Index

_

_conclude() (ectoolkits.analysis.atom_density.AtomDensity method) (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV method) _gen_connectivity() (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV method) _get_candidates_hbonds() (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV method)

_get_proton_transfer_cv() (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV method) _prepare() (ectoolkits.analysis.atom_density.AtomDensity method) (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV method) _single_frame() (ectoolkits.analysis.atom_density.AtomDensity method) (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV method)

A

add_adsorbate() (ectoolkits.structures.slab.Slab method) add_adsorbates() (ectoolkits.structures.slab.Slab method) ag (ectoolkits.analysis.atom_density.AtomDensity attribute) ag_H (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV attribute) ag_O (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV attribute)

align_to_slab_cent() (in module ectoolkits.analysis.band_align) all_z (ectoolkits.analysis.atom_density.AtomDensity attribute) analysis_run() (in module ectoolkits.analysis.atom_density) atom_density (ectoolkits.analysis.atom_density.AtomDensity attribute) atom_density_z (ectoolkits.analysis.atom_density.AtomDensity attribute) AtomDensity (class in ectoolkits.analysis.atom_density)

B

BandAlign (class in ectoolkits.analysis.band_align) be_data_to_she() (in module ectoolkits.plots.band_align)

bin_edges_to_grid() (in module ectoolkits.analysis.water) birch_murnaghan_equation() (in module ectoolkits.utils.math)

C

calc_FES() (in module ectoolkits.analysis.reweight) calc_one_FES_point() (in module ectoolkits.analysis.reweight) calc_one_property_point() (in module ectoolkits.analysis.reweight) calc_property_surface() (in module ectoolkits.analysis.reweight) cell (ectoolkits.analysis.water.WaterOrientation attribute) cellpar (ectoolkits.analysis.atom_density.AtomDensity attribute)

cellpar2volume() (in module ectoolkits.utils.rutile110) cn2disdeg() (ectoolkits.analysis.rutile110.RutileDisDeg static method) compute_bw_silverman() (in module ectoolkits.analysis.reweight) count_cn() (in module ectoolkits.utils.rutile110) count_heavy_atoms() (in module ectoolkits.structures.tools) counter_charge_model() (ectoolkits.analysis.finite_size_correction.UniformCharge static method) create_path() (in module ectoolkits.utils.utils)

D

d_unique_vecs() (in module ectoolkits.utils.rutile110) dAdBridge (class in ectoolkits.analysis.rutile110) del_from_range() (ectoolkits.structures.slab.Slab method) del_surf_layer() (ectoolkits.structures.slab.Slab method) delta_z() (ectoolkits.analysis.finite_size_correction.UniformCharge static method) Density (class in ectoolkits.analysis.atom_density) density() (in module ectoolkits.analysis.water) density_type (ectoolkits.analysis.atom_density.AtomDensity attribute)

DielProfile (class in ectoolkits.analysis.finite_size_correction) dInterLayer (class in ectoolkits.analysis.rutile110) dist2cn() (ectoolkits.analysis.rutile110.RutileDisDeg static method) dist2histo() (ectoolkits.analysis.rutile110.dObr_NearestH static method) (ectoolkits.analysis.rutile110.dObr_NearH static method) (ectoolkits.analysis.rutile110.RutileDisDeg static method) dObr_NearestH (class in ectoolkits.analysis.rutile110) dObr_NearH (class in ectoolkits.analysis.rutile110) dz (ectoolkits.analysis.water.WaterOrientation attribute)

E

ectoolkits module ectoolkits.analysis module ectoolkits.analysis.acidity module ectoolkits.analysis.atom_density module ectoolkits.analysis.band_align module ectoolkits.analysis.dielectric_constant module ectoolkits.analysis.finite_size_correction module ectoolkits.analysis.proton_transfer_cv module ectoolkits.analysis.reweight module ectoolkits.analysis.rutile110 module ectoolkits.analysis.uncertainty module ectoolkits.analysis.water module ectoolkits.log module ectoolkits.matplotlibstyle module

ectoolkits.plots module ectoolkits.plots.band_align module ectoolkits.plots.dpmd module ectoolkits.structures module ectoolkits.structures.interface module ectoolkits.structures.rutile110 module ectoolkits.structures.slab module ectoolkits.structures.tools module ectoolkits.utils module ectoolkits.utils.math module ectoolkits.utils.rutile110 module ectoolkits.utils.utils module ectoolkits.utils.vasp module enumerate_subplots() (in module ectoolkits.plots.band_align) exout_vasp() (in module ectoolkits.utils.vasp) extra_detail (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV attribute)

F

file_content() (in module ectoolkits.utils.utils) find_cn_idx() (in module ectoolkits.utils.rutile110) find_element_idx_list() (ectoolkits.structures.slab.Slab method) find_idx_from_range() (ectoolkits.structures.slab.Slab method)

find_outcar() (in module ectoolkits.utils.vasp) find_surf_idx() (ectoolkits.structures.slab.Slab method) FindSurfaceOadH (class in ectoolkits.analysis.rutile110) fit_line_vec() (in module ectoolkits.utils.math) fit_plane_normal() (in module ectoolkits.utils.math)

G

g_unique_vecs() (in module ectoolkits.utils.rutile110) GaussCharge (class in ectoolkits.analysis.finite_size_correction) gen_diel_profile() (ectoolkits.analysis.finite_size_correction.DielProfile method) generate_components_symmetry_box() (ectoolkits.structures.slab.Slab method) generate_interface() (ectoolkits.structures.slab.Slab method) generate_water_box() (ectoolkits.structures.slab.Slab method) get_alignment() (in module ectoolkits.analysis.band_align) get_alignment_vac() (in module ectoolkits.analysis.band_align) get_alignment_vac_2() (in module ectoolkits.analysis.band_align) get_alignment_water() (in module ectoolkits.analysis.band_align) get_alignment_water_2() (in module ectoolkits.analysis.band_align) get_all_z() (ectoolkits.analysis.atom_density.Density method) get_atom_density() (ectoolkits.analysis.atom_density.AtomDensity method), [1] (ectoolkits.analysis.atom_density.Density method) get_ave_density() (ectoolkits.analysis.atom_density.AtomDensity method) (ectoolkits.analysis.atom_density.Density method) get_cent_list() (ectoolkits.analysis.band_align.BandAlign method) get_cls_vib_fe() (in module ectoolkits.analysis.acidity) get_cum_mean() (in module ectoolkits.utils.utils) get_cus() (ectoolkits.structures.slab.Slab method) get_dab() (ectoolkits.analysis.rutile110.dAdBridge method) get_dielectric_constant() (in module ectoolkits.analysis.dielectric_constant) get_dielectric_constant_profile() (in module ectoolkits.analysis.dielectric_constant) get_dielectric_susceptibility() (in module ectoolkits.analysis.dielectric_constant) get_dipoles() (in module ectoolkits.analysis.water) get_dptest_data() (in module ectoolkits.plots.dpmd) get_dTiOad() (ectoolkits.analysis.rutile110.SurfTiOBondLenght method) get_dTiObr() (ectoolkits.analysis.rutile110.SurfTiOBondLenght method) get_dummy_insert_fe() (in module ectoolkits.analysis.acidity) get_dummy_insert_fe_hydronium() (in module ectoolkits.analysis.acidity) get_exclude_water_count() (in module ectoolkits.structures.tools) get_f_coarse_grained_data() (in module ectoolkits.analysis.uncertainty) get_gas_partition() (in module ectoolkits.analysis.acidity) get_idx_list() (ectoolkits.analysis.atom_density.AtomDensity method), [1] (ectoolkits.analysis.atom_density.Density method) get_idx_list_all() (ectoolkits.analysis.atom_density.AtomDensity method), [1] (ectoolkits.analysis.atom_density.Density method) get_idx_list_manual() (ectoolkits.analysis.atom_density.AtomDensity method), [1] (ectoolkits.analysis.atom_density.Density method) get_indices() (ectoolkits.structures.rutile110.Rutile110 method) (ectoolkits.structures.rutile110.Rutile1p11Edge method) get_induced_charge() (in module ectoolkits.analysis.dielectric_constant) get_integrated_array() (in module ectoolkits.analysis.dielectric_constant) get_layer_space_list() (in module ectoolkits.analysis.band_align) get_logger() (in module ectoolkits.log) get_mae() (in module ectoolkits.plots.dpmd) get_micro_electric_field() (in module ectoolkits.analysis.dielectric_constant) get_micro_polarization() (in module ectoolkits.analysis.dielectric_constant) get_min_OH() (ectoolkits.analysis.rutile110.dObr_NearestH method) get_n_trilayers() (ectoolkits.analysis.rutile110.dInterLayer static method) get_nearest_idx() (in module ectoolkits.analysis.band_align) get_neighbor_list() (ectoolkits.structures.slab.Slab method) get_neighbor_oxygen() (ectoolkits.analysis.rutile110.dAdBridge method) (ectoolkits.analysis.rutile110.RutileDisDeg method) (ectoolkits.analysis.rutile110.staleRutileDisDeg method) get_norm_vector() (in module ectoolkits.utils.math) get_octahedral_bonds() (in module ectoolkits.utils.rutile110)

get_OH_dist() (ectoolkits.analysis.rutile110.dObr_NearH method) (ectoolkits.analysis.rutile110.RutileDisDeg method) get_origin() (ectoolkits.analysis.water.WaterOrientation method) get_packmol_inp() (in module ectoolkits.structures.tools) get_pair() (in module ectoolkits.utils.rutile110) get_partition_ratio() (in module ectoolkits.analysis.acidity) get_partition_ratio_hydronium() (in module ectoolkits.analysis.acidity) get_pav_mav_traj_list_from_cube() (ectoolkits.analysis.band_align.BandAlign method) get_pav_mav_traj_list_from_file() (ectoolkits.analysis.band_align.BandAlign method) get_plane_distance() (in module ectoolkits.utils.math) get_plane_eq() (in module ectoolkits.utils.math) get_quant_vib_fe() (in module ectoolkits.analysis.acidity) get_quantum_correction() (in module ectoolkits.analysis.acidity) get_quantum_correction_hydronium() (in module ectoolkits.analysis.acidity) get_range_bool() (in module ectoolkits.analysis.band_align) get_rdf() (in module ectoolkits.utils.utils) get_rdf_list() (in module ectoolkits.utils.utils) get_ref() (ectoolkits.analysis.rutile110.dAdBridge method) get_rmse() (in module ectoolkits.plots.dpmd) get_rot_temp() (in module ectoolkits.analysis.acidity) get_rotM() (in module ectoolkits.utils.rutile110) get_rotM_edged_rutile110() (in module ectoolkits.utils.rutile110) get_slab() (ectoolkits.structures.slab.RutileSlab method) get_slab_cent() (in module ectoolkits.analysis.band_align) get_slab_obj() (ectoolkits.structures.rutile110.Rutile110 method) (ectoolkits.structures.rutile110.Rutile1p11Edge method) get_solid_hartree() (ectoolkits.analysis.band_align.BandAlign method) (in module ectoolkits.analysis.band_align) get_surf1_z_list() (ectoolkits.analysis.atom_density.Density method) get_surf2_z_list() (ectoolkits.analysis.atom_density.Density method) get_surf_o() (ectoolkits.structures.rutile110.SlabRutile110 method) (ectoolkits.structures.rutile110.SlabRutile1p11Edge method) get_surf_ti() (ectoolkits.structures.rutile110.SlabRutile110 method) (ectoolkits.structures.rutile110.SlabRutile1p11Edge method) get_surf_z_list() (ectoolkits.analysis.atom_density.AtomDensity method), [1] get_surface_indices() (ectoolkits.structures.rutile110.SlabRutile110 method) (ectoolkits.structures.rutile110.SlabRutile1p11Edge method) get_sym_edge() (in module ectoolkits.utils.rutile110) get_triangle() (in module ectoolkits.structures.rutile110) get_uncertainty() (in module ectoolkits.analysis.uncertainty) get_unit_conversion() (ectoolkits.analysis.atom_density.AtomDensity method) (ectoolkits.analysis.atom_density.AtomDensity static method) (ectoolkits.analysis.atom_density.Density method) get_vib_temp() (in module ectoolkits.analysis.acidity) get_wat() (ectoolkits.structures.rutile110.Rutile110 method) (ectoolkits.structures.rutile110.Rutile1p11Edge method) get_wat_thickness() (ectoolkits.analysis.rutile110.WatDensity method) get_water_cent_list() (ectoolkits.analysis.atom_density.AtomDensity method), [1] (ectoolkits.analysis.atom_density.Density method) get_water_center_list() (in module ectoolkits.analysis.band_align) get_water_hartree() (ectoolkits.analysis.band_align.BandAlign method) (in module ectoolkits.analysis.band_align) get_watOidx() (ectoolkits.analysis.rutile110.WatDensity method) (in module ectoolkits.utils.rutile110) get_z_density() (ectoolkits.analysis.rutile110.WatDensity method) get_z_histo() (ectoolkits.analysis.rutile110.dInterLayer static method) get_z_mean() (in module ectoolkits.analysis.band_align)

H

h_ag (ectoolkits.analysis.water.WaterOrientation attribute)

I

identify_water_molecules() (in module ectoolkits.analysis.water) idxs_type1_o (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV attribute) idxs_type2_o (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV attribute) idxs_water_o (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV attribute) idxslab2idxatoms() (ectoolkits.structures.rutile110.Rutile110 static method) (ectoolkits.structures.rutile110.Rutile1p11Edge static method)

ifmodel() (ectoolkits.analysis.finite_size_correction.DielProfile static method) insert_water() (in module ectoolkits.utils.utils) integer3D() (in module ectoolkits.analysis.finite_size_correction) Interface (class in ectoolkits.structures.interface) interface_2_slab() (in module ectoolkits.utils.rutile110) is_cross_z_boundary() (ectoolkits.structures.slab.Slab method)

M

make_grid() (in module ectoolkits.analysis.reweight) mic_1d() (in module ectoolkits.utils.utils) minimize_vectors_triclinic() (in module ectoolkits.utils.rutile110) module ectoolkits ectoolkits.analysis ectoolkits.analysis.acidity ectoolkits.analysis.atom_density ectoolkits.analysis.band_align ectoolkits.analysis.dielectric_constant ectoolkits.analysis.finite_size_correction ectoolkits.analysis.proton_transfer_cv ectoolkits.analysis.reweight ectoolkits.analysis.rutile110 ectoolkits.analysis.uncertainty ectoolkits.analysis.water ectoolkits.log ectoolkits.matplotlibstyle ectoolkits.plots ectoolkits.plots.band_align ectoolkits.plots.dpmd ectoolkits.structures ectoolkits.structures.interface ectoolkits.structures.rutile110 ectoolkits.structures.slab ectoolkits.structures.tools ectoolkits.utils ectoolkits.utils.math ectoolkits.utils.rutile110 ectoolkits.utils.utils ectoolkits.utils.vasp

N

n_atoms (ectoolkits.analysis.atom_density.AtomDensity attribute) n_results (ectoolkits.analysis.atom_density.AtomDensity attribute) (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV attribute)

normalized_vector() (in module ectoolkits.utils.rutile110) num_bridge (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV attribute) number_density2watdensity() (ectoolkits.analysis.rutile110.WatDensity static method)

O

o_ag (ectoolkits.analysis.water.WaterOrientation attribute)

oh_cutoff (ectoolkits.analysis.water.WaterOrientation attribute) origin (ectoolkits.analysis.water.WaterOrientation attribute)

P

pair_M5c_n_obr() (in module ectoolkits.utils.rutile110) pair_TiObr() (ectoolkits.analysis.rutile110.SurfTiOBondLenght static method) Paramcell (class in ectoolkits.analysis.finite_size_correction) PBCPoissonSolver (class in ectoolkits.analysis.finite_size_correction) perdz() (ectoolkits.analysis.finite_size_correction.DielProfile static method) plot_band_alignment() (in module ectoolkits.plots.band_align) plot_density() (ectoolkits.analysis.atom_density.AtomDensity method) (ectoolkits.analysis.atom_density.Density method) (ectoolkits.analysis.water.WaterOrientation method) plot_density_z() (ectoolkits.analysis.rutile110.WatDensity method)

plot_dptest() (in module ectoolkits.plots.dpmd) plot_error() (in module ectoolkits.plots.dpmd) plot_hartree_per_width() (ectoolkits.analysis.band_align.BandAlign method) plot_model_devi() (in module ectoolkits.plots.dpmd) plot_multiple_ba() (in module ectoolkits.plots.band_align) plot_multiple_ba_diff() (in module ectoolkits.plots.band_align) plot_one_ba_diff() (in module ectoolkits.plots.band_align) plot_one_ba_sc() (in module ectoolkits.plots.band_align) plot_orientation() (ectoolkits.analysis.water.WaterOrientation method) ProtonTransferCV (class in ectoolkits.analysis.proton_transfer_cv)

R

random() (in module ectoolkits.utils.utils) read_bias() (in module ectoolkits.analysis.reweight) read_cv() (in module ectoolkits.analysis.reweight) read_fes() (in module ectoolkits.analysis.reweight) refine_rotM() (ectoolkits.structures.rutile110.Rutile1p11Edge method) remove_cell_vacuum() (ectoolkits.structures.slab.Slab method) results (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV attribute) run() (ectoolkits.analysis.atom_density.Density method)

run_atom_density_analysis() (in module ectoolkits.analysis.atom_density) Rutile110 (class in ectoolkits.structures.rutile110) Rutile1p11Edge (class in ectoolkits.structures.rutile110) rutile_slab_001() (ectoolkits.structures.slab.RutileSlab method) rutile_slab_100() (ectoolkits.structures.slab.RutileSlab method) rutile_slab_101() (ectoolkits.structures.slab.RutileSlab method) rutile_slab_110() (ectoolkits.structures.slab.RutileSlab method) RutileDisDeg (class in ectoolkits.analysis.rutile110) RutileSlab (class in ectoolkits.structures.slab)

S

save_profiles() (ectoolkits.analysis.water.WaterOrientation method) scale_iso_cell() (in module ectoolkits.utils.vasp) sep_hobr() (ectoolkits.structures.rutile110.SlabRutile1p11Edge static method) sep_ocn2() (ectoolkits.structures.rutile110.SlabRutile1p11Edge method) sep_ticn5() (ectoolkits.structures.rutile110.SlabRutile1p11Edge method) sep_upper_lower() (ectoolkits.structures.rutile110.SlabRutile110 method) (ectoolkits.structures.rutile110.SlabRutile1p11Edge method) (in module ectoolkits.utils.rutile110) set_pbc() (in module ectoolkits.utils.utils) she_scale() (in module ectoolkits.plots.band_align) Slab (class in ectoolkits.structures.slab) SlabRutile110 (class in ectoolkits.structures.rutile110) SlabRutile1p11Edge (class in ectoolkits.structures.rutile110) smiles2xyz() (in module ectoolkits.structures.tools)

sort_by_rows() (in module ectoolkits.structures.rutile110) sort_idx() (ectoolkits.structures.rutile110.SlabRutile110 method) (ectoolkits.structures.rutile110.SlabRutile1p11Edge method) staleRutileDisDeg (class in ectoolkits.analysis.rutile110) strict (ectoolkits.analysis.water.WaterOrientation attribute) surf1 (ectoolkits.analysis.atom_density.AtomDensity attribute) surf1_ag (ectoolkits.analysis.water.WaterOrientation attribute) surf1_z (ectoolkits.analysis.atom_density.AtomDensity attribute) surf1_z_list (ectoolkits.analysis.atom_density.AtomDensity attribute) surf2 (ectoolkits.analysis.atom_density.AtomDensity attribute) surf2_ag (ectoolkits.analysis.water.WaterOrientation attribute) surf2_z (ectoolkits.analysis.atom_density.AtomDensity attribute) surf2_z_list (ectoolkits.analysis.atom_density.AtomDensity attribute) SurfTiOBondLenght (class in ectoolkits.analysis.rutile110)

T

trig_vec() (in module ectoolkits.structures.rutile110)

twoD (ectoolkits.analysis.atom_density.AtomDensity attribute)

U

u (ectoolkits.analysis.atom_density.AtomDensity attribute) (ectoolkits.analysis.proton_transfer_cv.ProtonTransferCV attribute)

UniformCharge (class in ectoolkits.analysis.finite_size_correction) update_pos() (ectoolkits.analysis.rutile110.dInterLayer static method) (ectoolkits.analysis.rutile110.WatDensity method)

V

vac_scale() (in module ectoolkits.plots.band_align)

volume (ectoolkits.analysis.atom_density.AtomDensity attribute)

W

WatDensity (class in ectoolkits.analysis.rutile110) water_cent_list (ectoolkits.analysis.atom_density.AtomDensity attribute) water_density() (in module ectoolkits.analysis.water)

water_dict (ectoolkits.analysis.water.WaterOrientation attribute) water_O_idx() (ectoolkits.analysis.atom_density.Density method) WaterOrientation (class in ectoolkits.analysis.water)

X

xy_area (ectoolkits.analysis.atom_density.AtomDensity attribute)