Added utilities for saving and loading RasCAL2 files....

examples/normalReflectivity/customLayers/R2_example/controls.json

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+{"procedure":"calculate","parallel":"single","numSimulationPoints":500,"resampleMinAngle":0.9,"resampleNPoints":50,"display":"iter","xTolerance":1E-6,"funcTolerance":1E-6,"maxFuncEvals":10000,"maxIterations":1000,"updateFreq":1,"updatePlotFreq":20,"populationSize":20,"fWeight":0.5,"crossoverProbability":0.8,"strategy":4,"targetValue":1,"numGenerations":500,"nLive":150,"nMCMC":0,"propScale":0.1,"nsTolerance":0.1,"nSamples":20000,"nChains":10,"jumpProbability":0.5,"pUnitGamma":0.2,"boundHandling":"reflect","adaptPCR":true}

examples/normalReflectivity/customLayers/R2_example/customBilayerDSPC.m

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+function [output,sub_rough] = customBilayerDSPC(params,bulk_in,bulk_out,contrast)
+%CUSTOMBILAYER  RASCAL Custom Layer Model File.
+%
+%
+% This file accepts 3 vectors containing the values for
+% Params, bulk in and bulk out
+% The final parameter is an index of the contrast being calculated
+% The m-file should output a matrix of layer values, in the form..
+% Output = [thick 1, SLD 1, Rough 1, Percent Hydration 1, Hydrate how 1
+%           ....
+%           thick n, SLD n, Rough n, Percent Hydration n, Hydration how n]
+% The "hydrate how" parameter decides if the layer is hydrated with
+% Bulk out or Bulk in phases. Set to 1 for Bulk out, zero for Bulk in.
+% Alternatively, leave out hydration and just return..
+% Output = [thick 1, SLD 1, Rough 1,
+%           ....
+%           thick n, SLD n, Rough n] };
+% The second output parameter should be the substrate roughness
+
+sub_rough = params(1);
+oxide_thick = params(2);
+oxide_hydration = params(3);
+lipidAPM = params(4);
+headHydration = params(5);
+bilayerHydration = params(6);
+bilayerRough = params(7);
+waterThick = params(8);
+
+
+% We have a constant SLD for the bilayer
+oxide_SLD = 3.41e-6;
+
+% Now make the lipid layers..
+% Use known lipid volume and compositions
+% to make the layers
+
+% define all the neutron b's.
+bc = 0.6646e-4;     %Carbon
+bo = 0.5843e-4;     %Oxygen
+bh = -0.3739e-4;	%Hydrogen
+bp = 0.513e-4;      %Phosphorus
+bn = 0.936e-4;      %Nitrogen
+bd = 0.6671e-4;     %Deuterium
+
+% Now make the lipid groups..
+COO = (4*bo) + (2*bc);
+GLYC = (3*bc) + (5*bh);
+CH3 = (2*bc) + (6*bh);             
+PO4 = (1*bp) + (4*bo);
+CH2 = (1*bc) + (2*bh);
+CHOL = (5*bc) + (12*bh) + (1*bn);
+
+% Group these into heads and tails:
+Head = CHOL + PO4 + GLYC + COO;
+Tails = (34*CH2) + (2*CH3);
+
+% We need volumes for each.
+% Use literature values:
+vHead = 319;
+vTail = 782;
+
+% we use the volumes to calculate the SLD's
+SLDhead = Head / vHead;
+SLDtail = Tails / vTail;
+
+% We calculate the layer thickness' from
+% the volumes and the APM...
+headThick = vHead / lipidAPM;
+tailThick = vTail / lipidAPM;
+
+% Manually deal with hydration for layers in
+% this example.
+oxSLD = (oxide_hydration * bulk_out(contrast)) + ((1 - oxide_hydration) * oxide_SLD);
+headSLD = (headHydration * bulk_out(contrast)) + ((1 - headHydration) * SLDhead);
+tailSLD = (bilayerHydration * bulk_out(contrast)) + ((1 - bilayerHydration) * SLDtail);
+
+% Make the layers
+oxide = [oxide_thick oxSLD sub_rough];
+water = [waterThick bulk_out(contrast) bilayerRough];
+head = [headThick headSLD bilayerRough];
+tail = [tailThick tailSLD bilayerRough];
+
+output = [oxide ; water ; head ; tail ; tail ; head];
+
+
+

examples/normalReflectivity/customLayers/R2_example_new/controls.json

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+{"procedure":"dream","parallel":"contrasts","numSimulationPoints":500,"resampleMinAngle":0.9,"resampleNPoints":50,"display":"iter","xTolerance":1E-6,"funcTolerance":1E-6,"maxFuncEvals":10000,"maxIterations":1000,"updateFreq":1,"updatePlotFreq":20,"populationSize":20,"fWeight":0.5,"crossoverProbability":0.8,"strategy":4,"targetValue":1,"numGenerations":500,"nLive":150,"nMCMC":0,"propScale":0.1,"nsTolerance":0.1,"nSamples":20000,"nChains":10,"jumpProbability":0.5,"pUnitGamma":0.2,"boundHandling":"reflect","adaptPCR":true}

examples/normalReflectivity/customLayers/R2_example_new/customBilayerDSPC.m

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+function [output,sub_rough] = customBilayerDSPC(params,bulk_in,bulk_out,contrast)
+%CUSTOMBILAYER  RASCAL Custom Layer Model File.
+%
+%
+% This file accepts 3 vectors containing the values for
+% Params, bulk in and bulk out
+% The final parameter is an index of the contrast being calculated
+% The m-file should output a matrix of layer values, in the form..
+% Output = [thick 1, SLD 1, Rough 1, Percent Hydration 1, Hydrate how 1
+%           ....
+%           thick n, SLD n, Rough n, Percent Hydration n, Hydration how n]
+% The "hydrate how" parameter decides if the layer is hydrated with
+% Bulk out or Bulk in phases. Set to 1 for Bulk out, zero for Bulk in.
+% Alternatively, leave out hydration and just return..
+% Output = [thick 1, SLD 1, Rough 1,
+%           ....
+%           thick n, SLD n, Rough n] };
+% The second output parameter should be the substrate roughness
+
+sub_rough = params(1);
+oxide_thick = params(2);
+oxide_hydration = params(3);
+lipidAPM = params(4);
+headHydration = params(5);
+bilayerHydration = params(6);
+bilayerRough = params(7);
+waterThick = params(8);
+
+
+% We have a constant SLD for the bilayer
+oxide_SLD = 3.41e-6;
+
+% Now make the lipid layers..
+% Use known lipid volume and compositions
+% to make the layers
+
+% define all the neutron b's.
+bc = 0.6646e-4;     %Carbon
+bo = 0.5843e-4;     %Oxygen
+bh = -0.3739e-4;	%Hydrogen
+bp = 0.513e-4;      %Phosphorus
+bn = 0.936e-4;      %Nitrogen
+bd = 0.6671e-4;     %Deuterium
+
+% Now make the lipid groups..
+COO = (4*bo) + (2*bc);
+GLYC = (3*bc) + (5*bh);
+CH3 = (2*bc) + (6*bh);             
+PO4 = (1*bp) + (4*bo);
+CH2 = (1*bc) + (2*bh);
+CHOL = (5*bc) + (12*bh) + (1*bn);
+
+% Group these into heads and tails:
+Head = CHOL + PO4 + GLYC + COO;
+Tails = (34*CH2) + (2*CH3);
+
+% We need volumes for each.
+% Use literature values:
+vHead = 319;
+vTail = 782;
+
+% we use the volumes to calculate the SLD's
+SLDhead = Head / vHead;
+SLDtail = Tails / vTail;
+
+% We calculate the layer thickness' from
+% the volumes and the APM...
+headThick = vHead / lipidAPM;
+tailThick = vTail / lipidAPM;
+
+% Manually deal with hydration for layers in
+% this example.
+oxSLD = (oxide_hydration * bulk_out(contrast)) + ((1 - oxide_hydration) * oxide_SLD);
+headSLD = (headHydration * bulk_out(contrast)) + ((1 - headHydration) * SLDhead);
+tailSLD = (bilayerHydration * bulk_out(contrast)) + ((1 - bilayerHydration) * SLDtail);
+
+% Make the layers
+oxide = [oxide_thick oxSLD sub_rough];
+water = [waterThick bulk_out(contrast) bilayerRough];
+head = [headThick headSLD bilayerRough];
+tail = [tailThick tailSLD bilayerRough];
+
+output = [oxide ; water ; head ; tail ; tail ; head];
+
+
+

utilities/misc/loadR2.m

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+
+function [problem,varargout] = loadR2(dirName)
+% Loads in a RasCAL2 project...
+
+% Load the project...
+projectFile = fullfile(dirName,'project.json');
+problem = jsonToProject(projectFile);
+
+% If there is a second argument, also load results..
+if nargout > 1
+    resultsFile = fullfile(dirName, 'results.json');
+    varargout{1} = jsonToResults(resultsFile);
+end
+
+end

utilities/misc/saveR2.m

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+
+function saveR2(dirName,problem,results,controls)
+
+% Saves the current project in RasCAL2 format...
+
+arguments
+    dirName {mustBeText}
+    problem {mustBeA(problem, 'projectClass')}
+    results 
+    controls {mustBeA(controls, 'controlsClass')}
+end
+
+% Check whether the save directory exists, create it if necessary
+if exist(dirName,'dir') ~= 7
+    mkdir(dirName);
+end
+currentDir = pwd; % Save the current directory name
+
+% Do some custom file housekeeping. We need to copy these to our new
+% folder if there are any..
+filesTable = problem.customFile.varTable;
+for i = size(filesTable,1)
+    thisFile = fullfile(filesTable{i,'Path'},filesTable{i,'Filename'});
+    copyfile(thisFile,dirName)
+
+    % Change the paths of our custom files in projectClass to point to our
+    % new files..
+    problem.setCustomFile(i,'path',fullfile(currentDir,dirName));
+end
+
+% Go to our new directory and export the jsons...
+cd(dirName);
+projectToJson(problem,'project.json');
+resultsToJson(results,'results.json');
+controlsToJson(controls,'controls.json');
+
+% Go back to our original dir and we are done...
+cd(currentDir);
+
+end