Source code for openmdao.jacobians.jacobian

"""Define the base Jacobian class."""
from __future__ import division
import numpy as np
from numpy.random import rand

from collections import OrderedDict, defaultdict
from scipy.sparse import issparse
from six import itervalues, iteritems

from openmdao.utils.name_maps import key2abs_key, rel_name2abs_name
from openmdao.matrices.matrix import sparse_types

    'rows': None,
    'cols': None,
    'value': None,
    'dependent': False,

_full_slice = slice(None)

[docs]class Jacobian(object): """ Base Jacobian class. This class provides a dictionary interface for sub-Jacobians and performs matrix-vector products when apply_linear is called. Attributes ---------- _system : <System> Pointer to the system that is currently operating on this Jacobian. _subjacs_info : dict Dictionary of the sub-Jacobian metadata keyed by absolute names. _override_checks : bool If we are approximating a jacobian at the top level and we have specified indices on the functions or designvars, then we need to disable the size checking temporarily so that we can assign a jacobian with less rows or columns than the variable sizes. _under_complex_step : bool When True, this Jacobian is under complex step, using a complex jacobian. _abs_keys : defaultdict A cache dict for key to absolute key. _randomize : bool If True, sparsity is being computed for simultaneous derivative coloring. _jac_summ : dict or None A dict containing a summation of some number of instantaneous absolute values of this jacobian, for use later to determine jacobian sparsity and simultaneous coloring. """
[docs] def __init__(self, system): """ Initialize all attributes. Parameters ---------- system : System Parent system to this jacobian. """ self._system = system self._subjacs_info = system._subjacs_info self._override_checks = False self._under_complex_step = False self._abs_keys = defaultdict(bool) self._randomize = False self._jac_summ = None
def _get_abs_key(self, key): abskey = self._abs_keys[key] if not abskey: self._abs_keys[key] = abskey = key2abs_key(self._system, key) return abskey def _abs_key2shape(self, abs_key): """ Return shape of sub-jacobian for variables making up the key tuple. Parameters ---------- abs_key : (str, str) Absolute name pair of sub-Jacobian. Returns ------- out_size : int local size of the output variable. in_size : int local size of the input variable. """ abs2meta = self._system._var_allprocs_abs2meta of, wrt = abs_key if self._system.comm.size > 1: if wrt in self._system._outputs._views: sz = abs2meta[wrt]['global_size'] else: sz = abs2meta[wrt]['size'] return (abs2meta[of]['global_size'], sz) return (abs2meta[of]['size'], abs2meta[wrt]['size'])
[docs] def __contains__(self, key): """ Return whether there is a subjac for the given promoted or relative name pair. Parameters ---------- key : (str, str) Promoted or relative name pair of sub-Jacobian. Returns ------- boolean return whether sub-Jacobian has been defined. """ return self._get_abs_key(key) in self._subjacs_info
[docs] def __getitem__(self, key): """ Get sub-Jacobian. Parameters ---------- key : (str, str) Promoted or relative name pair of sub-Jacobian. Returns ------- ndarray or spmatrix or list[3] sub-Jacobian as an array, sparse mtx, or AIJ/IJ list or tuple. """ abs_key = self._get_abs_key(key) if abs_key in self._subjacs_info: return self._subjacs_info[abs_key]['value'] else: msg = '{}: Variable name pair ("{}", "{}") not found.' raise KeyError(msg.format(self.msginfo, key[0], key[1]))
[docs] def __setitem__(self, key, subjac): """ Set sub-Jacobian. Parameters ---------- key : (str, str) Promoted or relative name pair of sub-Jacobian. subjac : int or float or ndarray or sparse matrix sub-Jacobian as a scalar, vector, array, or AIJ list or tuple. """ abs_key = self._get_abs_key(key) if abs_key is not None: # You can only set declared subjacobians. if abs_key not in self._subjacs_info: msg = '{}: Variable name pair ("{}", "{}") must first be declared.' raise KeyError(msg.format(self.msginfo, key[0], key[1])) subjacs_info = self._subjacs_info[abs_key] if issparse(subjac): subjacs_info['value'] = subjac else: # np.promote_types will choose the smallest dtype that can contain both arguments subjac = np.atleast_1d(subjac) safe_dtype = np.promote_types(subjac.dtype, float) subjac = subjac.astype(safe_dtype, copy=False) # Bail here so that we allow top level jacobians to be of reduced size when indices # are specified on driver vars. if self._override_checks: subjacs_info['value'] = subjac return rows = subjacs_info['rows'] if rows is None: # Dense subjac subjac = np.atleast_2d(subjac) if subjac.shape != (1, 1): shape = self._abs_key2shape(abs_key) subjac = subjac.reshape(shape) else: # Sparse subjac if subjac.shape != (1,) and subjac.shape != rows.shape: raise ValueError("{}: Sub-jacobian for key %s has " "the wrong shape (%s), expected (%s)." % (self.msginfo, abs_key, subjac.shape, rows.shape)) subjacs_info['value'][:] = subjac else: msg = '{}: Variable name pair ("{}", "{}") not found.' raise KeyError(msg.format(self.msginfo, key[0], key[1]))
[docs] def __iter__(self): """ Yield next name pair of sub-Jacobian. """ for key in self._subjacs_info.keys(): yield key
[docs] def items(self): """ Yield name pair and value of sub-Jacobian. """ for key, val in self._subjacs_info.items(): yield key, val['value']
@property def msginfo(self): """ Return info to prepend to messages. Returns ------- str Info to prepend to messages. """ if self._system is None: return type(self).__name__ return '{} in {}'.format(type(self).__name__, self._system.msginfo) def _update(self, system): """ Read the user's sub-Jacobians and set into the global matrix. Parameters ---------- system : System System that is updating this jacobian. """ pass def _apply(self, system, d_inputs, d_outputs, d_residuals, mode): """ Compute matrix-vector product. Parameters ---------- system : System System that is updating this jacobian. d_inputs : Vector inputs linear vector. d_outputs : Vector outputs linear vector. d_residuals : Vector residuals linear vector. mode : str 'fwd' or 'rev'. """ pass def _randomize_subjac(self, subjac, key): """ Return a subjac that is the given subjac filled with random values. Parameters ---------- subjac : ndarray or csc_matrix Sub-jacobian to be randomized. key : tuple (of, wrt) Key for subjac within the jacobian. Returns ------- ndarray or csc_matrix Randomized version of the subjac. """ if isinstance(subjac, sparse_types): # sparse sparse = subjac.copy() = rand( += 1.0 return sparse # if a subsystem has computed a dynamic partial or semi-total coloring, # we use that sparsity information to set the sparsity of the randomized # subjac. Otherwise all subjacs that didn't have sparsity declared by the # user will appear completely dense, which will lead to a total jacobian that # is more dense than it should be, causing any total coloring that we compute # to be overly conservative. subjac_info = self._subjacs_info[key] if 'sparsity' in subjac_info: assert subjac_info['rows'] is None rows, cols, shape = subjac_info['sparsity'] r = np.zeros(shape) val = rand(len(rows)) val += 1.0 r[rows, cols] = val else: r = rand(*subjac.shape) r += 1.0 return r def _save_sparsity(self, system): """ Add the current jacobian to a running absolute summation. Parameters ---------- system : System System owning this jacobian. """ subjacs = self._subjacs_info if self._jac_summ is None: # create _jac_summ structure self._jac_summ = summ = {} for key in subjacs: summ[key] = np.abs(subjacs[key]['value']) else: summ = self._jac_summ for key in subjacs: summ[key] += np.abs(subjacs[key]['value']) def _compute_sparsity(self, ordered_of_info, ordered_wrt_info, num_full_jacs, tol, orders): """ Compute a dense sparsity matrix for this jacobian using saved absolute summations. The sparsity matrix will contain only those columns that match the wrt variables in wrt_matches, but will contain rows for all outputs in the given system. Parameters ---------- ordered_of_info : list of (name, offset, end, idxs) Name, offset, etc. of row variables in the order that they appear in the jacobian. ordered_wrt_info : list of (name, offset, end, idxs) Name, offset, etc. of column variables in the order that they appear in the jacobian. num_full_jacs : int Number of times to compute partial jacobian when computing sparsity. tol : float Tolerance used to determine if an array entry is zero or nonzero. orders : int Number of orders +/- for the tolerance sweep. Returns ------- ndarray Boolean sparsity matrix. """ from openmdao.utils.coloring import _tol_sweep subjacs = self._subjacs_info summ = self._jac_summ rend = ordered_of_info[-1][2] cend = ordered_wrt_info[-1][2] J = np.zeros((rend, cend)) for of, roffset, rend, _ in ordered_of_info: for wrt, coffset, cend, _ in ordered_wrt_info: key = (of, wrt) if key in subjacs: meta = subjacs[key] if meta['rows'] is not None: rows = meta['rows'] + roffset cols = meta['cols'] + coffset J[rows, cols] = summ[key] elif issparse(summ[key]): raise NotImplementedError("{}: scipy sparse arrays are not " "supported yet.".format(self.msginfo)) else: J[roffset:rend, coffset:cend] = summ[key] J *= (1.0 / num_full_jacs) tol_info = _tol_sweep(J, tol, orders) boolJ = np.zeros(J.shape, dtype=bool) boolJ[J > tol_info['good_tol']] = True return boolJ, tol_info
[docs] def set_complex_step_mode(self, active): """ Turn on or off complex stepping mode. When turned on, the value in each subjac is cast as complex, and when turned off, they are returned to real values. Parameters ---------- active : bool Complex mode flag; set to True prior to commencing complex step. """ for meta in itervalues(self._subjacs_info): if active: meta['value'] = meta['value'].astype(np.complex) else: meta['value'] = meta['value'].real self._under_complex_step = active