HideyoshiNakazone/CrystalPol
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Adds Extra Parameter to Logs and Updates Version Variable

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This commit is contained in:
Vitor Hideyoshi
2024-07-24 00:47:58 -03:00
parent 95a88ccc34
commit 2192bac293
9 changed files with 427 additions and 433 deletions
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3
crystalpol/__init__.py
View File

@@ -0,0 +1,3 @@
from importlib import metadata
VERSION = metadata.version("crystalpol")

41
crystalpol/__main__.py
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@@ -1,19 +1,19 @@
from crystalpol import VERSION
from crystalpol.polarization import Polarization
from crystalpol.shared.config import Config
from crystalpol.shared.utils.log import Log
from yaml.loader import SafeLoader
from pathlib import Path
import setproctitle
import yaml
from yaml.loader import SafeLoader
import argparse
import logging
import yaml
import os
from pathlib import Path
__VERSION = "v0.0.1"
os.nice(+19)
setproctitle.setproctitle("crystalpol-{}".format(__VERSION))
setproctitle.setproctitle("crystalpol-{}".format(VERSION))
def main():
@@ -24,28 +24,31 @@ def main():
parser = argparse.ArgumentParser(prog="CrystalPol")
parser.add_argument(
"-v", "--version", action="version", version=f"crystalpol-{__VERSION}"
"-v", "--version", action="version", version=f"crystalpol-{VERSION}"
)
parser.add_argument(
"-c", "--config",
"-c",
"--config",
dest="config",
default="config.yml",
metavar="INFILE",
help="Config file of crystalpol [default = config.yml]"
help="Config file of crystalpol [default = config.yml]",
)
parser.add_argument(
"-i", "--input",
"-i",
"--input",
dest="infile",
default="crystal.xyz",
metavar="INFILE",
help="Input file of crystalpol [default = crystal.xyz]"
help="Input file of crystalpol [default = crystal.xyz]",
)
parser.add_argument(
"-o", "--output",
"-o",
"--output",
dest="outfile",
default="run.log",
metavar="OUTFILE",
help="Output file of crystalpol [default = run.log]"
help="Output file of crystalpol [default = run.log]",
)
args = parser.parse_args()
@@ -53,20 +56,16 @@ def main():
if log_file.exists():
log_file.rename(log_file.with_suffix(".log.backup"))
logging.basicConfig(
filename=args.outfile,
format='%(message)s',
level=logging.INFO
)
logging.basicConfig(filename=args.outfile, format="%(message)s", level=logging.INFO)
try:
with open(args.config) as file:
data = yaml.load(file, Loader=SafeLoader)
config = Config(**data.get('crystal_pol'))
config = Config(**data.get("crystal_pol"))
except IOError:
raise RuntimeError('Invalid or Missing Config File.')
raise RuntimeError("Invalid or Missing Config File.")
Log.make_header(__VERSION, config.to_dict())
Log.make_header(VERSION, config.to_dict())
pol = Polarization(args.infile, args.outfile, config)
pol.run()

38
crystalpol/polarization.py
View File

@@ -1,18 +1,16 @@
from crystalpol.shared.system.molecule import Molecule
from crystalpol.shared.system.crystal import Crystal
from crystalpol.shared.system.atom import Atom
from crystalpol.shared.config import Config
from crystalpol.gaussian import Gaussian
from typing import List, Tuple
from crystalpol.shared.config import Config
from crystalpol.shared.system.atom import Atom
from crystalpol.shared.system.crystal import Crystal
from crystalpol.shared.system.molecule import Molecule
from crystalpol.shared.utils.log import Log
import sys
from crystalpol.shared.utils.log import Log
from typing import List, Tuple
class Polarization:
__slots__ = ('geom_file', 'outfile', 'config', 'gaussian', 'crystal')
__slots__ = ("geom_file", "outfile", "config", "gaussian", "crystal")
def __init__(self, geom_file: str, outfile: str, config: Config) -> None:
self.crystal = None
@@ -33,21 +31,22 @@ class Polarization:
max_charge_diff = sys.float_info.max
while max_charge_diff >= self.config.charge_tolerance:
max_charge_diff, charge_diff = self.update_crystal_charges(
max_charge_diff, min_charge_diff, charge_diff = self.update_crystal_charges(
self.gaussian.run(cycle, self.crystal),
)
Log.make_run(
cycle,
max_charge_diff if cycle != 1 else 0,
min_charge_diff if cycle != 1 else 0,
charge_diff,
self.crystal
self.crystal,
)
cycle += 1
def read_crystal(self) -> None:
with open(self.geom_file, 'r') as geom_file:
with open(self.geom_file, "r") as geom_file:
lines = geom_file.readlines()
molecules = self._get_molecules_from_lines(lines)
@@ -57,7 +56,7 @@ class Polarization:
for molecule in molecules:
self.crystal.add_cell([molecule])
def update_crystal_charges(self, charges: List[float]) -> Tuple[float, list]:
def update_crystal_charges(self, charges: List[float]) -> Tuple[float, float, list]:
charge_diff = []
@@ -68,9 +67,12 @@ class Polarization:
charge_diff.append(abs(atom.chg - charges[index]))
atom.chg = charges[index]
max_charge_diff = abs(max(charge_diff, key=abs)) if charge_diff else sys.float_info.max
max_charge_diff = (
abs(max(charge_diff, key=abs)) if charge_diff else sys.float_info.max
)
min_charge_diff = abs(min(charge_diff, key=abs)) if charge_diff else 0
return max_charge_diff, charge_diff
return max_charge_diff, min_charge_diff, charge_diff
def _get_molecules_from_lines(self, lines: List[str]) -> List[Molecule]:
if (len(lines) % self.config.n_atoms) == 0:
@@ -82,7 +84,9 @@ class Polarization:
symbol, rx, ry, rz = tuple(atom_line.split())
mol.add_atom(
Atom(
rx, ry, rz,
rx,
ry,
rz,
symbol=symbol.ljust(2),
)
)
@@ -105,4 +109,4 @@ class Polarization:
@staticmethod
def split(array: List, partitions: int):
for i in range(0, len(array), partitions):
yield array[i: i + partitions]
yield array[i : i + partitions]

52
crystalpol/shared/utils/log.py
View File

@@ -19,31 +19,55 @@ class Log:
logger.info(f"Your python version is {sys.version}\n")
logger.info(f"Program started on {weekday_date_time()}\n")
logger.info("------------------------------------------------------------------------------------------")
logger.info(" CRYSTALPOL variables being used in this run: ")
logger.info("------------------------------------------------------------------------------------------\n")
logger.info(
"------------------------------------------------------------------------------------------"
)
logger.info(
" CRYSTALPOL variables being used in this run: "
)
logger.info(
"------------------------------------------------------------------------------------------\n"
)
for key, value in config_dict.items():
logger.info(f"\t{key} = {(value if value else 'Not set')}")
logger.info("------------------------------------------------------------------------------------------")
logger.info(f" RUN Results: ")
logger.info("------------------------------------------------------------------------------------------\n")
logger.info(
"------------------------------------------------------------------------------------------"
)
logger.info(
f" RUN Results: "
)
logger.info(
"------------------------------------------------------------------------------------------\n"
)
@staticmethod
def make_run(cycle, max_charge_diff, charge_diff, crystal, logger=None):
def make_run(
cycle, max_charge_diff, min_charge_diff, charge_diff, crystal, logger=None
):
if logger is None:
logger = logging.getLogger()
logger.info(f"cycle: {cycle}")
logger.info(f"\nMax charge diff: {max_charge_diff:.5f}")
logger.info(f"cycle: {cycle}\n")
logger.info(f"Max charge diff: {max_charge_diff:.5f}")
logger.info(f"Min charge diff: {min_charge_diff:.5f}")
logger.info(f"Charge Diff: {charge_diff}\n")
logger.info(f"------------------------------------------------------------------------------------------")
logger.info(f" S rx ry rz chg ")
logger.info(f"------------------------------------------------------------------------------------------")
logger.info(
f"------------------------------------------------------------------------------------------"
)
logger.info(
f" S rx ry rz chg "
)
logger.info(
f"------------------------------------------------------------------------------------------"
)
for atom in crystal[0][0]:
logger.info(
f" {atom.symbol.rjust(2)} {float(atom.rx):.6f} {float(atom.ry):.6f} {float(atom.rz):.6f} {float(atom.chg):.6f} ")
f" {atom.symbol.rjust(2)} {float(atom.rx):.6f} {float(atom.ry):.6f} {float(atom.rz):.6f} {float(atom.chg):.6f} "
)
logger.info("\n------------------------------------------------------------------------------------------\n")
logger.info(
"\n------------------------------------------------------------------------------------------\n"
)