def iron():
energy_range = list(linspace(-400.0, -200.0, 200)) \
+ list(linspace(-200.0, -30.0, 200)) \
+ list(linspace(-30.0, -5.0, 400)) \
+ list(linspace(-5.0, -0.0000001, 400)) \
# equidistant grid, use larger grid for heavy atoms
Z = 26
Nelec = 26
atomdft = PseudoAtomDFT(Z,Nelec,numerov_conv,en_conv=1.0e-4, grid_spacing="exponential", damping=0.6)
# iron has the electron configuration: [Ar] 3d^(6) 4s^2
occupation = [occ for occ in occupation_numbers(Nelec)]
assert occupation[-1] == (8,3-1,2) # 8e in 3d
occupation[-1] = (6,3-1,2) # put 6e in 3d
occupation.append( (2,4-1,0) ) # and 2e in 4s
atomdft.setOccupation(occupation)
atomdft.setRadialGrid(0.0000004, 16.0, 6000)
try:
from free_pseudo_atoms import fe
atomdft.initialDensityGuess((fe.r, fe.radial_density))
except ImportError:
atomdft.initialDensityGuess()
atomdft.setEnergyRange(energy_range)
atomdft.solveKohnSham()
fh = open(orbdir + "fe.py", "w")
atomdft.saveSolution(fh)
fh.close()
def silver():
energy_range = list(linspace(-1500.0, -800.0, 100)) \
+ list(linspace(-800.0, -200.0, 200)) \
+ list(linspace(-200.0, -30.0, 200)) \
+ list(linspace(-30.0, -5.0, 400)) \
+ list(linspace(-5.0, -0.0000001, 400)) \
# equidistant grid, use larger grid for heavy atoms
Z = 47
Nelec = 47
atomdft = PseudoAtomDFT(Z,Nelec,numerov_conv,en_conv=1.0e-4, grid_spacing="exponential", damping=0.6)
# In silver the 5s is filled before 4f: [Kr] 4d^(10) 5s^1
occupation = [occ for occ in occupation_numbers(Nelec)]
assert occupation[-1] == (1,4-1,3)
occupation[-1] = (1,5-1,0)
atomdft.setOccupation(occupation)
# I would like to include unoccupied f orbitals in minimal basis but
# sofar no Slater rules exist for f orbitals. So include 5p
atomdft.setValenceOrbitals(["4d", "5s","5p"], format="spectroscopic")
atomdft.setRadialGrid(0.000000001, 14.0, 20000)
try:
from free_pseudo_atoms import ag
atomdft.initialDensityGuess((ag.r, ag.radial_density))
except ImportError:
atomdft.initialDensityGuess()
atomdft.setEnergyRange(energy_range)
atomdft.solveKohnSham()
fh = open(orbdir + "ag.py", "w")
atomdft.saveSolution(fh)
fh.close()
def scandium():
energy_range = list(linspace(-400.0, -200.0, 200)) \
+ list(linspace(-200.0, -30.0, 200)) \
+ list(linspace(-30.0, -5.0, 400)) \
+ list(linspace(-5.0, -0.0000001, 400)) \
# equidistant grid, use larger grid for heavy atoms
Z = 21
Nelec = 21
atomdft = PseudoAtomDFT(Z,Nelec,numerov_conv,en_conv, grid_spacing="exponential") #, damping=0.6)
# scandium has the electron configuration: [Ar] 3d^1 4s^2
occupation = [occ for occ in occupation_numbers(Nelec)]
assert occupation[-1] == (3,3-1,2) # 3e in 3d
occupation[-1] = (1,3-1,2) # put 1e in 3d
occupation.append( (2,4-1,0) ) # and 2e in 4s
atomdft.setOccupation(occupation)
atomdft.setValenceOrbitals(["3d", "4s"], format="spectroscopic")
atomdft.setRadialGrid(0.0000004, 16.0, 6000)
try:
from free_pseudo_atoms import sc
atomdft.initialDensityGuess((sc.r, sc.radial_density))
#from free_pseudo_atoms import ti
# load density of titanium and scale it
#atomdft.initialDensityGuess((ti.r, ti.radial_density * float(Nelec)/float(ti.Nelec)))
except ImportError:
atomdft.initialDensityGuess()
atomdft.setEnergyRange(energy_range)
atomdft.solveKohnSham()
fh = open(orbdir + "sc.py", "w")
atomdft.saveSolution(fh)
fh.close()
def potassium():
energy_range = list(linspace(-135.0, -40.00, 100)) \
+list(linspace(-40, -13.0, 50)) \
+list(linspace(-13.0, -1.0, 200)) \
+list(linspace(-1.0, -0.0001, 200))
Z = 19
Nelec = 19
atomdft = PseudoAtomDFT(Z,Nelec,numerov_conv,en_conv, grid_spacing="exponential")
# in potassium 4s is filled before 3d: [Ar] 4s^1
occupation = [occ for occ in occupation_numbers(Nelec)]
assert occupation[-1] == (1, 3-1, 2) # 1e in 3d
occupation[-1] = (1,4-1,0) # 1e in 4s
atomdft.setOccupation(occupation)
atomdft.setRadialGrid(rmin, rmax_4th_row, Npts_4th_row)
try:
from free_pseudo_atoms import k
atomdft.initialDensityGuess((k.r, k.radial_density))
except ImportError:
atomdft.initialDensityGuess()
atomdft.setEnergyRange(energy_range)
atomdft.solveKohnSham()
fh = open(orbdir + "k.py", "w")
atomdft.saveSolution(fh)
fh.close()
def titanium():
energy_range = list(linspace(-400.0, -200.0, 200)) \
+ list(linspace(-200.0, -30.0, 200)) \
+ list(linspace(-30.0, -5.0, 400)) \
+ list(linspace(-5.0, 5.0, 200)) \
# equidistant grid, use larger grid for heavy atoms
Z = 22
Nelec = 22
atomdft = PseudoAtomDFT(Z,
Nelec,
numerov_conv,
100 * en_conv,
grid_spacing="exponential",
r0=confinement_radii_byZ[Z])
# titanium has the electron configuration: [Ar] 3d^2 4s^2
occupation = [occ for occ in occupation_numbers(Nelec)]
assert occupation[-1] == (4, 3 - 1, 2) # 4e in 3d
occupation[-1] = (2, 3 - 1, 2) # put 2e in 3d
occupation.append((2, 4 - 1, 0)) # and 2e in 4s
atomdft.setOccupation(occupation)
atomdft.setRadialGrid(0.0000004, 16.0, 6000)
try:
from confined_pseudo_atoms import ti
atomdft.initialDensityGuess((ti.r, ti.radial_density))
except ImportError:
atomdft.initialDensityGuess()
atomdft.setEnergyRange(energy_range)
atomdft.solveKohnSham()
fh = open(orbdir + "ti.py", "w")
atomdft.saveSolution(fh)
fh.close()
def ruthenium():
energy_range = list(linspace(-1500.0, -800.0, 100)) \
+ list(linspace(-800.0, -200.0, 200)) \
+ list(linspace(-200.0, -30.0, 200)) \
+ list(linspace(-30.0, -5.0, 400)) \
+ list(linspace(-5.0, 5.0, 400)) \
# equidistant grid, use larger grid for heavy atoms
Z = 44
Nelec = 44
atomdft = PseudoAtomDFT(Z,
Nelec,
numerov_conv,
en_conv,
grid_spacing="exponential",
r0=confinement_radii_byZ[Z],
damping=0.6)
# The electron configuration of ruthenium is [Kr] 4d^(7) 5s^(1)
occupation = [occ for occ in occupation_numbers(Nelec)]
# `occupation` is a list of tuples
# (nr.electrons, quantum number n + 1, quantum number l)
# that describe the occupied shells.
# In the default occupation, ruthenium would have the electronic configuration [Kr] 4d^(8).
assert occupation[-1] == (8, 4 - 1, 2)
# The default occupation is not correct, so we need to adjust it by
# removing one electron from 4d shell,
occupation[-1] = (7, 4 - 1, 2)
# and adding a 5s shell with 1 electron.
occupation.append((1, 5 - 1, 0))
# The new occupation is now [Kr] 4d^(7) 5s^(1)
atomdft.setOccupation(occupation)
atomdft.setValenceOrbitals(["4d", "5s"], format="spectroscopic")
atomdft.setRadialGrid(0.000000001, 14.0, 20000)
try:
"""
# If no initial density is available for Ru, we can take the density from silver
# and scale it, so that it integrates to the number of electrons in ruthenium.
from confined_pseudo_atoms import ag
atomdft.initialDensityGuess((ag.r, float(Nelec)/float(ag.Nelec) * ag.radial_density))
"""
# If an initial density is available for Ru, we use that one
from confined_pseudo_atoms import ru
atomdft.initialDensityGuess(
(ru.r, float(Nelec) / float(ru.Nelec) * ru.radial_density))
except ImportError:
atomdft.initialDensityGuess()
atomdft.setEnergyRange(energy_range)
atomdft.solveKohnSham()
fh = open(orbdir + "ru.py", "w")
atomdft.saveSolution(fh)
fh.close()
def ruthenium_2plus():
energy_range = list(linspace(-1500.0, -800.0, 100)) \
+ list(linspace(-800.0, -200.0, 200)) \
+ list(linspace(-200.0, -30.0, 200)) \
+ list(linspace(-30.0, -5.0, 400)) \
+ list(linspace(-5.0, 5.0, 400)) \
# equidistant grid, use larger grid for heavy atoms
Z = 44
Nelec = 42 # Ru^(2+)
atomdft = PseudoAtomDFT(Z,
Nelec,
numerov_conv,
en_conv,
grid_spacing="exponential",
r0=confinement_radii_byZ[Z],
damping=0.6)
# The electron configuration of Ru^(2+) is [Kr] 4d^(6)
occupation = [occ for occ in occupation_numbers(Nelec)]
# `occupation` is a list of tuples
# (nr.electrons, quantum number n + 1, quantum number l)
# that describe the occupied shells.
# In the default occupation, ruthenium would have the electronic configuration [Kr] 4d^(6),
# which is correct.
assert occupation[-1] == (6, 4 - 1, 2)
atomdft.setOccupation(occupation)
atomdft.setValenceOrbitals(["4d", "5s"], format="spectroscopic")
atomdft.setRadialGrid(0.000000001, 14.0, 20000)
try:
# If no initial density is available for Ru^(2+), we can take the density from silver
# and scale it, so that it integrates to the number of electrons in ruthenium 2+.
from confined_pseudo_atoms import ag
atomdft.initialDensityGuess(
(ag.r, float(Nelec) / float(ag.Nelec) * ag.radial_density))
"""
# If an initial density is available for Ru^(2+), we use that one
from confined_pseudo_atoms import ru
atomdft.initialDensityGuess((ru.r, ru.radial_density))
"""
except ImportError:
atomdft.initialDensityGuess()
atomdft.setEnergyRange(energy_range)
atomdft.solveKohnSham()
# Although we have calculated Ru^(2+), the pseudoorbitals still have to be saved under the name 'ru.py'.
# Only one oxidation state can be used for any atom at the same time.
fh = open(orbdir + "ru.py", "w")
atomdft.saveSolution(fh)
fh.close()