HideyoshiNakazone/CrystalPol
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Implements Better Tests and Logging

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This commit is contained in:
Vitor Hideyoshi
2023-03-01 02:49:28 -03:00
parent 32ca95086a
commit aea34bf214
17 changed files with 1147 additions and 72 deletions
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2
crystalpol/__main__.py
View File

@@ -69,7 +69,7 @@ def main():
except IOError:
raise RuntimeError('Invalid or Missing Config File.')
Log.make_header(__VERSION, data.get('crystal_pol'))
Log.make_header(__VERSION, config.to_dict())
pol = Polarization(args.infile, args.outfile, config)
pol.run()

11
crystalpol/gaussian.py
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@@ -81,9 +81,6 @@ class Gaussian:
with open(file, 'w+') as fh:
chk_path = file.with_suffix('.chk')
fh.write(f"%Chk={chk_path}\n")
fh.write(f"%Mem={self.config.mem}Gb\n")
fh.write(f"%Nprocs={self.config.n_procs}\n")
@@ -120,13 +117,13 @@ class Gaussian:
fh.seek(0)
return fh.read()
def make_gaussian_charges(self, fh: TextIO, crystal: Crystal) -> None:
@staticmethod
def make_gaussian_charges(fh: TextIO, crystal: Crystal) -> None:
for index_cell, cell in enumerate(crystal):
for index_mol, molecule in enumerate(cell):
if (index_cell == 0 and index_mol != 0) or (index_cell != 0):
for atom in molecule:
symbol = atom_symbol[atom.na]
fh.write(
f"{float(atom.rx):>10.5f} "
f"{float(atom.ry):>10.5f} "
@@ -134,8 +131,6 @@ class Gaussian:
f"{float(atom.chg):>10.5f}\n"
)
fh.write("\n")
def read_charges_from_gaussian_output(self, cycle, number_of_charges: int) -> List[float]:
step_dir = Path(
self.config.simulation_dir,
@@ -156,4 +151,4 @@ class Gaussian:
lines = lines[3:] # Consume 3 more lines
return list(map(lambda x: float(x.split()[2]), lines[:number_of_charges]))
return list(map(lambda x: float(x.split()[2]), lines[:number_of_charges]))

4
crystalpol/polarization.py
View File

@@ -33,7 +33,7 @@ class Polarization:
cycle = 1
max_charge_diff = sys.float_info.max
while max_charge_diff > self.config.charge_tolerance:
while max_charge_diff >= self.config.charge_tolerance:
max_charge_diff, charge_diff = self.update_crystal_charges(
self.gaussian.run(cycle, self.crystal),
@@ -41,7 +41,7 @@ class Polarization:
Log.make_run(
cycle,
max_charge_diff,
max_charge_diff if cycle != 1 else 0,
charge_diff,
self.crystal
)

11
crystalpol/shared/config/config.py
View File

@@ -1,9 +1,8 @@
from dataclasses import dataclass, field, fields
from dataclasses import dataclass, field, fields, asdict
@dataclass
class Config:
mem: int
level: str
n_atoms: int
@@ -31,13 +30,11 @@ class Config:
f'Memory must be a integer greater than 0.'
)
if self.level is None:
raise ValueError(
f'Invalid value for level. Level must not be none.'
)
if self.n_atoms is None or self.n_atoms <= 0:
raise ValueError(
f'Invalid value for n_atoms: {self.mem},'
f'Number of Atoms must be a integer greater than 0.'
)
def to_dict(self):
return asdict(self)

3
crystalpol/shared/system/atom.py
View File

@@ -18,6 +18,7 @@ class Atom:
ry: float,
rz: float,
na: int = None,
chg: float = None,
symbol: str = None,
) -> None:
@@ -42,5 +43,5 @@ class Atom:
self.rx = rx
self.ry = ry
self.rz = rz
self.chg = None
self.chg = chg
self.mass = atom_mass[self.na]

2
crystalpol/shared/utils/__init__.py
View File

@@ -2,4 +2,4 @@ import time
def weekday_date_time():
return time.strftime("%A, %d %b %Y at %H:%M:%S")
return time.strftime("%A, %d %b %Y at %H:%M:%S")

58
crystalpol/shared/utils/log.py
View File

@@ -1,45 +1,49 @@
import sys
from crystalpol.shared.config import Config
from crystalpol.shared.utils import weekday_date_time
import logging
from crystalpol.shared.utils import weekday_date_time
import sys
class Log:
@staticmethod
def make_header(version: str, config_dict: dict):
logging.info(
def make_header(version: str, config_dict: dict, logger=None):
if logger is None:
logger = logging.getLogger()
logger.info(
f"##########################################################################################\n"
f"############## Welcome to CRYSTALPOL version {version} ##############\n"
f"##########################################################################################\n"
)
logging.info(f"Your python version is {sys.version}\n")
logging.info(f"Program started on {weekday_date_time()}\n")
logger.info(f"Your python version is {sys.version}\n")
logger.info(f"Program started on {weekday_date_time()}\n")
logging.info("------------------------------------------------------------------------------------------")
logging.info(" CRYSTALPOL variables being used in this run: ")
logging.info("------------------------------------------------------------------------------------------\n")
logger.info("------------------------------------------------------------------------------------------")
logger.info(" CRYSTALPOL variables being used in this run: ")
logger.info("------------------------------------------------------------------------------------------\n")
for key, value in config_dict.items():
logging.info(f"\t{key} = {(key if key else 'Not set')}")
logger.info(f"\t{key} = {(value if value else 'Not set')}")
logging.info("------------------------------------------------------------------------------------------")
logging.info(f" RUN Results: ")
logging.info("------------------------------------------------------------------------------------------\n")
logger.info("------------------------------------------------------------------------------------------")
logger.info(f" RUN Results: ")
logger.info("------------------------------------------------------------------------------------------\n")
@staticmethod
def make_run(cycle, max_charge_diff, charge_diff, crystal):
logging.info(f"cycle: {cycle}")
logging.info(f"\nMax charge diff: {max_charge_diff}")
logging.info(f"Charge Diff: {charge_diff}\n")
def make_run(cycle, max_charge_diff, charge_diff, crystal, logger=None):
logging.info("------------------------------------------------------------------------------------------")
logging.info(f" S rx ry rz chg ")
logging.info("------------------------------------------------------------------------------------------")
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"Charge Diff: {charge_diff}\n")
logger.info(f"------------------------------------------------------------------------------------------")
logger.info(f" S rx ry rz chg ")
logger.info(f"------------------------------------------------------------------------------------------")
for atom in crystal[0][0]:
logging.info(f" {atom.symbol} {atom.rx} {atom.ry} {atom.rz} {atom.chg} ")
logging.info("\n------------------------------------------------------------------------------------------\n")
logger.info(
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")