Index

Symbols

--crosslinker-type pylimer-analyse-networks command line option --disable-primary-loops pylimer-generate-network command line option --disable-secondary-loops pylimer-generate-network command line option --functionalize-discrete pylimer-generate-network command line option --n-beads-per-chain-1 pylimer-generate-network command line option --n-beads-per-chain-2 pylimer-generate-network command line option --n-beads-per-solvent-chain pylimer-generate-network command line option --n-beads-per-xlink pylimer-generate-network command line option --n-chains-1 pylimer-generate-network command line option --n-chains-2 pylimer-generate-network command line option --n-chains-crosslinkers pylimer-generate-network command line option --n-mono-beads-per-chain pylimer-generate-network command line option

--n-mono-chains pylimer-generate-network command line option --n-solvent-chains pylimer-generate-network command line option --no-functionalize-discrete pylimer-generate-network command line option --parameter-type pylimer-generate-network command line option --polymer-name pylimer-analyse-networks command line option pylimer-generate-network command line option --remove-wsol pylimer-generate-network command line option --target-f pylimer-generate-network command line option --target-file pylimer-generate-network command line option --target-p pylimer-generate-network command line option --target-wsol pylimer-generate-network command line option --z-score-std-mult pylimer-generate-network command line option

_

__getattr__() (pylimer_tools.io.polymer_data.PolymerData method) (pylimer_tools.io.unit_styles.UnitStyle method) __getitem__() (pylimer_tools.io.polymer_data.PolymerData method) (pylimer_tools.io.polymer_data.PolymerDataFrame method)

__len__() (pylimer_tools.io.polymer_data.PolymerDataFrame method) __repr__() (pylimer_tools.io.polymer_data.PolymerDataFrame method)

A

add_angles() (pylimer_tools_cpp.Universe method) add_atoms() (pylimer_tools_cpp.Universe method) add_bonds() (pylimer_tools_cpp.Universe method) add_bonds_with_types() (pylimer_tools_cpp.Universe method) add_crosslinkers() (pylimer_tools_cpp.MCUniverseGenerator method) add_crosslinkers_at() (pylimer_tools_cpp.MCUniverseGenerator method) add_dihedral_angles() (pylimer_tools_cpp.Universe method) add_end_functionalized_strands() (pylimer_tools_cpp.MCUniverseGenerator method) add_functionalized_strands() (pylimer_tools_cpp.MCUniverseGenerator method) add_monofunctional_strands() (pylimer_tools_cpp.MCUniverseGenerator method) add_randomly_functionalized_strands() (pylimer_tools_cpp.MCUniverseGenerator method) add_regularly_spaced_functionalized_strands() (pylimer_tools_cpp.MCUniverseGenerator method) add_sliplinks() (pylimer_tools_cpp.MEHPForceBalance method) add_sliplinks_based_on_cycles() (pylimer_tools_cpp.MEHPForceBalance method) add_solvent_chains() (pylimer_tools_cpp.MCUniverseGenerator method) add_star_crosslinkers() (pylimer_tools_cpp.MCUniverseGenerator method) add_strands() (pylimer_tools_cpp.MCUniverseGenerator method) ALL (pylimer_tools_cpp.LinkSwappingMode attribute) ALL_CYCLE (pylimer_tools_cpp.LinkSwappingMode attribute) ALL_MC (pylimer_tools_cpp.LinkSwappingMode attribute) ALL_MC_CYCLE (pylimer_tools_cpp.LinkSwappingMode attribute) ALL_MC_TRY (pylimer_tools_cpp.LinkSwappingMode attribute)

ALL_MC_TRY_CYCLE (pylimer_tools_cpp.LinkSwappingMode attribute) ANGLE (pylimer_tools_cpp.AtomStyle attribute) append (pylimer_tools_cpp.OutputConfiguration attribute) apply_pbc() (pylimer_tools_cpp.Box method) apply_simple_shear() (pylimer_tools_cpp.Box method) apply_to_numeric_ignore_compat() (in module pylimer_tools.utils.data_utility) as_integer_ratio() (pylimer_tools_cpp.ComputedDoubleValues method) (pylimer_tools_cpp.ComputedIntValues method) (pylimer_tools_cpp.ExitReason method) assemble_gaussian_parameters_from_kuhn() (in module pylimer_tools.io.bead_spring_parameter_provider) assume_box_large_enough (pylimer_tools_cpp.SimplifiedNetwork attribute) assume_box_large_enough() (pylimer_tools_cpp.DPDSimulator method) (pylimer_tools_cpp.MEHPForceRelaxation method) assume_complete (pylimer_tools_cpp.SimplifiedNetwork attribute) at_index() (pylimer_tools_cpp.UniverseSequence method) Atom (class in pylimer_tools_cpp) ATOMIC (pylimer_tools_cpp.AtomStyle attribute) AtomPairEntanglements (class in pylimer_tools_cpp) AtomStyle (class in pylimer_tools_cpp) AUTO (pylimer_tools_cpp.NormalModeSolver attribute) autocorrelate_column() (pylimer_tools_cpp.AveFileReader method) autocorrelate_column_difference() (pylimer_tools_cpp.AveFileReader method) AveFileReader (class in pylimer_tools_cpp)

B

BackTrackStatus (class in pylimer_tools_cpp) BICGSTAB (pylimer_tools_cpp.SLESolver attribute) BICGSTAB_DIAGONALIZED (pylimer_tools_cpp.SLESolver attribute) BICGSTAB_IDENTITY (pylimer_tools_cpp.SLESolver attribute) BICGSTAB_INCOMPLETE_LU (pylimer_tools_cpp.SLESolver attribute) bit_count() (pylimer_tools_cpp.ComputedDoubleValues method) (pylimer_tools_cpp.ComputedIntValues method) (pylimer_tools_cpp.ExitReason method) bit_length() (pylimer_tools_cpp.ComputedDoubleValues method) (pylimer_tools_cpp.ComputedIntValues method) (pylimer_tools_cpp.ExitReason method)

BODY (pylimer_tools_cpp.AtomStyle attribute) BOND (pylimer_tools_cpp.AtomStyle attribute) Box (class in pylimer_tools_cpp) box_lengths (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) (pylimer_tools_cpp.SimplifiedNetwork attribute) BPM_SPHERE (pylimer_tools_cpp.AtomStyle attribute)

C

CHARGE (pylimer_tools_cpp.AtomStyle attribute) columns (pylimer_tools.io.polymer_data.PolymerDataFrame property) compute_angles() (pylimer_tools_cpp.Universe method) compute_bond_lengths() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) compute_bond_vectors() (pylimer_tools_cpp.Universe method) compute_chebyshev_moments_kpm() (pylimer_tools_cpp.NormalModeAnalyzer method) compute_crosslinker_conversion() (in module pylimer_tools.calc.structure_analysis) compute_cycle_rank() (in module pylimer_tools.calc.mehp_utilities) compute_density_of_states_kpm() (pylimer_tools_cpp.NormalModeAnalyzer method) compute_distance_autocorrelation_from_to() (pylimer_tools_cpp.UniverseSequence method) compute_distance_from_to_atoms() (pylimer_tools_cpp.UniverseSequence method) compute_dxs() (pylimer_tools_cpp.Universe method) compute_dys() (pylimer_tools_cpp.Universe method) compute_dzs() (pylimer_tools_cpp.Universe method) compute_effective_crosslinker_functionalities() (in module pylimer_tools.calc.structure_analysis) compute_effective_crosslinker_functionality() (in module pylimer_tools.calc.structure_analysis) compute_effective_nr_density_of_junctions() (in module pylimer_tools.calc.mehp_utilities) compute_effective_nr_density_of_network() (in module pylimer_tools.calc.mehp_utilities) compute_end_to_end_distance() (pylimer_tools_cpp.Molecule method) compute_end_to_end_distance_with_derived_image_flags() (pylimer_tools_cpp.Molecule method) compute_end_to_end_distances() (pylimer_tools_cpp.Universe method) compute_end_to_end_vector() (pylimer_tools_cpp.Molecule method) compute_end_to_end_vector_with_derived_image_flags() (pylimer_tools_cpp.Molecule method) compute_end_to_end_vectors() (in module pylimer_tools.calc.structure_analysis) compute_entanglement_modulus() (in module pylimer_tools.calc.miller_macosko_theory) compute_extent_of_reaction() (in module pylimer_tools.calc.structure_analysis) compute_extracted_modulus() (in module pylimer_tools.calc.miller_macosko_theory) compute_fraction_of_bifunctional_reactive_sites() (in module pylimer_tools.calc.structure_analysis) compute_junction_modulus() (in module pylimer_tools.calc.miller_macosko_theory) compute_mean_end_to_end_distance() (pylimer_tools_cpp.Universe method) compute_mean_end_to_end_distances() (in module pylimer_tools.calc.structure_analysis) compute_mean_end_to_end_vectors() (in module pylimer_tools.calc.structure_analysis) compute_mean_squared_end_to_end_distance() (pylimer_tools_cpp.Universe method) compute_mean_strand_length() (pylimer_tools_cpp.Universe method) compute_mean_universe_volume() (in module pylimer_tools.calc.mehp_utilities) compute_miller_macosko_probabilities() (in module pylimer_tools.calc.miller_macosko_theory) compute_modulus_decomposition() (in module pylimer_tools.calc.miller_macosko_theory) compute_msd_for_atom_properties() (pylimer_tools_cpp.UniverseSequence method) compute_msd_for_atoms() (pylimer_tools_cpp.UniverseSequence method) compute_number_average_molecular_weight() (pylimer_tools_cpp.Universe method) compute_number_fractions() (in module pylimer_tools.calc.stoichiometric_relationships) compute_polydispersity_index() (pylimer_tools_cpp.Universe method) compute_probability_that_bifunctional_monomer_is_dangling() (in module pylimer_tools.calc.miller_macosko_theory) compute_probability_that_bifunctional_monomer_is_effective() (in module pylimer_tools.calc.miller_macosko_theory) compute_probability_that_crosslink_is_dangling() (in module pylimer_tools.calc.miller_macosko_theory) compute_probability_that_crosslink_is_effective() (in module pylimer_tools.calc.miller_macosko_theory) compute_probability_that_crosslink_with_degree_is_dangling() (in module pylimer_tools.calc.miller_macosko_theory) compute_radius_of_gyration() (pylimer_tools_cpp.Molecule method) compute_radius_of_gyration_with_derived_image_flags() (pylimer_tools_cpp.Molecule method) compute_stoichiometric_imbalance() (in module pylimer_tools.calc.structure_analysis) compute_strand_number_density() (in module pylimer_tools.calc.stoichiometric_relationships) compute_temperature() (pylimer_tools_cpp.Universe method) compute_topological_factor() (in module pylimer_tools.calc.mehp_utilities) compute_total_length() (pylimer_tools_cpp.Molecule method) compute_total_mass() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) compute_total_vector() (pylimer_tools_cpp.Molecule method) compute_trapping_factor() (in module pylimer_tools.calc.miller_macosko_theory) compute_vector_from_to() (pylimer_tools_cpp.Molecule method) compute_vector_from_to_atoms() (pylimer_tools_cpp.UniverseSequence method) compute_vector_to() (pylimer_tools_cpp.Atom method) compute_weight_average_molecular_weight() (pylimer_tools_cpp.Universe method) compute_weight_fraction_of_backbone() (in module pylimer_tools.calc.miller_macosko_theory) compute_weight_fraction_of_dangling_chains() (in module pylimer_tools.calc.miller_macosko_theory) compute_weight_fraction_of_soluble_material() (in module pylimer_tools.calc.miller_macosko_theory)

compute_weight_fraction_of_soluble_material_from_weight_fractions() (in module pylimer_tools.calc.miller_macosko_theory) compute_weight_fractions() (in module pylimer_tools.calc.stoichiometric_relationships) (in module pylimer_tools.calc.structure_analysis) (pylimer_tools_cpp.Universe method) ComputedDoubleValues (class in pylimer_tools_cpp) ComputedIntValues (class in pylimer_tools_cpp) config_a() (pylimer_tools_cpp.DPDSimulator method) config_allow_relocation_in_network() (pylimer_tools_cpp.DPDSimulator method) config_assume_box_large_enough() (pylimer_tools_cpp.MEHPForceBalance method) config_assume_network_is_complete() (pylimer_tools_cpp.MEHPForceBalance2 method) config_atom_style() (pylimer_tools_cpp.DataFileWriter method) config_attempt_image_reset() (pylimer_tools_cpp.DataFileWriter method) config_auto_correlator_output() (pylimer_tools_cpp.DPDSimulator method) config_average_output() (pylimer_tools_cpp.DPDSimulator method) config_bond_formation() (pylimer_tools_cpp.DPDSimulator method) config_box_deformation() (pylimer_tools_cpp.DPDSimulator method) config_crosslinker_type() (pylimer_tools_cpp.DataFileWriter method) config_entanglement_type() (pylimer_tools_cpp.MEHPForceBalance method) config_include_angles() (pylimer_tools_cpp.DataFileWriter method) config_include_dihedral_angles() (pylimer_tools_cpp.DataFileWriter method) config_include_velocities() (pylimer_tools_cpp.DataFileWriter method) config_lambda() (pylimer_tools_cpp.DPDSimulator method) config_mean_bond_length() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) config_molecule_idx_for_swap() (pylimer_tools_cpp.DataFileWriter method) config_move_into_box() (pylimer_tools_cpp.DataFileWriter method) config_nr_of_mc_steps() (pylimer_tools_cpp.MCUniverseGenerator method) config_num_steps_dpd() (pylimer_tools_cpp.DPDSimulator method) config_num_steps_mc() (pylimer_tools_cpp.DPDSimulator method) config_primary_loop_probability() (pylimer_tools_cpp.MCUniverseGenerator method) config_reindex_atoms() (pylimer_tools_cpp.DataFileWriter method) config_rerun_epsilon() (pylimer_tools_cpp.MEHPForceRelaxation method) config_restart_output() (pylimer_tools_cpp.DPDSimulator method) config_secondary_loop_probability() (pylimer_tools_cpp.MCUniverseGenerator method) config_shift_one_at_a_time() (pylimer_tools_cpp.DPDSimulator method) config_shift_possibility_empty() (pylimer_tools_cpp.DPDSimulator method) config_sigma() (pylimer_tools_cpp.DPDSimulator method) config_simplification_frequency() (pylimer_tools_cpp.MEHPForceBalance method) config_slipspring_high_cutoff() (pylimer_tools_cpp.DPDSimulator method) config_slipspring_low_cutoff() (pylimer_tools_cpp.DPDSimulator method) config_spring_breaking_distance() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) config_spring_constant() (pylimer_tools_cpp.DPDSimulator method) (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) config_step_output() (pylimer_tools_cpp.DPDSimulator method) (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) conjugate() (pylimer_tools_cpp.ComputedDoubleValues method) (pylimer_tools_cpp.ComputedIntValues method) (pylimer_tools_cpp.ExitReason method) CONJUGATE_GRADIENT (pylimer_tools_cpp.SLESolver attribute) CONJUGATE_GRADIENT_DIAGONALIZED (pylimer_tools_cpp.SLESolver attribute) CONJUGATE_GRADIENT_IDENTITY (pylimer_tools_cpp.SLESolver attribute) CONJUGATE_GRADIENT_INCOMPLETE_CHOLESKY (pylimer_tools_cpp.SLESolver attribute) construct_with_random_sliplinks() (pylimer_tools_cpp.MEHPForceBalance static method) contract_vertices_along_bond_type() (pylimer_tools_cpp.Universe method) coordinates (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) (pylimer_tools_cpp.SimplifiedNetwork attribute) count_active_clustered_atoms() (pylimer_tools_cpp.MEHPForceRelaxation method) count_atom_types() (pylimer_tools_cpp.Universe method) count_atoms_in_skin_distance() (pylimer_tools_cpp.Universe method) count_loop_lengths() (pylimer_tools_cpp.Universe method) create_slip_springs() (pylimer_tools_cpp.DPDSimulator method)

D

DANGLING_CHAIN (pylimer_tools_cpp.MoleculeType attribute) DataFileReader (class in pylimer_tools_cpp) DataFileWriter (class in pylimer_tools_cpp) DEFAULT (pylimer_tools_cpp.SLESolver attribute) deform_to() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) denominator (pylimer_tools_cpp.ComputedDoubleValues attribute) (pylimer_tools_cpp.ComputedIntValues attribute) (pylimer_tools_cpp.ExitReason attribute) DENSE_EIGEN (pylimer_tools_cpp.NormalModeSolver attribute) DENSE_LAPACK (pylimer_tools_cpp.NormalModeSolver attribute) detect_angles() (pylimer_tools_cpp.Universe method) detect_dihedral_angles() (pylimer_tools_cpp.Universe method) detect_headers() (in module pylimer_tools.io.extract_thermo_data) determine_effective_functionality_per_type() (pylimer_tools_cpp.Universe method)

determine_functionality_per_type() (pylimer_tools_cpp.Universe method) DIELECTRIC (pylimer_tools_cpp.AtomStyle attribute) DIPOLE (pylimer_tools_cpp.AtomStyle attribute) disable_max_distance() (pylimer_tools_cpp.MCUniverseGenerator method) distance_to() (pylimer_tools_cpp.Atom method) distance_to_unwrapped() (pylimer_tools_cpp.Atom method) do_cache() (in module pylimer_tools.utils.cache_utility) do_linear_walk_chain_from_to() (in module pylimer_tools_cpp) do_random_walk() (in module pylimer_tools_cpp) do_random_walk_chain_from_to() (in module pylimer_tools_cpp) do_random_walk_chain_from_to_mc() (in module pylimer_tools_cpp) double_values (pylimer_tools_cpp.OutputConfiguration attribute) DPD (pylimer_tools_cpp.AtomStyle attribute) DPDSimulator (class in pylimer_tools_cpp) DumpFileReader (class in pylimer_tools_cpp)

E

EDPD (pylimer_tools_cpp.AtomStyle attribute) ELECTRON (pylimer_tools_cpp.AtomStyle attribute) ELLIPSOID (pylimer_tools_cpp.AtomStyle attribute) evaluate_force_set_gradient() (pylimer_tools_cpp.MEHPForceEvaluator method) (pylimer_tools_cpp.NonGaussianSpringForceEvaluator method) (pylimer_tools_cpp.SimpleSpringMEHPForceEvaluator method) evaluate_loss_modulus() (pylimer_tools_cpp.NormalModeAnalyzer method) evaluate_loss_modulus_kpm() (pylimer_tools_cpp.NormalModeAnalyzer method) evaluate_spring_distance() (pylimer_tools_cpp.MEHPForceBalance method) evaluate_spring_distance_from() (pylimer_tools_cpp.MEHPForceBalance method) evaluate_spring_distance_to() (pylimer_tools_cpp.MEHPForceBalance method)

evaluate_spring_vector() (pylimer_tools_cpp.MEHPForceBalance2 method) evaluate_spring_vector_from() (pylimer_tools_cpp.MEHPForceBalance2 method) evaluate_spring_vector_to() (pylimer_tools_cpp.MEHPForceBalance2 method) evaluate_storage_modulus() (pylimer_tools_cpp.NormalModeAnalyzer method) evaluate_storage_modulus_kpm() (pylimer_tools_cpp.NormalModeAnalyzer method) evaluate_stress_autocorrelation() (pylimer_tools_cpp.NormalModeAnalyzer method) evaluate_stress_autocorrelation_kpm() (pylimer_tools_cpp.NormalModeAnalyzer method) evaluate_stress_contribution() (pylimer_tools_cpp.MEHPForceEvaluator method) (pylimer_tools_cpp.NonGaussianSpringForceEvaluator method) (pylimer_tools_cpp.SimpleSpringMEHPForceEvaluator method) ExitReason (class in pylimer_tools_cpp) extract_thermo_params() (in module pylimer_tools.io.extract_thermo_data)

F

F_TOLERANCE (pylimer_tools_cpp.ExitReason attribute) FAILURE (pylimer_tools_cpp.ExitReason attribute) FILE pylimer-displace-randomly command line option filename (pylimer_tools_cpp.OutputConfiguration attribute) FILES pylimer-analyse-networks command line option pylimer-basic-lammps-stats command line option find_all_eigenvalues() (pylimer_tools_cpp.NormalModeAnalyzer method)

find_loops() (pylimer_tools_cpp.Universe method) find_minimal_order_loop_from() (pylimer_tools_cpp.Universe method) find_sparse_eigenvalues() (pylimer_tools_cpp.NormalModeAnalyzer method) forget_at_index() (pylimer_tools_cpp.UniverseSequence method) FREE_CHAIN (pylimer_tools_cpp.MoleculeType attribute) from_bytes() (pylimer_tools_cpp.ComputedDoubleValues class method) (pylimer_tools_cpp.ComputedIntValues class method) (pylimer_tools_cpp.ExitReason class method) FULL (pylimer_tools_cpp.AtomStyle attribute)

G

GAMMA (pylimer_tools_cpp.ComputedDoubleValues attribute) GAUSSIAN (pylimer_tools.io.bead_spring_parameter_provider.ParameterType attribute), [1] generate_structure() (in module pylimer_tools.generate_network) get() (pylimer_tools.io.bead_spring_parameter_provider.Parameters method) (pylimer_tools.io.polymer_data.PolymerData method) get_active_chains() (pylimer_tools_cpp.MEHPForceRelaxation method) get_all() (pylimer_tools_cpp.UniverseSequence method) get_angles() (pylimer_tools_cpp.Universe method) get_atom() (pylimer_tools_cpp.Universe method) get_atom_by_id() (pylimer_tools_cpp.Molecule method) get_atom_by_vertex_id() (pylimer_tools_cpp.Universe method) get_atom_by_vertex_idx() (pylimer_tools_cpp.Molecule method) get_atom_id_by_vertex_idx() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_atom_ids() (pylimer_tools_cpp.DataFileReader method) get_atom_nx() (pylimer_tools_cpp.DataFileReader method) get_atom_ny() (pylimer_tools_cpp.DataFileReader method) get_atom_nz() (pylimer_tools_cpp.DataFileReader method) get_atom_types() (pylimer_tools_cpp.DataFileReader method) (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_atom_x() (pylimer_tools_cpp.DataFileReader method) get_atom_y() (pylimer_tools_cpp.DataFileReader method) get_atom_z() (pylimer_tools_cpp.DataFileReader method) get_atoms() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_atoms_by_degree() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_atoms_by_type() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_atoms_close_to() (pylimer_tools_cpp.NeighbourList method) get_atoms_connected_to() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_atoms_connected_to_vertex() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_atoms_lined_up() (pylimer_tools_cpp.Molecule method) get_available_polymers() (in module pylimer_tools.io.polymer_data) (pylimer_tools.io.unit_styles.UnitStyleFactory method) get_average_contour_length() (pylimer_tools_cpp.MEHPForceRelaxation method) get_average_spring_length() (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_average_strand_length() (pylimer_tools_cpp.MEHPForceBalance method) get_base_distance_units() (pylimer_tools.io.bead_spring_parameter_provider.Parameters method) get_base_unit_of() (pylimer_tools.io.unit_styles.UnitStyle method) get_bead_density() (pylimer_tools.io.bead_spring_parameter_provider.Parameters method) get_bond_from() (pylimer_tools_cpp.DataFileReader method) get_bond_lengths() (pylimer_tools_cpp.DPDSimulator method) get_bond_to() (pylimer_tools_cpp.DataFileReader method) get_bond_types() (pylimer_tools_cpp.DataFileReader method) get_bonds() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_bounding_box() (pylimer_tools_cpp.Box method) get_box() (pylimer_tools_cpp.Universe method) get_cache_file_name() (in module pylimer_tools.utils.cache_utility) get_chains_with_crosslinker() (pylimer_tools_cpp.Universe method) get_clusters() (pylimer_tools_cpp.Universe method) get_column_names() (pylimer_tools_cpp.AveFileReader method) get_coordinates() (pylimer_tools_cpp.Atom method) (pylimer_tools_cpp.DPDSimulator method) (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_crosslinker_universe() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_current_crosslinker_conversion() (pylimer_tools_cpp.MCUniverseGenerator method) get_current_nr_of_atoms() (pylimer_tools_cpp.MCUniverseGenerator method) get_current_nr_of_bonds() (pylimer_tools_cpp.MCUniverseGenerator method) get_current_spring_distances() (pylimer_tools_cpp.MEHPForceRelaxation method) get_current_spring_lengths() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_current_spring_vectors() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_current_strand_conversion() (pylimer_tools_cpp.MCUniverseGenerator method) get_current_strand_vectors() (pylimer_tools_cpp.MEHPForceBalance method) get_current_timestep() (pylimer_tools_cpp.DPDSimulator method) get_dangling_weight_fraction() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_data() (pylimer_tools_cpp.AveFileReader method) get_default_mean_bond_length() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_default_r0_square() (pylimer_tools_cpp.MEHPForceRelaxation method) get_displacement_residual_norm() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_displacements() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_edge_ids_from() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_edge_ids_from_to() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_edges() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_effective_functionality_of_atoms() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_eigenvalues() (pylimer_tools_cpp.NormalModeAnalyzer method) get_eigenvectors() (pylimer_tools_cpp.NormalModeAnalyzer method) get_entanglement_density() (pylimer_tools.io.bead_spring_parameter_provider.Parameters method) get_everares_et_al_data() (pylimer_tools.io.unit_styles.UnitStyleFactory method) get_exit_reason() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_extra_data() (pylimer_tools_cpp.Atom method) get_fb_stress_conversion() (pylimer_tools.io.bead_spring_parameter_provider.Parameters method) get_force() (pylimer_tools_cpp.MEHPForceRelaxation method) get_force_balance() (pylimer_tools_cpp.MCUniverseGenerator method) get_force_balance2() (pylimer_tools_cpp.MCUniverseGenerator method) get_force_magnitude_vector() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_force_on() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_force_relaxation() (pylimer_tools_cpp.MCUniverseGenerator method) get_gamma_conversion_factor() (pylimer_tools.io.bead_spring_parameter_provider.Parameters method) get_gamma_factor() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_gamma_factors() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_gamma_factors_in_dir() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_gaussian_parameters_for_polymer() (in module pylimer_tools.io.bead_spring_parameter_provider) get_high_x() (pylimer_tools_cpp.Box method) (pylimer_tools_cpp.DataFileReader method) get_high_y() (pylimer_tools_cpp.Box method) (pylimer_tools_cpp.DataFileReader method) get_high_z() (pylimer_tools_cpp.Box method) (pylimer_tools_cpp.DataFileReader method) get_id() (pylimer_tools_cpp.Atom method) get_ids_of_active_nodes() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_initial_coordinates() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_kappa() (pylimer_tools.io.bead_spring_parameter_provider.Parameters method) get_key() (pylimer_tools_cpp.Molecule method) get_kg_lj_parameters_for_polymer() (in module pylimer_tools.io.bead_spring_parameter_provider) get_kuhn_parameters_for_polymer() (in module pylimer_tools.io.bead_spring_parameter_provider) get_l() (pylimer_tools_cpp.Box method) get_length() (pylimer_tools_cpp.DumpFileReader method) (pylimer_tools_cpp.UniverseSequence method) get_low_x() (pylimer_tools_cpp.Box method) (pylimer_tools_cpp.DataFileReader method) get_low_y() (pylimer_tools_cpp.Box method) (pylimer_tools_cpp.DataFileReader method) get_low_z() (pylimer_tools_cpp.Box method) (pylimer_tools_cpp.DataFileReader method) get_lx() (pylimer_tools_cpp.Box method) (pylimer_tools_cpp.DataFileReader method)

get_ly() (pylimer_tools_cpp.Box method) (pylimer_tools_cpp.DataFileReader method) get_lz() (pylimer_tools_cpp.Box method) (pylimer_tools_cpp.DataFileReader method) get_masses() (pylimer_tools_cpp.DataFileReader method) (pylimer_tools_cpp.Universe method) get_matrix() (pylimer_tools_cpp.NormalModeAnalyzer method) get_matrix_size() (pylimer_tools_cpp.NormalModeAnalyzer method) get_max_distance() (pylimer_tools_cpp.LinearMaxDistanceProvider method) (pylimer_tools_cpp.MaxDistanceProvider method) (pylimer_tools_cpp.NoMaxDistanceProvider method) (pylimer_tools_cpp.ZScoreMaxDistanceProvider method) get_mean_bead_distance() (pylimer_tools_cpp.MCUniverseGenerator method) get_mean_squared_bead_distance() (pylimer_tools_cpp.MCUniverseGenerator method) get_molecule_ids() (pylimer_tools_cpp.DataFileReader method) get_molecules() (pylimer_tools_cpp.Universe method) get_name() (pylimer_tools.io.bead_spring_parameter_provider.Parameters method) get_neighbour_link_indices() (pylimer_tools_cpp.MEHPForceBalance static method) (pylimer_tools_cpp.MEHPForceBalance2 static method) get_network_of_crosslinker() (pylimer_tools_cpp.Universe method) get_nr_of_active_nodes() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_nr_of_active_spring() (pylimer_tools_cpp.MEHPForceBalance2 method) get_nr_of_active_springs() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_nr_of_active_springs_connected() (pylimer_tools_cpp.MEHPForceRelaxation method) get_nr_of_active_springs_in_dir() (pylimer_tools_cpp.MEHPForceBalance2 method) get_nr_of_active_strands() (pylimer_tools_cpp.MEHPForceBalance method) get_nr_of_active_strands_in_dir() (pylimer_tools_cpp.MEHPForceBalance method) get_nr_of_angles() (pylimer_tools_cpp.Universe method) get_nr_of_atom_types() (pylimer_tools_cpp.DataFileReader method) get_nr_of_atoms() (pylimer_tools_cpp.DataFileReader method) (pylimer_tools_cpp.DPDSimulator method) (pylimer_tools_cpp.MCUniverseGenerator method) (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_nr_of_bond_types() (pylimer_tools_cpp.DataFileReader method) get_nr_of_bonds() (pylimer_tools_cpp.DataFileReader method) (pylimer_tools_cpp.DPDSimulator method) (pylimer_tools_cpp.MCUniverseGenerator method) (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_nr_of_bonds_of_atom() (pylimer_tools_cpp.Universe method) get_nr_of_bonds_of_vertex() (pylimer_tools_cpp.Universe method) get_nr_of_bonds_to_form() (pylimer_tools_cpp.DPDSimulator method) get_nr_of_columns() (pylimer_tools_cpp.AveFileReader method) get_nr_of_dihedral_angles() (pylimer_tools_cpp.Universe method) get_nr_of_edges_from_to() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_nr_of_extra_atoms() (pylimer_tools_cpp.DPDSimulator method) (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_nr_of_extra_bonds() (pylimer_tools_cpp.DPDSimulator method) (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_nr_of_intra_chain_sliplinks() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_nr_of_iterations() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_nr_of_nodes() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_nr_of_rows() (pylimer_tools_cpp.AveFileReader method) get_nr_of_slip_springs() (pylimer_tools_cpp.DPDSimulator method) get_nr_of_soluble_clusters() (pylimer_tools_cpp.NormalModeAnalyzer method) get_nr_of_springs() (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_nr_of_steps_dpd() (pylimer_tools_cpp.DPDSimulator method) get_nr_of_steps_mc() (pylimer_tools_cpp.DPDSimulator method) get_nr_of_strands() (pylimer_tools_cpp.MEHPForceBalance method) get_numeric_values_for_at() (pylimer_tools_cpp.DumpFileReader method) get_nx() (pylimer_tools_cpp.Atom method) get_ny() (pylimer_tools_cpp.Atom method) get_nz() (pylimer_tools_cpp.Atom method) get_offset() (pylimer_tools_cpp.Box method) get_overall_strand_lengths() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_parameters_for_polymer() (in module pylimer_tools.io.bead_spring_parameter_provider) get_polymer_by_name() (in module pylimer_tools.io.polymer_data) get_pressure() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_property() (pylimer_tools_cpp.Atom method) get_residual_norm() (pylimer_tools_cpp.MEHPForceRelaxation method) get_residuals() (pylimer_tools_cpp.MEHPForceRelaxation method) get_sampling_cutoff() (pylimer_tools.io.bead_spring_parameter_provider.Parameters method) get_shift_one_at_a_time() (pylimer_tools_cpp.DPDSimulator method) get_shift_possibility_empty() (pylimer_tools_cpp.DPDSimulator method) get_slip_spring_bond_type() (pylimer_tools_cpp.DPDSimulator method) get_soluble_weight_fraction() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_spring_constant() (pylimer_tools_cpp.DPDSimulator method) get_spring_contour_length() (pylimer_tools_cpp.MEHPForceRelaxation method) get_spring_distances() (pylimer_tools_cpp.MEHPForceRelaxation method) get_spring_lengths() (pylimer_tools_cpp.MEHPForceRelaxation method) get_strand_ends() (pylimer_tools_cpp.Molecule method) get_strand_partition_indices_of_sliplink() (pylimer_tools_cpp.MEHPForceBalance method) get_strand_partitions() (pylimer_tools_cpp.MEHPForceBalance method) get_strand_type() (pylimer_tools_cpp.Molecule method) get_stress_on() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_stress_tensor() (pylimer_tools_cpp.DPDSimulator method) (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) get_stress_tensor_link_based() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_string_values_for_at() (pylimer_tools_cpp.DumpFileReader method) get_supported_polymer_names() (in module pylimer_tools.io.bead_spring_parameter_provider) get_tail() (in module pylimer_tools.utils.data_utility) get_temperature() (pylimer_tools_cpp.DPDSimulator method) get_thermo_cache_name_suffix() (in module pylimer_tools.io.extract_thermo_data) get_timestep() (pylimer_tools_cpp.DPDSimulator method) (pylimer_tools_cpp.Universe method) get_type() (pylimer_tools_cpp.Atom method) get_underlying_unit_registry() (pylimer_tools.io.unit_styles.UnitStyle method) get_unit_registry() (pylimer_tools.io.bead_spring_parameter_provider.Parameters method) (pylimer_tools.io.unit_styles.UnitStyleFactory method) get_unit_style() (pylimer_tools.io.unit_styles.UnitStyleFactory method) get_universe() (pylimer_tools_cpp.DPDSimulator method) (pylimer_tools_cpp.MCUniverseGenerator method) get_unwrapped_coordinates() (pylimer_tools_cpp.Atom method) get_unwrapped_x() (pylimer_tools_cpp.Atom method) get_unwrapped_y() (pylimer_tools_cpp.Atom method) get_unwrapped_z() (pylimer_tools_cpp.Atom method) get_vertex_degrees() (pylimer_tools_cpp.Universe method) get_vertex_idx_by_atom_id() (pylimer_tools_cpp.Molecule method) (pylimer_tools_cpp.Universe method) get_volume() (pylimer_tools_cpp.Box method) (pylimer_tools_cpp.DPDSimulator method) (pylimer_tools_cpp.Universe method) get_weighted_spring_lengths() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) get_x() (pylimer_tools_cpp.Atom method) get_y() (pylimer_tools_cpp.Atom method) get_z() (pylimer_tools_cpp.Atom method) GRADIENT_DESCENT (pylimer_tools_cpp.SLESolver attribute) GRADIENT_DESCENT_BARZILAI_BORWEIN_LONG (pylimer_tools_cpp.SLESolver attribute) GRADIENT_DESCENT_BARZILAI_BORWEIN_MOMENTUM (pylimer_tools_cpp.SLESolver attribute) GRADIENT_DESCENT_BARZILAI_BORWEIN_SHORT (pylimer_tools_cpp.SLESolver attribute)

H

has_atom_with_id() (pylimer_tools_cpp.Universe method) has_infinite_strand() (pylimer_tools_cpp.Universe method) has_key() (pylimer_tools_cpp.DumpFileReader method)

hash_angle_type() (pylimer_tools_cpp.Universe method) hash_dihedral_angle_type() (pylimer_tools_cpp.Universe method) head() (pylimer_tools.io.polymer_data.PolymerDataFrame method) HYBRID (pylimer_tools_cpp.AtomStyle attribute)

I

imag (pylimer_tools_cpp.ComputedDoubleValues attribute) (pylimer_tools_cpp.ComputedIntValues attribute) (pylimer_tools_cpp.ExitReason attribute) INACTIVE_ONLY (pylimer_tools_cpp.StructureSimplificationMode attribute) INACTIVE_THEN_X2F (pylimer_tools_cpp.StructureSimplificationMode attribute) index (pylimer_tools.io.polymer_data.PolymerDataFrame property) initialize_from_data_sequence() (pylimer_tools_cpp.UniverseSequence method) initialize_from_dump_file() (pylimer_tools_cpp.UniverseSequence method) inspect_displacement_to_mean_position_update() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) inspect_parametrisation_optimsation_for_link() (pylimer_tools_cpp.MEHPForceBalance method) inspect_strand_partition_update() (pylimer_tools_cpp.MEHPForceBalance method) int_values (pylimer_tools_cpp.OutputConfiguration attribute)

interpolate_edges() (pylimer_tools_cpp.Universe method) INTERRUPT (pylimer_tools_cpp.ExitReason attribute) inverse_langevin() (in module pylimer_tools_cpp) is_2d (pylimer_tools_cpp.MEHPForceEvaluator attribute) (pylimer_tools_cpp.NonGaussianSpringForceEvaluator attribute) (pylimer_tools_cpp.SimpleSpringMEHPForceEvaluator attribute) is_active_network() (in module pylimer_tools.generate_network) is_current_cache() (in module pylimer_tools.utils.cache_utility) is_integer() (pylimer_tools_cpp.ComputedDoubleValues method) (pylimer_tools_cpp.ComputedIntValues method) (pylimer_tools_cpp.ExitReason method) is_valid_offset() (pylimer_tools_cpp.Box method) iterrows() (pylimer_tools.io.polymer_data.PolymerDataFrame method) itertuples() (pylimer_tools.io.polymer_data.PolymerDataFrame method)

K

key_has_column() (pylimer_tools_cpp.DumpFileReader method) key_has_directional_column() (pylimer_tools_cpp.DumpFileReader method)

KG_LJ (pylimer_tools.io.bead_spring_parameter_provider.ParameterType attribute), [1] KUHN (pylimer_tools.io.bead_spring_parameter_provider.ParameterType attribute), [1]

L

LazyUniverseSequenceIterator (class in pylimer_tools_cpp) LEAST_SQUARES_CONJUGATE_GRADIENT (pylimer_tools_cpp.SLESolver attribute) LEAST_SQUARES_CONJUGATE_GRADIENT_DIAGONALIZED (pylimer_tools_cpp.SLESolver attribute) LEAST_SQUARES_CONJUGATE_GRADIENT_IDENTITY (pylimer_tools_cpp.SLESolver attribute) LINE (pylimer_tools_cpp.AtomStyle attribute) LinearMaxDistanceProvider (class in pylimer_tools_cpp) link_is_entanglement (pylimer_tools_cpp.SimplifiedBalance2Network attribute) link_is_sliplink (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) link_strand() (pylimer_tools_cpp.MCUniverseGenerator method) link_strand_to() (pylimer_tools_cpp.MCUniverseGenerator method)

link_strand_to_strand() (pylimer_tools_cpp.MCUniverseGenerator method) link_strands_callback() (pylimer_tools_cpp.MCUniverseGenerator method) link_strands_to_conversion() (pylimer_tools_cpp.MCUniverseGenerator method) link_strands_to_soluble_fraction() (pylimer_tools_cpp.MCUniverseGenerator method) link_strands_to_strands_to_conversion() (pylimer_tools_cpp.MCUniverseGenerator method) links_of_strand (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) LinkSwappingMode (class in pylimer_tools_cpp) load_cache() (in module pylimer_tools.utils.cache_utility) load_everaers_et_al_data() (in module pylimer_tools.io.polymer_data)

M

MAX_B (pylimer_tools_cpp.ComputedDoubleValues attribute) MAX_DISPLACEMENT pylimer-displace-randomly command line option MAX_STEPS (pylimer_tools_cpp.ExitReason attribute) MaxDistanceProvider (class in pylimer_tools_cpp) MCUniverseGenerator (class in pylimer_tools_cpp) MDPD (pylimer_tools_cpp.AtomStyle attribute) MEAN_B (pylimer_tools_cpp.ComputedDoubleValues attribute) mean_position_with() (pylimer_tools_cpp.Atom method) mean_position_with_unwrapped() (pylimer_tools_cpp.Atom method) measure_lower_bound_weight_fraction_of_soluble_material() (in module pylimer_tools.calc.structure_analysis) measure_weight_fraction_of_backbone() (in module pylimer_tools.calc.structure_analysis) measure_weight_fraction_of_dangling_chains() (in module pylimer_tools.calc.structure_analysis) measure_weight_fraction_of_soluble_material() (in module pylimer_tools.calc.structure_analysis) MEHPForceBalance (class in pylimer_tools_cpp) MEHPForceBalance2 (class in pylimer_tools_cpp) MEHPForceEvaluator (class in pylimer_tools_cpp) MEHPForceRelaxation (class in pylimer_tools_cpp) module pylimer_tools pylimer_tools.analyse_networks pylimer_tools.basic_lammps_structure_stats pylimer_tools.calc pylimer_tools.calc.mehp_utilities pylimer_tools.calc.miller_macosko_theory pylimer_tools.calc.stoichiometric_relationships pylimer_tools.calc.structure_analysis pylimer_tools.displace_randomly pylimer_tools.generate_network pylimer_tools.io pylimer_tools.io.bead_spring_parameter_provider pylimer_tools.io.extract_thermo_data pylimer_tools.io.polymer_data pylimer_tools.io.read_lammps_output_file pylimer_tools.io.read_pylimer_tools_output_file pylimer_tools.io.unit_styles pylimer_tools.utils pylimer_tools.utils.cache_utility pylimer_tools.utils.data_utility pylimer_tools.utils.optimize_dataframe pylimer_tools_cpp

MOLECULAR (pylimer_tools_cpp.AtomStyle attribute) Molecule (class in pylimer_tools_cpp) MoleculeIterator (class in pylimer_tools_cpp) MoleculeType (class in pylimer_tools_cpp) move_sliplinks_to_their_best_branch() (pylimer_tools_cpp.MEHPForceBalance method) MSD (pylimer_tools_cpp.ComputedDoubleValues attribute)

N

NeighbourList (class in pylimer_tools_cpp) network (pylimer_tools_cpp.MEHPForceBalance attribute) (pylimer_tools_cpp.MEHPForceBalance2 attribute) (pylimer_tools_cpp.MEHPForceEvaluator attribute) (pylimer_tools_cpp.MEHPForceRelaxation attribute) (pylimer_tools_cpp.NonGaussianSpringForceEvaluator attribute) (pylimer_tools_cpp.SimpleSpringMEHPForceEvaluator attribute) NETWORK_STRAND (pylimer_tools_cpp.MoleculeType attribute) next() (pylimer_tools_cpp.UniverseSequence method) NO_SIMPLIFICATION (pylimer_tools_cpp.StructureSimplificationMode attribute) NO_STEPS_POSSIBLE (pylimer_tools_cpp.ExitReason attribute) NO_SWAPPING (pylimer_tools_cpp.LinkSwappingMode attribute) NoMaxDistanceProvider (class in pylimer_tools_cpp) NONE (pylimer_tools_cpp.AtomStyle attribute) NonGaussianSpringForceEvaluator (class in pylimer_tools_cpp) NormalModeAnalyzer (class in pylimer_tools_cpp) NormalModeSolver (class in pylimer_tools_cpp) nr_of_crosslink_swaps_endured (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) nr_of_crosslinks (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) (pylimer_tools_cpp.SimplifiedNetwork attribute)

nr_of_links (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) nr_of_nodes (pylimer_tools_cpp.SimplifiedNetwork attribute) nr_of_springs (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) (pylimer_tools_cpp.SimplifiedNetwork attribute) nr_of_strands (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) NUM_ATOMS (pylimer_tools_cpp.ComputedIntValues attribute) NUM_BONDS (pylimer_tools_cpp.ComputedIntValues attribute) NUM_BONDS_TO_FORM (pylimer_tools_cpp.ComputedIntValues attribute) NUM_EXTRA_ATOMS (pylimer_tools_cpp.ComputedIntValues attribute) NUM_EXTRA_BONDS (pylimer_tools_cpp.ComputedIntValues attribute) NUM_RELOC (pylimer_tools_cpp.ComputedIntValues attribute) NUM_SHIFT (pylimer_tools_cpp.ComputedIntValues attribute) numerator (pylimer_tools_cpp.ComputedDoubleValues attribute) (pylimer_tools_cpp.ComputedIntValues attribute) (pylimer_tools_cpp.ExitReason attribute)

O

old_atom_ids (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) (pylimer_tools_cpp.SimplifiedNetwork attribute) old_atom_types (pylimer_tools_cpp.SimplifiedBalance2Network attribute) optimize() (in module pylimer_tools.utils.optimize_dataframe)

optimize_floats() (in module pylimer_tools.utils.optimize_dataframe) optimize_ints() (in module pylimer_tools.utils.optimize_dataframe) optimize_objects() (in module pylimer_tools.utils.optimize_dataframe) OTHER (pylimer_tools_cpp.ExitReason attribute) output_every (pylimer_tools_cpp.OutputConfiguration attribute) OutputConfiguration (class in pylimer_tools_cpp)

P

pair_of_atom (pylimer_tools_cpp.AtomPairEntanglements attribute) pairs_of_atoms (pylimer_tools_cpp.AtomPairEntanglements attribute) Parameters (class in pylimer_tools.io.bead_spring_parameter_provider) ParameterType (class in pylimer_tools.io.bead_spring_parameter_provider) PERI (pylimer_tools_cpp.AtomStyle attribute) PolymerData (class in pylimer_tools.io.polymer_data) PolymerDataFrame (class in pylimer_tools.io.polymer_data) predict_gelation_point() (in module pylimer_tools.calc.miller_macosko_theory) predict_maximum_p() (in module pylimer_tools.calc.miller_macosko_theory) predict_number_density_of_junction_points() (in module pylimer_tools.calc.miller_macosko_theory) predict_number_density_of_network_strands() (in module pylimer_tools.calc.miller_macosko_theory) predict_p_from_w_sol() (in module pylimer_tools.calc.miller_macosko_theory) predict_shear_modulus() (in module pylimer_tools.calc.mehp_utilities) (in module pylimer_tools.calc.miller_macosko_theory) prepare_for_evaluations() (pylimer_tools_cpp.MEHPForceEvaluator method) (pylimer_tools_cpp.NonGaussianSpringForceEvaluator method) (pylimer_tools_cpp.SimpleSpringMEHPForceEvaluator method) prepare_structure_generation() (in module pylimer_tools.generate_network) PRESSURE (pylimer_tools_cpp.ComputedDoubleValues attribute) PRIMARY_LOOP (pylimer_tools_cpp.MoleculeType attribute) print_with_time() (in module pylimer_tools.generate_network) pylimer-analyse-networks command line option --crosslinker-type --polymer-name FILES pylimer-basic-lammps-stats command line option FILES pylimer-displace-randomly command line option FILE MAX_DISPLACEMENT pylimer-generate-network command line option --disable-primary-loops --disable-secondary-loops --functionalize-discrete --n-beads-per-chain-1 --n-beads-per-chain-2 --n-beads-per-solvent-chain --n-beads-per-xlink --n-chains-1 --n-chains-2 --n-chains-crosslinkers --n-mono-beads-per-chain --n-mono-chains --n-solvent-chains --no-functionalize-discrete --parameter-type --polymer-name --remove-wsol --target-f --target-file --target-p --target-wsol --z-score-std-mult

pylimer_tools module pylimer_tools.analyse_networks module pylimer_tools.basic_lammps_structure_stats module pylimer_tools.calc module pylimer_tools.calc.mehp_utilities module pylimer_tools.calc.miller_macosko_theory module pylimer_tools.calc.stoichiometric_relationships module pylimer_tools.calc.structure_analysis module pylimer_tools.displace_randomly module pylimer_tools.generate_network module pylimer_tools.io module pylimer_tools.io.bead_spring_parameter_provider module pylimer_tools.io.extract_thermo_data module pylimer_tools.io.polymer_data module pylimer_tools.io.read_lammps_output_file module pylimer_tools.io.read_pylimer_tools_output_file module pylimer_tools.io.unit_styles module pylimer_tools.utils module pylimer_tools.utils.cache_utility module pylimer_tools.utils.data_utility module pylimer_tools.utils.optimize_dataframe module pylimer_tools_cpp module

Q

query() (pylimer_tools.io.polymer_data.PolymerDataFrame method)

R

randomly_add_sliplinks() (pylimer_tools_cpp.MEHPForceBalance method) randomly_sample_entanglements() (in module pylimer_tools_cpp) read() (pylimer_tools_cpp.DataFileReader method) (pylimer_tools_cpp.DumpFileReader method) read_averages_file() (in module pylimer_tools.io.read_lammps_output_file) read_avg_file() (in module pylimer_tools.io.read_pylimer_tools_output_file) read_correlation_file() (in module pylimer_tools.io.read_lammps_output_file) read_data_file() (in module pylimer_tools.io.read_lammps_output_file) read_dump_file() (in module pylimer_tools.io.read_lammps_output_file) read_histogram_file() (in module pylimer_tools.io.read_lammps_output_file) read_log_file() (in module pylimer_tools.io.read_lammps_output_file) read_multi_section_separated_value_file() (in module pylimer_tools.io.extract_thermo_data) read_one_group() (in module pylimer_tools.io.extract_thermo_data) read_restart_file() (pylimer_tools_cpp.DPDSimulator static method) read_sectioned_averages_file() (in module pylimer_tools.io.read_lammps_output_file) real (pylimer_tools_cpp.ComputedDoubleValues attribute) (pylimer_tools_cpp.ComputedIntValues attribute) (pylimer_tools_cpp.ExitReason attribute) reduce_mem_usage() (in module pylimer_tools.utils.optimize_dataframe) refresh_current_state() (pylimer_tools_cpp.DPDSimulator method)

relax_crosslinks() (pylimer_tools_cpp.MCUniverseGenerator method) remove_all_angles() (pylimer_tools_cpp.Universe method) remove_all_dihedral_angles() (pylimer_tools_cpp.Universe method) remove_atom() (pylimer_tools_cpp.NeighbourList method) remove_atoms() (pylimer_tools_cpp.Universe method) remove_bonds() (pylimer_tools_cpp.Universe method) remove_bonds_by_type() (pylimer_tools_cpp.Universe method) remove_soluble_fraction() (pylimer_tools_cpp.MCUniverseGenerator method) replace_atom() (pylimer_tools_cpp.Universe method) replace_atom_type() (pylimer_tools_cpp.Universe method) requires_another_run() (pylimer_tools_cpp.MEHPForceRelaxation method) resample_velocities() (pylimer_tools_cpp.Universe method) reset_iterator() (pylimer_tools_cpp.UniverseSequence method) RESIDUAL (pylimer_tools_cpp.ComputedDoubleValues attribute) RHEO (pylimer_tools_cpp.AtomStyle attribute) RHEO_THERMAL (pylimer_tools_cpp.AtomStyle attribute) run_force_relaxation() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) (pylimer_tools_cpp.MEHPForceRelaxation method) run_simulation() (pylimer_tools_cpp.DPDSimulator method)

S

set_bead_distance() (pylimer_tools_cpp.MCUniverseGenerator method) set_box() (pylimer_tools_cpp.Universe method) set_box_lengths() (pylimer_tools_cpp.Universe method) set_custom_atom_format() (pylimer_tools_cpp.DataFileWriter method) set_data_file_atom_style() (pylimer_tools_cpp.UniverseSequence method) set_displacements() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) set_eigenvalues() (pylimer_tools_cpp.NormalModeAnalyzer method) set_eigenvectors() (pylimer_tools_cpp.NormalModeAnalyzer method) set_force_evaluator() (pylimer_tools_cpp.MEHPForceRelaxation method) set_mass() (pylimer_tools_cpp.Universe method) set_masses() (pylimer_tools_cpp.Universe method) set_mean_squared_bead_distance() (pylimer_tools_cpp.MCUniverseGenerator method) set_seed() (pylimer_tools_cpp.MCUniverseGenerator method) set_spring_contour_lengths() (pylimer_tools_cpp.MEHPForceBalance2 method) set_strand_contour_lengths() (pylimer_tools_cpp.MEHPForceBalance method) set_strand_partitions() (pylimer_tools_cpp.MEHPForceBalance method) set_timestep() (pylimer_tools_cpp.Universe method) set_universe_to_write() (pylimer_tools_cpp.DataFileWriter method) set_vertex_property() (pylimer_tools_cpp.Universe method) shape (pylimer_tools.io.polymer_data.PolymerDataFrame property) SimpleSpringMEHPForceEvaluator (class in pylimer_tools_cpp) SIMPLICIAL_LDLT (pylimer_tools_cpp.SLESolver attribute) SIMPLICIAL_LLT (pylimer_tools_cpp.SLESolver attribute) SimplifiedBalance2Network (class in pylimer_tools_cpp) SimplifiedBalanceNetwork (class in pylimer_tools_cpp) SimplifiedNetwork (class in pylimer_tools_cpp) simplify() (pylimer_tools_cpp.Universe method) SLESolver (class in pylimer_tools_cpp) SLIPLINKS_ONLY (pylimer_tools_cpp.LinkSwappingMode attribute) SMD (pylimer_tools_cpp.AtomStyle attribute) SPARSE_LU (pylimer_tools_cpp.SLESolver attribute) SPARSE_QR (pylimer_tools_cpp.SLESolver attribute) SPARSE_SLICING (pylimer_tools_cpp.NormalModeSolver attribute) SPH (pylimer_tools_cpp.AtomStyle attribute) SPHERE (pylimer_tools_cpp.AtomStyle attribute) SPIN (pylimer_tools_cpp.AtomStyle attribute) split_csv() (in module pylimer_tools_cpp) spring_box_offset (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute)

spring_contour_length (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedNetwork attribute) spring_coordinate_index_a (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) (pylimer_tools_cpp.SimplifiedNetwork attribute) spring_coordinate_index_b (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) (pylimer_tools_cpp.SimplifiedNetwork attribute) spring_index_a (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) (pylimer_tools_cpp.SimplifiedNetwork attribute) spring_index_b (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) (pylimer_tools_cpp.SimplifiedNetwork attribute) spring_is_entanglement (pylimer_tools_cpp.SimplifiedBalance2Network attribute) springs_of_strand (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) start_measuring_msd_for_atoms() (pylimer_tools_cpp.DPDSimulator method) STEP (pylimer_tools_cpp.ComputedIntValues attribute) STOP (in module pylimer_tools_cpp) (pylimer_tools_cpp.BackTrackStatus attribute) strand_contour_length (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) strand_coordinate_index_a (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) strand_coordinate_index_b (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) strand_index_a (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) strand_index_b (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) strand_of_spring (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) strands_of_link (pylimer_tools_cpp.SimplifiedBalance2Network attribute) (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) STRESS_NXY (pylimer_tools_cpp.ComputedDoubleValues attribute) STRESS_NXZ (pylimer_tools_cpp.ComputedDoubleValues attribute) STRESS_NYZ (pylimer_tools_cpp.ComputedDoubleValues attribute) STRESS_XX (pylimer_tools_cpp.ComputedDoubleValues attribute) STRESS_XY (pylimer_tools_cpp.ComputedDoubleValues attribute) STRESS_XZ (pylimer_tools_cpp.ComputedDoubleValues attribute) STRESS_YY (pylimer_tools_cpp.ComputedDoubleValues attribute) STRESS_YZ (pylimer_tools_cpp.ComputedDoubleValues attribute) STRESS_ZZ (pylimer_tools_cpp.ComputedDoubleValues attribute) StructureSimplificationMode (class in pylimer_tools_cpp) swap_sliplinks_incl_xlinks() (pylimer_tools_cpp.MEHPForceBalance method)

T

tail() (pylimer_tools.io.polymer_data.PolymerDataFrame method) TDPD (pylimer_tools_cpp.AtomStyle attribute) TEMPERATURE (pylimer_tools_cpp.ComputedDoubleValues attribute) TEMPLATE (pylimer_tools_cpp.AtomStyle attribute) TIME (pylimer_tools_cpp.ComputedDoubleValues attribute) TIMESTEP (pylimer_tools_cpp.ComputedDoubleValues attribute) to_bytes() (pylimer_tools_cpp.ComputedDoubleValues method) (pylimer_tools_cpp.ComputedIntValues method) (pylimer_tools_cpp.ExitReason method)

to_dict() (pylimer_tools.io.polymer_data.PolymerData method) TRACK_BACKWARD (in module pylimer_tools_cpp) (pylimer_tools_cpp.BackTrackStatus attribute) TRACK_FORWARD (in module pylimer_tools_cpp) (pylimer_tools_cpp.BackTrackStatus attribute) TRI (pylimer_tools_cpp.AtomStyle attribute)

U

UNDEFINED (pylimer_tools_cpp.MoleculeType attribute) unify_data_stepsizes() (in module pylimer_tools.utils.data_utility) unique() (pylimer_tools.io.polymer_data.PolymerDataFrame method) UnitStyle (class in pylimer_tools.io.unit_styles) UnitStyleFactory (class in pylimer_tools.io.unit_styles)

Universe (class in pylimer_tools_cpp) UniverseSequence (class in pylimer_tools_cpp) UNSET (pylimer_tools_cpp.ExitReason attribute) use_every (pylimer_tools_cpp.OutputConfiguration attribute) use_linear_max_distance() (pylimer_tools_cpp.MCUniverseGenerator method) use_zscore_max_distance() (pylimer_tools_cpp.MCUniverseGenerator method)

V

validate() (pylimer_tools_cpp.MCUniverseGenerator method) validate_neighbour_list() (pylimer_tools_cpp.DPDSimulator method) validate_network() (pylimer_tools_cpp.MEHPForceBalance method) (pylimer_tools_cpp.MEHPForceBalance2 method) validate_state() (pylimer_tools_cpp.DPDSimulator method)

vector_to_unwrapped() (pylimer_tools_cpp.Atom method) version_information() (in module pylimer_tools_cpp) VOLUME (pylimer_tools_cpp.ComputedDoubleValues attribute) volume (pylimer_tools_cpp.SimplifiedBalanceNetwork attribute) (pylimer_tools_cpp.SimplifiedNetwork attribute)

W

WAVEPACKET (pylimer_tools_cpp.AtomStyle attribute)

write_restart_file() (pylimer_tools_cpp.DPDSimulator method) write_to_file() (pylimer_tools_cpp.DataFileWriter method)

X

X1F_X2F_THEN_INACTIVE (pylimer_tools_cpp.StructureSimplificationMode attribute)

X2F_ONLY (pylimer_tools_cpp.StructureSimplificationMode attribute) X_TOLERANCE (pylimer_tools_cpp.ExitReason attribute)

Z

ZScoreMaxDistanceProvider (class in pylimer_tools_cpp)