def __init__(self, atomlist, Nst=2, **kwds):
"""
The DFTB module has many parameters which can be set from the command
line using options, e.g. --scf_conv=1.0e-10.
During the initialization
- the command line arguments are parsed for options
- Slater-Koster tables and repulsive potentials
are loaded for the atom pair present in the molecule
Parameters:
===========
atomlist: list of tuples (Zi,[xi,yi,zi]) for each atom in the molecule
Nst: number of electronic states (including ground state)
"""
usage = "Type --help to show all options for DFTB"
parser = optparse.OptionParserFuncWrapper([
DFTB2.__init__, DFTB2.runSCC, SolventCavity.__init__,
LR_TDDFTB.getEnergies
],
usage,
section_headers=["DFTBaby"],
unknown_options="ignore")
options, args = parser.parse_args(DFTB2.__init__)
self.atomlist = atomlist
self.tddftb = LR_TDDFTB(atomlist, **options)
solvent_options, args = parser.parse_args(SolventCavity.__init__)
solvent_cavity = SolventCavity(**solvent_options)
self.tddftb.dftb2.setSolventCavity(solvent_cavity)
self.grads = Gradients(self.tddftb)
self.tddftb.setGeometry(atomlist, charge=kwds.get("charge", 0.0))
self.options, args = parser.parse_args(self.tddftb.getEnergies)
self.scf_options, args = parser.parse_args(self.tddftb.dftb2.runSCC)
self.options.update(self.scf_options)
self.Nst = Nst
# # always use iterative diagonalizer for lowest Nst-1 excited states
self.options["nstates"] = Nst - 1
# save geometry, orbitals and TD-DFT coefficients from
# last calculation
self.last_calculation = None
# save transition dipoles from last calculation
self.tdip_old = None
def atomistic_dftb(atomlist):
"""
perform an atomistic tight-binding DFT calculation to get the ground state
and the molecular orbitals
"""
# get parameters controlling DFTB calculation from
# command line or configuration file
usage = "Type --help to show all options for DFTB"
parser = optparse.OptionParserFuncWrapper([
DFTB2.__init__, DFTB2.runSCC, SolventCavity.__init__,
MoldenExporter.export
],
usage,
section_headers=["DFTBaby"],
unknown_options="ignore")
options, args = parser.parse_args(DFTB2.__init__)
dftb2 = DFTB2(atomlist, **options)
(scf_options, args) = parser.parse_args(dftb2.runSCC)
# solvent cavity
(solvent_options, args) = parser.parse_args(SolventCavity.__init__)
solvent_cavity = SolventCavity(**solvent_options)
dftb2.setSolventCavity(solvent_cavity)
dftb2.setGeometry(atomlist, charge=0.0)
dftb2.getEnergy(**scf_options)
# export molden file with orbitals
(options, args) = parser.parse_args(MoldenExporter(None).export)
molden = MoldenExporter(dftb2)
molden.export(**options)
return dftb2
usage += " - `dftbaby.cfg` with the options controlling the TD-DFTB calculation and dynamics\n"
usage += " Output Files:\n"
usage += " - `dynamics.xyz`: geometries for each time step (in Angstrom)\n"
usage += " - `state.dat`: current electronic state\n"
usage += " - `energy_I.dat`: total energy of electronic state I in Hartree vs. time in fs.\n"
usage += " The ground state energy at time t=0 is subtracted from all later energies.\n"
usage += " - `nonadiabaticIJ.dat`: scalar non-adiabatic coupling between states I and J.\n"
# This wrapper makes the optional parameters of the python function __init__ visible
# as optional command line argument.
parser = optparse.OptionParserFuncWrapper(
[
# options for MD
MolecularDynamics.__init__,
# electronic structure options
DFTB2.__init__,
DFTB2.runSCC,
SolventCavity.__init__,
LR_TDDFTB.getEnergies
],
usage,
section_headers=["SurfaceHopping", "DFTBaby"])
# extract optional parameters from command line
(options, args) = parser.parse_args(MolecularDynamics.__init__)
md = MolecularDynamics(**options)
# run molecular dynamics - this takes a while
md.verlet()
print "FINISHED"
Examples:
GeometryOptimization.py molecule.xyz --state=0 --calc_hessian=1
optimizes the molecule on the ground state and computes the Hessian.
GeometryOptimization.py molecule.xyz --state=1 --coord_system='internal'
finds the minimum on the 1st excited state using redundant internal coordinates.
""" % os.path.basename(sys.argv[0])
# This wrapper makes the optional parameters of the python functions visible
# as optional command line argument.
parser = optparse.OptionParserFuncWrapper(
[
# options for geometry optimization
GeometryOptimization.__init__,
# electronic structure options
DFTB2.__init__,
DFTB2.runSCC,
SolventCavity.__init__,
LR_TDDFTB.getEnergies
],
usage,
section_headers=["DFTBaby", "GeometryOptimization"])
# extract optional parameters from command line
(options, args) = parser.parse_args(GeometryOptimization.__init__)
if len(args) < 1:
print(usage)
exit(-1)
GOpt = GeometryOptimization(**options)
#
xyz_file = args[0]