def _process_results(self, results):
assert len(results['states']) == 1
jsonprops = results['states'][0]['calculated']
if 'orbitals' in jsonprops:
wfn = self._make_wfn(results['states'][0])
else:
wfn = None
result = mdt.MolecularProperties(self.mol,
**self._json_to_quantities(jsonprops))
if wfn:
result['wfn'] = wfn
return result
def test_h2_calculation_caching(h2_harmonic):
h2 = h2_harmonic
h2.properties = mdt.MolecularProperties(h2)
true_energy = h2.calc_potential_energy()
assert 'potential_energy' in h2.properties
assert 'forces' in h2.properties
h2.potential_energy
h2.forces
h2.properties['potential_energy'] = 'banana'
assert h2.potential_energy == h2.calc_potential_energy() == 'banana'
props = h2.calculate()
assert props.potential_energy == h2.potential_energy == h2.calc_potential_energy(
) == 'banana'
props2 = h2.calculate(use_cache=False)
assert props2.potential_energy == h2.potential_energy == true_energy
assert h2.calc_potential_energy() == true_energy
def calculate(self, requests):
import openbabel as ob
self.prep()
for atom, pbatom in zip(self.mol.atoms, self._pbmol.atoms):
pbatom.OBAtom.SetVector(*atom.position.value_in(u.angstrom))
self._ff.SetCoordinates(self._pbmol.OBMol)
energy = self._ff.Energy(True)
self._ff.GetCoordinates(self._pbmol.OBMol)
# http://forums.openbabel.org/Doing-an-energ-force-calculation-with-openbabel-td1590730.html
data = ob.toConformerData(self._pbmol.OBMol.GetData(ob.ConformerData))
force_iterator = data.GetForces()[0]
forces = np.array([[f.GetX(), f.GetY(), f.GetZ()]
for f in force_iterator])
forces[np.abs(forces) < 1e-30] = 0.0 # prevent underflows
result = mdt.MolecularProperties(self.mol,
potential_energy=energy * self._units,
forces=forces * self._units /
u.angstrom)
return result
def _process_results(self, results):
assert len(results['states']) == 1
jsonprops = results['states'][0]['calculated']
result = mdt.MolecularProperties(self.mol,
**self._get_properties(jsonprops))
return result