Index

_

__contains__() (AKFReader method) __init__() (ChemicalSystem method) (InternalCoordinateManipulationPolicy method)

__iter__() (Bonds method) __len__() (Bonds method) (ChemicalSystem method) __str__() (ChemicalSystem method)

A

add_all_atoms_to_region() (ChemicalSystem method) add_atom() (ChemicalSystem method) add_atom_to_region() (ChemicalSystem method) add_atoms_to_region() (ChemicalSystem method) add_bond() (Bonds method), [1] add_bonds() (Bonds method), [1] add_hydrogen_atoms() (ChemicalSystem method) add_other() (ChemicalSystem method) adf (Atom property) adf_attribs (ChemicalSystem property) AKFReader (class in scm.akfreader) align_to() (ChemicalSystem method) all_from_input() (ChemicalSystem static method) amsprep module amsreport module any_bond_between() (Bonds method), [1]

apply_strain() (ChemicalSystem method) apply_strain_voigt() (ChemicalSystem method) Atom (class in scm.base) atom_attributes_enabled() (ChemicalSystem method) atom_EOL_string() (ChemicalSystem method) atom_index() (ChemicalSystem method) atom_is_in_ring() (ChemicalSystem method) AtomAttributesADF (class in base) AtomAttributesBAND (class in base) AtomAttributesDFTB (class in base) AtomAttributesForcefield (class in base) AtomAttributesGUI (class in base) AtomAttributesQE (class in base) AtomAttributesReaxFF (class in base) AtomAttributesVASP (class in base) atoms (ChemicalSystem property) atoms_are_bonded() (Bonds method), [1]

B

band (Atom property) band_attribs (ChemicalSystem property) Bond (class in base) (class in scm.base) bond_cuts_molecule() (ChemicalSystem method) bond_guess_connectors (Element property)

bond_guess_electro_negative (Element property) bond_guess_metallic (Element property) bond_index (Bonds property), [1] bonds (Bonds property), [1] (ChemicalSystem property) Bonds (class in scm.base) bounding_box_volume() (ChemicalSystem method)

C

cartesian_to_fractional() (Lattice method) center_of_mass() (ChemicalSystem method) charge (AtomAttributesForcefield property) (AtomAttributesReaxFF property) (ChemicalSystem property) check_molecule_symmetry() (ChemicalSystem method) ChemicalSystem (class in scm.base) ChgU (AtomAttributesADF property) clear() (AtomAttributesADF method) (AtomAttributesBAND method) (AtomAttributesDFTB method) (AtomAttributesForcefield method) (AtomAttributesGUI method) (AtomAttributesQE method) (AtomAttributesReaxFF method) (AtomAttributesVASP method) clear_bonds() (Bonds method), [1] (ChemicalSystem method) close() (KFFile method) close_var() (KFFile method) color (AtomAttributesGUI property) (Element property)

column_index (Bonds property), [1] contains_atom() (ChemicalSystem method) conversion_factor() (Units class method) coords (Atom property) (ChemicalSystem property) copy() (Atom method) (AtomAttributesADF method) (AtomAttributesBAND method) (AtomAttributesDFTB method) (AtomAttributesForcefield method) (AtomAttributesGUI method) (AtomAttributesQE method) (AtomAttributesReaxFF method) (AtomAttributesVASP method) (Bond method) (Bonds method) (ChemicalSystem method) (Lattice method) copy_section() (KFFile method) cpkf module create_section() (KFFile method) create_var() (KFFile method)

D

delete_file() (KFFile class method) delete_section() (KFFile method) delete_var() (KFFile method) density() (ChemicalSystem method) description() (AKFReader method) deselect_all() (ChemicalSystem method) deselect_atom() (ChemicalSystem method) deselect_atoms() (ChemicalSystem method)

deselect_atoms_if() (ChemicalSystem method) determine_species() (ChemicalSystem method) dftb (Atom property) dftb_attribs (ChemicalSystem property) disable_atom_attributes() (ChemicalSystem method) distance_matrix() (ChemicalSystem method) dmpkf module do_regions_intersect() (ChemicalSystem method)

E

electrostatic_embedding (ChemicalSystem property) element (Atom property) Element (class in scm.base) Elements (class in scm.base) empty() (AtomAttributesADF method) (AtomAttributesBAND method) (AtomAttributesDFTB method) (AtomAttributesForcefield method) (AtomAttributesGUI method) (AtomAttributesQE method) (AtomAttributesReaxFF method) (AtomAttributesVASP method)

enable_atom_attributes() (ChemicalSystem method) EpsU (AtomAttributesADF property) extract_atoms() (ChemicalSystem method)

F

f (AtomAttributesADF property) fg (AtomAttributesADF property) filename (KFFile property) forcefield (Atom property) forcefield_attribs (ChemicalSystem property) formula() (ChemicalSystem method) fractional_to_cartesian() (Lattice method) from_atomic_number() (Elements static method) from_in() (ChemicalSystem static method) from_input() (ChemicalSystem static method)

from_kf() (Bonds class method) (Bonds static method) (ChemicalSystem static method) (Lattice static method) from_list() (Bonds class method) (Bonds static method) from_sparse() (Bonds class method) (Bonds static method) from_symbol() (Elements static method) from_xyz() (ChemicalSystem static method) fs (AtomAttributesADF property)

G

geometric_center() (ChemicalSystem method) get() (InputFile method) get_3x3_lattice_vectors() (Lattice method) get_angle() (ChemicalSystem method) get_angles() (Lattice method) get_atomic_valencies() (Bonds method), [1] get_atoms_in_region() (ChemicalSystem method) get_atoms_outside_region() (ChemicalSystem method) get_bond_index() (Bonds method), [1] get_bonded_atoms() (Bonds method), [1] get_bonds_between_atoms() (Bonds method), [1] get_bonds_for_atom() (Bonds method), [1] get_canonical_name() (Units class method) get_category() (InputFile method) get_cell_depth() (Lattice method) get_dihedral() (ChemicalSystem method) get_distance() (ChemicalSystem method) get_distances_to_point() (ChemicalSystem method) get_entries_in_order() (InputFile method) get_fractional_coordinate() (ChemicalSystem method) get_fractional_coordinates() (ChemicalSystem method) get_freeblock() (InputFile method) get_header() (InputFile method)

get_int() (InputFile method) get_int_list() (InputFile method) get_inverted() (Bond method), [1] get_json() (InputFile method) get_label() (Units class method) get_lattice_translation() (Lattice method) get_lengths() (Lattice method) get_logical() (InputFile method) get_operands_in_region_expression() (ChemicalSystem static method) get_quantities() (Units class method) get_real() (InputFile method) get_real_list() (InputFile method) get_reciprocal_lattice_vectors() (Lattice method) get_regions_of_atom() (ChemicalSystem method) get_selected_atoms() (ChemicalSystem method) get_skeleton() (KFFile method) get_species() (ChemicalSystem method) get_string() (InputFile method) get_type() (InputFile method) get_units() (Units class method) get_volume() (Lattice method) guess_bonds() (ChemicalSystem method) gui (Atom property) gui_attribs (ChemicalSystem property)

H

has_bonds() (ChemicalSystem method) has_ghost_atoms() (ChemicalSystem method) has_identical_attributes() (Atom method) has_lattice() (ChemicalSystem method) has_region() (ChemicalSystem method)

has_same_atoms() (ChemicalSystem method) has_same_coords() (ChemicalSystem method) has_same_geometry() (ChemicalSystem method) has_same_regions() (ChemicalSystem method) has_same_selection() (ChemicalSystem method)

I

imol (AtomAttributesADF property) in_chemicalsystem() (Atom method) inertia_tensor() (ChemicalSystem method) InputError (class in base) InputFile (class in base) InputFile.EntryCategory (class in base) InputFile.EntryType (class in base) InternalCoordinateManipulationPolicy (class in scm.base.ChemicalSystem) invert_selection() (ChemicalSystem method) is_atom_in_region() (ChemicalSystem method) is_atom_outside_region() (ChemicalSystem method)

is_atom_selected() (ChemicalSystem method) is_close() (Lattice method) is_defined() (InputFile method) is_ghost (Atom property) is_kffile() (KFFile class method) is_linear() (ChemicalSystem method) is_ordered() (InputFile method) is_orthogonal() (Lattice method) is_present() (InputFile method) is_unique() (InputFile method) is_valid_region_name() (ChemicalSystem static method)

K

KF command line utilities KFError (class in base) KFFile (class in base)

KFFile.OpenMode (class in base) KFFile.StringSep (class in base) KFFile.VarType (class in base)

L

label (AtomAttributesQE property) (AtomAttributesVASP property) lattice (ChemicalSystem property)

Lattice (class in scm.base) lattice_displacements (Bond property), [1] lone_pairs (Element property)

M

make_conventional_cell() (ChemicalSystem method) make_primitive_cell() (ChemicalSystem method) make_selection_cappable() (ChemicalSystem method) make_slab_layers() (ChemicalSystem method) make_slab_thickness() (ChemicalSystem method) make_supercell() (ChemicalSystem method) make_supercell_trafo() (ChemicalSystem method) map_atoms() (ChemicalSystem method) map_atoms_around_atom() (ChemicalSystem method) map_atoms_continuous() (ChemicalSystem method)

map_vector_to_central_cell() (Lattice method) map_vectors_to_central_cell() (Lattice method) mass (Atom property) (Element property) molecule_indices() (ChemicalSystem method) molgraph_dijkstra() (ChemicalSystem method) moments_of_inertia() (ChemicalSystem method) moving_atoms_for_angle_change() (ChemicalSystem method) moving_atoms_for_dihedral_change() (ChemicalSystem method) moving_atoms_for_distance_change() (ChemicalSystem method)

N

name (InternalCoordinateManipulationPolicy property) nuclear_charge (AtomAttributesADF property) (AtomAttributesBAND property) num_atoms (Bonds property), [1] (ChemicalSystem property) num_atoms_in_region() (ChemicalSystem method) num_atoms_outside_region() (ChemicalSystem method) num_bonds() (Bonds method), [1]

num_lattice_vectors (Bonds property), [1] num_molecules() (ChemicalSystem method) num_regions (ChemicalSystem property) num_sections() (KFFile method) num_selected_atoms() (ChemicalSystem method) num_variables() (KFFile method) num_vectors (Lattice property) number_of_entries() (InputFile method)

O

open_var() (KFFile method)

order (Bond property), [1]

P

path (KFFile property) perturb_coordinates() (ChemicalSystem method)

perturb_lattice() (ChemicalSystem method) pkf module program (InputFile property)

Q

qe (Atom property)

qe_attribs (ChemicalSystem property)

R

R (AtomAttributesADF property) radius (AtomAttributesGUI property) (Element property) read() (AKFReader method) (InputFile method) (KFFile method) read_int() (KFFile method) read_ints() (KFFile method) read_ints_np() (KFFile method) read_logical() (KFFile method) read_logicals() (KFFile method) read_logicals_np() (KFFile method) read_real() (KFFile method) read_reals() (KFFile method) read_reals_np() (KFFile method) read_section() (KFFile method) read_string() (KFFile method) read_strings() (KFFile method) reaxff (Atom property) reaxff_attribs (ChemicalSystem property)

region_names (ChemicalSystem property) remove_all_regions() (ChemicalSystem method) remove_atom() (ChemicalSystem method) remove_atom_from_all_regions() (ChemicalSystem method) remove_atom_from_region() (ChemicalSystem method) remove_atoms() (ChemicalSystem method) remove_atoms_from_region() (ChemicalSystem method) remove_bond() (Bonds method), [1] remove_bonds() (Bonds method), [1] remove_bonds_between_atoms() (Bonds method), [1] remove_bonds_to_atom() (Bonds method), [1] remove_bonds_to_atoms() (Bonds method), [1] remove_region() (ChemicalSystem method) reorder_atoms() (ChemicalSystem method) rewind_var() (KFFile method) rmsd() (ChemicalSystem static method) rotate() (ChemicalSystem method) rotation_axis_for_angle_change() (ChemicalSystem method) rotation_matrix_minimizing_rmsd() (ChemicalSystem static method) row_offset (Bonds property), [1]

S

save() (KFFile method) section_exists() (KFFile method) sections() (AKFReader method) (KFFile method) select_all() (ChemicalSystem method) select_atom() (ChemicalSystem method) select_atom_close_to_origin() (ChemicalSystem method) select_atoms() (ChemicalSystem method) select_atoms_if() (ChemicalSystem method) select_atoms_of_same_type() (ChemicalSystem method) select_connected() (ChemicalSystem method) select_connected_if() (ChemicalSystem method) select_molecule() (ChemicalSystem method) select_molecule_if() (ChemicalSystem method) select_region() (ChemicalSystem method) select_within_radius() (ChemicalSystem method) set_angle() (ChemicalSystem method) set_atom() (ChemicalSystem method) set_atoms_in_region() (ChemicalSystem method) set_density() (ChemicalSystem method) set_dihedral() (ChemicalSystem method)

set_distance() (ChemicalSystem method) set_fractional_coordinates() (ChemicalSystem method) set_lattice_displacements_from_minimum_image_convention() (ChemicalSystem method) set_num_lattice_vectors() (ChemicalSystem method) set_selected_atoms() (ChemicalSystem method) shortest_path_between() (ChemicalSystem method) shortest_path_length_between() (ChemicalSystem method) shortest_path_lengths_from() (ChemicalSystem method) SigU (AtomAttributesADF property) skip_var() (KFFile method) sort_atoms() (ChemicalSystem method) sorted_atom_order() (ChemicalSystem method) split() (ChemicalSystem method) split_into_molecules() (ChemicalSystem method) squared_distance_matrix() (ChemicalSystem method) str_description() (AKFReader method) symbol (Atom property) (Element property) symmetrize() (ChemicalSystem method) symmetrize_cell() (ChemicalSystem method) symmetrize_molecule() (ChemicalSystem method) symmetrize_molecule_to() (ChemicalSystem method)

T

table_of_content() (AKFReader method) total_mass() (ChemicalSystem method) translate() (ChemicalSystem method)

transmute() (Atom method) type (AtomAttributesADF property) (AtomAttributesForcefield property)

U

udmpkf module Units (class in base)

units() (AKFReader method) units_summary_string() (Units class method) UnitsError (class in base)

V

var_exists() (KFFile method) var_length() (KFFile method) var_type() (KFFile method) var_used() (KFFile method) variables() (AKFReader method) (KFFile method)

variables_in_section() (AKFReader method) vasp (Atom property) vasp_attribs (ChemicalSystem property) vectors (Lattice property) Vext (AtomAttributesDFTB property)

W

write() (KFFile method) write_in() (ChemicalSystem method) write_kf() (Bonds method), [1] (ChemicalSystem method) (Lattice method)

write_xyz() (ChemicalSystem method)

X

x (AtomAttributesADF property)

Z

Z (Atom property)

z (AtomAttributesADF property) Z (Element property)