diff --git a/crystalpol/__main__.py b/crystalpol/__main__.py index a140c78..410dfdc 100644 --- a/crystalpol/__main__.py +++ b/crystalpol/__main__.py @@ -1,18 +1,15 @@ from crystalpol.polarization import Polarization from crystalpol.shared.config import Config +from crystalpol.shared.utils.log import Log from yaml.loader import SafeLoader -import yaml - from pathlib import Path import setproctitle import argparse import logging -import sys +import yaml import os -from crystalpol.shared.utils import weekday_date_time -from crystalpol.shared.utils.log import Log __VERSION = "v0.0.1" os.nice(+19) diff --git a/crystalpol/gaussian.py b/crystalpol/gaussian.py index 72572b1..240b552 100644 --- a/crystalpol/gaussian.py +++ b/crystalpol/gaussian.py @@ -27,7 +27,7 @@ class Gaussian: def run(self, cycle: int, crystal: Crystal) -> List[float]: file = Path( - "simfiles", + self.config.simulation_dir, f"crystal-{str(cycle).zfill(2)}", f"crystal-{str(cycle).zfill(2)}.gjf" ) @@ -151,4 +151,9 @@ 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] + ) + ) diff --git a/crystalpol/polarization.py b/crystalpol/polarization.py index 2ef7979..3f36138 100644 --- a/crystalpol/polarization.py +++ b/crystalpol/polarization.py @@ -1,5 +1,3 @@ -import os - from crystalpol.shared.system.molecule import Molecule from crystalpol.shared.system.crystal import Crystal from crystalpol.shared.system.atom import Atom diff --git a/crystalpol/shared/config/config.py b/crystalpol/shared/config/config.py index 910e82e..e35fcae 100644 --- a/crystalpol/shared/config/config.py +++ b/crystalpol/shared/config/config.py @@ -9,9 +9,9 @@ class Config: n_procs: int = 1 pop: str = "chelpg" - charge_tolerance = 0.02 comment: str = "crystalpol" - simulation_dir = "simfiles" + charge_tolerance: float = 0.02 + simulation_dir: str = "simfiles" mult: list = \ field(default_factory=lambda: [0, 1]) diff --git a/tests/shared/config/test_config.py b/tests/shared/config/test_config.py index 2510ce7..f449b80 100644 --- a/tests/shared/config/test_config.py +++ b/tests/shared/config/test_config.py @@ -53,3 +53,12 @@ class TestConfig(unittest.TestCase): level="b3lyp/aug-cc-pVDZ", n_atoms=0 ) + + def test_set_charge_tolerance(self): + config = Config( + mem=1, + level="b3lyp/aug-cc-pVDZ", + n_atoms=10, + charge_tolerance=0.001 + ) + self.assertEqual(config.charge_tolerance, 0.001)