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germselection.py
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germselection.py
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""" Functions for selecting a complete set of germs for a GST analysis."""
#***************************************************************************************************
# Copyright 2015, 2019 National Technology & Engineering Solutions of Sandia, LLC (NTESS).
# Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights
# in this software.
# Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0 or in the LICENSE file in the root pyGSTi directory.
#***************************************************************************************************
import warnings as _warnings
import numpy as _np
import numpy.linalg as _nla
from .. import objects as _objs
from .. import construction as _constr
from ..tools import mpitools as _mpit
from ..tools import slicetools as _slct
from . import grasp as _grasp
from . import scoring as _scoring
FLOATSIZE = 8 # in bytes: TODO: a better way
def generate_germs(target_model, randomize=True, randomizationStrength=1e-2,
numGSCopies=5, seed=None, candidateGermCounts=None,
candidateSeed=None, force="singletons", algorithm='greedy',
algorithm_kwargs=None, memLimit=None, comm=None,
profiler=None, verbosity=1):
"""
Generate a germ set for doing GST with a given target model.
This function provides a streamlined interface to a variety of germ
selection algorithms. It's goal is to provide a method that typical users
can run by simply providing a target model and leaving all other settings
at their default values, while providing flexibility for users desiring
more control to fine tune some of the general and algorithm-specific
details.
Currently, to break troublesome degeneracies and provide some confidence
that the chosen germ set is amplificationally complete (AC) for all
models in a neighborhood of the target model (rather than only the
target model), an ensemble of models with random unitary perturbations
to their gates must be provided or generated.
Parameters
----------
target_model : Model or list of Model
The model you are aiming to implement, or a list of models that are
copies of the model you are trying to implement (either with or
without random unitary perturbations applied to the models).
randomize : bool, optional
Whether or not to add random unitary perturbations to the model(s)
provided.
randomizationStrength : float, optional
The size of the random unitary perturbations applied to gates in the
model. See :meth:`~pygsti.objects.Model.randomize_with_unitary`
for more details.
numGSCopies : int, optional
The number of copies of the original model that should be used.
seed : int, optional
Seed for generating random unitary perturbations to models. Also
passed along to stochastic germ-selection algorithms.
candidateGermCounts : dict, optional
A dictionary of *germ_length* : *count* key-value pairs, specifying
the germ "candidate list" - a list of potential germs to draw from.
*count* is either an integer specifying the number of random germs
considered at the given *germ_length* or the special values `"all upto"`
that considers all of the of all non-equivalent germs of length up to
the corresponding *germ_length*. If None, all germs of up to length
6 are used, the equivalent of `{6: 'all upto'}`.
candidateSeed : int, optional
A seed value used when randomly selecting candidate germs. For each
germ length being randomly selected, the germ length is added to
the value of `candidateSeed` to get the actual seed used.
force : str or list, optional
A list of Circuits which *must* be included in the final germ set.
If set to the special string "singletons" then all length-1 strings will
be included. Seting to None is the same as an empty list.
algorithm : {'greedy', 'grasp', 'slack'}, optional
Specifies the algorithm to use to generate the germ set. Current
options are:
'greedy'
Add germs one-at-a-time until the set is AC, picking the germ that
improves the germ-set score by the largest amount at each step. See
:func:`build_up_breadth` for more details.
'grasp'
Use GRASP to generate random greedy germ sets and then locally
optimize them. See :func:`grasp_germ_set_optimization` for more
details.
'slack'
From a initial set of germs, add or remove a germ at each step in
an attempt to improve the germ-set score. Will allow moves that
degrade the score in an attempt to escape local optima as long as
the degredation is within some specified amount of "slack". See
:func:`optimize_integer_germs_slack` for more details.
algorithm_kwargs : dict
Dictionary of ``{'keyword': keyword_arg}`` pairs providing keyword
arguments for the specified `algorithm` function. See the documentation
for functions referred to in the `algorithm` keyword documentation for
what options are available for each algorithm.
memLimit : int, optional
A rough memory limit in bytes which restricts the amount of intermediate
values that are computed and stored.
comm : mpi4py.MPI.Comm, optional
When not None, an MPI communicator for distributing the computation
across multiple processors.
profiler : Profiler, optional
A profiler object used for to track timing and memory usage.
verbosity : int, optional
The verbosity level of the :class:`~pygsti.objects.VerbosityPrinter`
used to print log messages.
Returns
-------
list of Circuit
A list containing the germs making up the germ set.
"""
printer = _objs.VerbosityPrinter.build_printer(verbosity, comm)
modelList = setup_model_list(target_model, randomize,
randomizationStrength, numGSCopies, seed)
gates = list(target_model.operations.keys())
availableGermsList = []
if candidateGermCounts is None: candidateGermCounts = {6: 'all upto'}
for germLength, count in candidateGermCounts.items():
if count == "all upto":
availableGermsList.extend(_constr.list_all_circuits_without_powers_and_cycles(
gates, maxLength=germLength))
else:
seed = None if candidateSeed is None else candidateSeed + germLength
availableGermsList.extend(_constr.list_random_circuits_onelen(
gates, germLength, count, seed=seed))
if algorithm_kwargs is None:
# Avoid danger of using empty dict for default value.
algorithm_kwargs = {}
if algorithm == 'greedy':
printer.log('Using greedy algorithm.', 1)
# Define defaults for parameters that currently have no default or
# whose default we want to change.
default_kwargs = {
'germsList': availableGermsList,
'randomize': False,
'seed': seed,
'verbosity': max(0, verbosity - 1),
'force': force,
'scoreFunc': 'all',
'comm': comm,
'memLimit': memLimit,
'profiler': profiler
}
for key in default_kwargs:
if key not in algorithm_kwargs:
algorithm_kwargs[key] = default_kwargs[key]
germList = build_up_breadth(modelList=modelList,
**algorithm_kwargs)
if germList is not None:
germsetScore = calculate_germset_score(
germList, neighborhood=modelList,
scoreFunc=algorithm_kwargs['scoreFunc'])
printer.log('Constructed germ set:', 1)
printer.log(str([germ.str for germ in germList]), 1)
printer.log('Score: {}'.format(germsetScore), 1)
elif algorithm == 'grasp':
printer.log('Using GRASP algorithm.', 1)
# Define defaults for parameters that currently have no default or
# whose default we want to change.
default_kwargs = {
'alpha': 0.1, # No real reason for setting this value of alpha.
'germsList': availableGermsList,
'randomize': False,
'seed': seed,
'verbosity': max(0, verbosity - 1),
'force': force,
'returnAll': False,
'scoreFunc': 'all',
}
for key in default_kwargs:
if key not in algorithm_kwargs:
algorithm_kwargs[key] = default_kwargs[key]
germList = grasp_germ_set_optimization(modelList=modelList,
**algorithm_kwargs)
printer.log('Constructed germ set:', 1)
if algorithm_kwargs['returnAll'] and germList[0] is not None:
germsetScore = calculate_germset_score(
germList[0], neighborhood=modelList,
scoreFunc=algorithm_kwargs['scoreFunc'])
printer.log(str([germ.str for germ in germList[0]]), 1)
printer.log('Score: {}'.format(germsetScore))
elif not algorithm_kwargs['returnAll'] and germList is not None:
germsetScore = calculate_germset_score(germList,
neighborhood=modelList)
printer.log(str([germ.str for germ in germList]), 1)
printer.log('Score: {}'.format(germsetScore), 1)
elif algorithm == 'slack':
printer.log('Using slack algorithm.', 1)
# Define defaults for parameters that currently have no default or
# whose default we want to change.
default_kwargs = {
'germsList': availableGermsList,
'randomize': False,
'seed': seed,
'verbosity': max(0, verbosity - 1),
'force': force,
'scoreFunc': 'all',
}
if ('slackFrac' not in algorithm_kwargs
and 'fixedSlack' not in algorithm_kwargs):
algorithm_kwargs['slackFrac'] = 0.1
for key in default_kwargs:
if key not in algorithm_kwargs:
algorithm_kwargs[key] = default_kwargs[key]
germList = optimize_integer_germs_slack(modelList,
**algorithm_kwargs)
if germList is not None:
germsetScore = calculate_germset_score(
germList, neighborhood=modelList,
scoreFunc=algorithm_kwargs['scoreFunc'])
printer.log('Constructed germ set:', 1)
printer.log(str([germ.str for germ in germList]), 1)
printer.log('Score: {}'.format(germsetScore), 1)
else:
raise ValueError("'{}' is not a valid algorithm "
"identifier.".format(algorithm))
return germList
def calculate_germset_score(germs, target_model=None, neighborhood=None,
neighborhoodSize=5,
randomizationStrength=1e-2, scoreFunc='all',
opPenalty=0.0, l1Penalty=0.0):
"""Calculate the score of a germ set with respect to a model.
"""
def scoreFn(x): return _scoring.list_score(x, scoreFunc=scoreFunc)
if neighborhood is None:
neighborhood = [target_model.randomize_with_unitary(randomizationStrength)
for n in range(neighborhoodSize)]
scores = [compute_composite_germ_score(scoreFn, model=model,
partialGermsList=germs,
opPenalty=opPenalty,
l1Penalty=l1Penalty)
for model in neighborhood]
return max(scores)
def get_model_params(modelList):
"""Get the number of gates and gauge parameters of the models in a list.
Also verify all models have the same number of gates and gauge parameters.
Parameters
----------
modelList : list of Model
A list of models for which you want an AC germ set.
Returns
-------
reducedModelList : list of Model
The original list of models with SPAM removed
numGaugeParams : int
The number of non-SPAM gauge parameters for all models.
numNonGaugeParams : int
The number of non-SPAM non-gauge parameters for all models.
numOps : int
The number of gates for all models.
Raises
------
ValueError
If the number of gauge parameters or gates varies among the models.
"""
# We don't care about SPAM, since it can't be amplified.
reducedModelList = [removeSPAMVectors(model)
for model in modelList]
# All the models should have the same number of parameters and gates, but
# let's be paranoid here for the time being and make sure.
numGaugeParamsList = [reducedModel.num_gauge_params()
for reducedModel in reducedModelList]
numGaugeParams = numGaugeParamsList[0]
if not all([numGaugeParams == otherNumGaugeParams
for otherNumGaugeParams in numGaugeParamsList[1:]]):
raise ValueError("All models must have the same number of gauge "
"parameters!")
numNonGaugeParamsList = [reducedModel.num_nongauge_params()
for reducedModel in reducedModelList]
numNonGaugeParams = numNonGaugeParamsList[0]
if not all([numNonGaugeParams == otherNumNonGaugeParams
for otherNumNonGaugeParams in numNonGaugeParamsList[1:]]):
raise ValueError("All models must have the same number of non-gauge "
"parameters!")
numOpsList = [len(reducedModel.operations)
for reducedModel in reducedModelList]
numOps = numOpsList[0]
if not all([numOps == otherNumOps
for otherNumOps in numOpsList[1:]]):
raise ValueError("All models must have the same number of gates!")
return reducedModelList, numGaugeParams, numNonGaugeParams, numOps
def setup_model_list(modelList, randomize, randomizationStrength,
numCopies, seed):
"""
Sets up a list of randomize models (helper function).
"""
if not isinstance(modelList, (list, tuple)):
modelList = [modelList]
if len(modelList) > 1 and numCopies is not None:
_warnings.warn("Ignoring numCopies={} since multiple models were "
"supplied.".format(numCopies))
if randomize:
modelList = randomize_model_list(modelList, randomizationStrength,
numCopies, seed)
return modelList
def compute_composite_germ_score(scoreFn, thresholdAC=1e6, initN=1,
partialDerivDaggerDeriv=None, model=None,
partialGermsList=None, eps=None, numGaugeParams=None,
opPenalty=0.0, germLengths=None, l1Penalty=0.0):
"""
Compute the score for a germ set when it is not AC against a model.
Normally scores computed for germ sets against models for which they are
not AC will simply be astronomically large. This is fine if AC is all you
care about, but not so useful if you want to compare partial germ sets
against one another to see which is closer to being AC. This function
will see if the germ set is AC for the parameters corresponding to the
largest `N` eigenvalues for increasing `N` until it finds a value of `N`
for which the germ set is not AC or all the non gauge parameters are
accounted for and report the value of `N` as well as the score.
This allows partial germ set scores to be compared against one-another
sensibly, where a larger value of `N` always beats a smaller value of `N`,
and ties in the value of `N` are broken by the score for that value of `N`.
Parameters
----------
scoreFn : callable
A function that takes as input a list of sorted eigenvalues and returns
a score for the partial germ set based on those eigenvalues, with lower
scores indicating better germ sets. Usually some flavor of
:func:`~pygsti.algorithms.scoring.list_score`.
thresholdAC : float, optional
Value which the score (before penalties are applied) must be lower than
for the germ set to be considered AC.
initN : int
The number of largest eigenvalues to begin with checking.
partialDerivDaggerDeriv : numpy.array, optional
Array with three axes, where the first axis indexes individual germs
within the partial germ set and the remaining axes index entries in the
positive square of the Jacobian of each individual germ's parameters
with respect to the model parameters.
If this array is not supplied it will need to be computed from
`germsList` and `model`, which will take longer, so it is recommended
to precompute this array if this routine will be called multiple times.
model : Model, optional
The model against which the germ set is to be scored. Not needed if
`partialDerivDaggerDeriv` is provided.
partialGermsList : list of Circuit, optional
The list of germs in the partial germ set to be evaluated. Not needed
if `partialDerivDaggerDeriv` (and `germLengths` when
``opPenalty > 0``) are provided.
eps : float, optional
Used when calculating `partialDerivDaggerDeriv` to determine if two
eigenvalues are equal (see :func:`bulk_twirled_deriv` for details). Not
used if `partialDerivDaggerDeriv` is provided.
numGaugeParams : int
The number of gauge parameters of the model. Not needed if `model`
is provided.
opPenalty : float, optional
Coefficient for a penalty linear in the sum of the germ lengths.
germLengths : numpy.array, optional
The length of each germ. Not needed if `opPenalty` is ``0.0`` or
`partialGermsList` is provided.
l1Penalty : float, optional
Coefficient for a penalty linear in the number of germs.
Returns
-------
CompositeScore
The score for the germ set indicating how many parameters it amplifies
and its numerical score restricted to those parameters.
"""
if partialDerivDaggerDeriv is None:
if model is None or partialGermsList is None:
raise ValueError("Must provide either partialDerivDaggerDeriv or "
"(model, partialGermsList)!")
else:
pDDD_kwargs = {'model': model, 'germsList': partialGermsList}
if eps is not None:
pDDD_kwargs['eps'] = eps
if germLengths is not None:
pDDD_kwargs['germLengths'] = germLengths
partialDerivDaggerDeriv = calc_bulk_twirled_DDD(**pDDD_kwargs)
if numGaugeParams is None:
if model is None:
raise ValueError("Must provide either numGaugeParams or model!")
else:
numGaugeParams = removeSPAMVectors(model).num_gauge_params()
# Calculate penalty scores
numGerms = partialDerivDaggerDeriv.shape[0]
l1Score = l1Penalty * numGerms
opScore = 0.0
if opPenalty != 0.0:
if germLengths is None:
if partialGermsList is None:
raise ValueError("Must provide either germLengths or "
"partialGermsList when opPenalty != 0.0!")
else:
germLengths = _np.array([len(germ)
for germ in partialGermsList])
opScore = opPenalty * _np.sum(germLengths)
combinedDDD = _np.sum(partialDerivDaggerDeriv, axis=0)
sortedEigenvals = _np.sort(_np.real(_nla.eigvalsh(combinedDDD)))
observableEigenvals = sortedEigenvals[numGaugeParams:]
N_AC = 0
AC_score = _np.inf
for N in range(initN, len(observableEigenvals) + 1):
scoredEigenvals = observableEigenvals[-N:]
candidate_AC_score = scoreFn(scoredEigenvals)
if candidate_AC_score > thresholdAC:
break # We've found a set of parameters for which the germ set
# is not AC.
else:
AC_score = candidate_AC_score
N_AC = N
# OLD Apply penalties to the minor score; major part is just #amplified
#major_score = N_AC
#minor_score = AC_score + l1Score + opScore
# Apply penalties to the major score
major_score = -N_AC + opScore + l1Score
minor_score = AC_score
ret = _scoring.CompositeScore(major_score, minor_score, N_AC)
#DEBUG: ret.extra = {'opScore': opScore,
# 'sum(germLengths)': _np.sum(germLengths), 'l1': l1Score}
return ret
def calc_bulk_twirled_DDD(model, germsList, eps=1e-6, check=False,
germLengths=None, comm=None):
"""Calculate the positive squares of the germ Jacobians.
twirledDerivDaggerDeriv == array J.H*J contributions from each germ
(J=Jacobian) indexed by (iGerm, iModelParam1, iModelParam2)
size (nGerms, vec_model_dim, vec_model_dim)
"""
if germLengths is None:
germLengths = _np.array([len(germ) for germ in germsList])
twirledDeriv = bulk_twirled_deriv(model, germsList, eps, check, comm) / germLengths[:, None, None]
#OLD: slow, I think because conjugate *copies* a large tensor, causing a memory bottleneck
#twirledDerivDaggerDeriv = _np.einsum('ijk,ijl->ikl',
# _np.conjugate(twirledDeriv),
# twirledDeriv)
#NEW: faster, one-germ-at-a-time computation requires less memory.
nGerms, _, vec_model_dim = twirledDeriv.shape
twirledDerivDaggerDeriv = _np.empty((nGerms, vec_model_dim, vec_model_dim),
dtype=_np.complex)
for i in range(nGerms):
twirledDerivDaggerDeriv[i, :, :] = _np.dot(
twirledDeriv[i, :, :].conjugate().T, twirledDeriv[i, :, :])
return twirledDerivDaggerDeriv
def calc_twirled_DDD(model, germ, eps=1e-6):
"""Calculate the positive squares of the germ Jacobian.
twirledDerivDaggerDeriv == array J.H*J contributions from `germ`
(J=Jacobian) indexed by (iModelParam1, iModelParam2)
size (vec_model_dim, vec_model_dim)
"""
twirledDeriv = twirled_deriv(model, germ, eps) / len(germ)
#twirledDerivDaggerDeriv = _np.einsum('jk,jl->kl',
# _np.conjugate(twirledDeriv),
# twirledDeriv)
twirledDerivDaggerDeriv = _np.tensordot(_np.conjugate(twirledDeriv),
twirledDeriv, (0, 0))
return twirledDerivDaggerDeriv
def compute_score(weights, model_num, scoreFunc, derivDaggerDerivList,
forceIndices, forceScore,
nGaugeParams, opPenalty, germLengths, l1Penalty=1e-2,
scoreDict=None):
"""Returns a germ set "score" in which smaller is better. Also returns
intentionally bad score (`forceScore`) if `weights` is zero on any of
the "forced" germs (i.e. at any index in `forcedIndices`).
This function is included for use by :func:`optimize_integer_germs_slack`,
but is not convenient for just computing the score of a germ set. For that,
use :func:`calculate_germset_score`.
"""
if forceIndices is not None and _np.any(weights[forceIndices] <= 0):
score = forceScore
else:
#combinedDDD = _np.einsum('i,ijk', weights,
# derivDaggerDerivList[model_num])
combinedDDD = _np.squeeze(
_np.tensordot(_np.expand_dims(weights, 1),
derivDaggerDerivList[model_num], (0, 0)))
assert len(combinedDDD.shape) == 2
sortedEigenvals = _np.sort(_np.real(_nla.eigvalsh(combinedDDD)))
observableEigenvals = sortedEigenvals[nGaugeParams:]
score = (_scoring.list_score(observableEigenvals, scoreFunc)
+ l1Penalty * _np.sum(weights)
+ opPenalty * _np.dot(germLengths, weights))
if scoreDict is not None:
# Side effect: calling compute_score caches result in scoreDict
scoreDict[model_num, tuple(weights)] = score
return score
def randomize_model_list(modelList, randomizationStrength, numCopies,
seed=None):
"""
Applies random unitary perturbations to a models.
If `modelList` is a length-1 list, then `numCopies` determines how
many randomizations to create. If `modelList` containes multiple
models, then `numCopies` must be `None` and each model is
randomized once to create the corresponding returned model.
Parameters
----------
modelList : Model or list
A list of Model objects.
randomizationStrengh : float
The strength (input as the `scale` argument to
:func:`Model.randomize_with_unitary`) of random unitary
perturbations.
numCopies : int
The number of random perturbations of `modelList[0]` to generate when
`len(modelList) == 1`. A value of `None` will result in 1 copy. If
`len(modelList) > 1` then `numCopies` must be set to None.
seed : int, optional
Starting seed for randomization. Successive randomizations receive
successive seeds. `None` results in random seeds.
"""
if len(modelList) > 1 and numCopies is not None:
raise ValueError("Input multiple models XOR request multiple "
"copies only!")
newmodelList = []
if len(modelList) > 1:
for modelnum, model in enumerate(modelList):
newmodelList.append(model.randomize_with_unitary(
randomizationStrength,
seed=None if seed is None else seed + modelnum))
else:
for modelnum in range(numCopies if numCopies is not None else 1):
newmodelList.append(modelList[0].randomize_with_unitary(
randomizationStrength,
seed=None if seed is None else seed + modelnum))
return newmodelList
def checkGermsListCompleteness(modelList, germsList, scoreFunc, threshold):
"""Check to see if the germsList is amplificationally complete (AC)
Checks for AC with respect to all the Models in `modelList`, returning
the index of the first Model for which it is not AC or `-1` if it is AC
for all Models.
"""
for modelNum, model in enumerate(modelList):
initial_test = test_germ_list_infl(model, germsList,
scoreFunc=scoreFunc,
threshold=threshold)
if not initial_test:
return modelNum
# If the germsList is complete for all models, return -1
return -1
def removeSPAMVectors(model):
"""
Returns a copy of `model` with state preparations and effects removed.
Parameters
----------
model : Model
Returns
-------
Model
"""
reducedModel = model.copy()
for prepLabel in list(reducedModel.preps.keys()):
del reducedModel.preps[prepLabel]
for povmLabel in list(reducedModel.povms.keys()):
del reducedModel.povms[povmLabel]
return reducedModel
def num_non_spam_gauge_params(model):
"""
Return the number of non-gauge, non-SPAM parameters in `model`.
Equivalent to `removeSPAMVectors(model).num_gauge_params()`.
Parameters
---------
model : Model
Returns
-------
int
"""
return removeSPAMVectors(model).num_gauge_params()
# wrt is op_dim x op_dim, so is M, Minv, Proj
# so SOP is op_dim^2 x op_dim^2 and acts on vectorized *gates*
# Recall vectorizing identity (when vec(.) concats rows as flatten does):
# vec( A * X * B ) = A tensor B^T * vec( X )
def _SuperOpForPerfectTwirl(wrt, eps):
"""Return super operator for doing a perfect twirl with respect to wrt.
"""
assert wrt.shape[0] == wrt.shape[1] # only square matrices allowed
dim = wrt.shape[0]
SuperOp = _np.zeros((dim**2, dim**2), 'complex')
# Get spectrum and eigenvectors of wrt
wrtEvals, wrtEvecs = _np.linalg.eig(wrt)
wrtEvecsInv = _np.linalg.inv(wrtEvecs)
# We want to project X -> M * (Proj_i * (Minv * X * M) * Proj_i) * Minv,
# where M = wrtEvecs. So A = B = M * Proj_i * Minv and so
# superop = A tensor B^T == A tensor A^T
# NOTE: this == (A^T tensor A)^T while *Maple* germ functions seem to just
# use A^T tensor A -> ^T difference
for i in range(dim):
# Create projector onto i-th eigenspace (spanned by i-th eigenvector
# and other degenerate eigenvectors)
Proj_i = _np.diag([(1 if (abs(wrtEvals[i] - wrtEvals[j]) <= eps)
else 0) for j in range(dim)])
A = _np.dot(wrtEvecs, _np.dot(Proj_i, wrtEvecsInv))
#if _np.linalg.norm(A.imag) > 1e-6:
# print("DB: imag = ",_np.linalg.norm(A.imag))
#assert(_np.linalg.norm(A.imag) < 1e-6)
#A = _np.real(A)
# Need to normalize, because we are overcounting projectors onto
# subspaces of dimension d > 1, giving us d * Proj_i tensor Proj_i^T.
# We can fix this with a division by tr(Proj_i) = d.
SuperOp += _np.kron(A, A.T) / _np.trace(Proj_i)
# SuperOp += _np.kron(A.T,A) # Mimic Maple version (but I think this is
# wrong... or it doesn't matter?)
return SuperOp # a op_dim^2 x op_dim^2 matrix
def sq_sing_vals_from_deriv(deriv, weights=None):
"""Calculate the squared singulare values of the Jacobian of the germ set.
Parameters
----------
deriv : numpy.array
Array of shape ``(nGerms, flattened_op_dim, vec_model_dim)``. Each
sub-array corresponding to an individual germ is the Jacobian of the
vectorized gate representation of that germ raised to some power with
respect to the model parameters, normalized by dividing by the length
of each germ after repetition.
weights : numpy.array
Array of length ``nGerms``, giving the relative contributions of each
individual germ's Jacobian to the combined Jacobian (which is calculated
as a convex combination of the individual Jacobians).
Returns
-------
numpy.array
The sorted squared singular values of the combined Jacobian of the germ
set.
"""
# shape (nGerms, vec_model_dim, vec_model_dim)
derivDaggerDeriv = _np.einsum('ijk,ijl->ikl', _np.conjugate(deriv), deriv)
# awkward to convert to tensordot, so leave as einsum
# Take the average of the D^dagger*D/L^2 matrices associated with each germ
# with optional weights.
combinedDDD = _np.average(derivDaggerDeriv, weights=weights, axis=0)
sortedEigenvals = _np.sort(_np.real(_nla.eigvalsh(combinedDDD)))
return sortedEigenvals
def twirled_deriv(model, circuit, eps=1e-6):
"""Compute the "Twirled Derivative" of a circuit.
The twirled derivative is obtained by acting on the standard derivative of
a operation sequence with the twirling superoperator.
Parameters
----------
model : Model object
The Model which associates operation labels with operators.
circuit : Circuit object
The operation sequence to take a twirled derivative of.
eps : float, optional
Tolerance used for testing whether two eigenvectors are degenerate
(i.e. abs(eval1 - eval2) < eps ? )
Returns
-------
numpy array
An array of shape (op_dim^2, num_model_params)
"""
prod = model.product(circuit)
# flattened_op_dim x vec_model_dim
dProd = model.dproduct(circuit, flat=True)
# flattened_op_dim x flattened_op_dim
twirler = _SuperOpForPerfectTwirl(prod, eps)
# flattened_op_dim x vec_model_dim
return _np.dot(twirler, dProd)
def bulk_twirled_deriv(model, circuits, eps=1e-6, check=False, comm=None):
"""
Compute the "Twirled Derivative" of a set of circuits.
The twirled derivative is obtained by acting on the standard derivative of
a operation sequence with the twirling superoperator.
Parameters
----------
model : Model object
The Model which associates operation labels with operators.
circuits : list of Circuit objects
The operation sequence to take a twirled derivative of.
eps : float, optional
Tolerance used for testing whether two eigenvectors are degenerate
(i.e. abs(eval1 - eval2) < eps ? )
check : bool, optional
Whether to perform internal consistency checks, at the expense of
making the function slower.
comm : mpi4py.MPI.Comm, optional
When not None, an MPI communicator for distributing the computation
across multiple processors.
Returns
-------
numpy array
An array of shape (num_simplified_circuits, op_dim^2, num_model_params)
"""
if len(model.preps) > 0 or len(model.povms) > 0:
model = removeSPAMVectors(model)
# This function assumes model has no spam elements so `lookup` below
# gives indexes into products computed by evalTree.
evalTree, lookup, _ = model.bulk_evaltree(circuits)
dProds, prods = model.bulk_dproduct(evalTree, flat=True, bReturnProds=True, comm=comm)
op_dim = model.get_dimension()
fd = op_dim**2 # flattened gate dimension
nOrigStrs = len(circuits)
ret = _np.empty((nOrigStrs, fd, dProds.shape[1]), 'complex')
for iOrig in range(nOrigStrs):
iArray = _slct.as_array(lookup[iOrig])
assert(iArray.size == 1), ("Simplified lookup table should have length-1"
" element slices! Maybe you're using a"
" Model without SPAM elements removed?")
i = iArray[0] # get evalTree-final index (within dProds or prods)
# flattened_op_dim x flattened_op_dim
twirler = _SuperOpForPerfectTwirl(prods[i], eps)
# flattened_op_dim x vec_model_dim
ret[iOrig] = _np.dot(twirler, dProds[i * fd:(i + 1) * fd])
if check:
for i, circuit in enumerate(circuits):
chk_ret = twirled_deriv(model, circuit, eps)
if _nla.norm(ret[i] - chk_ret) > 1e-6:
_warnings.warn("bulk twirled derivative norm mismatch = "
"%g - %g = %g"
% (_nla.norm(ret[i]), _nla.norm(chk_ret),
_nla.norm(ret[i] - chk_ret))) # pragma: no cover
return ret # nSimplifiedCircuits x flattened_op_dim x vec_model_dim
def test_germ_list_finitel(model, germsToTest, L, weights=None,
returnSpectrum=False, tol=1e-6):
"""Test whether a set of germs is able to amplify all non-gauge parameters.
Parameters
----------
model : Model
The Model (associates operation matrices with operation labels).
germsToTest : list of Circuits
List of germs operation sequences to test for completeness.
L : int
The finite length to use in amplification testing. Larger
values take longer to compute but give more robust results.
weights : numpy array, optional
A 1-D array of weights with length equal len(germsToTest),
which multiply the contribution of each germ to the total
jacobian matrix determining parameter amplification. If
None, a uniform weighting of 1.0/len(germsToTest) is applied.
returnSpectrum : bool, optional
If True, return the jacobian^T*jacobian spectrum in addition
to the success flag.
tol : float, optional
Tolerance: an eigenvalue of jacobian^T*jacobian is considered
zero and thus a parameter un-amplified when it is less than tol.
Returns
-------
success : bool
Whether all non-gauge parameters were amplified.
spectrum : numpy array
Only returned when `returnSpectrum` is ``True``. Sorted array of
eigenvalues (from small to large) of the jacobian^T * jacobian
matrix used to determine parameter amplification.
"""
# Remove any SPAM vectors from model since we only want
# to consider the set of *gate* parameters for amplification
# and this makes sure our parameter counting is correct
model = removeSPAMVectors(model)
nGerms = len(germsToTest)
germToPowL = [germ * L for germ in germsToTest]
op_dim = model.get_dimension()
evt, lookup, _ = model.bulk_evaltree(germToPowL)
# shape (nGerms*flattened_op_dim, vec_model_dim)
dprods = model.bulk_dproduct(evt, flat=True)
dprods.shape = (evt.num_final_strings(), op_dim**2, dprods.shape[1])
prod_inds = [_slct.as_array(lookup[i]) for i in range(nGerms)]
assert(all([len(x) == 1 for x in prod_inds])), \
("Simplified lookup table should have length-1"
" element slices! Maybe you're using a"
" Model without SPAM elements removed?")
dprods = _np.take(dprods, _np.concatenate(prod_inds), axis=0)
# shape (nGerms, flattened_op_dim, vec_model_dim
germLengths = _np.array([len(germ) for germ in germsToTest], 'd')
normalizedDeriv = dprods / (L * germLengths[:, None, None])
sortedEigenvals = sq_sing_vals_from_deriv(normalizedDeriv, weights)
nGaugeParams = model.num_gauge_params()
observableEigenvals = sortedEigenvals[nGaugeParams:]
bSuccess = bool(_scoring.list_score(observableEigenvals, 'worst') < 1 / tol)
return (bSuccess, sortedEigenvals) if returnSpectrum else bSuccess
def test_germ_list_infl(model, germsToTest, scoreFunc='all', weights=None,
returnSpectrum=False, threshold=1e6, check=False):
"""Test whether a set of germs is able to amplify all non-gauge parameters.
Parameters
----------
model : Model
The Model (associates operation matrices with operation labels).
germsToTest : list of Circuit
List of germs operation sequences to test for completeness.
scoreFunc : string
Label to indicate how a germ set is scored. See
:func:`~pygsti.algorithms.scoring.list_score` for details.
weights : numpy array, optional
A 1-D array of weights with length equal len(germsToTest),
which multiply the contribution of each germ to the total
jacobian matrix determining parameter amplification. If
None, a uniform weighting of 1.0/len(germsToTest) is applied.
returnSpectrum : bool, optional
If ``True``, return the jacobian^T*jacobian spectrum in addition
to the success flag.
threshold : float, optional
An eigenvalue of jacobian^T*jacobian is considered zero and thus a
parameter un-amplified when its reciprocal is greater than threshold.
Also used for eigenvector degeneracy testing in twirling operation.
check : bool, optional
Whether to perform internal consistency checks, at the
expense of making the function slower.
Returns
-------
success : bool
Whether all non-gauge parameters were amplified.
spectrum : numpy array
Only returned when `returnSpectrum` is ``True``. Sorted array of
eigenvalues (from small to large) of the jacobian^T * jacobian
matrix used to determine parameter amplification.
"""
# Remove any SPAM vectors from model since we only want
# to consider the set of *gate* parameters for amplification
# and this makes sure our parameter counting is correct
model = removeSPAMVectors(model)
germLengths = _np.array([len(germ) for germ in germsToTest], _np.int64)
twirledDerivDaggerDeriv = calc_bulk_twirled_DDD(model, germsToTest,
1. / threshold, check,
germLengths)
# result[i] = _np.dot( twirledDeriv[i].H, twirledDeriv[i] ) i.e. matrix
# product
# result[i,k,l] = sum_j twirledDerivH[i,k,j] * twirledDeriv(i,j,l)
# result[i,k,l] = sum_j twirledDeriv_conj[i,j,k] * twirledDeriv(i,j,l)
if weights is None:
nGerms = len(germsToTest)
# weights = _np.array( [1.0/nGerms]*nGerms, 'd')
weights = _np.array([1.0] * nGerms, 'd')
#combinedTDDD = _np.einsum('i,ijk->jk', weights, twirledDerivDaggerDeriv)
combinedTDDD = _np.tensordot(weights, twirledDerivDaggerDeriv, (0, 0))
sortedEigenvals = _np.sort(_np.real(_np.linalg.eigvalsh(combinedTDDD)))
nGaugeParams = model.num_gauge_params()
observableEigenvals = sortedEigenvals[nGaugeParams:]
bSuccess = bool(_scoring.list_score(observableEigenvals, scoreFunc)
< threshold)
return (bSuccess, sortedEigenvals) if returnSpectrum else bSuccess
def build_up(modelList, germsList, randomize=True,
randomizationStrength=1e-3, numCopies=None, seed=0, opPenalty=0,
scoreFunc='all', tol=1e-6, threshold=1e6, check=False,
force="singletons", verbosity=0):
"""Greedy algorithm starting with 0 germs.
Tries to minimize the number of germs needed to achieve amplificational
completeness (AC). Begins with 0 germs and adds the germ that increases the
score used to check for AC by the largest amount at each step, stopping when
the threshold for AC is achieved.
"""
printer = _objs.VerbosityPrinter.build_printer(verbosity)
modelList = setup_model_list(modelList, randomize,
randomizationStrength, numCopies, seed)
(reducedModelList,
numGaugeParams, _, _) = get_model_params(modelList)
germLengths = _np.array([len(germ) for germ in germsList], _np.int64)
numGerms = len(germsList)
weights = _np.zeros(numGerms, _np.int64)
goodGerms = []
if force:
if force == "singletons":
weights[_np.where(germLengths == 1)] = 1
goodGerms = [germ for germ
in _np.array(germsList)[_np.where(germLengths == 1)]]
else: # force should be a list of Circuits
for opstr in force:
weights[germsList.index(opstr)] = 1
goodGerms = force[:]
undercompleteModelNum = checkGermsListCompleteness(modelList,
germsList,
scoreFunc,
threshold)
if undercompleteModelNum > -1:
printer.warning("Complete initial germ set FAILS on model "
+ str(undercompleteModelNum) + ". Aborting search.")
return None
printer.log("Complete initial germ set succeeds on all input models.", 1)
printer.log("Now searching for best germ set.", 1)
printer.log("Starting germ set optimization. Lower score is better.", 1)
twirledDerivDaggerDerivList = [calc_bulk_twirled_DDD(model, germsList, tol,
check, germLengths)
for model in modelList]