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averageSignals.m
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averageSignals.m
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%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function [SignalMean, experiment_time, ...
TM_powder,Order_n_SignalMean,Nuclei,statistics] ...
= ...
averageSignals( ...
System,Method,Data,OutputData,...
experiment_time, Nuclei,Clusters,...
Alpha,Beta,gridWeight,GridInfo,...
uncertainty,Progress)
Method.verbose = Method.verbose;
if Method.verbose
fprintf(' Computing cluster Hamiltonians and cluster signals.\n');
end
nOrientations = numel(Alpha);
if Method.verbose
fprintf("Calculating signal for %d orientations.\n",nOrientations);
end
nTimePoints = sum(System.nPoints);
[SignalsToCalculate,SignalMean,Order_n_SignalMean,...
TempSignals,Temp_Order_n_Signals,graphs,...
Signals,Order_n_Signals,Statistics,TM,AuxiliarySignal,...
Calculate_Signal,Ori_Clusters,Progress,saveAll,numberOfSignals] ...
= initializeSignals(System, Method, Data, OutputData,...
nOrientations,Progress,nTimePoints);
pool = setUpPool(Method);
% Loop over orientations
if Method.parallelComputing
parfor iOri = 1:numberOfSignals
[TempSignals_, AuxiliarySignal_,Temp_Order_n_Signals_,Statistics{iOri},...
graphs{iOri},Ori_Clusters{iOri}] ...
= getOrientationSignals(System,Method,Nuclei,Clusters, Alpha,Beta, ...
iOri,Method.verbose,OutputData,Data,Data.InputData,SignalsToCalculate,...
gridWeight,nOrientations);
TempSignals{iOri} = TempSignals_;
Temp_Order_n_Signals{iOri} = Temp_Order_n_Signals_;
if saveAll || Method.getContributions
AuxiliarySignal{iOri} = AuxiliarySignal_;
end
end
else
for iOri = 1:numberOfSignals
[TempSignals_, AuxiliarySignal_,Temp_Order_n_Signals_,Statistics{iOri},...
graphs{iOri},Ori_Clusters{iOri}] ...
= getOrientationSignals(System,Method,Nuclei,Clusters, Alpha,Beta, ...
iOri,Method.verbose,OutputData,Data,Data.InputData,SignalsToCalculate,...
gridWeight,nOrientations);
TempSignals{iOri} = TempSignals_;
Temp_Order_n_Signals{iOri} = Temp_Order_n_Signals_;
TempSignals{iOri} = TempSignals_;
Temp_Order_n_Signals{iOri} = Temp_Order_n_Signals_;
if saveAll || Method.getContributions
AuxiliarySignal{iOri} = AuxiliarySignal_;
end
end
end
% ========================================================================
% Save reselts
% ========================================================================
[SignalMean, experiment_time, ...
TM_powder,Order_n_SignalMean,Nuclei,statistics] ...
= saveSignalResults(Nuclei, Clusters,System, Method, Data,...
SignalMean,Order_n_SignalMean,...
experiment_time,OutputData,uncertainty,GridInfo,...
TempSignals,Temp_Order_n_Signals,graphs,...
Signals,Order_n_Signals,Statistics,TM,AuxiliarySignal,...
Calculate_Signal,Ori_Clusters,Progress,nOrientations);
if ~isempty(pool)
delete(pool);
end
% Delete temporary files
if ~Data.keep_temporary_files
for iOri = 1:nOrientations
temp_file = ['temp_', OutputData(1:end-4), '_sig_', num2str(iOri), '.mat'] ;
if isfile(temp_file)
delete(temp_file);
end
end
end
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function [pool,pc] = setUpPool(Method)
if ~Method.parallelComputing
pool = [];
pc = [];
return;
end
% remove current pool if it exists.
delete(gcp('nocreate'));
% determine number of cores available
numCores = min(feature('numcores'), Method.numberCores);
% create parallel pool
pc = parcluster('local');
if isfield(Method,'JobStorageLocation')
pc.JobStorageLocation = Method.JobStorageLocation;
end
pool = parpool(numCores);
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function [SignalsToCalculate,SignalMean,Order_n_SignalMean,...
TempSignals,Temp_Order_n_Signals,graphs,...
Signals,Order_n_Signals,Statistics,TM,AuxiliarySignal,...
Calculate_Signal,Ori_Clusters,Progress,saveAll,numberOfSignals] ...
= ...
initializeSignals(System, Method, Data, OutputData,...
nOrientations,Progress,nTimePoints)
% initialize result variables
Signals{nOrientations} = [];
TM(nOrientations) = 0;
AuxiliarySignal{nOrientations} = [];
Calculate_Signal{nOrientations} = true;
Ori_Clusters = cell(nOrientations,1);
% update progress
Progress.Order_n_Mean = 'pending';
Order_n_Signals{nOrientations} = [];
if strcmp(Method.method,'HD-CCE')
SignalMean = zeros(1,nTimePoints^System.dimensionality,...
length(System.deuteriumFraction));
else
SignalMean = zeros(1,nTimePoints^System.dimensionality);
end
% initialize
for iorder = Method.order:-1:1
if strcmp(System.experiment,'CPMG-2D')
Order_n_SignalMean{iorder} = zeros(1,nTimePoints^2);
else
Order_n_SignalMean{iorder} = zeros(1,nTimePoints);
end
end
SignalsToCalculate = zeros(nOrientations,1);
counter_SignalsToCalculate = 0;
saveAll = Data.saveLevel==2;
Statistics = cell(nOrientations,1);
% Check to see if file already exists.
for iOri = 1:nOrientations
% temporary file for partial saving
temp_file = ['temp_', OutputData(1:end-4), '_sig_', num2str(iOri), '.mat'] ;
Calculate_Signal{iOri} = true;
% check if file alread exists
if Method.partialSave && isfile(temp_file) ...
&& ~(saveAll || Method.getContributions)
try
% load partial save
if Method.Ori_cutoffs
load(temp_file,'signal','order_n','seed','statistics','iOri_Clusters');
else
load(temp_file,'signal','order_n','seed','statistics');
end
% check progress
if seed ~= Method.seed %&& progress_powder
error('RNG seeds do not match. Loaded data may be inconsistant.')
end
% use loaded data
if Method.verbose, fprintf(['Loading signal %d from ', ...
temp_file, '.\n'],iOri); end
% set values to simulation variables
Calculate_Signal{iOri} = false;
Signals{iOri} = signal;
Order_n_Signals{iOri} = order_n;
Statistics{iOri} = statistics;
if Method.Ori_cutoffs
Ori_Clusters{iOri} = iOri_Clusters;
end
catch
counter_SignalsToCalculate = counter_SignalsToCalculate + 1;
SignalsToCalculate(counter_SignalsToCalculate) = iOri;
end
else
counter_SignalsToCalculate = counter_SignalsToCalculate + 1;
SignalsToCalculate(counter_SignalsToCalculate) = iOri;
end
end
SignalsToCalculate(SignalsToCalculate==0) = [];
numberOfSignals = length(SignalsToCalculate);
TempSignals{numberOfSignals+1} = [];
Temp_Order_n_Signals{numberOfSignals+1} = [];
graphs = cell(numberOfSignals,1);
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
% ========================================================================
% Calculates signal for a set of orientations
% ========================================================================
function [TempSignals_, AuxiliarySignal_,Temp_Order_n_Signals_,...
Statistics_isignal,graphs_isignal,iOri_Clusters] ...
=...
getOrientationSignals(System,Method,Nuclei,inClusters, Alpha,Beta,...
isignal,verbose,OutputData,Data,InputData,SignalsToCalculate,...
gridWeight,iSignal_max)
% grid point indices
if System.newIsotopologuePerOrientation && ~Method.reparseNuclei
if Method.useCentralSpinSystem
error(['Error in getOrientationSignals(): ',...
'Method.useCentralSpinSystem is not yet compatible with',...
' System.newIsotopologuePerOrientation.']);
end
Nuclei = newHydronIsotopologue(Nuclei,System);
if verbose
fprintf('Generated a new hydron isotopologue for orientation %d.\n',...
isignal);
end
Clusters = inClusters;
else
Clusters = inClusters;
end
igrid = SignalsToCalculate(isignal);
sig_file = ['Ori_',OutputData(1:end-4),...
'_alpha_', num2str(Alpha(igrid)),'_beta_', num2str(Beta(igrid)),'.csv'];
batch_name = [];
if Method.save_orientation_signals && isfile(sig_file)
TempSignals_ = readmatrix(sig_file).';
AuxiliarySignal_ = [];
Temp_Order_n_Signals_ = [];
Statistics_isignal = [];
graphs_isignal = [];
iOri_Clusters = [];
else
% calculate coherence signal
[TempSignals_, AuxiliarySignal_,Temp_Order_n_Signals_,Statistics_isignal,...
graphs_isignal,iOri_Clusters,batch_name] ...
= beginCalculateSignal(System,Method,Nuclei,Clusters,...
Alpha(igrid),Beta(igrid),verbose,OutputData,Data,InputData,isignal);
if System.newIsotopologuePerOrientation && ~Method.reparseNuclei
Statistics_isignal.Isotopologue = Nuclei.Isotopologue;
end
% Order n signals
if ~ischar(Temp_Order_n_Signals_)
for iorder = 1:Method.order
% set the max amplitude to the weight
Temp_Order_n_Signals_{iorder} ...
= gridWeight(igrid)*Temp_Order_n_Signals_{iorder};
end
end
if Method.save_orientation_signals
T = array2table(TempSignals_.');
T.Properties.VariableNames(1) = {'signal'};
writetable(T,sig_file);
AuxiliarySignal_ = [];
Temp_Order_n_Signals_ = [];
Statistics_isignal = [];
graphs_isignal = [];
iOri_Clusters = [];
end
end
TempSignals_ = gridWeight(igrid)*TempSignals_;
if strcmp(Method.method,'full')
return
end
if verbose, fprintf('\nCompleted orientation %d/%d.\n',igrid,iSignal_max); end
% Save to file.
if Method.partialSave
temp_file = ['temp_', OutputData(1:end-4), '_sig_', num2str(igrid), '.mat'] ;
parsavefile = matfile(temp_file,'writable',true);
parsavefile.signal = TempSignals_;
parsavefile.order_n = Temp_Order_n_Signals_;
parsavefile.progress_powder = true;
parsavefile.seed = Method.seed;
parsavefile.statistics = Statistics_isignal;
if Method.Ori_cutoffs
parsavefile.iOri_Clusters = iOri_Clusters;
end
end
if ischar(batch_name) && isfile(batch_name)
delete(batch_name)
end
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
% ========================================================================
% Calculate signal for one orientation
% ========================================================================
function [Signal, AuxiliarySignal,Order_n_Signal,Statistics,graphs,...
Ori_Clusters,batch_name] = ...
beginCalculateSignal(System,Method,Nuclei,Clusters,Alpha,Beta,verbose,...
OutputData,Data,InputData,isignal)
% Get rotation matrix from PDB frame to lab frame, via Euler angles
R_pdb2lab = rotateZYZ(Alpha,Beta,0);
% Rotate nuclear coordinates.
Nuclei.Coordinates = Nuclei.Coordinates*R_pdb2lab';
Statistics = Nuclei.Statistics;
Ori_Clusters = [];
fprintf('\nOrientation: α = %d°; β = %d°.\n', Alpha*180/pi, Beta*180/pi);
if Method.Ori_cutoffs
isotopologueStatistics = [];
if Method.reparseNuclei
if isignal>1
[Nuclei, System] = parseNuclei(System, Method, Data, InputData);
end
isotopologueStatistics.number_1H_exchangeable ...
= Nuclei.number_1H_exchangeable;
isotopologueStatistics.number_1H_nonExchangeable ...
= Nuclei.number_1H_nonExchangeable;
isotopologueStatistics.number_2H_exchangeable ...
= Nuclei.number_2H_exchangeable;
isotopologueStatistics.number_2H_nonExchangeable ...
= Nuclei.number_2H_nonExchangeable;
end
StatisticsTemporary = getPairwiseStatistics(System, Method, Nuclei);
Nuclei.Statistics = StatisticsTemporary;
Adjacency = getAdjacencyMatrix(System, Nuclei,Method);
Nuclei.Adjacency = Adjacency;
Statistics.isotopologueStatistics = isotopologueStatistics;
Nuclei.Statistics = Statistics;
if ~Method.neighborCutoff.sizeDependent
Ori_Clusters = findClusters_treeSearch(Nuclei,Method.order,...
Method.extraOrder,{}, Method);
end
for clusterSize = 1:Method.order
if Method.neighborCutoff.sizeDependent
Ori_Clusters = findClusters_treeSearch(Nuclei,clusterSize,...
clusterSize,{}, Method);
end
% Combine arrays.
C = [Clusters{clusterSize}; Ori_Clusters{clusterSize}];
% Sort clusters
C = sortrows(C);
% Remove duplicates
keep = [true; any(C(1:end-1,:)~=C(2:end,:),2)];
if ~isempty(C)
Clusters{clusterSize} = C(keep,:);
elseif Method.emptyClusterSetsOkay
Clusters{clusterSize} = C;
else
error(['Error in beginCalculateSignal(): ', ...
'no clusters found.']);
end
Nuclei.numberClusters(clusterSize) = size(Clusters{clusterSize},1);
fprintf('Found %i clusters of size %i.\n', ...
size(Clusters{clusterSize},1),clusterSize);
end
sig_file = [OutputData(1:end-4),...
'_alpha_', num2str(Alpha),'_beta_', num2str(Beta)];
if Method.writeClusterStatistics
filename = [sig_file,...
'_cluster_statistics'];
r_max = write_cluster_statistics(Clusters,Nuclei,filename);
fprintf('Most distal spin: %d angstroms.\n', r_max*1e10);
end
end
% Rotate bath spin tensors.
for inucleus = 1:Nuclei.number
Nuclei.Atensor(inucleus,:) = reshape( ...
R_pdb2lab*reshape( full(Nuclei.Atensor(inucleus,:))',3,3)*R_pdb2lab' , ...
9,1);
if ~System.limitToSpinHalf
Nuclei.Qtensor(:,:,inucleus) ...
= R_pdb2lab*Nuclei.Qtensor(:,:,inucleus)*R_pdb2lab';
% Elementwise Qtensor manipulation used for testing.
% The default filter is ones(3);
Nuclei.Qtensor(:,:,inucleus) ...
= Nuclei.Qtensor(:,:,inucleus).*System.nuclear_quadrupole_filter;
end
end
% Rotate the g-matrix.
if isfield(System,'gFrame')
% Get rotation matrix.
g2MolRotation ...
= rotateZYZ(-System.gFrame(1),-System.gFrame(2),-System.gFrame(3));
% Rotate to molecular frame.
System.gMatrix = g2MolRotation*System.gMatrix_gFrame*g2MolRotation';
end
% Rotate the g-matrix to the lab frame.
System.gMatrix = R_pdb2lab*System.gMatrix_gFrame*R_pdb2lab';
% Get the g-value along the magnetic field direction.
System.Electron.g = System.gMatrix(3,3);
graphs = Nuclei.Adjacency;
% calculate restricted signal directly
if strcmp(Method.method,'rCE')
if verbose
fprintf('\nCalculating restricted Cluster Expansion.\n')
end
[Signal,AuxiliarySignal,Order_n_Signal] = ...
doRestrictedCE(System,Method, Nuclei, Method.r0, verbose);
if verbose
fprintf('\nComplete.\n')
end
return
elseif strcmp(Method.method,'rCCE')
if verbose
fprintf('\nCalculating restricted Cluster Correlation Expansion.\n')
end
batch_name = 'rCCE';
[Signal,AuxiliarySignal,Order_n_Signal] = ...
doRestrictedCCE(System,Method, Nuclei, verbose);
if verbose
fprintf('\nComplete.\n')
end
return
elseif strcmp(Method.method,'LCE')
if verbose
fprintf('\nCalculating Linked Cluster Expansion.\n')
end
[Signal,AuxiliarySignal,Order_n_Signal] = ...
doLCE(System,Method, Nuclei,Clusters);
if verbose
fprintf('\nComplete.\n')
end
return
end
timepoints = numel(System.Time);
% Calculate signal and save extra parameters (RAM intensive)
% Check if the theroy is the same for every cluster size.
if all(all(System.Theory)==any(System.Theory)) && ...
~strcmp(Method.method,'HD-CCE')
sig_file = [OutputData(1:end-4),...
'_alpha_', num2str(Alpha),'_beta_', num2str(Beta)];
[Signal, AuxiliarySignal, Signals,batch_name] ...
= calculate_signal(System, Method, Nuclei,Clusters,sig_file);
Order_n_Signal = cell(1,Method.order);
if ~isempty(Signals)
for ii = 1:Method.order
Order_n_Signal{ii} = Signals(1,ii);
end
end
else
Order_n_Signal = cell(1,Method.order);
AuxiliarySignal = cell(1,Method.order);
% Remember Method.order.
MethodOrder = Method.order;
new_order = 1;
% Loop over orders.
for iorder = 1:MethodOrder
if iorder < new_order
continue;
end
% Check for orders with the same theory.
for jorder = iorder:MethodOrder
if ~all( all( System.Theory(iorder:jorder,:),1 ) ...
== any(System.Theory(iorder:jorder,:),1 ) )
break;
end
new_order = jorder;
end
% Set new order to the highest order with the same theory as iorder.
Method.order = new_order;
% Calculate signals.
if strcmp(Method.method,'HD-CCE')
fractions = System.deuteriumFraction;
% Change all hydrons to protons.
System.deuteriumFraction = 0;
Nuclei = newHydronIsotopologue(Nuclei,System);
% Get proton auxiliary signals.
[ClusterArray, Coherences_1H,Coherences_2H,...
SubclusterIndices_2H,dimensionality,~] ...
= calculateSignal_forHDCCE(System, Method, Nuclei,Clusters);
% Change all hydrons to deuteron.
System.deuteriumFraction = 1;
Nuclei = newHydronIsotopologue(Nuclei,System);
% Get deuteron auxiliary signals.
[~, Coherences_1D,Coherences_2D,SubclusterIndices_2D,~,~] ...
= calculateSignal_forHDCCE(System, Method, Nuclei,Clusters);
[~, ...
~,~] = ...
doHydrogenIsotopologueCCE(...
Coherences_1H,Coherences_2H,Coherences_1D,Coherences_2D, ...
fractions, ClusterArray, ...
SubclusterIndices_2H,SubclusterIndices_2D,...
timepoints,dimensionality, Method.order,...
Nuclei.numberClusters,Nuclei.Exchangeable,Nuclei.MoleculeID);
System.deuteriumFraction = fractions;
else
[~, AuxiliarySignal_ofOrder, ~,batch_name] ...
= calculate_signal(System, Method, Nuclei,Clusters,sig_file);
end
% Record the appropraite signals.
for record_order = iorder:new_order
AuxiliarySignal{record_order} = AuxiliarySignal_ofOrder{record_order};
Order_n_Signal{record_order} = prod(AuxiliarySignal{record_order},1);
if record_order > 1
Order_n_Signal{record_order} = ...
Order_n_Signal{record_order}.*Order_n_Signal{record_order-1};
end
end
end
Signal = Order_n_Signal{MethodOrder};
end
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function [SignalMean, experiment_time, ...
TM_powder,Order_n_SignalMean,Nuclei,statistics] ...
=...
saveSignalResults(Nuclei, Clusters,System, Method, Data,...
SignalMean,Order_n_SignalMean,...
experiment_time,OutputData,uncertainty,GridInfo,...
TempSignals,Temp_Order_n_Signals,graphs,...
Signals,Order_n_Signals,Statistics,TM,AuxiliarySignal,...
Calculate_Signal,Ori_Clusters,Progress,nOrientations)
tempSignalIndex = 0;
for iOri = 1:nOrientations
if Calculate_Signal{iOri}
tempSignalIndex = tempSignalIndex +1;
Signals{iOri} = TempSignals{tempSignalIndex};
Order_n_Signals{iOri} = Temp_Order_n_Signals{tempSignalIndex};
end
if ~strcmp(Method.method,'HD-CCE') && ~isempty(Signals{iOri})
TM(iOri) = getTM(experiment_time,Signals{iOri});
end
end
clear('TempSignals');
if System.doPruneNuclei && ~Method.reparseNuclei
statistics = Nuclei.Isotopologue;
else
statistics.Statistics = Statistics;
statistics.uncertainty = uncertainty;
end
Nuclei.graphs = graphs;
if System.newIsotopologuePerOrientation
Nuclei.PowderStatistics.Isotopologue.Mean_TypeNumber = [0,0,0];
Nuclei.PowderStatistics.Isotopologue.Mean_Instance_2H_Number = [0,0,0];
Nuclei.PowderStatistics.Isotopologue.Mean_Instance_2H_Fraction = [0,0,0];
end
for iOri = 1:nOrientations
if ~Method.reparseNuclei && System.newIsotopologuePerOrientation
Nuclei.PowderStatistics.Isotopologue.Mean_TypeNumber ...
= Nuclei.PowderStatistics.Isotopologue.Mean_TypeNumber ...
+ Statistics{iOri}.Isotopologue.TypeNumber/nOrientations;
Nuclei.PowderStatistics.Isotopologue.Mean_Instance_2H_Number ...
= Nuclei.PowderStatistics.Isotopologue.Mean_Instance_2H_Number ...
+ Statistics{iOri}.Isotopologue.Instance_2H_Number/nOrientations;
Nuclei.PowderStatistics.Isotopologue.Mean_Instance_2H_Fraction ...
= Nuclei.PowderStatistics.Isotopologue.Mean_Instance_2H_Fraction ...
+ Statistics{iOri}.Isotopologue.InstanceFraction/nOrientations;
end
if Method.Ori_cutoffs
Clusters = combineClusters(Clusters,Ori_Clusters{iOri});
end
if ~isempty(Signals{iOri})
SignalMean = SignalMean + Signals{iOri};
end
%Signals{isignal} = abs(Signals{isignal});
for iorder = 1:Method.order
if min( numel(Order_n_Signals),numel(Order_n_SignalMean)) < iorder...
|| ischar(Order_n_SignalMean{iorder}) ...
|| isempty(Order_n_Signals{iorder})
continue;
end
try
Order_n_SignalMean{iorder} ...
= Order_n_SignalMean{iorder} + Order_n_Signals{iOri}{iorder};
catch
fprintf('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n');
fprintf('Error in Order %d mean at signal number %d.\n',iorder,iOri);
disp('Could not evaluate');
Order_n_Signals{iOri}{iorder} = nan(size(experiment_time));
Order_n_SignalMean{iorder} ...
= Order_n_SignalMean{iorder} + Order_n_Signals{iOri}{iorder};
fprintf('!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n');
end
end
% Signals{isignal} = Signals{isignal}/max(Signals{isignal});
end
for iSize=1:Method.order
Nuclei.numberClusters(iSize) = size(Clusters{iSize},1);
end
% update progress
if Progress.Order_n_Mean, Progress.Order_n_Mean = true; end
if System.dimensionality==2 && min(size(SignalMean))==1
SignalMean = reshape(SignalMean',nTimePoints,nTimePoints)';
for iorder = 1:Method.order
Order_n_SignalMean{iorder} ...
= reshape(Order_n_SignalMean{iorder}',nTimePoints,nTimePoints)';
end
end
% Save clusters if requested
if Method.exportClusters
if ~isempty(OutputData)
clusterSaveFile = [OutputData(1:end-4),'Clusters.mat'];
else
clusterSaveFile = 'Clusters.mat';
end
save(clusterSaveFile,'Clusters','Ori_Clusters');
end
if strcmp(Method.method,'count clusters')
SignalMean = SignalMean(1:Method.order);
experiment_time = 1:Method.order;
SignalMean = SignalMean/SignalMean(1)*double(Nuclei.number);
end
TM_powder = getTM(experiment_time,abs(SignalMean));
Progress.complete = true;
if Method.verbose
fprintf('Processing\n');
end
uncertainty = [];
% decide what to save
if ~isempty(OutputData)
T = array2table([experiment_time',SignalMean']);
T.Properties.VariableNames(1:2) = {'time','signal'};
writetable(T,[OutputData(1:end-4) , '.csv']);
if Data.save_mat_file
switch Data.saveLevel
case 0
save(OutputData,'SignalMean','Signals','TM','TM_powder',...
'Progress','uncertainty','GridInfo','-append');
case 1
save(OutputData,'SignalMean','Signals','TM','TM_powder','Progress',...
'Nuclei','Order_n_SignalMean','Order_n_Signals','uncertainty',...
'GridInfo','AuxiliarySignal','-append');
case 2
save(OutputData,'-v7.3');
end
end
end
% Calculate the contributions from each spin
% placed after the save since getSpinContributions() is still buggy
%NuclearContribution.findContributions = Method.getNuclearContributions;
if Method.getUncertainty
uncertainty = getClusterError([], ...
Nuclei, System, nOrientations, Clusters, AuxiliarySignal,Method, ...
gridWeight, Order_n_SignalMean, Order_n_Signals);
save(OutputData,'uncertainty','-append');
end
if Method.getNuclearSpinContributions
getNuclearSpinContributions([OutputData,'SpinContribution.mat'], ...
Nuclei, System, nOrientations, Clusters, Signals, AuxiliarySignal, ...
Method, experiment_time, gridWeight, TM_powder, Input, SignalMean, ...
Order_n_SignalMean);
end
if Method.getClusterContributions
if ~Method.Ori_cutoffs
getClusterContributions([OutputData,'ClusterContribution.mat'], ...
Nuclei, System, 1:nOrientations, Clusters, Signals, AuxiliarySignal, ...
Method, experiment_time, gridWeight, TM_powder, Input, SignalMean, ...
Order_n_SignalMean,Order_n_Signals);
else
for iOri = 1:nOrientations
getClusterContributions(...
[OutputData,'ClusterContribution_Ori_',num2str(iOri), '.mat'], ...
Nuclei, System, iOri, Ori_Clusters{iOri}, Signals, AuxiliarySignal, ...
Method, experiment_time, gridWeight, TM_powder, Input, SignalMean, ...
Order_n_SignalMean,Order_n_Signals);
end
end
end
if isfield(Method, 'getNuclearContributions') && Method.getNuclearContributions
if isnan(TM)
fprintf('Cannot find nuclear contributions whe TM is Nan.');
else
NuclearContribution = getSpinContributions(System, Nuclei, Signals, ...
AuxiliarySignal, Clusters,Method,OutputData,gridWeight, TM_powder);
save(OutputData,'NuclearContribution','-append');
end
end
if Method.verbose
fprintf('\nCompleted Nuclear Spin Diffusion\n');
fprintf('\nNuclear spin decoherence time = %f µs. \n',TM_powder/1e-6);
end
if Method.conserveMemory
if isfield(statistics,'Statistics')
for jj = 1:numel(statistics.Statistics)
if isfield(statistics.Statistics{jj},'Nuclear_Dipole')
statistics.Statistics{jj} = ...
rmfield(statistics.Statistics{jj},'Nuclear_Dipole');
end
if isfield(statistics.Statistics{jj},'Nuclear_Dipole_x_iy_Z')
statistics.Statistics{jj} = ...
rmfield(statistics.Statistics{jj},'Nuclear_Dipole_x_iy_Z');
end
end
end
end
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function [Signal,AuxiliarySignal,Order_n_Signal] = ...
doLCE(System,Method, Nuclei, Clusters)
MethylID = [];
Signal = zeros(size(System.Time));
Order_n_Signal = {ones(size(System.Time)),Signal};
tau1 = System.Time;
tau2 = System.Time';
if Method.conserveMemory
AuxiliarySignal = 'The auxiliary signals are not saved in memory conservation mode.';
end
cluster_size = 2;
for icluster = 1:Nuclei.numberClusters(cluster_size)
thisCluster = Clusters{cluster_size}(icluster,:);
[tensors,~] = pairwisetensors(Nuclei.Nuclear_g, Nuclei.Coordinates,...
thisCluster,Nuclei.Atensor, System.magneticField, System.ge, System.gMatrix(3,3), System.muB, System.muN, System.mu0, System.hbar,System.theory,MethylID);
b = -2*pi*tensors(3,3,2,3)/4; % rad/s.
omega = 2*pi*(tensors(3,3,1,2) - tensors(3,3,1,3))/2; % rad/s.
switch System.experiment
case 'Hahn'
case 'CPMG-2D'
V2 = - 4*(b/omega*(cos(omega.*tau1) - cos(omega.*tau2) )).^2;
AuxiliarySignal_ = V2;
Signal = Signal + AuxiliarySignal_;
end
% initialize the nth auxiliary signal
if ~Method.conserveMemory
AuxiliarySignal{icluster} = AuxiliarySignal_;
end
end
Signal = exp(Signal);
if System.dimensionality ==2
Signal = reshape(Signal.',1,[]);
end
Order_n_Signal{cluster_size} = Signal;
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function [Signal,AuxiliarySignal,Order_n_Signal] = doRestrictedCCE(System, Method, Nuclei,verbose)
% initialize
Hyperfine = zeros(Nuclei.number,1);
Signal = ones(size(System.Time));
Order_n_Signal{1} = Signal;
numberNuclei=Nuclei.number;
Adjacency = Nuclei.Adjacency;
if Method.conserveMemory
AuxiliarySignal = 'The auxiliary signals are not saved in memory conservation mode.';
end
if verbose
% threshold and counter for how often to display info
verboseThreshold = 0.05*numberNuclei;
verboseCounter = 0;
disp('Starting restricted CCE.');
end
if ~all(Nuclei.Spin==1/2)
warning('System has spins with I~=1/2. Restricted CCE is limited to spin-1/2 nuclei and will ignore them.');
end
% loop over all nuclei
for inucleus = 1:numberNuclei
if (abs(Nuclei.Spin(inucleus) -0.5)>1e-6)
continue;
end
% initialize the nth auxiliary signal
if ~Method.conserveMemory
AuxiliarySignal{inucleus} = ones(size(Signal));
end
% Calculating hyperfine coupling
gamma_e = -System.Electron.g*System.muB/System.hbar;
Rn = norm(Nuclei.Coordinates(inucleus,:) );
gamma_n = Nuclei.Nuclear_g(inucleus)*System.muN/System.hbar;
cosTheta2 = cosFieldAngle([0,0,0],Nuclei.Coordinates(inucleus,:));
cosTheta2 = cosTheta2*cosTheta2;
Hyperfine(inucleus) = Nuclei.FermiContact(inucleus)-(System.mu0/4/pi)*gamma_n*gamma_e*System.hbar*(1-3*cosTheta2)*Rn^-3;
% Calculating bath coupling
for jnucleus = 1:inucleus-1
% skip over I != 1/2
if Nuclei.Spin(inucleus)~=1/2, continue; end
if ~Adjacency(inucleus,jnucleus,2), continue; end
% calculate dipolar coupling
%{
cosThetaSquared = (cosFieldAngle(Nuclei.Coordinates(inucleus,:),Nuclei.Coordinates(jnucleus,:)))^2;
b = 0.25*(System.mu0/4/pi)*Nuclei.Nuclear_g(inucleus)*Nuclei.Nuclear_g(jnucleus)*System.muN^2; % J m^3.
r = norm(Nuclei.Coordinates(inucleus,:) - Nuclei.Coordinates(jnucleus,:));
r3 = r^3;
b = -b*(3*cosThetaSquared - 1)/r3; % J.
b = b/(System.hbar); % 1/s.
c = ( Hyperfine(inucleus)-Hyperfine(jnucleus) )/(4*b);
w = b*sqrt(1+c^2);
%}
modDepth = Nuclei.Statistics.Modulation_Depth_methyl(inucleus,jnucleus);
w = Nuclei.Statistics.Frequency_Pair_methyl(inucleus,jnucleus)*2*pi;
AuxiliarySignal_ = 1 - modDepth * sin(w*2*System.Time).^4;
Signal = Signal.*AuxiliarySignal_;
if ~Method.conserveMemory
AuxiliarySignal{inucleus} =AuxiliarySignal{inucleus}.*AuxiliarySignal_;
end
end
if verbose
verboseCounter = verboseCounter + 1;
if verboseCounter > verboseThreshold
verboseCounter = 0;
fprintf('Nuclei: %d/%d, (%s).\n',inucleus,numberNuclei,datetime);
end
end
Order_n_Signal{2} = Signal;
end
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
function cos_theta = cosFieldAngle(ParticleCoordinates_1,ParticleCoordinates_2)
R = ParticleCoordinates_2 - ParticleCoordinates_1;
cos_theta = R*[0;0;1]/norm(R);
end
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>