refactor

Author: jan-janssen

pyiron_dataclasses/v1/atomistic.py

@@ -0,0 +1,68 @@
+from dataclasses import dataclass
+import numpy as np
+from typing import Optional, List
+from pyiron_dataclasses.v1.dft import OutputGenericDFT
+
+
+@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 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/dft.py

@@ -0,0 +1,60 @@
+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 ChargeDensity:
+    total: np.ndarray

pyiron_dataclasses/v1/generic.py

@@ -12,6 +12,20 @@ class Executable:
     executable: Optional[str] = None
 
 
+@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 Server:
     user: str

pyiron_dataclasses/v1/job.py

@@ -2,14 +2,16 @@
 from typing import Optional, List
 
 
-from pyiron_dataclasses.v1.generic import (
-    GenericDict,
-    Interactive,
+from pyiron_dataclasses.v1.atomistic import (
     GenericInput,
     GenericOutput,
+    Structure,
+)
+from pyiron_dataclasses.v1.job import (
     Executable,
+    GenericDict,
+    Interactive,
     Server,
-    Structure,
 )
 
 

pyiron_dataclasses/v1/lammps.py

@@ -3,17 +3,21 @@
 from typing import List
 
 
-from pyiron_dataclasses.v1.generic import (
-    GenericDict,
-    Interactive,
+from pyiron_dataclasses.v1.atomistic import (
     GenericInput,
     GenericOutput,
-    Executable,
-    Server,
     Structure,
+)
+from pyiron_dataclasses.v1.dft import (
     ElectronicStructure,
     ChargeDensity,
 )
+from pyiron_dataclasses.v1.job import (
+    Executable,
+    GenericDict,
+    Interactive,
+    Server,
+)
 
 
 @dataclass

pyiron_dataclasses/v1/sphinx.py

@@ -2,17 +2,21 @@
 import numpy as np
 
 
-from pyiron_dataclasses.v1.generic import (
-    GenericDict,
-    Interactive,
+from pyiron_dataclasses.v1.atomistic import (
     GenericInput,
     GenericOutput,
-    Executable,
-    Server,
     Structure,
+)
+from pyiron_dataclasses.v1.dft import (
     ElectronicStructure,
     ChargeDensity,
 )
+from pyiron_dataclasses.v1.job import (
+    Executable,
+    GenericDict,
+    Interactive,
+    Server,
+)
 
 
 @dataclass