# It uses the adosorbtion system (REFERENCE_PDOS) to map gas molecular orbitals
# to adsorbate molecular orbitals. It then calculates the adsorption site
# atomic orbital energy overlaps with the adsorbate molecular orbital energies.
reference_indices, site_indices = get_adsorbate_indices(GAS_CONTCAR\
, ADSORBATE_CONTCAR)
#Initialize Coordination object. Repeat is necessary so it doesn't count itself
NO_overlap = PDOS_OVERLAP(GAS_PDOS, REFERENCE_PDOS, reference_indices\
, site_indices, min_occupation=1\
, upshift=0.5, energy_weight=3)
#######################################################################################
# Plot projected density
# ----------------------
#
# We plot the projected density of the gas, adsorbate, and adsorption site.
NO_overlap.plot_projected_density()
#######################################################################################
# Find the optimal upshift factor
# -------------------------------
#
# The optimal upshift factor shifts the gas molecular orbital energies to
# minimize the sum the orbital scores used in matching gas and adsorbate orbitals.
# This has the effect of increasing certainty and roughly corresponds to the
# average shift in molecular orbital energies when a gas adsorbs to the surface
optimized_upshift = NO_overlap.optimize_energy_shift(bound=[-10, 10]\
, reset=True, plot=True)
print(optimized_upshift)
#######################################################################################
# Print orbital CO_overlap attributes
# It uses the adosorbtion system (REFERENCE_PDOS) to map gas molecular orbitals
# to adsorbate molecular orbitals. It then calculates the adsorption site
# atomic orbital energy overlaps with the adsorbate molecular orbital energies.
reference_indices, site_indices = get_adsorbate_indices(GAS_CONTCAR\
, ADSORBATE_CONTCAR)
#Initialize Coordination object. Repeat is necessary so it doesn't count itself
C2H4_overlap = PDOS_OVERLAP(GAS_PDOS, REFERENCE_PDOS, reference_indices\
, site_indices, min_occupation=0.4\
, upshift=0.5, energy_weight=3)
#######################################################################################
# Plot projected density
# ----------------------
#
# We plot the projected density of the gas, adsorbate, and adsorption site.
C2H4_overlap.plot_projected_density()
#######################################################################################
# Find the optimal upshift factor
# -------------------------------
#
# The optimal upshift factor shifts the molecular orbital energies to
# minimize the sum the orbital scores used in matching gas and adsorbate orbitals.
# This has the effect of increasing certainty and roughly corresponds to the
# average shift in molecular orbital energies when a gas adsorbs to the surface
# as a fraction of the fermi energy.
"""
I need to fix this for NO
"""
optimized_upshift = C2H4_overlap.optimize_energy_shift(bound=[-10, 10]\
, reset=True, plot=True)
# It uses the adosorbtion system (REFERENCE_PDOS) to map gas molecular orbitals
# to adsorbate molecular orbitals. It then calculates the adsorption site
# atomic orbital energy overlaps with the adsorbate molecular orbital energies.
reference_indices, site_indices = get_adsorbate_indices(GAS_CONTCAR\
, ADSORBATE_CONTCAR)
#Initialize Coordination object. Repeat is necessary so it doesn't count itself
CO_overlap = PDOS_OVERLAP(GAS_PDOS, REFERENCE_PDOS, reference_indices\
, site_indices, min_occupation=1.5\
, upshift=0.5, energy_weight=4)
#######################################################################################
# Plot projected density
# ----------------------
#
# We plot the projected density of the gas, adsorbate, and adsorption site.
CO_overlap.plot_projected_density(figure_directory=Downloads_folder)
#######################################################################################
# Find the optimal upshift factor
# -------------------------------
#
# The optimal upshift factor shifts the gas molecular orbital energies to
# minimize the sum the orbital scores used in matching gas and adsorbate orbitals.
# This has the effect of increasing certainty and roughly corresponds to the
# average shift in molecular orbital energies when a gas adsorbs to the surface
optimized_upshift = CO_overlap.optimize_energy_shift(bound=[-10,10]\
, reset=True, plot=True)
print(optimized_upshift)
#######################################################################################
# Print orbital CO_overlap attributes
# It uses the adosorbtion system (REFERENCE_PDOS) to map gas molecular orbitals
# to adsorbate molecular orbitals. It then calculates the adsorption site
# atomic orbital energy overlaps with the adsorbate molecular orbital energies.
reference_indices, site_indices = get_adsorbate_indices(GAS_CONTCAR\
, ADSORBATE_CONTCAR)
#Initialize Coordination object. Repeat is necessary so it doesn't count itself
CO_overlap = PDOS_OVERLAP(GAS_PDOS, REFERENCE_PDOS, reference_indices\
, site_indices, min_occupation=0.9\
, upshift=0.5, energy_weight=4)
#######################################################################################
# Plot projected density
# ----------------------
#
# We plot the projected density of the gas, adsorbate, and adsorption site.
CO_overlap.plot_projected_density(figure_directory='print')
#######################################################################################
# Find the optimal upshift factor
# -------------------------------
#
# The optimal upshift factor shifts the gas molecular orbital energies to
# minimize the sum the orbital scores used in matching gas and adsorbate orbitals.
# This has the effect of increasing certainty and roughly corresponds to the
# average shift in molecular orbital energies when a gas adsorbs to the surface
optimized_upshift = CO_overlap.optimize_energy_shift(bound=[-10,10]\
, reset=True, plot=True)
print(optimized_upshift)
#######################################################################################
# Identify bonding orbitals
