ichor.core.files.pandora package

Submodules

ichor.core.files.pandora.morfi_output module

class MorfiDirectory(path: Path | str)

Bases: AnnotatedDirectory

classmethod check_path(path: Path) → bool

Implement if the path of the directory needs to be checked if it contains something specific

contents = {'mout': <class 'ichor.core.files.pandora.mout.MOUT'>}

dirname = 'morfi-2pdm'

path: Path | str

ichor.core.files.pandora.mout module

class AtomicMorfiOutput(ty: str, x: float, y: float, z: float, index: int | None = None, parent: ichor.core.atoms.Atoms | None = None, units: AtomicDistance = AtomicDistance.Angstroms)

Bases: Atom

bond_critical_points: List[BondCriticalPoint]

cage_critical_points: List[CageCriticalPoint]

interaction_energy: float = 0.0

maxsect: int

quadin: Quadrature | None

quadout: Quadrature | None

rho: float

ring_critical_points: List[RingCriticalPoint]

class BondCriticalPoint(A: Atom | None = None, B: Atom | None = None, pos: ndarray = array([4.68561279e-310, 0.00000000e+000, 8.69555537e-322]), rho: float = 0.0, lap: float = 0.0, lam: ndarray = array([4.68561277e-310, 0.00000000e+000, 1.58101007e-322]), ellip: float = 0.0, K_r: float = 0.0, G_r: float = 0.0, eig: ndarray = array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]), dA: float = 0.0, dB: float = 0.0, pA: float = 0.0, pB: float = 0.0)

Bases: CriticalPoint

class CageCriticalPoint(atoms: List[Atom] | None = None, pos: ndarray = array([4.68561286e-310, 0.00000000e+000, 1.58101007e-322]), rho: float = 0.0, lap: float = 0.0, lam: ndarray = array([6.94834959e-310, 4.68627909e-310, 1.58101007e-322]), dN: List[int] | None = None)

Bases: NCriticalPoint

class CriticalPoint(pos: ndarray = array([4.68561257e-310, 0.00000000e+000, 0.00000000e+000]), rho: float = 0.0, lap: float = 0.0, lam: ndarray = array([4.68561257e-310, 0.00000000e+000, 6.94833486e-310]))

Bases: VarReprMixin, ABC

class MOUT(path: Path, atoms: Atoms | None = None)

Bases: HasAtoms, HasData, ReadFile

items()

path: Path | str

property properties: Dict[str, Dict[str, float]]

class NCriticalPoint(atoms: List[Atom] | None = None, pos: ndarray = array([4.68561241e-310, 0.00000000e+000, 1.58101007e-322]), rho: float = 0.0, lap: float = 0.0, lam: ndarray = array([6.94834959e-310, 4.68627908e-310, 1.58101007e-322]), dN: List[int] | None = None)

Bases: CriticalPoint

class Quadrature(rad, theta, phi)

Bases: tuple

phi

Alias for field number 2

rad

Alias for field number 0

theta

Alias for field number 1

class RingCriticalPoint(atoms: List[Atom] | None = None, pos: ndarray = array([4.68561282e-310, 0.00000000e+000, 1.58101007e-322]), rho: float = 0.0, lap: float = 0.0, lam: ndarray = array([4.68561278e-310, 0.00000000e+000, 1.58101007e-322]), dN: List[int] | None = None)

Bases: NCriticalPoint

read_bcp(f, atom_names: List[Tuple[str, str]], xs: List[float], ys: List[float], zs: List[float], rhos: List[float], laps: List[float], lam1s: List[float], lam2s: List[float], lam3s: List[float], ellips: List[float], K_rs: List[float], G_rs: List[float], eig1xs: List[float], eig1ys: List[float], eig1zs: List[float], eig2xs: List[float], eig2ys: List[float], eig2zs: List[float], eig3xs: List[float], eig3ys: List[float], eig3zs: List[float], dAs: List[float], dBs: List[float], pAs: List[float], pBs: List[float])

read_ccp(f, atom_names, xs, ys, zs, rhos, laps, lam1s, lam2s, lam3s, dNs, line=None)

read_cp(f, xs: List[float], ys: List[float], zs: List[float], rhos: List[float], laps: List[float], lam1s: List[float], lam2s: List[float], lam3s: List[float], line=None)

read_cp_and_ncp(f, atom_names, xs, ys, zs, rhos, laps, lam1s, lam2s, lam3s, dNs, line=None)

read_ncp(f, atom_names, dNs)

read_rcp(f, atom_names, xs, ys, zs, rhos, laps, lam1s, lam2s, lam3s, dNs, line=None)

ichor.core.files.pandora.pandora_directory module

class PandoraDirectory(path: Path | str)

Bases: HasAtoms, AnnotatedDirectory

classmethod check_path(path: Path) → bool

Implement if the path of the directory needs to be checked if it contains something specific

contents = {'input': <class 'ichor.core.files.pandora.pandora_input.PandoraInput'>, 'morfi': <class 'ichor.core.files.pandora.morfi_output.MorfiDirectory'>, 'pyscf': <class 'ichor.core.files.pandora.pyscf_output.PySCFDirectory'>}

dirname = 'pandora'

path: Path | str

write()

ichor.core.files.pandora.pandora_input module

class PandoraCCSDmod(value)

Bases: Enum

An enumeration.

CCSD = 'ccsd'

CCSD_HF = 'ccsdHF'

CCSD_MULLER = 'ccsdM'

class PandoraInput(path: Path, atoms: Atoms | None = None, ccsdmod: PandoraCCSDmod = FileContents, morfi_grid_radial: float = FileContents, morfi_grid_angular: int = FileContents, morfi_grid_radial_h: float = FileContents, morfi_grid_angular_h: int = FileContents, method: str = FileContents, basis_set: str = FileContents)

Bases: HasAtoms, ReadFile, WriteFile

ccsdmod: PandoraCCSDmod

morfi_grid_angular: int

morfi_grid_angular_h: int

morfi_grid_radial: float

morfi_grid_radial_h: float

path: Path | str

ichor.core.files.pandora.pyscf_output module

class MorfiWFN(path: Path | str, method: str | None = None)

Bases: WFN

classmethod check_path(path: Path) → bool

Checks the suffix of the given path matches the filetype associated with class that subclasses from File :param path: A Path object to check :return: True if the Path object has the same suffix as the class filetype, False otherwise

path: Path | str

class PySCFDirectory(path: Path | str)

Bases: AnnotatedDirectory

classmethod check_path(path: Path) → bool

Implement if the path of the directory needs to be checked if it contains something specific

contents = {'aimall_wfn': <class 'ichor.core.files.gaussian.wfn.WFN'>, 'morfi_wfn': <class 'ichor.core.files.pandora.pyscf_output.MorfiWFN'>}

dirname = 'pyscf'

path: Path | str

Module contents

class MOUT(path: Path, atoms: Atoms | None = None)

Bases: HasAtoms, HasData, ReadFile

bond_critical_points: List[BondCriticalPoint]

cage_critical_points: List[CageCriticalPoint]

items()

nbcp: int

nccp: int

nnuc: int

nrcp: int

path: Path | str

property properties: Dict[str, Dict[str, float]]

ring_critical_points: List[RingCriticalPoint]

class MorfiDirectory(path: Path | str)

Bases: AnnotatedDirectory

classmethod check_path(path: Path) → bool

Implement if the path of the directory needs to be checked if it contains something specific

contents = {'mout': <class 'ichor.core.files.pandora.mout.MOUT'>}

dirname = 'morfi-2pdm'

path: Path | str

class PandoraDirectory(path: Path | str)

Bases: HasAtoms, AnnotatedDirectory

classmethod check_path(path: Path) → bool

Implement if the path of the directory needs to be checked if it contains something specific

contents = {'input': <class 'ichor.core.files.pandora.pandora_input.PandoraInput'>, 'morfi': <class 'ichor.core.files.pandora.morfi_output.MorfiDirectory'>, 'pyscf': <class 'ichor.core.files.pandora.pyscf_output.PySCFDirectory'>}

dirname = 'pandora'

path: Path | str

write()

class PandoraInput(path: Path, atoms: Atoms | None = None, ccsdmod: PandoraCCSDmod = FileContents, morfi_grid_radial: float = FileContents, morfi_grid_angular: int = FileContents, morfi_grid_radial_h: float = FileContents, morfi_grid_angular_h: int = FileContents, method: str = FileContents, basis_set: str = FileContents)

Bases: HasAtoms, ReadFile, WriteFile

ccsdmod: PandoraCCSDmod

morfi_grid_angular: int

morfi_grid_angular_h: int

morfi_grid_radial: float

morfi_grid_radial_h: float

path: Path | str

class PySCFDirectory(path: Path | str)

Bases: AnnotatedDirectory

classmethod check_path(path: Path) → bool

Implement if the path of the directory needs to be checked if it contains something specific

contents = {'aimall_wfn': <class 'ichor.core.files.gaussian.wfn.WFN'>, 'morfi_wfn': <class 'ichor.core.files.pandora.pyscf_output.MorfiWFN'>}

dirname = 'pyscf'

path: Path | str