chore: better project structure
This commit is contained in:
6
diceplayer/interface/__init__.py
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6
diceplayer/interface/__init__.py
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@@ -0,0 +1,6 @@
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from .__interface import Interface
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from .dice_interface import DiceInterface
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from .gaussian_interface import GaussianInterface
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__all__ = ["Interface", "DiceInterface", "GaussianInterface"]
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26
diceplayer/interface/__interface.py
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26
diceplayer/interface/__interface.py
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@@ -0,0 +1,26 @@
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from __future__ import annotations
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from diceplayer.config.player_config import PlayerConfig
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from diceplayer.environment.system import System
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from abc import ABC, abstractmethod
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class Interface(ABC):
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__slots__ = ["step", "system"]
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def __init__(self):
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self.system: System | None = None
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self.step: PlayerConfig | None = None
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@abstractmethod
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def configure(self, step: PlayerConfig, system: System):
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pass
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@abstractmethod
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def start(self, cycle: int):
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pass
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@abstractmethod
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def reset(self):
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pass
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389
diceplayer/interface/dice_interface.py
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389
diceplayer/interface/dice_interface.py
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@@ -0,0 +1,389 @@
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from __future__ import annotations
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from diceplayer import logger
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from diceplayer.config.player_config import PlayerConfig
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from diceplayer.environment.system import System
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from diceplayer.interface import Interface
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from setproctitle import setproctitle
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from typing_extensions import Final, TextIO
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import os
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import random
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import shutil
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import subprocess
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import sys
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import time
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from multiprocessing import Process, connection
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from pathlib import Path
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DICE_END_FLAG: Final[str] = "End of simulation"
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DICE_FLAG_LINE: Final[int] = -2
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UMAANG3_TO_GCM3: Final[float] = 1.6605
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MAX_SEED: Final[int] = 4294967295
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class DiceInterface(Interface):
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title = "Diceplayer run"
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def configure(self, step: PlayerConfig, system: System):
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self.step = step
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self.system = system
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def start(self, cycle: int):
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procs = []
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sentinels = []
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for proc in range(1, self.step.nprocs + 1):
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p = Process(target=self._simulation_process, args=(cycle, proc))
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p.start()
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procs.append(p)
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sentinels.append(p.sentinel)
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while procs:
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finished = connection.wait(sentinels)
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for proc_sentinel in finished:
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i = sentinels.index(proc_sentinel)
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status = procs[i].exitcode
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procs.pop(i)
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sentinels.pop(i)
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if status != 0:
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for p in procs:
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p.terminate()
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sys.exit(status)
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logger.info("\n")
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def reset(self):
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del self.step
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del self.system
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def _simulation_process(self, cycle: int, proc: int):
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setproctitle(f"diceplayer-step{cycle:0d}-p{proc:0d}")
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try:
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self._make_proc_dir(cycle, proc)
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self._make_dice_inputs(cycle, proc)
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self._run_dice(cycle, proc)
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except Exception as err:
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sys.exit(err)
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def _make_proc_dir(self, cycle, proc):
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simulation_dir = Path(self.step.simulation_dir)
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if not simulation_dir.exists():
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simulation_dir.mkdir(parents=True)
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proc_dir = Path(simulation_dir, f"step{cycle:02d}", f"p{proc:02d}")
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proc_dir.mkdir(parents=True, exist_ok=True)
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def _make_dice_inputs(self, cycle, proc):
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proc_dir = Path(self.step.simulation_dir, f"step{cycle:02d}", f"p{proc:02d}")
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self._make_potentials(proc_dir)
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random.seed(self._make_dice_seed())
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# This is logic is used to make the initial configuration file
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# for the next cycle using the last.xyz file from the previous cycle.
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if self.step.dice.randominit == "first" and cycle > 1:
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last_xyz = Path(
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self.step.simulation_dir,
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f"step{(cycle - 1):02d}",
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f"p{proc:02d}",
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"last.xyz",
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)
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if not last_xyz.exists():
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raise FileNotFoundError(f"File {last_xyz} not found.")
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with open(last_xyz, "r") as last_xyz_file:
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self._make_init_file(proc_dir, last_xyz_file)
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last_xyz_file.seek(0)
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self.step.dice.dens = self._new_density(last_xyz_file)
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else:
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self._make_nvt_ter(cycle, proc_dir)
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if len(self.step.dice.nstep) == 2:
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self._make_nvt_eq(cycle, proc_dir)
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elif len(self.step.dice.nstep) == 3:
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self._make_npt_ter(cycle, proc_dir)
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self._make_npt_eq(proc_dir)
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def _run_dice(self, cycle: int, proc: int):
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working_dir = os.getcwd()
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proc_dir = Path(self.step.simulation_dir, f"step{cycle:02d}", f"p{proc:02d}")
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logger.info(
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f"Simulation process {str(proc_dir)} initiated with pid {os.getpid()}"
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)
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os.chdir(proc_dir)
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if not (self.step.dice.randominit == "first" and cycle > 1):
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self.run_dice_file(cycle, proc, "NVT.ter")
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if len(self.step.dice.nstep) == 2:
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self.run_dice_file(cycle, proc, "NVT.eq")
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elif len(self.step.dice.nstep) == 3:
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self.run_dice_file(cycle, proc, "NPT.ter")
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self.run_dice_file(cycle, proc, "NPT.eq")
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os.chdir(working_dir)
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xyz_file = Path(proc_dir, "phb.xyz")
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last_xyz_file = Path(proc_dir, "last.xyz")
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if xyz_file.exists():
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shutil.copy(xyz_file, last_xyz_file)
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else:
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raise FileNotFoundError(f"File {xyz_file} not found.")
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@staticmethod
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def _make_dice_seed() -> int:
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num = time.time()
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num = (num - int(num)) * 1e6
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num = int((num - int(num)) * 1e6)
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return (os.getpid() * num) % (MAX_SEED + 1)
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def _make_init_file(self, proc_dir: Path, last_xyz_file: TextIO):
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xyz_lines = last_xyz_file.readlines()
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SECONDARY_MOLECULE_LENGTH = 0
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for i in range(1, len(self.step.dice.nmol)):
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SECONDARY_MOLECULE_LENGTH += self.step.dice.nmol[i] * len(
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self.system.molecule[i].atom
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)
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xyz_lines = xyz_lines[-SECONDARY_MOLECULE_LENGTH:]
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input_file = Path(proc_dir, self.step.dice.outname + ".xy")
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with open(input_file, "w") as f:
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for atom in self.system.molecule[0].atom:
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f.write(f"{atom.rx:>10.6f} {atom.ry:>10.6f} {atom.rz:>10.6f}\n")
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for line in xyz_lines:
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atom = line.split()
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rx = float(atom[1])
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ry = float(atom[2])
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rz = float(atom[3])
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f.write(f"{rx:>10.6f} {ry:>10.6f} {rz:>10.6f}\n")
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f.write("$end")
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def _new_density(self, last_xyz_file: TextIO):
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last_xyz_lines = last_xyz_file.readlines()
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box = last_xyz_lines[1].split()
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volume = float(box[-3]) * float(box[-2]) * float(box[-1])
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total_mass = 0
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for i in range(len(self.system.molecule)):
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total_mass += self.system.molecule[i].total_mass * self.step.dice.nmol[i]
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density = (total_mass / volume) * UMAANG3_TO_GCM3
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return density
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def _make_nvt_ter(self, cycle, proc_dir):
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file = Path(proc_dir, "NVT.ter")
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with open(file, "w") as f:
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f.write(f"title = {self.title} - NVT Thermalization\n")
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f.write(f"ncores = {self.step.ncores}\n")
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f.write(f"ljname = {self.step.dice.ljname}\n")
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f.write(f"outname = {self.step.dice.outname}\n")
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mol_string = " ".join(str(x) for x in self.step.dice.nmol)
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f.write(f"nmol = {mol_string}\n")
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f.write(f"dens = {self.step.dice.dens}\n")
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f.write(f"temp = {self.step.dice.temp}\n")
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if self.step.dice.randominit == "first" and cycle > 1:
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f.write("init = yesreadxyz\n")
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f.write(f"nstep = {self.step.altsteps}\n")
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else:
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f.write("init = yes\n")
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f.write(f"nstep = {self.step.dice.nstep[0]}\n")
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f.write("vstep = 0\n")
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f.write("mstop = 1\n")
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f.write("accum = no\n")
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f.write("iprint = 1\n")
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f.write("isave = 0\n")
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f.write("irdf = 0\n")
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seed = int(1e6 * random.random())
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f.write(f"seed = {seed}\n")
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f.write(f"upbuf = {self.step.dice.upbuf}")
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def _make_nvt_eq(self, cycle, proc_dir):
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file = Path(proc_dir, "NVT.eq")
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with open(file, "w") as f:
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f.write(f"title = {self.title} - NVT Production\n")
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f.write(f"ncores = {self.step.ncores}\n")
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f.write(f"ljname = {self.step.dice.ljname}\n")
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f.write(f"outname = {self.step.dice.outname}\n")
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mol_string = " ".join(str(x) for x in self.step.dice.nmol)
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f.write(f"nmol = {mol_string}\n")
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f.write(f"dens = {self.step.dice.dens}\n")
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f.write(f"temp = {self.step.dice.temp}\n")
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if self.step.dice.randominit == "first" and cycle > 1:
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f.write("init = yesreadxyz\n")
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else:
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f.write("init = no\n")
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f.write(f"nstep = {self.step.dice.nstep[1]}\n")
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f.write("vstep = 0\n")
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f.write("mstop = 1\n")
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f.write("accum = no\n")
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f.write("iprint = 1\n")
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f.write(f"isave = {self.step.dice.isave}\n")
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f.write(f"irdf = {10 * self.step.nprocs}\n")
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seed = int(1e6 * random.random())
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f.write("seed = {}\n".format(seed))
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def _make_npt_ter(self, cycle, proc_dir):
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file = Path(proc_dir, "NPT.ter")
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with open(file, "w") as f:
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f.write(f"title = {self.title} - NPT Thermalization\n")
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f.write(f"ncores = {self.step.ncores}\n")
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f.write(f"ljname = {self.step.dice.ljname}\n")
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f.write(f"outname = {self.step.dice.outname}\n")
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mol_string = " ".join(str(x) for x in self.step.dice.nmol)
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f.write(f"nmol = {mol_string}\n")
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f.write(f"press = {self.step.dice.press}\n")
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f.write(f"temp = {self.step.dice.temp}\n")
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if self.step.dice.randominit == "first" and cycle > 1:
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f.write("init = yesreadxyz\n")
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f.write(f"dens = {self.step.dice.dens:<8.4f}\n")
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f.write(f"vstep = {int(self.step.altsteps / 5)}\n")
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else:
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f.write("init = no\n")
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f.write(f"vstep = {int(self.step.dice.nstep[1] / 5)}\n")
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f.write("nstep = 5\n")
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f.write("mstop = 1\n")
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f.write("accum = no\n")
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f.write("iprint = 1\n")
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f.write("isave = 0\n")
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f.write("irdf = 0\n")
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seed = int(1e6 * random.random())
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f.write(f"seed = {seed}\n")
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def _make_npt_eq(self, proc_dir):
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file = Path(proc_dir, "NPT.eq")
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with open(file, "w") as f:
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f.write(f"title = {self.title} - NPT Production\n")
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f.write(f"ncores = {self.step.ncores}\n")
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f.write(f"ljname = {self.step.dice.ljname}\n")
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f.write(f"outname = {self.step.dice.outname}\n")
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mol_string = " ".join(str(x) for x in self.step.dice.nmol)
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f.write(f"nmol = {mol_string}\n")
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f.write(f"press = {self.step.dice.press}\n")
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f.write(f"temp = {self.step.dice.temp}\n")
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f.write("nstep = 5\n")
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f.write(f"vstep = {int(self.step.dice.nstep[2] / 5)}\n")
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f.write("init = no\n")
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f.write("mstop = 1\n")
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f.write("accum = no\n")
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f.write("iprint = 1\n")
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f.write(f"isave = {self.step.dice.isave}\n")
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f.write(f"irdf = {10 * self.step.nprocs}\n")
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seed = int(1e6 * random.random())
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f.write(f"seed = {seed}\n")
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def _make_potentials(self, proc_dir):
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fstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f}\n"
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file = Path(proc_dir, self.step.dice.ljname)
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with open(file, "w") as f:
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f.write(f"{self.step.dice.combrule}\n")
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f.write(f"{len(self.step.dice.nmol)}\n")
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nsites_qm = len(self.system.molecule[0].atom)
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f.write(f"{nsites_qm} {self.system.molecule[0].molname}\n")
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for atom in self.system.molecule[0].atom:
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f.write(
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fstr.format(
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atom.lbl,
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atom.na,
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atom.rx,
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atom.ry,
|
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atom.rz,
|
||||
atom.chg,
|
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atom.eps,
|
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atom.sig,
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)
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)
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for mol in self.system.molecule[1:]:
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f.write(f"{len(mol.atom)} {mol.molname}\n")
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for atom in mol.atom:
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f.write(
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fstr.format(
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atom.lbl,
|
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atom.na,
|
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atom.rx,
|
||||
atom.ry,
|
||||
atom.rz,
|
||||
atom.chg,
|
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atom.eps,
|
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atom.sig,
|
||||
)
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||||
)
|
||||
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def run_dice_file(self, cycle: int, proc: int, file_name: str):
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with (
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open(Path(file_name), "r") as infile,
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open(Path(file_name + ".out"), "w") as outfile,
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):
|
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if shutil.which("bash") is not None:
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||||
exit_status = subprocess.call(
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[
|
||||
"bash",
|
||||
"-c",
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f"exec -a dice-step{cycle}-p{proc} {self.step.dice.progname} < {infile.name} > {outfile.name}",
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||||
]
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||||
)
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||||
else:
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||||
exit_status = subprocess.call(
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self.step.dice.progname, stdin=infile, stdout=outfile
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)
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||||
|
||||
if exit_status != 0:
|
||||
raise RuntimeError(
|
||||
f"Dice process step{cycle:02d}-p{proc:02d} did not exit properly"
|
||||
)
|
||||
|
||||
with open(Path(file_name + ".out"), "r") as outfile:
|
||||
flag = outfile.readlines()[DICE_FLAG_LINE].strip()
|
||||
if flag != DICE_END_FLAG:
|
||||
raise RuntimeError(
|
||||
f"Dice process step{cycle:02d}-p{proc:02d} did not exit properly"
|
||||
)
|
||||
|
||||
logger.info(f"Dice {file_name} - step{cycle:02d}-p{proc:02d} exited properly")
|
||||
359
diceplayer/interface/gaussian_interface.py
Normal file
359
diceplayer/interface/gaussian_interface.py
Normal file
@@ -0,0 +1,359 @@
|
||||
from __future__ import annotations
|
||||
|
||||
from diceplayer import logger
|
||||
from diceplayer.config.player_config import PlayerConfig
|
||||
from diceplayer.environment.atom import Atom
|
||||
from diceplayer.environment.molecule import Molecule
|
||||
from diceplayer.environment.system import System
|
||||
from diceplayer.interface import Interface
|
||||
from diceplayer.utils.misc import date_time
|
||||
from diceplayer.utils.ptable import atomsymb
|
||||
|
||||
import numpy as np
|
||||
from nptyping import NDArray
|
||||
from typing_extensions import Any, Dict, List, Tuple
|
||||
|
||||
import os
|
||||
import shutil
|
||||
import subprocess
|
||||
import textwrap
|
||||
from pathlib import Path
|
||||
|
||||
|
||||
class GaussianInterface(Interface):
|
||||
def configure(self, step_dto: PlayerConfig, system: System):
|
||||
self.system = system
|
||||
self.step = step_dto
|
||||
|
||||
def start(self, cycle: int) -> Dict[str, NDArray]:
|
||||
self._make_qm_dir(cycle)
|
||||
|
||||
if cycle > 1:
|
||||
self._copy_chk_file_from_previous_step(cycle)
|
||||
|
||||
asec_charges = self.populate_asec_vdw(cycle)
|
||||
self._make_gaussian_input_file(cycle, asec_charges)
|
||||
|
||||
self._run_gaussian(cycle)
|
||||
self._run_formchk(cycle)
|
||||
|
||||
return_value = {}
|
||||
if self.step.opt:
|
||||
# return_value['position'] = np.array(
|
||||
# self._run_optimization(cycle)
|
||||
# )
|
||||
raise NotImplementedError("Optimization not implemented yet.")
|
||||
|
||||
else:
|
||||
return_value["charges"] = np.array(self._read_charges_from_fchk(cycle))
|
||||
|
||||
return return_value
|
||||
|
||||
def reset(self):
|
||||
del self.step
|
||||
del self.system
|
||||
|
||||
def _make_qm_dir(self, cycle: int):
|
||||
qm_dir_path = Path(self.step.simulation_dir, f"step{cycle:02d}", "qm")
|
||||
if not qm_dir_path.exists():
|
||||
qm_dir_path.mkdir()
|
||||
|
||||
def _copy_chk_file_from_previous_step(self, cycle: int):
|
||||
current_chk_file_path = Path(
|
||||
self.step.simulation_dir, f"step{cycle:02d}", "qm", "asec.chk"
|
||||
)
|
||||
if current_chk_file_path.exists():
|
||||
raise FileExistsError(f"File {current_chk_file_path} already exists.")
|
||||
|
||||
previous_chk_file_path = Path(
|
||||
self.step.simulation_dir, f"step{(cycle - 1):02d}", "qm", "asec.chk"
|
||||
)
|
||||
if not previous_chk_file_path.exists():
|
||||
raise FileNotFoundError(f"File {previous_chk_file_path} does not exist.")
|
||||
|
||||
shutil.copy(previous_chk_file_path, current_chk_file_path)
|
||||
|
||||
def populate_asec_vdw(self, cycle: int) -> list[dict]:
|
||||
norm_factor = self._calculate_norm_factor()
|
||||
|
||||
nsitesref = len(self.system.molecule[0].atom)
|
||||
|
||||
nsites_total = self._calculate_total_number_of_sites(nsitesref)
|
||||
|
||||
proc_charges = []
|
||||
for proc in range(1, self.step.nprocs + 1):
|
||||
proc_charges.append(self._read_charges_from_last_step(cycle, proc))
|
||||
|
||||
asec_charges, thickness, picked_mols = self._evaluate_proc_charges(
|
||||
nsites_total, proc_charges
|
||||
)
|
||||
|
||||
logger.info(
|
||||
f"In average, {(sum(picked_mols) / norm_factor):^7.2f} molecules\n"
|
||||
f"were selected from each of the {len(picked_mols)} configurations\n"
|
||||
f"of the production simulations to form the ASEC, comprising a shell with\n"
|
||||
f"minimum thickness of {(sum(thickness) / norm_factor):>6.2f} Angstrom\n"
|
||||
)
|
||||
|
||||
for charge in asec_charges:
|
||||
charge["chg"] = charge["chg"] / norm_factor
|
||||
|
||||
return asec_charges
|
||||
|
||||
def _calculate_norm_factor(self) -> int:
|
||||
if self.step.dice.nstep[-1] % self.step.dice.isave == 0:
|
||||
nconfigs = round(self.step.dice.nstep[-1] / self.step.dice.isave)
|
||||
else:
|
||||
nconfigs = int(self.step.dice.nstep[-1] / self.step.dice.isave)
|
||||
|
||||
return nconfigs * self.step.nprocs
|
||||
|
||||
def _calculate_total_number_of_sites(self, nsitesref) -> int:
|
||||
nsites_total = self.step.dice.nmol[0] * nsitesref
|
||||
for i in range(1, len(self.step.dice.nmol)):
|
||||
nsites_total += self.step.dice.nmol[i] * len(self.system.molecule[i].atom)
|
||||
|
||||
return nsites_total
|
||||
|
||||
def _read_charges_from_last_step(self, cycle: int, proc: int) -> list[str]:
|
||||
last_xyz_file_path = Path(
|
||||
self.step.simulation_dir, f"step{cycle:02d}", f"p{proc:02d}", "last.xyz"
|
||||
)
|
||||
if not last_xyz_file_path.exists():
|
||||
raise FileNotFoundError(f"File {last_xyz_file_path} does not exist.")
|
||||
|
||||
with open(last_xyz_file_path, "r") as last_xyz_file:
|
||||
lines = last_xyz_file.readlines()
|
||||
|
||||
return lines
|
||||
|
||||
def _evaluate_proc_charges(
|
||||
self, total_nsites: int, proc_charges: list[list[str]]
|
||||
) -> Tuple[List[Dict[str, float | Any]], List[float], List[int]]:
|
||||
asec_charges = []
|
||||
|
||||
thickness = []
|
||||
picked_mols = []
|
||||
|
||||
for charges in proc_charges:
|
||||
charges_nsites = int(charges.pop(0))
|
||||
if int(charges_nsites) != total_nsites:
|
||||
raise ValueError(
|
||||
"Number of sites does not match total number of sites."
|
||||
)
|
||||
|
||||
thickness.append(self._calculate_proc_thickness(charges))
|
||||
nsites_ref_mol = len(self.system.molecule[0].atom)
|
||||
charges = charges[nsites_ref_mol:]
|
||||
|
||||
mol_count = 0
|
||||
for type in range(len(self.step.dice.nmol)):
|
||||
if type == 0:
|
||||
# Reference Molecule must be ignored from type 0
|
||||
nmols = self.step.dice.nmol[type] - 1
|
||||
else:
|
||||
nmols = self.step.dice.nmol[type]
|
||||
|
||||
for mol in range(nmols):
|
||||
new_molecule = Molecule("ASEC TMP MOLECULE")
|
||||
for site in range(len(self.system.molecule[type].atom)):
|
||||
line = charges.pop(0).split()
|
||||
|
||||
if (
|
||||
line[0].title()
|
||||
!= atomsymb[
|
||||
self.system.molecule[type].atom[site].na
|
||||
].strip()
|
||||
):
|
||||
raise SyntaxError(
|
||||
"Error: Invalid Dice Output. Atom type does not match."
|
||||
)
|
||||
|
||||
new_molecule.add_atom(
|
||||
Atom(
|
||||
self.system.molecule[type].atom[site].lbl,
|
||||
self.system.molecule[type].atom[site].na,
|
||||
float(line[1]),
|
||||
float(line[2]),
|
||||
float(line[3]),
|
||||
self.system.molecule[type].atom[site].chg,
|
||||
self.system.molecule[type].atom[site].eps,
|
||||
self.system.molecule[type].atom[site].sig,
|
||||
)
|
||||
)
|
||||
|
||||
distance = self.system.molecule[0].minimum_distance(new_molecule)
|
||||
|
||||
if distance < thickness[-1]:
|
||||
for atom in new_molecule.atom:
|
||||
asec_charges.append(
|
||||
{
|
||||
"lbl": atomsymb[atom.na],
|
||||
"rx": atom.rx,
|
||||
"ry": atom.ry,
|
||||
"rz": atom.rz,
|
||||
"chg": atom.chg,
|
||||
}
|
||||
)
|
||||
mol_count += 1
|
||||
|
||||
picked_mols.append(mol_count)
|
||||
|
||||
return asec_charges, thickness, picked_mols
|
||||
|
||||
def _calculate_proc_thickness(self, charges: list[str]) -> float:
|
||||
box = charges.pop(0).split()[-3:]
|
||||
box = [float(box[0]), float(box[1]), float(box[2])]
|
||||
sizes = self.system.molecule[0].sizes_of_molecule()
|
||||
|
||||
return min(
|
||||
[
|
||||
(box[0] - sizes[0]) / 2,
|
||||
(box[1] - sizes[1]) / 2,
|
||||
(box[2] - sizes[2]) / 2,
|
||||
]
|
||||
)
|
||||
|
||||
def _make_gaussian_input_file(self, cycle: int, asec_charges: list[dict]) -> None:
|
||||
gaussian_input_file_path = Path(
|
||||
self.step.simulation_dir, f"step{cycle:02d}", "qm", "asec.gjf"
|
||||
)
|
||||
|
||||
with open(gaussian_input_file_path, "w") as gaussian_input_file:
|
||||
gaussian_input_file.writelines(
|
||||
self._generate_gaussian_input(cycle, asec_charges)
|
||||
)
|
||||
|
||||
def _generate_gaussian_input(
|
||||
self, cycle: int, asec_charges: list[dict]
|
||||
) -> list[str]:
|
||||
gaussian_input = ["%Chk=asec.chk\n"]
|
||||
|
||||
if self.step.mem is not None:
|
||||
gaussian_input.append(f"%Mem={self.step.mem}GB\n")
|
||||
|
||||
gaussian_input.append(f"%Nprocs={self.step.nprocs * self.step.ncores}\n")
|
||||
|
||||
kwords_line = f"#P {self.step.gaussian.level}"
|
||||
|
||||
if self.step.gaussian.keywords:
|
||||
kwords_line += " " + self.step.gaussian.keywords
|
||||
|
||||
if self.step.opt == "yes":
|
||||
kwords_line += " Force"
|
||||
|
||||
kwords_line += " NoSymm"
|
||||
kwords_line += f" Pop={self.step.gaussian.pop} Density=Current"
|
||||
|
||||
if cycle > 1:
|
||||
kwords_line += " Guess=Read"
|
||||
|
||||
gaussian_input.append(textwrap.fill(kwords_line, 90))
|
||||
gaussian_input.append("\n")
|
||||
|
||||
gaussian_input.append("\nForce calculation - Cycle number {}\n".format(cycle))
|
||||
gaussian_input.append("\n")
|
||||
gaussian_input.append(
|
||||
f"{self.step.gaussian.chgmult[0]},{self.step.gaussian.chgmult[1]}\n"
|
||||
)
|
||||
|
||||
for atom in self.system.molecule[0].atom:
|
||||
symbol = atomsymb[atom.na]
|
||||
gaussian_input.append(
|
||||
"{:<2s} {:>10.5f} {:>10.5f} {:>10.5f}\n".format(
|
||||
symbol, atom.rx, atom.ry, atom.rz
|
||||
)
|
||||
)
|
||||
|
||||
gaussian_input.append("\n")
|
||||
|
||||
for charge in asec_charges:
|
||||
gaussian_input.append(
|
||||
"{:>10.5f} {:>10.5f} {:>10.5f} {:>11.8f}\n".format(
|
||||
charge["rx"], charge["ry"], charge["rz"], charge["chg"]
|
||||
)
|
||||
)
|
||||
|
||||
gaussian_input.append("\n")
|
||||
|
||||
return gaussian_input
|
||||
|
||||
def _run_gaussian(self, cycle: int) -> None:
|
||||
qm_dir = Path(self.step.simulation_dir, f"step{(cycle):02d}", "qm")
|
||||
|
||||
working_dir = os.getcwd()
|
||||
os.chdir(qm_dir)
|
||||
|
||||
infile = "asec.gjf"
|
||||
|
||||
operation = None
|
||||
if self.step.opt:
|
||||
operation = "forces"
|
||||
else:
|
||||
operation = "charges"
|
||||
|
||||
logger.info(
|
||||
f"Calculation of {operation} initiated with Gaussian on {date_time()}\n"
|
||||
)
|
||||
|
||||
if shutil.which("bash") is not None:
|
||||
exit_status = subprocess.call(
|
||||
[
|
||||
"bash",
|
||||
"-c",
|
||||
"exec -a {}-step{} {} {}".format(
|
||||
self.step.gaussian.qmprog,
|
||||
cycle,
|
||||
self.step.gaussian.qmprog,
|
||||
infile,
|
||||
),
|
||||
]
|
||||
)
|
||||
else:
|
||||
exit_status = subprocess.call([self.step.gaussian.qmprog, infile])
|
||||
|
||||
if exit_status != 0:
|
||||
raise SystemError("Gaussian process did not exit properly")
|
||||
|
||||
logger.info(f"Calculation of {operation} finished on {date_time()}")
|
||||
|
||||
os.chdir(working_dir)
|
||||
|
||||
def _run_formchk(self, cycle: int):
|
||||
qm_dir = Path(self.step.simulation_dir, f"step{(cycle):02d}", "qm")
|
||||
|
||||
work_dir = os.getcwd()
|
||||
os.chdir(qm_dir)
|
||||
|
||||
logger.info("Formatting the checkpoint file... \n")
|
||||
|
||||
exit_status = subprocess.call(
|
||||
["formchk", "asec.chk"], stdout=subprocess.DEVNULL
|
||||
)
|
||||
|
||||
if exit_status != 0:
|
||||
raise SystemError("Formchk process did not exit properly")
|
||||
|
||||
logger.info("Done\n")
|
||||
|
||||
os.chdir(work_dir)
|
||||
|
||||
def _read_charges_from_fchk(self, cycle: int):
|
||||
fchk_file_path = Path("simfiles", f"step{cycle:02d}", "qm", "asec.fchk")
|
||||
with open(fchk_file_path) as fchk:
|
||||
fchkfile = fchk.readlines()
|
||||
|
||||
if self.step.gaussian.pop in ["chelpg", "mk"]:
|
||||
CHARGE_FLAG = "ESP Charges"
|
||||
else:
|
||||
CHARGE_FLAG = "ESP Charges"
|
||||
|
||||
start = fchkfile.pop(0).strip()
|
||||
while start.find(CHARGE_FLAG) != 0: # expression in begining of line
|
||||
start = fchkfile.pop(0).strip()
|
||||
|
||||
charges: List[float] = []
|
||||
while len(charges) < len(self.system.molecule[0].atom):
|
||||
charges.extend([float(x) for x in fchkfile.pop(0).split()])
|
||||
|
||||
return charges
|
||||
Reference in New Issue
Block a user