Initial Work on Reading Crystal and Creation Gaussian Input

crystalpol/polarization.py

@@ -0,0 +1,74 @@
+import os
+
+from crystalpol.shared.system.molecule import Molecule
+from crystalpol.shared.system.crystal import Crystal
+from crystalpol.shared.system.atom import Atom
+from crystalpol.shared.config import Config
+from crystalpol.gaussian import Gaussian
+
+from typing import List
+
+
+class Polarization:
+    __slots__ = ('geom_file', 'outfile', 'config', 'gaussian', 'crystal')
+
+    def __init__(self, geom_file: str, outfile: str, config: Config) -> None:
+        self.crystal = None
+
+        self.geom_file = geom_file
+        self.outfile = outfile
+        self.config = config
+
+        self.gaussian = Gaussian(config)
+
+    def run(self):
+
+        self.read_crystal()
+
+        self.gaussian.run(1, self.crystal)
+
+    def read_crystal(self) -> None:
+        with open(self.geom_file, 'r') as geom_file:
+            lines = geom_file.readlines()
+
+        molecules = self._get_molecules_from_lines(lines)
+        structure = self._get_crystal_structure(molecules[0])
+
+        self.crystal = Crystal([structure])
+        for molecule in molecules:
+            self.crystal.add_cell([molecule])
+
+    def _get_molecules_from_lines(self, lines: List[str]) -> List[Molecule]:
+        if (len(lines) % self.config.n_atoms) == 0:
+            molecules: List[Molecule] = []
+
+            for index, molecule in enumerate(split(lines, self.config.n_atoms)):
+                mol = Molecule(f"Molecule-{index}")
+                for atom_line in molecule:
+                    symbol, rx, ry, rz = tuple(atom_line.split())
+                    mol.add_atom(
+                        Atom(
+                            rx, ry, rz,
+                            symbol=symbol.ljust(2),
+                        )
+                    )
+                molecules.append(mol)
+
+            return molecules
+
+        else:
+            raise RuntimeError(
+                "Invalid Geom File, the number of atoms doesn't match the number of lines."
+            )
+
+    @staticmethod
+    def _get_crystal_structure(molecule: Molecule) -> List[str]:
+        structure: List[str] = []
+        for atom in molecule:
+            structure.append(atom.symbol)
+        return structure
+
+
+def split(array: List, partitions: int):
+    for i in range(0, len(array), partitions):
+        yield array[i: i + partitions]