Updated other wrappers and added tests

.gitignore

@@ -46,3 +46,9 @@ tests/.autode_calculations
 tests/data/complex_conf*.xyz
 
 tests/data/*.com
+
+tests/data/conformers/.autode_calculations
+
+tests/data/orca/.autode_calculations
+
+tests/data/xtb/.autode_calculations

autode/smiles/smiles.py

@@ -12,7 +12,9 @@
 
 
 def calc_multiplicity(molecule, n_radical_electrons):
-    """Calculate the spin multiplicity 2S + 1 where S is the number of unpaired electrons
+    """Calculate the spin multiplicity 2S + 1 where S is the number of
+    unpaired electrons
+
     Arguments:
         molecule (autode.molecule.Molecule):
         n_radical_electrons (int):
@@ -24,20 +26,23 @@ def calc_multiplicity(molecule, n_radical_electrons):
         return 1
 
     if molecule.mult == 1 and n_radical_electrons == 1:
-        # Cannot have multiplicity = 1 and 1 radical electrons – override default multiplicity
+        # Cannot have multiplicity = 1 and 1 radical electrons – override
+        # default multiplicity
         return 2
 
     if molecule.mult == 1 and n_radical_electrons > 1:
-        logger.warning('Diradicals by default singlets. Set mol.mult if it\'s any different')
+        logger.warning('Diradicals by default singlets. Set mol.mult if it\'s '
+                       'any different')
         return 1
 
     return molecule.mult
 
 
 def init_organic_smiles(molecule, smiles):
     """
-    Initialise a molecule from a SMILES string, set the charge, multiplicity (if it's not already specified) and the 3D
-    geometry using RDKit
+    Initialise a molecule from a SMILES string, set the charge, multiplicity (
+    if it's not already specified) and the 3D geometry using RDKit
+
     Arguments:
         molecule (autode.molecule.Molecule):
         smiles (str): SMILES string
@@ -114,7 +119,8 @@ def init_smiles(molecule, smiles):
 
 def check_bonds(molecule, bonds):
     """
-    Ensure the SMILES string and the 3D structure have the same bonds, but don't override
+    Ensure the SMILES string and the 3D structure have the same bonds,
+    but don't override
 
     Arguments:
         molecule (autode.molecule.Molecule):

autode/wrappers/G09.py

@@ -1,5 +1,6 @@
 from copy import deepcopy
 import numpy as np
+from autode.constants import Constants
 from autode.wrappers.base import ElectronicStructureMethod
 from autode.utils import run_external
 from autode.atoms import Atom
@@ -440,16 +441,20 @@ def get_gradients(self, calc):
                     gradients_section = False
 
             if gradients_section and len(line.split()) == 5:
-                _, _, x, y, z = line.split()
+                _, _, fx, fy, fz = line.split()
                 try:
-                    gradients.append([float(x), float(y), float(z)])
+                    # Ha / a0
+                    force = np.array([float(fx), float(fy), float(fz)])
+
+                    grad = -force / Constants.a02ang
+                    gradients.append(grad)
                 except ValueError:
                     pass
         for line in gradients:
             for i in range(3):
                 line[i] *= -1
 
-        return gradients
+        return np.array(gradients)
 
     def __init__(self):
         super().__init__(name='g09', path=Config.G09.path,

autode/wrappers/MOPAC.py

@@ -293,7 +293,7 @@ def get_gradients(self, calc):
                 _, _, _, _, _, _, value, _ = line.split()
                 gradients.append(value)
         grad_array = np.asarray(gradients)
-        grad_array *= Constants.a02ang/Constants.ha2kcalmol
+        grad_array /= Constants.ha2kcalmol  # From kcal mol-1 Å^-1 to Ha Å^-1
         grad_array.reshape((calc.molecule.n_atoms, 3))
 
         return grad_array.tolist()

autode/wrappers/NWChem.py

@@ -356,9 +356,11 @@ def get_gradients(self, calc):
 
             if gradients_section and len(line.split()) == 8:
                 x, y, z = line.split()[5:]
-                gradients.append([float(x), float(y), float(z)])
+                gradients.append(np.array([float(x), float(y), float(z)]))
 
-        return gradients
+        # Convert from Ha a0^-1 to Ha A-1
+        gradients = [grad / Constants.a02ang for grad in gradients]
+        return np.array(gradients)
 
     def __init__(self):
         super().__init__('nwchem', path=Config.NWChem.path,

doc/examples/molecules.rst

@@ -104,7 +104,8 @@ Calculations
 
 **autodE** provides wrappers around common electronic structure theory packages
 (ORCA, XTB, NWChem, MOPAC, Gaussian09) so geometries may be optimised and
-energies calculated.
+energies calculated. Energies are in atomic Hartrees and gradients in
+Ha / Å.
 
 For example, to optimise the geometry at the XTB level and then perform a
 single point energy evaluation with ORCA