ADSORBATE_DOSCAR = os.path.join(lobster_path, 'surfaces_noW/'+surface + '+'\
+ adsorbate + '/DOSCAR.lobster')
ADSORBATE_CONTCAR = os.path.join(lobster_path, 'surfaces_noW/'+surface + '+'\
+ adsorbate + '/CONTCAR')
BULK_DOSCAR = os.path.join(example_path,'Pt_nano/Pt147/DOSCAR')
# VASP_DOS objects for both the gas (vacuum) and the adsorbate+surface system
GAS_PDOS = VASP_DOS(GAS_DOSCAR)
REFERENCE_PDOS = VASP_DOS(ADSORBATE_DOSCAR)
BULK_PDOS = VASP_DOS(BULK_DOSCAR)
# Get adsorbate and site indices and initialize PDOS_OVERLAP object
adsorbate_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, adsorbate_indices\
, site_indices, min_occupation=1.5\
, upshift=0.5, energy_weight=3)
CO_overlap.optimize_energy_shift(bound=[-10, 10], reset=True)
GCNList = []
four_sigma_list = []
one_pi_list = []
five_sigma_list = []
DOSCAR_files, CONTCAR_files = get_all_VASP_files(\
r'C:\Users\lansf\Documents\Data\PROBE_PDOS\vasp_dos_files\Pt_nano')
for nano_DOSCAR, nano_CONTCAR in zip(DOSCAR_files, CONTCAR_files):
nano_indices, GCNs, atom_types = get_geometric_data(nano_CONTCAR)
GCNList += GCNs[atom_types[...] == 'surface'].tolist()
GAS_PDOS = VASP_DOS(GAS_DOSCAR)
REFERENCE_PDOS = VASP_DOS(ADSORBATE_DOSCAR)
#######################################################################################
# Get adsorbate and site indices and initialize PDOS_OVERLAP object
# -----------------------------------------------------------------
#
# This method utilizes two VASP_DOS objects, a gas and an adsorption system.
# 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.
REFERENCE_PDOS = VASP_DOS(ADSORBATE_DOSCAR)
#REFERENCE_PDOS.apply_gaussian_filter(10)
#######################################################################################
# Get adsorbate and site indices and initialize PDOS_OVERLAP object
# -----------------------------------------------------------------
#
# This method utilizes two VASP_DOS objects, a gas and an adsorption system.
# 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()
#######################################################################################
# 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.
ADSORBATE_DOSCAR = os.path.join(lobster_path, 'surfaces_noW/'+surface + '+'\
+ adsorbate + '/DOSCAR.lobster')
ADSORBATE_CONTCAR = os.path.join(lobster_path, 'surfaces_noW/'+surface + '+'\
+ adsorbate + '/CONTCAR')
BULK_DOSCAR = os.path.join(lobster_path,'nanoparticles_noW/Pt147/DOSCAR.lobster')
# VASP_DOS objects for both the gas (vacuum) and the adsorbate+surface system
GAS_PDOS = VASP_DOS(GAS_DOSCAR)
REFERENCE_PDOS = VASP_DOS(ADSORBATE_DOSCAR)
BULK_PDOS = VASP_DOS(BULK_DOSCAR)
# Get adsorbate and site indices and initialize PDOS_OVERLAP object
adsorbate_indices, site_indices = get_adsorbate_indices(GAS_CONTCAR\
, ADSORBATE_CONTCAR)
#Initialize Coordination object. Repeat is necessary so it doesn't count itself
Overlap = PDOS_OVERLAP(GAS_PDOS, REFERENCE_PDOS, adsorbate_indices\
, site_indices, min_occupation=0.5\
, upshift=0.5, energy_weight=4)
Overlap.optimize_energy_shift(bound=[-10, 10], reset=True)
GCNList = []
orbital_indices = [0, 3, 4, 5]
orbital_array = [[] for i in range(len(orbital_indices))]
DOSCAR_files, CONTCAR_files = get_all_VASP_files(os.path.join(lobster_path,'nanoparticles_noW'))
DOSCAR_files = [file_name + '.lobster' for file_name in DOSCAR_files]
for nano_DOSCAR, nano_CONTCAR in zip(DOSCAR_files, CONTCAR_files):
nano_indices, GCNs, atom_types = get_geometric_data(nano_CONTCAR)
GCNList += GCNs[atom_types[...] == 'surface'].tolist()
# read and return density of states object
nano_PDOS = VASP_DOS(nano_DOSCAR)
for atom_index in nano_indices[atom_types[...] == 'surface']:
for i, index in enumerate(orbital_indices):
GAS_PDOS = VASP_DOS(GAS_DOSCAR)
REFERENCE_PDOS = VASP_DOS(ADSORBATE_DOSCAR)
#######################################################################################
# Get adsorbate and site indices and initialize PDOS_OVERLAP object
# -----------------------------------------------------------------
#
# This method utilizes two VASP_DOS objects, a gas and an adsorption system.
# 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=1\
, 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(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.
REFERENCE_PDOS = VASP_DOS(ADSORBATE_DOSCAR)
#REFERENCE_PDOS.apply_gaussian_filter(10)
#######################################################################################
# Get adsorbate and site indices and initialize PDOS_OVERLAP object
# -----------------------------------------------------------------
#
# This method utilizes two VASP_DOS objects, a gas and an adsorption system.
# 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=0.55\
, 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.
GAS_PDOS = VASP_DOS(GAS_DOSCAR)
REFERENCE_PDOS = VASP_DOS(ADSORBATE_DOSCAR)
#######################################################################################
# Get adsorbate and site indices and initialize PDOS_OVERLAP object
# -----------------------------------------------------------------
#
# This method utilizes two VASP_DOS objects, a gas and an adsorption system.
# 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.
adsorbate_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, adsorbate_indices\
, site_indices, min_occupation=0.9\
, upshift=0.5, energy_weight=4)
# 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.
optimized_upshift = CO_overlap.optimize_energy_shift(bound=[-0.5,1.5]\
, reset=True, plot=True)
print(optimized_upshift)
# Print orbital CO_overlap attributes