Index

A

add_bin_dimension() (Frog.class_DiagramParameter.SingleDiagramParameter method) add_empty_diagram() (Frog.class_Diagrams.Diagram static method) (Frog.class_Molecule.MoleculeType method) add_empty_molecule() (Frog.class_Molecule.MoleculeType method) add_mean_dimension() (Frog.class_DiagramParameter.SingleDiagramParameter method) add_population() (Frog.class_Diagrams.Diagram method) add_single_contribution_electric_field_pbc() (in module Frog.electric_field_module) add_single_molecule_property() (Frog.class_Diagrams.Dia_alpha class method) (Frog.class_Diagrams.Dia_beta class method) (Frog.class_Diagrams.Dia_chi class method) (Frog.class_Diagrams.Dia_density class method) (Frog.class_Diagrams.Dia_effective_field class method) (Frog.class_Diagrams.Dia_electric_field class method) (Frog.class_Diagrams.Dia_hbond class method) (Frog.class_Diagrams.Dia_iota class method) (Frog.class_Diagrams.Dia_molecular_orientation class method) (Frog.class_Diagrams.Dia_rdf class method) (Frog.class_Diagrams.Prepare_run_QM class method)

add_value_to_diagram() (Frog.class_Diagrams.Dia_alpha method) (Frog.class_Diagrams.Dia_beta method) (Frog.class_Diagrams.Dia_chi method) (Frog.class_Diagrams.Dia_density method) (Frog.class_Diagrams.Dia_effective_field method) (Frog.class_Diagrams.Dia_electric_field method) (Frog.class_Diagrams.Dia_hbond method) (Frog.class_Diagrams.Dia_iota method) (Frog.class_Diagrams.Dia_molecular_orientation method) (Frog.class_Diagrams.Dia_rdf method) (Frog.class_Diagrams.Diagram method) add_value_to_mean() (Frog.class_Diagrams.Diagram method) all_possible_frequency_caligraphy() (in module Frog.toolbox) alpha_calculation_style (Frog.class_OpticalParameter.OpticalParameter property) analysis_type (Frog.class_DiagramParameter.SingleDiagramParameter property) axis_observable (Frog.class_Diagrams.Diagram property) axis_population (Frog.class_Diagrams.Diagram property) axis_space (Frog.class_Diagrams.Diagram property)

B

beta_calculation_style (Frog.class_OpticalParameter.OpticalParameter property) beta_order (Frog.class_OpticalParameter.OpticalParameter property) bin_size (Frog.class_DiagramParameter.SingleDiagramParameter property)

binarize_array() (in module Frog.toolbox) build_QM_file_localization() (in module Frog.dalton_manager_module) built_environment_first_shell_number() (in module Frog.universe_manager)

C

calculation_style (Frog.class_OpticalParameter.QMParameter property) centering_position_neighbourg() (in module Frog.universe_manager) centering_position_neighbourg_old() (in module Frog.universe_manager) change_bin_size_value() (Frog.class_DiagramParameter.SingleDiagramParameter method) change_tuple_component() (in module Frog.toolbox) check_file_write_read() (in module Frog.check) check_format() (Frog.class_DiagramParameter.SingleDiagramParameter method) check_GP_env_authorised_pbc_condition() (in module Frog.check) check_if_run_already_performed() (in module Frog.dalton_manager_module) check_if_run_done() (in module Frog.dalton_manager_module) check_input() (Frog.class_OpticalParameter.EFParameter method) check_input_qm() (Frog.class_OpticalParameter.QMParameter method) check_molecule_basics() (Frog.class_Molecule.MoleculeType method) check_molecule_geometry() (in module Frog.geometry_manager) check_molecule_position() (in module Frog.Molecules.Water_TIP4P2005_O) check_name_diagram_uniqueness() (in module Frog.check) check_pe_environement() (Frog.class_Molecule.MoleculeType method) check_polarizable_description() (Frog.class_Molecule.MoleculeType method) check_qm_target() (Frog.class_Molecule.MoleculeType method) closest_idx() (in module Frog.universe_manager) command_launch_job (Frog.class_GP.GlobalParameter attribute) compute_angle_3_atoms() (in module Frog.geometry_manager) compute_electric_field_from_electro_description() (in module Frog.electric_field_module) compute_electric_field_on_fly() (in module Frog.electric_field_module) compute_electric_field_PE (Frog.class_OpticalParameter.OpticalParameter property) compute_hbonds() (in module Frog.Molecules.Methanol_OPLSAA) (in module Frog.Molecules.Water_Osted2006_ESdescription) (in module Frog.Molecules.Water_PSPC) (in module Frog.Molecules.Water_RESD_Beerepoot2016) (in module Frog.Molecules.Water_TIP4P2005) (in module Frog.Molecules.Water_TIP4P2005_O) compute_mean_position() (Frog.class_Molecule.SingleMolecule method) (in module Frog.Molecules.Chlore) (in module Frog.Molecules.Ethanol_OPLSAA) (in module Frog.Molecules.Methanol_OPLSAA) (in module Frog.Molecules.Sodium) (in module Frog.Molecules.Water_Osted2006_ESdescription) (in module Frog.Molecules.Water_PSPC) (in module Frog.Molecules.Water_RESD_Beerepoot2016) (in module Frog.Molecules.Water_TIP4P2005) (in module Frog.Molecules.Water_TIP4P2005_O)

compute_molecular_orientation() (in module Frog.Molecules.Methanol_OPLSAA) (in module Frog.Molecules.Water_Osted2006_ESdescription) (in module Frog.Molecules.Water_PSPC) (in module Frog.Molecules.Water_RESD_Beerepoot2016) (in module Frog.Molecules.Water_TIP4P2005) (in module Frog.Molecules.Water_TIP4P2005_O) compute_rot_matrix() (Frog.class_Molecule.SingleMolecule method) compute_rotational_matrix() (in module Frog.Molecules.Chlore) (in module Frog.Molecules.Ethanol_OPLSAA) (in module Frog.Molecules.Methanol_OPLSAA) (in module Frog.Molecules.Sodium) (in module Frog.Molecules.Water_Osted2006_ESdescription) (in module Frog.Molecules.Water_PSPC) (in module Frog.Molecules.Water_RESD_Beerepoot2016) (in module Frog.Molecules.Water_TIP4P2005) (in module Frog.Molecules.Water_TIP4P2005_O) concatenate_bin() (in module Frog.toolbox) concatenate_path() (in module Frog.toolbox) construct_pbc_movement() (in module Frog.universe_manager) construct_pow_name_unit() (in module Frog.class_DiagramParameter) creat_beta_intrinsic() (in module Frog.toolbox) creat_beta_kleinman() (in module Frog.toolbox) creat_directory() (in module Frog.toolbox) creat_name_for_MT_module_load() (in module Frog.toolbox) create_submissionfile_array() (in module Frog.dalton_manager_module)

D

d_molecular_orientation (Frog.class_modules.SingleMoleculeParameter property) dalton_input_parameters() (in module Frog.Molecules.Water_TIP4P2005_O) dalton_version (Frog.class_OpticalParameter.QMParameter property) delete_file() (in module Frog.toolbox) Dia_alpha (class in Frog.class_Diagrams) Dia_beta (class in Frog.class_Diagrams) Dia_chi (class in Frog.class_Diagrams) Dia_density (class in Frog.class_Diagrams) Dia_effective_field (class in Frog.class_Diagrams) Dia_electric_field (class in Frog.class_Diagrams) Dia_hbond (class in Frog.class_Diagrams)

Dia_iota (class in Frog.class_Diagrams) Dia_molecular_orientation (class in Frog.class_Diagrams) Dia_rdf (class in Frog.class_Diagrams) Diagram (class in Frog.class_Diagrams) DiagramParameter (class in Frog.class_DiagramParameter) diff_time() (in module Frog.toolbox) dir_mol_times (Frog.class_GP.GlobalParameter attribute) dir_submission_file (Frog.class_GP.GlobalParameter attribute) dir_torun_QM (Frog.class_GP.GlobalParameter attribute) discretization_space() (in module Frog.geometry_manager) discretization_type (Frog.class_DiagramParameter.SingleDiagramParameter property) dparameter (Frog.class_Molecule.MoleculeTypeParameter property)

E

e_100() (in module Frog.error_messages) e_101() (in module Frog.error_messages) e_102() (in module Frog.error_messages) e_103() (in module Frog.error_messages) e_104() (in module Frog.error_messages) e_105() (in module Frog.error_messages) e_106() (in module Frog.error_messages) e_107() (in module Frog.error_messages) e_108() (in module Frog.error_messages) e_109() (in module Frog.error_messages) e_110() (in module Frog.error_messages) e_111() (in module Frog.error_messages) e_112() (in module Frog.error_messages) e_113() (in module Frog.error_messages) e_114() (in module Frog.error_messages) e_115() (in module Frog.error_messages) e_116() (in module Frog.error_messages) e_117() (in module Frog.error_messages) e_118() (in module Frog.error_messages) e_119() (in module Frog.error_messages) e_120() (in module Frog.error_messages) e_121() (in module Frog.error_messages) e_122() (in module Frog.error_messages) e_123() (in module Frog.error_messages) e_124() (in module Frog.error_messages) e_125() (in module Frog.error_messages) e_126() (in module Frog.error_messages) e_127_a() (in module Frog.error_messages) e_127_b() (in module Frog.error_messages) e_128_a() (in module Frog.error_messages) e_128_b() (in module Frog.error_messages) e_129() (in module Frog.error_messages) e_130() (in module Frog.error_messages) e_131() (in module Frog.error_messages) e_132() (in module Frog.error_messages) e_133() (in module Frog.error_messages) e_134_a() (in module Frog.error_messages) e_134_b() (in module Frog.error_messages) e_134_c() (in module Frog.error_messages) e_135() (in module Frog.error_messages) e_136() (in module Frog.error_messages) e_137() (in module Frog.error_messages) e_138() (in module Frog.error_messages) e_139() (in module Frog.error_messages) e_140() (in module Frog.error_messages) e_141() (in module Frog.error_messages) e_142() (in module Frog.error_messages) e_143() (in module Frog.error_messages) e_144() (in module Frog.error_messages) e_145() (in module Frog.error_messages) e_146() (in module Frog.error_messages) e_147() (in module Frog.error_messages)

e_148() (in module Frog.error_messages) e_149() (in module Frog.error_messages) e_150() (in module Frog.error_messages) e_151() (in module Frog.error_messages) e_152() (in module Frog.error_messages) e_153() (in module Frog.error_messages) e_154() (in module Frog.error_messages) e_155() (in module Frog.error_messages) e_156() (in module Frog.error_messages) e_157() (in module Frog.error_messages) e_158() (in module Frog.error_messages) e_159() (in module Frog.error_messages) e_90() (in module Frog.error_messages) e_91() (in module Frog.error_messages) e_92() (in module Frog.error_messages) e_94() (in module Frog.error_messages) e_95() (in module Frog.error_messages) e_96() (in module Frog.error_messages) e_97() (in module Frog.error_messages) e_98() (in module Frog.error_messages) e_99() (in module Frog.error_messages) effective_field_polarization (Frog.class_OpticalParameter.QMParameter property) EFParameter (class in Frog.class_OpticalParameter) electric_field_from_one_order_0_description() (in module Frog.electric_field_module) electrostatic_description() (in module Frog.Molecules.Chlore) (in module Frog.Molecules.Ethanol_OPLSAA) (in module Frog.Molecules.Methanol_OPLSAA) (in module Frog.Molecules.Sodium) (in module Frog.Molecules.Water_Osted2006_ESdescription) (in module Frog.Molecules.Water_PSPC) (in module Frog.Molecules.Water_RESD_Beerepoot2016) (in module Frog.Molecules.Water_TIP4P2005) (in module Frog.Molecules.Water_TIP4P2005_O) ElectrostaticDescription (class in Frog.class_OpticalParameter) end_diagram() (Frog.class_Diagrams.Diagram method) (Frog.class_Molecule.MoleculeType method) end_frame_diagram() (Frog.class_Diagrams.Dia_alpha method) (Frog.class_Diagrams.Dia_beta method) (Frog.class_Diagrams.Dia_chi method) (Frog.class_Diagrams.Dia_density method) (Frog.class_Diagrams.Dia_effective_field method) (Frog.class_Diagrams.Dia_electric_field method) (Frog.class_Diagrams.Dia_hbond method) (Frog.class_Diagrams.Dia_iota method) (Frog.class_Diagrams.Dia_molecular_orientation method) (Frog.class_Diagrams.Dia_rdf method) (Frog.class_Diagrams.Diagram method) end_initialize() (Frog.class_Molecule.MoleculeType method) env_authorised_pbc_condition (Frog.class_GP.GlobalParameter attribute) environement_builder_return_position() (in module Frog.universe_manager) ewald_factor (Frog.class_OpticalParameter.QMParameter property) extract_file_name() (in module Frog.toolbox)

F

file_template_script_run_QM (Frog.class_GP.GlobalParameter attribute) fill_2nd_order_tensor() (in module Frog.dalton_manager_module) fill_beta_dipole_quadru() (in module Frog.dalton_manager_module) fill_beta_quadru_dipole() (in module Frog.dalton_manager_module) fill_beta_quadru_zero_freq() (in module Frog.dalton_manager_module) find_1st_order_tensor_component() (in module Frog.dalton_manager_module) find_2nd_order_tensor() (in module Frog.dalton_manager_module) find_beta_dipole_quadru() (in module Frog.dalton_manager_module) find_beta_quadru_dipole() (in module Frog.dalton_manager_module) find_closest_position_threw_pbc() (in module Frog.geometry_manager) Frog module Frog.check module Frog.class_DiagramParameter module Frog.class_Diagrams module Frog.class_modules module Frog.class_Molecule module Frog.class_OpticalParameter module Frog.dalton_manager_module module Frog.electric_field_module module Frog.error_messages module Frog.first_part module Frog.frog_class module Frog.frog_data_analysis module Frog.geometry_manager module Frog.main module

Frog.messages module Frog.Molecules module Frog.Molecules.Chlore module Frog.Molecules.Ethanol_OPLSAA module Frog.Molecules.Methanol_OPLSAA module Frog.Molecules.Sodium module Frog.Molecules.Water_Osted2006_ESdescription module Frog.Molecules.Water_PSPC module Frog.Molecules.Water_RESD_Beerepoot2016 module Frog.Molecules.Water_TIP4P2005 module Frog.Molecules.Water_TIP4P2005_O module Frog.second_part module Frog.third_part module Frog.toolbox module Frog.universe_manager module frog_authors() (in module Frog.messages) frog_axis (class in Frog.class_DiagramParameter) frog_format_time() (in module Frog.toolbox) frog_licence() (in module Frog.messages) frog_logo() (in module Frog.messages) frog_run() (in module Frog.main) frog_run_from_shell() (in module Frog.main) frog_title() (in module Frog.messages) functional (Frog.class_OpticalParameter.QMParameter property)

G

gaussian_fct() (in module Frog.frog_data_analysis) gaussian_fit() (in module Frog.frog_data_analysis) general_path (Frog.class_GP.GlobalParameter attribute) generate_inp_dal() (in module Frog.dalton_manager_module)

generate_inp_mol() (in module Frog.dalton_manager_module) generate_inp_pot() (in module Frog.dalton_manager_module) give_class_diagram_name() (in module Frog.class_modules) global_basis_value (Frog.class_OpticalParameter.QMParameter property)

H

how_many_QM_jobs_are_left() (in module Frog.second_part)

I

info_molecule() (in module Frog.Molecules.Chlore) (in module Frog.Molecules.Ethanol_OPLSAA) (in module Frog.Molecules.Methanol_OPLSAA) (in module Frog.Molecules.Sodium) (in module Frog.Molecules.Water_Osted2006_ESdescription) (in module Frog.Molecules.Water_PSPC) (in module Frog.Molecules.Water_RESD_Beerepoot2016) (in module Frog.Molecules.Water_TIP4P2005) (in module Frog.Molecules.Water_TIP4P2005_O) info_molecule_for_layer() (in module Frog.Molecules.Methanol_OPLSAA) (in module Frog.Molecules.Water_TIP4P2005) info_molecule_typical_size() (in module Frog.Molecules.Chlore) (in module Frog.Molecules.Ethanol_OPLSAA) (in module Frog.Molecules.Methanol_OPLSAA) (in module Frog.Molecules.Sodium) (in module Frog.Molecules.Water_Osted2006_ESdescription) (in module Frog.Molecules.Water_PSPC) (in module Frog.Molecules.Water_RESD_Beerepoot2016) (in module Frog.Molecules.Water_TIP4P2005) (in module Frog.Molecules.Water_TIP4P2005_O)

init_plane_axis() (in module Frog.geometry_manager) initial_msg_welcome() (in module Frog.messages) initialize_empty_for_frame() (Frog.class_Molecule.MoleculeType method) initialize_single_molecule() (Frog.class_Diagrams.Dia_alpha class method) (Frog.class_Diagrams.Dia_beta class method) (Frog.class_Diagrams.Dia_chi class method) (Frog.class_Diagrams.Dia_density class method) (Frog.class_Diagrams.Dia_effective_field class method) (Frog.class_Diagrams.Dia_electric_field class method) (Frog.class_Diagrams.Dia_hbond class method) (Frog.class_Diagrams.Dia_iota class method) (Frog.class_Diagrams.Dia_molecular_orientation class method) (Frog.class_Diagrams.Dia_rdf class method) (Frog.class_Diagrams.Prepare_run_QM class method) input_section_check_update() (Frog.class_Molecule.MoleculeType method) input_section_checks (Frog.class_Molecule.MoleculeType property) IS_density (Frog.class_DiagramParameter.DiagramParameter property) is_it_python_file() (in module Frog.check) IS_rot_mat (Frog.class_DiagramParameter.DiagramParameter property) IS_run_QM (Frog.class_OpticalParameter.OpticalParameter property)

L

L_allowed_molecule (Frog.class_DiagramParameter.DiagramParameter property) L_alpha_ref (Frog.class_OpticalParameter.OpticalParameter property) L_atom_type (Frog.class_OpticalParameter.QMDescription property) L_beta_ref (Frog.class_OpticalParameter.OpticalParameter property) L_charge_order_0 (Frog.class_OpticalParameter.ElectrostaticDescription property) L_charge_order_1 (Frog.class_OpticalParameter.ElectrostaticDescription property) L_charge_order_2 (Frog.class_OpticalParameter.ElectrostaticDescription property) L_coordinate (Frog.class_OpticalParameter.QMDescription property) L_diagram (Frog.class_DiagramParameter.DiagramParameter property) L_key_mol (Frog.class_Molecule.MoleculeType property) L_key_selection_traj (Frog.class_Molecule.MoleculeType property) L_localization_site (Frog.class_OpticalParameter.ElectrostaticDescription property) L_localization_type (Frog.class_OpticalParameter.ElectrostaticDescription property) L_molecule (Frog.class_Molecule.MoleculeType property) L_molecule_tracked (Frog.class_OpticalParameter.OpticalParameter property) L_polarization_exclude (Frog.class_OpticalParameter.ElectrostaticDescription property)

L_polarization_order_1_1 (Frog.class_OpticalParameter.ElectrostaticDescription property) L_possible_diagram (Frog.class_DiagramParameter.DiagramParameter property) L_QM_todo (Frog.class_OpticalParameter.OpticalParameter property) L_reassignation_selection (Frog.class_DiagramParameter.SingleDiagramParameter property) L_type_atom (Frog.class_modules.SingleMoleculeParameter property) launch_first_part() (in module Frog.main) launch_second_part() (in module Frog.main) launch_third_part() (in module Frog.main) layer_which_radii_MT (Frog.class_GP.GlobalParameter attribute) load_chi() (in module Frog.dalton_manager_module) load_iota() (in module Frog.dalton_manager_module) load_iota_from_1st_order_calculation() (in module Frog.dalton_manager_module) load_iota_from_2nd_order_calculation() (in module Frog.dalton_manager_module) load_qm_results_one_frame() (in module Frog.third_part) load_result() (in module Frog.frog_data_analysis) long_range_distance_switch (Frog.class_OpticalParameter.QMParameter property) long_range_switch (Frog.class_OpticalParameter.QMParameter property)

M

max_distance_atom (Frog.class_modules.SingleMoleculeParameter property) max_iter_scf (Frog.class_OpticalParameter.QMParameter property) max_pe_distance_neigh (Frog.class_OpticalParameter.QMParameter property) max_pe_polarization_distance_neigh (Frog.class_OpticalParameter.QMParameter property) max_qm_box_distance_neigh (Frog.class_OpticalParameter.QMParameter property) max_submission_QM (Frog.class_GP.GlobalParameter attribute) MD_convertion_to_angstrom (Frog.class_GP.GlobalParameter attribute) MD_cut_trajectory (Frog.class_GP.GlobalParameter attribute) MD_file_name_topology (Frog.class_GP.GlobalParameter attribute) MD_file_name_traj (Frog.class_GP.GlobalParameter attribute) MD_file_type (Frog.class_GP.GlobalParameter attribute) md_parameters() (in module Frog.Molecules.Water_TIP4P2005_O) mean (Frog.class_Diagrams.Diagram property) mean_size (Frog.class_DiagramParameter.SingleDiagramParameter property) merge_diagram() (Frog.class_Diagrams.Diagram method) merge_frame() (Frog.class_Molecule.MoleculeType method) merge_mol() (Frog.class_OpticalParameter.ElectrostaticDescription method) (Frog.class_OpticalParameter.QMDescription method) merge_qmparameter() (Frog.class_OpticalParameter.QMParameter method) message_with_hashtag() (in module Frog.messages) module Frog Frog.check Frog.class_DiagramParameter Frog.class_Diagrams Frog.class_modules Frog.class_Molecule Frog.class_OpticalParameter Frog.dalton_manager_module Frog.electric_field_module Frog.error_messages Frog.first_part Frog.frog_class Frog.frog_data_analysis Frog.geometry_manager Frog.main Frog.messages Frog.Molecules Frog.Molecules.Chlore Frog.Molecules.Ethanol_OPLSAA Frog.Molecules.Methanol_OPLSAA Frog.Molecules.Sodium Frog.Molecules.Water_Osted2006_ESdescription Frog.Molecules.Water_PSPC Frog.Molecules.Water_RESD_Beerepoot2016 Frog.Molecules.Water_TIP4P2005 Frog.Molecules.Water_TIP4P2005_O Frog.second_part Frog.third_part Frog.toolbox Frog.universe_manager

module_binarized_array() (in module Frog.toolbox) MoleculeType (class in Frog.class_Molecule) MoleculeTypeParameter (class in Frog.class_Molecule) move_previous_results() (in module Frog.dalton_manager_module) mtparameter (Frog.class_Molecule.MoleculeType property) multipole_order (Frog.class_OpticalParameter.ElectrostaticDescription property)

N

name (Frog.class_DiagramParameter.SingleDiagramParameter property) (Frog.class_Diagrams.Diagram property) (Frog.class_Molecule.MoleculeType property) name_mt (Frog.class_modules.SingleMoleculeParameter property) nbr_analysis() (Frog.class_DiagramParameter.DiagramParameter method)

nbr_atom (Frog.class_modules.SingleMoleculeParameter property) nbr_job_parr_QM (Frog.class_GP.GlobalParameter attribute) nbr_parra (Frog.class_GP.GlobalParameter attribute) nbr_time_step (Frog.class_GP.GlobalParameter attribute) nbr_type_atom() (Frog.class_OpticalParameter.QMDescription method) NotAnOptionError

O

open_pickle() (in module Frog.toolbox) OpticalParameter (class in Frog.class_OpticalParameter)

optparameter (Frog.class_Molecule.MoleculeTypeParameter property) optparameter_selection_tool_molecule() (in module Frog.geometry_manager) optparameter_where_to_run_QM_molecule() (in module Frog.geometry_manager)

P

parallelize_fct() (in module Frog.toolbox) pass_first_part (Frog.class_GP.GlobalParameter attribute) PBC (class in Frog.geometry_manager) pbc_condition() (in module Frog.geometry_manager) pbc_condition_neigh() (in module Frog.universe_manager) PE_k_vector_range (Frog.class_OpticalParameter.QMParameter property) pe_level (Frog.class_OpticalParameter.OpticalParameter property) (Frog.class_OpticalParameter.QMParameter property) perform_effective_field_one_frame() (in module Frog.third_part) perform_effective_field_one_frame_old() (in module Frog.third_part) polarizability_response (Frog.class_OpticalParameter.QMParameter property)

polarization_order (Frog.class_OpticalParameter.ElectrostaticDescription property) population (Frog.class_Diagrams.Diagram property) (Frog.class_Molecule.MoleculeType property) preference_functional (Frog.class_GP.GlobalParameter attribute) Prepare_run_QM (class in Frog.class_Diagrams) prepare_submission_scripts() (in module Frog.second_part) print_diagram_info() (in module Frog.frog_data_analysis) print_general_info() (in module Frog.frog_data_analysis) print_info_QM_file_localization() (in module Frog.dalton_manager_module) print_typical_position() (Frog.class_Molecule.SingleMolecule method) print_unit() (Frog.class_DiagramParameter.unit method)

Q

QM_preparation_PE_and_PE_plus_QMBox() (in module Frog.universe_manager) QM_preparation_PE_long() (in module Frog.universe_manager) qm_target_description() (in module Frog.Molecules.Chlore) (in module Frog.Molecules.Ethanol_OPLSAA) (in module Frog.Molecules.Methanol_OPLSAA) (in module Frog.Molecules.Sodium) (in module Frog.Molecules.Water_Osted2006_ESdescription) (in module Frog.Molecules.Water_PSPC) (in module Frog.Molecules.Water_RESD_Beerepoot2016) (in module Frog.Molecules.Water_TIP4P2005) (in module Frog.Molecules.Water_TIP4P2005_O)

QMDescription (class in Frog.class_OpticalParameter) QMParameter (class in Frog.class_OpticalParameter) qmparameter (Frog.class_OpticalParameter.OpticalParameter property)

R

rcut_PE_direct (Frog.class_OpticalParameter.QMParameter property) rcut_PE_smoth (Frog.class_OpticalParameter.QMParameter property) read_diagram_input() (Frog.class_DiagramParameter.DiagramParameter method) (Frog.class_Molecule.MoleculeType method) read_input() (Frog.class_Diagrams.Dia_alpha static method) (Frog.class_Diagrams.Dia_beta static method) (Frog.class_Diagrams.Dia_chi static method) (Frog.class_Diagrams.Dia_density static method) (Frog.class_Diagrams.Dia_effective_field static method) (Frog.class_Diagrams.Dia_electric_field static method) (Frog.class_Diagrams.Dia_hbond static method) (Frog.class_Diagrams.Dia_iota static method) (Frog.class_Diagrams.Dia_molecular_orientation static method) (Frog.class_Diagrams.Dia_rdf static method) (in module Frog.main) read_optic_properties_input() (Frog.class_Molecule.MoleculeType method) (Frog.class_OpticalParameter.OpticalParameter method) real_space_discretization_bin_number (Frog.class_DiagramParameter.SingleDiagramParameter property) recurcive_pbc_movement_constructor() (in module Frog.universe_manager) redo_QM (Frog.class_GP.GlobalParameter attribute)

ref_polarizability() (in module Frog.Molecules.Water_Osted2006_ESdescription) (in module Frog.Molecules.Water_PSPC) (in module Frog.Molecules.Water_RESD_Beerepoot2016) rescale_values() (Frog.class_OpticalParameter.ElectrostaticDescription method) restart (Frog.class_OpticalParameter.QMParameter property) return_component_dipole() (in module Frog.dalton_manager_module) return_component_quadrupole() (in module Frog.dalton_manager_module) return_diagram() (in module Frog.frog_data_analysis) return_time() (in module Frog.toolbox) rotate_1st_order_tensor() (in module Frog.toolbox) rotate_2nd_order_tensor() (in module Frog.toolbox) rotate_3rd_order_tensor() (in module Frog.toolbox) rotate_4th_order_tensor() (in module Frog.toolbox) RUN_electric_field (Frog.class_OpticalParameter.QMParameter property) RUN_integral (Frog.class_OpticalParameter.QMParameter property) RUN_pe (Frog.class_OpticalParameter.QMParameter property) RUN_polarization (Frog.class_OpticalParameter.QMParameter property) RUN_properties (Frog.class_OpticalParameter.QMParameter property) RUN_response (Frog.class_OpticalParameter.QMParameter property) RUN_shg (Frog.class_OpticalParameter.QMParameter property) run_third_part() (in module Frog.third_part)

S

save_pickle() (in module Frog.toolbox) scratch_dir (Frog.class_GP.GlobalParameter attribute) sd (Frog.class_Diagrams.Diagram property) sdparameter_create_axis() (in module Frog.class_DiagramParameter) selection_absolute_position() (in module Frog.geometry_manager) selection_relative_position() (in module Frog.geometry_manager) selection_tool (Frog.class_OpticalParameter.OpticalParameter property) shg_response (Frog.class_OpticalParameter.QMParameter property) single_neighbour_find_position_PBC() (in module Frog.universe_manager) single_neighbour_return_position() (in module Frog.universe_manager) SingleDiagramParameter (class in Frog.class_DiagramParameter) SingleMolecule (class in Frog.class_Molecule) SingleMoleculeParameter (class in Frog.class_modules) size (Frog.class_Diagrams.Diagram property) size_typical_molecule (Frog.class_modules.SingleMoleculeParameter property) SM_attribute_name() (Frog.class_Diagrams.Dia_alpha static method) (Frog.class_Diagrams.Dia_beta static method) (Frog.class_Diagrams.Dia_chi static method) (Frog.class_Diagrams.Dia_density static method) (Frog.class_Diagrams.Dia_effective_field static method) (Frog.class_Diagrams.Dia_electric_field static method) (Frog.class_Diagrams.Dia_hbond static method) (Frog.class_Diagrams.Dia_iota static method) (Frog.class_Diagrams.Dia_molecular_orientation static method) (Frog.class_Diagrams.Dia_rdf static method) (Frog.class_Diagrams.Prepare_run_QM static method)

smparameter (Frog.class_Molecule.MoleculeTypeParameter property) special_selection (Frog.class_DiagramParameter.DiagramParameter property) special_selection_assignement_for_molecules() (in module Frog.geometry_manager) special_selection_reassignation_list_creation() (Frog.class_DiagramParameter.SingleDiagramParameter method) static_electric_field (Frog.class_OpticalParameter.QMParameter property) static_electric_field_direction (Frog.class_OpticalParameter.QMParameter property) str_to_class() (in module Frog.class_Diagrams) strong_remarks() (in module Frog.messages) submit_qm_calculation() (in module Frog.dalton_manager_module) switch_for_given_unit() (Frog.class_DiagramParameter.unit method) switch_unit() (Frog.class_DiagramParameter.unit method) switch_unit_diagram() (Frog.class_Diagrams.Diagram method) symetryse_beta_dipole_quadrupole() (in module Frog.dalton_manager_module) symetryse_beta_quadrupole_dipole() (in module Frog.dalton_manager_module)

T

test_electrostatic() (in module Frog.Molecules.Water_Osted2006_ESdescription) (in module Frog.Molecules.Water_PSPC) (in module Frog.Molecules.Water_RESD_Beerepoot2016) (in module Frog.Molecules.Water_TIP4P2005) (in module Frog.Molecules.Water_TIP4P2005_O) theory_lv (Frog.class_OpticalParameter.QMParameter property) to_store_electric_field() (in module Frog.electric_field_module) total_charge (Frog.class_OpticalParameter.QMParameter property) trajectory_load() (in module Frog.universe_manager) trajectory_load_old() (in module Frog.universe_manager) trajectory_selection_for_residues() (in module Frog.universe_manager) treat_block_of_frame() (in module Frog.first_part)

treat_one_frame() (in module Frog.first_part) trotter_step (Frog.class_GP.GlobalParameter attribute) type_basis (Frog.class_OpticalParameter.QMParameter property) typical_geometry() (in module Frog.Molecules.Chlore) (in module Frog.Molecules.Ethanol_OPLSAA) (in module Frog.Molecules.Methanol_OPLSAA) (in module Frog.Molecules.Sodium) (in module Frog.Molecules.Water_Osted2006_ESdescription) (in module Frog.Molecules.Water_PSPC) (in module Frog.Molecules.Water_RESD_Beerepoot2016) (in module Frog.Molecules.Water_TIP4P2005) (in module Frog.Molecules.Water_TIP4P2005_O)

U

unit (class in Frog.class_DiagramParameter) (Frog.class_Diagrams.Diagram property) user_frendly_1() (in module Frog.messages) user_frendly_10() (in module Frog.messages) user_frendly_11() (in module Frog.messages) user_frendly_12() (in module Frog.messages) user_frendly_13() (in module Frog.messages) user_frendly_14_a() (in module Frog.messages) user_frendly_14_b() (in module Frog.messages) user_frendly_15() (in module Frog.messages) user_frendly_16() (in module Frog.messages) user_frendly_17() (in module Frog.messages) user_frendly_18() (in module Frog.messages) user_frendly_19() (in module Frog.messages) user_frendly_2() (in module Frog.messages) user_frendly_20() (in module Frog.messages) user_frendly_21() (in module Frog.messages) user_frendly_22() (in module Frog.messages) user_frendly_23() (in module Frog.messages) user_frendly_24_a() (in module Frog.messages) user_frendly_24_b() (in module Frog.messages) user_frendly_25() (in module Frog.messages) user_frendly_26() (in module Frog.messages) user_frendly_27() (in module Frog.messages) user_frendly_28() (in module Frog.messages) user_frendly_29() (in module Frog.messages) user_frendly_3() (in module Frog.messages) user_frendly_30() (in module Frog.messages) user_frendly_31() (in module Frog.messages) user_frendly_32() (in module Frog.messages) user_frendly_33() (in module Frog.messages) user_frendly_34_a() (in module Frog.messages) user_frendly_34_b() (in module Frog.messages) user_frendly_34_c() (in module Frog.messages) user_frendly_34_d() (in module Frog.messages) user_frendly_35() (in module Frog.messages) user_frendly_36() (in module Frog.messages) user_frendly_37() (in module Frog.messages) user_frendly_38() (in module Frog.messages) user_frendly_39() (in module Frog.messages) user_frendly_4() (in module Frog.messages) user_frendly_40() (in module Frog.messages) user_frendly_41() (in module Frog.messages) user_frendly_42_a() (in module Frog.messages) user_frendly_42_b() (in module Frog.messages) user_frendly_43() (in module Frog.messages) user_frendly_44() (in module Frog.messages) user_frendly_45() (in module Frog.messages) user_frendly_46() (in module Frog.messages) user_frendly_47() (in module Frog.messages) user_frendly_48() (in module Frog.messages) user_frendly_49() (in module Frog.messages) user_frendly_5() (in module Frog.messages) user_frendly_50_a() (in module Frog.messages) user_frendly_50_b() (in module Frog.messages) user_frendly_51_a() (in module Frog.messages) user_frendly_52_a() (in module Frog.messages) user_frendly_52_b() (in module Frog.messages) user_frendly_53_a() (in module Frog.messages) user_frendly_53_c() (in module Frog.messages) user_frendly_54_a() (in module Frog.messages)

user_frendly_54_b() (in module Frog.messages) user_frendly_54_c() (in module Frog.messages) user_frendly_55_a() (in module Frog.messages) user_frendly_55_b() (in module Frog.messages) user_frendly_55_c() (in module Frog.messages) user_frendly_56_a() (in module Frog.messages) user_frendly_56_b() (in module Frog.messages) user_frendly_56_c() (in module Frog.messages) user_frendly_57() (in module Frog.messages) user_frendly_58_a() (in module Frog.messages) user_frendly_58_b() (in module Frog.messages) user_frendly_59() (in module Frog.messages) user_frendly_6() (in module Frog.messages) user_frendly_60_a() (in module Frog.messages) user_frendly_60_b() (in module Frog.messages) user_frendly_60_c() (in module Frog.messages) user_frendly_61_a() (in module Frog.messages) user_frendly_61_b() (in module Frog.messages) user_frendly_62_a() (in module Frog.messages) user_frendly_62_b() (in module Frog.messages) user_frendly_62_c() (in module Frog.messages) user_frendly_63_a() (in module Frog.messages) user_frendly_63_b() (in module Frog.messages) user_frendly_63_c() (in module Frog.messages) user_frendly_63_d() (in module Frog.messages) user_frendly_64() (in module Frog.messages) user_frendly_65() (in module Frog.messages) user_frendly_66_a() (in module Frog.messages) user_frendly_66_b() (in module Frog.messages) user_frendly_66_c() (in module Frog.messages) user_frendly_67_a() (in module Frog.messages) user_frendly_67_b() (in module Frog.messages) user_frendly_67_c() (in module Frog.messages) user_frendly_68_a() (in module Frog.messages) user_frendly_68_b() (in module Frog.messages) user_frendly_69() (in module Frog.messages) user_frendly_7() (in module Frog.messages) user_frendly_70() (in module Frog.messages) user_frendly_71_a() (in module Frog.messages) user_frendly_71_b() (in module Frog.messages) user_frendly_71_c() (in module Frog.messages) user_frendly_72() (in module Frog.messages) user_frendly_73() (in module Frog.messages) user_frendly_74() (in module Frog.messages) user_frendly_75() (in module Frog.messages) user_frendly_76() (in module Frog.messages) user_frendly_77() (in module Frog.messages) user_frendly_78() (in module Frog.messages) user_frendly_79() (in module Frog.messages) user_frendly_8() (in module Frog.messages) user_frendly_80() (in module Frog.messages) user_frendly_81() (in module Frog.messages) user_frendly_82() (in module Frog.messages) user_frendly_83() (in module Frog.messages) user_frendly_84() (in module Frog.messages) user_frendly_85() (in module Frog.messages) user_frendly_86() (in module Frog.messages) user_frendly_87() (in module Frog.messages) user_frendly_88() (in module Frog.messages) user_frendly_89() (in module Frog.messages) user_frendly_9() (in module Frog.messages)

V

value (Frog.class_Diagrams.Diagram property)

valuesquare (Frog.class_Diagrams.Diagram property)

W

where_are_molecules (Frog.class_Molecule.MoleculeType property) where_to_run_QM (Frog.class_OpticalParameter.OpticalParameter property)

write_beta_quadrupole_dalton_shortcut() (in module Frog.dalton_manager_module) write_xyz_environment (Frog.class_OpticalParameter.QMParameter property) write_xyz_mol() (in module Frog.toolbox)