agox 3.10.2rc1__tar.gz → 3.11.0__tar.gz

agox-3.11.0/.gitignore

@@ -0,0 +1,29 @@
+# Python related:
+**/__pycache__
+.ipynb_checkpoints/
+pip-wheel-metadata/
+agox.egg-info
+
+# Cython related
+*.c
+*.so
+.o
+
+# Documentation related:
+docs/build/
+docs/old_stuff/
+
+# Test related:
+agox/test/run_tests/expected_outputs/*/*.png
+BA_data/
+
+# VSCode related:
+.vscode/
+.venv
+.venv/
+
+# CI Related
+.gitlab-ci-local/
+
+# Other
+uv.lock

agox-3.11.0/.gitlab/build.yml

@@ -0,0 +1,27 @@
+build-dist:
+  stage: build
+  image: python:3.11
+  rules:
+    - if: $CI_COMMIT_TAG          # run only on tag pipelines in Phase 1
+    - if: $CI_PIPELINE_SOURCE == 'merge_request_event'
+      when: manual
+    # If you also want this on main to catch issues early, add:
+    # - if: '$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 (replace DISTNAME)
+    - 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-3.11.0/.gitlab/defaults.yml

@@ -0,0 +1,25 @@
+variables:
+  OMP_NUM_THREADS: "1"
+  DEFAULT_PYTHON_VERSION: "3.11"
+
+stages:
+  - test
+  - docs
+  - build
+  - verify
+  - publish
+
+.install_agox:
+  before_script:
+    - pip install virtualenv
+    - virtualenv venv
+    - source venv/bin/activate
+    - pip install --upgrade pip setuptools 
+    - pip install pytest coverage
+    - pip install -e .[test]
+    - pip list
+
+.install_docs:    
+  before_script:
+    - !reference [.install_agox, before_script]
+    - pip install -e .[docs]

agox-3.11.0/.gitlab/docs.yml

@@ -0,0 +1,28 @@
+build_pages:
+  stage: docs
+  extends: .install_docs
+  needs: []
+  image: python:3.10
+  script:
+    - make -C docs html
+  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-3.11.0/.gitlab/publish.yml

@@ -0,0 +1,37 @@
+# Release to PyPi
+publish-pypi:
+  stage: publish
+  needs: [build-dist, verify-install]
+  image: python:${DEFAULT_PYTHON_VERSION}
+  environment:
+    name: release           
+    action: start
+  when: manual
+  rules:
+    - if: '$CI_COMMIT_TAG =~ /^v\d+\.\d+\.\d+$/'
+  id_tokens:
+    PYPI_ID_TOKEN:
+      aud: pypi
+  script:
+    - python -m pip install -U twine
+    # Should fix to include wheels.
+    - twine upload dist/*.tar.gz
+
+# Prelease - to TestPyPI
+publish-testpypi:
+  stage: publish
+  needs: [build-dist, verify-install]
+  image: python:${PYTHON_VERSION}
+  environment:
+    name: release                  
+    action: start
+  rules:
+    - if: '$CI_COMMIT_TAG =~ /^v.*(a|b|rc)\d+$/'
+  when: manual
+  id_tokens:
+    PYPI_ID_TOKEN:
+      aud: testpypi                   
+  script:
+    - python -m pip install --upgrade twine
+    # Should fix to include wheels
+    - twine upload --repository-url https://test.pypi.org/legacy/ dist/*.tar.gz

agox-3.11.0/.gitlab/tests.yml

@@ -0,0 +1,55 @@
+.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

agox-3.11.0/.gitlab/verify.yml

@@ -0,0 +1,32 @@
+verify-install:
+  stage: verify
+  needs: [build-dist]                     
+  image: python:${DEFAULT_PYTHON_VERSION}
+  variables:
+    DIST_NAME: "agox"                  
+  script:
+    - set -euo pipefail
+    - python -m pip install -U pip
+    # Prefer wheel if present; otherwise fall back to sdist
+    - if ls dist/*.whl >/dev/null 2>&1; then
+        pip install dist/*.whl;
+      else
+        pip install dist/*.tar.gz;
+      fi
+    # Check if the package is installed correctly by running the CLI
+    - agox --version
+    - agox --help
+
+  rules:
+    # Pre-releases (required on tags)
+    - if: '$CI_COMMIT_TAG =~ /^v.*(a|b|rc)\d+$/'
+      when: on_success
+      allow_failure: false
+    # Stable releases (required on tags)
+    - if: '$CI_COMMIT_TAG =~ /^v\d+\.\d+\.\d+$/'
+      when: on_success
+      allow_failure: false
+    # Merge requests: optional/manual
+    - if: $CI_PIPELINE_SOURCE == 'merge_request_event'
+      when: manual
+      allow_failure: true

agox-3.11.0/.gitlab-ci.yml

@@ -0,0 +1,8 @@
+include:
+  - local: .gitlab/defaults.yml
+  - local: .gitlab/tests.yml
+  - local: .gitlab/docs.yml
+  - local: .gitlab/build.yml
+  - local: .gitlab/verify.yml
+  - local: .gitlab/publish.yml
+  

agox-3.11.0/CHANGELOG.md

@@ -0,0 +1,254 @@
+# 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]
+
+## [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-3.10.2rc1 → agox-3.11.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: agox
-Version: 3.10.2rc1
+Version: 3.11.0
 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>
@@ -13,7 +13,6 @@ 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
@@ -40,6 +39,7 @@ 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"
 Provides-Extra: torchjax
 Requires-Dist: torch; extra == "torchjax"
 Requires-Dist: jax; extra == "torchjax"

{agox-3.10.2rc1 → agox-3.11.0}/agox/__init__.py

@@ -1,14 +1,5 @@
 import os
 
-# Versioning
-__version_info__ = (3, 10, 2)
-__version__ = "{}.{}.{}".format(*__version_info__)
-
-# Extra versioning - Mainly for managing Pypi releases.
-version_extra = os.environ.get("AGOX_VERSION_EXTRA", None)
-if version_extra:
-    __version__ = "{}{}".format(__version__, version_extra)
-
 try:  # When installing the package we don't need to actually import.
     from agox.module import Module  # noqa
     from agox.observer import Observer

agox-3.11.0/agox/acquisitors/GFE_aquisitor.py

@@ -0,0 +1,60 @@
+
+import numpy as np
+
+from agox.acquisitors import LowerConfidenceBoundAcquisitor
+from agox.utils.thermodynamics import ThermodynamicsData, gibbs_free_energy
+
+
+class GibbsFreeEnergyAquisitor(LowerConfidenceBoundAcquisitor):
+    name = "GFEacquisitor"
+
+    def __init__(
+        self,
+        thermo_data: ThermodynamicsData,
+        model: object,
+        kappa: float = 1,
+        **kwargs,
+    ):
+        super().__init__(model, kappa, **kwargs)
+        self.thermo_data = thermo_data
+
+    def calculate_acquisition_function(
+        self, candidates: list
+    ) -> np.array:
+        fitness = np.zeros(len(candidates))
+
+        # Attach calculator and get model_energy
+        for i, candidate in enumerate(candidates):
+            E, sigma = self.model.predict_energy_and_uncertainty(candidate)
+
+            fitness[i] = gibbs_free_energy(candidate=candidate, total_energy=self.acquisition_function(E, sigma), 
+                                           thermo_data=self.thermo_data)
+
+            # For printing:
+            comp = candidate.get_search_formula()
+
+            ##------------------------------
+            candidate.add_meta_information("model_energy", E)
+            candidate.add_meta_information("uncertainty", sigma)
+            candidate.add_meta_information("model_gfe", fitness[i])
+            candidate.add_meta_information("gfe_composition", comp)
+
+        return fitness
+
+    def print_information(self, candidates, acquisition_values):
+        if self.model.ready_state:
+            for i, candidate in enumerate(candidates):
+                fitness = acquisition_values[i]
+
+                GFEmodel = candidate.get_meta_information("model_gfe")
+                composition = candidate.get_meta_information("gfe_composition")
+                Emodel = candidate.get_meta_information("model_energy")
+                sigma = candidate.get_meta_information("uncertainty")
+                description = candidate.get_meta_information("description")
+                self.writer(
+                    "Candidate "
+                    + composition
+                    + ": GFE={:8.3f}, E={:8.3f}, s={:8.3f}, F={:8.3f}, {}".format(
+                        GFEmodel, Emodel, sigma, fitness, description
+                    )
+                )

{agox-3.10.2rc1 → agox-3.11.0}/agox/acquisitors/__init__.py

@@ -23,6 +23,7 @@ Acquisitor: TypeAlias = AcquisitorBaseClass
 from .LCB import LowerConfidenceBoundAcquisitor
 from .LCB_penalty import LCBPenaltyAcquisitor
 from .LCB_power import PowerLowerConfidenceBoundAcquisitor
+from .GFE_aquisitor import GibbsFreeEnergyAquisitor
 from .meta_acquisitor import MetaInformationAcquisitor
 from .replica_exchange.default import ReplicaExchangeAcquisitor
 
@@ -34,5 +35,6 @@ __all__ = [
     "PowerLowerConfidenceBoundAcquisitor",
     "AcquisitonCalculatorBaseClass",
     "MetaInformationAcquisitor",
+    'GibbsFreeEnergyAquisitor',
     "ReplicaExchangeAcquisitor",
 ]

{agox-3.10.2rc1 → agox-3.11.0}/agox/analysis/property/free_energy.py

@@ -2,7 +2,7 @@ import numpy as np
 
 from agox.utils.thermodynamics import ThermodynamicsData, gibbs_free_energy
 
-from .property import ArrayPropertyData, Property
+from .property import ArrayPropertyData, Property, SearchData
 
 
 class FreeEnergyProperty(Property):
@@ -18,15 +18,31 @@ class FreeEnergyProperty(Property):
         self.thermo_data = thermo_data
         self.time_axis = time_axis
 
-    def compute(self, search_data) -> np.array:
-        """
-        Get the energy of the system as a np.array of shape [restarts, iterations].
-        """
+    def get_time_axis(self, search_data: SearchData) -> str:
+        axis_name = self.time_axis.capitalize()
 
         if self.time_axis == "indices":
             indices = search_data.get_all("indices", fill=np.nan)
         elif self.time_axis == "iterations":
             indices = search_data.get_all("iterations", fill=np.nan)
+        else:
+            indices = search_data.get_all("times", fill=np.nan) / self.unit * self.cost_factor
+            if self.cost_factor == 1:
+                axis_name = axis_name + f" [{self.time_unit_symbol}]"
+            else:
+                axis_name = f"CPU cost [{self.time_unit_symbol}]"
+
+        if self.time_axis in ["indices", "iterations"]:
+            axis_name = f"{axis_name} [#]"
+
+        return axis_name, indices
+
+    def compute(self, search_data) -> np.array:
+        """
+        Get the energy of the system as a np.array of shape [restarts, iterations].
+        """
+
+        axis_name, indices = self.get_time_axis(search_data)
 
         candidates = search_data.get_all_candidates()
         energy = search_data.get_all("energies", fill=np.inf)
@@ -40,8 +56,9 @@ class FreeEnergyProperty(Property):
                 free_energy[restart, observation] = gibbs_free_energy(candidate=candidate, thermo_data=self.thermo_data)
 
         free_energy_property = ArrayPropertyData(
-            array=free_energy,
-            property_shape=("Restarts", self.time_axis.copy().capitalize()),
+            data=free_energy,
+            name='Free Energy',
+            shape=("Restarts", axis_name),
             array_axis=(search_data.get_all_identifiers(), indices),
         )