# first geometry
atomlist = XYZ.read_xyz(geom_file)[0]
# read charge from title line in .xyz file
kwds = XYZ.extract_keywords_xyz(geom_file)
charge = kwds.get("charge", opts.charge)
pes = PotentialEnergySurfaces(atomlist, charge=charge)
# dftbaby needs one excited states calculation to set all variables
x = XYZ.atomlist2vector(atomlist)
pes.getEnergies(x)
for i, atomlist in enumerate(XYZ.read_xyz(geom_file)):
# compute electronic ground state forces with DFTB
x = XYZ.atomlist2vector(atomlist)
en = pes.getEnergy_S0(x)
# total ground state energy including repulsive potential
en_tot = en[0]
print("Structure %d enTot= %s Hartree" % (i, en_tot))
# electronic energy without repulsive potential
en_elec = pes.tddftb.dftb2.getEnergies()[2]
gradVrep, gradE0, gradExc = pes.grads.gradient(I=0)
# exclude repulsive potential from forces
grad = gradE0 + gradExc
forces = XYZ.vector2atomlist(-grad, atomlist)
if i == 0:
mode = 'w'
else:
mode = 'a'
print("%2.7f" % en_elec, file=fh_en)
# Read the geometry from the xyz-file
atomlists = XYZ.read_xyz(xyz_file)
atomlist = atomlists[0]
# read the charge of the molecule from the comment line in the xyz-file
kwds = XYZ.extract_keywords_xyz(xyz_file)
# initialize the TD-DFTB calculator
pes = PotentialEnergySurfaces(atomlist, Nst=Nst, **kwds)
fh = open(dat_file, "w")
for i, atomlist in enumerate(atomlists):
print "SCAN geometry %d of %d" % (i + 1, len(atomlists))
# convert geometry to a vector
x = XYZ.atomlist2vector(atomlist)
try:
if Nst == 1:
ens = pes.getEnergy_S0(x)
else:
ens = pes.getEnergies(x)
except ExcitedStatesError as e:
print "WARNING: %s" % e
print "%d-th point is skipped" % i
continue
if i == 0:
E0 = ens[0]
# subtract ground state energy at first geometry
ens -= E0
# convert to eV
ens *= AtomicData.hartree_to_eV
print >> fh, "%d " % i,
for ei in ens:
print >> fh, "%3.7f " % ei,