def test():
# bond length in bohr
dist = 2.0
# positions of protons
posH1 = (0.0, 0.0, -dist / 2.0)
posH2 = (0.0, 0.0, +dist / 2.0)
atomlist = [(1, posH1), (1, posH2)]
# Set resolution of multicenter grid
settings.radial_grid_factor = 20
settings.lebedev_order = 23
# energy of continuum orbital
E = 1.0
# same functional as used in the calculation of pseudo orbitals
xc = XCFunctionals.libXCFunctional(Parameters.pseudo_orbital_x,
Parameters.pseudo_orbital_c)
dft = BasissetFreeDFT(atomlist, xc)
print "initial orbital guess from DFTB calculation"
orbitals = dft.getOrbitalGuess()
norb = len(orbitals)
# all orbitals are doubly occupied
nelec = 2 * norb
bound_orbitals = dft.getOrbitalGuess()
# effective potential
rho = density_func(bound_orbitals)
veff = effective_potential_func(atomlist, rho, xc, nelec=nelec)
# radius that separates inner from outer region
r0 = vdw_sphere_radius(atomlist, fac=2.0)
# basis sets
bs_core = AtomicBasisSet(atomlist, orbital_set="core")
bs_valence = AtomicBasisSet(atomlist, orbital_set="valence")
bs_continuum = AtomicScatteringBasisSet(atomlist, E, lmax=1)
# combine basis functions from all basis sets
bfs = bs_core.bfs + bs_valence.bfs + bs_continuum.bfs
A, D, S = fvvm_matrix_elements(atomlist, bfs, veff, E, r0)
# solve generalized eigenvalue problem
# A.C = b.D.C
b, C = sla.eigh(A, D)
return b, C
def test_h2_continuum_orbital():
"""
The sigma continuum orbital is approximated as a linear
combination of two s continuum orbitals and is then
improved iteratively
"""
# bond length in bohr
dist = 2.0
# positions of protons
posH1 = (0.0, 0.0, -dist / 2.0)
posH2 = (0.0, 0.0, +dist / 2.0)
atomlist = [(1, posH1), (1, posH2)]
# Set resolution of multicenter grid
settings.radial_grid_factor = 20
settings.lebedev_order = 23
# energy of continuum orbital
E = 1.0
# same functional as used in the calculation of pseudo orbitals
xc = XCFunctionals.libXCFunctional(Parameters.pseudo_orbital_x,
Parameters.pseudo_orbital_c)
dft = BasissetFreeDFT(atomlist, xc)
print("initial orbital guess from DFTB calculation")
orbitals = dft.getOrbitalGuess()
norb = len(orbitals)
# all orbitals are doubly occupied
nelec = 2 * norb
bound_orbitals = dft.getOrbitalGuess()
# electron density (closed shell)
rho = density_func(bound_orbitals)
# effective Kohn-Sham potential
veff = effective_potential_func(atomlist,
rho,
xc,
nelec=nelec,
nuclear=True)
# effective Kohn-Sham potential without nuclear attraction
# (only electron-electron interaction)
veff_ee = effective_potential_func(atomlist,
rho,
xc,
nelec=nelec,
nuclear=False)
ps = AtomicPotentialSet(atomlist)
lmax = 0
bs = AtomicScatteringBasisSet(atomlist, E, lmax=lmax)
#test_AO_basis(atomlist, bs, ps, E)
R = residual2_matrix(atomlist, veff, ps, bs)
S = continuum_overlap(bs.bfs, E)
print("continuum overlap")
print(S)
print("residual^2 matrix")
print(R)
eigvals, eigvecs = sla.eigh(R, S)
print(eigvals)
print("eigenvector belonging to lowest eigenvalue")
print(eigvecs[:, 0])
# LCAO continuum orbitals
continuum_orbitals = orbital_transformation(atomlist, bs.bfs, eigvecs)
# improve continuum orbital by adding a correction term
#
# phi = phi0 + dphi
#
# The orbital correction dphi is the solution of the inhomogeneous
# Schroedinger equation
#
# (H-E)dphi = -(H-E)phi0
#
print("orbital correction...")
phi0 = continuum_orbitals[0]
phi = improve_continuum_orbital(atomlist, phi0, veff_ee, E)
def lithium_cation_continuum(l, m, k):
"""
compute continuum orbital in the electrostatic potential of the Li^+ core
Parameters
----------
l,m : angular quantum numbers of asymptotic solution
e.g. l=0,m=0 s-orbital
l=1,m=+1 px-orbital
k : length of wavevector in a.u., the energy of the
continuum orbital is E=1/2 k^2
"""
# Li^+ atom
atomlist = [(3, (0.0, 0.0, 0.0))]
charge = +1
# choose resolution of multicenter grids for bound orbitals
settings.radial_grid_factor = 20 # controls size of radial grid
settings.lebedev_order = 25 # controls size of angular grid
# 1s core orbitals for Li+^ atom
RDFT = BasissetFreeDFT(atomlist, None, charge=charge)
# bound_orbitals = RDFT.getOrbitalGuess()
Etot, bound_orbitals, orbital_energies = RDFT.solveKohnSham()
# choose resolution of multicenter grids for continuum orbitals
settings.radial_grid_factor = 120 # controls size of radial grid
settings.lebedev_order = 41 # controls size of angular grid
# show number of radial and angular points in multicenter grid
print_grid_summary(atomlist, settings.lebedev_order,
settings.radial_grid_factor)
print "electron density..."
# electron density of two electrons in the 1s core orbital
rho = density_func(bound_orbitals)
print "effective potential..."
# potential energy for Li nucleus and 2 core electrons
potential = effective_potential_func(atomlist, rho, None, nelec=2)
def v0(x, y, z):
r = np.sqrt(x * x + y * y + z * z)
return -1.0 / r
def v1(x, y, z):
return potential(x, y, z) - v0(x, y, z)
# The continuum orbital is specified by its energy and asymptotic
# angular momentum (E,l,m)
# energy of continuum orbital
E = 0.5 * k**2
# angular quantum numbers of asymptotic solution
assert abs(m) <= l
print " "
print "Asymptotic continuum wavefunction"
print "================================="
print " energy E= %e Hartree ( %e eV )" % (
E, E * AtomicData.hartree_to_eV)
print " wavevector k= %e a.u." % k
print " angular moment l= %d m= %+d" % (l, m)
print " "
# asymptotically correct solution for V0 = -1/r (hydrogen)
Cf = regular_coulomb_func(E, charge, l, m, 0.0)
phi0 = Cf
# right-hand side of inhomogeneous Schroedinger equation
def source(x, y, z):
return -v1(x, y, z) * phi0(x, y, z)
#
# solve (H0 + V1 - E) dphi = - V1 phi0
# for orbital correction dphi
atomic_numbers, atomic_coordinates = atomlist2arrays(atomlist)
print "Schroedinger equation..."
dphi = multicenter_inhomogeneous_schroedinger(
potential,
source,
E,
atomic_coordinates,
atomic_numbers,
radial_grid_factor=settings.radial_grid_factor,
lebedev_order=settings.lebedev_order)
# Combine asymptotically correct solution with correction
# phi = phi0 + dphi
phi = add_two_functions(atomlist, phi0, dphi, 1.0, 1.0)
# residual for phi0 R0 = (H-E)phi0
residual0 = residual_func(atomlist, phi0, potential, E)
# residual for final solution R = (H-E)phi
residual = residual_func(atomlist, phi, potential, E)
# spherical average of residual function
residual_avg = spherical_average_residual_func(atomlist[0], residual)
# The phase shift is determined by matching the radial wavefunction
# to a shifted and scaled Coulomb function at a number of radial
# sampling points drawn from the interval [rmin, rmax].
# On the one hand rmin < rmax should be chosen large enough,
# so that the continuum orbital approaches its asymptotic form,
# on the other hand rmax should be small enough that the accuracy
# of the solution due to the sparse r-grid is still high enough.
# A compromise has to be struck depending on the size of the radial grid.
# The matching points are spread over several periods,
# but not more than 30 bohr.
wavelength = 2.0 * np.pi / k
print "wavelength = %e" % wavelength
rmin = 70.0
rmax = rmin + max(10 * wavelength, 30.0)
Npts = 100
# determine phase shift and scaling factor by a least square
# fit the the regular Coulomb function
scale, delta = phaseshift_lstsq(atomlist, phi, E, charge, l, m, rmin, rmax,
Npts)
print "scale factor (relative to Coulomb wave) = %s" % scale
print "phase shift (relative to Coulomb wave) = %e " % delta
# normalize wavefunction, so that 1/scale phi(x,y,z) approaches
# asymptotically a phase-shifted Coulomb wave
phi_norm = multicenter_operation(
[phi],
lambda fs: fs[0] / scale,
atomic_coordinates,
atomic_numbers,
radial_grid_factor=settings.radial_grid_factor,
lebedev_order=settings.lebedev_order)
# The continuum orbital should be orthogonal to the bound
# orbitals belonging to the same Hamiltonian. I think this
# should come out correctly by default.
print " "
print " Overlaps between bound orbitals and continuum orbital"
print " ====================================================="
for ib, bound_orbital in enumerate(bound_orbitals):
olap_bc = overlap(atomlist, bound_orbital, phi_norm)
print " <bound %d| continuum> = %e" % (ib + 1, olap_bc)
print ""
# shifted regular coulomb function
Cf_shift = regular_coulomb_func(E, charge, l, m, delta)
# save radial wavefunctions and spherically averaged residual
# radial part of Coulomb wave without phase shift
phi0_rad = radial_wave_func(atomlist, phi0, l, m)
# radial part of shifted Coulomb wave
Cf_shift_rad = radial_wave_func(atomlist, Cf_shift, l, m)
# radial part of scattering solution
phi_norm_rad = radial_wave_func(atomlist, phi_norm, l, m)
print ""
print "# RADIAL_WAVEFUNCTIONS"
print "# Asymptotic wavefunction:"
print "# charge Z= %+d" % charge
print "# energy E= %e k= %e" % (E, k)
print "# angular momentum l= %d m= %+d" % (l, m)
print "# phase shift delta= %e rad" % delta
print "# "
print "# R/bohr Coulomb Coulomb radial wavefunction spherical avg. residual"
print "# shifted R_{l,m}(r) <|(H-E)phi|^2>"
import sys
# write table to console
r = np.linspace(1.0e-3, 100, 1000)
data = np.vstack((r, phi0_rad(r), Cf_shift_rad(r), phi_rad(r),
residual_avg(r))).transpose()
np.savetxt(sys.stdout, data, fmt=" %+e ")
print "# END"
print ""
def test_lcao_continuum():
import matplotlib.pyplot as plt
# bond length in bohr
dist = 2.0
# positions of protons
posH1 = (0.0, 0.0, -dist / 2.0)
posH2 = (0.0, 0.0, +dist / 2.0)
atomlist = [(1, posH1), (1, posH2)]
# Set resolution of multicenter grid
settings.radial_grid_factor = 20
settings.lebedev_order = 23
# energy of continuum orbital
E = 1.0
# same functional as used in the calculation of pseudo orbitals
xc = XCFunctionals.libXCFunctional(Parameters.pseudo_orbital_x,
Parameters.pseudo_orbital_c)
dft = BasissetFreeDFT(atomlist, xc)
print("initial orbital guess from DFTB calculation")
orbitals = dft.getOrbitalGuess()
norb = len(orbitals)
# all orbitals are doubly occupied
nelec = 2 * norb
bound_orbitals = dft.getOrbitalGuess()
# effective potential
rho = density_func(bound_orbitals)
veff = effective_potential_func(atomlist, rho, xc, nelec=nelec)
ps = AtomicPotentialSet(atomlist)
r = np.linspace(-15.0, 15.0, 10000)
x = 0.0 * r
y = 0.0 * r
z = r
for lmax in [0, 1, 2, 3]:
bs = AtomicScatteringBasisSet(atomlist, E, lmax=lmax)
#test_AO_basis(atomlist, bs, ps, E)
R = residual2_matrix(atomlist, veff, ps, bs)
S = continuum_overlap(bs.bfs, E)
print("continuum overlap")
print(S)
print("residual^2 matrix")
print(R)
eigvals, eigvecs = sla.eigh(R, S)
print(eigvals)
print("eigenvector belonging to lowest eigenvalue")
print(eigvecs[:, 0])
# LCAO continuum orbitals
continuum_orbitals = orbital_transformation(atomlist, bs.bfs, eigvecs)
# improve continuum orbital by adding a correction term
#
# phi = phi0 + dphi
#
# The orbital correction dphi is the solution of the inhomogeneous
# Schroedinger equation
#
# (H-E)dphi = -(H-E)phi0
#
print("orbital correction...")
phi0 = continuum_orbitals[0]
phi = improve_continuum_orbital(atomlist, phi0, veff, E)
exit(-1)
residual_0 = residual_func(atomlist, phi0, veff, E)
def source(x, y, z):
return -residual_0(x, y, z)
delta_phi = inhomogeneous_schroedinger(atomlist, veff, source, E)
residual_d = residual_func(atomlist, delta_phi, veff, E)
a, b = variational_mixture_continuum(atomlist, phi0, delta_phi, veff,
E)
phi = add_two_functions(atomlist, phi0, delta_phi, a, b)
residual = residual_func(atomlist, phi, veff, E)
plt.plot(r, 1.0 / np.sqrt(2.0) * bs.bfs[0](x, y, z), label=r"AO")
plt.plot(r, phi0(x, y, z), label=r"$\phi_0$")
plt.plot(r, delta_phi(x, y, z), label=r"$\Delta \phi$")
plt.plot(r, phi(x, y, z), label=r"$\phi_0 + \Delta \phi$")
plt.legend()
plt.show()
"""
dphi = delta_phi(x,y,z)
imin = np.argmin(abs(r-1.0))
dphi[abs(r) < 1.0] = dphi[imin] - (dphi[abs(r) < 1.0] - dphi[imin])
plt.plot(r, dphi, label=r"$\Delta \phi$")
"""
plt.plot(r, residual_0(x, y, z), label=r"$(H-E) \phi_0$")
plt.plot(r, residual_d(x, y, z), label=r"$(H-E)\Delta \phi$")
plt.plot(r,
residual(x, y, z),
label=r"$(H-E)(a \phi_0 + b \Delta \phi)$")
plt.plot(r,
a * residual_0(x, y, z) + b * residual_d(x, y, z),
ls="-.",
label=r"$(H-E)(a \phi_0 + b \Delta \phi)$ (separate)")
plt.legend()
plt.show()
averaged_angular_distribution(atomlist, bound_orbitals,
continuum_orbitals, E)
# save continuum MOs to cubefiles
for i, phi in enumerate(continuum_orbitals):
def func(grid, dV):
x, y, z = grid
return phi(x, y, z)
Cube.function_to_cubefile(
atomlist,
func,
filename="/tmp/cmo_lmax_%2.2d_orb%4.4d.cube" % (lmax, i),
ppb=5.0)
#
for i, phi in enumerate(continuum_orbitals):
residual = residual_func(atomlist, phi, veff, E)
delta_e = energy_correction(atomlist,
residual,
phi,
method="Becke")
print(" orbital %d energy <%d|H-E|%d> = %e" % (i, i, i, delta_e))
l, = plt.plot(r,
phi(x, y, z),
label=r"$\phi_{%d}$ ($l_{max}$ = %d)" % (i, lmax))
plt.plot(r,
residual(x, y, z),
ls="-.",
label=r"$(H-E)\phi_{%d}$" % i,
color=l.get_color())
plt.legend()
plt.show()
print("effective potential...")
# List of (exchange, correlation) functionals implemented
# in libXC
functionals = [
("lda_x", "lda_c_xalpha"),
("lda_x_erf", "lda_c_xalpha"),
("lda_x_rae", "lda_c_xalpha"),
("gga_x_lb", "lda_c_xalpha"),
]
r = np.linspace(0.1, 100.0, 1000)
plt.xlabel(r"distance r / bohr")
plt.ylabel(r"potential / Hartree")
# correct asymptotic HF potential
plt.plot(r, -2.0 / r, "-.", lw=2, label=r"$-2/r$")
for (x_func, c_func) in functionals:
xc = XCFunctionals.libXCFunctional(x_func, c_func)
# potential energy for Li nucleus and 2 core electrons
potential = effective_potential_func(atomlist, rho, xc)
plt.plot(r,
potential(r, 0 * r, 0 * r),
label=r"%s, %s" % (x_func, c_func))
plt.ylim((-5.0, +0.1))
plt.legend()
plt.show()
def hmi_variational_kohn():
# H2^+
# bond length in bohr
R = 2.0
# positions of protons
posH1 = (0.0, 0.0, -R/2.0)
posH2 = (0.0, 0.0, +R/2.0)
# center of charge
center = (0.0, 0.0, 0.0)
atomlist = [(1, posH1),
(1, posH2)]
charge = +2
# choose resolution of multicenter grids for continuum orbitals
settings.radial_grid_factor = 10 # controls size of radial grid
settings.lebedev_order = 21 # controls size of angular grid
# energy of continuum orbital (in Hartree)
E = 10.0
# angular momentum quantum numbers
l,m = 0,0
rho = None
xc = None
print "effective potential..."
V = effective_potential_func(atomlist, rho, xc, nelec=0)
# basis functions
u1 = regular_coulomb_func(E, +1, l, m, 0.0,
center=posH1)
eta1 = 0.0
u2 = regular_coulomb_func(E, +1, l, m, 0.0,
center=posH2)
eta2 = 0.0
# asymptotic solutions
s0 = regular_coulomb_func(E, charge, l, m, 0.0,
center=center)
# c0 = irregular_coulomb_func(E, charge, l, m, 0.0,
# center=center)
c0 = regular_coulomb_func(E, charge, l, m, np.pi/2.0,
center=center)
# switching function
# g(0) = 0 g(oo) = 1
def g(r):
r0 = 3.0 # radius at which the switching happens
gr = 0*r
gr[r > 0] = 1.0/(1.0+np.exp(-(1-r0/r[r > 0])))
return gr
def s(x,y,z):
r = np.sqrt(x*x+y*y+z*z)
return g(r) * s0(x,y,z)
def c(x,y,z):
r = np.sqrt(x*x+y*y+z*z)
return g(r) * c0(x,y,z)
free = [s,c]
# basis potentials
def V1(x,y,z):
r2 = (x-posH1[0])**2 + (y-posH1[1])**2 + (z-posH1[2])**2
return -1.0/np.sqrt(r2)
def V2(x,y,z):
r2 = (x-posH2[0])**2 + (y-posH2[1])**2 + (z-posH2[2])**2
return -1.0/np.sqrt(r2)
basis = [u1,u2]
basis_potentials = [V1,V2]
# number of basis functions
nb = len(basis)
# matrix elements between basis functions
Lbb = np.zeros((nb,nb))
for i in range(0, nb):
ui = basis[i]
for j in range(0, nb):
print "i= %d j= %d" % (i,j)
uj = basis[j]
Vj = basis_potentials[j]
def integrand(x,y,z):
return ui(x,y,z) * (V(x,y,z) - Vj(x,y,z)) * uj(x,y,z)
Lbb[i,j] = integral(atomlist, integrand)
print Lbb
# matrix elements between unbound functions
Lff = np.zeros((2,2))
for i in range(0, 2):
fi = free[i]
for j in range(0, 2):
print "i= %d j= %d" % (i,j)
fj = free[j]
Lff[i,j] = kinetic(atomlist, fi,fj) + nuclear(atomlist, fi,fj) - E * overlap(atomlist, fi,fj)
print Lff
# matrix elements between bound and unbound functions
Lbf = np.zeros((nb,2))
Lfb = np.zeros((2,nb))
for i in range(0, nb):
ui = basis[i]
for j in range(0, 2):
fj = free[j]
print "i= %d j= %d" % (i,j)
Lbf[i,j] = kinetic(atomlist, ui,fj) + nuclear(atomlist, ui,fj) - E * overlap(atomlist, ui,fj)
Lfb[j,i] = kinetic(atomlist, fj,ui) + nuclear(atomlist, fj,ui) - E * overlap(atomlist, fj,ui)
print Lbf
print Lfb
#
coeffs = -np.dot(la.inv(Lbb), Lbf)
M = Lff - np.dot(Lfb, np.dot(la.inv(Lbb), Lbf))
print "M"
print M
# The equation
#
# M. (1) = 0
# (t)
# cannot be fulfilled, usually.
t0 = -M[0,0]/M[0,1]
tans = np.array([np.tan(eta1), np.tan(eta2)])
t = (t0 + np.sum(coeffs[:,0]*tans) + t0*np.sum(coeffs[:,1]*tans)) \
/ (1 + np.sum(coeffs[:,0]) + t0*np.sum(coeffs[:,1]))
eta = np.arctan(t)
# Because a global phase is irrelevant, the phase shift is only determined
# modulo pi. sin(pi+eta) = -sin(eta)
while eta < 0.0:
eta += np.pi
print "eta= %s" % eta
bc0 = linear_combination(atomlist, basis, coeffs[:,0])
bc1 = linear_combination(atomlist, basis, coeffs[:,1])
#u = s + np.dot(basis, coeffs[:,0]) + t0 * (c + np.dot(basis, coeffs[:,1]))
orbitals = [s, bc0, c, bc1]
nrm = (1 + np.sum(coeffs[:,0]) + t0*np.sum(coeffs[:,1]))
orb_coeffs = np.array([ 1.0, 1.0, t0, t0 ]) / nrm
phi = linear_combination(atomlist, orbitals, orb_coeffs)
residual = residual_func(atomlist, phi, V, E)
import matplotlib.pyplot as plt
r = np.linspace(-50.0, 50.0, 5000)
x = 0.0*r
y = 0.0*r
z = r
plt.plot(r, phi(x,y,z), label=r"$\phi$")
plt.plot(r, residual(x,y,z), label=r"residual $(H-E)\phi$")
plt.plot(r, V(x,y,z), label=r"potential")
phi_lcao = linear_combination(atomlist, basis, [1.0/np.sqrt(2.0), 1.0/np.sqrt(2.0)])
residual_lcao = residual_func(atomlist, phi_lcao, V, E)
plt.plot(r, phi_lcao(x,y,z), label=r"$\phi_{LCAO}$")
plt.plot(r, residual_lcao(x,y,z), label=r"residual $(H-E)\phi_{LCAO}$")
plt.legend()
plt.show()
