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getAdjacencyMatrix.m
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getAdjacencyMatrix.m
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function Adjacency = getAdjacencyMatrix(System, Nuclei,Method)
pwstat = Nuclei.Statistics;
% Orientation dependent cutoffs
Ori_cutoffs = Method.Ori_cutoffs;
% Get the highest spin value.
Nuclei.maxSpin = max(Nuclei.Spin);
% Initialize a matrix of valid edges.
Adjacency = true(Nuclei.number,Nuclei.number,Method.extraOrder);
for isize = 1:Method.extraOrder
Adjacency(:,:,isize) = Nuclei.valid'*Nuclei.valid > 0;
if ~Method.allowHDcoupling
Adjacency(:,:,isize) = Adjacency(:,:,isize).*pwstat.Same_g;
end
% Loop over all criteria used to determine an edge.
num_criteria = numel(Method.Criteria);
for ii = 1:num_criteria
idx = -1;
switch Method.Criteria{ii}
case 'rMax'
idx = min(isize, numel( Method.neighborCutoff.rMax ));
Max_R_ = pwstat.DistanceMatrix <= Method.neighborCutoff.rMax(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Max_R_;
case 'rMin'
idx = min(isize, numel( Method.neighborCutoff.rMin ));
Min_R_ = pwstat.DistanceMatrix > Method.neighborCutoff.rMin(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_R_;
case 'modulation'
idx = min(isize, numel( Method.neighborCutoff.modulation ));
if Ori_cutoffs
Min_Mod_ ...
= pwstat.Modulation_Depth_methyl >= Method.neighborCutoff.modulation(isize);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_Mod_;
else
Min_Mod_ = pwstat.Modulation_Depth_p ...
>= Method.neighborCutoff.modulation(isize);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_Mod_;
end
case 'dipole'
idx = min(isize, numel( Method.neighborCutoff.dipole ));
J = -2/3*Nuclei.methylTunnelingSplitting;
if Ori_cutoffs
Min_dipole_ = abs(pwstat.Nuclear_Dipole - 2*J) ...
>= Method.neighborCutoff.dipole(isize);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_dipole_;
else
Min_dipole_ = abs(pwstat.Nuclear_Dipole_perpendicular - 2*J) ...
>= Method.neighborCutoff.dipole(isize);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_dipole_;
end
case 'dipoleHalf'
idx = min(isize, numel( Method.neighborCutoff.dipoleHalf ));
Min_dipole_ = Nuclei.Spin == 1/2;
Min_dipole_ = Min_dipole_ & Min_dipole_';
if Ori_cutoffs
Min_dipole_ = ~Min_dipole_ ...
| (Min_dipole_ & abs(pwstat.Nuclear_Dipole) ...
>= Method.neighborCutoff.dipoleHalf(idx));
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_dipole_;
else
Min_dipole_ = ~Min_dipole_ ...
| (Min_dipole_ & abs(pwstat.Nuclear_Dipole_perpendicular) ...
>= Method.neighborCutoff.dipoleHalf(idx));
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_dipole_;
end
case 'dipoleOne'
idx = min(isize, numel( Method.neighborCutoff.dipoleOne ));
Min_dipole_ = Nuclei.Spin == 1;
Min_dipole_ = Min_dipole_ & Min_dipole_';
if Ori_cutoffs
Min_dipole_ = ~Min_dipole_ | (Min_dipole_ ...
& abs(pwstat.Nuclear_Dipole)...
>= Method.neighborCutoff.dipoleOne(idx));
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_dipole_;
else
Min_dipole_ = ~Min_dipole_ | (Min_dipole_ ...
& abs(pwstat.Nuclear_Dipole_perpendicular) ...
>= Method.neighborCutoff.dipoleOne(idx));
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_dipole_;
end
case 'bAmax'
idx = min(isize, numel( Method.neighborCutoff.bAmax ));
Min_bAmax_ = abs(pwstat.bAmax) >= Method.neighborCutoff.bAmax(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_bAmax_;
case 'minAmax'
idx = min(isize, numel( Method.neighborCutoff.minAmax ));
Min_Amax_ = abs(pwstat.Amax) >= Method.neighborCutoff.minAmax(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_Amax_;
case 'maxAmax'
idx = min(isize, numel( Method.neighborCutoff.maxAmax ));
Max_Amax_ = abs(pwstat.Amax) <= Method.neighborCutoff.maxAmax(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Max_Amax_;
case 'minimum-frequency'
idx = min(isize, numel( Method.neighborCutoff.minimum_frequency ));
if Ori_cutoffs
Min_Freq_ = abs(pwstat.Frequency_Pair_methyl) ...
> Method.neighborCutoff.minimum_frequency(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_Freq_;
else
Min_Freq_ = abs(pwstat.Frequency_Pair_p) ...
> Method.neighborCutoff.minimum_frequency(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_Freq_;
end
case 'delta hyperfine'
idx = min(isize, numel( Method.neighborCutoff.DeltaHyperfine ));
if Ori_cutoffs
DeltaHyperfine = pwstat.Hyperfine - pwstat.Hyperfine';
Min_DeltaA_ = abs(DeltaHyperfine) ...
> Method.neighborCutoff.DeltaHyperfine(idx);
%Max_DeltaA_ = abs(DeltaHyperfine) ...
% < Method.neighborCutoff.hyperfine_sup(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_DeltaA_;%.*Max_DeltaA_;
clear('DeltaHyperfine');
else
DeltaHyperfine_perpendicular = pwstat.Hyperfine_perpendicular ...
- pwstat.Hyperfine_perpendicular';
Min_DeltaA_ = abs(DeltaHyperfine_perpendicular) ...
> Method.neighborCutoff.hyperfine_inf(idx);
%Max_DeltaA_ = abs(DeltaHyperfine_perpendicular) ...
% < Method.neighborCutoff.hyperfine_sup(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_DeltaA_;%.*Max_DeltaA_;
clear('DeltaHyperfine_perpendicular');
end
case 'Hahn: k*omega^4'
if ~Ori_cutoffs
error("Please set Ori_cutoffs = true.");
end
idx = min(isize, numel( Method.neighborCutoff.modDepthFreq4 ));
kom4 = pwstat.Modulation_Depth_methyl.*(2*pi*pwstat.Frequency_Pair_methyl).^4;
selection = kom4 >= Method.neighborCutoff.modDepthFreq4(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*selection;
case 'Hahn: k*sin^4(omega*1us)'
if ~Ori_cutoffs
error("Please set Ori_cutoffs = true.");
end
idx = min(isize, numel( Method.neighborCutoff.Hahn_1us));
ks4 = pwstat.ModulationDepth.*sin(2*pi*pwstat.Frequency_Pair*1e-6).^4;
selection = ks4 >= Method.neighborCutoff.Hahn_1us(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*selection;
case 'Gaussian RMSD'
idx = min(isize, numel( Method.neighborCutoff.gaussianRMSD ));
if Ori_cutoffs
Min_gRMSD = pwstat.GaussianRMSD ...
> Method.neighborCutoff.gaussianRMSD(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_gRMSD;
else
Min_gRMSD = pwstat.GaussianRMSD_p ...
> Method.neighborCutoff.gaussianRMSD(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Min_gRMSD;
end
case 'radius_nonSpinHalf'
idx = min(isize, numel( Method.vertexCutoff.radius_nonSpinHalf ));
maxDistance = vecnorm(Nuclei.Coordinates,2,2);
maxDistance = max(maxDistance,maxDistance');
MaxR_ = Nuclei.Spin == 1/2;
MaxR_ = MaxR_ & MaxR_';
MaxR_ = MaxR_ | maxDistance ...
<= Method.vertexCutoff.radius_nonSpinHalf(idx);
Adjacency(:,:,isize) = Adjacency(:,:,isize).*MaxR_;
clear('maxDistance');
case 'same g'
Adjacency(:,:,isize) = Adjacency(:,:,isize).*pwstat.Same_g;
case 'spin 1/2 only'
Sele_ = Nuclei.Spin == 1/2;
Sele_ = Sele_ & Sele_';
Adjacency(:,:,isize) = Adjacency(:,:,isize).*Sele_;
end
end
if System.Methyl.method == 1
isMethylHydron = Nuclei.MethylID > 0;
Adjacency(isMethylHydron,:,isize) = false;
Adjacency(:,isMethylHydron,isize) = false;
elseif System.Methyl.method == 2
if Method.fullyConnectedMethyls
% Protons within a methyl group should always be connected to each
% other.
isMethylHydron = Nuclei.MethylID > 0;
isMethylHydron = (isMethylHydron + isMethylHydron')>0;
isSameMethyl = (Nuclei.MethylID==Nuclei.MethylID');
Sele_ = isMethylHydron.*isSameMethyl;
Adjacency(:,:,isize) = (Adjacency(:,:,isize) + Sele_) > 0;
end
isMethylCarbon = strcmp(Nuclei.Type,'CH3');
Adjacency(isMethylCarbon,:,isize) = false;
Adjacency(:,isMethylCarbon,isize) = false;
end
end
end