Index

A

analyse_all_angles() (in module carmm.analyse.angles) analyse_all_bonds() (in module carmm.analyse.bonds) analyse_angles() (in module carmm.analyse.angles) analyse_bonds() (in module carmm.analyse.bonds)

analyse_chelation() (in module carmm.analyse.bonds) Atom (class in carmm.analyse.mulliken) atom_mesh_build_mask() (in module carmm.analyse.meshgrid.meshgrid_functions) average_distribution_function() (in module carmm.analyse.distribution_functions)

B

bulk_identifier() (in module carmm.build.slab_consistent_bulk_generator)

C

calculate_energy_ghost_compatible() (in module carmm.analyse.counterpoise_onepot) calculate_formula() (in module carmm.analyse.molecules) calculate_molecules() (in module carmm.analyse.molecules) carmm module carmm.analyse module carmm.analyse.angles module carmm.analyse.bonds module carmm.analyse.colormaps module carmm.analyse.counterpoise_onepot module carmm.analyse.distribution_functions module carmm.analyse.forces module carmm.analyse.graphs module carmm.analyse.hirshfeld module carmm.analyse.images module carmm.analyse.meshgrid module carmm.analyse.meshgrid.meshgrid_functions module carmm.analyse.meshgrid.meshgrid_mesh module carmm.analyse.meshgrid.meshgrid_void module carmm.analyse.molecules module carmm.analyse.mulliken module carmm.analyse.neighbours module carmm.analyse.pickle_dos module carmm.analyse.planes module

carmm.analyse.surface_area module carmm.build module carmm.build.adsorbate_placer module carmm.build.adsorbate_placer_gui module carmm.build.cutout module carmm.build.facets module carmm.build.neb module carmm.build.neb.bond_length_scan module carmm.build.neb.ilm module carmm.build.neb.indices module carmm.build.neb.interpolation module carmm.build.neb.symmetry module carmm.build.neb.WIP_neb_preselection module carmm.build.slab_consistent_bulk_generator module carmm.run module carmm.run.aims_calculator module carmm.run.aims_path module check_and_convert_id() (in module carmm.analyse.counterpoise_onepot) check_interpolation() (in module carmm.build.neb.interpolation) color_bar() (in module carmm.analyse.colormaps) compare_structures() (in module carmm.analyse.bonds) comparing_bonds_lengths() (in module carmm.analyse.bonds) counterpoise_calc() (in module carmm.analyse.counterpoise_onepot) cutout_sphere() (in module carmm.build.cutout)

D

dissociation() (in module carmm.build.neb.bond_length_scan) distance_between_centers_of_mass() (in module carmm.analyse.planes)

distance_meshgrid2point() (in module carmm.analyse.meshgrid.meshgrid_functions) distance_point2point() (in module carmm.analyse.meshgrid.meshgrid_functions)

E

element_radial_distribution_function() (in module carmm.analyse.distribution_functions) establish_planes() (in module carmm.analyse.planes)

extract_hirshfeld() (in module carmm.analyse.hirshfeld) extract_mulliken_charge() (in module carmm.analyse.mulliken) extract_mulliken_spin() (in module carmm.analyse.mulliken)

F

find_adsorbate_normal() (carmm.build.adsorbate_placer.RotationBox method) find_adsorbate_rotation_axes() (carmm.build.adsorbate_placer.RotationBox method)

find_generic_normal() (carmm.build.adsorbate_placer.RotationBox method) find_site_normal() (carmm.build.adsorbate_placer.RotationBox method)

G

gather_info_for_write_input() (in module carmm.analyse.counterpoise_onepot) generate() (in module carmm.build.facets) get_aims_and_sockets_calculator() (in module carmm.run.aims_calculator) get_aims_calculator() (in module carmm.run.aims_calculator) get_all_plot_data() (carmm.analyse.mulliken.MullikenData method) get_close_contacts() (in module carmm.analyse.planes) get_data_integrity() (carmm.analyse.mulliken.MullikenData method) get_energy_dryrun() (in module carmm.analyse.counterpoise_onepot) get_graph_colour() (in module carmm.analyse.graphs) get_graph_linetype() (in module carmm.analyse.graphs) get_graph_xlabel() (carmm.analyse.mulliken.MullikenData method) get_hirshfeld_line() (in module carmm.analyse.hirshfeld)

get_homo() (carmm.analyse.mulliken.MullikenData method) get_indices_of_elements() (in module carmm.analyse.bonds) get_interplane_distances() (in module carmm.analyse.planes) get_k_grid() (in module carmm.run.aims_calculator) get_lattice_constant() (in module carmm.build.neb.symmetry) get_natoms() (carmm.analyse.mulliken.MullikenData method) get_nkpts() (carmm.analyse.mulliken.MullikenData method) get_nspin() (carmm.analyse.mulliken.MullikenData method) get_nstates() (carmm.analyse.mulliken.MullikenData method) get_orbital_plot_data() (carmm.analyse.mulliken.MullikenData method) get_plot_data() (carmm.analyse.mulliken.MullikenData method) get_rotations() (in module carmm.build.adsorbate_placer_gui) get_sorted_distances() (in module carmm.analyse.bonds)

I

is_close_to_integer() (in module carmm.build.slab_consistent_bulk_generator)

is_converged() (in module carmm.analyse.forces)

K

Kpt (class in carmm.analyse.mulliken)

L

load_xyz_data_from_csv() (in module carmm.analyse.graphs)

M

main_ase_gui() (in module carmm.build.adsorbate_placer_gui) Mesh (class in carmm.analyse.meshgrid.meshgrid_mesh) midpoint_points() (in module carmm.analyse.meshgrid.meshgrid_functions) mirror() (in module carmm.build.neb.symmetry) module carmm carmm.analyse carmm.analyse.angles carmm.analyse.bonds carmm.analyse.colormaps carmm.analyse.counterpoise_onepot carmm.analyse.distribution_functions carmm.analyse.forces carmm.analyse.graphs carmm.analyse.hirshfeld carmm.analyse.images carmm.analyse.meshgrid carmm.analyse.meshgrid.meshgrid_functions carmm.analyse.meshgrid.meshgrid_mesh carmm.analyse.meshgrid.meshgrid_void carmm.analyse.molecules carmm.analyse.mulliken carmm.analyse.neighbours carmm.analyse.pickle_dos carmm.analyse.planes carmm.analyse.surface_area carmm.build carmm.build.adsorbate_placer carmm.build.adsorbate_placer_gui carmm.build.cutout carmm.build.facets carmm.build.neb carmm.build.neb.bond_length_scan carmm.build.neb.ilm carmm.build.neb.indices carmm.build.neb.interpolation carmm.build.neb.symmetry carmm.build.neb.WIP_neb_preselection carmm.build.slab_consistent_bulk_generator carmm.run carmm.run.aims_calculator carmm.run.aims_path

mol_mesh_pbc_check() (in module carmm.analyse.meshgrid.meshgrid_functions) MullikenData (class in carmm.analyse.mulliken) multiple_local_extrema() (in module carmm.build.neb.ilm)

N

neb_identify_local_minima() (in module carmm.build.neb.ilm) neighbour_cutout_sphere() (in module carmm.analyse.neighbours)

neighbours() (in module carmm.analyse.neighbours) normal_rotation_matrix() (carmm.build.adsorbate_placer.RotationBox method)

P

parse_mulliken_file() (in module carmm.analyse.mulliken) place_adsorbate() (carmm.build.adsorbate_placer.RotationBox method) plane_of_best_fit() (in module carmm.analyse.planes) plot_distribution_function() (in module carmm.analyse.distribution_functions)

plot_energy_profile() (in module carmm.analyse.graphs) print_angles_table_header() (in module carmm.analyse.angles) print_bond_table_header() (in module carmm.analyse.bonds) print_position() (in module carmm.build.adsorbate_placer_gui)

R

radial_distribution_function() (in module carmm.analyse.distribution_functions) radius_of_gyration() (in module carmm.analyse.distribution_functions) read_cube_file() (carmm.analyse.meshgrid.meshgrid_mesh.Mesh method) read_dos_from_old_pickle() (in module carmm.analyse.pickle_dos) read_hirshfeld() (in module carmm.analyse.hirshfeld)

rotate() (carmm.build.adsorbate_placer.RotationBox method) rotate_ads2site_vec() (carmm.build.adsorbate_placer.RotationBox method) rotate_and_place_adsorbate() (carmm.build.adsorbate_placer.RotationBox method) rotate_fcc() (in module carmm.build.neb.symmetry) RotationBox (class in carmm.build.adsorbate_placer) rotationbox_gui() (in module carmm.build.adsorbate_placer_gui)

S

search_abnormal_bonds() (in module carmm.analyse.bonds) set_aims_command() (in module carmm.run.aims_path) set_graph_axes_heatmap() (in module carmm.analyse.graphs) set_graph_axes_mulliken() (in module carmm.analyse.graphs) sort_by_symbols() (in module carmm.build.neb.indices) sort_by_xyz() (in module carmm.build.neb.symmetry)

sort_z() (in module carmm.build.neb.symmetry) Spin (class in carmm.analyse.mulliken) start_ase_gui() (in module carmm.build.adsorbate_placer_gui) surface_area() (in module carmm.analyse.surface_area) surface_coordination() (in module carmm.analyse.neighbours) switch_all_indices() (in module carmm.build.neb.indices) switch_indices() (in module carmm.build.neb.indices)

T

translation() (in module carmm.build.neb.symmetry)

transpose() (in module carmm.build.cutout)

V

vmd_out() (in module carmm.analyse.hirshfeld) void_analysis() (in module carmm.analyse.meshgrid.meshgrid_void)

void_build_mask() (in module carmm.analyse.meshgrid.meshgrid_void) void_find() (in module carmm.analyse.meshgrid.meshgrid_void)

W

wrap_fcc() (in module carmm.build.neb.symmetry) write_dos_to_csv() (in module carmm.analyse.mulliken)

write_hirshfeld() (in module carmm.analyse.hirshfeld) write_to_povray() (in module carmm.analyse.images)