Index

A

alloy (geom.classes.input_class.input_class attribute) alloy_perc (geom.classes.input_class.input_class attribute) alloy_string (geom.classes.input_class.input_class attribute) angle (geom.classes.input_class.input_class attribute) angles (geom.classes.input_class.input_class attribute) angles_input (geom.classes.input_class.input_class attribute) atomic_arrangement (geom.classes.parameters.parameters attribute), [1]

atoms (geom.classes.molecule.molecule attribute), [1] atomtype (geom.classes.input_class.input_class attribute) atomtype_in (geom.classes.input_class.input_class attribute) atomtype_out (geom.classes.input_class.input_class attribute) atomtypes_alloys (geom.classes.input_class.input_class attribute) atomtypes_core_shell (geom.classes.input_class.input_class attribute) axes (geom.classes.input_class.input_class attribute)

C

calc_min_distance() (in module geom.functions.tools) change_atomtype() (geom.classes.molecule.molecule method) change_trans_sense() (geom.classes.input_class.input_class method) check_dir_axis() (in module geom.functions.general) check_FCC() (in module geom.functions.general) check_FCC_or_BCC() (in module geom.functions.general) check_file_exists() (in module geom.functions.general) check_file_extension() (in module geom.functions.general) check_input_case() (geom.classes.input_class.input_class method) compare_mesh_files() (in module geom.tests.test_) cone() (in module geom.functions.create_geom) convergence (geom.classes.parameters.parameters attribute), [1] convergence_step (geom.classes.parameters.parameters attribute), [1] copy_geometry_file() (in module geom.functions.tools)

create_alloy() (geom.classes.molecule.molecule method) create_ase_bulk (geom.classes.input_class.input_class attribute) create_ase_bulk_graphene() (in module geom.functions.create_geom) create_ase_bulk_metal() (in module geom.functions.create_geom) create_bowtie (geom.classes.input_class.input_class attribute) create_bowtie() (in module geom.functions.tools) create_cuboctahedra() (geom.classes.molecule.molecule method) create_decahedra() (geom.classes.molecule.molecule method) create_dimer (geom.classes.input_class.input_class attribute) create_dimer() (in module geom.functions.tools) create_geom (geom.classes.input_class.input_class attribute) create_icosahedra() (geom.classes.molecule.molecule method) create_results_geom() (in module geom.functions.general) cto() (in module geom.functions.create_geom)

D

delete_all_files() (in module geom.functions.tools) delete_geometry_file() (in module geom.functions.tools) determine_sphere_center() (in module geom.functions.tools) dimer_distance (geom.classes.input_class.input_class attribute)

dir_axis_input (geom.classes.input_class.input_class attribute) dir_factor (geom.classes.input_class.input_class attribute) direction (geom.classes.input_class.input_class attribute) distances (geom.classes.input_class.input_class attribute) distances_input (geom.classes.input_class.input_class attribute)

E

elliptic_parabola_a (geom.classes.input_class.input_class attribute) elliptic_parabola_b (geom.classes.input_class.input_class attribute)

elliptic_parabola_c (geom.classes.input_class.input_class attribute) error() (in module geom.functions.output) error_dir_axis() (in module geom.functions.output)

F

file_geom2_translated (geom.classes.input_class.input_class attribute) file_geom_rotated (geom.classes.input_class.input_class attribute) filter_xyz_graphene_to_disk() (geom.classes.molecule.molecule method) filter_xyz_graphene_to_ribbon() (geom.classes.molecule.molecule method) filter_xyz_graphene_to_ring() (geom.classes.molecule.molecule method)

filter_xyz_graphene_to_triangle() (geom.classes.molecule.molecule method) filter_xyz_in_cone() (geom.classes.molecule.molecule method) filter_xyz_in_cylinder() (geom.classes.molecule.molecule method) filter_xyz_in_elliptic_paraboloid() (geom.classes.molecule.molecule method) filter_xyz_in_pyramid() (geom.classes.molecule.molecule method) filter_xyz_in_sphere() (geom.classes.molecule.molecule method)

G

gen_3d_mesh (geom.classes.input_class.input_class attribute) gen_3d_mesh_rod (geom.classes.input_class.input_class attribute) gen_3d_mesh_sphere (geom.classes.input_class.input_class attribute) gen_cone (geom.classes.input_class.input_class attribute) gen_core_shell (geom.classes.input_class.input_class attribute) gen_cto (geom.classes.input_class.input_class attribute) gen_graphene (geom.classes.input_class.input_class attribute) gen_icosahedra (geom.classes.input_class.input_class attribute) gen_idh (geom.classes.input_class.input_class attribute) gen_microscope (geom.classes.input_class.input_class attribute) gen_pyramid (geom.classes.input_class.input_class attribute) gen_rod (geom.classes.input_class.input_class attribute) gen_rod_core_shell (geom.classes.input_class.input_class attribute) gen_sphere (geom.classes.input_class.input_class attribute) gen_sphere_core_shell (geom.classes.input_class.input_class attribute) gen_tip (geom.classes.input_class.input_class attribute) geom module geom.__main__ module geom.classes module geom.classes.input_class module geom.classes.molecule module geom.classes.parameters module geom.functions module

geom.functions.create_geom module geom.functions.general module geom.functions.output module geom.functions.rotate module geom.functions.tools module geom.functions.translate module geom.functions.various module geom.tests module geom.tests.test_ module geom1_file (geom.classes.input_class.input_class attribute) geom2_file (geom.classes.input_class.input_class attribute) geom_center (geom.classes.input_class.input_class attribute) geom_center() (in module geom.functions.various) geom_file (geom.classes.input_class.input_class attribute) geom_specular (geom.classes.input_class.input_class attribute) geom_specular() (in module geom.functions.various) get_layers() (in module geom.functions.create_geom) graphene() (in module geom.functions.create_geom) graphene_edge_type (geom.classes.input_class.input_class attribute) graphene_edge_types (geom.classes.input_class.input_class attribute) graphene_structure (geom.classes.input_class.input_class attribute) graphene_structures (geom.classes.input_class.input_class attribute)

I

icosahedra() (in module geom.functions.create_geom)

idh() (in module geom.functions.create_geom) input_class (class in geom.classes.input_class)

L

lattice_constant (geom.classes.parameters.parameters attribute), [1]

logfile_close() (in module geom.functions.output) logfile_init() (in module geom.functions.output)

M

main() (in module geom.__main__) merge (geom.classes.input_class.input_class attribute) merge_cutoff (geom.classes.input_class.input_class attribute) merge_geoms() (in module geom.functions.tools) (in module geom.functions.various) mesh_output (geom.classes.input_class.input_class attribute) mesh_size (geom.classes.input_class.input_class attribute) metal_atomtypes (geom.classes.parameters.parameters attribute), [1] microscope() (in module geom.functions.create_geom) min_dist (geom.classes.input_class.input_class attribute) (geom.classes.parameters.parameters attribute), [1] min_dist() (in module geom.functions.various) min_dist_translate (geom.classes.parameters.parameters attribute), [1] module geom geom.__main__ geom.classes geom.classes.input_class geom.classes.molecule geom.classes.parameters geom.functions geom.functions.create_geom geom.functions.general geom.functions.output geom.functions.rotate geom.functions.tools geom.functions.translate geom.functions.various geom.tests geom.tests.test_

molecule (class in geom.classes.molecule) move_created_geom() (in module geom.tests.test_) move_geom_1_to_000 (geom.classes.input_class.input_class attribute) move_geom_2_to_000 (geom.classes.input_class.input_class attribute) move_geom_to_000 (geom.classes.input_class.input_class attribute) move_input_geom() (in module geom.tests.test_) move_managed_geom() (in module geom.tests.test_)

N

nAtoms (geom.classes.molecule.molecule attribute), [1]

O

origin_CM (geom.classes.input_class.input_class attribute)

origin_CM_1 (geom.classes.input_class.input_class attribute) origin_CM_2 (geom.classes.input_class.input_class attribute)

P

param (in module geom.functions.translate) parameters (class in geom.classes.parameters) parse_alloy_arguments() (in module geom.functions.general) parse_bowtie_argument() (in module geom.functions.general) parse_center() (in module geom.functions.general) parse_create() (in module geom.functions.general) parse_dimer_argument() (in module geom.functions.general) parse_merge() (in module geom.functions.general) parse_min() (in module geom.functions.general) parse_mirror() (in module geom.functions.general) parse_rotation() (in module geom.functions.general)

parse_translation() (in module geom.functions.general) print_computed_distance() (in module geom.functions.output) print_convergence_achieved() (in module geom.functions.output) print_geom() (in module geom.functions.output) print_geom_center() (in module geom.functions.output) print_help() (in module geom.functions.general) print_min_dist() (in module geom.functions.output) print_normal_termination() (in module geom.functions.output) print_optimization_starts() (in module geom.functions.output) print_optimizing_distance() (in module geom.functions.output) pyramid() (in module geom.functions.create_geom)

R

radius (geom.classes.input_class.input_class attribute) radius_in (geom.classes.input_class.input_class attribute) radius_out (geom.classes.input_class.input_class attribute) read_command_line() (in module geom.functions.general) read_geom() (geom.classes.molecule.molecule method) read_input() (geom.classes.input_class.input_class method) remove_dangling_atoms_metals() (geom.classes.molecule.molecule method) remove_dangling_bonds_graphene() (geom.classes.molecule.molecule method) rod() (in module geom.functions.create_geom) rod_3d_mesh() (in module geom.functions.create_geom) rod_core_shell() (in module geom.functions.create_geom)

rod_length (geom.classes.input_class.input_class attribute) rod_length_in (geom.classes.input_class.input_class attribute) rod_length_out (geom.classes.input_class.input_class attribute) rod_width (geom.classes.input_class.input_class attribute) rod_width_in (geom.classes.input_class.input_class attribute) rod_width_out (geom.classes.input_class.input_class attribute) rotate (geom.classes.input_class.input_class attribute) rotate() (in module geom.functions.tools) rotate_1 (geom.classes.input_class.input_class attribute) rotate_1() (in module geom.functions.rotate) rotate_angles (geom.classes.input_class.input_class attribute) rotate_angles() (in module geom.functions.rotate)

S

save_distance_opt() (in module geom.functions.output) select_case() (in module geom.functions.create_geom) (in module geom.functions.rotate) (in module geom.functions.translate) (in module geom.functions.various) side_length (geom.classes.input_class.input_class attribute)

small_tasks (geom.classes.input_class.input_class attribute) sphere() (in module geom.functions.create_geom) sphere_3d_mesh() (in module geom.functions.create_geom) sphere_center (geom.classes.input_class.input_class attribute) sphere_core_shell() (in module geom.functions.create_geom) subtract_geoms() (in module geom.functions.tools)

T

test_controlled_distance() (in module geom.tests.test_) test_controlled_rotation() (in module geom.tests.test_) test_create_bowtie() (in module geom.tests.test_) test_create_cone() (in module geom.tests.test_) test_create_cuboctahedra() (in module geom.tests.test_) test_create_decahedra() (in module geom.tests.test_) test_create_dimer() (in module geom.tests.test_) test_create_graphene_disk() (in module geom.tests.test_) test_create_graphene_ribbon() (in module geom.tests.test_) test_create_graphene_ring() (in module geom.tests.test_) test_create_graphene_triangle_armchair() (in module geom.tests.test_) test_create_graphene_triangle_zigzag() (in module geom.tests.test_) test_create_icosahedra() (in module geom.tests.test_) test_create_microscope() (in module geom.tests.test_) test_create_pyramid() (in module geom.tests.test_)

test_create_rod() (in module geom.tests.test_) test_create_rod_core_shell() (in module geom.tests.test_) test_create_sphere() (in module geom.tests.test_) test_create_sphere_core_shell() (in module geom.tests.test_) test_create_tip() (in module geom.tests.test_) test_folder_path (in module geom.tests.test_) test_specular_geometry() (in module geom.tests.test_) tip() (in module geom.functions.create_geom) tmp_folder (geom.classes.input_class.input_class attribute) trans_geom_center_to_000() (geom.classes.molecule.molecule method) translate (geom.classes.input_class.input_class attribute) translate_1 (geom.classes.input_class.input_class attribute) translate_1() (in module geom.functions.translate) translate_controlled_distance (geom.classes.input_class.input_class attribute) translate_controlled_distance() (in module geom.functions.translate) translate_geom() (geom.classes.molecule.molecule method)

V

verbose (geom.classes.input_class.input_class attribute)

verbose_inp (geom.classes.input_class.input_class attribute)

X

X_length (geom.classes.input_class.input_class attribute) xyz_center (geom.classes.molecule.molecule attribute), [1]

xyz_max (geom.classes.molecule.molecule attribute), [1] xyz_min (geom.classes.molecule.molecule attribute), [1] xyz_output (geom.classes.input_class.input_class attribute)

Y

Y_length (geom.classes.input_class.input_class attribute)

Z

z_max (geom.classes.input_class.input_class attribute) z_max_paraboloid (geom.classes.input_class.input_class attribute)

z_max_pyramid (geom.classes.input_class.input_class attribute) z_min (geom.classes.input_class.input_class attribute)