np.set_printoptions(linewidth=100)
#These files are too large to store in the examples directory
lobster_path = r'C:\Users\lansf\Documents\Data\PROBE_PDOS\lobster_files'
GAS_DOSCAR = os.path.join(lobster_path, gas + '/DOSCAR.lobster')
GAS_CONTCAR = os.path.join(lobster_path, gas + '/CONTCAR')
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')
#######################################################################################
# Generate VASP_DOS objects
# -------------------------
#
# 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)
#######################################################################################
# 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\
gas = 'CO'
adsorbate='CO'
surface = 'Pt111'
set_figure_settings('paper')
np.set_printoptions(linewidth=100)
example_path = r'C:\Users\lansf\Documents\Data\PROBE_PDOS\vasp_dos_files'
lobster_path = r'C:\Users\lansf\Documents\Data\PROBE_PDOS\lobster_files'
GAS_DOSCAR = os.path.join(lobster_path, gas + '/DOSCAR.lobster')
GAS_CONTCAR = os.path.join(lobster_path, gas + '/CONTCAR')
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 = []
import matplotlib.pyplot as plt
from pdos_overlap.vasp_dos import get_example_data
from pdos_overlap.vasp_dos import VASP_DOS
from pdos_overlap.plotting_tools import set_figure_settings
#######################################################################################
# Load DOSCAR file
# ----------------
#
# First we will, get the example data, load a DOSCAR file and use it to
# instantiate a VASP_DOS object.
set_figure_settings('paper')
example_path = get_example_data()
DOSCAR = os.path.join(example_path, 'C2H4/DOSCAR')
PDOS = VASP_DOS(DOSCAR)
#######################################################################################
# Obtain projected density
# ------------------------
#
# We get the site and spin orbital projected density. We sum the individual
# spin orbital densities to get energy sub-level site projected densities.
orbitals, projected_density = PDOS.get_site_dos(atom_indices=np.arange(-6,0)\
, orbital_list=['s', 'p', 'd']\
, sum_density = True)
#######################################################################################
# Plot projected density
# ----------------------
occupied_band_list = []
unoccupied_band_list = []
filling_list = []
second_moment_list = []
bond_energy_list = []
#DOSCAR_files, CONTCAR_files = get_all_VASP_files(\
# r'C:\Users\lansf\Documents\Data\PROBE_PDOS\lobster_files\nanoparticles_noW')
DOSCAR_files, CONTCAR_files = get_all_VASP_files(\
r'C:\Users\lansf\Documents\Data\PROBE_PDOS\vasp_dos_files/Pt_nano')
for DOSCAR, CONTCAR in zip(DOSCAR_files, CONTCAR_files):
indices, GCNs, atom_types = get_geometric_data(CONTCAR)
GCNList += GCNs.tolist()
atom_type += atom_types.tolist()
# read and return densityofstates object
PDOS = VASP_DOS(DOSCAR, add_p2s=True)
for atom_index in indices:
band_center = PDOS.get_band_center(atom_index, ['s','d']\
, sum_density=True) - PDOS.e_fermi
occupied_band_center = PDOS.get_band_center(atom_index, ['s','d']\
, sum_density=True, max_energy=PDOS.e_fermi) - PDOS.e_fermi
unoccupied_band_center = PDOS.get_band_center(atom_index, ['s','d']\
, sum_density=True, min_energy=PDOS.e_fermi) - PDOS.e_fermi
band_width = PDOS.get_center_width(PDOS.e_fermi, atom_index, ['s','d']\
, sum_density=True)
second_moment = PDOS.get_second_moment(atom_index, ['s','d']\
, sum_density=True)
bond_energy = PDOS.get_bond_energy(atom_index, ['s','d']\
, sum_density=True)
import os
from pdos_overlap.vasp_dos import get_example_data
from pdos_overlap.vasp_dos import VASP_DOS
from pdos_overlap.plotting_tools import set_figure_settings
#######################################################################################
# Load DOSCAR file
# ----------------
#
# First we will, get the example data, load a DOSCAR file and use it to
# instantiate a VASP_DOS object.
set_figure_settings('paper')
example_path = get_example_data()
DOSCAR = os.path.join(example_path, 'C2H4/DOSCAR')
PDOS = VASP_DOS(DOSCAR)
#######################################################################################
# Calculate and print band centers
# --------------------------------
#
# This method uses the the site and spin orbital projected density. It sums the
# spin orbital densities to get energy sub-level band centers.
orbitals = [
key for key in PDOS.orbital_dictionary.keys() if 's' in key or 'p' in key
]
band_centers = PDOS.get_band_center([0], orbital_list=orbitals\
, max_energy=PDOS.e_fermi, sum_spin=False)
