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