mod: enable MOPAC and openbabel for ONIOM

pysisyphus/calculators/MOPAC.py

@@ -104,7 +104,7 @@ def prepare_input(self, atoms, coords, calc_type, opt=False):
         )
         return inp
 
-    def get_energy(self, atoms, coords):
+    def get_energy(self, atoms, coords, **prepare_kwargs):
         calc_type = "energy"
         inp = self.prepare_input(atoms, coords, calc_type)
         # with open("inp.mop", "w") as handle:
@@ -113,18 +113,21 @@ def get_energy(self, atoms, coords):
         results = self.run(inp, calc="energy")
         return results
 
-    def get_forces(self, atoms, coords):
+    def get_forces(self, atoms, coords, **prepare_kwargs):
         calc_type = "gradient"
         inp = self.prepare_input(atoms, coords, calc_type, opt=True)
         results = self.run(inp, calc="grad")
         return results
 
-    def get_hessian(self, atoms, coords):
+    def get_hessian(self, atoms, coords, **prepare_kwargs):
         calc_type = "hessian"
         inp = self.prepare_input(atoms, coords, calc_type, opt=True)
         results = self.run(inp, calc="hessian")
         return results
 
+    def run_calculation(self, atoms, coords, **prepare_kwargs):
+        return self.get_energy(atoms, coords, **prepare_kwargs)
+
     def read_aux(self, path):
         with open(path / self.aux_fn) as handle:
             text = handle.read()

pysisyphus/calculators/OBabel.py

@@ -1,10 +1,14 @@
+import warnings
+
 import numpy as np
 
 try:
     from openbabel import openbabel as ob
     from openbabel import pybel
 except ModuleNotFoundError:
     pass
+except ImportError:
+    pass
 
 from pysisyphus.calculators.Calculator import Calculator
 from pysisyphus.constants import BOHR2ANG, AU2KJPERMOL, AU2KCALPERMOL
@@ -30,7 +34,7 @@ def __init__(self, ff="gaff", mol=None, **kwargs):
         super().__init__(**kwargs)
 
         if self.charge != 0:
-            print("'charge' keyword is currently ignored!")
+            warnings.warn("'charge' keyword is currently ignored!")
 
         self.ff_name = ff
         avail_ffs = _getplugins(

pysisyphus/calculators/ONIOMv2.py

@@ -32,6 +32,8 @@
 from pysisyphus.calculators import (
     Composite,
     Gaussian16,
+    MOPAC,
+    OBabel,
     OpenMolcas,
     ORCA,
     ORCA5,
@@ -52,6 +54,8 @@
     "composite": Composite,
     "g16": Gaussian16,
     "openmolcas": OpenMolcas.OpenMolcas,
+    "mopac": MOPAC,
+    "obabel": OBabel,
     "orca": ORCA.ORCA,
     "orca5": ORCA5.ORCA5,
     "psi4": Psi4,

pysisyphus/calculators/__init__.py

@@ -19,6 +19,7 @@
     "LennardJones",
     "MOPAC",
     "MultiCalc",
+    "OBabel",
     "ONIOM",
     "OpenMolcas",
     "ORCA",
@@ -53,6 +54,7 @@
 from pysisyphus.calculators.MultiCalc import MultiCalc
 from pysisyphus.calculators.MOPAC import MOPAC
 from pysisyphus.calculators.Psi4 import Psi4
+from pysisyphus.calculators.OBabel import OBabel
 from pysisyphus.calculators.ONIOMv2 import ONIOM
 from pysisyphus.calculators.OpenMolcas import OpenMolcas
 from pysisyphus.calculators.ORCA import ORCA

pysisyphus/run.py

@@ -88,6 +88,7 @@
     "ipiserver": IPIServer,
     "mopac": MOPAC,
     "multi": MultiCalc,
+    "obabel": OBabel,
     "oniom": ONIOM,
     "openmolcas": OpenMolcas,
     "orca": ORCA,