usage += " see --help for all options\n"
parser = OptionParser(usage)
parser.add_option("--transition_charges", dest="transition_charges", type=str, default="", help="Path to .chromo file with excitation energies, transition charges and magnetic transition dipoles for building a Frenckel exciton model. [default: %default]")
parser.add_option("--spectrum_file", dest="spectrum_file", type=str, default="exciton_spectrum.dat", help="Save excitonic absorption and circular dichroism spectra to this file [default: %default]")
parser.add_option("--state", dest="state", type=int, default=0, help="Excitonic state for which the gradient should be calculated (0 for ground state). [default: %default]")
parser.add_option("--plot_spectra", dest="plot_spectra", type=str, default="", help="Choose units ('nm', 'Hartree', 'cm-1' or 'eV') for plotting absorption and circular dichroism spectra. [default: %default]")
(opts,args) = parser.parse_args()
if len(args) < 1:
print usage
exit(-1)
ff_file = args[0] #"h2.ff" #"ethene.ff" #"pyrene_crystal_expanded.ff" #
# read force field definition
atomlist, atomtypes, partial_charges, lattice_vectors = read_force_field(ff_file)
# read transition charge for exciton model (if available)
if opts.transition_charges != "":
chromophores = list(read_transition_charges(opts.transition_charges))
else:
chromophores = []
pff = PeriodicForceField(atomlist, atomtypes, partial_charges, lattice_vectors, chromophores)
coords = XYZ.atomlist2vector(atomlist)
# evaluate force field once
energy, grad = pff.getEnergyAndGradient(coords, state=opts.state)
print "Total energy: %s" % energy
print "|gradient| : %s" % la.norm(grad)
# compute exciton spectrum
en, T, M = pff.getTransitionDipoles(verbose=1)
save_exciton_spectrum(opts.spectrum_file, en, T, M)
def __init__(self, atomlist_full, inner_indeces, embedding="electrostatic", pff_file=None, verbose=0):
"""
Parameters:
===========
atomlist_full: list of tuples (Zi,[xi,yi,zi]) for all atoms (QM + MM)
inner_indeces: list of the indeces which belong to the QM atoms
"""
assert embedding in ["mechanical", "electrostatic"]
if "-" in inner_indeces:
# index list contains ranges such as "9-14"
inner_indeces = parseAtomTags(inner_indeces)
else:
inner_indeces = list(eval(inner_indeces))
inner_indeces = list(set(inner_indeces)) # remove duplicate indeces
inner_indeces.sort()
if verbose > 0:
print("Indeces of QM atoms:")
print(inner_indeces)
print("number of QM atoms: %d" % len(inner_indeces))
# counting in the partitioning file starts at 1
inner_indeces = np.asarray(inner_indeces, dtype=int)-1
Nat = len(atomlist_full)
all_indeces = set(range(0, Nat))
outer_indeces = list(all_indeces - set(inner_indeces))
outer_indeces.sort()
self.inner_indeces = inner_indeces
self.outer_indeces = outer_indeces
# sort atoms into inner and outer region
self.atomlist_full = atomlist_full
self.atomlist_inner = [self.atomlist_full[i] for i in self.inner_indeces]
self.atomlist_outer = [self.atomlist_full[i] for i in self.outer_indeces]
if (pff_file == None):
#
# prepare the drivers for the UFF calculations
# E^MM(I+O)
self.FF_full = Gaussian.UFF_handler(self.atomlist_full,
embedding=embedding, verbose=verbose, unique_tmp=True)
# E^MM(I)
self.FF_inner = Gaussian.UFF_handler(self.atomlist_inner,
embedding=embedding, verbose=verbose, unique_tmp=True)
else:
# load definitions for periodic force field
if verbose > 0:
print("periodic MM calculations with DREIDING")
atomlist_full_ff, atomtypes_full, charges_full, lattice_vectors = read_force_field(pff_file)
atomtypes_inner = [atomtypes_full[i] for i in self.inner_indeces]
charges_inner = [charges_full[i] for i in self.inner_indeces]
if (len(atomlist_full_ff) != Nat):
raise ValueError("Wrong number of atoms in '%s'. Expected %d atoms but got %d !" \
% (pff_file, Nat, len(atomlist)))
# prepare drivers for DREIDING calculations
# E^MM(I+O)
self.FF_full = PeriodicForceField(self.atomlist_full, atomtypes_full, charges_full,
lattice_vectors, [], verbose=verbose)
# E^MM(I)
self.FF_inner = PeriodicForceField(self.atomlist_inner, atomtypes_inner, charges_inner,
lattice_vectors, [], verbose=verbose)
self.charge = 0