agox 3.11.0__tar.gz → 3.11.1__tar.gz

agox-3.11.1/.gitignore

@@ -0,0 +1,28 @@
+# Python related:
+**/__pycache__
+.ipynb_checkpoints/
+pip-wheel-metadata/
+agox.egg-info
+
+# Cython related
+*.c
+*.so
+.o
+
+# Documentation related:
+docs/build/
+docs/_build/
+docs/source/autoapi
+
+
+# Test related:
+agox/test/run_tests/expected_outputs/*/*.png
+BA_data/
+
+# VSCode related:
+.vscode/
+.venv
+.venv/
+
+# CI Related
+.gitlab-ci-local/

agox-3.11.1/.gitlab/build.yml

@@ -0,0 +1,29 @@
+build-dist:
+  stage: build
+  image: python:3.11
+  rules:
+    - if: $CI_COMMIT_TAG
+      allow_failure: false
+    - if: $CI_PIPELINE_SOURCE == 'merge_request_event'
+      when: manual
+      allow_failure: true
+    # If you also want this on main to catch issues early, add:
+    # - if: '$CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH'
+  variables:
+    GIT_STRATEGY: fetch
+    GIT_DEPTH: "0"           # make tags visible to hatch-vcs / setuptools-scm
+  before_script:
+    - apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*
+    - python -m pip install -U pip build twine
+  script:
+    - git describe --tags --always || true
+    - python -m build --sdist --wheel --outdir dist
+    - twine check dist/*
+    # Sanity: print the version inside the built wheel
+    - python -c "import importlib.metadata as m; print('wheel version:', m.version('agox'))"
+  artifacts:
+    paths: [dist/]
+    expire_in: 1 week
+  needs:
+    - job: tests
+      optional: true   # if your tests job exists; remove if not needed

agox-3.11.1/.gitlab/docs.yml

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+build_pages:
+  stage: docs
+  extends: .install_docs
+  needs: []
+  image: python:3.10
+  script:
+    - make -C docs html
+  artifacts:
+    paths:
+      - docs/build/html/
+    expire_in: 3 days
+    expose_as: "Docs preview"
+  rules:
+    - if: $CI_PIPELINE_SOURCE == 'merge_request_event'
+  when: manual
+
+pages:
+  stage: docs
+  extends: .install_docs
+  image: python:3.10
+  needs:
+    - test-python3.10
+  script:
+    - coverage html -d docs/source/_static/htmlcov
+    - make -C docs html
+  when: on_success
+  artifacts:
+    paths:
+      - docs/build/html
+  publish: docs/build/html
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'dev'
+

agox-3.11.1/.gitlab/tests.yml

@@ -0,0 +1,57 @@
+.test:
+  extends: .install_agox
+  stage: test
+  script: 
+  - coverage run -m pytest -rsv --junit-xml=report.xml # Generate test report in junit format
+  - coverage report # for displaying coverage in job logs
+  - coverage xml    # for generating coverage.xml report
+  coverage: '/^TOTAL.+?(\d+\%)$/'
+  artifacts:
+    when: always
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+      junit: report.xml
+  interruptible: true
+  rules:
+    # Scheduled pipelines: required
+    - if: $CI_PIPELINE_SOURCE == 'schedule'
+      allow_failure: false
+    # Pre-releases (required on tags)
+    - if: '$CI_COMMIT_TAG =~ /^v.*(a|b|rc)\d+$/'
+      allow_failure: false
+    # Stable releases (required on tags)
+    - if: '$CI_COMMIT_TAG =~ /^v\d+\.\d+\.\d+$/'
+      allow_failure: false
+    # Merge requests: optional/manual
+    - if: $CI_PIPELINE_SOURCE == 'merge_request_event'
+      when: manual
+      allow_failure: true
+
+test-python3.10:
+  extends: .test
+  image: python:3.10
+  rules:
+    - if: $CI_COMMIT_BRANCH == 'dev'
+    - if: $CI_PIPELINE_SOURCE == 'merge_request_event'
+    - if: $CI_PIPELINE_SOURCE == 'schedule'
+    - if: '$CI_COMMIT_TAG =~ /^v\d+\.\d+\.\d+$/'
+    - if: '$CI_COMMIT_TAG =~ /^v.*(a|b|rc)\d+$/'
+  artifacts:
+    paths:
+      - .coverage
+
+test-python3.11:
+  extends: .test
+  image: python:3.11
+
+test-python3.12:
+  extends: .test
+  image: python:3.12
+
+test-python3.13:
+  extends: .test
+  image: python:3.13
+  when: manual
+  allow_failure: true

agox-3.11.1/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+* Removed upperbound on NumPy, affects only sparingly used matscipy neighbourlist that will fallback to using ASE. 
+
+## [3.11.0] - 2025-08-15
+
+* Moved build system to CI for making it easier to manage releases.
+* Added Grand Canonical modules.
+
+## [3.10.2] - 2025-06-24
+
+* Fixed issue with package discovery breaking non-editable installs.
+
+## [3.10.1] - 2025-06-24 
+
+* Yanked this release.
+* Failure
+
+## [3.10.0]
+
+### Added
+
+* `CalculatorModel` and `CompositionModel` both intended for use with universal potentials.
+* Added replica exchange modules: a sampler, a collector and an acquisitor. 
+* Added replica exchange documentation with two scripts: one short test script and one real DFT script.
+
+### Fixed
+
+* Fixed LCB-penalty acquisition function after changes in 3.9.0
+* Added `check_callback` to allow calculations to be discarded according to user defined criteria. 
+
+## [3.9.0] - 2024-10-23
+
+### Changed
+
+* Analysis code refactored into several modules and classes, rather than monolithic `batch_analysis`
+* Analysis code has almost full test coverage now.
+* Updated CLI tools to use `click` rather than `ArgumentParser` some changes to flags.
+* Python version requirement increased to `3.10` or higher. Tests will run on `3.10` for merge requests to `dev` or `stable` and weekly tests will run `3.10`, `3.11`, `3.12`. Motivated by newest Scipy and Numpy 
+version not support `3.8` or `3.9`.
+* Numpy version locked to `<2` at least until `GPAW` releases a version that allows `>2`.
+* Added ruff rules to `pyproject.toml`
+* Refactoring of Observer code into several modules and some clean up of the logic, should be more approachable now. 
+* Removal of 'Tracker' as it was an entirely unused feature. 
+* Rewritten and simplified `Writer` using `rich` for easy construction of more elaborate output layouts. 
+* Refactoring of `Confinement`-class - is now not inherited from but created by classes that use it. Simplifies inheritance patterns and 
+makes the `Confinement`-class more versatile.
+* Installation problem fixed with changes to `pyproject.toml`. 
+
+## [3.8.0] - 2024-8-26
+
+### Added
+
+* Added surface centering postprocessor
+* Added adsorption site-aware Voronoi graph descriptor
+* Added LCB-penalty acquisition function
+* Added Ray-based Parallel Tempering implementation and renamed old implementation to Concurrent Tempering.
+
+## [3.7.0] - 2024-8-2
+
+### Added
+
+* Improved Ray stability by trying to avoid asking for too many resources at once and refactored a bit more.
+* Added additional plotting utility to more easily create plots with custom color schemes.
+* Fixed issue with BoxConstraint lacking methods used by ASE's VASP calculator.
+* Added parity plot functionality and some simple metrics.
+* Revamped some tests and added examples with different calculators to documentation.
+* Added Ensemble LGPR model.
+
+## [3.6.0] - 2024-4-2
+
+### Added
+
+* Added symmetry generators.
+* Changed the internal workings of generators & samplers. Better support for generators that have multiple parents.
+* Removed use of custom docker image for testing, added testing pipelines for other python versions.
+* Scheduling functionality for the SparseGPR to control how often sparsification is done during a search.
+* Printing of git commit sha with the version with the AGOX logo at the start of a run.
+* Sparse GPR no longer trains projected process uncertainty by default, as it can be very slow.
+* Sparse GPR saves fewer attributes with model.save, resulting in much smaller files.
+* Plots produced by generators now indicate atoms that are fixed.
+* Block generators added that place blocks of atoms (rattle and random
+  implemented)
+* MD generator added.
+
+### Changed
+
+* Changelog using Keep a Changelog guidelines.
+
+### Fixed
+
+* Fixed bug in visual ordering of atoms plotted with `plot_atoms` when the `repeat` option is used.
+
+## [3.5.3] - 2023-12-19
+
+### Added
+
+* Added wrap keyword in BoxConstraint to control if atoms are wrapped
+  inside periodic confinement directions. Default is false to conform
+  with BFGS.
+
+## [3.5.2] - 2023-11-16
+
+### Added
+
+* Added SafeBFGS which fixes an issue where relaxations take an indefinite amount of time due the Hessian becoming singular and the optimization step containing nans.
+
+## [3.5.1] - 2023-11-15
+
+### Fixed
+
+* Fixes issue where jobs using Ray often crash at the very beginning of the run.
+
+## [3.5.0] - 2023-11-07
+
+### Changed
+
+* Small updates to Ray, but installing Ray with more dependencies easist option is to do `pip install ray[default]`.
+
+## [3.4.0] - 2023-10-26
+
+### Added
+
+* Added a postprocessor to filter disjoint candidates.
+
+## [3.3.0] - 2023-10-17
+
+### Added
+
+* Added coverage report to gitlab CI.
+
+## [3.2.5] - 2023-10-17
+
+### Added
+
+* Added a method to make it easier handle transfer and regular data with the sparse GPR.
+
+## [3.2.4] - 2023-10-16
+
+### Changed
+
+* Minor documentation fixes.
+
+## [3.2.3] - 2023-10-09
+
+### Fixed
+
+* Bug fixes for sparsifiers and added a test for sparsifiers.
+
+## [3.2.2] - 2023-09-22
+
+### Fixed
+
+* Bug fixes related to Cython release of 3+
+
+## [3.2.1] - 2023-09-14
+
+### Changed
+
+* Pin Cython to 0.29.36
+
+## [3.2.0] - 2023-09-08
+
+### Added
+
+* Added possibility to train sparse GPRs on energies and forces.
+
+## [3.1.2] - 2023-09-08
+
+### Fixed
+
+* Fixed bug where the DescriptorBaseClass takes kwargs and therefore wouldnt throw an error for unused keyword arguments leading to unintended behaviour.
+
+## [3.1.1] - 2023-08-07
+
+### Fixed
+
+* Bugfix for `_make_local_sigma` method
+
+## [3.1.0] - 2023-07-18
+
+### Added
+
+* Updated documentation about Ray and about using filters to analyze structures, both are in bonus topics.
+* Added FeatureDistanceFilter and a test for it.
+
+## [3.0.0] - 2023-07-10
+
+### Changed
+
+* Rewritten GPR and SparseGPR models able to handle both global and local descriptors
+* GPR kernels inheriting from Scikit-learn, but with added functionality
+* Descriptor initialization has changed to better fit into standard AGOX use.
+
+### Added
+
+* Parallel hyperparameter optimization using Ray.
+* Filters and sparsifiers to use with GPR models
+* Ability to add validation data to models.
+* New and improved save/load format for models
+* Analytical forces
+* Uncertainty quantification with projected process for Sparse GPR
+* Analytical uncertainty forces
+* Marginal likelihood for Sparse GPR
+* Monte Carlo hyperparameter optimization for Sparse GPR
+
+## [2.3.0] - 2023-05-02
+
+### Changed
+
+* Gitlab CI now enabled.
+* Plotting code cleaned up.
+* Replaced the logger with a more general tracker module.
+
+### Fixed
+
+* GPAW_IO bug fixes.
+* Bug fixes for parallel collector with updatable generators.
+
+### Added
+
+* Complemenetary Energy Generator added.
+* Cache for e.g. descriptors added.
+
+### Removed
+
+* Removed 'test_scripts' directory which was not supposed to be used anymore.
+
+[Unreleased]: https://gitlab.com/agox/agox/-/compare/v3.9.0...dev
+[3.9.0]: https://gitlab.com/agox/agox/-/compare/v3.8.0...v3.9.0
+[3.8.0]: https://gitlab.com/agox/agox/-/compare/v3.7.0...v3.8.0
+[3.7.0]: https://gitlab.com/agox/agox/-/compare/v3.6.0...v3.7.0
+[3.6.0]: https://gitlab.com/agox/agox/-/compare/v3.5.2...v3.6.0
+[3.5.2]: https://gitlab.com/agox/agox/-/compare/v3.5.1...v3.5.2
+[3.5.1]: https://gitlab.com/agox/agox/-/compare/v3.5.0...v3.5.1
+[3.5.0]: https://gitlab.com/agox/agox/-/compare/v3.4.0...v3.5.0
+[3.4.0]: https://gitlab.com/agox/agox/-/compare/v3.3.0...v3.4.0
+[3.3.0]: https://gitlab.com/agox/agox/-/compare/v3.2.5...v3.3.0
+[3.2.5]: https://gitlab.com/agox/agox/-/compare/v3.2.4...v3.2.5
+[3.2.4]: https://gitlab.com/agox/agox/-/compare/v3.2.3...v3.2.4
+[3.2.3]: https://gitlab.com/agox/agox/-/compare/v3.2.2...v3.2.3
+[3.2.2]: https://gitlab.com/agox/agox/-/compare/v3.2.1...v3.2.2
+[3.2.1]: https://gitlab.com/agox/agox/-/compare/v3.2.0...v3.2.1
+[3.2.0]: https://gitlab.com/agox/agox/-/compare/v3.1.2...v3.2.0
+[3.1.2]: https://gitlab.com/agox/agox/-/compare/v3.1.1...v3.1.2
+[3.1.1]: https://gitlab.com/agox/agox/-/compare/v3.1.0...v3.1.1
+[3.1.0]: https://gitlab.com/agox/agox/-/compare/v3.0.0...v3.1.0
+[3.0.0]: https://gitlab.com/agox/agox/-/compare/v2.3.0...v3.0.0
+[2.3.0]: https://gitlab.com/agox/agox/-/compare/v2.2.1...v2.3.0

agox-3.11.1/PKG-INFO

@@ -0,0 +1,111 @@
+Metadata-Version: 2.4
+Name: agox
+Version: 3.11.1
+Summary: Atomistic Global Optimziation X is a framework for structure optimization in materials science.
+Author: AGOX Developers
+Author-email: "Mads-Peter V. Christiansen" <machri@phys.au.dk>, Nikolaj Rønne <nronne@phys.au.dk>, Bjørk Hammer <hammer@phys.au.dk>
+License-Expression: GPL-3.0-only
+Project-URL: homepage, https://agox.gitlab.io/agox/
+Project-URL: Repository, https://gitlab.com/agox/agox
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: numpy>=2
+Requires-Dist: scipy
+Requires-Dist: ase
+Requires-Dist: matplotlib
+Requires-Dist: cymem
+Requires-Dist: scikit-learn
+Requires-Dist: h5py
+Requires-Dist: dscribe>=2.0.0
+Requires-Dist: ray
+Requires-Dist: rich-click>=1.8.3
+Requires-Dist: pydantic>=2.11.7
+Requires-Dist: ase-ga>=1.0.3
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-mock; extra == "test"
+Requires-Dist: pytest-regressions; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: furo; extra == "docs"
+Requires-Dist: sphinx-autoapi; extra == "docs"
+Requires-Dist: sphinx-copybutton; extra == "docs"
+Requires-Dist: sphinx-tabs; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Requires-Dist: sphinx-autobuild; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Requires-Dist: myst-nb; extra == "docs"
+Requires-Dist: sphinx-substitution-extensions; extra == "docs"
+Requires-Dist: ipywidgets; extra == "docs"
+Provides-Extra: torchjax
+Requires-Dist: torch; extra == "torchjax"
+Requires-Dist: jax; extra == "torchjax"
+Requires-Dist: jaxlib; extra == "torchjax"
+Requires-Dist: typing_extensions; extra == "torchjax"
+Requires-Dist: matscipy; extra == "torchjax"
+Provides-Extra: all
+Requires-Dist: agox[docs,test]; extra == "all"
+Dynamic: license-file
+
+# Atomistic Global Optimization X (AGOX)
+
+![logo](docs/source/logos/logo-carbon.gif)
+
+
+AGOX is a package for global optimization of atomic system using e.g. the energy 
+calculated from density functional theory as the objective function. AGOX interfaces 
+with the Atomistic Simulation Environment (ASE) and as such supports any of 
+calculators in ASE as objectives for optimization. 
+
+AGOX is built to be flexible, consisting of modules that can be put together to 
+create an optimization algorithm, from simple random searches to Bayesian searches 
+guided by a surrogate model and many more. 
+
+Check out the documentation at 
+
+https://agox.gitlab.io/agox/
+
+## Installation
+
+AGOX can be installed from PyPI 
+
+```
+pip install agox
+```
+
+Or from source by cloning the repo.
+
+## Contributions & Issues 
+
+Feel free to make a fork and submit a merge request! 
+
+If you have an issue or a question please post it on the issue board! 
+
+## Authors 
+
+The main AGOX framework has been written by 
+* Mads-Peter Verner Christiansen
+* Nikolaj Rønne
+* Bjørk Hammer
+
+with inspiration and help from current and previous members of the Hammer group at Aarhus University, Denmark.
+Parts of the code have been contributed by
+
+* Andreas Slavensky (Complementary Energy Generator)
+* Florian Brix (Symmetry generators)
+* Joe Pitfield (Replica-exchange)
+* Jon Eunan Quinlivan Dominguez (Grand canonical)
+
+## License
+
+AGOX is released under the GPLv3 license. 
+
+

agox-3.11.1/README.md

@@ -0,0 +1,54 @@
+# Atomistic Global Optimization X (AGOX)
+
+![logo](docs/source/logos/logo-carbon.gif)
+
+
+AGOX is a package for global optimization of atomic system using e.g. the energy 
+calculated from density functional theory as the objective function. AGOX interfaces 
+with the Atomistic Simulation Environment (ASE) and as such supports any of 
+calculators in ASE as objectives for optimization. 
+
+AGOX is built to be flexible, consisting of modules that can be put together to 
+create an optimization algorithm, from simple random searches to Bayesian searches 
+guided by a surrogate model and many more. 
+
+Check out the documentation at 
+
+https://agox.gitlab.io/agox/
+
+## Installation
+
+AGOX can be installed from PyPI 
+
+```
+pip install agox
+```
+
+Or from source by cloning the repo.
+
+## Contributions & Issues 
+
+Feel free to make a fork and submit a merge request! 
+
+If you have an issue or a question please post it on the issue board! 
+
+## Authors 
+
+The main AGOX framework has been written by 
+* Mads-Peter Verner Christiansen
+* Nikolaj Rønne
+* Bjørk Hammer
+
+with inspiration and help from current and previous members of the Hammer group at Aarhus University, Denmark.
+Parts of the code have been contributed by
+
+* Andreas Slavensky (Complementary Energy Generator)
+* Florian Brix (Symmetry generators)
+* Joe Pitfield (Replica-exchange)
+* Jon Eunan Quinlivan Dominguez (Grand canonical)
+
+## License
+
+AGOX is released under the GPLv3 license. 
+
+

agox-3.11.1/agox/acquisitors/EI.py

@@ -0,0 +1,54 @@
+import numpy as np
+from scipy.stats import norm
+
+from agox.acquisitors import AcquisitorBaseClass
+from agox.observer import Observer
+
+
+class ExpectedImprovementAcquisitor(AcquisitorBaseClass):
+    name = "EIAcquisitor"
+
+    def __init__(self, model, database, xi=0.01, **kwargs):
+        super().__init__(**kwargs)
+        self.model = model
+        self.xi = xi
+        self.lowest_energy = 10e10
+        self.add_observer_method(self.update, sets={}, gets={}, order=0, handler_identifier="database")
+        self.attach(database)
+
+    def calculate_acquisition_function(self, candidates):
+        fitness = np.zeros(len(candidates))
+        for i, candidate in enumerate(candidates):
+            E, sigma = self.model.predict_energy_and_uncertainty(candidate)
+            fitness[i] = self.acquisition_function(E, sigma)
+            candidate.add_meta_information("model_energy", E)
+            candidate.add_meta_information("uncertainty", sigma)
+        return fitness
+
+    def acquisition_function(self, E, sigma):
+        mu = E
+        mu_opt = self.lowest_energy
+        with np.errstate(divide="warn"):
+            imp = mu_opt - mu - self.xi
+            Z = imp / sigma
+            ei = imp * norm.cdf(Z) + sigma * norm.pdf(Z)
+        return -ei
+
+    def print_information(self, candidates, acquisition_values):
+        if self.do_check():
+            for i, candidate in enumerate(candidates):
+                fitness = acquisition_values[i]
+                E = candidate.get_meta_information("model_energy")
+                sigma = candidate.get_meta_information("uncertainty")
+                self.writer(f"Candidate {i}: E = {E:8.3f}, s = {sigma:8.3f}, EI = {fitness:8.6f}")
+
+    @Observer.observer_method
+    def update(self, database, state):
+        self.lowest_energy = database.get_best_energy()
+        self.writer("Lowest energy: {}".format(self.lowest_energy))
+
+    def do_check(self, **kwargs):
+        return self.model.ready_state
+    
+    def get_acquisition_calculator(self):
+        return self.model

agox-3.11.1/agox/algorithms/__init__.py

@@ -0,0 +1,39 @@
+# ruff: noqa: I001, E402
+from agox.algorithms.config import ProblemConfig, RunConfig, BaseConfig
+
+from agox.algorithms.parallel_composable import ParallelAlgorithm
+from agox.algorithms.algorithm import Algorithm, AlgorithmConfig
+
+from agox.algorithms.rss import RandomStructureSearch, RandomSearchConfig
+from agox.algorithms.rss_surrogate import SurrogateRandomStructureSearch, SurrogateRandomSearchConfig
+from agox.algorithms.gofee import GOFEE, GOFEEConfig
+from agox.algorithms.basin_hopping import BasinHopping, BasinHoppingConfig
+from agox.algorithms.basin_hopping_surrogate import SurrogateBasinHopping, SurrogateBasinHoppingConfig
+from agox.algorithms.replica_exchange import ReplicaExchange, ReplicaExchangeConfig
+
+from agox.algorithms.api import create_search
+
+__all__ = [
+    # Algorithm configurations
+    'BaseConfig',
+    'ProblemConfig',
+    'RunConfig',
+    'AlgorithmConfig',
+    'ParallelAlgorithm',
+    'Algorithm',
+    # Algorithm implementations
+    'RandomStructureSearch',
+    'RandomSearchConfig',
+    'SurrogateRandomStructureSearch',
+    'SurrogateRandomSearchConfig',
+    'GOFEE',
+    'GOFEEConfig',
+    'BasinHopping',
+    'BasinHoppingConfig',
+    'SurrogateBasinHopping',
+    'SurrogateBasinHoppingConfig',
+    'ReplicaExchange',
+    'ReplicaExchangeConfig',
+    # Algorithm API
+    'create_search'
+]