OptParametersProcess

A class for managing the optimization of parameters within molecular dynamics simulations.

Attributes

  • system_topology (dict): Stores the system’s molecular topology information.

  • opt_term_parse (dict): Contains details on which parameters are to be optimized.

  • equivalent_term_id_list (list): Maps parameters to their equivalent terms for optimization purposes.

  • equivalent_term_boundary_value_dict (dict): Specifies boundary values for equivalent optimization terms.

  • opt_parameter_boundary_array (numpy.ndarray): An array containing the lower and upper boundaries for each optimization parameter.

Methods

  • __init__(self, system_topology, opt_term_parse, equivalent_term_id_list=None, equivalent_term_boundary_value_dict=None): Initializes the OptParametersProcess class with the system topology and optimization parameters.

  • pack_opt_parameters_to_boundary_array(self): Converts the optimization parameters defined in the system topology into a structured array that delineates their lower and upper boundaries.

  • unpack_updated_parameters_to_top(self, updated_parameters_array): Updates the system topology with the optimized parameter values obtained from the optimization process.

  • adjust_for_equivalent_terms(self, boundary_array): (Private Method) Adjusts the parameter boundary array to account for equivalent terms as defined by equivalent_term_id_list.

  • get_optimized_parameters(self): Retrieves the optimized parameters from the current system topology.

  • save_optimized_parameters(self, filepath): Saves the optimized parameters to a specified file.

  • load_optimized_parameters(self, filepath): Loads optimized parameters from a specified file into the system topology.