Merge pull request #7 from HideyoshiNakazone/bug-fixes

Bug Fixes on Simfiles Directory and Config File

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)

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]
+            )
+        )

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

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])
 

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)