53 lines
2.1 KiB
Python
53 lines
2.1 KiB
Python
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from __future__ import annotations
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import numpy as np
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from pathlib import Path
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from nptyping import NDArray, Shape, Number
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class ACF:
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def __init__(self,
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coords: NDArray[Shape['Natoms, 3'], Number],
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nelec_per_atom: NDArray[Shape['Natoms'], Number],
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spin_per_atom: NDArray[Shape['Natoms'], Number] = None):
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self.coords = coords
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self.nelec_per_atom = nelec_per_atom
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self.nelec_per_isolated_atom = None
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self.spin_per_atom = spin_per_atom
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@staticmethod
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def from_file(filepath: str | Path):
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if isinstance(filepath, str):
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filepath = Path(filepath)
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file = open(filepath)
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file.readline()
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line = file.readline()
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ncols = len(line.split('+'))
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if '+' in line:
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if ncols == 7:
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data = np.genfromtxt(filepath, skip_header=2, skip_footer=5, delimiter='|')
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return ACF(data[:, 1:4], data[:, 4])
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elif ncols == 8:
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data = np.genfromtxt(filepath, skip_header=2, skip_footer=7, delimiter='|')
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return ACF(data[:, 1:4], data[:, 4], data[:, 5])
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else:
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raise IOError(f'Can parse ACF.dat with 7 or 8 columns, but {ncols=} was given')
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else:
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data = np.genfromtxt(filepath, skip_header=2, skip_footer=4)
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return ACF(data[:, 1:4], data[:, 4])
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def get_charge(self,
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nelec_per_isolated_atom: NDArray[Shape['Natoms'], Number] | None = None):
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if nelec_per_isolated_atom is not None:
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return nelec_per_isolated_atom - self.nelec_per_atom
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else:
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if self.nelec_per_isolated_atom is not None:
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return self.nelec_per_isolated_atom - self.nelec_per_atom
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else:
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raise ValueError('nelec_per_isolated_atom should be defined either as argument of '
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'this function or as self.nelec_per_isolated_atom')
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def get_delta_elec(self,
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nelec_per_isolated_atom: NDArray[Shape['Natoms'], Number]):
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return self.nelec_per_atom - nelec_per_isolated_atom
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