Index

Symbols

--center cube_radial_distribution command line option --criteria measure_mols command line option --criterion boltzmann_population command line option --data cube_radial_distribution command line option --decontaminate gen_spectrum command line option --dr cube_radial_distribution command line option --dummy ct_analysis command line option --each gen_spectrum command line option --excited ct_analysis command line option --exclude gen_spectrum command line option thermochemistry_analysis command line option --factor boltzmann_population command line option thermochemistry_analysis command line option --ground ct_analysis command line option --guess-symmetry thermochemistry_analysis command line option --help boltzmann_population command line option check_chemistry_file command line option ct_analysis command line option cube_radial_distribution command line option electrical_derivatives command line option excitations command line option gen_character_table command line option gen_spectrum command line option geometrical_derivatives command line option measure_mols command line option symmetrise command line option thermochemistry_analysis command line option to_xyz command line option --impulses gen_spectrum command line option --include gen_spectrum command line option --limit excitations command line option --limit-CSFs excitations command line option --limit-impulses gen_spectrum command line option --limits gen_spectrum command line option --maximums gen_spectrum command line option --n-azimuthal cube_radial_distribution command line option --n-polar cube_radial_distribution command line option --no-vibs geometrical_derivatives command line option --normalize gen_spectrum command line option --not-trust-extension check_chemistry_file command line option --output ct_analysis command line option --output-with-diff ct_analysis command line option --pressure boltzmann_population command line option thermochemistry_analysis command line option --property check_chemistry_file command line option --same-output symmetrise command line option --scale gen_spectrum command line option thermochemistry_analysis command line option --square ct_analysis command line option cube_radial_distribution command line option --symmetrise symmetrise command line option --symmetry-number thermochemistry_analysis command line option --temperature boltzmann_population command line option thermochemistry_analysis command line option --tolerance symmetrise command line option --uniques symmetrise command line option --unit excitations command line option --verbose thermochemistry_analysis command line option --version boltzmann_population command line option check_chemistry_file command line option ct_analysis command line option cube_radial_distribution command line option electrical_derivatives command line option excitations command line option gen_character_table command line option gen_spectrum command line option geometrical_derivatives command line option measure_mols command line option symmetrise command line option thermochemistry_analysis command line option to_xyz command line option

-c boltzmann_population command line option cube_radial_distribution command line option measure_mols command line option -D ct_analysis command line option gen_spectrum command line option -d ct_analysis command line option cube_radial_distribution command line option -E excitations command line option gen_spectrum command line option -e ct_analysis command line option gen_spectrum command line option -f boltzmann_population command line option thermochemistry_analysis command line option -g ct_analysis command line option thermochemistry_analysis command line option -h boltzmann_population command line option check_chemistry_file command line option ct_analysis command line option cube_radial_distribution command line option electrical_derivatives command line option excitations command line option gen_character_table command line option gen_spectrum command line option geometrical_derivatives command line option measure_mols command line option symmetrise command line option thermochemistry_analysis command line option to_xyz command line option -I gen_spectrum command line option -i gen_spectrum command line option -L excitations command line option gen_spectrum command line option -l excitations command line option gen_spectrum command line option -m gen_spectrum command line option -N geometrical_derivatives command line option -n gen_spectrum command line option thermochemistry_analysis command line option -o ct_analysis command line option -p boltzmann_population command line option check_chemistry_file command line option thermochemistry_analysis command line option -S ct_analysis command line option cube_radial_distribution command line option symmetrise command line option -s gen_spectrum command line option symmetrise command line option thermochemistry_analysis command line option -T check_chemistry_file command line option -t boltzmann_population command line option symmetrise command line option thermochemistry_analysis command line option -u symmetrise command line option -V thermochemistry_analysis command line option -v boltzmann_population command line option check_chemistry_file command line option ct_analysis command line option cube_radial_distribution command line option electrical_derivatives command line option excitations command line option gen_character_table command line option gen_spectrum command line option geometrical_derivatives command line option measure_mols command line option symmetrise command line option thermochemistry_analysis command line option to_xyz command line option -x thermochemistry_analysis command line option

A

AABoundingBox (class in qcip_tools.bounding) add_atomic_basis_set() (qcip_tools.basis_set.BasisSet method) add_basis_function() (qcip_tools.basis_set.AtomicBasisSet method) add_primitive() (qcip_tools.basis_set.Function method) ak_shifted() (in module qcip_tools.numerical_differentiation) alike() (qcip_tools.chemistry_files.gaussian.Cube method) ALLOWED_DERIVATIVES (in module qcip_tools.derivatives) ALLOWED_LEVEL_0_MODULES (in module qcip_tools.chemistry_files.dalton) amplitude_error() (qcip_tools.numerical_differentiation.RombergTriangle method) AMUToElectronMass (in module qcip_tools.quantities) angle() (in module qcip_tools.math) angle_vector() (in module qcip_tools.math) anisotropic_value() (qcip_tools.derivatives_e.PolarisabilityTensor method) antiprismatic (qcip_tools.symmetry.PointGroupType attribute) apply() (qcip_tools.symmetry.Operation method) apply_function() (qcip_tools.chemistry_files.ChemistryLogFile method) apply_over_list() (in module qcip_tools.chemistry_files) apply_permutation() (qcip_tools.derivatives.Derivative class method) ArchiveOutput (class in qcip_tools.chemistry_files.dalton) Atom (class in qcip_tools.atom)

atom() (qcip_tools.molecule.Molecule method) AtomicBasisSet (class in qcip_tools.basis_set) atoms() (qcip_tools.molecule.Molecule method) attempt_identification() (qcip_tools.chemistry_files.chemistry_datafile.ChemistryDataFile class method) (qcip_tools.chemistry_files.crystal.Output class method) (qcip_tools.chemistry_files.csv_tensor.CSVTensor class method) (qcip_tools.chemistry_files.dalton.ArchiveOutput class method) (qcip_tools.chemistry_files.dalton.Input class method) (qcip_tools.chemistry_files.dalton.MoleculeInput class method) (qcip_tools.chemistry_files.dalton.Output class method) (qcip_tools.chemistry_files.gamess.Input class method) (qcip_tools.chemistry_files.gamess.Output class method) (qcip_tools.chemistry_files.gaussian.Cube class method) (qcip_tools.chemistry_files.gaussian.FCHK class method) (qcip_tools.chemistry_files.gaussian.Input class method) (qcip_tools.chemistry_files.gaussian.Output class method) (qcip_tools.chemistry_files.pdb.File class method) (qcip_tools.chemistry_files.WithIdentificationMixin class method) (qcip_tools.chemistry_files.xyz.File class method) AuToAngstrom (in module qcip_tools.quantities)

B

BadChemistryDataFile BaseElectricalDerivativeTensor (class in qcip_tools.derivatives_e) BaseGeometricalDerivativeTensor (class in qcip_tools.derivatives_g) BasisSet (class in qcip_tools.basis_set) (class in qcip_tools.chemistry_files.gaussian) BasisSetFormatError beta_EOP_from_fchk() (in module qcip_tools.chemistry_files.gaussian) beta_hrs() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) beta_kerr() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) beta_parallel() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) beta_perpendicular() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) beta_SHG_from_fchk() (in module qcip_tools.chemistry_files.gaussian) beta_squared_zxx() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) beta_squared_zzz() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) beta_vector() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) BinaryOperation (class in qcip_tools.symmetry) BLA() (in module qcip_tools.math) boltzmann_population command line option --criterion --factor --help --pressure --temperature --version -c -f -h -p -t -v infiles

Bond (class in qcip_tools.molecule) bonds() (qcip_tools.molecule.Molecule method) bounding_box() (qcip_tools.molecule.Molecule method) BoundingObject (class in qcip_tools.bounding) BoundingSet (class in qcip_tools.bounding) BoundingSphere (class in qcip_tools.bounding)

C

C() (qcip_tools.symmetry.Operation class method) C_n() (qcip_tools.symmetry.PointGroup class method) C_nh() (qcip_tools.symmetry.PointGroup class method) C_nv() (qcip_tools.symmetry.PointGroup class method) cartesian_tensor() (qcip_tools.symmetry.SymmetryFinder static method) center_of_charges() (qcip_tools.molecule.Molecule method) center_of_mass() (qcip_tools.molecule.Molecule method) character_table() (qcip_tools.symmetry.Group method) (qcip_tools.symmetry.PointGroup method) characters (qcip_tools.symmetry.ReducibleRepresentation property) CharacterTable (class in qcip_tools.symmetry) CharacterTableError charge() (qcip_tools.atom.Atom method) ChargeTransferInformation (class in qcip_tools.chemistry_files.gaussian) check_associativity() (qcip_tools.symmetry.BinaryOperation method) check_chemistry_file command line option --help --not-trust-extension --property --version -h -p -T -v infile check_closure() (qcip_tools.symmetry.BinaryOperation method) check_module() (in module qcip_tools.chemistry_files.dalton) check_surjectivity() (qcip_tools.symmetry.BinaryOperation method) chemistry_datafile__property__electrical_derivatives() (in module qcip_tools.chemistry_files.chemistry_datafile) chemistry_datafile__property__geometrical_derivatives() (in module qcip_tools.chemistry_files.chemistry_datafile) chemistry_file__property__file_type() (in module qcip_tools.chemistry_files) chemistry_file__property__molecule() (in module qcip_tools.chemistry_files) ChemistryDataFile (class in qcip_tools.chemistry_files.chemistry_datafile) ChemistryFile (class in qcip_tools.chemistry_files) ChemistryLogFile (class in qcip_tools.chemistry_files) choose_p_for_centered() (qcip_tools.numerical_differentiation.Coefficients static method) chunk_exists() (qcip_tools.chemistry_files.ChemistryLogFile method) class_matrices() (qcip_tools.symmetry.Group method) class_matrix() (qcip_tools.symmetry.Group method) closest_fraction() (in module qcip_tools.math) closest_int() (in module qcip_tools.math) Coefficients (class in qcip_tools.numerical_differentiation) components_to_flatten_component() (qcip_tools.derivatives.Derivative method) compute_charge_transfer() (qcip_tools.chemistry_files.gaussian.Cube method) compute_derivative_of_function() (in module qcip_tools.numerical_differentiation) compute_enthalpy() (qcip_tools.derivatives_g.MassWeightedHessian method) compute_entropy() (qcip_tools.derivatives_g.MassWeightedHessian method) compute_gibbs_free_energy() (qcip_tools.derivatives_g.MassWeightedHessian method) compute_internal_energy() (qcip_tools.derivatives_g.MassWeightedHessian method) compute_numerical_derivative_of_tensor() (in module qcip_tools.derivatives) compute_partition_functions() (qcip_tools.derivatives_g.MassWeightedHessian method) compute_properties() (qcip_tools.derivatives_e.ElectricDipole method) (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) (qcip_tools.derivatives_e.PolarisabilityTensor method) (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) compute_sum() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method)

compute_zpva() (qcip_tools.derivatives_g.MassWeightedHessian method) Configuration (class in qcip_tools.derivatives_exci) ConfigurationStateFunction (class in qcip_tools.derivatives_exci) conjugacy_class() (qcip_tools.symmetry.Group method) conjugate() (in module qcip_tools.math) connectivities() (qcip_tools.molecule.Molecule method) contains() (qcip_tools.bounding.AABoundingBox method) (qcip_tools.bounding.BoundingObject method) (qcip_tools.bounding.BoundingSet method) (qcip_tools.bounding.BoundingSphere method) convert() (in module qcip_tools.quantities) convert_energy_to() (in module qcip_tools.derivatives_e) convert_frequency_from_string() (in module qcip_tools.derivatives_e) COORDINATES (in module qcip_tools.derivatives) correct_components() (qcip_tools.derivatives.Derivative class method) create_open_chemistry_file_action() (in module qcip_tools.chemistry_files.helpers) crystal__output__property__electrical_derivatives() (in module qcip_tools.chemistry_files.crystal) CSVTensor (class in qcip_tools.chemistry_files.csv_tensor) csvtensor__property__electrical_derivatives() (in module qcip_tools.chemistry_files.csv_tensor) csvtensor__property__excitations() (in module qcip_tools.chemistry_files.csv_tensor) csvtensor__property__geometrical_derivatives() (in module qcip_tools.chemistry_files.csv_tensor) ct_analysis command line option --dummy --excited --ground --help --output --output-with-diff --square --version -D -d -e -g -h -o -S -v Cube (class in qcip_tools.chemistry_files.gaussian) cube_radial_distribution command line option --center --data --dr --help --n-azimuthal --n-polar --square --version -c -d -h -S -v infile CubeFormatError cyclic (qcip_tools.symmetry.PointGroupType attribute)

D

D_n() (qcip_tools.symmetry.PointGroup class method) D_nd() (qcip_tools.symmetry.PointGroup class method) D_nh() (qcip_tools.symmetry.PointGroup class method) dalton__archive_output__property__computed_energies() (in module qcip_tools.chemistry_files.dalton) dalton__archive_output__property__electrical_derivatives() (in module qcip_tools.chemistry_files.dalton) dalton__archive_output__property__excitations() (in module qcip_tools.chemistry_files.dalton) dalton__archive_output__property__geometrical_derivatives() (in module qcip_tools.chemistry_files.dalton) dalton__output__computed_energies() (in module qcip_tools.chemistry_files.dalton) dalton__output__get_geometrical_derivatives() (in module qcip_tools.chemistry_files.dalton) degeneracies() (qcip_tools.symmetry.SymmetryFinder static method) degree (qcip_tools.symmetry.IrreducibleRepresentation property) depolarization_ratio() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method)

Derivative (class in qcip_tools.derivatives) differentiate() (qcip_tools.derivatives.Derivative method) dihedral (qcip_tools.symmetry.PointGroupType attribute) dimension() (qcip_tools.derivatives.Derivative method) DimensionAreNotEquals dipolar_contribution() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) dipolar_contribution_squared() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) dispatch() (qcip_tools.mixins.Dispatcher method) Dispatcher (class in qcip_tools.mixins) distance() (in module qcip_tools.math) distances() (qcip_tools.molecule.Molecule method) dot() (qcip_tools.symmetry.IrreducibleRepresentation method) dV() (qcip_tools.chemistry_files.gaussian.Cube method)

E

E() (qcip_tools.symmetry.Operation class method) electrical_derivatives command line option --help --version -h -v infile ElectricDipole (class in qcip_tools.derivatives_e) ENERGY_IN_AU_CONVERSION (qcip_tools.derivatives_g.MassWeightedHessian attribute) Excitations (class in qcip_tools.derivatives_exci) excitations command line option --help --limit --limit-CSFs --unit --version -E -h -l -L -v infile

exclude() (qcip_tools.bounding.BoundingSet method) expend_list() (qcip_tools.derivatives.Derivative class method)

F

FCHK (class in qcip_tools.chemistry_files.gaussian) FCHKChunkInformation (class in qcip_tools.chemistry_files.gaussian) FCHKFormatError fields_to_str() (in module qcip_tools.derivatives_e) File (class in qcip_tools.chemistry_files.pdb) (class in qcip_tools.chemistry_files.xyz) file_type (qcip_tools.chemistry_files.chemistry_datafile.ChemistryDataFile attribute) (qcip_tools.chemistry_files.crystal.Output attribute) (qcip_tools.chemistry_files.dalton.ArchiveOutput attribute) (qcip_tools.chemistry_files.dalton.Input attribute) (qcip_tools.chemistry_files.dalton.MoleculeInput attribute) (qcip_tools.chemistry_files.dalton.Output attribute) (qcip_tools.chemistry_files.gamess.Input attribute) (qcip_tools.chemistry_files.gamess.Output attribute) (qcip_tools.chemistry_files.gaussian.Cube attribute) (qcip_tools.chemistry_files.gaussian.FCHK attribute) (qcip_tools.chemistry_files.gaussian.Input attribute) (qcip_tools.chemistry_files.gaussian.Output attribute) (qcip_tools.chemistry_files.pdb.File attribute) (qcip_tools.chemistry_files.xyz.File attribute) find_best_value() (qcip_tools.numerical_differentiation.RombergTriangle method) find_best_x_axis() (qcip_tools.symmetry.SymmetryFinder method)

find_c_highest() (qcip_tools.symmetry.SymmetryFinder method) find_probable_parallel_mirrors() (qcip_tools.symmetry.SymmetryFinder method) find_probable_rotations() (qcip_tools.symmetry.SymmetryFinder method) find_symmetry() (qcip_tools.symmetry.SymmetryFinder method) find_textual_axis() (qcip_tools.symmetry.OperationDescription static method) FirstHyperpolarisabilityTensor (class in qcip_tools.derivatives_e) flatten_component_to_components() (qcip_tools.derivatives.Derivative method) FormatError formula() (qcip_tools.molecule.Molecule method) from_axangle() (qcip_tools.symmetry.Operation class method) from_cartesian_hessian() (qcip_tools.derivatives_g.MassWeightedHessian method) from_molecule() (qcip_tools.chemistry_files.chemistry_datafile.ChemistryDataFile class method) (qcip_tools.chemistry_files.dalton.ArchiveOutput class method) (qcip_tools.chemistry_files.dalton.MoleculeInput class method) (qcip_tools.chemistry_files.gamess.Input class method) (qcip_tools.chemistry_files.gaussian.Cube class method) (qcip_tools.chemistry_files.gaussian.FCHK class method) (qcip_tools.chemistry_files.gaussian.Input class method) (qcip_tools.chemistry_files.pdb.File class method) (qcip_tools.chemistry_files.WithMoleculeMixin class method) (qcip_tools.chemistry_files.xyz.File class method) from_string() (qcip_tools.chemistry_files.gamess.InputModule static method) Function (class in qcip_tools.basis_set)

G

gamess__log__property__computed_energies() (in module qcip_tools.chemistry_files.gamess) gamess__log__property__geometrical_derivatives() (in module qcip_tools.chemistry_files.gamess) gamma_from_gaussian() (in module qcip_tools.chemistry_files.gaussian) gamma_kerr() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) gamma_parallel() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) gamma_perpendicular() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) gamma_squared_zxxx() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) gamma_squared_zzzz() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) gamma_ths() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) gaussian__fchk__property__computed_energies() (in module qcip_tools.chemistry_files.gaussian) gaussian__fchk__property__electrical_derivatives() (in module qcip_tools.chemistry_files.gaussian) gaussian__fchk__property__excitations() (in module qcip_tools.chemistry_files.gaussian) gaussian__fchk__property__geometrical_derivatives() (in module qcip_tools.chemistry_files.gaussian) gaussian__output__get_computed_energies() (in module qcip_tools.chemistry_files.gaussian) gaussian__output__property__electrical_derivatives() (in module qcip_tools.chemistry_files.gaussian) gaussian__output__property__excitations() (in module qcip_tools.chemistry_files.gaussian) gen_character_table command line option --help --version -h -v group gen_character_table() (qcip_tools.symmetry.Group method) gen_molecule_from_unique_atoms() (in module qcip_tools.molecule) gen_point_group() (qcip_tools.symmetry.PointGroupDescription method) gen_spectrum command line option --decontaminate --each --exclude --help --impulses --include --limit-impulses --limits --maximums --normalize --scale --version -D -e -E -h -I -i -l -L -m -n -s -v infile subparser_name

generate() (qcip_tools.symmetry.BinaryOperation class method) (qcip_tools.symmetry.PointGroup class method) geometrical_derivatives command line option --help --no-vibs --version -h -N -v infile get() (qcip_tools.chemistry_files.gaussian.FCHK method) get_description() (qcip_tools.symmetry.Operation method) get_file() (qcip_tools.chemistry_files.dalton.ArchiveOutput method) get_inputs() (qcip_tools.chemistry_files.dalton.Output method) get_mirrors() (qcip_tools.symmetry.SymmetryFinder method) get_molecule() (qcip_tools.chemistry_files.WithMoleculeMixin method) get_perpendicular_C2() (qcip_tools.symmetry.SymmetryFinder method) get_symmetry() (qcip_tools.symmetry.SymmetryFinder method) group gen_character_table command line option Group (class in qcip_tools.symmetry) group_points() (qcip_tools.symmetry.SymmetryFinder static method) GroupElement (class in qcip_tools.symmetry) GroupError

H

HARTREE_TO_WAVENUMBER_CONVERSION (qcip_tools.derivatives_g.MassWeightedHessian attribute) has_improper_rotation() (qcip_tools.symmetry.SymmetryFinder method) has_inversion() (qcip_tools.symmetry.SymmetryFinder method) has_mirror() (qcip_tools.symmetry.SymmetryFinder method)

has_property() (qcip_tools.chemistry_files.ChemistryFile method) has_rotation() (qcip_tools.symmetry.SymmetryFinder method) hexadecapolar_contribution() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) hexadecapolar_contribution_squared() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method)

I

i() (qcip_tools.symmetry.Operation class method) I() (qcip_tools.symmetry.PointGroup class method) I_h() (qcip_tools.symmetry.PointGroup class method) icosahedral_achiral (qcip_tools.symmetry.PointGroupType attribute) icosahedral_chiral (qcip_tools.symmetry.PointGroupType attribute) identifiable_chemistry_file_objects() (in module qcip_tools.chemistry_files.helpers) identity (qcip_tools.symmetry.OperationType attribute) identity() (qcip_tools.symmetry.Group method) (qcip_tools.transformations.TransformationMatrix static method) image() (qcip_tools.symmetry.BinaryOperation method) ImmutableRotatable (class in qcip_tools.transformations) ImmutableScalable (class in qcip_tools.transformations) ImmutableTransformable (class in qcip_tools.transformations) ImmutableTranslatable (class in qcip_tools.transformations) improper_rotation (qcip_tools.symmetry.OperationType attribute) (qcip_tools.symmetry.PointGroupType attribute) include() (qcip_tools.bounding.BoundingSet method) INERTIA_CONVERSION (qcip_tools.derivatives_g.MassWeightedHessian attribute) inertia_tensor_moments() (qcip_tools.symmetry.SymmetryFinder static method) infile check_chemistry_file command line option cube_radial_distribution command line option electrical_derivatives command line option excitations command line option gen_spectrum command line option geometrical_derivatives command line option symmetrise command line option thermochemistry_analysis command line option to_xyz command line option

infiles boltzmann_population command line option measure_mols command line option Input (class in qcip_tools.chemistry_files.dalton) (class in qcip_tools.chemistry_files.gamess) (class in qcip_tools.chemistry_files.gaussian) InputCard (class in qcip_tools.chemistry_files.dalton) InputFormatError, [1], [2] InputModule (class in qcip_tools.chemistry_files.dalton) (class in qcip_tools.chemistry_files.gamess) InputModuleError insert() (qcip_tools.molecule.Molecule method) inverse() (qcip_tools.symmetry.Group method) inverse_smart_iterator() (qcip_tools.derivatives.Derivative method) inversion (qcip_tools.symmetry.OperationType attribute) IrreducibleRepresentation (class in qcip_tools.symmetry) is_diffuse() (qcip_tools.basis_set.Function method) is_dummy() (qcip_tools.atom.Atom method) is_electrical() (in module qcip_tools.derivatives) is_excitation() (in module qcip_tools.derivatives) is_geometrical() (in module qcip_tools.derivatives) is_shg() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) is_thg() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) isotropic_contribution() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) isotropic_contribution_squared() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) isotropic_value() (qcip_tools.derivatives_e.PolarisabilityTensor method) iteration_error() (qcip_tools.numerical_differentiation.RombergTriangle method)

L

LIMIT (qcip_tools.symmetry.CharacterTable attribute) linear() (qcip_tools.molecule.Molecule method)

LinkCalled (class in qcip_tools.chemistry_files.gaussian) list_of_atoms() (qcip_tools.molecule.Molecule method) local_coordinates() (qcip_tools.bounding.BoundingObject method)

M

make_cartesian_hessian_from_fchk() (in module qcip_tools.chemistry_files.gaussian) mass() (qcip_tools.molecule.Molecule method) MASS_CONVERSION (qcip_tools.derivatives_g.MassWeightedHessian attribute) MassWeightedHessian (class in qcip_tools.derivatives_g) matrix_representation() (qcip_tools.symmetry.Operation method) maximum() (qcip_tools.bounding.AABoundingBox method) measure_mols command line option --criteria --help --version -c -h -v infiles missing() (qcip_tools.derivatives_exci.ConfigurationStateFunction method) MO_to_str() (qcip_tools.molecule.Molecule method) module qcip_tools qcip_tools.atom qcip_tools.basis_set qcip_tools.bounding qcip_tools.chemistry_files qcip_tools.chemistry_files.chemistry_datafile qcip_tools.chemistry_files.crystal qcip_tools.chemistry_files.csv_tensor qcip_tools.chemistry_files.dalton qcip_tools.chemistry_files.gamess qcip_tools.chemistry_files.gaussian qcip_tools.chemistry_files.helpers qcip_tools.chemistry_files.pdb qcip_tools.chemistry_files.xyz qcip_tools.derivatives qcip_tools.derivatives_e qcip_tools.derivatives_exci qcip_tools.derivatives_g qcip_tools.math qcip_tools.mixins qcip_tools.molecule qcip_tools.numerical_differentiation qcip_tools.quantities qcip_tools.symmetry qcip_tools.transformations

MolecularSymmetryError MolecularSymmetryFinder (class in qcip_tools.molecule) Molecule (class in qcip_tools.molecule) MoleculeInput (class in qcip_tools.chemistry_files.dalton) moments_of_inertia() (qcip_tools.molecule.Molecule method) MutableRotatable (class in qcip_tools.transformations) MutableScalable (class in qcip_tools.transformations) MutableTransformable (class in qcip_tools.transformations) MutableTranslatable (class in qcip_tools.transformations)

N

n() (qcip_tools.derivatives_exci.Configuration method) nonlinear_anisotropy() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) norm() (qcip_tools.derivatives_e.ElectricDipole method) normalize() (in module qcip_tools.math) NotAValidAngularMomentum NotInGroup NotSHG NotTHG

num_of_unique_permutations() (in module qcip_tools.math) number_of_core_electrons() (qcip_tools.atom.Atom method) number_of_data() (qcip_tools.chemistry_files.gaussian.Cube method) number_of_electrons() (qcip_tools.atom.Atom method) (qcip_tools.molecule.Molecule method) number_of_protons() (qcip_tools.atom.Atom method) number_of_records() (qcip_tools.chemistry_files.gaussian.Cube method) number_of_valence_electrons() (qcip_tools.atom.Atom method)

O

O() (qcip_tools.symmetry.PointGroup class method) O_h() (qcip_tools.symmetry.PointGroup class method) octahedral_achiral (qcip_tools.symmetry.PointGroupType attribute) octahedral_chiral (qcip_tools.symmetry.PointGroupType attribute) octupolar_contribution() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) octupolar_contribution_squared() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) open_chemistry_file() (in module qcip_tools.chemistry_files.helpers) Operation (class in qcip_tools.symmetry) OperationDescription (class in qcip_tools.symmetry) OperationType (class in qcip_tools.symmetry) order() (qcip_tools.derivatives.Derivative method)

ORDERS (in module qcip_tools.derivatives) orient_molecule() (qcip_tools.molecule.MolecularSymmetryFinder method) oscillator_strength() (qcip_tools.derivatives_exci.Excitations method) Output (class in qcip_tools.chemistry_files.crystal) (class in qcip_tools.chemistry_files.dalton) (class in qcip_tools.chemistry_files.gamess) (class in qcip_tools.chemistry_files.gaussian) output_atoms() (qcip_tools.molecule.Molecule method) output_displacements() (qcip_tools.derivatives_g.MassWeightedHessian method) OutputFormatError, [1], [2] OutputSection (class in qcip_tools.chemistry_files.dalton) OutputStep (class in qcip_tools.chemistry_files.gamess)

P

pass_trough() (qcip_tools.symmetry.SymmetryFinder method) PointGroup (class in qcip_tools.symmetry) PointGroupDescription (class in qcip_tools.symmetry) PointGroupError PointGroupType (class in qcip_tools.symmetry) PolarisabilityTensor (class in qcip_tools.derivatives_e) polarization_angle_dependant_intensity() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) position_matrix() (qcip_tools.molecule.Molecule method) positions() (qcip_tools.chemistry_files.gaussian.Cube method) possible_file_extensions() (qcip_tools.chemistry_files.chemistry_datafile.ChemistryDataFile class method) (qcip_tools.chemistry_files.ChemistryLogFile class method) (qcip_tools.chemistry_files.csv_tensor.CSVTensor class method) (qcip_tools.chemistry_files.dalton.ArchiveOutput class method) (qcip_tools.chemistry_files.dalton.Input class method) (qcip_tools.chemistry_files.dalton.MoleculeInput class method) (qcip_tools.chemistry_files.gamess.Input class method) (qcip_tools.chemistry_files.gaussian.Cube class method) (qcip_tools.chemistry_files.gaussian.FCHK class method) (qcip_tools.chemistry_files.gaussian.Input class method) (qcip_tools.chemistry_files.pdb.File class method) (qcip_tools.chemistry_files.WithIdentificationMixin class method) (qcip_tools.chemistry_files.xyz.File class method)

prefactor() (qcip_tools.numerical_differentiation.Coefficients method) Primitive (class in qcip_tools.basis_set) principal_axes() (qcip_tools.molecule.Molecule method) prismatic (qcip_tools.symmetry.PointGroupType attribute) ProbablyNotAChemistryFile prod() (in module qcip_tools.math) product() (qcip_tools.symmetry.PointGroup static method) project_over_normal_modes() (qcip_tools.derivatives.Tensor method) proper_rotation (qcip_tools.symmetry.OperationType attribute) property() (qcip_tools.chemistry_files.ChemistryFile method) PropertyNotDefined PropertyNotPresent pyramidal (qcip_tools.symmetry.PointGroupType attribute) pyritohedral (qcip_tools.symmetry.PointGroupType attribute)

Q

Q_ (in module qcip_tools.quantities) qcip_tools module qcip_tools.atom module qcip_tools.basis_set module qcip_tools.bounding module qcip_tools.chemistry_files module qcip_tools.chemistry_files.chemistry_datafile module qcip_tools.chemistry_files.crystal module qcip_tools.chemistry_files.csv_tensor module qcip_tools.chemistry_files.dalton module qcip_tools.chemistry_files.gamess module qcip_tools.chemistry_files.gaussian module qcip_tools.chemistry_files.helpers module qcip_tools.chemistry_files.pdb module

qcip_tools.chemistry_files.xyz module qcip_tools.derivatives module qcip_tools.derivatives_e module qcip_tools.derivatives_exci module qcip_tools.derivatives_g module qcip_tools.math module qcip_tools.mixins module qcip_tools.molecule module qcip_tools.numerical_differentiation module qcip_tools.quantities module qcip_tools.symmetry module qcip_tools.transformations module quadrupolar_contribution() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) quadrupolar_contribution_squared() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method)

R

rank() (qcip_tools.derivatives_e.BaseElectricalDerivativeTensor method) raw_representation() (qcip_tools.derivatives.Derivative method) read() (qcip_tools.chemistry_files.chemistry_datafile.ChemistryDataFile method) (qcip_tools.chemistry_files.ChemistryLogFile method) (qcip_tools.chemistry_files.crystal.Output method) (qcip_tools.chemistry_files.dalton.ArchiveOutput method) (qcip_tools.chemistry_files.dalton.Input method) (qcip_tools.chemistry_files.dalton.MoleculeInput method) (qcip_tools.chemistry_files.dalton.Output method) (qcip_tools.chemistry_files.gamess.Input method) (qcip_tools.chemistry_files.gamess.Output method) (qcip_tools.chemistry_files.gaussian.BasisSet method) (qcip_tools.chemistry_files.gaussian.Cube method) (qcip_tools.chemistry_files.gaussian.FCHK method) (qcip_tools.chemistry_files.gaussian.Input method) (qcip_tools.chemistry_files.gaussian.Output method) (qcip_tools.chemistry_files.pdb.File method) read_derivative_from_dataset() (qcip_tools.chemistry_files.chemistry_datafile.ChemistryDataFile static method) read_derivatives_from_group() (qcip_tools.chemistry_files.chemistry_datafile.ChemistryDataFile static method)

real_fields() (in module qcip_tools.numerical_differentiation) ReducibleRepresentation (class in qcip_tools.symmetry) reflexion (qcip_tools.symmetry.PointGroupType attribute) reflexion_plane (qcip_tools.symmetry.OperationType attribute) remove_atom() (qcip_tools.molecule.Molecule method) representation() (qcip_tools.derivatives.Derivative method) representation_to_operator() (in module qcip_tools.derivatives) RepresentationError, [1] REPRESENTATIONS (in module qcip_tools.derivatives_e) (in module qcip_tools.derivatives_g) response_to_electric_field() (qcip_tools.derivatives_e.BaseElectricalDerivativeTensor method) romberg_triangle_repr() (qcip_tools.numerical_differentiation.RombergTriangle method) RombergTriangle (class in qcip_tools.numerical_differentiation) rotate_around_axis() (qcip_tools.transformations.ImmutableRotatable method) (qcip_tools.transformations.TransformationMatrix static method) rotate_around_axis_self() (qcip_tools.transformations.MutableRotatable method) rotate_euler() (qcip_tools.transformations.ImmutableRotatable method) (qcip_tools.transformations.TransformationMatrix static method) rotate_euler_self() (qcip_tools.transformations.MutableRotatable method) rotational_temperature() (qcip_tools.derivatives_g.MassWeightedHessian static method)

S

S() (qcip_tools.symmetry.Operation class method) S_n() (qcip_tools.symmetry.PointGroup class method) scale() (qcip_tools.transformations.ImmutableScalable method) (qcip_tools.transformations.TransformationMatrix static method) scale_self() (qcip_tools.transformations.MutableScalable method) scale_uniform() (qcip_tools.transformations.ImmutableScalable method) (qcip_tools.transformations.TransformationMatrix static method) scale_uniform_self() (qcip_tools.transformations.MutableScalable method) search() (qcip_tools.chemistry_files.ChemistryLogFile method) SecondHyperpolarizabilityTensor (class in qcip_tools.derivatives_e) Set (class in qcip_tools.symmetry) set_input_card() (qcip_tools.chemistry_files.dalton.InputModule method) set_submodule() (qcip_tools.chemistry_files.dalton.InputModule method) set_to_inertia_axes() (qcip_tools.molecule.Molecule method) shape() (qcip_tools.derivatives.Derivative method) SHELL_TO_TAM (in module qcip_tools.basis_set) ShiftedIndexError sigma() (qcip_tools.symmetry.Operation class method) SIMPLIFIED_NAMES (in module qcip_tools.derivatives_e) (in module qcip_tools.derivatives_g) simultaneous_diagonalization() (in module qcip_tools.symmetry) size (qcip_tools.symmetry.CharacterTable property) (qcip_tools.symmetry.ReducibleRepresentation property) slice() (qcip_tools.chemistry_files.gaussian.Cube method) smart_iterator() (qcip_tools.derivatives.Derivative method) spherical_J0_contribution_squared() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) spherical_J1_contribution_squared() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) spherical_J1a_contribution_squared() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) spherical_J1ab_contribution_squared() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method)

spherical_J1b_contribution_squared() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) spherical_J2_contribution_squared() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) spherical_J2a_contribution_squared() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) spherical_J2ab_contribution_squared() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) spherical_J2b_contribution_squared() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) spherical_J3_contribution_squared() (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) spherical_J4_contribution_squared() (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) square_of_spin_angular_moment() (qcip_tools.molecule.Molecule method) subparser_name gen_spectrum command line option sum_density_of_sets() (qcip_tools.chemistry_files.gaussian.Cube method) symmetric_for() (qcip_tools.symmetry.SymmetryFinder method) symmetrise command line option --help --same-output --symmetrise --tolerance --uniques --version -h -s -S -t -u -v infile symmetrise_molecule() (qcip_tools.molecule.MolecularSymmetryFinder method) SymmetryFinder (class in qcip_tools.symmetry) SymmetryFinderError

T

T() (qcip_tools.symmetry.PointGroup class method) T_d() (qcip_tools.symmetry.PointGroup class method) T_h() (qcip_tools.symmetry.PointGroup class method) TAM_TO_SHELL (in module qcip_tools.basis_set) Tensor (class in qcip_tools.derivatives) tetrahedral_achiral (qcip_tools.symmetry.PointGroupType attribute) tetrahedral_chiral (qcip_tools.symmetry.PointGroupType attribute) thermochemistry_analysis command line option --exclude --factor --guess-symmetry --help --pressure --scale --symmetry-number --temperature --verbose --version -f -g -h -n -p -s -t -v -V -x infile

to_name() (qcip_tools.derivatives_e.BaseElectricalDerivativeTensor method) (qcip_tools.derivatives_g.BaseGeometricalDerivativeTensor method) to_string() (qcip_tools.chemistry_files.dalton.MoleculeInput method) (qcip_tools.chemistry_files.gaussian.BasisSet method) (qcip_tools.chemistry_files.gaussian.Cube method) (qcip_tools.chemistry_files.gaussian.Input method) (qcip_tools.chemistry_files.pdb.File method) (qcip_tools.derivatives.Tensor method) (qcip_tools.derivatives_e.BaseElectricalDerivativeTensor method) (qcip_tools.derivatives_e.ElectricDipole method) (qcip_tools.derivatives_e.FirstHyperpolarisabilityTensor method) (qcip_tools.derivatives_e.PolarisabilityTensor method) (qcip_tools.derivatives_e.SecondHyperpolarizabilityTensor method) (qcip_tools.derivatives_exci.ConfigurationStateFunction method) to_xyz command line option --help --version -h -v infile torsion_angle() (in module qcip_tools.math) TransformationMatrix (class in qcip_tools.transformations) transition_dipole() (qcip_tools.derivatives_exci.Excitations method) transition_energy() (qcip_tools.derivatives_exci.Excitations method) translate() (qcip_tools.transformations.ImmutableTranslatable method) (qcip_tools.transformations.TransformationMatrix static method) translate_self() (qcip_tools.transformations.MutableTranslatable method) translate_self_to_center_of_charges() (qcip_tools.molecule.Molecule method) translate_self_to_center_of_mass() (qcip_tools.molecule.Molecule method)

U

unique_everseen() (in module qcip_tools.math) unique_permutations() (in module qcip_tools.math) update() (qcip_tools.bounding.AABoundingBox method) (qcip_tools.bounding.BoundingObject method) (qcip_tools.bounding.BoundingSphere method) (qcip_tools.chemistry_files.dalton.Input method) (qcip_tools.chemistry_files.dalton.InputModule method)

ureg (in module qcip_tools.quantities)

V

ValueOutsideDomain vec_in_vecs() (qcip_tools.symmetry.SymmetryFinder static method)

VIB_ENERGY_CONVERSION (qcip_tools.derivatives_g.MassWeightedHessian attribute) vibrational_temperature() (qcip_tools.derivatives_g.MassWeightedHessian static method)

W

WithIdentificationMixin (class in qcip_tools.chemistry_files) WithMoleculeMixin (class in qcip_tools.chemistry_files) WithOutputMixin (class in qcip_tools.chemistry_files) write() (qcip_tools.chemistry_files.dalton.MoleculeInput method) (qcip_tools.chemistry_files.gaussian.Input method)

write_derivative_in_dataset() (qcip_tools.chemistry_files.chemistry_datafile.ChemistryDataFile static method) write_derivatives_in_group() (qcip_tools.chemistry_files.chemistry_datafile.ChemistryDataFile static method) WrongNumberOfData

X

XYZFormatError