overlap_population¶
The write_lobsterin function¶
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write_lobsterin(directory='.', adsorbate_atoms=['C', 'H', 'O', 'N'], basisSet='pbeVaspFit2015', basisfunctions={'C': '2s 2p', 'H': '1s', 'N': '2s 2p', 'O': '2s 2p', 'Pt': '5d 6s'}, gaussianSmearingWidth=0.003)[source]¶ Write a lobster input file
- Parameters
directory (str) – directory to write the lobsterin file. Must also contain a CONTCAR and DOSCAR file
adsorbate_atoms (list[str or int]) – adsorbate atom symbols or indices
basisSet (str) – basis used to projected density onto orbitals
basisfunctions (dict) – dictionary of atomic symbols and corresponding basis functions
gaussianSmearingWidth (float) – float if Gaussian smearing is used. If tetrahedron method is used then set to None
The get_example_data function¶
The get_all_lobster_files function¶
The get_bonding_states function¶
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get_bonding_states(orbital_indices, dos_energies, pcoop, pcoop_energies, set_antibonding_zero=False, emax=inf)[source]¶ method for obtaining bonding fraction of dos or dos-like array
- Parameters
orbital_indices (list[list]) – list of orbital indices for each molecular orbital
dos_energies (numpy.ndarray) – energies at which dos is calculated
pcoop (numpy.ndarray) – projected orbital overlap populations
pcoop_energies (numpy.ndarray) – energies at which the pcoop is calculated
set_antibonding_zero (bool) – if true, set antibonding populations to zero to look at total instead of net bonding characteristics
- Returns
dos_bonding – 1-D array of the relative bonding for either dos-like array
- Return type
The OVERLAP_POPULATION class¶
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class
OVERLAP_POPULATION(file_name='COOPCAR.lobster')[source]¶ Class for analyzing overlap population bonding data
- Parameters
file_name (str) – full lobster file location
- Variables
emax (float) – maximum energy level
emin (float) – minimum energy level
ndos (int) – number of descritized energy levels
e_fermi (float) – highest occupied energy level
is_spin (bool) – indicates if projected density is spin resolved
num_interactions (int) – number of interactions in COOP
interactions (list[str]) – list of the interactions included in the file
Methods
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_read_coopcar(file_name='COOPCAR.lobster')[source]¶ Read lobster COOPCAR and extract projected overlap
- Parameters
file_name (str) – file location of the COOPCAR.lobster file file
- Variables
_pcoop (numpy.ndarray) – numpy array that contains the energy of levels and the projected crystal orbital overlap population densities
- Returns
emax (float) – maximum energy level
emin (float) – minimum energy level
ndos (int) – number of descritized energy levels
e_fermi (float) – highest occupied energy level
is_spin (bool) – indicates if projected density is spin resolved
num_interactions (int) – number of interactions in COOP
interactions (list[str]) – list of the interactions included in the file
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apply_gaussian_filter(sigma)[source]¶ Applies Gaussian filter to self._pcoop
- Parameters
sigma (float) – standard deviation of Gaussian Kernel
- Variables
_pcoop_original (numpy.ndarray) – self._pcoop array without filter
Notes
Understand carefully what this does before using it. It applies a Gaussian filter to the average and integrated PCOOP and the PCOOP such that the average and integrated PCOOP may become meaningless
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get_average_int_pcoop(sum_spin=True)[source]¶ obtain average integrated overlap population for all atom pairs
- Parameters
sum_spin (bool) – indicates whether data of different spins should be summed
- Returns
average_int_pcoop – 1-D or 2-D array of average integrated pcoop for all interactions
- Return type
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get_average_pcoop(sum_spin=True)[source]¶ obtain average overlap population for all atom pairs
- Parameters
sum_spin (bool) – indicates whether data of different spins should be summed
- Returns
average_pcoop – 1-D or 2-D array of average pcoop for all interactions
- Return type
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get_bonding_states(orbital_indices, dos_energies, interactions=[], set_antibonding_zero=False, emax=inf)[source]¶ method for obtaining bonding fraction of dos or dos-like array
- Parameters
orbital_indices (list[list]) – list of energy indices for each molecular orbital
dos_energies (numpy.ndarray) – energies at which dos is calculated
interactions (list) – indices of interactions for which to find the integrated pcoop
set_antibonding_zero (bool) – if true, set antibonding populations to zero to look at total instead of net bonding characteristics
emax (float) – maximum energy level
- Returns
dos_bonding – 1-D array of the relative bonding for either dos-like array
- Return type
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get_energies()[source]¶ method for obtaining energy levels
- Returns
energies – 1-D array of energies
- Return type
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get_integrated_pcoop(interactions=[], sum_pcoop=False, sum_spin=True, set_antibonding_zero=False)[source]¶ obtain integrated projected crystal orbital overlap populations
- Parameters
interactions (list) – indices of interactions for which to find the integrated pcoop
sum_pcoop (bool) – indicates whether all pcoop should be summed
sum_spin (bool) – indicates whether data of different spins should be summed
set_antibonding_zero (bool) – if true, set antibonding populations to zero to look at total instead of net bonding characteristics
- Returns
integrated_pcoop – 1-D, 2-D, or 3-D array of integrated pcoop for all interactions
- Return type
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get_pcoop(interactions=[], sum_pcoop=False, sum_spin=True, set_antibonding_zero=False)[source]¶ method for obtaining projected crystal orbital overlap populations
- Parameters
interactions (list) – indices of interactions for which to find the integrated pcoop
sum_pcoop (bool) – indicates whether all pcoop should be summed
sum_spin (bool) – indicates whether data of different spins should be summed
set_antibonding_zero (bool) – if true, set antibonding populations to zero to look at total instead of net bonding characteristics
- Returns
pcoop – 1-D or 2-D array of pcoop for all interactions
- Return type