Index

A

add_density_entries_from_fcf() (in module xharpy.io) add_from_cif() (in module xharpy.io) angle_between() (in module xharpy.f0j_sources.nosphera2_orca_source) atom1 (xharpy.restraints.FixedDistanceRestraint attribute) (xharpy.restraints.RigidADPRestraint attribute) (xharpy.restraints.SameADPRestraint attribute) atom1_index (xharpy.restraints.RigidADPRestrInd attribute) (xharpy.restraints.SameADPRestrInd attribute)

atom2 (xharpy.restraints.FixedDistanceRestraint attribute) (xharpy.restraints.RigidADPRestraint attribute) (xharpy.restraints.SameADPRestraint attribute) atom2_index (xharpy.restraints.RigidADPRestrInd attribute) (xharpy.restraints.SameADPRestrInd attribute) atom_pair_indexes (xharpy.restraints.SameDistanceRestrInd attribute) atom_pairs (xharpy.restraints.SameDistanceRestraint attribute)

B

bench_colors (in module xharpy.paper)

box_options() (in module xharpy.paper)

C

calc_f() (in module xharpy.refine) calc_f0j() (in module xharpy.f0j_sources.gpaw_mpi_source) (in module xharpy.f0j_sources.gpaw_source) (in module xharpy.f0j_sources.iam_source) (in module xharpy.f0j_sources.nosphera2_orca_source) (in module xharpy.f0j_sources.qe_source) calc_f0j_core() (in module xharpy.f0j_sources.gpaw_mpi_source) (in module xharpy.f0j_sources.gpaw_source) (in module xharpy.f0j_sources.iam_source) (in module xharpy.f0j_sources.nosphera2_orca_source) (in module xharpy.f0j_sources.qe_source) calc_lsq_factory() (in module xharpy.refine) calc_s12() (in module xharpy.paper) calc_sin_theta_ov_lambda() (in module xharpy.conversion) calc_var_cor_mat() (in module xharpy.refine) calc_weights() (in module xharpy.weighting) calculate_agreement() (in module xharpy.paper) calculate_drk() (in module xharpy.quality) calculate_egross() (in module xharpy.quality) calculate_quality_indicators() (in module xharpy.quality) cell_constants_to_M() (in module xharpy.conversion) cif2atom_type_table_string() (in module xharpy.io) cif2data() (in module xharpy.io) cif2space_group_table_string() (in module xharpy.io)

cif2tsc() (in module xharpy.io) cif_entry_string() (in module xharpy.io) ciflike_to_dict() (in module xharpy.io) corr_uij_cubic() (in module xharpy.paper) corr_uij_cubic_nosc() (in module xharpy.paper) corr_uij_hexa() (in module xharpy.paper) corr_uij_hexa_nosc() (in module xharpy.paper) corr_uij_mono() (in module xharpy.paper) corr_uij_mono_nosc() (in module xharpy.paper) corr_uij_ortho() (in module xharpy.paper) corr_uij_ortho_nosc() (in module xharpy.paper) corr_uij_tetra() (in module xharpy.paper) corr_uij_tetra_nosc() (in module xharpy.paper) corr_uij_tric() (in module xharpy.paper) corr_uij_tric_nosc() (in module xharpy.paper) create_angle_table() (in module xharpy.io) create_aniso_table_string() (in module xharpy.io) create_atom_site_table_string() (in module xharpy.io) create_diff_density_entries() (in module xharpy.io) create_distance_table() (in module xharpy.io) create_extinction_entries() (in module xharpy.io) create_fcf4_table() (in module xharpy.io) create_gc3_table_string() (in module xharpy.io) create_gc4_table_string() (in module xharpy.io) create_restraint_instructions() (in module xharpy.restraints)

D

diff_density_values() (in module xharpy.quality)

distance (xharpy.restraints.FixedDistanceRestraint attribute)

E

entries2atom_string() (in module xharpy.io) esd (xharpy.restraints.FixedDistanceRestraint attribute) (xharpy.restraints.RigidADPRestraint attribute) (xharpy.restraints.RigidADPRestrInd attribute) (xharpy.restraints.SameADPRestraint attribute) (xharpy.restraints.SameADPRestrInd attribute) (xharpy.restraints.SameDistanceRestraint attribute) (xharpy.restraints.SameDistanceRestrInd attribute)

expand_symm_unique() (in module xharpy.conversion)

F

f0j2tsc() (in module xharpy.io) f_core_from_spline() (in module xharpy.f0j_sources.gpaw_source) fcf2hkl_pd() (in module xharpy.io)

figure_height() (in module xharpy.paper) FixedDistanceRestraint (class in xharpy.restraints) FixedDistanceRestrInd (in module xharpy.restraints)

G

gen_lsq() (in module xharpy.paper) generate_cif_output() (in module xharpy.f0j_sources.gpaw_mpi_source) (in module xharpy.f0j_sources.gpaw_source) (in module xharpy.f0j_sources.iam_source) (in module xharpy.f0j_sources.nosphera2_orca_source) (in module xharpy.f0j_sources.qe_source) generate_cluster_file() (in module xharpy.f0j_sources.nosphera2_orca_source) generate_core_refinement_string() (in module xharpy.io)

generate_cube_shell() (in module xharpy.f0j_sources.nosphera2_orca_source) generate_hm() (in module xharpy.quality) get_calculator() (xharpy.f0j_sources.gpaw_source.HirshfeldPartitioning method) get_charges() (xharpy.f0j_sources.gpaw_source.HirshfeldPartitioning method) get_density() (xharpy.f0j_sources.gpaw_source.HirshfeldDensity method) get_effective_volume_ratio() (xharpy.f0j_sources.gpaw_source.HirshfeldPartitioning method) get_effective_volume_ratios() (xharpy.f0j_sources.gpaw_source.HirshfeldPartitioning method) get_multiplication_instructions() (in module xharpy.f0j_sources.real_spher_harm) get_weight() (xharpy.f0j_sources.gpaw_source.HirshfeldPartitioning method)

H

HirshfeldDensity (class in xharpy.f0j_sources.gpaw_source)

HirshfeldPartitioning (class in xharpy.f0j_sources.gpaw_source)

I

initialize() (xharpy.f0j_sources.gpaw_source.HirshfeldPartitioning method)

instructions_to_constraints() (in module xharpy.io)

L

lst2constraint_dict() (in module xharpy.io)

M

module xharpy xharpy.conversion xharpy.f0j_sources xharpy.f0j_sources.gpaw_mpi_source xharpy.f0j_sources.gpaw_source xharpy.f0j_sources.iam_source xharpy.f0j_sources.nosphera2_orca_source xharpy.f0j_sources.qe_source xharpy.f0j_sources.real_spher_harm xharpy.f0j_sources.rho xharpy.io xharpy.paper xharpy.quality xharpy.refine xharpy.restraints xharpy.weighting

mult (xharpy.restraints.RigidADPRestraint attribute) (xharpy.restraints.RigidADPRestrInd attribute) (xharpy.restraints.SameADPRestraint attribute) (xharpy.restraints.SameADPRestrInd attribute)

P

plot_heatmap() (in module xharpy.paper)

Q

qe_atomic_density() (in module xharpy.f0j_sources.qe_source) qe_density() (in module xharpy.f0j_sources.qe_source)

qe_entry_string() (in module xharpy.f0j_sources.qe_source) qe_pp_file() (in module xharpy.f0j_sources.qe_source) qe_pw_file() (in module xharpy.f0j_sources.qe_source)

R

read_xsf_density() (in module xharpy.f0j_sources.qe_source) refine() (in module xharpy.refine)

resolve_restraints() (in module xharpy.restraints) RigidADPRestraint (class in xharpy.restraints) RigidADPRestrInd (class in xharpy.restraints)

S

SameADPRestraint (class in xharpy.restraints) SameADPRestrInd (class in xharpy.restraints) SameDistanceRestraint (class in xharpy.restraints) SameDistanceRestrInd (class in xharpy.restraints) set_positions() (xharpy.f0j_sources.gpaw_source.HirshfeldDensity method) shelxl_hkl2pd() (in module xharpy.io)

single_core_function() (in module xharpy.f0j_sources.qe_source) site_symm2mat_vec() (in module xharpy.io) spherical_bessel() (in module xharpy.f0j_sources.real_spher_harm) spherical_harmonic() (in module xharpy.f0j_sources.real_spher_harm) split_error() (in module xharpy.io) symm_to_matrix_vector() (in module xharpy.io)

U

ucif2ucart() (in module xharpy.conversion)

V

value_with_esd() (in module xharpy.io)

W

write_cif() (in module xharpy.io)

write_fcf() (in module xharpy.io) write_res() (in module xharpy.io)

X

xd_hkl2pd() (in module xharpy.io) xharpy module xharpy.conversion module xharpy.f0j_sources module xharpy.f0j_sources.gpaw_mpi_source module xharpy.f0j_sources.gpaw_source module xharpy.f0j_sources.iam_source module xharpy.f0j_sources.nosphera2_orca_source module xharpy.f0j_sources.qe_source module

xharpy.f0j_sources.real_spher_harm module xharpy.f0j_sources.rho module xharpy.io module xharpy.paper module xharpy.quality module xharpy.refine module xharpy.restraints module xharpy.weighting module