Index

_

_supported_files (dfttoolkit.parameters.Parameters attribute)

A

add_atoms() (dfttoolkit.geometry.Geometry method) add_geometry() (dfttoolkit.geometry.Geometry method) add_keywords() (dfttoolkit.parameters.AimsControl method) add_multipoles() (dfttoolkit.geometry.Geometry method) add_top_comment() (dfttoolkit.geometry.Geometry method) aims_bin_path_prompt() (in module dfttoolkit.utils.file_utils) AimsControl (class in dfttoolkit.parameters) AimsGeometry (class in dfttoolkit.geometry) AimsOutput (class in dfttoolkit.output) AimsVibrations (class in dfttoolkit.vibrations)

align_cartiesian_axis_to_vector() (dfttoolkit.geometry.Geometry method) align_into_xy_plane() (dfttoolkit.geometry.Geometry method) align_lattice_vector_to_vector() (dfttoolkit.geometry.Geometry method) align_main_axis_along_xyz() (dfttoolkit.geometry.Geometry method) align_vector_to_vector() (dfttoolkit.geometry.Geometry method) align_with_view_direction() (dfttoolkit.geometry.Geometry method) align_with_z_vector() (dfttoolkit.geometry.Geometry method) apply_gaussian_window() (in module dfttoolkit.utils.math_utils) apply_hann_window() (in module dfttoolkit.utils.math_utils) average_with() (dfttoolkit.geometry.Geometry method)

B

BaseParser (class in dfttoolkit.base_parser)

benchmark_dirs (dfttoolkit.benchmarking.BenchmarkAims attribute) BenchmarkAims (class in dfttoolkit.benchmarking)

C

center_coordinates() (dfttoolkit.geometry.Geometry method) check_exit_normal() (dfttoolkit.output.AimsOutput method) check_required_files() (in module dfttoolkit.utils.file_utils) check_spin_polarised() (dfttoolkit.output.AimsOutput method) check_symmetry() (dfttoolkit.geometry.Geometry method)

convergence() (dfttoolkit.visualise.VisualiseAims method), [1] crop() (dfttoolkit.geometry.Geometry method) crop_inverse() (dfttoolkit.geometry.Geometry method) crop_to_unit_cell() (dfttoolkit.geometry.Geometry method) CustomAims (class in dfttoolkit.custom_ase)

D

dfttoolkit module dfttoolkit.base_parser module dfttoolkit.benchmarking module dfttoolkit.custom_ase module dfttoolkit.geometry module dfttoolkit.output module dfttoolkit.parameters module dfttoolkit.utils module dfttoolkit.utils.file_crawler module

dfttoolkit.utils.file_utils module dfttoolkit.utils.geometry_utils module dfttoolkit.utils.math_utils module dfttoolkit.utils.periodic_table module dfttoolkit.utils.run_utils module dfttoolkit.utils.units module dfttoolkit.utils.vibrations_utils module dfttoolkit.vibrations module dfttoolkit.visualise module displace_atoms() (dfttoolkit.geometry.Geometry method)

E

eigenvalues (dfttoolkit.vibrations.Vibrations property)

eigenvectors (dfttoolkit.vibrations.Vibrations property) ELSIOutput (class in dfttoolkit.output)

F

file_contents (dfttoolkit.base_parser.BaseParser attribute) file_paths (dfttoolkit.base_parser.BaseParser attribute) find_aims_output_file() (in module dfttoolkit.utils.file_crawler) find_all_aims_output_files() (in module dfttoolkit.utils.file_crawler) find_file() (in module dfttoolkit.utils.file_crawler)

find_vasp_output_file() (in module dfttoolkit.utils.file_crawler) free_all_calculate_friction() (dfttoolkit.geometry.Geometry method) free_all_constraints() (dfttoolkit.geometry.Geometry method) free_all_external_forces() (dfttoolkit.geometry.Geometry method) free_homogeneous_field() (dfttoolkit.geometry.Geometry method)

G

gaussian_window() (in module dfttoolkit.utils.math_utils) Geometry (class in dfttoolkit.geometry) get_adsorbate_indices() (dfttoolkit.geometry.Geometry method) get_adsorbates() (dfttoolkit.geometry.Geometry method) get_all_ks_eigenvalues() (dfttoolkit.output.AimsOutput method) get_angle_between_vectors() (in module dfttoolkit.utils.math_utils) get_area() (dfttoolkit.geometry.Geometry method) get_area_in_atom_numbers() (dfttoolkit.geometry.Geometry method) get_as_ase() (dfttoolkit.geometry.Geometry method) get_atom_layers_indices() (dfttoolkit.geometry.Geometry method) get_atom_layers_indices_by_height() (dfttoolkit.geometry.Geometry method) get_atom_type_index() (dfttoolkit.vibrations.Vibrations method) get_atomic_mass() (dfttoolkit.utils.periodic_table.PeriodicTable method) get_atomic_masses() (dfttoolkit.geometry.Geometry method) get_atomic_number() (dfttoolkit.utils.periodic_table.PeriodicTable method) get_atomic_numbers_of_atoms() (dfttoolkit.geometry.Geometry method) get_atoms_by_indices() (dfttoolkit.geometry.Geometry method) get_atoms_by_species() (dfttoolkit.geometry.Geometry method) get_autocorrelation_function_manual_lag() (in module dfttoolkit.utils.math_utils) get_bond_lengths() (dfttoolkit.geometry.Geometry method) get_cartesian_coords() (in module dfttoolkit.utils.math_utils) get_center_of_mass() (dfttoolkit.geometry.Geometry method) get_change_of_forces() (dfttoolkit.output.AimsOutput method) get_change_of_sum_of_eigenvalues() (dfttoolkit.output.AimsOutput method) get_change_of_total_energy() (dfttoolkit.output.AimsOutput method) get_chemical_symbol() (dfttoolkit.utils.periodic_table.PeriodicTable method) get_closest_atoms() (dfttoolkit.geometry.Geometry method) get_colliding_groups() (dfttoolkit.geometry.Geometry method) get_constrained_atoms() (dfttoolkit.geometry.Geometry method) get_convergence_parameters() (dfttoolkit.output.AimsOutput method) get_coupling_matrix() (dfttoolkit.vibrations.Vibrations method) get_covalent_radius() (dfttoolkit.utils.periodic_table.PeriodicTable method) get_cropped_geometry() (dfttoolkit.geometry.Geometry method) get_cropping_indices() (dfttoolkit.geometry.Geometry method) get_cross_correlation_function() (dfttoolkit.vibrations.Vibrations method) (in module dfttoolkit.utils.math_utils) (in module dfttoolkit.utils.vibrations_utils) get_cross_spectrum() (dfttoolkit.vibrations.Vibrations method) (in module dfttoolkit.utils.vibrations_utils) get_cross_spectrum_mem() (in module dfttoolkit.utils.vibrations_utils) get_cx_potential_correction() (dfttoolkit.output.AimsOutput method) get_density_embedding_energy() (dfttoolkit.output.AimsOutput method) get_displaced_atoms() (dfttoolkit.geometry.Geometry method) get_displacements() (dfttoolkit.vibrations.Vibrations method) get_distance_between_all_atoms() (dfttoolkit.geometry.Geometry method) get_distance_between_two_atoms() (dfttoolkit.geometry.Geometry method) get_distance_to_equivalent_atoms() (dfttoolkit.geometry.Geometry method) get_eigenvalues_and_eigenvectors() (dfttoolkit.vibrations.Vibrations method) get_eigenvalues_in_Hz() (dfttoolkit.vibrations.Vibrations method) get_eigenvalues_in_inverse_cm() (dfttoolkit.vibrations.Vibrations method) get_electrostatic_energy() (dfttoolkit.output.AimsOutput method) get_element_dict() (dfttoolkit.utils.periodic_table.PeriodicTable method) get_elsi_csc_header() (dfttoolkit.output.ELSIOutput method) get_energy_corrected() (dfttoolkit.output.AimsOutput method) get_energy_uncorrected() (dfttoolkit.output.AimsOutput method) get_energy_without_vdw() (dfttoolkit.output.AimsOutput method) get_entropy_correction() (dfttoolkit.output.AimsOutput method) get_exchange_correlation_energy() (dfttoolkit.output.AimsOutput method) get_external_embedding_energy() (dfttoolkit.output.AimsOutput method) get_file_format_from_ending() (in module dfttoolkit.geometry) get_final_energy() (dfttoolkit.output.AimsOutput method) get_final_ks_eigenvalues() (dfttoolkit.output.AimsOutput method) get_forces() (dfttoolkit.output.AimsOutput method) get_fourier_transform() (in module dfttoolkit.utils.math_utils) get_fractional_coords() (dfttoolkit.geometry.Geometry method) (in module dfttoolkit.utils.math_utils) get_fractional_lattice_vectors() (dfttoolkit.geometry.Geometry method) get_free_atom_electrostatic_energy() (dfttoolkit.output.AimsOutput method) get_from_ase_atoms_object() (dfttoolkit.geometry.Geometry method) get_geometric_center() (dfttoolkit.geometry.Geometry method) get_geometry() (dfttoolkit.output.AimsOutput method) get_geometry_steps_of_optimisation() (dfttoolkit.output.AimsOutput method) get_hartree_energy_correction() (dfttoolkit.output.AimsOutput method)

get_hessian() (dfttoolkit.vibrations.Vibrations method) get_HOMO_energy() (dfttoolkit.output.AimsOutput method) get_homogeneous_field() (dfttoolkit.geometry.Geometry method) get_i_scf_conv_acc() (dfttoolkit.output.AimsOutput method) get_indices_of_all_atoms() (dfttoolkit.geometry.Geometry method) get_indices_of_metal() (dfttoolkit.geometry.Geometry method) get_indices_of_molecules() (dfttoolkit.geometry.Geometry method) get_indices_of_species() (dfttoolkit.geometry.Geometry method) get_instance_of_other_type() (dfttoolkit.geometry.Geometry method) (dfttoolkit.vibrations.Vibrations method) get_ionic_embedding_energy() (dfttoolkit.output.AimsOutput method) get_is_periodic() (dfttoolkit.geometry.Geometry method) get_keywords() (dfttoolkit.parameters.AimsControl method) get_kinetic_energy() (dfttoolkit.output.AimsOutput method) get_largest_atom_distance() (dfttoolkit.geometry.Geometry method) get_last_maximum() (in module dfttoolkit.utils.vibrations_utils) get_layers() (dfttoolkit.geometry.Geometry method) get_line_widths() (in module dfttoolkit.utils.vibrations_utils) get_list_of_neighbouring_atoms() (dfttoolkit.geometry.Geometry method) get_LUMO_energy() (dfttoolkit.output.AimsOutput method) get_main_axes() (dfttoolkit.geometry.Geometry method) get_mass_tensor() (dfttoolkit.vibrations.Vibrations method) get_maximum_force() (dfttoolkit.output.AimsOutput method) get_mirror_matrix() (in module dfttoolkit.utils.math_utils) get_moving_average() (in module dfttoolkit.utils.math_utils) get_n_initial_ks_states() (dfttoolkit.output.AimsOutput method) get_n_relaxation_steps() (dfttoolkit.output.AimsOutput method) get_n_scf_iters() (dfttoolkit.output.AimsOutput method) get_nonlocal_embedding_energy() (dfttoolkit.output.AimsOutput method) get_normal_mode_decomposition() (dfttoolkit.vibrations.Vibrations method) (in module dfttoolkit.utils.vibrations_utils) get_number_of_atom_layers() (dfttoolkit.geometry.Geometry method) get_number_of_atoms() (dfttoolkit.output.AimsOutput method) get_number_of_electrons() (dfttoolkit.geometry.Geometry method) get_orientation_of_main_axis() (dfttoolkit.geometry.Geometry method) get_parameters() (dfttoolkit.output.AimsOutput method) get_peak_parameters() (in module dfttoolkit.utils.vibrations_utils) get_periodic_replica() (dfttoolkit.geometry.Geometry method) get_pert_soc_ks_eigenvalues() (dfttoolkit.output.AimsOutput method) get_primitive_slab() (dfttoolkit.geometry.Geometry method) get_principal_moments_of_inertia() (dfttoolkit.geometry.Geometry method) get_reassembled_molecule() (dfttoolkit.geometry.Geometry method) get_reciprocal_lattice_vectors() (dfttoolkit.geometry.Geometry method) get_rotation_matrix() (in module dfttoolkit.utils.math_utils) get_rotation_matrix_around_axis() (in module dfttoolkit.utils.math_utils) get_rotation_matrix_around_z_axis() (in module dfttoolkit.utils.math_utils) get_scaled_copy() (dfttoolkit.geometry.Geometry method) get_slab() (dfttoolkit.geometry.Geometry method) get_species_colors() (dfttoolkit.utils.periodic_table.PeriodicTable method) get_spglib_cell() (dfttoolkit.geometry.Geometry method) get_split_into_molecules() (dfttoolkit.geometry.Geometry method) get_substrate() (dfttoolkit.geometry.Geometry method) get_substrate_indices() (dfttoolkit.geometry.Geometry method) get_substrate_indices_from_parts() (dfttoolkit.geometry.Geometry method) get_substrate_layers() (dfttoolkit.geometry.Geometry method) get_sum_of_eigenvalues() (dfttoolkit.output.AimsOutput method) get_symmetries() (dfttoolkit.geometry.Geometry method) get_symmetrized_hessian() (dfttoolkit.vibrations.Vibrations method) get_text() (dfttoolkit.geometry.AimsGeometry method) (dfttoolkit.geometry.Geometry method) (dfttoolkit.geometry.VaspGeometry method) (dfttoolkit.geometry.XSFGeometry method) (dfttoolkit.geometry.XYZGeometry method) get_time_per_scf() (dfttoolkit.output.AimsOutput method) get_timings_per_benchmark() (dfttoolkit.benchmarking.BenchmarkAims method) get_total_energy_T0() (dfttoolkit.output.AimsOutput method) get_total_mass() (dfttoolkit.geometry.Geometry method) get_transformation_indices() (dfttoolkit.geometry.Geometry method) get_unconstrained_atoms() (dfttoolkit.geometry.Geometry method) get_unit_cell_parameters() (dfttoolkit.geometry.Geometry method) get_vdw_energy() (dfttoolkit.output.AimsOutput method) get_velocity_mass_average() (dfttoolkit.vibrations.Vibrations method) get_volume_of_unit_cell() (dfttoolkit.geometry.Geometry method)

H

hann_window() (in module dfttoolkit.utils.math_utils)

hessian (dfttoolkit.vibrations.Vibrations property)

I

is_equivalent() (dfttoolkit.geometry.Geometry method)

is_equivalent_up_to_translation() (dfttoolkit.geometry.Geometry method)

L

lines (dfttoolkit.base_parser.BaseParser property) (dfttoolkit.output.AimsOutput attribute) (dfttoolkit.output.ELSIOutput attribute) (dfttoolkit.parameters.AimsControl attribute)

load() (dfttoolkit.utils.periodic_table.PeriodicTable method) lorentzian() (in module dfttoolkit.utils.math_utils) lorentzian_fit() (in module dfttoolkit.utils.vibrations_utils)

M

mae() (in module dfttoolkit.utils.math_utils) map_center_of_atoms_to_first_unit_cell() (dfttoolkit.geometry.Geometry method) map_to_first_unit_cell() (dfttoolkit.geometry.Geometry method) mirror_through_plane() (dfttoolkit.geometry.Geometry method) module dfttoolkit dfttoolkit.base_parser dfttoolkit.benchmarking dfttoolkit.custom_ase dfttoolkit.geometry dfttoolkit.output dfttoolkit.parameters dfttoolkit.utils dfttoolkit.utils.file_crawler dfttoolkit.utils.file_utils dfttoolkit.utils.geometry_utils dfttoolkit.utils.math_utils dfttoolkit.utils.periodic_table dfttoolkit.utils.run_utils dfttoolkit.utils.units dfttoolkit.utils.vibrations_utils dfttoolkit.vibrations dfttoolkit.visualise

move_adsorbates() (dfttoolkit.geometry.Geometry method) move_all_atoms() (dfttoolkit.geometry.Geometry method) move_all_atoms_by_fractional_coords() (dfttoolkit.geometry.Geometry method) move_multipoles() (dfttoolkit.geometry.Geometry method)

N

n_basis (dfttoolkit.output.ELSIOutput attribute) (dfttoolkit.output.ELSIOutput property) n_non_zero (dfttoolkit.output.ELSIOutput attribute) (dfttoolkit.output.ELSIOutput property)

no_repeat() (in module dfttoolkit.utils.run_utils) norm_matrix_by_dagonal() (in module dfttoolkit.utils.math_utils)

O

Output (class in dfttoolkit.output)

output_cross_spectrum() (dfttoolkit.vibrations.Vibrations method)

P

Parameters (class in dfttoolkit.parameters) parse() (dfttoolkit.geometry.AimsGeometry method) (dfttoolkit.geometry.Geometry method) (dfttoolkit.geometry.VaspGeometry method) (dfttoolkit.geometry.XYZGeometry method)

path (dfttoolkit.base_parser.BaseParser property) (dfttoolkit.output.AimsOutput attribute) (dfttoolkit.parameters.AimsControl attribute) PeriodicTable (class in dfttoolkit.utils.periodic_table) project_onto_wave_vector() (dfttoolkit.vibrations.Vibrations method)

R

read_elsi_as_csc() (dfttoolkit.output.ELSIOutput method) read_from_file() (dfttoolkit.geometry.Geometry method) read_xyz_animation() (in module dfttoolkit.utils.geometry_utils) rel_mae() (in module dfttoolkit.utils.math_utils) rel_rmse() (in module dfttoolkit.utils.math_utils) remove_adsorbates() (dfttoolkit.geometry.Geometry method) remove_atoms() (dfttoolkit.geometry.Geometry method) remove_atoms_by_species() (dfttoolkit.geometry.Geometry method) remove_collisions() (dfttoolkit.geometry.Geometry method) remove_constrained_atoms() (dfttoolkit.geometry.Geometry method)

remove_keywords() (dfttoolkit.parameters.AimsControl method) remove_metal_atoms() (dfttoolkit.geometry.Geometry method) remove_non_metallic_atoms() (dfttoolkit.geometry.Geometry method) remove_periodicity() (dfttoolkit.geometry.Geometry method) remove_substrate() (dfttoolkit.geometry.Geometry method) remove_unconstrained_atoms() (dfttoolkit.geometry.Geometry method) reorder_atoms() (dfttoolkit.geometry.Geometry method) rmse() (in module dfttoolkit.utils.math_utils) rotate_coords_around_axis() (dfttoolkit.geometry.Geometry method) rotate_lattice_around_axis() (dfttoolkit.geometry.Geometry method)

S

save_to_file() (dfttoolkit.geometry.Geometry method) scf_conv_acc_params (dfttoolkit.visualise.VisualiseAims attribute) set_calculate_friction() (dfttoolkit.geometry.Geometry method) set_constraints() (dfttoolkit.geometry.Geometry method) set_constraints_based_on_space() (dfttoolkit.geometry.Geometry method) set_external_forces() (dfttoolkit.geometry.Geometry method) set_homogeneous_field() (dfttoolkit.geometry.Geometry method) set_multipoles_charge() (dfttoolkit.geometry.Geometry method)

set_vacuum_height() (dfttoolkit.geometry.Geometry method) set_vacuum_level() (dfttoolkit.geometry.Geometry method) shift_to_bottom() (dfttoolkit.geometry.Geometry method) supported_files (dfttoolkit.output.Output attribute) (dfttoolkit.output.Output property) (dfttoolkit.parameters.Parameters property) swap_lattice_vectors() (dfttoolkit.geometry.Geometry method) symmetrize() (dfttoolkit.geometry.Geometry method)

T

transform() (dfttoolkit.geometry.Geometry method) transform_fractional() (dfttoolkit.geometry.Geometry method)

transform_lattice() (dfttoolkit.geometry.Geometry method) transform_lattice_fractional() (dfttoolkit.geometry.Geometry method) truncate() (dfttoolkit.geometry.Geometry method)

V

VaspGeometry (class in dfttoolkit.geometry) VaspVibrations (class in dfttoolkit.vibrations) vibration_coords (dfttoolkit.vibrations.Vibrations property)

vibration_forces (dfttoolkit.vibrations.Vibrations property) Vibrations (class in dfttoolkit.vibrations) visualise() (dfttoolkit.geometry.Geometry method) VisualiseAims (class in dfttoolkit.visualise)

W

write_input() (dfttoolkit.custom_ase.CustomAims method)

X

XSFGeometry (class in dfttoolkit.geometry)

XYZGeometry (class in dfttoolkit.geometry)