Source code for openmdao.drivers.genetic_algorithm_driver

Driver for a simple genetic algorithm.

This is the Simple Genetic Algorithm implementation based on 2009 AAE550: MDO Lecture notes of
Prof. William A. Crossley.

This basic GA algorithm is compartmentalized into the GeneticAlgorithm class so that it can be
used in more complicated driver.

The following reference is only for the automatic population sizing:
Williams E.A., Crossley W.A. (1998) Empirically-Derived Population Size and Mutation Rate
Guidelines for a Genetic Algorithm with Uniform Crossover. In: Chawdhry P.K., Roy R., Pant R.K.
(eds) Soft Computing in Engineering Design and Manufacturing. Springer, London.

The following reference is only for the penalty function:
Smith, A. E., Coit, D. W. (1995) Penalty functions. In: Handbook of Evolutionary Computation, 97(1).

The following reference is only for weighted sum multi-objective optimization:
Sobieszczanski-Sobieski, J., Morris, A. J., van Tooren, M. J. L. (2015)
Multidisciplinary Design Optimization Supported by Knowledge Based Engineering.
John Wiley & Sons, Ltd.
import os
import copy

import numpy as np
from pyDOE2 import lhs

from openmdao.core.constants import INF_BOUND
from openmdao.core.driver import Driver, RecordingDebugging
from openmdao.utils.concurrent import concurrent_eval
from openmdao.utils.mpi import MPI
from openmdao.core.analysis_error import AnalysisError

[docs]class SimpleGADriver(Driver): """ Driver for a simple genetic algorithm. Parameters ---------- **kwargs : dict of keyword arguments Keyword arguments that will be mapped into the Driver options. Attributes ---------- _problem_comm : MPI.Comm or None The MPI communicator for the Problem. _concurrent_pop_size : int Number of points to run concurrently when model is a parallel one. _concurrent_color : int Color of current rank when running a parallel model. _desvar_idx : dict Keeps track of the indices for each desvar, since GeneticAlgorithm sees an array of design variables. _ga : <GeneticAlgorithm> Main genetic algorithm lies here. _randomstate : np.random.RandomState, int Random state (or seed-number) which controls the seed and random draws. """
[docs] def __init__(self, **kwargs): """ Initialize the SimpleGADriver driver. """ super().__init__(**kwargs) # What we support self.supports['integer_design_vars'] = True self.supports['inequality_constraints'] = True self.supports['equality_constraints'] = True self.supports['multiple_objectives'] = True # What we don't support yet self.supports['two_sided_constraints'] = False self.supports['linear_constraints'] = False self.supports['simultaneous_derivatives'] = False self.supports['active_set'] = False self.supports['distributed_design_vars'] = False self.supports._read_only = True self._desvar_idx = {} self._ga = None # random state can be set for predictability during testing if 'SimpleGADriver_seed' in os.environ: self._randomstate = int(os.environ['SimpleGADriver_seed']) else: self._randomstate = None # Support for Parallel models. self._concurrent_pop_size = 0 self._concurrent_color = 0
def _declare_options(self): """ Declare options before kwargs are processed in the init method. """ self.options.declare('bits', default={}, types=(dict), desc='Number of bits of resolution. Default is an empty dict, where ' 'every unspecified variable is assumed to be integer, and the number ' 'of bits is calculated automatically. If you have a continuous var, ' 'you should set a bits value as a key in this dictionary.') self.options.declare('elitism', types=bool, default=True, desc='If True, replace worst performing point with best from previous' ' generation each iteration.') self.options.declare('gray', types=bool, default=False, desc='If True, use Gray code for binary encoding. Gray coding makes' ' the binary representation of adjacent integers differ by one bit.') self.options.declare('cross_bits', types=bool, default=False, desc='If True, crossover swaps single bits instead the default' ' k-point crossover.') self.options.declare('max_gen', default=100, desc='Number of generations before termination.') self.options.declare('pop_size', default=0, desc='Number of points in the GA. Set to 0 and it will be computed ' 'as four times the number of bits.') self.options.declare('run_parallel', types=bool, default=False, desc='Set to True to execute the points in a generation in parallel.') self.options.declare('procs_per_model', default=1, lower=1, desc='Number of processors to give each model under MPI.') self.options.declare('penalty_parameter', default=10., lower=0., desc='Penalty function parameter.') self.options.declare('penalty_exponent', default=1., desc='Penalty function exponent.') self.options.declare('Pc', default=0.1, lower=0., upper=1., desc='Crossover rate.') self.options.declare('Pm', default=0.01, lower=0., upper=1., allow_none=True, desc='Mutation rate.') self.options.declare('multi_obj_weights', default={}, types=(dict), desc='Weights of objectives for multi-objective optimization.' 'Weights are specified as a dictionary with the absolute names' 'of the objectives. The same weights for all objectives are assumed, ' 'if not given.') self.options.declare('multi_obj_exponent', default=1., lower=0., desc='Multi-objective weighting exponent.') self.options.declare('compute_pareto', default=False, types=(bool, ), desc='When True, compute a set of non-dominated points based on all ' 'given objectives and update it each generation. The multi-objective ' 'weight and exponents are ignored because the algorithm uses all ' 'objective values instead of a composite.') def _setup_driver(self, problem): """ Prepare the driver for execution. This is the final thing to run during setup. Parameters ---------- problem : <Problem> Pointer to the containing problem. """ super()._setup_driver(problem) # check design vars and constraints for invalid bounds for name, meta in self._designvars.items(): lower, upper = meta['lower'], meta['upper'] for param in (lower, upper): if param is None or np.all(np.abs(param) >= INF_BOUND): msg = (f"Invalid bounds for design variable '{name}'. When using " f"{self.__class__.__name__}, values for both 'lower' and 'upper' " f"must be specified between +/-INF_BOUND ({INF_BOUND}), " f"but they are: lower={lower}, upper={upper}.") raise ValueError(msg) for name, meta in self._cons.items(): equals, lower, upper = meta['equals'], meta['lower'], meta['upper'] if ((equals is None or np.all(np.abs(equals) >= INF_BOUND)) and (lower is None or np.all(np.abs(lower) >= INF_BOUND)) and (upper is None or np.all(np.abs(upper) >= INF_BOUND))): msg = (f"Invalid bounds for constraint '{name}'. " f"When using {self.__class__.__name__}, the value for 'equals', " f"'lower' or 'upper' must be specified between +/-INF_BOUND " f"({INF_BOUND}), but they are: " f"equals={equals}, lower={lower}, upper={upper}.") raise ValueError(msg) model_mpi = None comm = problem.comm if self._concurrent_pop_size > 0: model_mpi = (self._concurrent_pop_size, self._concurrent_color) elif not self.options['run_parallel']: comm = None self._ga = GeneticAlgorithm(self.objective_callback, comm=comm, model_mpi=model_mpi) def _setup_comm(self, comm): """ Perform any driver-specific setup of communicators for the model. Here, we generate the model communicators. Parameters ---------- comm : MPI.Comm or <FakeComm> or None The communicator for the Problem. Returns ------- MPI.Comm or <FakeComm> or None The communicator for the Problem model. """ self._problem_comm = comm procs_per_model = self.options['procs_per_model'] if MPI and self.options['run_parallel']: full_size = comm.size size = full_size // procs_per_model if full_size != size * procs_per_model: raise RuntimeError("The total number of processors is not evenly divisible by the " "specified number of processors per model.\n Provide a " "number of processors that is a multiple of %d, or " "specify a number of processors per model that divides " "into %d." % (procs_per_model, full_size)) color = comm.rank % size model_comm = comm.Split(color) # Everything we need to figure out which case to run. self._concurrent_pop_size = size self._concurrent_color = color return model_comm self._concurrent_pop_size = 0 self._concurrent_color = 0 return comm def _setup_recording(self): """ Set up case recording. """ if MPI: run_parallel = self.options['run_parallel'] procs_per_model = self.options['procs_per_model'] for recorder in self._rec_mgr: if run_parallel: # write cases only on procs up to the number of parallel models # (i.e. on the root procs for the cases) if procs_per_model == 1: recorder.record_on_process = True else: size = self._problem_comm.size // procs_per_model if self._problem_comm.rank < size: recorder.record_on_process = True elif self._problem_comm.rank == 0: # if not running cases in parallel, then just record on proc 0 recorder.record_on_process = True super()._setup_recording() def _get_name(self): """ Get name of current Driver. Returns ------- str Name of current Driver. """ return "SimpleGA"
[docs] def run(self): """ Execute the genetic algorithm. Returns ------- bool Failure flag; True if failed to converge, False is successful. """ model = self._problem().model ga = self._ga ga.elite = self.options['elitism'] ga.gray_code = self.options['gray'] ga.cross_bits = self.options['cross_bits'] pop_size = self.options['pop_size'] max_gen = self.options['max_gen'] user_bits = self.options['bits'] compute_pareto = self.options['compute_pareto'] Pm = self.options['Pm'] # if None, it will be calculated in execute_ga() Pc = self.options['Pc'] self._check_for_missing_objective() if compute_pareto: self._ga.nobj = len(self._objs) # Size design variables. desvars = self._designvars desvar_vals = self.get_design_var_values() count = 0 for name, meta in desvars.items(): if name in self._designvars_discrete: val = desvar_vals[name] if np.ndim(val) == 0: size = 1 else: size = len(val) else: size = meta['size'] self._desvar_idx[name] = (count, count + size) count += size lower_bound = np.empty((count, )) upper_bound = np.empty((count, )) outer_bound = np.full((count, ), np.inf) bits = np.empty((count, ), dtype=np.int_) x0 = np.empty(count) # Figure out bounds vectors and initial design vars for name, meta in desvars.items(): i, j = self._desvar_idx[name] lower_bound[i:j] = meta['lower'] upper_bound[i:j] = meta['upper'] x0[i:j] = desvar_vals[name] # Bits of resolution abs2prom = model._var_abs2prom['output'] for name, meta in desvars.items(): i, j = self._desvar_idx[name] if name in abs2prom: prom_name = abs2prom[name] else: prom_name = name if name in user_bits: val = user_bits[name] elif prom_name in user_bits: val = user_bits[prom_name] else: # If the user does not declare a bits for this variable, we assume they want it to # be encoded as an integer. Encoding requires a power of 2 in the range, so we need # to pad additional values above the upper range, and adjust accordingly. Design # points with values above the upper bound will be discarded by the GA. log_range = np.log2(upper_bound[i:j] - lower_bound[i:j] + 1) val = log_range # default case -- no padding required mask = log_range % 2 > 0 # mask for vars requiring padding val[mask] = np.ceil(log_range[mask]) outer_bound[i:j][mask] = upper_bound[i:j][mask] upper_bound[i:j][mask] = 2**np.ceil(log_range[mask]) - 1 + lower_bound[i:j][mask] bits[i:j] = val # Automatic population size. if pop_size == 0: pop_size = 4 * np.sum(bits) desvar_new, obj, nfit = ga.execute_ga(x0, lower_bound, upper_bound, outer_bound, bits, pop_size, max_gen, self._randomstate, Pm, Pc) if compute_pareto: # Just save the non-dominated points. self.desvar_nd = desvar_new self.obj_nd = obj else: # Pull optimal parameters back into framework and re-run, so that # framework is left in the right final state for name in desvars: i, j = self._desvar_idx[name] val = desvar_new[i:j] self.set_design_var(name, val) with RecordingDebugging(self._get_name(), self.iter_count, self) as rec: model.run_solve_nonlinear() rec.abs = 0.0 rec.rel = 0.0 self.iter_count += 1 return False
[docs] def objective_callback(self, x, icase): r""" Evaluate problem objective at the requested point. In case of multi-objective optimization, a simple weighted sum method is used: .. math:: f = (\sum_{k=1}^{N_f} w_k \cdot f_k)^a where :math:`N_f` is the number of objectives and :math:`a>0` is an exponential weight. Choosing :math:`a=1` is equivalent to the conventional weighted sum method. The weights given in the options are normalized, so: .. math:: \sum_{k=1}^{N_f} w_k = 1 If one of the objectives :math:`f_k` is not a scalar, its elements will have the same weights, and it will be normed with length of the vector. Takes into account constraints with a penalty function. All constraints are converted to the form of :math:`g_i(x) \leq 0` for inequality constraints and :math:`h_i(x) = 0` for equality constraints. The constraint vector for inequality constraints is the following: .. math:: g = [g_1, g_2 \dots g_N], g_i \in R^{N_{g_i}} h = [h_1, h_2 \dots h_N], h_i \in R^{N_{h_i}} The number of all constraints: .. math:: N_g = \sum_{i=1}^N N_{g_i}, N_h = \sum_{i=1}^N N_{h_i} The fitness function is constructed with the penalty parameter :math:`p` and the exponent :math:`\kappa`: .. math:: \Phi(x) = f(x) + p \cdot \sum_{k=1}^{N^g}(\delta_k \cdot g_k)^{\kappa} + p \cdot \sum_{k=1}^{N^h}|h_k|^{\kappa} where :math:`\delta_k = 0` if :math:`g_k` is satisfied, 1 otherwise .. note:: The values of :math:`\kappa` and :math:`p` can be defined as driver options. Parameters ---------- x : ndarray Value of design variables. icase : int Case number, used for identification when run in parallel. Returns ------- float Objective value. bool Success flag, True if successful. int Case number, used for identification when run in parallel. """ model = self._problem().model success = 1 objs = self.get_objective_values() nr_objectives = len(objs) # Single objective, if there is only one objective, which has only one element if nr_objectives > 1: is_single_objective = False else: for obj in objs.items(): is_single_objective = len(obj) == 1 break obj_exponent = self.options['multi_obj_exponent'] if self.options['multi_obj_weights']: # not empty obj_weights = self.options['multi_obj_weights'] else: # Same weight for all objectives, if not specified obj_weights = {name: 1. for name in objs.keys()} sum_weights = sum(obj_weights.values()) for name in self._designvars: i, j = self._desvar_idx[name] self.set_design_var(name, x[i:j]) # a very large number, but smaller than the result of nan_to_num in Numpy almost_inf = INF_BOUND # Execute the model with RecordingDebugging(self._get_name(), self.iter_count, self) as rec: self.iter_count += 1 try: model.run_solve_nonlinear() # Tell the optimizer that this is a bad point. except AnalysisError: model._clear_iprint() success = 0 obj_values = self.get_objective_values() if is_single_objective: # Single objective optimization for i in obj_values.values(): obj = i # First and only key in the dict elif self.options['compute_pareto']: obj = np.array([val for val in obj_values.values()]).flatten() else: # Multi-objective optimization with weighted sums weighted_objectives = np.array([]) for name, val in obj_values.items(): # element-wise multiplication with scalar # takes the average, if an objective is a vector try: weighted_obj = val * obj_weights[name] / val.size except KeyError: msg = ('Name "{}" in "multi_obj_weights" option ' 'is not an absolute name of an objective.') raise KeyError(msg.format(name)) weighted_objectives = np.hstack((weighted_objectives, weighted_obj)) obj = sum(weighted_objectives / sum_weights)**obj_exponent # Parameters of the penalty method penalty = self.options['penalty_parameter'] exponent = self.options['penalty_exponent'] if penalty == 0: fun = obj else: constraint_violations = np.array([]) for name, val in self.get_constraint_values().items(): con = self._cons[name] # The not used fields will either None or a very large number if (con['lower'] is not None) and np.any(con['lower'] > -almost_inf): diff = val - con['lower'] violation = np.array([0. if d >= 0 else abs(d) for d in diff]) elif (con['upper'] is not None) and np.any(con['upper'] < almost_inf): diff = val - con['upper'] violation = np.array([0. if d <= 0 else abs(d) for d in diff]) elif (con['equals'] is not None) and np.any(np.abs(con['equals']) < almost_inf): diff = val - con['equals'] violation = np.absolute(diff) constraint_violations = np.hstack((constraint_violations, violation)) fun = obj + penalty * sum(np.power(constraint_violations, exponent)) # Record after getting obj to assure they have # been gathered in MPI. rec.abs = 0.0 rec.rel = 0.0 # print("Functions calculated") # print(x) # print(obj) return fun, success, icase
[docs]class GeneticAlgorithm(object): """ Simple Genetic Algorithm. This is the Simple Genetic Algorithm implementation based on 2009 AAE550: MDO Lecture notes of Prof. William A. Crossley. It can be used standalone or as part of the OpenMDAO Driver. Parameters ---------- objfun : function Objective callback function. comm : MPI communicator or None The MPI communicator that will be used objective evaluation for each generation. model_mpi : None or tuple If the model in objfun is also parallel, then this will contain a tuple with the the total number of population points to evaluate concurrently, and the color of the point to evaluate on this rank. Attributes ---------- comm : MPI communicator or None The MPI communicator that will be used objective evaluation for each generation. elite : bool Elitism flag. gray_code : bool Gray code binary representation flag. cross_bits : bool Crossover swaps bits instead of tails flag. Swapping bits is similar to mutation, so when used Pc should be increased and Pm reduced. lchrom : int Chromosome length. model_mpi : None or tuple If the model in objfun is also parallel, then this will contain a tuple with the the total number of population points to evaluate concurrently, and the color of the point to evaluate on this rank. nobj : int Number of objectives. npop : int Population size. objfun : function Objective function callback. """
[docs] def __init__(self, objfun, comm=None, model_mpi=None): """ Initialize genetic algorithm object. """ self.objfun = objfun self.comm = comm self.lchrom = 0 self.npop = 0 self.nobj = 1 self.elite = True self.gray_code = False self.cross_bits = False self.model_mpi = model_mpi
[docs] def execute_ga(self, x0, vlb, vub, vob, bits, pop_size, max_gen, random_state, Pm=None, Pc=0.5): """ Perform the genetic algorithm. Parameters ---------- x0 : ndarray Initial design values. vlb : ndarray Lower bounds array. vub : ndarray Upper bounds array. This includes over-allocation so that every point falls on an integer value. vob : ndarray Outer bounds array. This is purely for bounds check. bits : ndarray Number of bits to encode the design space for each element of the design vector. pop_size : int Number of points in the population. max_gen : int Number of generations to run the GA. random_state : np.random.RandomState, int Random state (or seed-number) which controls the seed and random draws. Pm : float or None Mutation rate. Pc : float Crossover rate. Returns ------- ndarray Best design point. float Objective value at best design point. int Number of successful function evaluations. """ comm = self.comm nobj = self.nobj self.lchrom = int(np.sum(bits)) if nobj > 1: xopt = [] fopt = [] # Needs to be divisible by number of objectives because of tournament selection # strategy. if np.mod(pop_size, nobj) > 0: pop_size += nobj - np.mod(pop_size, nobj) else: xopt = copy.deepcopy(vlb) fopt = np.inf # Needs to be divisible by two because tournament selection pits one half of the # population against the other half. if np.mod(pop_size, 2) == 1: pop_size += 1 self.npop = int(pop_size) fitness = np.zeros((self.npop, nobj)) # If mutation rate is not provided as input if Pm is None: Pm = (self.lchrom + 1.0) / (2.0 * pop_size * np.sum(bits)) elite = self.elite new_gen = np.round(lhs(self.lchrom, self.npop, criterion='center', random_state=random_state)) new_gen[0] = self.encode(x0, vlb, vub, bits) # Main Loop nfit = 0 for generation in range(max_gen + 1): old_gen = copy.deepcopy(new_gen) x_pop = self.decode(old_gen, vlb, vub, bits) # Evaluate fitness of points in this generation. if comm is not None: # Parallel # Since GA is random, ranks generate different new populations, so just take one # and use it on all. x_pop = comm.bcast(x_pop, root=0) cases = [((item, ii), None) for ii, item in enumerate(x_pop) if np.all(item - vob <= 0)] # Pad the cases with some dummy cases to make the cases divisible amongst the procs. # TODO: Add a load balancing option to this driver. extra = len(cases) % comm.size if extra > 0: for j in range(comm.size - extra): cases.append(cases[-1]) results = concurrent_eval(self.objfun, cases, comm, allgather=True, model_mpi=self.model_mpi) fitness[:] = np.inf for result in results: returns, traceback = result if returns: val, success, ii = returns if success: fitness[ii, :] = val nfit += 1 else: # Print the traceback if it fails print('A case failed:') print(traceback) else: # Serial for ii in range(self.npop): x = x_pop[ii] if np.any(x - vob > 0): # Exceeded bounds for integer variables that are over-allocated. success = False else: fitness[ii, :], success, _ = self.objfun(x, 0) if success: nfit += 1 else: fitness[ii, :] = np.inf # Find Pareto front. if nobj > 1: xopt, fopt = self.eval_pareto(x_pop, fitness, xopt, fopt) # Find best objective. else: # Elitism means replace worst performing point with best from # previous generation. if elite and generation > 0: max_index = np.argmax(fitness[:, 0]) old_gen[max_index] = min_gen x_pop[max_index] = min_x fitness[max_index, 0] = min_fit # Find best performing point in this generation. min_fit = np.min(fitness) min_index = np.argmin(fitness) min_gen = old_gen[min_index] min_x = x_pop[min_index] if min_fit < fopt: fopt = min_fit xopt = min_x # Evolve new generation. if nobj > 1: new_gen, new_obj = self.tournament_multi_obj(old_gen, fitness) else: new_gen = self.tournament(old_gen, fitness[:, 0]) new_gen = self.crossover(new_gen, Pc) new_gen = self.mutate(new_gen, Pm) return xopt, fopt, nfit
[docs] def eval_pareto(self, x, obj, x_nd, obj_nd): """ Produce a set of non dominated designs. Parameters ---------- x : ndarray Design points from new generation. obj : ndarray Objective values from new generation. x_nd : ndarray Non dominated design points from previous pareto evaluation. obj_nd : ndarray Non dominated objective values from previous pareto evaluation. Returns ------- ndarray Nondominated design points. ndarray Objective at nondominated design points. """ if len(x_nd) > 1: ypop = np.concatenate((np.array(obj_nd), obj), axis=0) xpop = np.concatenate((x_nd, x), axis=0) else: ypop = obj xpop = x n_pts = ypop.shape[0] i = 0 pot_idx = np.arange(n_pts) while i < len(ypop): nd_point_mask = np.any(ypop < ypop[i, :], axis=1) nd_point_mask[i] = True # Remove dominated points pot_idx = pot_idx[nd_point_mask] ypop = ypop[nd_point_mask] i = np.sum(nd_point_mask[:i]) + 1 return xpop[pot_idx, :], ypop
[docs] def tournament(self, old_gen, fitness): """ Apply tournament selection and keep the best points. Parameters ---------- old_gen : ndarray Points in current generation. fitness : ndarray Objective value of each point. Returns ------- ndarray New generation with best points. """ new_gen = [] idx = np.array(range(0, self.npop - 1, 2)) for j in range(2): old_gen, i_shuffled = self.shuffle(old_gen) fitness = fitness[i_shuffled] # Each point competes with its neighbor; save the best. i_min = np.argmin(np.array([[fitness[idx]], [fitness[idx + 1]]]), axis=0) selected = i_min + idx new_gen.append(old_gen[selected]) return np.concatenate(np.array(new_gen), axis=1).reshape(old_gen.shape)
[docs] def tournament_multi_obj(self, old_gen, obj_val): """ Apply tournament selection and keep the best points. This method is used if there are multiple objectives and the non-dominated set is being kept. Parameters ---------- old_gen : ndarray Points in current generation. obj_val : ndarray Objective value of each point. Returns ------- ndarray New generation with best points. ndarray Corresponding objective values. """ nobj = self.nobj npop = self.npop nrow = npop // nobj new_gen = [] new_obj = [] idx = np.array(range(0, npop - 1, nobj)) for j in np.arange(nobj): old_gen, i_shuffled = self.shuffle(old_gen) obj_val = obj_val[i_shuffled] # Each point competes with its neighbor; save the best. i_min = np.argmin(obj_val[:, j].reshape((nrow, nobj)), axis=1) selected = i_min + idx new_gen.append(old_gen[selected]) new_obj.append(obj_val[selected]) return np.concatenate(np.array(new_gen), axis=1).reshape(old_gen.shape), \ np.concatenate(np.array(new_obj), axis=1).reshape(obj_val.shape)
[docs] def crossover(self, old_gen, Pc): """ Apply crossover to the current generation. Crossover swaps tails (k-point crossover) of two adjacent genes. Parameters ---------- old_gen : ndarray Points in current generation. Pc : float Probability of crossover. Returns ------- ndarray Current generation with crossovers applied. """ new_gen = copy.deepcopy(old_gen) num_sites = self.npop // 2 sites = np.random.rand(num_sites, self.lchrom) idx, idy = np.where(sites < Pc) for ii, jj in zip(idx, idy): i = 2 * ii j = i + 1 if self.cross_bits: # swap single bit new_gen[i][jj] = old_gen[j][jj] new_gen[j][jj] = old_gen[i][jj] else: # swap remainder new_gen[i][jj:] = old_gen[j][jj:] new_gen[j][jj:] = old_gen[i][jj:] return new_gen
[docs] def mutate(self, current_gen, Pm): """ Apply mutations to the current generation. A mutation flips the state of the gene from 0 to 1 or 1 to 0. Parameters ---------- current_gen : ndarray Points in current generation. Pm : float Probability of mutation. Returns ------- ndarray Current generation with mutations applied. """ temp = np.random.rand(self.npop, self.lchrom) idx, idy = np.where(temp < Pm) current_gen[idx, idy] = 1 - current_gen[idx, idy] return current_gen
[docs] def shuffle(self, old_gen): """ Shuffle (reorder) the points in the population. Used in tournament selection. Parameters ---------- old_gen : ndarray Old population. Returns ------- ndarray New shuffled population. ndarray( Index array that maps the shuffle from old to new. """ temp = np.random.rand(self.npop) index = np.argsort(temp) return old_gen[index], index
[docs] def decode(self, gen, vlb, vub, bits): """ Decode from binary array to real value array. Parameters ---------- gen : ndarray Population of points, encoded. vlb : ndarray Lower bound array. vub : ndarray Upper bound array. bits : ndarray( Number of bits for decoding. Returns ------- ndarray Decoded design variable values. """ pts = gen.copy() if self.gray_code: for i in range(np.shape(gen)[0]): pts[i] = self.from_gray(gen[i]) num_desvar = len(bits) interval = (vub - vlb) / (2**bits - 1) x = np.empty((self.npop, num_desvar)) sbit = 0 ebit = 0 for jj in range(num_desvar): exponents = 2**np.array(range(bits[jj] - 1, -1, -1)) ebit += bits[jj] fact = exponents * (pts[:, sbit:ebit]) x[:, jj] = np.einsum('ij->i', fact) * interval[jj] + vlb[jj] sbit = ebit return x
[docs] def encode(self, x, vlb, vub, bits): """ Encode array of real values to array of binary arrays. The array of arrays represents a single population member. Parameters ---------- x : ndarray Design variable values. vlb : ndarray Lower bound array. vub : ndarray Upper bound array. bits : ndarray( Number of bits for decoding. Returns ------- ndarray Single population member, encoded. """ interval = (vub - vlb) / (2**bits - 1) x = np.maximum(x, vlb) x = np.minimum(x, vub) x = np.round((x - vlb) / interval).astype(np.int_) byte_str = [("0" * b + bin(i)[2:])[-b:] for i, b in zip(x, bits)] result = np.array([int(c) for s in byte_str for c in s]) if self.gray_code: result = self.to_gray(result) return result
[docs] @staticmethod def to_gray(g): """ Convert a binary array representing a single population member to Gray code. Parameters ---------- g : binary array Normal binary array, e.g. np.array([0, 0, 1, 0]). Returns ------- ndarray Binary array using Gray code, e.g. np.array([0, 0, 1, 1]). """ s = ''.join([str(x) for x in g]) # convert to binary string: '0010' i = int(s, 2) # convert to Integer: 2 gi = i ^ (i >> 1) # compute gray code Integer: 3 gs = np.binary_repr(gi, len(g)) # convert to binary string: '0011' return np.array([0 if q == '0' else 1 for q in gs]) # convert to np.array: [0, 0, 1, 1]
[docs] @staticmethod def from_gray(g): """ Convert a Gray coded binary array to normal binary coding. The input and output arrays represent a single population member. Parameters ---------- g : binary array Gray coded binary array, e.g. np.array([0, 0, 1, 1]). Returns ------- ndarray Binary array using normal coding, e.g. np.array([0, 0, 1, 0]). """ b = g.copy() for i in range(1, len(g)): prev = 1 if b[i - 1] == 0 else 0 b[i] = b[i - 1] if g[i] == 0 else prev return b