337 lines
12 KiB
Python
337 lines
12 KiB
Python
from diceplayer.shared.interface.gaussian_interface import GaussianInterface
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from diceplayer.shared.interface.dice_interface import DiceInterface
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from diceplayer.shared.utils.dataclass_protocol import Dataclass
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from diceplayer.shared.config.gaussian_dto import GaussianDTO
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from diceplayer.shared.environment.molecule import Molecule
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from diceplayer.shared.utils.misc import weekday_date_time
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from diceplayer.shared.config.player_dto import PlayerDTO
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from diceplayer.shared.environment.system import System
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from diceplayer.shared.config.step_dto import StepDTO
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from diceplayer.shared.config.dice_dto import DiceDTO
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from diceplayer.shared.environment.atom import Atom
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from diceplayer import logger
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from dataclasses import fields
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from pathlib import Path
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from typing import Type
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import logging
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import yaml
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import sys
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import os
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ENV = ["OMP_STACKSIZE"]
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class Player:
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def __init__(self, infile: str):
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config_data = self.read_keywords(infile)
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self.system = System()
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self.config = self.set_config(
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config_data.get("diceplayer")
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)
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self.gaussian = GaussianInterface(config_data.get("gaussian"))
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self.dice = DiceInterface(config_data.get("dice"))
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def start(self, initial_cycle: int = 1):
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self.print_keywords()
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self.create_simulation_dir()
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self.read_potentials()
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self.print_potentials()
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for cycle in range(initial_cycle, self.config.maxcyc + 1):
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self.dice_start(cycle)
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def create_simulation_dir(self):
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simulation_dir_path = Path(self.config.simulation_dir)
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if simulation_dir_path.exists():
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raise FileExistsError(
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f"Error: a file or a directory {self.config.simulation_dir} already exists,"
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f" move or delete the simfiles directory to continue."
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)
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simulation_dir_path.mkdir()
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def print_keywords(self) -> None:
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def log_keywords(config: Dataclass, dto: Type[Dataclass]):
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for key in sorted(list(map(lambda f: f.name, fields(dto)))):
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if getattr(config, key) is not None:
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if isinstance(getattr(config, key), list):
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string = " ".join(str(x) for x in getattr(config, key))
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logger.info(f"{key} = [ {string} ]")
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else:
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logger.info(f"{key} = {getattr(config, key)}")
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logger.info(
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"##########################################################################################\n"
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"############# Welcome to DICEPLAYER version 1.0 #############\n"
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"##########################################################################################\n"
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"\n"
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)
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logger.info("Your python version is {}\n".format(sys.version))
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logger.info("\n")
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logger.info("Program started on {}\n".format(weekday_date_time()))
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logger.info("\n")
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logger.info("Environment variables:\n")
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for var in ENV:
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logger.info(
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"{} = {}\n".format(
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var, (os.environ[var] if var in os.environ else "Not set")
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)
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)
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logger.info(
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"\n==========================================================================================\n"
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" CONTROL variables being used in this run:\n"
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"------------------------------------------------------------------------------------------\n"
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"\n"
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)
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logger.info("\n")
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logger.info(
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"------------------------------------------------------------------------------------------\n"
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" DICE variables being used in this run:\n"
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"------------------------------------------------------------------------------------------\n"
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"\n"
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)
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log_keywords(self.dice.config, DiceDTO)
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logger.info("\n")
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logger.info(
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"------------------------------------------------------------------------------------------\n"
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" GAUSSIAN variables being used in this run:\n"
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"------------------------------------------------------------------------------------------\n"
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"\n"
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)
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log_keywords(self.gaussian.config, GaussianDTO)
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logger.info("\n")
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def read_potentials(self):
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ljname_path = Path(self.dice.config.ljname)
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if ljname_path.exists():
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with open(self.dice.config.ljname) as file:
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ljc_data = file.readlines()
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else:
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raise RuntimeError(
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f"Potential file {self.dice.config.ljname} not found."
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)
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combrule = ljc_data.pop(0).split()[0]
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if combrule not in ("*", "+"):
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sys.exit(
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"Error: expected a '*' or a '+' sign in 1st line of file {}".format(
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self.dice.config.ljname
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)
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)
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self.dice.config.combrule = combrule
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ntypes = ljc_data.pop(0).split()[0]
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if not ntypes.isdigit():
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sys.exit(
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"Error: expected an integer in the 2nd line of file {}".format(
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self.dice.config.ljname
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)
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)
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ntypes = int(ntypes)
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if ntypes != len(self.dice.config.nmol):
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sys.exit(
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f"Error: number of molecule types in file {self.dice.config.ljname} "
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f"must match that of 'nmol' keyword in config file"
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)
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for i in range(ntypes):
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try:
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nsites, molname = ljc_data.pop(0).split()[:2]
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except ValueError:
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raise ValueError(
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f"Error: expected nsites and molname for the molecule type {i+1}"
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)
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if not nsites.isdigit():
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raise ValueError(
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f"Error: expected nsites to be an integer for molecule type {i+1}"
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)
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nsites = int(nsites)
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self.system.add_type(nsites, Molecule(molname))
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atom_fields = ["lbl", "na", "rx", "ry", "rz", "chg", "eps", "sig"]
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for j in range(nsites):
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new_atom = dict(zip(
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atom_fields,
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ljc_data.pop(0).split()
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))
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self.system.molecule[i].add_atom(
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Atom(**self.validate_atom_dict(i, j, new_atom))
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)
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def print_potentials(self) -> None:
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formatstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f} {:>9.4f}"
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logger.info(
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"==========================================================================================\n"
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)
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logger.info(
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f" Potential parameters from file {self.dice.config.ljname}:"
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)
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logger.info(
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"------------------------------------------------------------------------------------------"
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"\n"
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)
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logger.info(f"Combination rule: {self.dice.config.combrule}")
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logger.info(
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f"Types of molecules: {len(self.system.molecule)}\n"
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)
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i = 0
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for mol in self.system.molecule:
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i += 1
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logger.info(
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"{} atoms in molecule type {}:".format(len(mol.atom), i)
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)
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logger.info(
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"---------------------------------------------------------------------------------"
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)
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logger.info(
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"Lbl AN X Y Z Charge Epsilon Sigma Mass"
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)
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logger.info(
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"---------------------------------------------------------------------------------"
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)
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for atom in mol.atom:
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logger.info(
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formatstr.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,
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atom.chg,
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atom.eps,
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atom.sig,
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atom.mass,
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)
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)
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logger.info("\n")
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logger.info(
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"=========================================================================================="
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)
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def dice_start(self, cycle: int):
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self.dice.configure(
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StepDTO(
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ncores=self.config.ncores,
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nprocs=self.config.nprocs,
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simulation_dir=self.config.simulation_dir,
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altsteps=self.config.altsteps,
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molecule=self.system.molecule,
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nmol=self.system.nmols,
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)
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)
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self.dice.start(cycle)
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self.dice.reset()
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def gaussian_start(self, cycle: int):
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self.gaussian.start(cycle)
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@staticmethod
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def validate_atom_dict(molecule_type, molecule_site, atom_dict: dict) -> dict:
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molecule_type += 1
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molecule_site += 1
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if len(atom_dict) < 8:
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raise ValueError(
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f'Invalid number of fields for site {molecule_site} for molecule type {molecule_type}.'
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)
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try:
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atom_dict['lbl'] = int(atom_dict['lbl'])
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except Exception:
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raise ValueError(
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f'Invalid lbl fields for site {molecule_site} for molecule type {molecule_type}.'
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)
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try:
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atom_dict['na'] = int(atom_dict['na'])
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except Exception:
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raise ValueError(
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f'Invalid na fields for site {molecule_site} for molecule type {molecule_type}.'
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)
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try:
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atom_dict['rx'] = float(atom_dict['rx'])
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except Exception:
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raise ValueError(
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f'Invalid rx fields for site {molecule_site} for molecule type {molecule_type}. '
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f'Value must be a float.'
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)
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try:
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atom_dict['ry'] = float(atom_dict['ry'])
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except Exception:
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raise ValueError(
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f'Invalid ry fields for site {molecule_site} for molecule type {molecule_type}. '
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f'Value must be a float.'
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)
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try:
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atom_dict['rz'] = float(atom_dict['rz'])
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except Exception:
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raise ValueError(
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f'Invalid rz fields for site {molecule_site} for molecule type {molecule_type}. '
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f'Value must be a float.'
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)
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try:
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atom_dict['chg'] = float(atom_dict['chg'])
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except Exception:
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raise ValueError(
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f'Invalid chg fields for site {molecule_site} for molecule type {molecule_type}. '
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f'Value must be a float.'
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)
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try:
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atom_dict['eps'] = float(atom_dict['eps'])
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except Exception:
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raise ValueError(
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f'Invalid eps fields for site {molecule_site} for molecule type {molecule_type}. '
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f'Value must be a float.'
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)
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try:
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atom_dict['sig'] = float(atom_dict['sig'])
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except Exception:
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raise ValueError(
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f'Invalid sig fields for site {molecule_site} for molecule type {molecule_type}. '
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f'Value must be a float.'
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)
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return atom_dict
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@staticmethod
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def set_config(data: dict) -> PlayerDTO:
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return PlayerDTO.from_dict(data)
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@staticmethod
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def read_keywords(infile) -> dict:
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with open(infile, 'r') as yml_file:
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return yaml.load(yml_file, Loader=yaml.SafeLoader)
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