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‎.github/workflows/black.yml‎

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# This workflow is used to check the differences and find conflict markers or whitespace errors
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name: Black
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on:
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push:
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branches: [ main ]
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pull_request:
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: psf/black@stable
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with:
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options: "--check --diff"
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src: ./${{ github.event.repository.name }}

‎.github/workflows/deploy.yml‎

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# This workflow is used to upload and deploy a new release to PyPi
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# Based on https://github.com/pypa/gh-action-pypi-publish
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name: PyPi Release
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on:
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push:
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pull_request:
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workflow_dispatch:
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jobs:
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build:
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if: startsWith(github.event.ref, 'refs/tags') || github.event_name == 'release'
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/${{ github.event.repository.name }}
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permissions:
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id-token: write
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steps:
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- uses: actions/checkout@v4
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- name: Build
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shell: bash -l {0}
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run: |
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pip install versioneer[toml]==0.29
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python setup.py sdist bdist_wheel
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- name: Publish distribution 📦 to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.6.8
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hooks:
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- id: ruff
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name: ruff lint
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args: ["--select", "I", "--fix"]
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files: ^pyiron_dataclasses/
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- id: ruff-format
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name: ruff format

‎CODE_OF_CONDUCT.md‎

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# Contributor Covenant Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to making participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, sex characteristics, gender identity and expression,
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level of experience, education, socio-economic status, nationality, personal
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appearance, race, religion, or sexual identity and orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment
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include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic
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address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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## Scope
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This Code of Conduct applies both within project spaces and in public spaces
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when an individual is representing the project or its community. Examples of
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representing a project or community include using an official project e-mail
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address, posting via an official social media account, or acting as an appointed
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representative at an online or offline event. Representation of a project may be
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further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the project team at pyiron@mpie.de. All
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complaints will be reviewed and investigated and will result in a response that
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is deemed necessary and appropriate to the circumstances. The project team is
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obligated to maintain confidentiality with regard to the reporter of an incident.
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Further details of specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
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available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
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[homepage]: https://www.contributor-covenant.org
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For answers to common questions about this code of conduct, see
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https://www.contributor-covenant.org/faq

‎LICENSE‎

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BSD 3-Clause License
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Copyright (c) 2018, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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* Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎MANIFEST.in‎

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include LICENSE

‎pyiron_dataclasses/__init__.py‎

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‎pyiron_dataclasses/v1/__init__.py‎

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‎pyiron_dataclasses/v1/calculation.py‎

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from dataclasses import dataclass
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from typing import List, Optional, Union
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@dataclass
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class CalculateMolecularDynamics:
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temperature: float
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pressure: Optional[Union[float, List[float]]]
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n_ionic_steps: int
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time_step: float
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n_print: int
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temperature_damping_timescale: float
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pressure_damping_timescale: float
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seed: Optional[int]
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tloop: Optional[float]
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initial_temperature: Optional[float]
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langevin: bool
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delta_temp: Optional[float]
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delta_press: Optional[float]
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@dataclass
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class CalculateMinimize:
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ionic_energy_tolerance: float
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ionic_force_tolerance: float
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e_tol: Optional[float]
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f_tol: Optional[float]
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max_iter: int
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pressure: Optional[Union[float, List[float]]]
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n_print: int
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style: str

‎pyiron_dataclasses/v1/generic.py‎

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from dataclasses import dataclass
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import numpy as np
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from typing import Optional, List
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@dataclass
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class DensityOfStates:
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energies: str
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int_densities: str
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tot_densities: str
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@dataclass
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class ElectronicStructure:
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efermi: float
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eig_matrix: np.ndarray
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k_points: np.ndarray
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k_weights: np.ndarray
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occ_matrix: np.ndarray
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dos: DensityOfStates
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@dataclass
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class OutputGenericDFT:
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energy_free: np.ndarray
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energy_int: np.ndarray
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energy_zero: np.ndarray
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scf_energy_free: np.ndarray
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scf_energy_int: np.ndarray
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scf_energy_zero: np.ndarray
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cbm_list: Optional[np.ndarray]
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e_fermi_list: Optional[np.ndarray]
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final_magmoms: Optional[np.ndarray]
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magnetization: Optional[np.ndarray]
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n_elect: Optional[float]
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n_valence: Optional[dict]
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potentiostat_output: Optional[np.ndarray]
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bands_k_weights: Optional[np.ndarray]
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kpoints_cartesian: Optional[np.ndarray]
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bands_e_fermi: Optional[np.ndarray]
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bands_occ: Optional[np.ndarray]
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bands_eigen_values: Optional[np.ndarray]
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scf_convergence: Optional[List[bool]]
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scf_dipole_mom: Optional[np.ndarray]
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scf_computation_time: Optional[np.ndarray]
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valence_charges: Optional[np.ndarray]
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vbm_list: Optional[np.ndarray]
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bands: Optional[ElectronicStructure]
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scf_energy_band: Optional[np.ndarray]
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scf_electronic_entropy: Optional[np.ndarray]
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scf_residue: Optional[np.ndarray]
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computation_time: Optional[np.ndarray]
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energy_band: Optional[np.ndarray]
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electronic_entropy: Optional[np.ndarray]
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residue: Optional[np.ndarray]
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@dataclass
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class GenericOutput:
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cells: np.ndarray # N_steps * 3 *3 [Angstrom]
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energy_pot: np.ndarray # N_steps [eV]
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energy_tot: np.ndarray # N_steps [eV]
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forces: np.ndarray # N_steps * N_atoms * 3 [eV/Angstrom]
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positions: np.ndarray # N_steps * N_atoms * 3 [Angstrom]
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volume: np.ndarray # N_steps
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indices: Optional[np.ndarray] # N_steps * N_atoms
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natoms: Optional[np.ndarray] # N_steps
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pressures: Optional[np.ndarray] # N_steps * 3 * 3
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steps: Optional[np.ndarray] # N_steps
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stresses: Optional[np.ndarray] # N_steps
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temperature: Optional[np.ndarray] # N_steps
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unwrapped_positions: Optional[np.ndarray] # N_steps * N_atoms * 3 [Angstrom]
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velocities: Optional[np.ndarray] # N_steps * N_atoms * 3 [Angstrom/fs]
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dft: Optional[OutputGenericDFT]
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elastic_constants: Optional[np.ndarray]
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@dataclass
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class ChargeDensity:
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total: np.ndarray
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@dataclass
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class Server:
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user: str
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host: str
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run_mode: str
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cores: int
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threads: int
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new_h5: bool
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accept_crash: bool
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run_time: int # [seconds]
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structure_id: Optional[int]
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memory_limit: Optional[str]
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queue: Optional[str]
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qid: Optional[int]
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@dataclass
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class Executable:
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version: str
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name: str
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operation_system_nt: bool
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executable: Optional[str]
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mpi: bool
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accepted_return_codes: List[int]
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@dataclass
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class GenericDict:
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restart_file_list: list
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restart_file_dict: dict
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exclude_nodes_hdf: list
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exclude_groups_hdf: list
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@dataclass
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class Interactive:
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interactive_flush_frequency: int
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interactive_write_frequency: int
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@dataclass
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class GenericInput:
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calc_mode: str
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structure: str
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fix_symmetry: Optional[bool]
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k_mesh_spacing: Optional[float]
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k_mesh_center_shift: Optional[np.ndarray]
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reduce_kpoint_symmetry: Optional[bool]
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restart_for_band_structure: Optional[bool]
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path_name: Optional[str]
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n_path: Optional[str]
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fix_spin_constraint: Optional[bool]
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max_iter: Optional[int]
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temperature: Optional[float]
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n_ionic_steps: Optional[int]
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n_print: Optional[int]
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temperature_damping_timescale: Optional[float]
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pressure_damping_timescale: Optional[float]
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time_step: Optional[int]
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@dataclass
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class Units:
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length: str
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mass: str
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@dataclass
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class Cell:
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cell: np.ndarray # 3 * 3 [Angstrom]
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pbc: np.ndarray # 3
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@dataclass
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class Structure:
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dimension: int
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indices: np.array
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info: dict
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positions: np.ndarray # N_atoms * 3 [Angstrom]
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species: List[str]
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cell: Cell
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units: Units

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