Initial Work on Reading Crystal and Creation Gaussian Input

crystalpol/gaussian.py

@@ -0,0 +1,114 @@
+from crystalpol.shared.utils.ptable import atom_symbol
+from crystalpol.shared.system.crystal import Crystal
+from crystalpol.shared.config import Config
+
+from pathlib import Path, PosixPath
+from typing import TextIO
+import subprocess
+import textwrap
+import shutil
+import os
+
+
+class Gaussian:
+    __slots__ = ('qmprog', 'config', 'keywords')
+
+    def __init__(self, config: Config) -> None:
+        self.qmprog = "g16"
+        self.config = config
+
+        self.check_keyword()
+
+    def check_keyword(self):
+        if self.config.pop not in ["chelpg", "mk", "nbo"]:
+            self.config.pop = "chelpg"
+
+    def run(self, cycle: int, crystal: Crystal) -> None:
+
+        file = Path("simfiles", f"crystal-{str(cycle).zfill(2)}.gjf")
+
+        self.make_gaussian_input(cycle, file, crystal)
+
+        if shutil.which("bash") is not None:
+            exit_status = subprocess.call(
+                [
+                    "bash",
+                    "-c",
+                    "exec -a {}-step{} {} {}".format(
+                        self.qmprog, cycle, self.qmprog, file.name
+                    ),
+                ]
+            )
+        else:
+            exit_status = subprocess.call([self.qmprog, file.name])
+
+        if exit_status != 0:
+            raise RuntimeError("Gaussian process did not exit properly")
+
+        return self.read_charges_from_gaussian_output()
+
+    def create_simulation_dir(self):
+        if not os.path.exists(self.config.simulation_dir):
+            os.makedirs(self.config.simulation_dir)
+        else:
+            raise RuntimeError(
+                f"Simulation directory '{self.config.simulation_dir}' already exists. "
+                f"Please remove it before proceeding."
+            )
+
+    def make_gaussian_input(self, cycle: int, file: PosixPath, crystal: Crystal) -> str:
+
+        with open(file, 'w+') as fh:
+
+            fh.write(f"%Mem={self.config.mem}MB\n")
+
+            fh.write(f"%Nprocs={self.config.n_procs}\n")
+
+            kwords_line = f"#P {self.config.level} " \
+                          f"Pop = {self.config.pop} " \
+                          f"Density = Current " \
+                          f"NoSymm "
+
+            if cycle > 1:
+                kwords_line += f"charge"
+
+            fh.write(textwrap.fill(kwords_line, 90))
+            fh.write("\n")
+
+            fh.write(f"\n{self.config.comment} - Cycle number {cycle}\n")
+            fh.write("\n")
+            fh.write(f"{self.config.mult[0]}, {self.config.mult[1]}\n")
+
+            for atom in crystal[0][0]:
+                symbol = atom_symbol[atom.na]
+                fh.write(
+                    f"{symbol:<2s}    "
+                    f"{atom.rx:>10.5f}   "
+                    f"{atom.ry:>10.5f}   "
+                    f"{atom.rz:>10.5f}\n"
+                )
+
+            if cycle > 1:
+                self.make_gaussian_charges(fh, crystal)
+
+            fh.seek(0)
+            return fh.read()
+
+    def make_gaussian_charges(self, fh: TextIO, crystal: Crystal) -> None:
+
+        fh.write("\n")
+
+        for index_cell, cell in enumerate(crystal):
+            for index_mol, molecule in enumerate(cell):
+                if (index_cell == 0 and index_mol != 0) or (index_cell != 0):
+                    for atom in molecule:
+                        symbol = atom_symbol[atom.na]
+                        fh.write(
+                            f"{symbol:<2s}    "
+                            f"{atom.rx:>10.5f}   "
+                            f"{atom.ry:>10.5f}   "
+                            f"{atom.rz:>10.5f}\n"
+                        )
+
+    def read_charges_from_gaussian_output(self) -> None:
+        pass