init

electrochemistry/echem/io_data/bader.py

@@ -0,0 +1,52 @@
+from __future__ import annotations
+import numpy as np
+from pathlib import Path
+from nptyping import NDArray, Shape, Number
+
+
+class ACF:
+    def __init__(self,
+                 coords: NDArray[Shape['Natoms, 3'], Number],
+                 nelec_per_atom: NDArray[Shape['Natoms'], Number],
+                 spin_per_atom: NDArray[Shape['Natoms'], Number] = None):
+        self.coords = coords
+        self.nelec_per_atom = nelec_per_atom
+        self.nelec_per_isolated_atom = None
+        self.spin_per_atom = spin_per_atom
+
+    @staticmethod
+    def from_file(filepath: str | Path):
+        if isinstance(filepath, str):
+            filepath = Path(filepath)
+
+        file = open(filepath)
+        file.readline()
+        line = file.readline()
+        ncols = len(line.split('+'))
+        if '+' in line:
+            if ncols == 7:
+                data = np.genfromtxt(filepath, skip_header=2, skip_footer=5, delimiter='|')
+                return ACF(data[:, 1:4], data[:, 4])
+            elif ncols == 8:
+                data = np.genfromtxt(filepath, skip_header=2, skip_footer=7, delimiter='|')
+                return ACF(data[:, 1:4], data[:, 4], data[:, 5])
+            else:
+                raise IOError(f'Can parse ACF.dat with 7 or 8 columns, but {ncols=} was given')
+        else:
+            data = np.genfromtxt(filepath, skip_header=2, skip_footer=4)
+            return ACF(data[:, 1:4], data[:, 4])
+
+    def get_charge(self,
+                   nelec_per_isolated_atom: NDArray[Shape['Natoms'], Number] | None = None):
+        if nelec_per_isolated_atom is not None:
+            return nelec_per_isolated_atom - self.nelec_per_atom
+        else:
+            if self.nelec_per_isolated_atom is not None:
+                return self.nelec_per_isolated_atom - self.nelec_per_atom
+            else:
+                raise ValueError('nelec_per_isolated_atom should be defined either as argument of '
+                                 'this function or as self.nelec_per_isolated_atom')
+
+    def get_delta_elec(self,
+                       nelec_per_isolated_atom: NDArray[Shape['Natoms'], Number]):
+        return self.nelec_per_atom - nelec_per_isolated_atom