Cumulative update.

Spelling and grammer fixes in comments.
Tools for dividing problems and running them in parallel through bash.
Fixed a bug with using ismembertol when order matters.

Author: JBurniston

.gitignore

@@ -1,10 +1,18 @@
 # ignore .mat files
 *.mat
+
 # ignore figures
 *.fig
-*.DS_Store
-# ignore folder for comparision to old software
+*.png
+*.jpg
+*.eps
 
+# Ignore log files
+*.log
+*.out
+
+# Don't know where this is from but it keeps comming up
+*.DS_Store
 
 # Default good practice MATLAB ignores:
 # Windows default autosave extension
@@ -18,4 +26,4 @@
 
 # Packaged app and toolbox files
 *.mlappinstall
-*.mltbx
+*.mltbx

BasicProtocols/BasicBB84Alice2D/BasicBB84Alice2DChannelFunc.m

@@ -1,6 +1,6 @@
 function [newParams, modParser]= BasicBB84Alice2DChannelFunc(params,options,debugInfo)
 % BasicBB84Alice2DChannelFunc a simple channel function for a qubit based
-% BB84 protocol with no loss. This channel model allows for depolariztion
+% BB84 protocol with no loss. This channel model allows for depolarization
 % and misalignment between Alice and Bob's detectors. Here, Schmidt
 % decomposition was used to shrink Alice from a 4d space to a 2d space.
 % With this, we can model Alice and Bob through a maximally entangled
@@ -12,30 +12,31 @@
 % * dimB: The dimension of Bob's system. In this channel it is assumed to
 %   be 2.
 % * observablesJoint: The joint observables from Alice and Bob's
-%   measurments which they perform on the (idealy) max entangled state. The
-%   observables must be hermitian and each must be the size dimA*dimB by
-%   dimA*dimB. The observables assume the spaces are ordered A \otimes B.
-%   They also should be positive semi-definite and should sum to identity,
-%   but this is hard to check because of machine precision issues.
+%   measurements which they perform on the (ideally) max entangled state.
+%   The observables must be Hermitian and each must be the size dimA*dimB
+%   by dimA*dimB. The observables assume the spaces are ordered A \otimes
+%   B. They also should be positive semi-definite and should sum to
+%   identity, but this is hard to check because of machine precision
+%   issues.
 % * depolarization (0): The amount of depolarization applied to the signal
-%   Alice sends to Bob. At maximum depolarization (depolariztion =1) a pure
-%   qubit state is converted to a maximally mixed state. Depolarization
-%   should be between 0 and 1.
+%   Alice sends to Bob. At maximum depolarization (depolarization =1) a
+%   pure qubit state is converted to a maximally mixed state.
+%   Depolarization should be between 0 and 1.
 % * misalignmentAngle (0): Angle Alice and Bob's bases are misaligned by
 %   around the Y-axis. For example, Bob's detectors could be slightly
 %   rotated away from the incoming signals. Although calculations are done
 %   on the Bloch sphere, angles should not be given in that form (period
 %   4pi). This angle is measured as the physical rotation of the device
 %   (period 2pi).
 % Output parameters:
-% * expectationsJoint: The joint epxectations for Alice and Bob's
+% * expectationsJoint: The joint expectations for Alice and Bob's
 %   measurement of the signals. Simply formed by taking the
 %   observablesJoint and applying them to a simulated rhoAB.
 % Options:
 % * none
 % DebugInfo:
 % * rhoAB: Alice and Bob's shared density matrix after the channel has
-%   acted on it. Usefull for checking the channel has been applied
+%   acted on it. Useful for checking the channel has been applied
 %   correctly.
 %
 % See also QKDChannelModule, makeGlobalOptionsParser
@@ -88,7 +89,7 @@
 % generate joint density operator
 % This should technically be rhoAAprime until we act the channels on
 % it.
-rhoAB = MaxEntangled(dimA,false,false); %This is really the only differnce between 2D and 4D Alice
+rhoAB = MaxEntangled(dimA,false,false); %This is really the only difference between 2D and 4D Alice
 
 rhoAB = (rhoAB*rhoAB')/dimA;
 
@@ -97,7 +98,7 @@
 rhoAB = PartialMap(rhoAB,depolChoiMat,2,[dimA,dimB]);
 
 %Rotation
-%When using QetLab's PartialMap function, kraus operators need to be
+%When using QetLab's PartialMap function, Kraus operators need to be
 %passed in as a cell array. If you don't, It will try and use it as a
 %Choi matrix.
 rotationKrausOps = {Qudit.rotateStateZXY(params.misalignmentAngle,[0,0,1],"angleOnBlochSphere",false)};

BasicProtocols/BasicBB84Alice2D/BasicBB84Alice2DDescriptionFunc.m

@@ -5,9 +5,9 @@
 % 2d space. This is used with BasicKeyRateFunc.
 %
 % Input parameters:
-% * pz: The probability that ALice measures in the Z-basis (for this protocol,
-%   it's also the probability that Bob measures in the Z-basis aswell). It
-%   must be between 0 and 1.
+% * pz: The probability that Alice measures in the Z-basis (for this
+%   protocol, it's also the probability that Bob measures in the Z-basis as
+%   well). It must be between 0 and 1.
 % Output parameters:
 % * observablesJoint: The joint observables for Alice and Bob's measurement
 %   of the signals.
@@ -27,7 +27,7 @@
 %   outcome to key bits (May be written with Strings).
 % * krausOps: A cell array of matrices. The Kraus operators that form the G
 %   map on Alice and Bob's joint system. These should form a completely
-%   postive trace non-increasing linear map. Each Kraus operator must be
+%   positive trace non-increasing linear map. Each Kraus operator must be
 %   the same size.
 % * keyProj:  A cell array of projection operators that extract the key
 %   from G(\rho). These projection operators should sum to identity. This
@@ -77,7 +77,7 @@
 %% rhoA for source replacement scheme
 newParams.rhoA = eye(dimA)/dimA;
 
-%% joint obserables
+%% joint observables
 POVMsA = {pz*diag([1,0]),pz*diag([0,1]),(1-pz)*(ketP*ketP'),(1-pz)*(ketM*ketM')};
 POVMsB = POVMsA;
 newParams.POVMA = POVMsA;
@@ -101,10 +101,10 @@
 %% Kraus Ops (for G map)
 % A: Alice's system, B: Bob's System, C: announcement register, R:
 % key register.
-% The Kraus operators are matrices from ABC \rightarrow RBC. Here we
-% used an isometry to shrink the Kraus operators from outputing on RABC
-% to just RBC. This lets us save time on computing eigen values later.
-% The factor of pz comes from a \sqrt(pz) from Alice's measurements(from Schmidt
+% The Kraus operators are matrices from ABC \rightarrow RBC. Here we used
+% an isometry to shrink the Kraus operators from outputting on RABC to just
+% RBC. This lets us save time on computing eigen values later. The factor
+% of pz comes from a \sqrt(pz) from Alice's measurements(from Schmidt
 % reduction) and \sqrt(pz) from Bob's measurements.
 krausOpZ = pz*kron(diag([1,0])+diag([0,1]),kron(eye(dimB),zket(2,1)));
 krausOpX = (1-pz)*kron(zket(2,1)*ketP'+zket(2,2)*ketM',kron(eye(dimB),zket(2,2)));
@@ -128,7 +128,7 @@
 proj1 = kron(diag([0,1]),eye(dimB*2));
 keyProj = {proj0,proj1};
 
-%% set kraus ops and key projection in new parameters
+%% set Kraus ops and key projection in new parameters
 newParams.krausOps = krausOps;
 newParams.keyProj = keyProj;
 

BasicProtocols/BasicBB84Alice2D/BasicBB84Alice2DPreset.m

@@ -1,18 +1,18 @@
 function qkdInput = BasicBB84Alice2DPreset()
 % BasicBB84Alice2DPreset A preset that describes a qubit based BB84 protocol
-% using source replacement. In this implementation, there is no tranmission
-% loss modeled. Alice and Bob have the same probability of choosing the
-% Z-basis (and same for the X-basis). Here, Schmidt decomposition was used
-% to shrink Alice from a 4d space to a 2d space.
+% using source replacement. In this implementation, there is no
+% transmission loss modeled. Alice and Bob have the same probability of
+% choosing the Z-basis (and same for the X-basis). Here, Schmidt
+% decomposition was used to shrink Alice from a 4d space to a 2d space.
 
 qkdInput = QKDSolverInput();
 
 %% Parameters
 
 %Here we start by setting what are the initial parameters we will use with
 %the protocol. These parameters help define what needs to be fixed, what we
-%want to scan over (usualy for graphing), and what needs to be optimized to
-%extract more key.
+%want to scan over (usually for graphing), and what needs to be optimized
+%to extract more key.
 %
 %How do we know what parameters can be set? Each module (the section after
 %this) has a series of inputs they request. If they aren't given by a
@@ -39,10 +39,10 @@
 % then they transmit / measure in the X-basis.
 qkdInput.addFixedParameter("pz",1/2);
 
-% fEC: Efficiency of error correction. Real error correction protocols don't
-% reach the Shannon limit. f is a scalar muliple, that scales up the amount
-% of information leaked to fix a single bit. fEC=1, is the Shannon limit.
-% fEC=1.16 is a more realistic value.
+% fEC: Efficiency of error correction. Real error correction protocols
+% don't reach the Shannon limit. f is a scalar multiple, that scales up the
+% amount of information leaked to fix a single bit. fEC=1, is the Shannon
+% limit. fEC=1.16 is a more realistic value.
 qkdInput.addFixedParameter("fEC",1);
 
 %% modules
@@ -57,11 +57,10 @@
 % This module works with the keyRate module to describe the class of
 % protocols that the keyRate module can solve. Usually code goes here
 % because it is likely to change to work on flavors of other protocols or
-% when parts of the protocol are usefull for a channel model to have access
-% to.
-% This description only provides the joint observables so that the channel
-% module can use them. It's useful when we want to swap out what our
-% measuremnts are.
+% when parts of the protocol are useful for a channel model to have access
+% to. This description only provides the joint observables so that the
+% channel module can use them. It's useful when we want to swap out what
+% our measurements are.
 descriptionModule = QKDDescriptionModule(@BasicBB84Alice2DDescriptionFunc);
 qkdInput.setDescriptionModule(descriptionModule);
 
@@ -78,17 +77,17 @@
 keyRateModule = QKDKeyRateModule(@BasicKeyRateFunc);
 qkdInput.setKeyRateModule(keyRateModule);
 
-% The optimizer module is designed to tweak perameters to increase your
+% The optimizer module is designed to tweak parameters to increase your
 % keyrate. It's not used in this protocol, though use cases can include
 % tweaking the intensity of coherent pulses used by Alice.
 optimizerMod = QKDOptimizerModule(@coordinateDescentFunc,struct("verboseLevel",0),struct("verboseLevel",0));
 qkdInput.setOptimizerModule(optimizerMod);
 
 
 % The mathSolver module takes in a description of linear equality, linear
-% ineqaulity, trace norm constraints, Kraus operators (for the G map) and
+% inequality, trace norm constraints, Kraus operators (for the G map) and
 % projectors for the key map (also known as the Z map). It then determine
-% the worst case senario and produces the minimum relaive entropy between
+% the worst case scenario and produces the minimum relative entropy between
 % the key and Eve's information.
 mathSolverOptions = struct();
 mathSolverOptions.initMethod = 1; %closest to maximally mixed.
@@ -109,7 +108,7 @@
 % * verboseLevel (default 1): Non-negative integer telling the program how
 %   much information it should display in the command window. 0, minimum; 1
 %   basic information; 2, full details, including CVX output.
-% * errorHandling (2): ErrorHandling object (unit8 or convertable),
+% * errorHandling (2): ErrorHandling object (unit8 or convertible),
 %   detailing how the program should handle run time errors. CatchSilent 1:
 %   catch but don't warn the user and the error message is appended to the
 %   debug info. CatchWarn 2: catch and warn the user. The key rate for the

BasicProtocols/BasicBB84Alice2D/mainBasicBB84Alice2D.m

@@ -1,5 +1,5 @@
-% qubit BB84 prepare and measure. We use schmidt decomposition to reduce
-% the dimension of Alice's state for enchanced speed and stability.
+% qubit BB84 prepare and measure. We use Schmidt decomposition to reduce
+% the dimension of Alice's state for enhanced speed and stability.
 qkdInput = BasicBB84Alice2DPreset();
 
 %run the QKDSolver with this input

BasicProtocols/BasicBB84Alice2DFinite/BasicBB84Alice2DFiniteKeyRateFunc.m

@@ -14,39 +14,43 @@
 %   outcome to key bits (May be written with Strings).
 % * krausOps: A cell array of matrices. The Kraus operators that form the G
 %   map on Alice and Bob's joint system. These should form a completely
-%   postive trace non-increasing linear map. Each Kraus operator must be
+%   positive trace non-increasing linear map. Each Kraus operator must be
 %   the same size.
 % * keyProj:  A cell array of projection operators that perform the pinching map 
 %   key on  G(\rho). These projection operators should sum to identity.
-% * fEC: error correction effiency. Set to 1 means for Shannon limit. 
+% * fEC: error correction efficiency. Set to 1 means for Shannon limit. 
 % * observablesJoint: The joint observables of Alice and Bob's
-%   measurments. The observables must be hermitian and each must be the size 
-%   dimA*dimB by dimA*dimB. The observables assume the spaces are ordered A \otimes B.
-%   They also should be positive semi-definite and should sum to identity. 
+%   measurements. The observables must be Hermitian and each must be the
+%   size dimA*dimB by dimA*dimB. The observables assume the spaces are
+%   ordered A \otimes B. They also should be positive semi-definite and
+%   should sum to identity.
 % * expectationsJoint: The joint expectations (as an array) from Alice and
 %   Bob's measurements that line up with it's corresponding observable in
-%   observablesJoint. These values should be betwen 0 and 1.
+%   observablesJoint. These values should be between 0 and 1.
 % * rhoA (nan): The fixed known density matrix on Alice's side for
 %   prepare-and-measure protocols.
-% * epsilonPA : epsilon for privacy amplification.
-% * epsilonAT : epsilon for acceptance test.
-% * epsilonEC : epsilon for error-verification.
-% * epsilonBar : epsilon for smoothing.
-% * numSignals : total number of signals sent.
-% * pTest : pTest*numSignals is the number of signals used for testing
-% * tExp : finite-size parameter determining the size of the acceptance
+% * epsilonPA: epsilon for privacy amplification.
+% * epsilonAT: epsilon for acceptance test.
+% * epsilonEC: epsilon for error-verification.
+% * epsilonBar: epsilon for smoothing.
+% * numSignals: total number of signals sent.
+% * pTest: pTest*numSignals is the number of signals used for testing
+% * tExp: finite-size parameter determining the size of the acceptance
 %   set.
 
 % Outputs:
 % * keyrate: Key rate of the QKD protocol.
+%
 % Options:
 % * verboseLevel: (global option) See makeGlobalOptionsParser for details.
 % * errorHandling: (global option) See makeGlobalOptionsParser for details.
+%
 % DebugInfo:
-% * relEnt : The computed lower bound on the relative entropy.
-% * keyRateRelEntStep2Linearization : The relative entropy at the
-% linearization point.
-% See also QKDKeyRateModule, PM46DescriptionFunc, makeGlobalOptionsParser
+% * relEnt: The computed lower bound on the relative entropy.
+% * keyRateRelEntStep2Linearization: The relative entropy at the
+%   linearization point.
+%
+% See also QKDKeyRateModule, makeGlobalOptionsParser
 arguments
     params (1,1) struct
     options (1,1) struct

BasicProtocols/BasicBB84Alice4D/BasicBB84Alice4DChannelFunc.m

@@ -1,6 +1,6 @@
 function [newParams, modParser]= BasicBB84Alice4DChannelFunc(params,options,debugInfo)
 % BasicBB84Alice4DChannelFunc a simple channel function for a qubit based
-% BB84 protocol with no loss. This channel model allows for depolariztion
+% BB84 protocol with no loss. This channel model allows for depolarization
 % and misalignment between Alice and Bob's detectors.
 %
 % Input parameters:
@@ -9,30 +9,31 @@
 % * dimB: The dimension of Bob's system. In this channel it is assumed to
 %   be 2.
 % * observablesJoint: The joint observables from Alice and Bob's
-%   measurments which they perform on the (idealy) max entangled state. The
-%   observables must be hermitian and each must be the size dimA*dimB by
-%   dimA*dimB. The observables assume the spaces are ordered A \otimes B.
-%   They also should be positive semi-definite and should sum to identity,
-%   but this is hard to check because of machine precision issues.
+%   measurements which they perform on the (ideally) max entangled state.
+%   The observables must be Hermitian and each must be the size dimA*dimB
+%   by dimA*dimB. The observables assume the spaces are ordered A \otimes
+%   B. They also should be positive semi-definite and should sum to
+%   identity, but this is hard to check because of machine precision
+%   issues.
 % * depolarization (0): The amount of depolarization applied to the signal
-%   Alice sends to Bob. At maximum depolarization (depolariztion =1) a pure
-%   qubit state is converted to a maximally mixed state. Depolarization
-%   should be between 0 and 1.
+%   Alice sends to Bob. At maximum depolarization (depolarization =1) a
+%   pure qubit state is converted to a maximally mixed state.
+%   Depolarization should be between 0 and 1.
 % * misalignmentAngle (0): Angle Alice and Bob's bases are misaligned by
 %   around the Y-axis. For example, Bob's detectors could be slightly
 %   rotated away from the incoming signals. Although calculations are done
 %   on the Bloch sphere, angles should not be given in that form (period
 %   4pi). This angle is measured as the physical rotation of the device
 %   (period 2pi).
 % Output parameters:
-% * expectationsJoint: The joint epxectations for Alice and Bob's
+% * expectationsJoint: The joint expectations for Alice and Bob's
 %   measurement of the signals. Simply formed by taking the
 %   observablesJoint and applying them to a simulated rhoAB.
 % Options:
 % * none
 % DebugInfo:
 % * rhoAB: Alice and Bob's shared density matrix after the channel has
-%   acted on it. Usefull for checking the channel has been applied
+%   acted on it. Useful for checking the channel has been applied
 %   correctly.
 %
 % See also QKDChannelModule
@@ -91,7 +92,7 @@
     ketM = 1/sqrt(2) * [1;-1];
 
     % generate joint density operator. Technically this should be rhoAAPrime
-    % untill the channels transform it.
+    % until the channels transform it.
     rhoAB = sqrt(pz/2) * (kron(zket(dimA,1), zket(dimB,1)) + kron(zket(dimA,2), zket(dimB,2)))... 
               +sqrt((1-pz)/2) * (kron(zket(dimA,3), ketP) + kron(zket(dimA,4), ketM));
 
@@ -103,7 +104,7 @@
     rhoAB = PartialMap(rhoAB,depolChoiMat,2,[dimA,dimB]);
 
     %Rotation
-    %When using QetLab's PartialMap function, kraus operators need to be
+    %When using QetLab's PartialMap function, Kraus operators need to be
     %passed in as a cell array. If you don't, It will try and use it as a
     %Choi matrix.
     rotationKrausOps = {Qudit.rotateStateZXY(params.misalignmentAngle,[0,0,1],"angleOnBlochSphere",false)};