def test_dipole_prepared_continuum():
"""
see
G. Fronzoni, M. Stener, S. Furlan, P. Decleva
Chemical Physics 273 (2001) 117-133
"""
from DFTB.LR_TDDFTB import LR_TDDFTB
from DFTB import XYZ
from DFTB.Scattering import slako_tables_scattering
# BOUND ORBITAL = H**O
atomlist = XYZ.read_xyz("./water.xyz")[0]
tddftb = LR_TDDFTB(atomlist)
tddftb.setGeometry(atomlist, charge=0)
options = {"nstates": 1}
tddftb.getEnergies(**options)
valorbs, radial_val = load_pseudo_atoms(atomlist)
H**O, LUMO = tddftb.dftb2.getFrontierOrbitals()
bound_orbs = tddftb.dftb2.getKSCoefficients()
# polarization direction of E-field
epol = np.array([0.0, 1.0, 0.0])
# according to Koopman's theorem the electron is ionized from the H**O
mo_indx = range(0, len(bound_orbs))
nmo = len(mo_indx)
for imo in range(0, nmo):
mo_bound = bound_orbs[:, mo_indx[imo]]
# CONTINUUM ORBITALS at energy E
for E in slako_tables_scattering.energies:
bs = AtomicScatteringBasisSet(atomlist, E)
SKT_bf, SKT_ff = load_slako_scattering(atomlist, E)
Dipole = ScatteringDipoleMatrix(atomlist, valorbs, SKT_bf)
# projection of dipoles onto polarization direction
Dipole_projected = np.zeros((Dipole.shape[0], Dipole.shape[1]))
for xyz in [0, 1, 2]:
Dipole_projected += Dipole[:, :, xyz] * epol[xyz]
# unnormalized coefficients of dipole-prepared continuum orbitals
mo_scatt = np.dot(mo_bound, Dipole_projected)
nrm2 = np.dot(mo_scatt, mo_scatt)
# normalized coefficients
mo_scatt /= np.sqrt(nrm2)
Cube.orbital2grid(atomlist, bs.bfs, mo_scatt, \
filename="/tmp/scattering_orbital_%d_to_%s.cube" % (imo, str(E).replace(".", "p")), dbuff=25.0)
delattr(Cube.orbital_amplitude, "cached_grid")
def test_averaged_asymptotic_density():
from DFTB.LR_TDDFTB import LR_TDDFTB
from DFTB import XYZ
from DFTB.Scattering import slako_tables_scattering
from DFTB.Scattering import PAD
# BOUND ORBITAL = H**O
atomlist = XYZ.read_xyz("./water.xyz")[0]
tddftb = LR_TDDFTB(atomlist)
tddftb.setGeometry(atomlist, charge=0)
options = {"nstates": 1}
tddftb.getEnergies(**options)
valorbs, radial_val = load_pseudo_atoms(atomlist)
H**O, LUMO = tddftb.dftb2.getFrontierOrbitals()
bound_orbs = tddftb.dftb2.getKSCoefficients()
# polarization direction of E-field
epol = np.array([0.0, 0.0, 1.0])
# according to Koopman's theorem the electron is ionized from the H**O
mo_indx = range(0, len(bound_orbs))
nmo = len(mo_indx)
for imo in range(0, nmo):
print "IMO = %s" % imo
import time
time.sleep(1)
mo_bound = bound_orbs[:, mo_indx[imo]]
# CONTINUUM ORBITALS at energy E
for E in slako_tables_scattering.energies[-2:-1]:
bs = AtomicScatteringBasisSet(atomlist, E)
SKT_bf, SKT_ff = load_slako_scattering(atomlist, E)
Dipole = ScatteringDipoleMatrix(atomlist, valorbs, SKT_bf)
PAD.averaged_asymptotic_density(mo_bound, Dipole, bs, 20.0, E)
def averaged_pad_scan(xyz_file, dyson_file,
selected_orbitals, npts_euler, npts_theta, nskip, inter_atomic, sphere_radius):
molecule_name = os.path.basename(xyz_file).replace(".xyz", "")
atomlist = XYZ.read_xyz(xyz_file)[-1]
# shift molecule to center of mass
print "shift molecule to center of mass"
pos = XYZ.atomlist2vector(atomlist)
masses = AtomicData.atomlist2masses(atomlist)
pos_com = MolCo.shift_to_com(pos, masses)
atomlist = XYZ.vector2atomlist(pos_com, atomlist)
# compute molecular orbitals with DFTB
tddftb = LR_TDDFTB(atomlist)
tddftb.setGeometry(atomlist, charge=0)
options={"nstates": 1}
try:
tddftb.getEnergies(**options)
except DFTB.Solver.ExcitedStatesNotConverged:
pass
valorbs, radial_val = load_pseudo_atoms(atomlist)
if dyson_file == None:
print "tight-binding Kohn-Sham orbitals are taken as Dyson orbitals"
H**O, LUMO = tddftb.dftb2.getFrontierOrbitals()
bound_orbs = tddftb.dftb2.getKSCoefficients()
if selected_orbitals == None:
# all orbitals
selected_orbitals = range(0,bound_orbs.shape[1])
else:
selected_orbitals = eval(selected_orbitals, {}, {"H**O": H**O+1, "LUMO": LUMO+1})
print "Indeces of selected orbitals (counting from 1): %s" % selected_orbitals
orbital_names = ["orb_%s" % o for o in selected_orbitals]
selected_orbitals = np.array(selected_orbitals, dtype=int)-1 # counting from 0
dyson_orbs = bound_orbs[:,selected_orbitals]
ionization_energies = -tddftb.dftb2.getKSEnergies()[selected_orbitals]
else:
print "coeffients for Dyson orbitals are read from '%s'" % dyson_file
orbital_names, ionization_energies, dyson_orbs = load_dyson_orbitals(dyson_file)
ionization_energies = np.array(ionization_energies) / AtomicData.hartree_to_eV
print ""
print "*******************************************"
print "* PHOTOELECTRON ANGULAR DISTRIBUTIONS *"
print "*******************************************"
print ""
# determine the radius of the sphere where the angular distribution is calculated. It should be
# much larger than the extent of the molecule
(xmin,xmax),(ymin,ymax),(zmin,zmax) = Cube.get_bbox(atomlist, dbuff=0.0)
dx,dy,dz = xmax-xmin,ymax-ymin,zmax-zmin
Rmax = max([dx,dy,dz]) + sphere_radius
Npts = max(int(Rmax),1) * 50
print "Radius of sphere around molecule, Rmax = %s bohr" % Rmax
print "Points on radial grid, Npts = %d" % Npts
nr_dyson_orbs = len(orbital_names)
# compute PADs for all selected orbitals
for iorb in range(0, nr_dyson_orbs):
print "computing photoangular distribution for orbital %s" % orbital_names[iorb]
data_file = "betas_" + molecule_name + "_" + orbital_names[iorb] + ".dat"
pad_data = []
print " SCAN"
nskip = max(1, nskip)
# save table
fh = open(data_file, "w")
print " Writing table with betas to %s" % data_file
print>>fh, "# ionization from orbital %s IE = %6.3f eV" % (orbital_names[iorb], ionization_energies[iorb]*AtomicData.hartree_to_eV)
print>>fh, "# inter_atomic: %s npts_euler: %s npts_theta: %s rmax: %s" % (inter_atomic, npts_euler, npts_theta, Rmax)
print>>fh, "# PKE/eV sigma beta1 beta2 beta3 beta4"
for i,E in enumerate(slako_tables_scattering.energies):
if i % nskip != 0:
continue
print " PKE = %6.6f Hartree (%4.4f eV)" % (E, E*AtomicData.hartree_to_eV)
k = np.sqrt(2*E)
wavelength = 2.0 * np.pi/k
bs_free = AtomicScatteringBasisSet(atomlist, E, rmin=0.0, rmax=Rmax+2*wavelength, Npts=Npts)
SKT_bf, SKT_ff = load_slako_scattering(atomlist, E)
Dipole = ScatteringDipoleMatrix(atomlist, valorbs, SKT_bf, inter_atomic=inter_atomic).real
orientation_averaging = PAD.OrientationAveraging_small_memory(Dipole, bs_free, Rmax, E, npts_euler=npts_euler, npts_theta=npts_theta)
pad,betasE = orientation_averaging.averaged_pad(dyson_orbs[:,iorb])
pad_data.append( [E*AtomicData.hartree_to_eV] + list(betasE) )
# save PAD for this energy
print>>fh, "%10.6f %10.6e %+10.6e %+10.6f %+10.6e %+10.6e" % tuple(pad_data[-1])
fh.flush()
fh.close()
def test_photoangular_distribution():
from DFTB.LR_TDDFTB import LR_TDDFTB
from DFTB import XYZ
from DFTB.Scattering import slako_tables_scattering
# BOUND ORBITAL = H**O
atomlist = XYZ.read_xyz("./h2.xyz")[0]
tddftb = LR_TDDFTB(atomlist)
tddftb.setGeometry(atomlist, charge=0)
options = {"nstates": 1}
tddftb.getEnergies(**options)
valorbs, radial_val = load_pseudo_atoms(atomlist)
H**O, LUMO = tddftb.dftb2.getFrontierOrbitals()
bound_orbs = tddftb.dftb2.getKSCoefficients()
# according to Koopman's theorem the electron is ionized from the H**O
mo_indx = range(0, len(bound_orbs))
nmo = len(mo_indx)
energies = [[] for i in range(0, nmo)]
sigmas = [[] for i in range(0, nmo)]
betas = [[] for i in range(0, nmo)]
tdip2s = [[] for i in range(0, nmo)]
for imo in range(0, nmo):
mo_bound = bound_orbs[:, mo_indx[imo]]
# CONTINUUM ORBITALS at energy E
for E in slako_tables_scattering.energies:
SKT_bf, SKT_ff = load_slako_scattering(atomlist, E)
S_bb, H0_bb = tddftb.dftb2._constructH0andS()
S_bf, H0_bf = ScatteringHamiltonianMatrix(atomlist, valorbs,
SKT_bf)
#
invS_bb = la.inv(S_bb)
# (H-E*S)^t . Id . (H-E*S)
HmE2 = np.dot(H0_bf.conjugate().transpose(), np.dot(invS_bb, H0_bf)) \
- E * np.dot( S_bf.conjugate().transpose(), np.dot(invS_bb, H0_bf)) \
- E * np.dot(H0_bf.conjugate().transpose(), np.dot(invS_bb, S_bf)) \
+ E**2 * np.dot(S_bf.conjugate().transpose(), np.dot(invS_bb, S_bf))
#
scat_lambdas, scat_orbs = sla.eigh(HmE2)
print "PKE = %s" % E
print "lambdas = %s" % scat_lambdas
# photoangular distribution averaged over isotropically oriented ensemble of molecules
Dipole = ScatteringDipoleMatrix(atomlist, valorbs, SKT_bf)
sigma = 0.0
beta = 0.0
tdip2 = 0.0
olap = 0.0
for i in range(0, len(scat_lambdas)):
if abs(scat_lambdas[i]) > 1.0e-10:
print "%d lambda = %s" % (i, scat_lambdas[i])
mo_scatt = scat_orbs[:, i]
sigma_i, beta_i = angular_distribution(
atomlist, valorbs, mo_bound, mo_scatt, Dipole)
sigma += sigma_i
beta += sigma_i * beta_i
tdip_i = np.zeros(3, dtype=complex)
for xyz in range(0, 3):
tdip_i[xyz] += np.dot(
mo_bound, np.dot(Dipole[:, :, xyz], mo_scatt))
tdip2 += np.sum(abs(tdip_i)**2)
print "tdip2 = %s" % tdip2
beta /= sigma
####
#sigma_test, beta_test = angular_distribution_old2(atomlist, valorbs, mo_bound, mo_scatt, Dipole)
#assert abs(sigma-sigma_test) < 1.0e-10
#assert abs(beta-beta_test) < 1.0e-10
####
print "E= %s sigma=%s beta= %s" % (E, sigma, beta)
energies[imo].append(E)
sigmas[imo].append(sigma.real)
betas[imo].append(beta.real)
tdip2s[imo].append(tdip2)
energies = np.array(energies)
sigmas = np.array(sigmas)
betas = np.array(betas)
from matplotlib import pyplot as plt
# total cross section
plt.xlabel("PKE / eV")
plt.ylabel("total photoionization cross section $\sigma$")
for imo in range(0, nmo):
plt.plot(energies[imo] * 27.211, sigmas[imo], lw=2)
#plt.plot(energies[imo]*27.211, tdip2s[imo], lw=2, ls="-.")
plt.show()
# anisotropy
plt.cla()
plt.ylim((-1.0, 2.0))
plt.xlabel("PKE / eV")
plt.ylabel("anisotropy $\\beta_2$")
for imo in range(0, nmo):
plt.plot(energies[imo] * 27.211, betas[imo], lw=2, label="%d" % imo)
plt.legend()
plt.show()
return energies, sigmas, betas
def test_scattering_orbitals():
from DFTB.LR_TDDFTB import LR_TDDFTB
from DFTB import XYZ
atomlist = XYZ.read_xyz("h2.xyz")[0]
tddftb = LR_TDDFTB(atomlist)
tddftb.setGeometry(atomlist, charge=0)
options = {"nstates": 1}
tddftb.getEnergies(**options)
valorbs, radial_val = load_pseudo_atoms(atomlist)
E = 5.0 / 27.211
bs = AtomicScatteringBasisSet(atomlist, E)
print bs.bfs
SKT_bf, SKT_ff = load_slako_scattering(atomlist, E)
S_bb, H0_bb = tddftb.dftb2._constructH0andS()
S_bf, H0_bf = ScatteringHamiltonianMatrix(atomlist, valorbs, SKT_bf)
#
invS_bb = la.inv(S_bb)
# (H-E*S)^t . Id . (H-E*S)
HmE2 = np.dot(H0_bf.conjugate().transpose(), np.dot(invS_bb, H0_bf)) \
- E * np.dot( S_bf.conjugate().transpose(), np.dot(invS_bb, H0_bf)) \
- E * np.dot(H0_bf.conjugate().transpose(), np.dot(invS_bb, S_bf)) \
+ E**2 * np.dot(S_bf.conjugate().transpose(), np.dot(invS_bb, S_bf))
Scont = continuum_flux(atomlist, SKT_bf)
S2 = np.dot(S_bf.conjugate().transpose(), np.dot(la.inv(S_bb), S_bf))
"""
#
H2 = np.dot(H0_bf.transpose(), np.dot(la.inv(S_bb), H0_bf))
S2 = np.dot( S_bf.transpose(), np.dot(la.inv(S_bb), S_bf))
print "H2"
print H2
print "S2"
print S2
scat_orbe2, scat_orbs = sla.eig(H2) #, S2)
print "PKE = %s" % E
print "Energies^2 = %s" % scat_orbe2
scat_orbe = np.sqrt(scat_orbe2)
sort_indx = np.argsort(scat_orbe)
scat_orbe = scat_orbe[sort_indx]
scat_orbs = scat_orbs[:,sort_indx]
print "Energies of scattering orbitals: %s" % scat_orbe
orbE = np.argmin(abs(scat_orbe-E))
"""
assert np.sum(abs(HmE2.conjugate().transpose() - HmE2)) < 1.0e-10
assert np.sum(abs(S2.conjugate().transpose() - S2)) < 1.0e-10
lambdas, scat_orbs = sla.eigh(HmE2)
print "lambdas = %s" % lambdas
from DFTB.Scattering import PAD
for i in range(0, len(lambdas)):
if abs(lambdas[i]) > 1.0e-8:
print "%d lambda = %s" % (i, lambdas[i])
###
def wavefunction(grid, dV):
# evaluate orbital
amp = Cube.orbital_amplitude(grid,
bs.bfs,
scat_orbs[:, i],
cache=False)
return amp
PAD.asymptotic_density(wavefunction, 20, E)
###
for (flm, l, m) in classify_lm(bs, scat_orbs[:, i]):
if abs(flm).max() > 1.0e-4:
print " %s %s %s" % (l, m, abs(flm))
Cube.orbital2grid(atomlist, bs.bfs, scat_orbs[:,i], \
filename="/tmp/scattering_orbital_%d.cube" % i, dbuff=25.0)
delattr(Cube.orbital_amplitude, "cached_grid")
#test_dipole_prepared_continuum()
test_averaged_asymptotic_density()
#test_photoangular_distribution()
exit(-1)
#atomlist = [(8,(0,0,0))]
atomlist = [(1, (0, 0, 0)), (1, (0, 0, 3.0))]
energies = []
sigmas = []
betas = []
for E in np.linspace(0.001, 5.0 / 27.211, 20):
SKT_bf, SKT_ff = load_slako_scattering(atomlist, E)
#print SKT
valorbs, radial_val = load_pseudo_atoms(atomlist)
Dipole = ScatteringDipoleMatrix(atomlist, valorbs, SKT_bf)
#print Dipole
mos_bound = np.array([1.0, 1.0])
#mos_bound = np.array([1.0,-1.0])
mos_bound /= la.norm(mos_bound)
mos_scatt = np.array([0.0, 1.0, 1.0, 1.0] + [0.0, 1.0, 1.0, 1.0])
#mos_scatt = np.array([0.0, 1.0,1.0,1.0] + [0.0, 1.0,1.0,1.0])
mos_scatt /= la.norm(mos_scatt)
#sigma, beta = angular_distribution_old(atomlist, valorbs, mos_bound, mos_scatt, Dipole)
#print "OLD E= %s sigma=%s beta= %s" % (E,sigma, beta)
sigma, beta = angular_distribution(atomlist, valorbs, mos_bound,
mos_scatt, Dipole)
def atomic_pz_orbital(Z, data_file):
atomlist = [(Z, (0.0, 0.0, 0.0))]
# compute molecular orbitals with DFTB
print "compute molecular orbitals with tight-binding DFT"
tddftb = LR_TDDFTB(atomlist)
tddftb.setGeometry(atomlist, charge=0)
options = {"nstates": 1}
try:
tddftb.getEnergies(**options)
except DFTB.Solver.ExcitedStatesNotConverged:
pass
valorbs, radial_val = load_pseudo_atoms(atomlist)
bound_orbs = tddftb.dftb2.getKSCoefficients()
# order of orbitals s, py,pz,px, dxy,dyz,dz2,dzx,dx2y2, so the pz-orbital has index 2
mo_bound = bound_orbs[:, 2]
tdipole_data = []
for iE, E in enumerate(slako_tables_scattering.energies):
print "PKE = %s" % E
try:
SKT_bf, SKT_ff = load_slako_scattering(atomlist, E)
except ImportError:
break
Dipole = ScatteringDipoleMatrix(atomlist, valorbs, SKT_bf).real
# dipole between bound orbital and the continuum AO basis orbitals
dipole_bf = np.tensordot(mo_bound, Dipole, axes=(0, 0))
tdip_pz_to_s = dipole_bf[0, 2] # points along z-axis
tdip_pz_to_dyz = dipole_bf[5, 1] # points along y-axis
tdip_pz_to_dz2 = dipole_bf[6, 2] # points along z-axis
tdip_pz_to_dzx = dipole_bf[7, 0] # points along x-axis
tdipole_data.append(
[E * AtomicData.hartree_to_eV] +
[tdip_pz_to_s, tdip_pz_to_dyz, tdip_pz_to_dz2, tdip_pz_to_dzx])
####
# determine the radius of the sphere where the angular distribution is calculated. It should be
# much larger than the extent of the molecule
(xmin, xmax), (ymin, ymax), (zmin, zmax) = Cube.get_bbox(atomlist,
dbuff=0.0)
dx, dy, dz = xmax - xmin, ymax - ymin, zmax - zmin
Rmax = max([dx, dy, dz]) + 500.0
print "Radius of sphere around molecule, Rmax = %s bohr" % Rmax
k = np.sqrt(2 * E)
wavelength = 2.0 * np.pi / k
print "wavelength = %s" % wavelength
valorbsE, radial_valE = load_pseudo_atoms_scattering(atomlist,
E,
rmin=0.0,
rmax=Rmax +
2 * wavelength,
Npts=90000)
# Plot radial wavefunctions
import matplotlib.pyplot as plt
plt.ion()
r = np.linspace(0.0, Rmax + 2 * wavelength, 5000)
for i, (Zi, posi) in enumerate(atomlist):
for indx, (ni, li, mi) in enumerate(valorbsE[Zi]):
# only plot the dz2 continuum orbital
if li == 2 and mi == 0 and (iE % 10 == 0):
R_spl = radial_valE[Zi][indx]
radial_orbital_wfn = R_spl(r)
plt.plot(r,
radial_orbital_wfn,
label="Z=%s n=%s l=%s m=%s E=%s" %
(Zi, ni, li, mi, E))
plt.plot(r, np.sin(k * r) / r, ls="-.")
#plt.plot(r, np.sin(k*r + 1.0/k * np.log(2*k*r))/r, ls="--", lw=2)
plt.plot(r,
np.array([
float(mpmath.coulombf(li, -1.0 / k, k * rx)) /
rx for rx in r
]),
ls="--",
lw=2,
label="CoulombF l=%s E=%s" % (li, E))
plt.draw()
####
# save table
fh = open(data_file, "w")
print >> fh, "# PKE/eV pz->s pz->dyz pz->dz2 pz->dzx"
np.savetxt(fh, tdipole_data)
fh.close()
print "Wrote table with transition dipoles to %s" % data_file
# show radial wavefunctions
plt.ioff()
plt.show()
def build_water_cluster(atomlist_template, orbital_names, phases):
"""
build a cluster orbital as a linear combination of monomer orbitals with the correct orientation.
The position and orientation of the water molecules is taken from the template.
Parameters:
===========
atomlist_template: molecular geometry for cluster with n water molecules
orbital_names: list of orbital names ('1b1', '3a1', '1b2' or '2a1') for each of the n water molecules
phases: list of +1 or -1's for each orbital
Returns:
========
water_cluster: molecular geometry of the cluster
orb_cluster: cluster orbital, that is a linear combination of the monomer orbitals.
"""
# water geometry in bohr
water_std = [(1, (0.0, 0.8459947982381987, -1.4473477675908173)),
(8, (0.0, -0.21392561795490195, 0.0 )),
(1, (0.0, 0.8459947982381987, 1.4473477675908173))]
valorbs, radial_val = load_pseudo_atoms(water_std)
# Orbitals for H2O monomer in standard orientation:
# molecular plane = yz-plane, oxygen lies on the negative y-axis, H-H bond is parallel to z-axis
# H1-1s O-2s O-2py O-2pz O-2px H2-1s
monomer_orbitals = {
"1b1": np.array([ 0.0000, 0.0000, 0.0000, 0.0000, 1.0000, 0.0000]),
"3a1": np.array([ 0.7816,-0.6842, 0.6989, 0.0000, 0.0000, 0.7816]),
"1b2": np.array([-0.7264, 0.0000, 0.0000, 0.9429, 0.0000, 0.7264]),
"2a1": np.array([ 0.1730, 0.8662, 0.0393, 0.0000, 0.0000, 0.1730])
}
# First the individual water molecules in the template are identified and their positions
# and orientations are extracted.
fragments = MolecularGraph.disconnected_fragments(atomlist_template)
assert len(fragments) == len(orbital_names) == len(phases), "For each water fragment in the cluster you need to specify one fragment orbital ('1b1', '3a1', '1b2' or '2a1') and its phase"
orb_cluster = [] # list of MO coefficients
water_cluster = [] # list of atoms
for i,water in enumerate(fragments):
# the Euler angles (a,b,g) specify the orientation of the i-th water molecule
water_std_i, (a,b,g), cm = MolCo.molecular_frame_transformation(water)
print "WATER STANDARD"
for (Zi,posi) in water_std:
print " %s %8.6f %8.6f %8.6f" % (Zi, posi[0], posi[1], posi[2])
print "WATER STANDARD %d" % i
for (Zi,posi) in water_std_i:
print " %s %8.6f %8.6f %8.6f" % (Zi, posi[0], posi[1], posi[2])
# The desired orbital is placed on the i-th water molecule and is
# rotated to match the orientation of the molecule.
orb_monomer = monomer_orbitals[orbital_names[i]]
# rotate orbital
orb_monomer_rot = OrbitalRotations.rotate_orbitals(water_std, valorbs, orb_monomer, (a,b,g))
# add orbital with desired phase to cluster MOs
orb_cluster += list(phases[i] * orb_monomer_rot)
# rotate geometry
water_rot = MolCo.transform_molecule(water_std, (a,b,g), cm)
XYZ.write_xyz("/tmp/water_std.xyz", [water_std, water_rot])
water_cluster += water_rot
# Assuming that the overlap between orbitals on different water molecules is negligible,
# we can normalize the cluster orbital by dividing through sqrt(number of water molecules)
n = np.sum(abs(np.array(phases))) # a phase of 0 indicates no orbital
orb_cluster /= np.sqrt(n)
return water_cluster, orb_cluster
def __init__(self, xyz_file, dyson_file=None):
super(Main, self).__init__()
self.settings = Settings({
"Continuum Orbital": {
"Ionization transitions":
[0, ["only intra-atomic", "inter-atomic"]]
},
"Averaging": {
"Euler angle grid points": 5,
"polar angle grid points": 1000,
"sphere radius Rmax": 300.0,
},
"Scan": {
"nr. points": 20
},
"Cube": {
"extra space / bohr": 15.0,
"points per bohr": 3.0
}
})
# perform DFTB calculation
# BOUND ORBITAL = H**O
self.atomlist = XYZ.read_xyz(xyz_file)[0]
# shift molecule to center of mass
print "shift molecule to center of mass"
pos = XYZ.atomlist2vector(self.atomlist)
masses = AtomicData.atomlist2masses(self.atomlist)
pos_com = MolCo.shift_to_com(pos, masses)
self.atomlist = XYZ.vector2atomlist(pos_com, self.atomlist)
self.tddftb = LR_TDDFTB(self.atomlist)
self.tddftb.setGeometry(self.atomlist, charge=0)
options = {"nstates": 1}
try:
self.tddftb.getEnergies(**options)
except DFTB.Solver.ExcitedStatesNotConverged:
pass
self.valorbs, radial_val = load_pseudo_atoms(self.atomlist)
if dyson_file == None:
# Kohn-Sham orbitals are taken as Dyson orbitals
self.H**O, self.LUMO = self.tddftb.dftb2.getFrontierOrbitals()
self.bound_orbs = self.tddftb.dftb2.getKSCoefficients()
self.orbe = self.tddftb.dftb2.getKSEnergies()
orbital_names = []
norb = len(self.orbe)
for o in range(0, norb):
if o < self.H**O:
name = "occup."
elif o == self.H**O:
name = "H**O"
elif o == self.LUMO:
name = "LUMO "
else:
name = "virtual"
name = name + " " + str(o).rjust(4) + (
" %+10.3f eV" % (self.orbe[o] * 27.211))
orbital_names.append(name)
initially_selected = self.H**O
else:
# load coefficients of Dyson orbitals from file
names, ionization_energies, self.bound_orbs = load_dyson_orbitals(
dyson_file)
self.orbe = np.array(ionization_energies) / 27.211
orbital_names = []
norb = len(self.orbe)
for o in range(0, norb):
name = names[o] + " " + str(o).rjust(4) + (
" %4.2f eV" % (self.orbe[o] * 27.211))
orbital_names.append(name)
initially_selected = 0
self.photo_kinetic_energy = slako_tables_scattering.energies[0]
self.epol = np.array([15.0, 0.0, 0.0])
# Build Graphical User Interface
main = QtGui.QWidget()
mainLayout = QtGui.QHBoxLayout(main)
#
selectionFrame = QtGui.QFrame()
selectionFrame.setSizePolicy(QtGui.QSizePolicy.Fixed,
QtGui.QSizePolicy.Preferred)
mainLayout.addWidget(selectionFrame)
selectionLayout = QtGui.QVBoxLayout(selectionFrame)
#
label = QtGui.QLabel(selectionFrame)
label.setText("Select bound MO:")
selectionLayout.addWidget(label)
# bound orbitals
self.orbitalSelection = QtGui.QListWidget(selectionFrame)
self.orbitalSelection.itemSelectionChanged.connect(
self.selectBoundOrbital)
norb = len(self.orbe)
self.orbital_dict = {}
for o in range(0, norb):
name = orbital_names[o]
self.orbital_dict[name] = o
item = QtGui.QListWidgetItem(name, self.orbitalSelection)
if o == initially_selected:
selected_orbital_item = item
selectionLayout.addWidget(self.orbitalSelection)
### VIEWS
center = QtGui.QWidget()
mainLayout.addWidget(center)
centerLayout = QtGui.QGridLayout(center)
#
boundFrame = QtGui.QFrame()
centerLayout.addWidget(boundFrame, 1, 1)
boundLayout = QtGui.QVBoxLayout(boundFrame)
# "Bound Orbital"
label = QtGui.QLabel(boundFrame)
label.setText("Bound Orbital")
boundLayout.addWidget(label)
#
self.boundOrbitalViewer = QCubeViewerWidget(boundFrame)
boundLayout.addWidget(self.boundOrbitalViewer)
# continuum orbital
continuumFrame = QtGui.QFrame()
centerLayout.addWidget(continuumFrame, 1, 2)
continuumLayout = QtGui.QVBoxLayout(continuumFrame)
# "Dipole-Prepared Continuum Orbital"
label = QtGui.QLabel(continuumFrame)
label.setText("Dipole-Prepared Continuum Orbital")
continuumLayout.addWidget(label)
self.continuumOrbitalViewer = QCubeViewerWidget(continuumFrame)
continuumLayout.addWidget(self.continuumOrbitalViewer)
self.efield_objects = []
self.efield_actors = []
self.selected = None
# picker
self.picker = self.continuumOrbitalViewer.visualization.scene.mayavi_scene.on_mouse_pick(
self.picker_callback)
self.picker.tolerance = 0.01
# PHOTO KINETIC ENERGY
sliderFrame = QtGui.QFrame(continuumFrame)
continuumLayout.addWidget(sliderFrame)
sliderLayout = QtGui.QHBoxLayout(sliderFrame)
# label
self.pke_label = QtGui.QLabel()
self.pke_label.setText("PKE: %6.4f eV" %
(self.photo_kinetic_energy * 27.211))
sliderLayout.addWidget(self.pke_label)
# Slider for changing the PKE
self.pke_slider = QtGui.QSlider(QtCore.Qt.Horizontal)
self.pke_slider.setMinimum(0)
self.pke_slider.setMaximum(len(slako_tables_scattering.energies) - 1)
self.pke_slider.setValue(0)
self.pke_slider.sliderReleased.connect(self.changePKE)
self.pke_slider.valueChanged.connect(self.searchPKE)
sliderLayout.addWidget(self.pke_slider)
#
# molecular frame photoangular distribution
mfpadFrame = QtGui.QFrame()
centerLayout.addWidget(mfpadFrame, 2, 1)
mfpadLayout = QtGui.QVBoxLayout(mfpadFrame)
mfpadLayout.addWidget(QtGui.QLabel("Molecular Frame PAD"))
mfpadTabs = QtGui.QTabWidget()
mfpadLayout.addWidget(mfpadTabs)
# 2D map
mfpadFrame2D = QtGui.QFrame()
mfpadTabs.addTab(mfpadFrame2D, "2D")
mfpadLayout2D = QtGui.QVBoxLayout(mfpadFrame2D)
self.MFPADfig2D = Figure()
self.MFPADCanvas2D = FigureCanvas(self.MFPADfig2D)
mfpadLayout2D.addWidget(self.MFPADCanvas2D)
self.MFPADCanvas2D.draw()
NavigationToolbar(self.MFPADCanvas2D, mfpadFrame2D, coordinates=True)
# 3D
mfpadFrame3D = QtGui.QFrame()
mfpadTabs.addTab(mfpadFrame3D, "3D")
mfpadLayout3D = QtGui.QVBoxLayout(mfpadFrame3D)
self.MFPADfig3D = Figure()
self.MFPADCanvas3D = FigureCanvas(self.MFPADfig3D)
mfpadLayout3D.addWidget(self.MFPADCanvas3D)
self.MFPADCanvas3D.draw()
NavigationToolbar(self.MFPADCanvas3D, mfpadFrame3D, coordinates=True)
# orientation averaged photoangular distribution
avgpadFrame = QtGui.QFrame()
centerLayout.addWidget(avgpadFrame, 2, 2)
avgpadLayout = QtGui.QVBoxLayout(avgpadFrame)
self.activate_average = QtGui.QCheckBox("Orientation Averaged PAD")
self.activate_average.setToolTip(
"Check this box to start averaging of the molecular frame PADs over all orientations. This can take a while."
)
self.activate_average.setCheckState(QtCore.Qt.Unchecked)
self.activate_average.stateChanged.connect(self.activateAveragedPAD)
avgpadLayout.addWidget(self.activate_average)
avgpadTabs = QtGui.QTabWidget()
avgpadLayout.addWidget(avgpadTabs)
# 1D map
avgpadFrame1D = QtGui.QFrame()
avgpadTabs.addTab(avgpadFrame1D, "1D")
avgpadLayout1D = QtGui.QVBoxLayout(avgpadFrame1D)
self.AvgPADfig1D = Figure()
self.AvgPADCanvas1D = FigureCanvas(self.AvgPADfig1D)
avgpadLayout1D.addWidget(self.AvgPADCanvas1D)
self.AvgPADCanvas1D.draw()
NavigationToolbar(self.AvgPADCanvas1D, avgpadFrame1D, coordinates=True)
# 2D map
avgpadFrame2D = QtGui.QFrame()
avgpadFrame2D.setToolTip(
"The averaged PAD should have no phi-dependence anymore. A phi-dependence is a sign of incomplete averaging."
)
avgpadTabs.addTab(avgpadFrame2D, "2D")
avgpadLayout2D = QtGui.QVBoxLayout(avgpadFrame2D)
self.AvgPADfig2D = Figure()
self.AvgPADCanvas2D = FigureCanvas(self.AvgPADfig2D)
avgpadLayout2D.addWidget(self.AvgPADCanvas2D)
self.AvgPADCanvas2D.draw()
NavigationToolbar(self.AvgPADCanvas2D, avgpadFrame2D, coordinates=True)
# Table
avgpadFrameTable = QtGui.QFrame()
avgpadTabs.addTab(avgpadFrameTable, "Table")
avgpadLayoutTable = QtGui.QVBoxLayout(avgpadFrameTable)
self.avgpadTable = QtGui.QTableWidget(0, 6)
self.avgpadTable.setToolTip(
"Activate averaging and move the PKE slider above to add a new row with beta values. After collecting betas for different energies you can save the table or plot a curve beta(PKE) for the selected orbital."
)
self.avgpadTable.setHorizontalHeaderLabels(
["PKE / eV", "sigma", "beta1", "beta2", "beta3", "beta4"])
avgpadLayoutTable.addWidget(self.avgpadTable)
# Buttons
buttonFrame = QtGui.QFrame()
avgpadLayoutTable.addWidget(buttonFrame)
buttonLayout = QtGui.QHBoxLayout(buttonFrame)
deleteButton = QtGui.QPushButton("Delete")
deleteButton.setToolTip("clear table")
deleteButton.clicked.connect(self.deletePADTable)
buttonLayout.addWidget(deleteButton)
buttonLayout.addSpacing(3)
scanButton = QtGui.QPushButton("Scan")
scanButton.setToolTip(
"fill table by scanning automatically through all PKE values")
scanButton.clicked.connect(self.scanPADTable)
buttonLayout.addWidget(scanButton)
saveButton = QtGui.QPushButton("Save")
saveButton.setToolTip("save table as a text file")
saveButton.clicked.connect(self.savePADTable)
buttonLayout.addWidget(saveButton)
plotButton = QtGui.QPushButton("Plot")
plotButton.setToolTip("plot beta2 column as a function of PKE")
plotButton.clicked.connect(self.plotPADTable)
buttonLayout.addWidget(plotButton)
"""
# DOCKS
self.setDockOptions(QtGui.QMainWindow.AnimatedDocks | QtGui.QMainWindow.AllowNestedDocks)
#
selectionDock = QtGui.QDockWidget(self)
selectionDock.setWidget(selectionFrame)
selectionDock.setFeatures(QtGui.QDockWidget.DockWidgetFloatable | QtGui.QDockWidget.DockWidgetMovable)
self.addDockWidget(QtCore.Qt.DockWidgetArea(1), selectionDock)
#
boundDock = QtGui.QDockWidget(self)
boundDock.setWidget(boundFrame)
boundDock.setFeatures(QtGui.QDockWidget.DockWidgetFloatable | QtGui.QDockWidget.DockWidgetMovable)
boundDock.setSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Preferred)
self.addDockWidget(QtCore.Qt.DockWidgetArea(2), boundDock)
#
continuumDock = QtGui.QDockWidget(self)
continuumDock.setWidget(continuumFrame)
continuumDock.setFeatures(QtGui.QDockWidget.DockWidgetFloatable | QtGui.QDockWidget.DockWidgetMovable)
continuumDock.setSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Preferred)
self.addDockWidget(QtCore.Qt.DockWidgetArea(2), continuumDock)
"""
self.setCentralWidget(main)
self.status_bar = QtGui.QStatusBar(main)
self.setStatusBar(self.status_bar)
self.default_message = "Click on the tip of the green arrow in the top right figure to change the orientation of the E-field"
self.statusBar().showMessage(self.default_message)
# Menu bar
menubar = self.menuBar()
exitAction = QtGui.QAction('&Exit', self)
exitAction.setShortcut('Ctrl+Q')
exitAction.setStatusTip('Exit program')
exitAction.triggered.connect(exit)
fileMenu = menubar.addMenu('&File')
fileMenu.addAction(exitAction)
settingsMenu = menubar.addMenu('&Edit')
settingsAction = QtGui.QAction('&Settings...', self)
settingsAction.setStatusTip('Edit settings')
settingsAction.triggered.connect(self.editSettings)
settingsMenu.addAction(settingsAction)
self.loadContinuum()
# select H**O
selected_orbital_item.setSelected(True)