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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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38
crystalpol/polarization.py
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@@ -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]