Initial Work on Reading Crystal and Creation Gaussian Input

crystalpol/shared/system/atom.py

@@ -0,0 +1,46 @@
+from crystalpol.shared.utils.ptable import atom_mass, atom_symbol
+
+
+class Atom:
+    """
+    Atom class declaration. This class is used throughout the DicePlayer program to represent atoms.
+    Attributes:
+        na (int): Atomic number of the represented atom.
+        symbol (str): Atomic symbol of the represented atom.
+        rx (float): x cartesian coordinates of the represented atom.
+        ry (float): y cartesian coordinates of the represented atom.
+        rz (float): z cartesian coordinates of the represented atom.
+    """
+
+    def __init__(
+            self,
+            rx: float,
+            ry: float,
+            rz: float,
+            na: int = None,
+            symbol: str = None,
+
+    ) -> None:
+        """
+        The constructor function __init__ is used to create new instances of the Atom class.
+        Args:
+            na (int): Atomic number of the represented atom.
+            symbol (str): Atomic symbol of the represented atom.
+            rx (float): x cartesian coordinates of the represented atom.
+            ry (float): y cartesian coordinates of the represented atom.
+            rz (float): z cartesian coordinates of the represented atom.
+        """
+
+        if na is not None:
+            self.na = na
+            self.symbol = atom_symbol[self.na]
+
+        if symbol is not None and symbol in atom_symbol:
+            self.symbol = symbol
+            self.na = atom_symbol.index(self.symbol)
+
+        self.rx = rx
+        self.ry = ry
+        self.rz = rz
+        self.chg = None
+        self.mass = atom_mass[self.na]