Index

A

Aadhaar (class in esta.general.aadhaar), [1], [2] add_vacuum() (in module esta.general.add_vacuum_to_unit_cell), [1], [2] (in module esta.vaspBag.add_vacuum_to_unit_cell)

affine_map() (in module esta.general.affine), [1], [2] atom_distance_density (class in esta.plot.atomic_distance_density_class2) AtomicStructure (class in esta.general.manipulate), [1], [2] atomtypes_outpot() (in module esta.vaspBag.inout.xml_vasp_ASE), [1]

B

bfgs_line() (in module esta.transitionState.optimizer), [1] boltzmann_dist() (in module esta.general.boltzmann), [1], [2]

boltzmann_dist_() (in module esta.general.boltzmann), [1], [2] boltzmann_factor() (in module esta.general.boltzmann), [1], [2]

C

centroid() (esta.general.manipulate.Manipulate method), [1], [2] (in module esta.general.shift), [1], [2] (in module esta.general.shift0), [1], [2] change_basis_mesh() (in module esta.general.affine), [1], [2] change_of_basis() (in module esta.general.affine), [1], [2] checkEqual_list() (in module esta.plot.plot_pdos_Natoms_contribution_adv_both_spin_possible) (in module esta.plot.plot_pdos_with_atoms_contribution_2plots_qe)

cif() (in module esta.spaceGroup.read_cif) com() (in module esta.general.get_com), [1], [2] com_slightly_slow() (in module esta.general.get_com), [1], [2] conf_surf() (in module esta.surfReact.conformer), [1] conjugate_gradient() (in module esta.transitionState.optimizer), [1] contour_plot() (in module esta.plot.plot2D) CrystalLattice (class in esta.general.crystal_latticee), [1], [2] (class in esta.vaspBag.inout.crystal_lattice), [1]

D

data_exist() (in module esta.grrmBag.plot_strs_energy), [1], [2] data_from() (in module esta.extract_data) DataStore (class in esta.plot.multiplot) delete_atomic_strs() (esta.general.manipulate.Manipulate method), [1], [2] delete_atoms() (esta.general.manipulate.Manipulate method), [1], [2] delete_pseudo_pot() (in module esta.qeBag.gen_qeinput), [1], [2] (in module esta.qeBag.gen_qeinput2), [1], [2] (in module esta.qeBag.gen_qeinput_adv), [1], [2]

diameter_nanowire() (in module esta.vaspBag.inout.diameter_or_area_nanowire), [1] direction_indx_to_str() (in module esta.general.direction_index2str), [1], [2] distance_array() (esta.plot.atomic_distance_density_class2.atom_distance_density method) distance_atom_pairs() (in module esta.general.distance_matrix_PBC), [1], [2] distances_pbc_ase() (in module esta.general.distances_ase_esa), [1], [2] dos() (esta.plot.atomic_distance_density_class2.atom_distance_density method) double() (in module esta.general.conversion_factors), [1], [2] (in module esta.measure.conversion_factors), [1]

E

elements_data() (in module esta.element) energies_kpts() (in module esta.qeBag.bands_kpts_band_gap), [1], [2] (in module esta.qeBag.get_bands_kpts_band_gap_adv3), [1], [2] (in module esta.qeBag.xbands_kpts_band_gap), [1], [2] esta module esta.abinitBag module esta.bonds module esta.c module esta.dict_to_xlsx_csv module esta.element module esta.element_data module esta.externalBag module esta.extract_data module esta.fortran module esta.gamessBag module esta.gaussianBag module esta.gaussianBag.input_gaussian module esta.gaussianBag.input_gaussian_TODO module esta.gaussianBag.input_grrm module esta.gaussianBag.input_grrm_advv module esta.gaussianBag.output_gaussian_adv module esta.gaussianBag.output_gaussian_adv0 module esta.general module, [1], [2] esta.general.aadhaar module, [1], [2] esta.general.add_const_to_dict module, [1], [2] esta.general.add_vacuum_to_unit_cell module, [1], [2] esta.general.affine module, [1], [2] esta.general.b module, [1], [2] esta.general.bending_nanoribbon module, [1], [2] esta.general.boltzmann module, [1], [2] esta.general.cartAndSpherical module, [1], [2] esta.general.compare_scalar module, [1], [2] esta.general.conversion_factors module, [1], [2] esta.general.crystal_latticee module, [1], [2] esta.general.direction_index2str module, [1], [2] esta.general.distance_matrix_PBC module, [1], [2] esta.general.distances_ase_esa module, [1], [2] esta.general.entropy_data module, [1], [2] esta.general.filter_vib_freq module, [1], [2] esta.general.from_pos2xyz module, [1], [2] esta.general.get_com module, [1], [2] esta.general.get_configs module, [1], [2] esta.general.get_configs_btw2strs module, [1], [2] esta.general.get_labelling_atoms module, [1], [2] esta.general.get_moved_atom_n_symb module, [1], [2] esta.general.get_range_from_intervals module, [1], [2] esta.general.get_rotation_matrix module, [1], [2] esta.general.integration1D_over_a_cutoff module, [1], [2] esta.general.list_grouped_and_unique module, [1], [2] esta.general.manipulate module, [1], [2] esta.general.metric_tensor module, [1], [2] esta.general.min_trans_rot module, [1], [2] esta.general.niggli_reduce module, [1], [2] esta.general.operation module, [1], [2] esta.general.peak_position_and_average_1D module, [1], [2] esta.general.pseudo_info module, [1], [2] esta.general.rate_const_IS0_TS1 module, [1], [2] esta.general.read_force_constant module, [1], [2] esta.general.read_jmol module, [1], [2] esta.general.read_kappa module, [1], [2] esta.general.read_xyz module, [1], [2] esta.general.reciprocal_lattice module, [1], [2] esta.general.rename module, [1], [2] esta.general.reverse_array module, [1], [2] esta.general.shift module, [1], [2] esta.general.shift0 module, [1], [2] esta.general.shift_poscar module, [1], [2] esta.general.sum_dictionaries module, [1], [2] esta.general.symbol_from_atm_number module, [1], [2] esta.general.thermo module, [1], [2] esta.general.thermo2 module, [1], [2] esta.general.unique_array module, [1], [2] esta.general.use_pbc_ASE module, [1], [2] esta.general.xsf2cube module, [1], [2] esta.general.xyz module, [1], [2] esta.general.xyz_grouped module, [1], [2] esta.general.xyz_images module, [1], [2] esta.grrmBag module, [1], [2] esta.grrmBag.a module, [1], [2] esta.grrmBag.com2xyz module, [1], [2] esta.grrmBag.get_IRC_path module, [1], [2] esta.grrmBag.get_LUP module, [1], [2] esta.grrmBag.get_LUP_profile_advv module, [1], [2] esta.grrmBag.get_LUPINP module, [1], [2] esta.grrmBag.get_nTS_nEQ_nPT module, [1], [2] esta.grrmBag.input_grrm module, [1], [2] esta.grrmBag.input_grrm_advv module, [1], [2] esta.grrmBag.LUPINP module, [1], [2] esta.grrmBag.output_grrm module, [1], [2] esta.grrmBag.output_grrm_init module, [1], [2] esta.grrmBag.output_grrm_ITR_adv module, [1], [2] esta.grrmBag.output_grrm_ITR_adv1 module, [1], [2] esta.grrmBag.output_grrm_ITR_adv2 module, [1], [2] esta.grrmBag.output_grrm_ITR_adv3 module, [1], [2] esta.grrmBag.output_grrm_ITR_adv4 module, [1], [2] esta.grrmBag.output_grrm_ITR_adv5 module, [1], [2] esta.grrmBag.output_grrm_PT module, [1], [2] esta.grrmBag.output_grrm_RxnMap6 module, [1], [2] esta.grrmBag.output_grrm_TS module, [1], [2] esta.grrmBag.plot_strs_energy module, [1], [2] esta.grrmBag.search_structure2 module, [1], [2] esta.grrmBag.search_structure2_mod module, [1], [2] esta.grrmBag.search_structure3 module, [1], [2] esta.grrmBag.to_location module, [1], [2] esta.grrmBag.to_location_adv module, [1], [2] esta.grrmBag.write_xyz module, [1], [2] esta.grrmBag.x module, [1], [2] esta.interval2Range module esta.kspace module esta.kspace.kgrid module esta.log module

esta.measure module, [1] esta.measure.atomic_units module, [1] esta.measure.conversion_factors module, [1] esta.mlBag module, [1] esta.orcaBag module esta.phonon module, [1] esta.phonon.atm_displacements module, [1] esta.phonon.atm_displacements_selective module, [1] esta.phonon.atm_displacements_selective_general_disp module, [1] esta.phonon.fc_and_freq_selected_atoms module, [1] esta.phonon.force_constant_and_frequencies_selective_subspace_ module, [1] esta.phonon.forces module, [1] esta.phonon.forces_selective module, [1] esta.phonon.x_error_force_constant_and_frequencies_selective_subspace module, [1] esta.phonon.yaml_read_band module, [1] esta.phononBag module esta.phononBag.intensity module esta.phononBag.ir_intensity module esta.phononBag.phonopy module esta.phononBag.phonopy.eigen_vector module esta.phononBag.phonopy.eigenvector module esta.phononBag.phonopy.get_phonon_disp_with_phdos module esta.phononBag.phonopy.phonon_dispersion module esta.phononBag.phonopy.projected_phonon_dos module esta.phononBag.phonopy.read_force_constant module esta.phononBag.read_force_constant module esta.plot module esta.plot.atomic_distance_density_class2 module esta.plot.broken_axis_plot__most_done_only_axis_allignmnet_left module esta.plot.free_energy_2 module esta.plot.multiplot module esta.plot.plot2D module esta.plot.plot_2Ddata_NEB module esta.plot.plot_2Ddata_NEB_adv module esta.plot.plot_free_energy_vs_reaction_coordinate_adv module esta.plot.plot_pdos_Natoms_contribution_adv_both_spin_possible module esta.plot.plot_pdos_with_atoms_contribution_2plots_qe module esta.plot.plot_xanes_ module esta.plot.plotxy module esta.plot.plotxy0 module esta.plot.plotxy1 module esta.plot.plotxy_adv module esta.plot.plotxy_advv module esta.plot.polar_plot module esta.plot.tex_demo module esta.pointGroup module, [1] esta.qeBag module, [1], [2] esta.qeBag.23 module, [1], [2] esta.qeBag.bands_kpts_band_gap module, [1], [2] esta.qeBag.gen_qeinput module, [1], [2] esta.qeBag.gen_qeinput2 module, [1], [2] esta.qeBag.gen_qeinput_adv module, [1], [2] esta.qeBag.get_bands_kpts_band_gap_adv3 module, [1], [2] esta.qeBag.get_output_qe module, [1], [2] esta.qeBag.get_xyz_from_qe_rlxout module, [1], [2] esta.qeBag.neb_qe module, [1], [2] esta.qeBag.neb_qe1 module, [1], [2] esta.qeBag.parse_pseudo module, [1], [2] esta.qeBag.pspot_core_states module, [1], [2] esta.qeBag.rate_const_adv module, [1], [2] esta.qeBag.read_dynmat_adv module, [1], [2] esta.qeBag.read_write module, [1], [2] esta.qeBag.read_write0 module, [1], [2] esta.qeBag.sum_pdos_atom module, [1], [2] esta.qeBag.xbands_kpts_band_gap module, [1], [2] esta.qeBag.xml_qe module, [1], [2] esta.qeBag.zpe module, [1], [2] esta.siestaBag module esta.spaceGroup module esta.spaceGroup.read_cif module esta.spaceGroup.transform module esta.spaceGroup.transform_adv module esta.surfReact module, [1] esta.surfReact.conformer module, [1] esta.to_format module esta.to_yaml module esta.transitionState module, [1] esta.transitionState.associated_legendre module, [1] esta.transitionState.neb module, [1] esta.transitionState.optimizer module, [1] esta.transitionState.potential_2D module, [1] esta.turbomoleBag module esta.vaspBag module esta.vaspBag.add_vacuum_to_unit_cell module esta.vaspBag.band_gap module esta.vaspBag.inout module, [1] esta.vaspBag.inout.crystal_lattice module, [1] esta.vaspBag.inout.diameter_or_area_nanowire module, [1] esta.vaspBag.inout.get_labelling_atoms module, [1] esta.vaspBag.inout.lattice module, [1] esta.vaspBag.inout.old_reciprocal_lattice module, [1] esta.vaspBag.inout.read_eigenval module, [1] esta.vaspBag.inout.read_eigenval_file module, [1] esta.vaspBag.inout.read_outcar module, [1] esta.vaspBag.inout.read_outcar_file module, [1] esta.vaspBag.inout.read_poscar module, [1] esta.vaspBag.inout.reciprocal_lattice module, [1] esta.vaspBag.inout.xml_vasp module, [1] esta.vaspBag.inout.xml_vasp_ASE module, [1] esta.vaspBag.inout.xml_vasp_hse module, [1] esta.vaspBag.postproc module esta.vaspBag.postproc.band_gap module esta.vaspBag.postproc.planarAverage module esta.vaspBag.postproc.planarAverage.grid_data_reading_ module esta.vaspBag.postproc.planarAverage.input_data module esta.vaspBag.postproc.planarAverage.planar_average_ module esta.xtbBag module extract_atomic_strs() (esta.general.manipulate.Manipulate method), [1], [2] extract_atomic_strs_() (esta.general.manipulate.Manipulate method), [1], [2]

F

filter_vib_freq() (in module esta.general.filter_vib_freq), [1], [2] find_VBMin_CBMax() (in module esta.vaspBag.band_gap) (in module esta.vaspBag.postproc.band_gap) flags_grrm() (esta.gaussianBag.input_grrm.GenerateCom method) (esta.gaussianBag.input_grrm_advv.GenerateCom method) (esta.grrmBag.input_grrm.GenerateCom method), [1], [2] (esta.grrmBag.input_grrm_advv.GenerateCom method), [1], [2]

freeze_atoms() (esta.general.manipulate.Manipulate method), [1], [2] freeze_notfreeze_atoms() (esta.grrmBag.input_grrm_advv.GenerateCom method), [1], [2]

G

gauss (class in esta.gaussianBag.output_gaussian_adv) (class in esta.gaussianBag.output_gaussian_adv0) gaussian_distribution() (esta.plot.atomic_distance_density_class2.atom_distance_density method) gen_disp() (in module esta.phonon.atm_displacements), [1] (in module esta.phonon.atm_displacements_selective), [1] (in module esta.phonon.atm_displacements_selective_general_disp), [1] gen_kgrid() (in module esta.kspace.kgrid) general_find_mic() (in module esta.general.use_pbc_ASE), [1], [2] GenerateCom (class in esta.gaussianBag.input_gaussian) (class in esta.gaussianBag.input_grrm) (class in esta.gaussianBag.input_grrm_advv) (class in esta.grrmBag.input_grrm), [1], [2] (class in esta.grrmBag.input_grrm_advv), [1], [2] get_all_atomic_positions() (esta.gaussianBag.output_gaussian_adv.gauss method) (esta.gaussianBag.output_gaussian_adv0.gauss method) (esta.grrmBag.output_grrm_RxnMap6.grrm method), [1], [2] get_all_atomic_positions_from_EQ_list() (esta.grrmBag.output_grrm.grrm method), [1], [2] (esta.grrmBag.output_grrm_init.grrm method), [1], [2] (esta.grrmBag.x.grrm method), [1], [2] get_all_atomic_positions_from_ITR_list() (esta.grrmBag.output_grrm_ITR_adv.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv1.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv2.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv3.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv4.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv5.grrm method), [1], [2] get_all_atomic_positions_from_PT_list() (esta.grrmBag.output_grrm_PT.grrm method), [1], [2] get_all_atomic_positions_from_TS_list() (esta.grrmBag.output_grrm_TS.grrm method), [1], [2] get_all_atoms_labels() (esta.general.crystal_latticee.CrystalLattice method), [1], [2] (esta.vaspBag.inout.crystal_lattice.CrystalLattice method), [1] get_all_atoms_lebels() (in module esta.general.get_labelling_atoms), [1], [2] (in module esta.vaspBag.inout.get_labelling_atoms), [1] get_all_xyz_file() (esta.gaussianBag.output_gaussian_adv.gauss method) (esta.gaussianBag.output_gaussian_adv0.gauss method) (esta.grrmBag.output_grrm.grrm method), [1], [2] (esta.grrmBag.output_grrm_init.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv1.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv2.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv3.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv4.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv5.grrm method), [1], [2] (esta.grrmBag.output_grrm_PT.grrm method), [1], [2] (esta.grrmBag.output_grrm_RxnMap6.grrm method), [1], [2] (esta.grrmBag.output_grrm_TS.grrm method), [1], [2] (esta.grrmBag.x.grrm method), [1], [2] (in module esta.grrmBag.write_xyz), [1], [2] get_all_xyz_in_a_file() (esta.gaussianBag.output_gaussian_adv.gauss method) (esta.gaussianBag.output_gaussian_adv0.gauss method) (esta.general.aadhaar.Aadhaar method), [1], [2] (esta.grrmBag.output_grrm.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv1.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv2.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv3.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv4.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv5.grrm method), [1], [2] (esta.grrmBag.output_grrm_PT.grrm method), [1], [2] (esta.grrmBag.output_grrm_TS.grrm method), [1], [2] (in module esta.grrmBag.write_xyz), [1], [2] get_all_xyz_in_a_file_() (esta.general.aadhaar.Aadhaar method), [1], [2] get_asr() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] get_atm_indices_constraint() (esta.general.manipulate.Manipulate method), [1], [2] get_atm_positions() (esta.general.xyz_grouped.RWpwo method), [1], [2] (esta.qeBag.read_write.RWpwo method), [1], [2] (esta.qeBag.read_write0.RWpwo method), [1], [2] get_atm_type (esta.vaspBag.inout.crystal_lattice.CrystalLattice property), [1] get_atomic_configurations() (in module esta.general.get_configs), [1], [2] (in module esta.general.get_configs_btw2strs), [1], [2] (in module esta.general.xyz_images), [1], [2] get_atomic_positions() (esta.gaussianBag.output_gaussian_adv.gauss method) (esta.gaussianBag.output_gaussian_adv0.gauss method) (esta.grrmBag.output_grrm.grrm method), [1], [2] (esta.grrmBag.output_grrm_init.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv1.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv2.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv3.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv4.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv5.grrm method), [1], [2] (esta.grrmBag.output_grrm_PT.grrm method), [1], [2] (esta.grrmBag.output_grrm_RxnMap6.grrm method), [1], [2] (esta.grrmBag.output_grrm_TS.grrm method), [1], [2] (esta.grrmBag.x.grrm method), [1], [2] (in module esta.gaussianBag.input_gaussian_TODO) get_atomtypes() (in module esta.vaspBag.inout.xml_vasp_ASE), [1] get_atomtypes_from_formula() (in module esta.vaspBag.inout.xml_vasp_ASE), [1] get_bader_data() (in module esta.plot.broken_axis_plot__most_done_only_axis_allignmnet_left) get_bandgap_from_eigenval() (in module esta.vaspBag.band_gap) (in module esta.vaspBag.postproc.band_gap) get_bandgap_from_outcar() (in module esta.vaspBag.band_gap) (in module esta.vaspBag.postproc.band_gap) get_bare_energy() (esta.grrmBag.output_grrm_ITR_adv2.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv3.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv4.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv5.grrm method), [1], [2] get_bent_structure() (in module esta.general.bending_nanoribbon), [1], [2] get_bond_length() (in module esta.bonds) get_broken_axis_plot() (in module esta.plot.broken_axis_plot__most_done_only_axis_allignmnet_left) get_cell_matrix() (esta.vaspBag.inout.crystal_lattice.CrystalLattice method), [1] get_cell_parameters() (esta.general.xyz_grouped.RWpwo method), [1], [2] (esta.qeBag.read_write.RWpwo method), [1], [2] (esta.qeBag.read_write0.RWpwo method), [1], [2] get_cell_vectors (esta.vaspBag.inout.crystal_lattice.CrystalLattice property), [1] get_com_oniom() (esta.general.aadhaar.Aadhaar method), [1], [2] get_com_oniom_frozen() (esta.general.aadhaar.Aadhaar method), [1], [2] get_com_oniom_min() (esta.general.aadhaar.Aadhaar method), [1], [2] get_connection() (esta.grrmBag.output_grrm_RxnMap6.grrm method), [1], [2] get_coord() (in module esta.grrmBag.com2xyz), [1], [2] get_coord_grrm_kin() (in module esta.grrmBag.com2xyz), [1], [2] get_cube_from_xsf() (in module esta.general.xsf2cube), [1], [2] get_cutoff_wfc_rho() (in module esta.qeBag.gen_qeinput2), [1], [2] get_dispPOSCAR() (esta.vaspBag.inout.crystal_lattice.CrystalLattice method), [1] get_dynamical_matrix() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.forces), [1] (in module esta.phonon.forces_selective), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] get_E_vib() (esta.general.thermo.ThermoDyn method), [1], [2] (esta.general.thermo.ThermoHarmonic method), [1], [2] (esta.general.thermo2.ThermoDyn method), [1], [2] (esta.general.thermo2.ThermoHarmonic method), [1], [2] get_each_atm_type (esta.vaspBag.inout.crystal_lattice.CrystalLattice property), [1] get_eigen() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.forces), [1] (in module esta.phonon.forces_selective), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] get_eigen_() (in module esta.phonon.fc_and_freq_selected_atoms), [1] get_element_label() (esta.general.xyz_grouped.RWpwo method), [1], [2] (esta.qeBag.read_write.RWpwo method), [1], [2] (esta.qeBag.read_write0.RWpwo method), [1], [2] get_energies() (esta.gaussianBag.output_gaussian_adv.gauss method) (esta.gaussianBag.output_gaussian_adv0.gauss method) get_energies_and_kpt() (esta.general.xyz_grouped.RWpwo method), [1], [2] (esta.qeBag.read_write.RWpwo method), [1], [2] (esta.qeBag.read_write0.RWpwo method), [1], [2] get_energy() (esta.grrmBag.output_grrm.grrm method), [1], [2] (esta.grrmBag.output_grrm_init.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv1.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv2.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv3.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv4.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv5.grrm method), [1], [2] (esta.grrmBag.output_grrm_PT.grrm method), [1], [2] (esta.grrmBag.output_grrm_RxnMap6.grrm method), [1], [2] (esta.grrmBag.output_grrm_TS.grrm method), [1], [2] (esta.grrmBag.x.grrm method), [1], [2] (in module esta.grrmBag.get_IRC_path), [1], [2] get_energy_general() (esta.grrmBag.output_grrm_RxnMap6.grrm method), [1], [2] get_enthalpy() (esta.general.thermo.ThermoIdealGas method), [1], [2] (esta.general.thermo2.ThermoIdealGas method), [1], [2] (in module esta.grrmBag.get_IRC_path), [1], [2] get_entropy() (esta.general.thermo.ThermoIdealGas method), [1], [2] (esta.general.thermo2.ThermoIdealGas method), [1], [2] get_EQ_IRC() (in module esta.grrmBag.a), [1], [2] (in module esta.grrmBag.get_IRC_path), [1], [2] get_EQ_TS_IRC() (in module esta.grrmBag.a), [1], [2] (in module esta.grrmBag.get_IRC_path), [1], [2] get_fermi() (in module esta.plot.plot_pdos_Natoms_contribution_adv_both_spin_possible) (in module esta.plot.plot_pdos_with_atoms_contribution_2plots_qe) (in module esta.plot.plot_xanes_) (in module esta.qeBag.get_output_qe), [1], [2] get_fermi2() (in module esta.qeBag.get_output_qe), [1], [2] get_fermi_from_dos() (in module esta.plot.plot_pdos_Natoms_contribution_adv_both_spin_possible) (in module esta.plot.plot_pdos_with_atoms_contribution_2plots_qe) get_force_ci (esta.transitionState.neb.Neb property), [1] get_force_perpen() (esta.transitionState.neb.Neb method), [1] get_forceconstant_matrix() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.forces), [1] (in module esta.phonon.forces_selective), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] get_forces() (esta.gaussianBag.output_gaussian_adv.gauss method) (esta.gaussianBag.output_gaussian_adv0.gauss method) (in module esta.qeBag.get_output_qe), [1], [2] get_forces_central() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.forces), [1] (in module esta.phonon.forces_selective), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] get_forces_dict() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.forces), [1] (in module esta.phonon.forces_selective), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] get_forces_dict_parta() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] get_forces_minus() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.forces), [1] (in module esta.phonon.forces_selective), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] get_forces_plus() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.forces), [1] (in module esta.phonon.forces_selective), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] get_free_energy() (esta.plot.free_energy_2.GibbsFreeEnergy method) (in module esta.grrmBag.a), [1], [2] (in module esta.grrmBag.get_IRC_path), [1], [2] get_freq() (in module esta.qeBag.zpe), [1], [2] get_freq_intensity_plot_data() (in module esta.phononBag.intensity) (in module esta.phononBag.ir_intensity) get_Gibbs_free_energy() (esta.general.thermo.ThermoIdealGas method), [1], [2] (esta.general.thermo2.ThermoIdealGas method), [1], [2] get_grouped_list() (esta.general.operation.transform method), [1], [2] (esta.general.xyz_grouped.RWpwi method), [1], [2] (esta.general.xyz_grouped.RWpwo method), [1], [2] (esta.qeBag.neb_qe.neb method), [1], [2] (esta.qeBag.read_write.RWpwi method), [1], [2] (esta.qeBag.read_write.RWpwo method), [1], [2] (esta.qeBag.read_write0.RWpwi method), [1], [2] (esta.qeBag.read_write0.RWpwo method), [1], [2] (esta.vaspBag.inout.crystal_lattice.CrystalLattice method), [1] (in module esta.general.list_grouped_and_unique), [1], [2]

get_grouped_xyz() (esta.general.operation.transform method), [1], [2] (esta.spaceGroup.transform.Transform method) (esta.spaceGroup.transform_adv.transform method) get_Helmholtz_free_energy() (esta.general.thermo.ThermoHarmonic method), [1], [2] (esta.general.thermo2.ThermoHarmonic method), [1], [2] get_homo_lumo() (esta.gaussianBag.output_gaussian_adv.gauss method) get_idatm_iddir_iddispl() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.forces), [1] (in module esta.phonon.forces_selective), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] get_input_parameters() (in module esta.qeBag.gen_qeinput), [1], [2] (in module esta.qeBag.gen_qeinput_adv), [1], [2] get_integrated_electrons() (in module esta.general.integration1D_over_a_cutoff), [1], [2] get_internal_energy() (esta.general.thermo.ThermoHarmonic method), [1], [2] (esta.general.thermo2.ThermoHarmonic method), [1], [2] get_irc_path() (in module esta.grrmBag.a), [1], [2] (in module esta.grrmBag.get_IRC_path), [1], [2] get_kgrid() (in module esta.kspace.kgrid) get_list_of_string_and_float() (in module esta.gaussianBag.input_gaussian_TODO) get_location_peak_and_average() (in module esta.general.peak_position_and_average_1D), [1], [2] get_lup_inp() (in module esta.grrmBag.get_LUP), [1], [2] (in module esta.grrmBag.get_LUPINP), [1], [2] get_lup_out() (in module esta.grrmBag.get_LUP), [1], [2] get_lup_profile() (in module esta.grrmBag.get_LUP_profile_advv), [1], [2] get_lup_profile2() (in module esta.grrmBag.get_LUP_profile_advv), [1], [2] get_LUPINP() (in module esta.grrmBag.LUPINP), [1], [2] get_map() (esta.grrmBag.output_grrm_RxnMap6.grrm method), [1], [2] get_map2() (esta.grrmBag.output_grrm_RxnMap6.grrm method), [1], [2] get_metric_tensor() (in module esta.general.metric_tensor), [1], [2] get_moment_inertia() (esta.general.thermo.ThermoDyn method), [1], [2] (esta.general.thermo2.ThermoDyn method), [1], [2] get_moved_atoms_and_symbols() (in module esta.general.get_moved_atom_n_symb), [1], [2] get_N1_N2_N3_in_MP_grid() (in module esta.qeBag.gen_qeinput), [1], [2] (in module esta.qeBag.gen_qeinput2), [1], [2] (in module esta.qeBag.gen_qeinput_adv), [1], [2] get_natm_type (esta.vaspBag.inout.crystal_lattice.CrystalLattice property), [1] get_natoms() (esta.general.xyz_grouped.RWpwo method), [1], [2] (esta.qeBag.read_write.RWpwo method), [1], [2] (esta.qeBag.read_write0.RWpwo method), [1], [2] (in module esta.qeBag.get_output_qe), [1], [2] get_natoms_dummy() (esta.gaussianBag.output_gaussian_adv.gauss method) (esta.gaussianBag.output_gaussian_adv0.gauss method) get_natoms_IRC() (in module esta.grrmBag.a), [1], [2] (in module esta.grrmBag.get_IRC_path), [1], [2] get_neach_type() (esta.general.operation.transform method), [1], [2] (esta.general.xyz_grouped.RWpwi method), [1], [2] (esta.general.xyz_grouped.RWpwo method), [1], [2] (esta.qeBag.neb_qe.neb method), [1], [2] (esta.qeBag.read_write.RWpwi method), [1], [2] (esta.qeBag.read_write.RWpwo method), [1], [2] (esta.qeBag.read_write0.RWpwi method), [1], [2] (esta.qeBag.read_write0.RWpwo method), [1], [2] (esta.spaceGroup.transform.Transform method) (esta.spaceGroup.transform_adv.transform method) (esta.vaspBag.inout.crystal_lattice.CrystalLattice method), [1] get_neb_plot() (in module esta.plot.plot_2Ddata_NEB) (in module esta.plot.plot_2Ddata_NEB_adv) get_nEQ() (in module esta.grrmBag.get_nTS_nEQ_nPT), [1], [2] get_nPT() (in module esta.grrmBag.get_nTS_nEQ_nPT), [1], [2] get_nTS() (in module esta.grrmBag.get_nTS_nEQ_nPT), [1], [2] get_nudged_force (esta.transitionState.neb.Neb property), [1] get_parameters_pseudo() (in module esta.qeBag.gen_qeinput), [1], [2] (in module esta.qeBag.gen_qeinput_adv), [1], [2] get_pdos_files() (in module esta.plot.plot_pdos_Natoms_contribution_adv_both_spin_possible) (in module esta.plot.plot_pdos_with_atoms_contribution_2plots_qe) get_plot() (in module esta.plot.plotxy) (in module esta.plot.plotxy0) (in module esta.plot.plotxy1) (in module esta.plot.plotxy_adv) (in module esta.plot.plotxy_advv) get_plot1() (in module esta.plot.plotxy) (in module esta.plot.plotxy_advv) get_plot_multiple() (in module esta.plot.plotxy) (in module esta.plot.plotxy_advv) get_plots() (in module esta.plot.plot_pdos_Natoms_contribution_adv_both_spin_possible) (in module esta.plot.plot_pdos_with_atoms_contribution_2plots_qe) (in module esta.plot.plot_xanes_) get_plots1() (in module esta.plot.plot_pdos_Natoms_contribution_adv_both_spin_possible) (in module esta.plot.plot_pdos_with_atoms_contribution_2plots_qe) get_poscar() (esta.general.aadhaar.Aadhaar method), [1], [2] (esta.general.crystal_latticee.CrystalLattice method), [1], [2] (esta.general.xyz_grouped.RWpwi method), [1], [2] (esta.general.xyz_grouped.RWpwo method), [1], [2] (esta.qeBag.read_write.RWpwi method), [1], [2] (esta.qeBag.read_write.RWpwo method), [1], [2] (esta.qeBag.read_write0.RWpwi method), [1], [2] (esta.qeBag.read_write0.RWpwo method), [1], [2] (esta.vaspBag.inout.crystal_lattice.CrystalLattice method), [1] (in module esta.qeBag.xml_qe), [1], [2] (in module esta.vaspBag.inout.read_poscar), [1] get_poscar_images() (in module esta.general.get_configs), [1], [2] (in module esta.general.get_configs_btw2strs), [1], [2] get_potential_energy() (in module esta.transitionState.potential_2D), [1] get_pressure() (in module esta.qeBag.get_output_qe), [1], [2] get_pseudo_tags() (in module esta.general.pseudo_info), [1], [2] get_qe_input() (in module esta.general.b), [1], [2] (in module esta.qeBag.gen_qeinput), [1], [2] (in module esta.qeBag.gen_qeinput2), [1], [2] (in module esta.qeBag.gen_qeinput_adv), [1], [2] get_range_int_from_intervals() (in module esta.general.get_range_from_intervals), [1], [2] (in module esta.interval2Range) (in module esta.plot.plot_pdos_Natoms_contribution_adv_both_spin_possible) (in module esta.plot.plot_pdos_with_atoms_contribution_2plots_qe) get_rate_constant() (in module esta.qeBag.rate_const_adv), [1], [2] get_reciprocal_lattice() (esta.vaspBag.inout.crystal_lattice.CrystalLattice method), [1] get_rVolume (esta.vaspBag.inout.crystal_lattice.CrystalLattice property), [1] get_S_vib() (esta.general.thermo.ThermoDyn method), [1], [2] (esta.general.thermo.ThermoHarmonic method), [1], [2] (esta.general.thermo2.ThermoDyn method), [1], [2] (esta.general.thermo2.ThermoHarmonic method), [1], [2] get_selectivePOSCAR() (esta.vaspBag.inout.crystal_lattice.CrystalLattice method), [1] get_sposcar() (esta.general.operation.transform method), [1], [2] (esta.spaceGroup.transform.Transform method) (esta.spaceGroup.transform_adv.transform method) get_spring_force_parallel() (esta.transitionState.neb.Neb method), [1] get_sqrt_mass_array() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.forces), [1] (in module esta.phonon.forces_selective), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] get_str() (esta.grrmBag.search_structure2.struct method), [1], [2] (esta.grrmBag.search_structure2_mod.struct method), [1], [2] (esta.grrmBag.search_structure3.struct method), [1], [2] get_str_and_float() (in module esta.gaussianBag.input_gaussian_TODO) get_str_info() (esta.grrmBag.search_structure2.strInfo method), [1], [2] (esta.grrmBag.search_structure2_mod.strInfo method), [1], [2] (esta.grrmBag.search_structure3.strInfo method), [1], [2] get_str_info1() (esta.grrmBag.search_structure3.strInfo method), [1], [2] get_supercell() (esta.general.operation.transform method), [1], [2] (esta.spaceGroup.transform.Transform method) (esta.spaceGroup.transform_adv.transform method) get_symbol_from_atomic_number() (esta.qeBag.neb_qe.neb method), [1], [2] (in module esta.general.symbol_from_atm_number), [1], [2] get_symmetrized_force_constant_matrix() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.forces), [1] (in module esta.phonon.forces_selective), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] get_tangent() (esta.transitionState.neb.Neb method), [1] get_total_energy() (in module esta.qeBag.get_output_qe), [1], [2] get_uniq_freq_n_intensity() (in module esta.phononBag.intensity) (in module esta.phononBag.ir_intensity) get_unique_array() (in module esta.general.unique_array), [1], [2] get_unique_list() (esta.general.operation.transform method), [1], [2] (esta.general.xyz_grouped.RWpwi method), [1], [2] (esta.general.xyz_grouped.RWpwo method), [1], [2] (esta.qeBag.neb_qe.neb method), [1], [2] (esta.qeBag.read_write.RWpwi method), [1], [2] (esta.qeBag.read_write.RWpwo method), [1], [2] (esta.qeBag.read_write0.RWpwi method), [1], [2] (esta.qeBag.read_write0.RWpwo method), [1], [2] (esta.vaspBag.inout.crystal_lattice.CrystalLattice method), [1] (in module esta.general.list_grouped_and_unique), [1], [2] get_xlsx_csv_file() (in module esta.dict_to_xlsx_csv) get_xyz() (in module esta.qeBag.get_xyz_from_qe_rlxout), [1], [2] get_xyz_all() (in module esta.qeBag.get_xyz_from_qe_rlxout), [1], [2] get_xyz_data() (in module esta.general.read_jmol), [1], [2] get_xyz_file() (esta.gaussianBag.output_gaussian_adv.gauss method) (esta.gaussianBag.output_gaussian_adv0.gauss method) (esta.general.aadhaar.Aadhaar method), [1], [2] (esta.general.xyz_grouped.RWpwo method), [1], [2] (esta.grrmBag.output_grrm.grrm method), [1], [2] (esta.grrmBag.output_grrm_init.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv1.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv2.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv3.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv4.grrm method), [1], [2] (esta.grrmBag.output_grrm_ITR_adv5.grrm method), [1], [2] (esta.grrmBag.output_grrm_PT.grrm method), [1], [2] (esta.grrmBag.output_grrm_RxnMap6.grrm method), [1], [2] (esta.grrmBag.output_grrm_TS.grrm method), [1], [2] (esta.grrmBag.x.grrm method), [1], [2] (esta.qeBag.read_write.RWpwo method), [1], [2] (esta.qeBag.read_write0.RWpwo method), [1], [2] (in module esta.grrmBag.com2xyz), [1], [2] get_xyz_frozen() (esta.general.aadhaar.Aadhaar method), [1], [2] get_xyz_grouped() (esta.general.aadhaar.Aadhaar method), [1], [2] get_xyz_grouped_file() (esta.general.xyz_grouped.RWpwo method), [1], [2] (esta.qeBag.read_write.RWpwo method), [1], [2] (esta.qeBag.read_write0.RWpwo method), [1], [2] get_xyz_oniom_file() (esta.general.aadhaar.Aadhaar method), [1], [2] get_zpe() (esta.general.thermo.ThermoDyn method), [1], [2] (esta.general.thermo.ThermoHarmonic method), [1], [2] (esta.general.thermo2.ThermoDyn method), [1], [2] (esta.general.thermo2.ThermoHarmonic method), [1], [2] GibbsFreeEnergy (class in esta.plot.free_energy_2) grid_data_read() (in module esta.vaspBag.postproc.planarAverage.grid_data_reading_) grrm (class in esta.grrmBag.output_grrm), [1], [2] (class in esta.grrmBag.output_grrm_init), [1], [2] (class in esta.grrmBag.output_grrm_ITR_adv), [1], [2] (class in esta.grrmBag.output_grrm_ITR_adv1), [1], [2] (class in esta.grrmBag.output_grrm_ITR_adv2), [1], [2] (class in esta.grrmBag.output_grrm_ITR_adv3), [1], [2] (class in esta.grrmBag.output_grrm_ITR_adv4), [1], [2] (class in esta.grrmBag.output_grrm_ITR_adv5), [1], [2] (class in esta.grrmBag.output_grrm_PT), [1], [2] (class in esta.grrmBag.output_grrm_RxnMap6), [1], [2] (class in esta.grrmBag.output_grrm_TS), [1], [2] (class in esta.grrmBag.x), [1], [2]

I

id_orb2_indx() (in module esta.qeBag.pspot_core_states), [1], [2] invert_atoms() (esta.general.manipulate.Manipulate method), [1], [2] is_basis() (in module esta.general.affine), [1], [2]

is_cartesian (esta.vaspBag.inout.crystal_lattice.CrystalLattice property), [1] is_crystal (esta.vaspBag.inout.crystal_lattice.CrystalLattice property), [1] is_rotation_matrix() (in module esta.general.affine), [1], [2] is_selective_dynamics (esta.vaspBag.inout.crystal_lattice.CrystalLattice property), [1]

L

lattice (class in esta.vaspBag.inout.lattice), [1]

log_footer() (in module esta.log) log_header() (in module esta.log)

M

Manipulate (class in esta.general.manipulate), [1], [2] mass_weighted_distance() (in module esta.general.get_configs), [1], [2] (in module esta.general.get_configs_btw2strs), [1], [2] max_scalarlist() (in module esta.general.compare_scalar), [1], [2] (in module esta.qeBag.gen_qeinput), [1], [2] (in module esta.qeBag.gen_qeinput2), [1], [2] (in module esta.qeBag.gen_qeinput_adv), [1], [2] merge() (esta.general.manipulate.Manipulate method), [1], [2] min_scalarlist() (in module esta.general.compare_scalar), [1], [2] (in module esta.qeBag.gen_qeinput), [1], [2] (in module esta.qeBag.gen_qeinput2), [1], [2] (in module esta.qeBag.gen_qeinput_adv), [1], [2] minimize_rotation_and_translation() (in module esta.general.min_trans_rot), [1], [2] minimum_image_distance() (in module esta.general.affine), [1], [2] module esta esta.abinitBag esta.bonds esta.c esta.dict_to_xlsx_csv esta.element esta.element_data esta.externalBag esta.extract_data esta.fortran esta.gamessBag esta.gaussianBag esta.gaussianBag.input_gaussian esta.gaussianBag.input_gaussian_TODO esta.gaussianBag.input_grrm esta.gaussianBag.input_grrm_advv esta.gaussianBag.output_gaussian_adv esta.gaussianBag.output_gaussian_adv0 esta.general, [1], [2] esta.general.aadhaar, [1], [2] esta.general.add_const_to_dict, [1], [2] esta.general.add_vacuum_to_unit_cell, [1], [2] esta.general.affine, [1], [2] esta.general.b, [1], [2] esta.general.bending_nanoribbon, [1], [2] esta.general.boltzmann, [1], [2] esta.general.cartAndSpherical, [1], [2] esta.general.compare_scalar, [1], [2] esta.general.conversion_factors, [1], [2] esta.general.crystal_latticee, [1], [2] esta.general.direction_index2str, [1], [2] esta.general.distance_matrix_PBC, [1], [2] esta.general.distances_ase_esa, [1], [2] esta.general.entropy_data, [1], [2] esta.general.filter_vib_freq, [1], [2] esta.general.from_pos2xyz, [1], [2] esta.general.get_com, [1], [2] esta.general.get_configs, [1], [2] esta.general.get_configs_btw2strs, [1], [2] esta.general.get_labelling_atoms, [1], [2] esta.general.get_moved_atom_n_symb, [1], [2] esta.general.get_range_from_intervals, [1], [2] esta.general.get_rotation_matrix, [1], [2] esta.general.integration1D_over_a_cutoff, [1], [2] esta.general.list_grouped_and_unique, [1], [2] esta.general.manipulate, [1], [2] esta.general.metric_tensor, [1], [2] esta.general.min_trans_rot, [1], [2] esta.general.niggli_reduce, [1], [2] esta.general.operation, [1], [2] esta.general.peak_position_and_average_1D, [1], [2] esta.general.pseudo_info, [1], [2] esta.general.rate_const_IS0_TS1, [1], [2] esta.general.read_force_constant, [1], [2] esta.general.read_jmol, [1], [2] esta.general.read_kappa, [1], [2] esta.general.read_xyz, [1], [2] esta.general.reciprocal_lattice, [1], [2] esta.general.rename, [1], [2] esta.general.reverse_array, [1], [2] esta.general.shift, [1], [2] esta.general.shift0, [1], [2] esta.general.shift_poscar, [1], [2] esta.general.sum_dictionaries, [1], [2] esta.general.symbol_from_atm_number, [1], [2] esta.general.thermo, [1], [2] esta.general.thermo2, [1], [2] esta.general.unique_array, [1], [2] esta.general.use_pbc_ASE, [1], [2] esta.general.xsf2cube, [1], [2] esta.general.xyz, [1], [2] esta.general.xyz_grouped, [1], [2] esta.general.xyz_images, [1], [2] esta.grrmBag, [1], [2] esta.grrmBag.a, [1], [2] esta.grrmBag.com2xyz, [1], [2] esta.grrmBag.get_IRC_path, [1], [2] esta.grrmBag.get_LUP, [1], [2] esta.grrmBag.get_LUP_profile_advv, [1], [2] esta.grrmBag.get_LUPINP, [1], [2] esta.grrmBag.get_nTS_nEQ_nPT, [1], [2] esta.grrmBag.input_grrm, [1], [2] esta.grrmBag.input_grrm_advv, [1], [2] esta.grrmBag.LUPINP, [1], [2] esta.grrmBag.output_grrm, [1], [2] esta.grrmBag.output_grrm_init, [1], [2] esta.grrmBag.output_grrm_ITR_adv, [1], [2] esta.grrmBag.output_grrm_ITR_adv1, [1], [2] esta.grrmBag.output_grrm_ITR_adv2, [1], [2] esta.grrmBag.output_grrm_ITR_adv3, [1], [2] esta.grrmBag.output_grrm_ITR_adv4, [1], [2] esta.grrmBag.output_grrm_ITR_adv5, [1], [2] esta.grrmBag.output_grrm_PT, [1], [2] esta.grrmBag.output_grrm_RxnMap6, [1], [2] esta.grrmBag.output_grrm_TS, [1], [2] esta.grrmBag.plot_strs_energy, [1], [2] esta.grrmBag.search_structure2, [1], [2] esta.grrmBag.search_structure2_mod, [1], [2] esta.grrmBag.search_structure3, [1], [2] esta.grrmBag.to_location, [1], [2] esta.grrmBag.to_location_adv, [1], [2] esta.grrmBag.write_xyz, [1], [2] esta.grrmBag.x, [1], [2] esta.interval2Range esta.kspace esta.kspace.kgrid esta.log esta.measure, [1] esta.measure.atomic_units, [1] esta.measure.conversion_factors, [1] esta.mlBag, [1] esta.orcaBag esta.phonon, [1] esta.phonon.atm_displacements, [1] esta.phonon.atm_displacements_selective, [1] esta.phonon.atm_displacements_selective_general_disp, [1] esta.phonon.fc_and_freq_selected_atoms, [1] esta.phonon.force_constant_and_frequencies_selective_subspace_, [1] esta.phonon.forces, [1] esta.phonon.forces_selective, [1] esta.phonon.x_error_force_constant_and_frequencies_selective_subspace, [1] esta.phonon.yaml_read_band, [1] esta.phononBag esta.phononBag.intensity esta.phononBag.ir_intensity esta.phononBag.phonopy esta.phononBag.phonopy.eigen_vector esta.phononBag.phonopy.eigenvector esta.phononBag.phonopy.get_phonon_disp_with_phdos esta.phononBag.phonopy.phonon_dispersion esta.phononBag.phonopy.projected_phonon_dos esta.phononBag.phonopy.read_force_constant esta.phononBag.read_force_constant esta.plot esta.plot.atomic_distance_density_class2 esta.plot.broken_axis_plot__most_done_only_axis_allignmnet_left esta.plot.free_energy_2 esta.plot.multiplot esta.plot.plot2D esta.plot.plot_2Ddata_NEB esta.plot.plot_2Ddata_NEB_adv esta.plot.plot_free_energy_vs_reaction_coordinate_adv esta.plot.plot_pdos_Natoms_contribution_adv_both_spin_possible esta.plot.plot_pdos_with_atoms_contribution_2plots_qe esta.plot.plot_xanes_ esta.plot.plotxy esta.plot.plotxy0 esta.plot.plotxy1 esta.plot.plotxy_adv esta.plot.plotxy_advv esta.plot.polar_plot esta.plot.tex_demo esta.pointGroup, [1] esta.qeBag, [1], [2] esta.qeBag.23, [1], [2] esta.qeBag.bands_kpts_band_gap, [1], [2] esta.qeBag.gen_qeinput, [1], [2] esta.qeBag.gen_qeinput2, [1], [2] esta.qeBag.gen_qeinput_adv, [1], [2] esta.qeBag.get_bands_kpts_band_gap_adv3, [1], [2] esta.qeBag.get_output_qe, [1], [2] esta.qeBag.get_xyz_from_qe_rlxout, [1], [2] esta.qeBag.neb_qe, [1], [2] esta.qeBag.neb_qe1, [1], [2] esta.qeBag.parse_pseudo, [1], [2] esta.qeBag.pspot_core_states, [1], [2] esta.qeBag.rate_const_adv, [1], [2] esta.qeBag.read_dynmat_adv, [1], [2] esta.qeBag.read_write, [1], [2] esta.qeBag.read_write0, [1], [2] esta.qeBag.sum_pdos_atom, [1], [2] esta.qeBag.xbands_kpts_band_gap, [1], [2] esta.qeBag.xml_qe, [1], [2] esta.qeBag.zpe, [1], [2] esta.siestaBag esta.spaceGroup esta.spaceGroup.read_cif esta.spaceGroup.transform esta.spaceGroup.transform_adv esta.surfReact, [1] esta.surfReact.conformer, [1] esta.to_format esta.to_yaml esta.transitionState, [1] esta.transitionState.associated_legendre, [1] esta.transitionState.neb, [1] esta.transitionState.optimizer, [1] esta.transitionState.potential_2D, [1] esta.turbomoleBag esta.vaspBag esta.vaspBag.add_vacuum_to_unit_cell esta.vaspBag.band_gap esta.vaspBag.inout, [1] esta.vaspBag.inout.crystal_lattice, [1] esta.vaspBag.inout.diameter_or_area_nanowire, [1] esta.vaspBag.inout.get_labelling_atoms, [1] esta.vaspBag.inout.lattice, [1] esta.vaspBag.inout.old_reciprocal_lattice, [1] esta.vaspBag.inout.read_eigenval, [1] esta.vaspBag.inout.read_eigenval_file, [1] esta.vaspBag.inout.read_outcar, [1] esta.vaspBag.inout.read_outcar_file, [1] esta.vaspBag.inout.read_poscar, [1] esta.vaspBag.inout.reciprocal_lattice, [1] esta.vaspBag.inout.xml_vasp, [1] esta.vaspBag.inout.xml_vasp_ASE, [1] esta.vaspBag.inout.xml_vasp_hse, [1] esta.vaspBag.postproc esta.vaspBag.postproc.band_gap esta.vaspBag.postproc.planarAverage esta.vaspBag.postproc.planarAverage.grid_data_reading_ esta.vaspBag.postproc.planarAverage.input_data esta.vaspBag.postproc.planarAverage.planar_average_ esta.xtbBag

move_to_location() (in module esta.grrmBag.to_location), [1], [2] (in module esta.grrmBag.to_location_adv), [1], [2]

N

neb (class in esta.qeBag.neb_qe), [1], [2] (class in esta.qeBag.neb_qe1), [1], [2] Neb (class in esta.transitionState.neb), [1] niggli_reduce() (in module esta.general.niggli_reduce), [1], [2]

np (esta.gaussianBag.input_gaussian.GenerateCom attribute) (esta.gaussianBag.input_grrm.GenerateCom attribute) (esta.grrmBag.input_grrm.GenerateCom attribute), [1], [2] (esta.qeBag.neb_qe.neb attribute), [1], [2] (esta.qeBag.neb_qe1.neb attribute), [1], [2]

P

parse_pseudoUPF() (in module esta.qeBag.parse_pseudo), [1], [2] planar_average_3D() (in module esta.vaspBag.postproc.planarAverage.planar_average_) plot_free_energy() (in module esta.plot.plot_free_energy_vs_reaction_coordinate_adv) plot_kappa() (in module esta.general.read_kappa), [1], [2] plot_multiplot_in_1column() (in module esta.plot.multiplot)

plot_phonon_disp_with_phdos() (in module esta.phononBag.phonopy.get_phonon_disp_with_phdos) plot_polar() (in module esta.plot.polar_plot) pos2xyz() (in module esta.general.from_pos2xyz), [1], [2] process_colums() (in module esta.plot.plot_pdos_Natoms_contribution_adv_both_spin_possible) (in module esta.plot.plot_pdos_with_atoms_contribution_2plots_qe) process_data() (in module esta.grrmBag.plot_strs_energy), [1], [2]

Q

q_partition() (in module esta.general.rate_const_IS0_TS1), [1], [2] (in module esta.qeBag.rate_const_adv), [1], [2]

qe_warning() (in module esta.qeBag.get_output_qe), [1], [2] quaternion_to_matrix() (in module esta.general.min_trans_rot), [1], [2] quick_min() (in module esta.transitionState.optimizer), [1]

R

read_axsf() (esta.qeBag.neb_qe.neb method), [1], [2] (esta.qeBag.neb_qe1.neb method), [1], [2] read_data() (esta.plot.multiplot.DataStore method) read_dynamical_matrix_q0() (in module esta.qeBag.read_dynmat_adv), [1], [2] read_eigenval() (in module esta.vaspBag.inout.read_eigenval), [1] (in module esta.vaspBag.inout.read_eigenval_file), [1] read_eigenvector() (in module esta.phononBag.phonopy.eigen_vector) (in module esta.phononBag.phonopy.eigenvector) read_eigenvector_dat() (in module esta.phononBag.phonopy.eigen_vector) (in module esta.phononBag.phonopy.eigenvector) read_force_constant_phonopy() (in module esta.general.read_force_constant), [1], [2] (in module esta.phononBag.phonopy.read_force_constant) (in module esta.phononBag.read_force_constant) read_freq_data() (in module esta.general.rate_const_IS0_TS1), [1], [2] (in module esta.qeBag.rate_const_adv), [1], [2] read_freq_eigenvector_dat() (in module esta.phononBag.phonopy.eigen_vector) read_outcar() (in module esta.vaspBag.inout.read_outcar), [1] (in module esta.vaspBag.inout.read_outcar_file), [1] read_path() (esta.qeBag.neb_qe.neb method), [1], [2] (esta.qeBag.neb_qe1.neb method), [1], [2] read_phonon_disp() (in module esta.phononBag.phonopy.phonon_dispersion) read_poscar() (esta.vaspBag.inout.crystal_lattice.CrystalLattice method), [1] read_projected_phonon_dos() (in module esta.phononBag.phonopy.projected_phonon_dos) read_qe_xml() (in module esta.qeBag.xml_qe), [1], [2] read_UPF_xml() (in module esta.qeBag.pspot_core_states), [1], [2] read_vasp() (in module esta.vaspBag.inout.xml_vasp_ASE), [1] read_vasp_out() (in module esta.vaspBag.inout.xml_vasp_ASE), [1] read_vasp_xdatcar() (in module esta.vaspBag.inout.xml_vasp_ASE), [1] read_vasp_xml() (in module esta.vaspBag.inout.xml_vasp), [1] (in module esta.vaspBag.inout.xml_vasp_ASE), [1] (in module esta.vaspBag.inout.xml_vasp_hse), [1] read_xsf() (esta.qeBag.neb_qe.neb method), [1], [2] read_xyz() (esta.gaussianBag.input_gaussian.GenerateCom method) (esta.gaussianBag.input_grrm.GenerateCom method) (esta.gaussianBag.input_grrm_advv.GenerateCom method) (esta.general.aadhaar.Aadhaar method), [1], [2] (esta.general.xyz.Xyz method), [1], [2] (esta.grrmBag.input_grrm.GenerateCom method), [1], [2] (esta.grrmBag.input_grrm_advv.GenerateCom method), [1], [2] (esta.grrmBag.search_structure2.struct method), [1], [2] (esta.grrmBag.search_structure2_mod.struct method), [1], [2] (esta.grrmBag.search_structure3.struct method), [1], [2] (esta.qeBag.neb_qe.neb method), [1], [2] (esta.qeBag.neb_qe1.neb method), [1], [2]

read_xyz2() (esta.gaussianBag.input_grrm.GenerateCom method) (esta.gaussianBag.input_grrm_advv.GenerateCom method) (esta.grrmBag.input_grrm.GenerateCom method), [1], [2] (esta.grrmBag.input_grrm_advv.GenerateCom method), [1], [2] read_xyz_all() (esta.general.aadhaar.Aadhaar method), [1], [2] (esta.general.xyz.Xyz method), [1], [2] read_xyz_file() (in module esta.general.read_xyz), [1], [2] read_yaml_band() (in module esta.phonon.yaml_read_band), [1] ReadKappaCSV() (in module esta.general.read_kappa), [1], [2] reciprocal_lattice() (esta.general.crystal_latticee.CrystalLattice method), [1], [2] (esta.vaspBag.inout.crystal_lattice.CrystalLattice method), [1] (in module esta.general.reciprocal_lattice), [1], [2] (in module esta.vaspBag.inout.old_reciprocal_lattice), [1] (in module esta.vaspBag.inout.reciprocal_lattice), [1] remove_duplicate() (esta.plot.atomic_distance_density_class2.atom_distance_density method) replace() (esta.general.manipulate.Manipulate method), [1], [2] reshape_dyn() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.forces), [1] (in module esta.phonon.forces_selective), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1] reverse_array() (in module esta.general.reverse_array), [1], [2] rosenbrock_2D() (in module esta.plot.plot2D) rot_trans() (esta.general.operation.transform method), [1], [2] (esta.spaceGroup.transform.Transform method) (esta.spaceGroup.transform_adv.transform method) rotation_matrix() (in module esta.general.affine), [1], [2] (in module esta.general.get_rotation_matrix), [1], [2] rotation_matrix_from_points() (in module esta.general.min_trans_rot), [1], [2] RWpwi (class in esta.general.xyz_grouped), [1], [2] (class in esta.qeBag.read_write), [1], [2] (class in esta.qeBag.read_write0), [1], [2] RWpwo (class in esta.general.xyz_grouped), [1], [2] (class in esta.qeBag.read_write), [1], [2] (class in esta.qeBag.read_write0), [1], [2]

S

save_ev() (in module esta.phononBag.phonopy.eigen_vector) (in module esta.phononBag.phonopy.eigenvector) shift() (esta.general.manipulate.Manipulate method), [1], [2] (in module esta.general.shift), [1], [2] (in module esta.general.shift0), [1], [2] shift_poscar() (in module esta.general.shift_poscar), [1], [2] shift_to_origin() (esta.general.manipulate.Manipulate method), [1], [2] (in module esta.general.shift), [1], [2] (in module esta.general.shift0), [1], [2] split_string() (in module esta.general.rename), [1], [2]

steepest_descent() (in module esta.transitionState.optimizer), [1] strInfo (class in esta.grrmBag.search_structure2), [1], [2] (class in esta.grrmBag.search_structure2_mod), [1], [2] (class in esta.grrmBag.search_structure3), [1], [2] struct (class in esta.grrmBag.search_structure2), [1], [2] (class in esta.grrmBag.search_structure2_mod), [1], [2] (class in esta.grrmBag.search_structure3), [1], [2] substitute() (esta.general.manipulate.Manipulate method), [1], [2] sum_dictionaries() (in module esta.general.sum_dictionaries), [1], [2] sum_pdos() (in module esta.qeBag.sum_pdos_atom), [1], [2] surface_plot() (in module esta.plot.plot2D)

T

test() (in module esta.transitionState.associated_legendre), [1] ThermoDyn (class in esta.general.thermo), [1], [2] (class in esta.general.thermo2), [1], [2] ThermoHarmonic (class in esta.general.thermo), [1], [2] (class in esta.general.thermo2), [1], [2] ThermoHindredRotVib (class in esta.general.thermo), [1], [2] (class in esta.general.thermo2), [1], [2] ThermoIdealGas (class in esta.general.thermo), [1], [2] (class in esta.general.thermo2), [1], [2] ThermoLattice (class in esta.general.thermo), [1], [2] (class in esta.general.thermo2), [1], [2] to_cartesian (esta.vaspBag.inout.crystal_lattice.CrystalLattice property), [1] to_cartesian() (in module esta.general.cartAndSpherical), [1], [2] to_crystal (esta.vaspBag.inout.crystal_lattice.CrystalLattice property), [1] to_file() (in module esta.general.rename), [1], [2]

to_format() (in module esta.to_format) to_poscar() (esta.qeBag.neb_qe.neb method), [1], [2] to_spherical() (in module esta.general.cartAndSpherical), [1], [2] to_xyz_file() (esta.qeBag.neb_qe.neb method), [1], [2] to_xyz_files() (esta.qeBag.neb_qe.neb method), [1], [2] (esta.qeBag.neb_qe1.neb method), [1], [2] to_xyz_plus_delta_files() (esta.qeBag.neb_qe.neb method), [1], [2] (esta.qeBag.neb_qe1.neb method), [1], [2] to_yaml() (in module esta.to_yaml) transform (class in esta.general.operation), [1], [2] Transform (class in esta.spaceGroup.transform) transform (class in esta.spaceGroup.transform_adv) transform() (in module esta.general.affine), [1], [2] translation_matrix() (in module esta.general.affine), [1], [2] translation_rotation_matrix() (in module esta.general.affine), [1], [2]

V

vector_prod() (esta.general.xyz_grouped.RWpwo class method), [1], [2] (esta.qeBag.read_write.RWpwo class method), [1], [2] (esta.qeBag.read_write0.RWpwo class method), [1], [2]

W

write_com() (esta.gaussianBag.input_gaussian.GenerateCom method) (esta.gaussianBag.input_grrm.GenerateCom method) (esta.gaussianBag.input_grrm_advv.GenerateCom method) (esta.grrmBag.input_grrm.GenerateCom method), [1], [2] (esta.grrmBag.input_grrm_advv.GenerateCom method), [1], [2] write_com_2xyz() (esta.gaussianBag.input_gaussian.GenerateCom method) (esta.gaussianBag.input_grrm.GenerateCom method) (esta.gaussianBag.input_grrm_advv.GenerateCom method) (esta.grrmBag.input_grrm.GenerateCom method), [1], [2] (esta.grrmBag.input_grrm_advv.GenerateCom method), [1], [2] write_forces() (in module esta.phonon.fc_and_freq_selected_atoms), [1] (in module esta.phonon.force_constant_and_frequencies_selective_subspace_), [1] (in module esta.phonon.forces), [1] (in module esta.phonon.forces_selective), [1] (in module esta.phonon.x_error_force_constant_and_frequencies_selective_subspace), [1]

write_inp() (esta.gaussianBag.input_gaussian.GenerateCom method) (esta.gaussianBag.input_grrm_advv.GenerateCom method) (esta.grrmBag.input_grrm_advv.GenerateCom method), [1], [2] write_input_oniom() (esta.gaussianBag.input_gaussian.GenerateCom method) (esta.gaussianBag.input_grrm_advv.GenerateCom method) (esta.grrmBag.input_grrm_advv.GenerateCom method), [1], [2] write_position_card() (esta.qeBag.neb_qe.neb method), [1], [2] (esta.qeBag.neb_qe1.neb method), [1], [2] write_vasp() (in module esta.vaspBag.inout.xml_vasp_ASE), [1] write_xyz_all_separate() (esta.general.aadhaar.Aadhaar method), [1], [2]

X

Xyz (class in esta.general.xyz), [1], [2]