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Implements Refactoring in Player Class and Initial Working Version

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This commit is contained in:
Vitor Hideyoshi
2023-06-02 20:20:38 -03:00
parent b440a0f05d
commit 33612f2d7b
21 changed files with 1193 additions and 983 deletions
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198
diceplayer/player.py
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@@ -1,19 +1,18 @@
from diceplayer.shared.interface.gaussian_interface import GaussianInterface
from diceplayer.shared.interface.dice_interface import DiceInterface
from diceplayer.shared.utils.dataclass_protocol import Dataclass
from diceplayer.shared.config.gaussian_dto import GaussianDTO
from diceplayer.shared.environment.molecule import Molecule
from diceplayer.shared.config.gaussian_config import GaussianDTO
from diceplayer.shared.config.player_config import PlayerConfig
from diceplayer.shared.config.dice_config import DiceConfig
from diceplayer.shared.utils.misc import weekday_date_time
from diceplayer.shared.config.player_dto import PlayerDTO
from diceplayer.shared.environment.molecule import Molecule
from diceplayer.shared.environment.system import System
from diceplayer.shared.config.step_dto import StepDTO
from diceplayer.shared.config.dice_dto import DiceDTO
from diceplayer.shared.environment.atom import Atom
from diceplayer import logger
from dataclasses import fields
from pathlib import Path
from typing import Type
from typing import Type, List
import logging
import yaml
import sys
@@ -33,20 +32,50 @@ class Player:
config_data.get("diceplayer")
)
self.gaussian = GaussianInterface(config_data.get("gaussian"))
self.dice = DiceInterface(config_data.get("dice"))
self.dice_interface = DiceInterface()
self.gaussian_interface = GaussianInterface()
def start(self, initial_cycle: int = 1):
self.print_keywords()
self.create_simulation_dir()
self.read_potentials()
self.print_potentials()
logger.info(
"==========================================================================================\n"
"Starting the iterative process.\n"
"==========================================================================================\n"
)
for cycle in range(initial_cycle, self.config.maxcyc + 1):
logger.info(
f"------------------------------------------------------------------------------------------\n"
f" Step # {cycle}\n"
f"------------------------------------------------------------------------------------------\n"
)
self.dice_start(cycle)
try:
self.gaussian_start(cycle)
except StopIteration as e:
break
def prepare_system(self):
for i, mol in enumerate(self.system.molecule):
logger.info(
f"Molecule {i + 1} - {mol.molname}"
)
mol.print_mol_info()
logger.info(
"\n Translating and rotating molecule to standard orientation..."
)
mol.standard_orientation()
logger.info("\n Done")
logger.info("\nNew values:\n")
mol.print_mol_info()
logger.info("\n")
def create_simulation_dir(self):
simulation_dir_path = Path(self.config.simulation_dir)
if simulation_dir_path.exists():
@@ -71,13 +100,10 @@ class Player:
"##########################################################################################\n"
"############# Welcome to DICEPLAYER version 1.0 #############\n"
"##########################################################################################\n"
"\n"
)
logger.info("Your python version is {}\n".format(sys.version))
logger.info("\n")
logger.info("Program started on {}\n".format(weekday_date_time()))
logger.info("\n")
logger.info("Environment variables:\n")
logger.info("Environment variables:")
for var in ENV:
logger.info(
"{} = {}\n".format(
@@ -85,68 +111,55 @@ class Player:
)
)
logger.info(
"\n==========================================================================================\n"
" CONTROL variables being used in this run:\n"
"------------------------------------------------------------------------------------------\n"
"\n"
)
logger.info("\n")
logger.info(
"------------------------------------------------------------------------------------------\n"
" DICE variables being used in this run:\n"
"------------------------------------------------------------------------------------------\n"
"\n"
)
log_keywords(self.dice.config, DiceDTO)
logger.info("\n")
log_keywords(self.config.dice, DiceConfig)
logger.info(
"------------------------------------------------------------------------------------------\n"
" GAUSSIAN variables being used in this run:\n"
"------------------------------------------------------------------------------------------\n"
"\n"
)
log_keywords(self.gaussian.config, GaussianDTO)
log_keywords(self.config.gaussian, GaussianDTO)
logger.info("\n")
def read_potentials(self):
ljname_path = Path(self.dice.config.ljname)
ljname_path = Path(self.config.dice.ljname)
if ljname_path.exists():
with open(self.dice.config.ljname) as file:
with open(self.config.dice.ljname) as file:
ljc_data = file.readlines()
else:
raise RuntimeError(
f"Potential file {self.dice.config.ljname} not found."
f"Potential file {self.config.dice.ljname} not found."
)
combrule = ljc_data.pop(0).split()[0]
if combrule not in ("*", "+"):
sys.exit(
"Error: expected a '*' or a '+' sign in 1st line of file {}".format(
self.dice.config.ljname
self.config.dice.ljname
)
)
self.dice.config.combrule = combrule
self.config.dice.combrule = combrule
ntypes = ljc_data.pop(0).split()[0]
if not ntypes.isdigit():
sys.exit(
"Error: expected an integer in the 2nd line of file {}".format(
self.dice.config.ljname
self.config.dice.ljname
)
)
ntypes = int(ntypes)
if ntypes != len(self.dice.config.nmol):
if ntypes != len(self.config.dice.nmol):
sys.exit(
f"Error: number of molecule types in file {self.dice.config.ljname} "
f"Error: number of molecule types in file {self.config.dice.ljname} "
f"must match that of 'nmol' keyword in config file"
)
@@ -165,7 +178,7 @@ class Player:
)
nsites = int(nsites)
self.system.add_type(nsites, Molecule(molname))
self.system.add_type(Molecule(molname))
atom_fields = ["lbl", "na", "rx", "ry", "rz", "chg", "eps", "sig"]
for j in range(nsites):
@@ -178,20 +191,15 @@ class Player:
)
def print_potentials(self) -> None:
formatstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f} {:>9.4f}"
logger.info(
"==========================================================================================\n"
)
logger.info(
f" Potential parameters from file {self.dice.config.ljname}:"
)
logger.info(
f" Potential parameters from file {self.config.dice.ljname}:\n"
"------------------------------------------------------------------------------------------"
"\n"
)
logger.info(f"Combination rule: {self.dice.config.combrule}")
logger.info(f"Combination rule: {self.config.dice.combrule}")
logger.info(
f"Types of molecules: {len(self.system.molecule)}\n"
)
@@ -229,28 +237,50 @@ class Player:
logger.info("\n")
logger.info(
"=========================================================================================="
)
def dice_start(self, cycle: int):
self.dice.configure(
StepDTO(
ncores=self.config.ncores,
nprocs=self.config.nprocs,
simulation_dir=self.config.simulation_dir,
altsteps=self.config.altsteps,
molecule=self.system.molecule,
nmol=self.system.nmols,
)
self.dice_interface.configure(
self.config,
self.system,
)
self.dice.start(cycle)
self.dice_interface.start(cycle)
self.dice.reset()
self.dice_interface.reset()
def gaussian_start(self, cycle: int):
self.gaussian.start(cycle)
self.gaussian_interface.configure(
self.config,
self.system,
)
result = self.gaussian_interface.start(cycle)
self.gaussian_interface.reset()
if self.config.opt:
if 'position' not in result:
raise RuntimeError(
'Optimization failed. No position found in result.'
)
self.system.update_molecule(result['position'])
else:
if 'charges' not in result:
raise RuntimeError(
'Charges optimization failed. No charges found in result.'
)
diff = self.system.molecule[0]\
.update_charges(result['charges'])
self.system.print_charges_and_dipole(cycle)
if diff < self.config.gaussian.chg_tol:
logger.info(
f'Charges converged after {cycle} cycles.'
)
raise StopIteration()
@staticmethod
def validate_atom_dict(molecule_type, molecule_site, atom_dict: dict) -> dict:
@@ -326,9 +356,43 @@ class Player:
return atom_dict
def print_results(self):
formatstr = "{:<3d} {:>3d} {:>10.5f} {:>10.5f} {:>10.5f} {:>10.6f} {:>9.5f} {:>7.4f} {:>9.4f}"
mol = self.system.molecule[0]
logger.info(
"{} atoms in molecule type {}:".format(len(mol.atom), 1)
)
logger.info(
"---------------------------------------------------------------------------------"
)
logger.info(
"Lbl AN X Y Z Charge Epsilon Sigma Mass"
)
logger.info(
"---------------------------------------------------------------------------------"
)
for atom in mol.atom:
logger.info(
formatstr.format(
atom.lbl,
atom.na,
atom.rx,
atom.ry,
atom.rz,
atom.chg,
atom.eps,
atom.sig,
atom.mass,
)
)
logger.info("\n")
@staticmethod
def set_config(data: dict) -> PlayerDTO:
return PlayerDTO.from_dict(data)
def set_config(data: dict) -> PlayerConfig:
return PlayerConfig.from_dict(data)
@staticmethod
def read_keywords(infile) -> dict: