chore: switches from black and isort to ruff
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@@ -1 +1,4 @@
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from .__interface import Interface
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__all__ = ["Interface"]
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@@ -17,6 +17,7 @@ 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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@@ -206,10 +207,10 @@ class DiceInterface(Interface):
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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(f"init = yesreadxyz\n")
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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(f"init = yes\n")
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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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@@ -301,7 +302,7 @@ class DiceInterface(Interface):
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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(f"nstep = 5\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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@@ -60,13 +60,13 @@ class GaussianInterface(Interface):
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def _copy_chk_file_from_previous_step(self, cycle: int):
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current_chk_file_path = Path(
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self.step.simulation_dir, f"step{cycle:02d}", "qm", f"asec.chk"
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self.step.simulation_dir, f"step{cycle:02d}", "qm", "asec.chk"
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)
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if current_chk_file_path.exists():
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raise FileExistsError(f"File {current_chk_file_path} already exists.")
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previous_chk_file_path = Path(
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self.step.simulation_dir, f"step{(cycle - 1):02d}", "qm", f"asec.chk"
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self.step.simulation_dir, f"step{(cycle - 1):02d}", "qm", "asec.chk"
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)
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if not previous_chk_file_path.exists():
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raise FileNotFoundError(f"File {previous_chk_file_path} does not exist.")
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@@ -139,7 +139,7 @@ class GaussianInterface(Interface):
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charges_nsites = int(charges.pop(0))
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if int(charges_nsites) != total_nsites:
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raise ValueError(
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f"Number of sites does not match total number of sites."
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"Number of sites does not match total number of sites."
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)
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thickness.append(self._calculate_proc_thickness(charges))
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@@ -166,7 +166,7 @@ class GaussianInterface(Interface):
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].strip()
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):
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raise SyntaxError(
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f"Error: Invalid Dice Output. Atom type does not match."
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"Error: Invalid Dice Output. Atom type does not match."
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)
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new_molecule.add_atom(
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@@ -216,7 +216,7 @@ class GaussianInterface(Interface):
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def _make_gaussian_input_file(self, cycle: int, asec_charges: list[dict]) -> None:
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gaussian_input_file_path = Path(
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self.step.simulation_dir, f"step{cycle:02d}", "qm", f"asec.gjf"
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self.step.simulation_dir, f"step{cycle:02d}", "qm", "asec.gjf"
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)
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with open(gaussian_input_file_path, "w") as gaussian_input_file:
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