besmarts.mechanics namespace

Submodules

• besmarts.mechanics.fits module
  • calc_tier_distributed()
  • chemical_objective()
  • chemical_system_cluster_angles()
  • chemical_system_cluster_bonds()
  • chemical_system_cluster_data()
  • chemical_system_cluster_force_constants()
  • chemical_system_cluster_geom()
  • compute_config
    • compute_config.prepare_systems()
    • compute_config.run()
  • compute_config_energy_sapt
    • compute_config_energy_sapt.run()
  • compute_config_energy_total
    • compute_config_energy_total.run()
  • compute_config_gradient
    • compute_config_gradient.run()
  • compute_config_hessian
    • compute_config_hessian.run()
  • compute_config_penalty
    • compute_config_penalty.run()
  • compute_config_position
    • compute_config_position.run()
  • ff_optimize()
  • finite_difference_central_2()
  • finite_difference_forward_1()
  • fit()
  • forcefield_optimization_strategy
    • forcefield_optimization_strategy.build_steps()
    • forcefield_optimization_strategy.macro_iteration()
  • forcefield_optimization_strategy_build_macro_iterations()
  • forcefield_optimization_strategy_default()
  • gdb_to_physical_systems()
  • generate_candidates()
  • insert_candidates()
  • objective_config
    • objective_config.compute_diff()
    • objective_config.compute_gradient()
    • objective_config.get_task()
  • objective_config_energy_sapt
    • objective_config_energy_sapt.compute_diff()
    • objective_config_energy_sapt.compute_gradient()
    • objective_config_energy_sapt.get_task()
  • objective_config_energy_total
    • objective_config_energy_total.compute_diff()
    • objective_config_energy_total.compute_gradient()
    • objective_config_energy_total.get_task()
  • objective_config_gradient
    • objective_config_gradient.compute_diff()
    • objective_config_gradient.compute_gradient()
    • objective_config_gradient.get_task()
  • objective_config_hessian
    • objective_config_hessian.compute_diff()
    • objective_config_hessian.compute_gradient()
    • objective_config_hessian.get_task()
  • objective_config_penalty
    • objective_config_penalty.compute_diff()
    • objective_config_penalty.compute_gradient()
    • objective_config_penalty.compute_hessian()
    • objective_config_penalty.get_task()
  • objective_config_position
    • objective_config_position.get_task()
  • objective_run_distributed()
  • objective_tier
    • objective_tier.key_filter()
  • objective_tier_get_keys()
  • objective_tier_run()
  • perform_operations()
  • print_chemical_system()
  • print_xyz()
  • process_accepted_candidates()
  • process_tiers()
  • project_torsions()
  • reset()
  • reset_project_dihedrals()
  • reset_project_torsions()
  • reset_unique()
  • reset_unique_dihedral()
  • select_best_accepted()
  • smiles_assignment_force_constants()
• besmarts.mechanics.force_harmonic module
  • chemical_model_angle_harmonic()
  • chemical_model_bond_harmonic()
  • energy_function_spring()
  • force_function_spring()
  • force_gradient_function_spring()
  • force_gradient_system_spring()
  • force_system_spring()
  • smiles_assignment_energy_function_spring()
  • smiles_assignment_energy_function_spring_matrix()
• besmarts.mechanics.force_pairwise module
  • chemical_model_coulomb()
  • chemical_model_lennard_jones()
  • chemical_model_procedure_antechamber
    • chemical_model_procedure_antechamber.assign()
  • chemical_model_procedure_combine_coulomb
    • chemical_model_procedure_combine_coulomb.assign()
  • chemical_model_procedure_combine_lj_lorentz_berthelot
    • chemical_model_procedure_combine_lj_lorentz_berthelot.assign()
  • energy_function_coulomb_mix()
  • energy_function_lennard_jones_combined()
  • force_function_coulomb_mix()
  • force_function_lennard_jones_combined()
  • force_gradient_function_coulomb_mix()
  • force_gradient_function_lennard_jones_combined()
  • force_gradient_system_coulomb_mix()
  • force_gradient_system_lennard_jones_combined()
  • force_system_coulomb_mix()
  • force_system_lennard_jones_combined()
• besmarts.mechanics.force_periodic module
  • chemical_model_outofplane_periodic()
  • chemical_model_torsion_periodic()
  • energy_function_periodic_cosine_2term()
  • force_function_periodic_cosine_2term()
  • force_gradient_function_periodic_cosine_2term()
  • force_gradient_system_periodic_cosine_2term()
  • force_system_periodic_cosine_2term()
  • init_dihedral_common()
• besmarts.mechanics.hessians module
  • hessian_frequencies()
  • hessian_project_onto_ics()
  • hessian_transform()
  • project_gradient()
  • project_ics()
  • project_onto_ics_from_data()
  • remove_tr()
  • subtract_projection()
  • transform()
  • transform_v2()
  • transform_v3()
• besmarts.mechanics.masses module
  • chemical_model_mass_smarts()
• besmarts.mechanics.molecular_models module
  • chemical_model
  • chemical_model_iter_smarts_hierarchies()
  • chemical_model_iter_smarts_hierarchies_nodes()
  • chemical_model_procedure
    • chemical_model_procedure.assign()
    • chemical_model_procedure.get_term_labels()
    • chemical_model_procedure.get_term_values()
  • chemical_model_procedure_smarts_assignment
    • chemical_model_procedure_smarts_assignment.assign()
    • chemical_model_procedure_smarts_assignment.get_term_labels()
    • chemical_model_procedure_smarts_assignment.get_term_values()
  • chemical_model_smarts_hierarchy_add_node()
  • chemical_model_smarts_hierarchy_copy_node()
  • chemical_model_smarts_hierarchy_remove_node()
  • chemical_system
  • chemical_system_get_angle_means()
  • chemical_system_get_angles()
  • chemical_system_get_bond_length_means()
  • chemical_system_get_bond_lengths()
  • chemical_system_get_ic_measure()
  • chemical_system_get_ic_measure_means()
  • chemical_system_get_node_hierarchy()
  • chemical_system_get_node_model()
  • chemical_system_get_smarts_node()
  • chemical_system_get_value()
  • chemical_system_get_value_list()
  • chemical_system_groupby_names()
  • chemical_system_iter_keys()
  • chemical_system_iter_smarts_hierarchies()
  • chemical_system_iter_smarts_hierarchies_nodes()
  • chemical_system_print()
  • chemical_system_reset_angles()
  • chemical_system_reset_bond_lengths()
  • chemical_system_set_value()
  • chemical_system_set_value_list()
  • chemical_system_smarts_complexity()
  • chemical_system_smarts_hierarchy_add_node()
  • chemical_system_smarts_hierarchy_get_node_keys()
  • chemical_system_to_physical_system()
  • forcefield
    • forcefield.metadata
    • forcefield.models
    • forcefield.perception
  • forcefield_metadata
  • physical_model
    • physical_model.labels
    • physical_model.positions
    • physical_model.topology
    • physical_model.values
  • physical_model_procedure
    • physical_model_procedure.assign()
    • physical_model_procedure.get_term_labels()
    • physical_model_procedure.get_term_values()
  • physical_model_values_copy()
  • physical_system
  • physical_system_iter_keys()
  • physical_system_set_value()
  • smiles_assignment_function()
  • smiles_assignment_matrix_function()
  • system_term
  • topology_term
    • topology_term.copy()
  • topology_term_copy()
• besmarts.mechanics.objectives module
  • array_flatten_assignment()
  • array_flatten_matrix_assignment()
  • array_geom_energy()
  • array_geom_energy_gradient()
  • array_geom_force()
  • array_geom_gradient()
  • array_geom_hessian()
  • physical_model_energy()
  • physical_model_internal_energy()
  • physical_system_bmatrix()
  • physical_system_energy()
  • physical_system_force()
  • physical_system_force_gradient()
  • physical_system_force_gradient_internal()
  • physical_system_force_internal()
  • physical_system_force_system()
  • physical_system_gradient()
  • physical_system_gradient_gradient_internal()
  • physical_system_gradient_internal()
  • physical_system_gradient_system()
  • physical_system_hessian()
  • physical_system_hessian_analytic()
  • physical_system_internals()
• besmarts.mechanics.smirnoff_models module
  • chemical_model_angle_harmonic_smirnoff()
  • chemical_model_bond_harmonic_smirnoff()
  • chemical_model_dihedral_periodic_smirnoff()
  • chemical_model_electrostatics_smirnoff()
  • chemical_model_outofplane_periodic_smirnoff()
  • chemical_model_to_xml_dict()
  • chemical_model_torsion_periodic_smirnoff()
  • chemical_model_vdw_smirnoff()
  • parent_id_add()
  • smirnoff_dihedral_load()
  • smirnoff_load()
  • smirnoff_write_version_0p3()
• besmarts.mechanics.smirnoff_xml module
  • smirnoff_xml_read()
  • smirnoff_xml_write()
• besmarts.mechanics.vibration module
  • angular_momentum()
  • center_of_mass()
  • converteig()
  • gram_schmidt()
  • gs()
  • gs2()
  • hessian_modes()
  • hessian_transform_mass_weighted()
  • inertia_tensor()
  • mode_COM_to_xyz()
  • mode_to_xyz()
  • printmat()
  • printortho()
  • save_xyz()
  • trans_rot_modes()