def run(self, geom, multiplicity, state, verbose=False):
#print('running!')
#sys.stdout.flush()
coords = manage_xyz.xyz_to_np(geom)
# convert to bohr
positions = coords * units.ANGSTROM_TO_AU
calc = Calculator(get_method("GFN2-xTB"),
self.numbers,
positions,
charge=self.charge)
calc.set_output('lot_jobs_{}.txt'.format(self.node_id))
res = calc.singlepoint() # energy printed is only the electronic part
calc.release_output()
# energy in hartree
self._Energies[(multiplicity,
state)] = self.Energy(res.get_energy(), 'Hartree')
# grad in Hatree/Bohr
self._Gradients[(multiplicity,
state)] = self.Gradient(res.get_gradient(),
'Hartree/Bohr')
# write E to scratch
self.write_E_to_file()
self.hasRanForCurrentCoords = True
return res
def run(self, coords, multiplicity, state, verbose=False):
#print('running!')
#sys.stdout.flush()
self.E = []
self.grada = []
# convert to angstrom
positions = coords * units.ANGSTROM_TO_AU
calc = Calculator(get_method("GFN2-xTB"), self.numbers, positions)
calc.set_output('lot_jobs_{}.txt'.format(self.node_id))
res = calc.singlepoint() # energy printed is only the electronic part
calc.release_output()
# energy in hartree
self.E.append((multiplicity, state, res.get_energy()))
# grad in Hatree/Bohr
self.grada.append((multiplicity, state, res.get_gradient()))
# write E to scratch
with open('scratch/E_{}.txt'.format(self.node_id), 'w') as f:
for E in self.E:
f.write('{} {:9.7f}\n'.format(E[0], E[2]))
self.hasRanForCurrentCoords = True
return res