/calculators/turbomole/reader.py 3.26.0-1/ase/calculators/turbomole/reader.py --- 3.24.0-1/ase/calculators/turbomole/reader.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/turbomole/reader.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Functions to read from control file and from turbomole standard output""" import os diff -pruN 3.24.0-1/ase/calculators/turbomole/turbomole.py 3.26.0-1/ase/calculators/turbomole/turbomole.py --- 3.24.0-1/ase/calculators/turbomole/turbomole.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/turbomole/turbomole.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # type: ignore """ This module defines an ASE interface to Turbomole: http://www.turbomole.com/ diff -pruN 3.24.0-1/ase/calculators/turbomole/writer.py 3.26.0-1/ase/calculators/turbomole/writer.py --- 3.24.0-1/ase/calculators/turbomole/writer.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/turbomole/writer.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Module containing code to manupulate control file""" import subprocess diff -pruN 3.24.0-1/ase/calculators/vasp/__init__.py 3.26.0-1/ase/calculators/vasp/__init__.py --- 3.24.0-1/ase/calculators/vasp/__init__.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/vasp/__init__.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from .interactive import VaspInteractive from .vasp import Vasp from .vasp2 import Vasp2 diff -pruN 3.24.0-1/ase/calculators/vasp/create_input.py 3.26.0-1/ase/calculators/vasp/create_input.py --- 3.24.0-1/ase/calculators/vasp/create_input.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/vasp/create_input.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Copyright (C) 2008 CSC - Scientific Computing Ltd. """This module defines an ASE interface to VASP. @@ -22,11 +24,12 @@ import os import shutil import warnings from os.path import isfile, islink, join -from typing import List, Sequence, Tuple +from typing import List, Sequence, TextIO, Tuple, Union import numpy as np import ase +from ase import Atoms from ase.calculators.calculator import kpts2ndarray from ase.calculators.vasp.setups import get_default_setups from ase.config import cfg @@ -117,22 +120,27 @@ def set_ldau(ldau_param, luj_params, sym return ldau_dct -def test_nelect_charge_compitability(nelect, charge, nelect_from_ppp): - # We need to determine the nelect resulting from a given - # charge in any case if it's != 0, but if nelect is - # additionally given explicitly, then we need to determine it - # even for net charge of 0 to check for conflicts - if charge is not None and charge != 0: +def _calc_nelect_from_charge( + nelect: Union[float, None], + charge: Union[float, None], + nelect_from_ppp: float, +) -> Union[float, None]: + """Determine nelect resulting from a given charge if charge != 0.0. + + If nelect is additionally given explicitly, then we need to determine it + even for net charge of 0 to check for conflicts. + + """ + if charge is not None and charge != 0.0: nelect_from_charge = nelect_from_ppp - charge if nelect and nelect != nelect_from_charge: - raise ValueError('incompatible input parameters: ' - f'nelect={nelect}, but charge={charge} ' - '(neutral nelect is ' - f'{nelect_from_ppp})') - print(nelect_from_charge) + raise ValueError( + 'incompatible input parameters: ' + f'nelect={nelect}, but charge={charge} ' + f'(neutral nelect is {nelect_from_ppp})' + ) return nelect_from_charge - else: - return nelect + return nelect # NELECT explicitly given in INCAR (`None` if not given) def get_pp_setup(setup) -> Tuple[dict, Sequence[int]]: @@ -1496,7 +1504,7 @@ class GenerateVaspInput: raise RuntimeError(msg) return ppp_list - def initialize(self, atoms): + def initialize(self, atoms: Atoms) -> None: """Initialize a VASP calculation Constructs the POTCAR file (does not actually write it). @@ -1534,32 +1542,34 @@ class GenerateVaspInput: # Check if the necessary POTCAR files exists and # create a list of their paths. atomtypes = atoms.get_chemical_symbols() - self.symbol_count = [] + self.symbol_count: list[tuple[str, int]] = [] for m in special_setups: - self.symbol_count.append([atomtypes[m], 1]) - for m in symbols: - self.symbol_count.append([m, symbolcount[m]]) + self.symbol_count.append((atomtypes[m], 1)) + for s in symbols: + self.symbol_count.append((s, symbolcount[s])) # create pseudopotential list - self.ppp_list = self._build_pp_list(atoms, - setups=setups, - special_setups=special_setups) + self.ppp_list = self._build_pp_list( + atoms, + setups=setups, + special_setups=special_setups, + ) self.converged = None self.setups_changed = None - def default_nelect_from_ppp(self): + def default_nelect_from_ppp(self) -> float: """ Get default number of electrons from ppp_list and symbol_count "Default" here means that the resulting cell would be neutral. """ - symbol_valences = [] + symbol_valences: list[tuple[str, float]] = [] for filename in self.ppp_list: with open_potcar(filename=filename) as ppp_file: r = read_potcar_numbers_of_electrons(ppp_file) symbol_valences.extend(r) assert len(self.symbol_count) == len(symbol_valences) - default_nelect = 0 + default_nelect = 0.0 for ((symbol1, count), (symbol2, valence)) in zip(self.symbol_count, symbol_valences): assert symbol1 == symbol2 @@ -1639,7 +1649,7 @@ class GenerateVaspInput: if 'charge' in self.input_params and self.input_params[ 'charge'] is not None: - nelect_val = test_nelect_charge_compitability( + nelect_val = _calc_nelect_from_charge( self.float_params['nelect'], self.input_params['charge'], self.default_nelect_from_ppp()) @@ -1780,6 +1790,8 @@ class GenerateVaspInput: raise ValueError("KSPACING value {} is not allowable. " "Please use None or a positive number." "".format(self.float_params['kspacing'])) + if self.input_params['kpts'] is None: + return kpointstring = format_kpoints( kpts=self.input_params['kpts'], @@ -2073,21 +2085,27 @@ def open_potcar(filename): raise ValueError(f'Invalid POTCAR filename: "{filename}"') -def read_potcar_numbers_of_electrons(file_obj): - """ Read list of tuples (atomic symbol, number of valence electrons) - for each atomtype from a POTCAR file.""" - nelect = [] - lines = file_obj.readlines() +def read_potcar_numbers_of_electrons(fd: TextIO, /) -> list[tuple[str, float]]: + """Read number of valence electrons for each atomtype from a POTCAR file. + + Returns + ------- + list[tuple[str, float]] + List of (atomic symbol, number of valence electrons). + + """ + nelect: list[tuple[str, float]] = [] + lines = fd.readlines() for n, line in enumerate(lines): if 'TITEL' in line: symbol = line.split('=')[1].split()[1].split('_')[0].strip() - valence = float( - lines[n + 4].split(';')[1].split('=')[1].split()[0].strip()) - nelect.append((symbol, valence)) + linep4 = lines[n + 4] + zval = float(linep4.split(';')[1].split('=')[1].split()[0].strip()) + nelect.append((symbol, zval)) return nelect -def count_symbols(atoms, exclude=()): +def count_symbols(atoms: Atoms, exclude=()) -> tuple[list[str], dict[str, int]]: """Count symbols in atoms object, excluding a set of indices Parameters: @@ -2108,8 +2126,8 @@ def count_symbols(atoms, exclude=()): >>> count_symbols(atoms, exclude=(1, 2, 3)) (['Na', 'Cl'], {'Na': 3, 'Cl': 2}) """ - symbols = [] - symbolcount = {} + symbols: list[str] = [] + symbolcount: dict[str, int] = {} for m, symbol in enumerate(atoms.symbols): if m in exclude: continue diff -pruN 3.24.0-1/ase/calculators/vasp/interactive.py 3.26.0-1/ase/calculators/vasp/interactive.py --- 3.24.0-1/ase/calculators/vasp/interactive.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/vasp/interactive.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import os import time from subprocess import PIPE, Popen diff -pruN 3.24.0-1/ase/calculators/vasp/setups.py 3.26.0-1/ase/calculators/vasp/setups.py --- 3.24.0-1/ase/calculators/vasp/setups.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/vasp/setups.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import copy _setups_defaults = { diff -pruN 3.24.0-1/ase/calculators/vasp/vasp.py 3.26.0-1/ase/calculators/vasp/vasp.py --- 3.24.0-1/ase/calculators/vasp/vasp.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/vasp/vasp.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Copyright (C) 2008 CSC - Scientific Computing Ltd. """This module defines an ASE interface to VASP. @@ -1196,7 +1198,7 @@ class Vasp(GenerateVaspInput, Calculator i_freq.append(float(data[-2])) return freq, i_freq - def _read_massweighted_hessian_xml(self) -> np.ndarray: + def _read_massweighted_hessian_xml(self): """Read the Mass Weighted Hessian from vasprun.xml. Returns: diff -pruN 3.24.0-1/ase/calculators/vasp/vasp_auxiliary.py 3.26.0-1/ase/calculators/vasp/vasp_auxiliary.py --- 3.24.0-1/ase/calculators/vasp/vasp_auxiliary.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/vasp/vasp_auxiliary.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import os import re @@ -87,12 +89,17 @@ class VaspChargeDensity: self.augdiff = '' while True: try: - atoms = aiv.read_vasp(fd) + atoms = aiv.read_vasp_configuration(fd) except (KeyError, RuntimeError, ValueError): # Probably an empty line, or we tried to read the # augmentation occupancies in CHGCAR break + + # Note: We continue reading from the same file, and + # this relies on read_vasp() to read no more lines + # than it currently does. fd.readline() + ngr = fd.readline().split() ng = (int(ngr[0]), int(ngr[1]), int(ngr[2])) chg = np.empty(ng) diff -pruN 3.24.0-1/ase/calculators/vasp/vasp_data.py 3.26.0-1/ase/calculators/vasp/vasp_data.py --- 3.24.0-1/ase/calculators/vasp/vasp_data.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/vasp/vasp_data.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # flake8: noqa diff -pruN 3.24.0-1/ase/calculators/vdwcorrection.py 3.26.0-1/ase/calculators/vdwcorrection.py --- 3.24.0-1/ase/calculators/vdwcorrection.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/calculators/vdwcorrection.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """van der Waals correction schemes for DFT""" import numpy as np from scipy.special import erfc, erfinv diff -pruN 3.24.0-1/ase/cell.py 3.26.0-1/ase/cell.py --- 3.24.0-1/ase/cell.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cell.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from typing import Mapping, Sequence, Union import numpy as np @@ -328,14 +330,19 @@ class Cell: permuted = Cell(self[permutation][:, permutation]) return permuted - def standard_form(self): - """Rotate axes such that unit cell is lower triangular. The cell + def standard_form(self, form='lower'): + """Rotate axes such that unit cell is lower/upper triangular. The cell handedness is preserved. A lower-triangular cell with positive diagonal entries is a canonical (i.e. unique) description. For a left-handed cell the diagonal entries are negative. + Parameters: + + form: str + 'lower' or 'upper' triangular form. The default is 'lower'. + Returns: rcell: the standardized cell object @@ -353,9 +360,16 @@ class Cell: # Q is an orthogonal matrix and L is a lower triangular matrix. The # decomposition is a unique description if the diagonal elements are # all positive (negative for a left-handed cell). - Q, L = np.linalg.qr(self.T) - Q = Q.T - L = L.T + if form == 'lower': + Q, L = np.linalg.qr(self.T) + Q = Q.T + L = L.T + elif form == 'upper': + Q, L = np.linalg.qr(self.T[::-1, ::-1]) + Q = Q.T[::-1, ::-1] + L = L.T[::-1, ::-1] + else: + raise ValueError('form must be either "lower" or "upper"') # correct the signs of the diagonal elements signs = np.sign(np.diag(L)) diff -pruN 3.24.0-1/ase/cli/band_structure.py 3.26.0-1/ase/cli/band_structure.py --- 3.24.0-1/ase/cli/band_structure.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/band_structure.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Note: # Try to avoid module level import statements here to reduce # import time during CLI execution diff -pruN 3.24.0-1/ase/cli/build.py 3.26.0-1/ase/cli/build.py --- 3.24.0-1/ase/cli/build.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/build.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Note: # Try to avoid module level import statements here to reduce # import time during CLI execution @@ -18,7 +20,7 @@ class CLICommand: ase build ... where must be one of the formulas known to ASE - (see here: https://wiki.fysik.dtu.dk/ase/ase/build/build.html#molecules). + (see here: https://ase-lib.org/ase/build/build.html#molecules). Bulk: diff -pruN 3.24.0-1/ase/cli/complete.py 3.26.0-1/ase/cli/complete.py --- 3.24.0-1/ase/cli/complete.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/complete.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,4 +1,6 @@ #!/usr/bin/env python3 +# fmt: off + """Bash completion for ase. Put this in your .bashrc:: @@ -73,10 +75,6 @@ commands = { ['--files', '-v', '--verbose', '--formats', '--calculators'], 'nebplot': ['--nimages', '--share-x', '--share-y'], - 'nomad-get': - [], - 'nomad-upload': - ['-t', '--token', '-n', '--no-save-token', '-0', '--dry-run'], 'reciprocal': [], 'run': diff -pruN 3.24.0-1/ase/cli/completion.py 3.26.0-1/ase/cli/completion.py --- 3.24.0-1/ase/cli/completion.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/completion.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """TAB-completion sub-command and update helper funtion. Run this when ever options are changed:: @@ -54,6 +56,9 @@ def update(path: Path, dct[command].extend(arg for arg in args if arg.startswith('-')) + def add_argument_group(self, name): + return self + def add_mutually_exclusive_group(self, required=False): return self diff -pruN 3.24.0-1/ase/cli/convert.py 3.26.0-1/ase/cli/convert.py --- 3.24.0-1/ase/cli/convert.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/convert.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Note: # Try to avoid module level import statements here to reduce # import time during CLI execution diff -pruN 3.24.0-1/ase/cli/db.py 3.26.0-1/ase/cli/db.py --- 3.24.0-1/ase/cli/db.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/db.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Note: # Try to avoid module level import statements here to reduce # import time during CLI execution @@ -31,7 +33,7 @@ class CLICommand: 2.2=10 - See also: https://wiki.fysik.dtu.dk/ase/ase/db/db.html. + See also: https://ase-lib.org/ase/db/db.html. """ @staticmethod diff -pruN 3.24.0-1/ase/cli/diff.py 3.26.0-1/ase/cli/diff.py --- 3.24.0-1/ase/cli/diff.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/diff.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Note: # Try to avoid module level import statements here to reduce # import time during CLI execution diff -pruN 3.24.0-1/ase/cli/dimensionality.py 3.26.0-1/ase/cli/dimensionality.py --- 3.24.0-1/ase/cli/dimensionality.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/dimensionality.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Note: # Try to avoid module level import statements here to reduce # import time during CLI execution diff -pruN 3.24.0-1/ase/cli/exec.py 3.26.0-1/ase/cli/exec.py --- 3.24.0-1/ase/cli/exec.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/exec.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Note: # Try to avoid module level import statements here to reduce # import time during CLI execution diff -pruN 3.24.0-1/ase/cli/find.py 3.26.0-1/ase/cli/find.py --- 3.24.0-1/ase/cli/find.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/find.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Note: # Try to avoid module level import statements here to reduce # import time during CLI execution @@ -9,7 +11,7 @@ class CLICommand: Search through files known to ASE applying a query to filter the results. - See https://wiki.fysik.dtu.dk/ase/ase/db/db.html#querying for more + See https://ase-lib.org/ase/db/db.html#querying for more informations on how to construct the query string. """ diff -pruN 3.24.0-1/ase/cli/info.py 3.26.0-1/ase/cli/info.py --- 3.24.0-1/ase/cli/info.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/info.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Note: # Try to avoid module level import statements here to reduce # import time during CLI execution diff -pruN 3.24.0-1/ase/cli/main.py 3.26.0-1/ase/cli/main.py --- 3.24.0-1/ase/cli/main.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/main.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import argparse import textwrap from importlib import import_module @@ -28,8 +30,6 @@ commands = [ ('ulm', 'ase.cli.ulm'), ('find', 'ase.cli.find'), ('nebplot', 'ase.cli.nebplot'), - ('nomad-upload', 'ase.cli.nomad'), - ('nomad-get', 'ase.cli.nomadget'), ('convert', 'ase.cli.convert'), ('reciprocal', 'ase.cli.reciprocal'), ('completion', 'ase.cli.completion'), diff -pruN 3.24.0-1/ase/cli/nebplot.py 3.26.0-1/ase/cli/nebplot.py --- 3.24.0-1/ase/cli/nebplot.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/nebplot.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Note: # Try to avoid module level import statements here to reduce # import time during CLI execution diff -pruN 3.24.0-1/ase/cli/nomad.py 3.26.0-1/ase/cli/nomad.py --- 3.24.0-1/ase/cli/nomad.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/nomad.py 1970-01-01 00:00:00.000000000 +0000 @@ -1,75 +0,0 @@ -# Note: -# Try to avoid module level import statements here to reduce -# import time during CLI execution - - -class CLICommand: - """Upload files to NOMAD. - - Upload all data within specified folders to the Nomad repository - using authentication token given by the --token option or, - if no token is given, the token stored in ~/.ase/nomad-token. - - To get an authentication token, you create a Nomad repository account - and use the 'Uploads' button on that page while logged in: - - https://repository.nomad-coe.eu/ - """ - - @staticmethod - def add_arguments(parser): - parser.add_argument('folders', nargs='*', metavar='folder') - parser.add_argument('-t', '--token', - help='Use given authentication token and save ' - 'it to ~/.ase/nomad-token unless ' - '--no-save-token') - parser.add_argument('-n', '--no-save-token', action='store_true', - help='do not save the token if given') - parser.add_argument('-0', '--dry-run', action='store_true', - help='print command that would upload files ' - 'without uploading anything') - - @staticmethod - def run(args): - import os - import os.path as op - import subprocess - - dotase = op.expanduser('~/.ase') - tokenfile = op.join(dotase, 'nomad-token') - - if args.token: - token = args.token - if not args.no_save_token: - if not op.isdir(dotase): - os.mkdir(dotase) - with open(tokenfile, 'w') as fd: - print(token, file=fd) - os.chmod(tokenfile, 0o600) - print('Wrote token to', tokenfile) - else: - try: - with open(tokenfile) as fd: - token = fd.readline().strip() - except OSError as err: # py2/3 discrepancy - from ase.cli.main import CLIError - msg = ('Could not find authentication token in {}. ' - 'Use the --token option to specify a token. ' - 'Original error: {}' - .format(tokenfile, err)) - raise CLIError(msg) - - cmd = ('tar cf - {} | ' - 'curl -XPUT -# -HX-Token:{} ' - '-N -F file=@- http://nomad-repository.eu:8000 | ' - 'xargs echo').format(' '.join(args.folders), token) - - if not args.folders: - print('No folders specified -- another job well done!') - elif args.dry_run: - print(cmd) - else: - print('Uploading {} folder{} ...' - .format(len(args.folders), - 's' if len(args.folders) != 1 else '')) - subprocess.check_call(cmd, shell=True) diff -pruN 3.24.0-1/ase/cli/nomadget.py 3.26.0-1/ase/cli/nomadget.py --- 3.24.0-1/ase/cli/nomadget.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/nomadget.py 1970-01-01 00:00:00.000000000 +0000 @@ -1,28 +0,0 @@ -# Note: -# Try to avoid module level import statements here to reduce -# import time during CLI execution - - -class CLICommand: - """Get calculations from NOMAD and write to JSON files. - - ... - """ - - @staticmethod - def add_arguments(p): - p.add_argument('uri', nargs='+', metavar='nmd://', - help='URIs to get') - - @staticmethod - def run(args): - import json - - from ase.nomad import download - for uri in args.uri: - calculation = download(uri) - identifier = calculation.hash.replace('/', '.') - fname = f'nmd.{identifier}.nomad-json' - with open(fname, 'w') as fd: - json.dump(calculation, fd) - print(uri) diff -pruN 3.24.0-1/ase/cli/reciprocal.py 3.26.0-1/ase/cli/reciprocal.py --- 3.24.0-1/ase/cli/reciprocal.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/reciprocal.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Note: # Try to avoid module level import statements here to reduce # import time during CLI execution diff -pruN 3.24.0-1/ase/cli/run.py 3.26.0-1/ase/cli/run.py --- 3.24.0-1/ase/cli/run.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/run.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import sys from typing import Any, Dict diff -pruN 3.24.0-1/ase/cli/template.py 3.26.0-1/ase/cli/template.py --- 3.24.0-1/ase/cli/template.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/template.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import string import numpy as np diff -pruN 3.24.0-1/ase/cli/ulm.py 3.26.0-1/ase/cli/ulm.py --- 3.24.0-1/ase/cli/ulm.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cli/ulm.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # Note: # Try to avoid module level import statements here to reduce # import time during CLI execution diff -pruN 3.24.0-1/ase/cluster/__init__.py 3.26.0-1/ase/cluster/__init__.py --- 3.24.0-1/ase/cluster/__init__.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cluster/__init__.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Module for creating clusters.""" from ase.cluster.cluster import Cluster diff -pruN 3.24.0-1/ase/cluster/base.py 3.26.0-1/ase/cluster/base.py --- 3.24.0-1/ase/cluster/base.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cluster/base.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np diff -pruN 3.24.0-1/ase/cluster/cluster.py 3.26.0-1/ase/cluster/cluster.py --- 3.24.0-1/ase/cluster/cluster.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cluster/cluster.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import math import numpy as np diff -pruN 3.24.0-1/ase/cluster/compounds.py 3.26.0-1/ase/cluster/compounds.py --- 3.24.0-1/ase/cluster/compounds.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cluster/compounds.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase.cluster.cubic import SimpleCubicFactory diff -pruN 3.24.0-1/ase/cluster/cubic.py 3.26.0-1/ase/cluster/cubic.py --- 3.24.0-1/ase/cluster/cubic.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cluster/cubic.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ Function-like objects that creates cubic clusters. """ diff -pruN 3.24.0-1/ase/cluster/decahedron.py 3.26.0-1/ase/cluster/decahedron.py --- 3.24.0-1/ase/cluster/decahedron.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cluster/decahedron.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase import Atoms diff -pruN 3.24.0-1/ase/cluster/factory.py 3.26.0-1/ase/cluster/factory.py --- 3.24.0-1/ase/cluster/factory.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cluster/factory.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from typing import List, Optional import numpy as np diff -pruN 3.24.0-1/ase/cluster/hexagonal.py 3.26.0-1/ase/cluster/hexagonal.py --- 3.24.0-1/ase/cluster/hexagonal.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cluster/hexagonal.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ Function-like objects that creates cubic clusters. """ diff -pruN 3.24.0-1/ase/cluster/icosahedron.py 3.26.0-1/ase/cluster/icosahedron.py --- 3.24.0-1/ase/cluster/icosahedron.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cluster/icosahedron.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase import Atoms diff -pruN 3.24.0-1/ase/cluster/octahedron.py 3.26.0-1/ase/cluster/octahedron.py --- 3.24.0-1/ase/cluster/octahedron.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cluster/octahedron.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ Function-like objects that creates cubic clusters. """ diff -pruN 3.24.0-1/ase/cluster/util.py 3.26.0-1/ase/cluster/util.py --- 3.24.0-1/ase/cluster/util.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cluster/util.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from ase.data import atomic_numbers, chemical_symbols, reference_states diff -pruN 3.24.0-1/ase/cluster/wulff.py 3.26.0-1/ase/cluster/wulff.py --- 3.24.0-1/ase/cluster/wulff.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/cluster/wulff.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np delta = 1e-10 diff -pruN 3.24.0-1/ase/codes.py 3.26.0-1/ase/codes.py --- 3.24.0-1/ase/codes.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/codes.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from dataclasses import dataclass # Note: There could be more than one "calculator" for any given code; diff -pruN 3.24.0-1/ase/collections/collection.py 3.26.0-1/ase/collections/collection.py --- 3.24.0-1/ase/collections/collection.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/collections/collection.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import os.path as op from ase.db.row import AtomsRow diff -pruN 3.24.0-1/ase/collections/create.py 3.26.0-1/ase/collections/create.py --- 3.24.0-1/ase/collections/create.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/collections/create.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import os import ase.db diff -pruN 3.24.0-1/ase/config.py 3.26.0-1/ase/config.py --- 3.24.0-1/ase/config.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/config.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import configparser import os import shlex diff -pruN 3.24.0-1/ase/constraints.py 3.26.0-1/ase/constraints.py --- 3.24.0-1/ase/constraints.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/constraints.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Constraints""" from typing import Sequence from warnings import warn diff -pruN 3.24.0-1/ase/data/__init__.py 3.26.0-1/ase/data/__init__.py --- 3.24.0-1/ase/data/__init__.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/__init__.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np from ase.data.vdw import vdw_radii diff -pruN 3.24.0-1/ase/data/cccbdb_ip.py 3.26.0-1/ase/data/cccbdb_ip.py --- 3.24.0-1/ase/data/cccbdb_ip.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/cccbdb_ip.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # flake8: noqa """ Experimental ionization energies from CCCBDB at diff -pruN 3.24.0-1/ase/data/cohesive_energies.py 3.26.0-1/ase/data/cohesive_energies.py --- 3.24.0-1/ase/data/cohesive_energies.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/cohesive_energies.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import numpy as np # http://metal.elte.hu/~groma/Anyagtudomany/kittel.pdf diff -pruN 3.24.0-1/ase/data/colors.py 3.26.0-1/ase/data/colors.py --- 3.24.0-1/ase/data/colors.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/colors.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # flake8: noqa import numpy as np diff -pruN 3.24.0-1/ase/data/dbh24.py 3.26.0-1/ase/data/dbh24.py --- 3.24.0-1/ase/data/dbh24.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/dbh24.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # flake8: noqa """ The following contains a database of 24 gas-phase reaction barrier heights for small molecules. diff -pruN 3.24.0-1/ase/data/extra_molecules.py 3.26.0-1/ase/data/extra_molecules.py --- 3.24.0-1/ase/data/extra_molecules.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/extra_molecules.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # flake8: noqa """ Database of molecules outside the G2_1 set diff -pruN 3.24.0-1/ase/data/g2.py 3.26.0-1/ase/data/g2.py --- 3.24.0-1/ase/data/g2.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/g2.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """The following contains a database of small molecules Data for the G2/97 database are from diff -pruN 3.24.0-1/ase/data/g2_1.py 3.26.0-1/ase/data/g2_1.py --- 3.24.0-1/ase/data/g2_1.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/g2_1.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # flake8: noqa """ The following contains a database of small molecules diff -pruN 3.24.0-1/ase/data/g2_2.py 3.26.0-1/ase/data/g2_2.py --- 3.24.0-1/ase/data/g2_2.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/g2_2.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # flake8: noqa """ The following contains a database of small molecules diff -pruN 3.24.0-1/ase/data/isotopes.py 3.26.0-1/ase/data/isotopes.py --- 3.24.0-1/ase/data/isotopes.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/isotopes.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """Isotope data extracted from NIST public website. Source data has been compiled by NIST: diff -pruN 3.24.0-1/ase/data/pubchem.py 3.26.0-1/ase/data/pubchem.py --- 3.24.0-1/ase/data/pubchem.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/pubchem.py 2025-08-12 11:26:23.000000000 +0000 @@ -2,7 +2,7 @@ import json import urllib.request import warnings from collections import namedtuple -from io import BytesIO, StringIO +from io import StringIO from urllib.error import HTTPError, URLError from ase.io import read @@ -28,7 +28,7 @@ class PubchemData: return self.data -def search_pubchem_raw(search, field, silent=False, mock_test=False): +def search_pubchem_raw(search, field, silent=False): """ A helper function for searching pubchem. @@ -49,33 +49,27 @@ def search_pubchem_raw(search, field, si data (str): a string containing the raw response from pubchem. """ - if mock_test: # for testing only - r = BytesIO(test_output) - else: - suffix = 'sdf?record_type=3d' - - url = ( - f'{base_url}/{field}/{search!s}/{suffix}' - if field == 'conformers' - else f'{base_url}/compound/{field}/{search!s}/{suffix}' - ) - try: - r = urllib.request.urlopen(url) - except HTTPError as e: - raise ValueError( - f'the search term {search} could not be found for the field ' - f'{field}' - ) from e - except URLError as e: - raise ValueError( - 'Couldn\'t reach the pubchem servers, check' - ' your internet connection' - ) from e + suffix = 'sdf?record_type=3d' + + url = ( + f'{base_url}/{field}/{search!s}/{suffix}' + if field == 'conformers' + else f'{base_url}/compound/{field}/{search!s}/{suffix}' + ) + try: + r = urllib.request.urlopen(url) + except HTTPError as e: + raise ValueError( + f'the search term {search} could not be found for the field {field}' + ) from e + except URLError as e: + raise ValueError( + "Couldn't reach the pubchem servers, check your internet connection" + ) from e # check if there are confomers and warn them if there are if field != 'conformers' and not silent: - conformer_ids = available_conformer_search(search, field, - mock_test=mock_test) + conformer_ids = available_conformer_search(search, field) if len(conformer_ids) > 1: warnings.warn( f'The structure "{search}" has more than one conformer in ' @@ -105,8 +99,7 @@ def parse_pubchem_raw(data): """ if 'PUBCHEM_COMPOUND_CID' not in data: - raise Exception('There was a problem with the data returned by ' - 'PubChem') + raise Exception('There was a problem with the data returned by PubChem') f_like = StringIO(data) atoms = read(f_like, format='sdf') @@ -133,7 +126,7 @@ def parse_pubchem_raw(data): # the first entry just contains the number of atoms with charges charges = pubchem_data['PUBCHEM_MMFF94_PARTIAL_CHARGES'][1:] # each subsequent entry contains the index and charge of the atoms - atom_charges = [0.] * len(atoms) + atom_charges = [0.0] * len(atoms) for charge in charges: i, charge = charge.split() # indices start at 1 @@ -142,8 +135,9 @@ def parse_pubchem_raw(data): return atoms, pubchem_data -def analyze_input(name=None, cid=None, smiles=None, conformer=None, - silent=False): +def analyze_input( + name=None, cid=None, smiles=None, conformer=None, silent=False +): """ helper function to translate keyword arguments from intialization and searching into the search and field that is being asked for @@ -162,23 +156,31 @@ def analyze_input(name=None, cid=None, s input_fields = ['name', 'cid', 'smiles', 'conformers'] if inputs_check.count(True) > 1: - raise ValueError('Only one search term my be entered a time.' - ' Please pass in only one of the following: ' - 'name, cid, smiles, confomer') - elif inputs_check.count(True) == 1: - # Figure out which input has been passed in - index = inputs_check.index(True) - field = input_fields[index] - search = inputs[index] - else: - raise ValueError('No search was entered.' - ' Please pass in only one of the following: ' - 'name, cid, smiles, confomer') + raise ValueError( + 'Only one search term my be entered a time.' + ' Please pass in only one of the following: ' + 'name, cid, smiles, confomer' + ) + if inputs_check.count(True) == 0: + raise ValueError( + 'No search was entered.' + ' Please pass in only one of the following: ' + 'name, cid, smiles, confomer' + ) + + # Figure out which input has been passed in + index = inputs_check.index(True) + field = input_fields[index] + search = inputs[index] + + # convert hash (triple bond) to hex for URL + if isinstance(search, str): + search = search.replace('#', '%23') return PubchemSearch(search, field) -def available_conformer_search(search, field, mock_test=False): +def available_conformer_search(search, field) -> list: """ Helper function to get the conformer IDs. This searches pubchem for the conformers of a given structure and returns all the confomer ids @@ -204,27 +206,24 @@ def available_conformer_search(search, f """ suffix = 'conformers/JSON' url = f'{base_url}/compound/{field}/{search!s}/{suffix}' - if mock_test: - r = BytesIO(test_conformer_output) - else: - try: - r = urllib.request.urlopen(url) - except HTTPError as e: - err = ValueError( - f'the search term {search} could not be found for the field ' - f'{field}' - ) - raise err from e - except URLError as e: - err = ValueError('Couldn\'t reach the pubchem servers, check' - ' your internet connection') - raise err from e + try: + r = urllib.request.urlopen(url) + except HTTPError as e: + err = ValueError( + f'the search term {search} could not be found for the field {field}' + ) + raise err from e + except URLError as e: + err = ValueError( + "Couldn't reach the pubchem servers, check your internet connection" + ) + raise err from e record = r.read().decode('utf-8') record = json.loads(record) return record['InformationList']['Information'][0]['ConformerID'] -def pubchem_search(*args, mock_test=False, **kwargs): +def pubchem_search(*args, **kwargs) -> PubchemData: """ Search PubChem for the field and search input on the argument passed in returning a PubchemData object. Note that only one argument may be passed @@ -245,14 +244,13 @@ def pubchem_search(*args, mock_test=Fals a pubchem data object containing the information on the requested entry """ - search, field = analyze_input(*args, **kwargs) - raw_pubchem = search_pubchem_raw(search, field, mock_test=mock_test) + raw_pubchem = search_pubchem_raw(search, field) atoms, data = parse_pubchem_raw(raw_pubchem) return PubchemData(atoms, data) -def pubchem_conformer_search(*args, mock_test=False, **kwargs): +def pubchem_conformer_search(*args, **kwargs) -> list: """ Search PubChem for all the conformers of a given compound. Note that only one argument may be passed in at a time. @@ -265,15 +263,9 @@ def pubchem_conformer_search(*args, mock a list containing the PubchemData objects of all the conformers for your search """ - search, field = analyze_input(*args, **kwargs) - - conformer_ids = available_conformer_search(search, field, - mock_test=mock_test) - return [ - pubchem_search(mock_test=mock_test, conformer=id_) - for id_ in conformer_ids - ] + conformer_ids = available_conformer_search(search, field) + return [pubchem_search(conformer=id_) for id_ in conformer_ids] def pubchem_atoms_search(*args, **kwargs): @@ -309,7 +301,3 @@ def pubchem_atoms_conformer_search(*args conformers = pubchem_conformer_search(*args, **kwargs) conformers = [conformer.get_atoms() for conformer in conformers] return conformers - - -test_output = b'222\n -OEChem-10071914343D\n\n 4 3 0 0 0 0 0 0 0999 V2000\n 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4417 0.2906 0.8711 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7256 0.6896 -0.1907 H 0 0 0 0 0 0 0 0 0 0 0 0\n 0.4875 -0.8701 0.2089 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 1 3 1 0 0 0 0\n 1 4 1 0 0 0 0\nM END\n> \n222\n\n> \n0.4\n\n> \n1\n\n> \n4\n1 -1.08\n2 0.36\n3 0.36\n4 0.36\n\n> \n0\n\n> \n1\n1 1 cation\n\n> \n1\n\n> \n0\n\n> \n0\n\n> \n0\n\n> \n0\n\n> \n0\n\n> \n1\n\n> \n1\n\n> \n000000DE00000001\n\n> \n0\n\n> \n5.074\n\n> \n260 1 18410856563934756871\n\n> \n15.6\n0.51\n0.51\n0.51\n0\n0\n0\n0\n0\n0\n0\n0\n0\n0\n\n> \n14.89\n\n> \n15.6\n\n> \n2\n5\n10\n\n$$$$\n' # noqa -test_conformer_output = b'{\n "InformationList": {\n "Information": [\n {\n "CID": 222,\n "ConformerID": [\n "000000DE00000001"\n ]\n }\n ]\n }\n}\n' # noqa diff -pruN 3.24.0-1/ase/data/s22.py 3.26.0-1/ase/data/s22.py --- 3.24.0-1/ase/data/s22.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/s22.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # flake8: noqa """ The following contains the S22 and s26 databases of weakly interacting dimers and complexes diff -pruN 3.24.0-1/ase/data/vdw.py 3.26.0-1/ase/data/vdw.py --- 3.24.0-1/ase/data/vdw.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/vdw.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """ Van der Waals radii in [A] taken from http://www.webelements.com/periodicity/van_der_waals_radius/ and the references given there. diff -pruN 3.24.0-1/ase/data/vdw_alvarez.py 3.26.0-1/ase/data/vdw_alvarez.py --- 3.24.0-1/ase/data/vdw_alvarez.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/data/vdw_alvarez.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + # flake8: noqa """ Van der Waals radii in [A] taken from: A cartography of the van der Waals territories diff -pruN 3.24.0-1/ase/db/app.py 3.26.0-1/ase/db/app.py --- 3.24.0-1/ase/db/app.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/app.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """WSGI Flask-app for browsing a database. :: diff -pruN 3.24.0-1/ase/db/cli.py 3.26.0-1/ase/db/cli.py --- 3.24.0-1/ase/db/cli.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/cli.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import json import sys from collections import defaultdict @@ -291,7 +293,7 @@ def row2str(row) -> str: fmt = (' {0}| {1}|{2[0]:>11}|{2[1]:>11}|{2[2]:>11}|' + '{3:>10}|{4:>10}') for p, axis, L, A in zip(row.pbc, t['cell'], t['lengths'], t['angles']): - S.append(fmt.format(c, [' no', 'yes'][p], axis, L, A)) + S.append(fmt.format(c, [' no', 'yes'][int(p)], axis, L, A)) c += 1 S.append('') diff -pruN 3.24.0-1/ase/db/convert.py 3.26.0-1/ase/db/convert.py --- 3.24.0-1/ase/db/convert.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/convert.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import optparse import os diff -pruN 3.24.0-1/ase/db/core.py 3.26.0-1/ase/db/core.py --- 3.24.0-1/ase/db/core.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/core.py 2025-08-12 11:26:23.000000000 +0000 @@ -50,8 +50,10 @@ class KeyDescription: def __repr__(self): cls = type(self).__name__ - return (f'{cls}({self.key!r}, {self.shortdesc!r}, {self.longdesc!r}, ' - f'unit={self.unit!r})') + return ( + f'{cls}({self.key!r}, {self.shortdesc!r}, {self.longdesc!r}, ' + f'unit={self.unit!r})' + ) # The templates like to sort key descriptions by shortdesc. def __eq__(self, other): @@ -63,24 +65,31 @@ class KeyDescription: def get_key_descriptions(): KD = KeyDescription - return {keydesc.key: keydesc for keydesc in [ - KD('id', 'ID', 'Uniqe row ID'), - KD('age', 'Age', 'Time since creation'), - KD('formula', 'Formula', 'Chemical formula'), - KD('pbc', 'PBC', 'Periodic boundary conditions'), - KD('user', 'Username'), - KD('calculator', 'Calculator', 'ASE-calculator name'), - KD('energy', 'Energy', 'Total energy', unit='eV'), - KD('natoms', 'Number of atoms'), - KD('fmax', 'Maximum force', unit='eV/Å'), - KD('smax', 'Maximum stress', 'Maximum stress on unit cell', - unit='eV/ų'), - KD('charge', 'Charge', 'Net charge in unit cell', unit='|e|'), - KD('mass', 'Mass', 'Sum of atomic masses in unit cell', unit='au'), - KD('magmom', 'Magnetic moment', unit='μ_B'), - KD('unique_id', 'Unique ID', 'Random (unique) ID'), - KD('volume', 'Volume', 'Volume of unit cell', unit='ų') - ]} + return { + keydesc.key: keydesc + for keydesc in [ + KD('id', 'ID', 'Uniqe row ID'), + KD('age', 'Age', 'Time since creation'), + KD('formula', 'Formula', 'Chemical formula'), + KD('pbc', 'PBC', 'Periodic boundary conditions'), + KD('user', 'Username'), + KD('calculator', 'Calculator', 'ASE-calculator name'), + KD('energy', 'Energy', 'Total energy', unit='eV'), + KD('natoms', 'Number of atoms'), + KD('fmax', 'Maximum force', unit='eV/Å'), + KD( + 'smax', + 'Maximum stress', + 'Maximum stress on unit cell', + unit='eV/ų', + ), + KD('charge', 'Charge', 'Net charge in unit cell', unit='|e|'), + KD('mass', 'Mass', 'Sum of atomic masses in unit cell', unit='au'), + KD('magmom', 'Magnetic moment', unit='μ_B'), + KD('unique_id', 'Unique ID', 'Random (unique) ID'), + KD('volume', 'Volume', 'Volume of unit cell', unit='ų'), + ] + } def now(): @@ -88,48 +97,69 @@ def now(): return (time() - T2000) / YEAR -seconds = {'s': 1, - 'm': 60, - 'h': 3600, - 'd': 86400, - 'w': 604800, - 'M': 2629800, - 'y': YEAR} - -longwords = {'s': 'second', - 'm': 'minute', - 'h': 'hour', - 'd': 'day', - 'w': 'week', - 'M': 'month', - 'y': 'year'} - -ops = {'<': operator.lt, - '<=': operator.le, - '=': operator.eq, - '>=': operator.ge, - '>': operator.gt, - '!=': operator.ne} +seconds = { + 's': 1, + 'm': 60, + 'h': 3600, + 'd': 86400, + 'w': 604800, + 'M': 2629800, + 'y': YEAR, +} + +longwords = { + 's': 'second', + 'm': 'minute', + 'h': 'hour', + 'd': 'day', + 'w': 'week', + 'M': 'month', + 'y': 'year', +} + +ops = { + '<': operator.lt, + '<=': operator.le, + '=': operator.eq, + '>=': operator.ge, + '>': operator.gt, + '!=': operator.ne, +} invop = {'<': '>=', '<=': '>', '>=': '<', '>': '<=', '=': '!=', '!=': '='} word = re.compile('[_a-zA-Z][_0-9a-zA-Z]*$') -reserved_keys = set(all_properties + - all_changes + - list(atomic_numbers) + - ['id', 'unique_id', 'ctime', 'mtime', 'user', - 'fmax', 'smax', - 'momenta', 'constraints', 'natoms', 'formula', 'age', - 'calculator', 'calculator_parameters', - 'key_value_pairs', 'data']) +reserved_keys = set( + all_properties + + all_changes + + list(atomic_numbers) + + [ + 'id', + 'unique_id', + 'ctime', + 'mtime', + 'user', + 'fmax', + 'smax', + 'momenta', + 'constraints', + 'natoms', + 'formula', + 'age', + 'calculator', + 'calculator_parameters', + 'key_value_pairs', + 'data', + ] +) numeric_keys = {'id', 'energy', 'magmom', 'charge', 'natoms'} def check(key_value_pairs): for key, value in key_value_pairs.items(): - if key == "external_tables": + if key == 'external_tables': # Checks for external_tables are not # performed continue @@ -145,19 +175,23 @@ def check(key_value_pairs): 'It is best not to use keys ({0}) that are also a ' 'chemical formula. If you do a "db.select({0!r})",' 'you will not find rows with your key. Instead, you wil get ' - 'rows containing the atoms in the formula!'.format(key)) + 'rows containing the atoms in the formula!'.format(key) + ) if not isinstance(value, (numbers.Real, str, np.bool_)): raise ValueError(f'Bad value for {key!r}: {value}') if isinstance(value, str): for t in [bool, int, float]: if str_represents(value, t): raise ValueError( - 'Value ' + value + ' is put in as string ' + - 'but can be interpreted as ' + - f'{t.__name__}! Please convert ' + - f'to {t.__name__} before ' + - 'writing to the database OR change ' + - 'to a different string.') + 'Value ' + + value + + ' is put in as string ' + + 'but can be interpreted as ' + + f'{t.__name__}! Please convert ' + + f'to {t.__name__} before ' + + 'writing to the database OR change ' + + 'to a different string.' + ) def str_represents(value, t=int): @@ -165,21 +199,30 @@ def str_represents(value, t=int): return isinstance(new_value, t) -def connect(name, type='extract_from_name', create_indices=True, - use_lock_file=True, append=True, serial=False): +def connect( + name, + type='extract_from_name', + create_indices=True, + use_lock_file=True, + append=True, + serial=False, + **db_kwargs, +): """Create connection to database. name: str Filename or address of database. type: str - One of 'json', 'db', 'postgresql', - (JSON, SQLite, PostgreSQL). + One of 'json', 'db', 'postgresql', 'mysql', 'aselmdb' + (JSON, SQLite, PostgreSQL, MYSQL, ASELMDB). Default is 'extract_from_name', which will guess the type from the name. use_lock_file: bool You can turn this off if you know what you are doing ... append: bool Use append=False to start a new database. + db_kwargs: dict + Optional extra kwargs to pass on to the underlying db """ if isinstance(name, PurePath): @@ -190,8 +233,7 @@ def connect(name, type='extract_from_nam type = None elif not isinstance(name, str): type = 'json' - elif (name.startswith('postgresql://') or - name.startswith('postgres://')): + elif name.startswith('postgresql://') or name.startswith('postgres://'): type = 'postgresql' elif name.startswith('mysql://') or name.startswith('mariadb://'): type = 'mysql' @@ -201,7 +243,7 @@ def connect(name, type='extract_from_nam raise ValueError('No file extension or database type given') if type is None: - return Database() + return Database(**db_kwargs) if not append and world.rank == 0: if isinstance(name, str) and os.path.isfile(name): @@ -212,23 +254,37 @@ def connect(name, type='extract_from_nam if type == 'json': from ase.db.jsondb import JSONDatabase - return JSONDatabase(name, use_lock_file=use_lock_file, serial=serial) + + return JSONDatabase( + name, use_lock_file=use_lock_file, serial=serial, **db_kwargs + ) if type == 'db': from ase.db.sqlite import SQLite3Database - return SQLite3Database(name, create_indices, use_lock_file, - serial=serial) + + return SQLite3Database( + name, create_indices, use_lock_file, serial=serial, **db_kwargs + ) if type == 'postgresql': - from ase.db.postgresql import PostgreSQLDatabase - return PostgreSQLDatabase(name) + from ase_db_backends.postgresql import PostgreSQLDatabase + + return PostgreSQLDatabase(name, **db_kwargs) if type == 'mysql': - from ase.db.mysql import MySQLDatabase - return MySQLDatabase(name) + from ase_db_backends.mysql import MySQLDatabase + + return MySQLDatabase(name, **db_kwargs) + + if type == 'aselmdb': + from ase_db_backends.aselmdb import LMDBDatabase + + return LMDBDatabase(name, **db_kwargs) + raise ValueError('Unknown database type: ' + type) def lock(method): """Decorator for using a lock-file.""" + @functools.wraps(method) def new_method(self, *args, **kwargs): if self.lock is None: @@ -236,6 +292,7 @@ def lock(method): else: with self.lock: return method(self, *args, **kwargs) + return new_method @@ -287,8 +344,9 @@ def parse_selection(selection, **kwargs) except ValueError: keys.append(expression) else: - comparisons.extend((symbol, '>', n - 1) - for symbol, n in count.items()) + comparisons.extend( + (symbol, '>', n - 1) for symbol, n in count.items() + ) continue key, value = expression.split(op) comparisons.append((key, op, value)) @@ -307,15 +365,17 @@ def parse_selection(selection, **kwargs) raise ValueError('Use fomula=...') f = Formula(value) count = f.count() - cmps.extend((atomic_numbers[symbol], '=', n) - for symbol, n in count.items()) + cmps.extend( + (atomic_numbers[symbol], '=', n) for symbol, n in count.items() + ) key = 'natoms' value = len(f) elif key in atomic_numbers: key = atomic_numbers[key] value = int(value) elif isinstance(value, str): - value = convert_str_to_int_float_bool_or_str(value) + if key != 'unique_id': + value = convert_str_to_int_float_bool_or_str(value) if key in numeric_keys and not isinstance(value, (int, float)): msg = 'Wrong type for "{}{}{}" - must be a number' raise ValueError(msg.format(key, op, value)) @@ -327,8 +387,13 @@ def parse_selection(selection, **kwargs) class Database: """Base class for all databases.""" - def __init__(self, filename=None, create_indices=True, - use_lock_file=False, serial=False): + def __init__( + self, + filename: str = None, + create_indices: bool = True, + use_lock_file: bool = False, + serial: bool = False, + ): """Database object. serial: bool @@ -340,14 +405,13 @@ class Database: filename = os.path.expanduser(filename) self.filename = filename self.create_indices = create_indices + self.lock = None if use_lock_file and isinstance(filename, str): self.lock = Lock(filename + '.lock', world=DummyMPI()) - else: - self.lock = None self.serial = serial # Decription of columns and other stuff: - self._metadata: Dict[str, Any] = None + self._metadata = None @property def metadata(self) -> Dict[str, Any]: @@ -403,9 +467,9 @@ class Database: anything and return None. """ - for _ in self._select([], - [(key, '=', value) - for key, value in key_value_pairs.items()]): + for _ in self._select( + [], [(key, '=', value) for key, value in key_value_pairs.items()] + ): return None atoms = Atoms() @@ -435,8 +499,9 @@ class Database: def __delitem__(self, id): self.delete([id]) - def get_atoms(self, selection=None, - add_additional_information=False, **kwargs): + def get_atoms( + self, selection=None, add_additional_information=False, **kwargs + ): """Get Atoms object. selection: int, str or list @@ -467,9 +532,19 @@ class Database: return rows[0] @parallel_generator - def select(self, selection=None, filter=None, explain=False, - verbosity=1, limit=None, offset=0, sort=None, - include_data=True, columns='all', **kwargs): + def select( + self, + selection=None, + filter=None, + explain=False, + verbosity=1, + limit=None, + offset=0, + sort=None, + include_data=True, + columns='all', + **kwargs, + ): """Select rows. Return AtomsRow iterator with results. Selection is done @@ -516,11 +591,17 @@ class Database: sort += 'name' keys, cmps = parse_selection(selection, **kwargs) - for row in self._select(keys, cmps, explain=explain, - verbosity=verbosity, - limit=limit, offset=offset, sort=sort, - include_data=include_data, - columns=columns): + for row in self._select( + keys, + cmps, + explain=explain, + verbosity=verbosity, + limit=limit, + offset=offset, + sort=sort, + include_data=include_data, + columns=columns, + ): if filter is None or filter(row): yield row @@ -540,8 +621,9 @@ class Database: @parallel_function @lock - def update(self, id, atoms=None, delete_keys=[], data=None, - **add_key_value_pairs): + def update( + self, id, atoms=None, delete_keys=[], data=None, **add_key_value_pairs + ): """Update and/or delete key-value pairs of row(s). id: int @@ -560,11 +642,13 @@ class Database: if not isinstance(id, numbers.Integral): if isinstance(id, list): - err = ('First argument must be an int and not a list.\n' - 'Do something like this instead:\n\n' - 'with db:\n' - ' for id in ids:\n' - ' db.update(id, ...)') + err = ( + 'First argument must be an int and not a list.\n' + 'Do something like this instead:\n\n' + 'with db:\n' + ' for id in ids:\n' + ' db.update(id, ...)' + ) raise ValueError(err) raise TypeError('id must be an int') @@ -667,15 +751,14 @@ def o2b(obj: Any, parts: List[bytes]): if isinstance(obj, (list, tuple)): return [o2b(value, parts) for value in obj] if isinstance(obj, np.ndarray): - assert obj.dtype != object, \ + assert obj.dtype != object, ( 'Cannot convert ndarray of type "object" to bytes.' + ) offset = sum(len(part) for part in parts) if not np.little_endian: obj = obj.byteswap() parts.append(obj.tobytes()) - return {'__ndarray__': [obj.shape, - obj.dtype.name, - offset]} + return {'__ndarray__': [obj.shape, obj.dtype.name, offset]} if isinstance(obj, complex): return {'__complex__': [obj.real, obj.imag]} objtype = obj.ase_objtype @@ -683,8 +766,9 @@ def o2b(obj: Any, parts: List[bytes]): dct = o2b(obj.todict(), parts) dct['__ase_objtype__'] = objtype return dct - raise ValueError('Objects of type {type} not allowed' - .format(type=type(obj))) + raise ValueError( + 'Objects of type {type} not allowed'.format(type=type(obj)) + ) def b2o(obj: Any, b: bytes) -> Any: @@ -705,7 +789,7 @@ def b2o(obj: Any, b: bytes) -> Any: shape, name, offset = x dtype = np.dtype(name) size = dtype.itemsize * np.prod(shape).astype(int) - a = np.frombuffer(b[offset:offset + size], dtype) + a = np.frombuffer(b[offset : offset + size], dtype) a.shape = shape if not np.little_endian: a = a.byteswap() diff -pruN 3.24.0-1/ase/db/jsondb.py 3.26.0-1/ase/db/jsondb.py --- 3.24.0-1/ase/db/jsondb.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/jsondb.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + import os import sys from contextlib import ExitStack diff -pruN 3.24.0-1/ase/db/mysql.py 3.26.0-1/ase/db/mysql.py --- 3.24.0-1/ase/db/mysql.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/mysql.py 1970-01-01 00:00:00.000000000 +0000 @@ -1,280 +0,0 @@ -import json -import sys -from copy import deepcopy - -import numpy as np -from pymysql import connect -from pymysql.err import ProgrammingError - -import ase.io.jsonio -from ase.db.postgresql import insert_nan_and_inf, remove_nan_and_inf -from ase.db.sqlite import VERSION, SQLite3Database, init_statements - - -class Connection: - """ - Wrapper for the MySQL connection - - Arguments - ========= - host: str - Hostname. For a local database this is localhost. - user: str - Username. - passwd: str - Password - db_name: str - Name of the database - port: int - Port - binary_prefix: bool - MySQL checks if an argument can be interpreted as a UTF-8 string. This - check fails for binary values. Binary values need to have _binary - prefix in MySQL. By setting this to True, the prefix is automatically - added for binary values. - """ - - def __init__(self, host=None, user=None, passwd=None, port=3306, - db_name=None, binary_prefix=False): - self.con = connect(host=host, user=user, passwd=passwd, db=db_name, - binary_prefix=binary_prefix, port=port) - - def cursor(self): - return MySQLCursor(self.con.cursor()) - - def commit(self): - self.con.commit() - - def close(self): - self.con.close() - - def rollback(self): - self.con.rollback() - - -class MySQLCursor: - """ - Wrapper for the MySQL cursor. The most important task performed by this - class is to translate SQLite queries to MySQL. Translation is needed - because ASE DB uses some field names that are reserved words in MySQL. - Thus, these has to mapped onto other field names. - """ - sql_replace = [ - (' key TEXT', ' attribute_key TEXT'), - ('(key TEXT', '(attribute_key TEXT'), - ('SELECT key FROM', 'SELECT attribute_key FROM'), - ('SELECT DISTINCT key FROM keys', - 'SELECT DISTINCT attribute_key FROM attribute_keys'), - ('?', '%s'), - (' keys ', ' attribute_keys '), - (' key=', ' attribute_key='), - ('table.key', 'table.attribute_key'), - (' IF NOT EXISTS', '')] - - def __init__(self, cur): - self.cur = cur - - def execute(self, sql, params=None): - - # Replace external table key -> attribute_key - for substibution in self.sql_replace: - sql = sql.replace(substibution[0], substibution[1]) - - if params is None: - params = () - - self.cur.execute(sql, params) - - def fetchone(self): - return self.cur.fetchone() - - def fetchall(self): - return self.cur.fetchall() - - def _replace_nan_inf_kvp(self, values): - for item in values: - if not np.isfinite(item[1]): - item[1] = sys.float_info.max / 2 - return values - - def executemany(self, sql, values): - if 'number_key_values' in sql: - values = self._replace_nan_inf_kvp(values) - - for substibution in self.sql_replace: - sql = sql.replace(substibution[0], substibution[1]) - self.cur.executemany(sql, values) - - -class MySQLDatabase(SQLite3Database): - """ - ASE interface to a MySQL database (via pymysql package). - - Arguments - ========== - url: str - URL to the database. It should have the form - mysql://username:password@host:port/database_name. - Example URL with the following credentials - username: john - password: johnspasswd - host: localhost (i.e. server is running locally) - database: johns_calculations - port: 3306 - mysql://john:johnspasswd@localhost:3306/johns_calculations - create_indices: bool - Carried over from parent class. Currently indices are not - created for MySQL, as TEXT fields cannot be hashed by MySQL. - use_lock_file: bool - See SQLite - serial: bool - See SQLite - """ - type = 'mysql' - default = 'DEFAULT' - - def __init__(self, url=None, create_indices=True, - use_lock_file=False, serial=False): - super().__init__( - url, create_indices, use_lock_file, serial) - - self.host = None - self.username = None - self.passwd = None - self.db_name = None - self.port = 3306 - self._parse_url(url) - - def _parse_url(self, url): - """ - Parse the URL - """ - url = url.replace('mysql://', '') - url = url.replace('mariadb://', '') - - splitted = url.split(':', 1) - self.username = splitted[0] - - splitted = splitted[1].split('@') - self.passwd = splitted[0] - - splitted = splitted[1].split('/') - host_and_port = splitted[0].split(':') - self.host = host_and_port[0] - self.port = int(host_and_port[1]) - self.db_name = splitted[1] - - def _connect(self): - return Connection(host=self.host, user=self.username, - passwd=self.passwd, db_name=self.db_name, - port=self.port, binary_prefix=True) - - def _initialize(self, con): - if self.initialized: - return - - cur = con.cursor() - - information_exists = True - self._metadata = {} - try: - cur.execute("SELECT 1 FROM information") - except ProgrammingError: - information_exists = False - - if not information_exists: - # We need to initialize the DB - # MySQL require that id is explicitly set as primary key - # in the systems table - init_statements_cpy = deepcopy(init_statements) - init_statements_cpy[0] = init_statements_cpy[0][:-1] + \ - ', PRIMARY KEY(id))' - - statements = schema_update(init_statements_cpy) - for statement in statements: - cur.execute(statement) - con.commit() - self.version = VERSION - else: - cur.execute('select * from information') - - for name, value in cur.fetchall(): - if name == 'version': - self.version = int(value) - elif name == 'metadata': - self._metadata = json.loads(value) - - self.initialized = True - - def blob(self, array): - if array is None: - return None - return super().blob(array).tobytes() - - def get_offset_string(self, offset, limit=None): - sql = '' - if not limit: - # mysql does not allow for setting limit to -1 so - # instead we set a large number - sql += '\nLIMIT 10000000000' - sql += f'\nOFFSET {offset}' - return sql - - def get_last_id(self, cur): - cur.execute('select max(id) as ID from systems') - last_id = cur.fetchone()[0] - return last_id - - def create_select_statement(self, keys, cmps, - sort=None, order=None, sort_table=None, - what='systems.*'): - sql, value = super().create_select_statement( - keys, cmps, sort, order, sort_table, what) - - for subst in MySQLCursor.sql_replace: - sql = sql.replace(subst[0], subst[1]) - return sql, value - - def encode(self, obj, binary=False): - return ase.io.jsonio.encode(remove_nan_and_inf(obj)) - - def decode(self, obj, lazy=False): - return insert_nan_and_inf(ase.io.jsonio.decode(obj)) - - -def schema_update(statements): - for i, statement in enumerate(statements): - for a, b in [('REAL', 'DOUBLE'), - ('INTEGER PRIMARY KEY AUTOINCREMENT', - 'INT NOT NULL AUTO_INCREMENT')]: - statements[i] = statement.replace(a, b) - - # MySQL does not support UNIQUE constraint on TEXT - # need to use VARCHAR. The unique_id is generated with - # randint(16**31, 16**32-1) so it will contain 32 - # hex-characters - statements[0] = statements[0].replace('TEXT UNIQUE', 'VARCHAR(32) UNIQUE') - - # keys is a reserved word in MySQL redefine this table name to - # attribute_keys - statements[2] = statements[2].replace('keys', 'attribute_keys') - - txt2jsonb = ['calculator_parameters', 'key_value_pairs'] - - for column in txt2jsonb: - statements[0] = statements[0].replace( - f'{column} TEXT,', - f'{column} JSON,') - - statements[0] = statements[0].replace('data BLOB,', 'data JSON,') - - tab_with_key_field = ['attribute_keys', 'number_key_values', - 'text_key_values'] - - # key is a reserved word in MySQL redefine this to attribute_key - for i, statement in enumerate(statements): - for tab in tab_with_key_field: - if tab in statement: - statements[i] = statement.replace( - 'key TEXT', 'attribute_key TEXT') - return statements diff -pruN 3.24.0-1/ase/db/postgresql.py 3.26.0-1/ase/db/postgresql.py --- 3.24.0-1/ase/db/postgresql.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/postgresql.py 1970-01-01 00:00:00.000000000 +0000 @@ -1,215 +0,0 @@ -import json - -import numpy as np -from psycopg2 import connect -from psycopg2.extras import execute_values - -from ase.db.sqlite import ( - VERSION, - SQLite3Database, - index_statements, - init_statements, -) -from ase.io.jsonio import create_ase_object, create_ndarray -from ase.io.jsonio import encode as ase_encode - -jsonb_indices = [ - 'CREATE INDEX idxkeys ON systems USING GIN (key_value_pairs);', - 'CREATE INDEX idxcalc ON systems USING GIN (calculator_parameters);'] - - -def remove_nan_and_inf(obj): - if isinstance(obj, float) and not np.isfinite(obj): - return {'__special_number__': str(obj)} - if isinstance(obj, list): - return [remove_nan_and_inf(x) for x in obj] - if isinstance(obj, dict): - return {key: remove_nan_and_inf(value) for key, value in obj.items()} - if isinstance(obj, np.ndarray) and not np.isfinite(obj).all(): - return remove_nan_and_inf(obj.tolist()) - return obj - - -def insert_nan_and_inf(obj): - if isinstance(obj, dict) and '__special_number__' in obj: - return float(obj['__special_number__']) - if isinstance(obj, list): - return [insert_nan_and_inf(x) for x in obj] - if isinstance(obj, dict): - return {key: insert_nan_and_inf(value) for key, value in obj.items()} - return obj - - -class Connection: - def __init__(self, con): - self.con = con - - def cursor(self): - return Cursor(self.con.cursor()) - - def commit(self): - self.con.commit() - - def close(self): - self.con.close() - - -class Cursor: - def __init__(self, cur): - self.cur = cur - - def fetchone(self): - return self.cur.fetchone() - - def fetchall(self): - return self.cur.fetchall() - - def execute(self, statement, *args): - self.cur.execute(statement.replace('?', '%s'), *args) - - def executemany(self, statement, *args): - if len(args[0]) > 0: - N = len(args[0][0]) - else: - return - if 'INSERT INTO systems' in statement: - q = 'DEFAULT' + ', ' + ', '.join('?' * N) # DEFAULT for id - else: - q = ', '.join('?' * N) - statement = statement.replace(f'({q})', '%s') - q = '({})'.format(q.replace('?', '%s')) - - execute_values(self.cur, statement.replace('?', '%s'), - argslist=args[0], template=q, page_size=len(args[0])) - - -def insert_ase_and_ndarray_objects(obj): - if isinstance(obj, dict): - objtype = obj.pop('__ase_objtype__', None) - if objtype is not None: - return create_ase_object(objtype, - insert_ase_and_ndarray_objects(obj)) - data = obj.get('__ndarray__') - if data is not None: - return create_ndarray(*data) - return {key: insert_ase_and_ndarray_objects(value) - for key, value in obj.items()} - if isinstance(obj, list): - return [insert_ase_and_ndarray_objects(value) for value in obj] - return obj - - -class PostgreSQLDatabase(SQLite3Database): - type = 'postgresql' - default = 'DEFAULT' - - def encode(self, obj, binary=False): - return ase_encode(remove_nan_and_inf(obj)) - - def decode(self, obj, lazy=False): - return insert_ase_and_ndarray_objects(insert_nan_and_inf(obj)) - - def blob(self, array): - """Convert array to blob/buffer object.""" - - if array is None: - return None - if len(array) == 0: - array = np.zeros(0) - if array.dtype == np.int64: - array = array.astype(np.int32) - return array.tolist() - - def deblob(self, buf, dtype=float, shape=None): - """Convert blob/buffer object to ndarray of correct dtype and shape. - - (without creating an extra view).""" - if buf is None: - return None - return np.array(buf, dtype=dtype) - - def _connect(self): - return Connection(connect(self.filename)) - - def _initialize(self, con): - if self.initialized: - return - - self._metadata = {} - - cur = con.cursor() - cur.execute("show search_path;") - schema = cur.fetchone()[0].split(', ') - if schema[0] == '"$user"': - schema = schema[1] - else: - schema = schema[0] - - cur.execute(""" - SELECT EXISTS(select * from information_schema.tables where - table_name='information' and table_schema='{}'); - """.format(schema)) - - if not cur.fetchone()[0]: # information schema doesn't exist. - # Initialize database: - sql = ';\n'.join(init_statements) - sql = schema_update(sql) - cur.execute(sql) - if self.create_indices: - cur.execute(';\n'.join(index_statements)) - cur.execute(';\n'.join(jsonb_indices)) - con.commit() - self.version = VERSION - else: - cur.execute('select * from information;') - for name, value in cur.fetchall(): - if name == 'version': - self.version = int(value) - elif name == 'metadata': - self._metadata = json.loads(value) - - assert 5 < self.version <= VERSION - - self.initialized = True - - def get_offset_string(self, offset, limit=None): - # postgresql allows you to set offset without setting limit; - # very practical - return f'\nOFFSET {offset}' - - def get_last_id(self, cur): - cur.execute('SELECT last_value FROM systems_id_seq') - id = cur.fetchone()[0] - return int(id) - - -def schema_update(sql): - for a, b in [('REAL', 'DOUBLE PRECISION'), - ('INTEGER PRIMARY KEY AUTOINCREMENT', - 'SERIAL PRIMARY KEY')]: - sql = sql.replace(a, b) - - arrays_1D = ['numbers', 'initial_magmoms', 'initial_charges', 'masses', - 'tags', 'momenta', 'stress', 'dipole', 'magmoms', 'charges'] - - arrays_2D = ['positions', 'cell', 'forces'] - - txt2jsonb = ['calculator_parameters', 'key_value_pairs'] - - for column in arrays_1D: - if column in ['numbers', 'tags']: - dtype = 'INTEGER' - else: - dtype = 'DOUBLE PRECISION' - sql = sql.replace(f'{column} BLOB,', - f'{column} {dtype}[],') - for column in arrays_2D: - sql = sql.replace(f'{column} BLOB,', - f'{column} DOUBLE PRECISION[][],') - for column in txt2jsonb: - sql = sql.replace(f'{column} TEXT,', - f'{column} JSONB,') - - sql = sql.replace('data BLOB,', 'data JSONB,') - - return sql diff -pruN 3.24.0-1/ase/db/project.py 3.26.0-1/ase/db/project.py --- 3.24.0-1/ase/db/project.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/project.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from pathlib import Path from ase.db.core import KeyDescription diff -pruN 3.24.0-1/ase/db/row.py 3.26.0-1/ase/db/row.py --- 3.24.0-1/ase/db/row.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/row.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,4 +1,6 @@ -from random import randint +# fmt: off + +import uuid from typing import Any, Dict import numpy as np @@ -35,7 +37,7 @@ def atoms2dict(atoms): dct = { 'numbers': atoms.numbers, 'positions': atoms.positions, - 'unique_id': '%x' % randint(16**31, 16**32 - 1)} + 'unique_id': uuid.uuid4().hex} if atoms.pbc.any(): dct['pbc'] = atoms.pbc if atoms.cell.any(): diff -pruN 3.24.0-1/ase/db/sqlite.py 3.26.0-1/ase/db/sqlite.py --- 3.24.0-1/ase/db/sqlite.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/sqlite.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + """SQLite3 backend. Versions: diff -pruN 3.24.0-1/ase/db/table.py 3.26.0-1/ase/db/table.py --- 3.24.0-1/ase/db/table.py 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/table.py 2025-08-12 11:26:23.000000000 +0000 @@ -1,3 +1,5 @@ +# fmt: off + from typing import List, Optional import numpy as np @@ -58,11 +60,17 @@ def cutlist(lst, length): class Table: - def __init__(self, connection, unique_key='id', verbosity=1, cut=35): + def __init__( + self, + connection, + unique_key: str = 'id', + verbosity: int = 1, + cut: int = 35, + ): self.connection = connection self.verbosity = verbosity self.cut = cut - self.rows = [] + self.rows: list[Row] = [] self.columns = None self.id = None self.right = None diff -pruN 3.24.0-1/ase/db/templates/js.html 3.26.0-1/ase/db/templates/js.html --- 3.24.0-1/ase/db/templates/js.html 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/templates/js.html 2025-08-12 11:26:23.000000000 +0000 @@ -1,9 +1,7 @@ - - - - - - - - - \ No newline at end of file + + + + + + + diff -pruN 3.24.0-1/ase/db/templates/layout.html 3.26.0-1/ase/db/templates/layout.html --- 3.24.0-1/ase/db/templates/layout.html 2024-12-28 21:22:10.000000000 +0000 +++ 3.26.0-1/ase/db/templates/layout.html 2025-08-12 11:26:23.000000000 +0000 @@ -3,8 +3,8 @@ -{% include 'ase/db/templates/js.html' %} {% include 'ase/db/templates/style.html' %} +{% include 'ase/db/templates/js.html' %} {% block head %} {% endblock %} @@ -14,9 +14,9 @@ -
+
-