Refactor Gaussian class to use pop method for parameter removal and update test setup to utilize utility functions for directory paths

Author: calvinp0

autotst/calculator/gaussian.py

@@ -179,7 +179,7 @@ def get_rotor_calc(self,
             addsec=[addsec[:-1]])
 
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        ase_gaussian.parameters.pop("force", None)
         return ase_gaussian
 
     def get_conformer_calc(self):
@@ -232,7 +232,7 @@ def get_conformer_calc(self):
             extra=f"opt=(calcfc,maxcycles=900,{self.convergence}) freq IOP(7/33=1,2/16=3) scf=(maxcycle=900)",
             multiplicity=self.conformer.rmg_molecule.multiplicity)
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        ase_gaussian.parameters.pop("force", None)
         return ase_gaussian
 
     def get_shell_calc(self):
@@ -293,7 +293,7 @@ def get_shell_calc(self):
             addsec=[combos]
         )
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        ase_gaussian.parameters.pop("force", None)
 
         return ase_gaussian
 
@@ -353,7 +353,7 @@ def get_center_calc(self):
             addsec=[addsec[:-1]]
         )
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        ase_gaussian.parameters.pop("force", None)
 
         return ase_gaussian
 
@@ -399,7 +399,7 @@ def get_overall_calc(self):
             extra="opt=(ts,calcfc,noeigentest,maxcycles=900) freq scf=(maxcycle=900) IOP(7/33=1,2/16=3)",
             multiplicity=self.conformer.rmg_molecule.multiplicity)
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        ase_gaussian.parameters.pop("force", None)
 
         return ase_gaussian
 
@@ -444,7 +444,7 @@ def get_irc_calc(self):
             multiplicity=self.conformer.rmg_molecule.multiplicity
         )
         ase_gaussian.atoms = self.conformer.ase_molecule
-        del ase_gaussian.parameters['force']
+        ase_gaussian.parameters.pop("force", None)
 
         return ase_gaussian
 

autotst/calculator/gaussian_test.py

@@ -38,6 +38,7 @@
 from ..species import Species, Conformer
 from ..geometry import Torsion
 from .gaussian import Gaussian
+from ..utils.paths import project_root, test_bin_dir
 
 import ase
 import ase.calculators.gaussian
@@ -48,7 +49,7 @@
 
 class TestGaussian(unittest.TestCase):
     def setUp(self):
-        os.environ["PATH"] = os.path.expandvars("$AUTOTST/test/bin:") + os.environ["PATH"]
+        os.environ["PATH"] = f"{test_bin_dir()}:{os.environ['PATH']}"
         rxn = Reaction(label='C+[O]O_[CH3]+OO')
         ts = rxn.ts["forward"][0]
         ts.get_molecules()
@@ -105,12 +106,14 @@ def test_irc_calc(self):
         self.assertIsInstance(calc_dict,dict)
 
     def tearDown(self):
-        if os.path.exists(os.path.expandvars("$AUTOTST/autotst/calculator/ts")):
-            shutil.rmtree(os.path.expandvars("$AUTOTST/autotst/calculator/ts"))
-        if os.path.exists(os.path.expandvars("$AUTOTST/autotst/calculator/species")):
-            shutil.rmtree(os.path.expandvars("$AUTOTST/autotst/calculator/species"))
+        ts_dir = project_root() / "autotst" / "calculator" / "ts"
+        species_dir = project_root() / "autotst" / "calculator" / "species"
+        if os.path.exists(ts_dir):
+            shutil.rmtree(ts_dir)
+        if os.path.exists(species_dir):
+            shutil.rmtree(species_dir)
 
 if __name__ == "__main__":
     unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))
 
-    
+    

test/bin/g16

@@ -1,16 +1,17 @@
 #!/usr/bin/env python
 
 import os, sys, shutil, time
+from pathlib import Path
 
 input_file = sys.argv[1].split("/")[-1] + ".log"
 directory_path = sys.argv[1].strip(input_file)
 log_file = input_file.replace(".com", ".log")
-log_path = os.path.expandvars("$AUTOTST/test/bin/log-files")
+project_root = Path(__file__).resolve().parents[2]
+log_path = project_root / "test" / "bin" / "log-files"
 
 if os.path.join(log_path, log_file):
     shutil.copy(
         os.path.join(log_path, log_file),
         os.path.join(directory_path, log_file)
     )
 
-