initial commit

.github/workflows/black.yml

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+# This workflow is used to check the differences and find conflict markers or whitespace errors
+
+name: Black
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: psf/black@stable
+      with:
+        options: "--check --diff"
+        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
+# Based on https://github.com/pypa/gh-action-pypi-publish
+
+name: PyPi Release
+
+on:
+    push:
+    pull_request:
+    workflow_dispatch:
+
+jobs:
+  build:
+    if: startsWith(github.event.ref, 'refs/tags') || github.event_name == 'release'
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/${{ github.event.repository.name }}
+    permissions:
+      id-token: write
+    steps:
+    - uses: actions/checkout@v4
+    - name: Build
+      shell: bash -l {0}
+      run: |
+        pip install versioneer[toml]==0.29
+        python setup.py sdist bdist_wheel
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

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

CODE_OF_CONDUCT.md

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

LICENSE

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

MANIFEST.in

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+include LICENSE

pyiron_dataclasses/v1/calculation.py

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

pyiron_dataclasses/v1/generic.py

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

pyiron_dataclasses/v1/job.py

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+from dataclasses import dataclass
+from typing import List, Optional
+
+
+@dataclass
+class Executable:
+    name: str
+    operation_system_nt: bool
+    mpi: bool
+    accepted_return_codes: List[int]
+    version: Optional[str] = None
+    executable: Optional[str] = None
+
+
+@dataclass
+class Server:
+    user: str
+    host: str
+    run_mode: str
+    cores: int
+    threads: Optional[int] = 1
+    new_hdf: Optional[bool] = True
+    accept_crash: Optional[bool] = False
+    additional_arguments: Optional[dict] = None
+    gpus: Optional[int] = None
+    run_time: Optional[int] = None  # [seconds]
+    memory_limit: Optional[str] = None
+    queue: Optional[str] = None
+    qid: Optional[int] = None
+    conda_environment_name: Optional[str] = None
+    conda_environment_path: Optional[str] = None