From 90dd950e2d8c1495f2be34bbf1629b2fd82b93ae Mon Sep 17 00:00:00 2001
From: Stephen Nneji <steve.nneji@gmail.com>
Date: Mon, 6 Jul 2026 10:09:18 +0100
Subject: [PATCH 1/3] Refactors NS and Dream to exist quicker when stopped

---
 minimisers/DREAM/functions/DREAM.m | 2 +-
 minimisers/DREAM/runDREAM.m        | 6 ++++++
 minimisers/NS/nestedSampler.m      | 3 ++-
 minimisers/NS/runNestedSampler.m   | 5 +++++
 4 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/minimisers/DREAM/functions/DREAM.m b/minimisers/DREAM/functions/DREAM.m
index e6481e570..df486d910 100644
--- a/minimisers/DREAM/functions/DREAM.m
+++ b/minimisers/DREAM/functions/DREAM.m
@@ -222,7 +222,7 @@
         if ~strcmpi(controls.display, coderEnums.displayOptions.Off)
             triggerEvent(coderEnums.eventTypes.Message, sprintf('Optimisation terminated by user\n'));
         end
-        break;
+        return;
     end
 end
 
diff --git a/minimisers/DREAM/runDREAM.m b/minimisers/DREAM/runDREAM.m
index 73e98ea05..c2845dd6a 100644
--- a/minimisers/DREAM/runDREAM.m
+++ b/minimisers/DREAM/runDREAM.m
@@ -87,6 +87,12 @@
 % Run the sampler....
 [chain,dreamOutput,~] = DREAM(DREAMPar,ParInfo,ratInputs);
 
+if isRATStopped(controls.IPCFilePath)
+    result = makeEmptyResultStruct(problemStruct.numberOfContrasts, length(problemStruct.fitParams), domains);
+    outProblemStruct = problemStruct;
+    return
+end
+
 % Combine all chains....
 nChains = DREAMPar.nChains;
 nParams = DREAMPar.nParams;
diff --git a/minimisers/NS/nestedSampler.m b/minimisers/NS/nestedSampler.m
index e7a4f98b4..f7ce16ea7 100644
--- a/minimisers/NS/nestedSampler.m
+++ b/minimisers/NS/nestedSampler.m
@@ -263,7 +263,8 @@
         if ~strcmpi(controls.display, coderEnums.displayOptions.Off)
             triggerEvent(coderEnums.eventTypes.Message, sprintf('Optimisation terminated by user\n'));
         end
-        break;
+        post_samples = [];
+        return;
     end
     % update counter    
     j = j+1;
diff --git a/minimisers/NS/runNestedSampler.m b/minimisers/NS/runNestedSampler.m
index 0a8310e72..1ab17893c 100644
--- a/minimisers/NS/runNestedSampler.m
+++ b/minimisers/NS/runNestedSampler.m
@@ -49,6 +49,11 @@
 [logZ, nestSamples, postSamples, H] = nestedSampler(data, nLive, nMCMC,...
     tolerance, likelihood, model, priorList, fitNames);
 
+if isRATStopped(controls.IPCFilePath)
+    result = makeEmptyResultStruct(problemStruct.numberOfContrasts, length(problemStruct.fitParams), domains);
+    return
+end
+
 % Process the results...
 nParams = length(fitNames);
 % chain = nest_samples(:,1:end-1);

From 84c10c9b39a4b72bb7008d496c89d4e275e48924 Mon Sep 17 00:00:00 2001
From: Stephen Nneji <steve.nneji@gmail.com>
Date: Wed, 8 Jul 2026 14:31:40 +0100
Subject: [PATCH 2/3] Refactors alignALProfiles and make it work for bayes and
 live plot.

---
 API/events/triggerEvent.m            | 10 +++-
 utilities/plotting/alignALProfiles.m | 71 ++++++++++++++++++++++++++++
 utilities/plotting/bayesShadedPlot.m |  9 ++--
 utilities/plotting/plotRefSLD.m      | 64 ++-----------------------
 4 files changed, 87 insertions(+), 67 deletions(-)
 create mode 100644 utilities/plotting/alignALProfiles.m

diff --git a/API/events/triggerEvent.m b/API/events/triggerEvent.m
index 7fe8ecd49..ba13892c1 100644
--- a/API/events/triggerEvent.m
+++ b/API/events/triggerEvent.m
@@ -30,13 +30,15 @@ function triggerEvent(eventType, varargin)
             problemStruct = varargin{2};
             plotData.reflectivity = result.reflectivity;
             plotData.shiftedData = result.shiftedData;
-            plotData.sldProfiles = result.sldProfiles;
-            plotData.resampledLayers = result.resampledLayers;
             plotData.subRoughs = result.contrastParams.subRoughs;
             plotData.resample = problemStruct.resample;
             plotData.dataPresent = problemStruct.dataPresent;
             plotData.modelType = problemStruct.modelType;
             plotData.contrastNames = problemStruct.names.contrasts;
+            
+            [slds, resampledLayers, ~] = alignALProfiles(problemStruct.geometry, problemStruct.modelType, result.sldProfiles, result.resampledLayers, {});
+            plotData.sldProfiles = slds;
+            plotData.resampledLayers = resampledLayers;
              
             eventManager.notify(eventType, plotData);
         end
@@ -62,6 +64,10 @@ function triggerEvent(eventType, varargin)
             elseif eventType == coderEnums.eventTypes.Plot
                 result = varargin{1};
                 problemStruct = varargin{2};
+                [slds, resampledLayers, ~] = alignALProfiles(problemStruct.geometry, problemStruct.modelType, result.sldProfiles, result.resampledLayers, {});
+                result.sldProfiles = slds;
+                result.resampledLayers = resampledLayers;
+
                 subRoughs = result.contrastParams.subRoughs;
                 nContrast = length(result.reflectivity);
                 [reflect, nReflect] = packCellArray(result.reflectivity, 1);
diff --git a/utilities/plotting/alignALProfiles.m b/utilities/plotting/alignALProfiles.m
new file mode 100644
index 000000000..3b1511bb1
--- /dev/null
+++ b/utilities/plotting/alignALProfiles.m
@@ -0,0 +1,71 @@
+function [sldProfiles, resampledLayers, pIntervals] = alignALProfiles(geometry, modelType, sldProfiles, resampledLayers, pIntervals)
+% Aligns the A/L SLD profiles so that the substrates line up by padding the
+% start of any shorter than the longest profile. Also adjusts resampled
+% layers and prediction interval slds as necessary.
+%
+% Parameters
+% ----------
+% geometry : geometryOptions
+%    The geometry.
+% modelType : modelTypes
+%    The model type. 
+% sldProfiles : cell
+%    The sld profiles.
+% resampledLayers : cell
+%    The resampled layers. 
+% pIntervals : cell
+%    The slds in the prediction intervals.
+%
+% Returns
+% -------
+% sldProfiles : cell
+%    The sld profiles, adjusted if necessary.
+% resampledLayers : cell
+%    The resampled layers, adjusted if necessary. 
+% pIntervals : cell
+%    The slds in the prediction intervals, adjusted if necessary.
+
+if ~strcmpi(geometry,'air/substrate') || strcmpi(modelType,'custom xy')
+    return
+end
+
+% Find the length of the longest profile.
+lengths = zeros(size(sldProfiles));
+for i = 1:numel(sldProfiles)
+    lengths(i) = size(sldProfiles{i}, 1);
+end
+% Get max length and its index
+[maxLen, maxPos] = max(lengths);
+maxPos = maxPos(1);
+maxLen  = maxLen (1);
+
+maxXValue = sldProfiles{maxPos}(end,1);
+
+% Get the longest profile...
+maxX = sldProfiles{maxPos}(:,1);
+
+% Pad the start of any profiles that are shorter than this
+for i = 1:numel(sldProfiles)
+    thisSLD = sldProfiles{i};
+    thisLen = size(thisSLD,1);
+    if thisLen < maxLen
+        diffLen = maxLen - thisLen;
+        pad = zeros(diffLen,1);
+        newY = [pad ; thisSLD(:,2)];
+        sldProfiles{i} = [maxX(:,1) newY(:)];
+        
+        % For resampled layers, the pad is just one big layer at the start
+        thisResam = resampledLayers{i};
+        if any(thisResam,'all')      % not all zeros
+            totLength = sum(thisResam(:,1));
+            padLength = maxXValue - totLength;
+            resamPad = [padLength 0 0];
+            resampledLayers{i} = [resamPad ; thisResam]; 
+        end
+
+        if ~isempty(pIntervals)
+            pIntervals{i} = [zeros(5, diffLen), pIntervals{i}];
+        end
+    end
+end
+end
diff --git a/utilities/plotting/bayesShadedPlot.m b/utilities/plotting/bayesShadedPlot.m
index 38351a8e1..b3141cfa6 100644
--- a/utilities/plotting/bayesShadedPlot.m
+++ b/utilities/plotting/bayesShadedPlot.m
@@ -50,10 +50,11 @@ function bayesShadedPlot(project, result, options)
 
 controls = controlsClass();
 [projectStruct,~] = parseClassToStructs(project,controls);
+[sldProfiles, ~, pIntervals] = alignALProfiles(projectStruct.geometry, projectStruct.modelType, result.sldProfiles, result.resampledLayers, result.predictionIntervals.sld);
 
 % Get the reflectivities and SLDs
 reflectivityValues = result.predictionIntervals.reflectivity;
-sldValues = result.predictionIntervals.sld;
+sldValues = pIntervals;
 
 shiftedData = result.shiftedData;
 numberOfContrasts = length(shiftedData);
@@ -118,7 +119,7 @@ function bayesShadedPlot(project, result, options)
 subplot(1,2,2); hold on; box on
 xlabel('$\textrm{Z} (\AA)$','Interpreter','Latex')
 ylabel('$\textrm{SLD} (\AA^{-2})$','Interpreter','Latex')
-nColumns = size(result.sldProfiles, 2);
+nColumns = size(sldProfiles, 2);
 lines = cell(numberOfContrasts * nColumns, 1);
 names = cell(numberOfContrasts * nColumns, 1);
 
@@ -128,7 +129,7 @@ function bayesShadedPlot(project, result, options)
 
         sld = sldValues{i}(3,:);
         limits = sldValues{i};
-        sldXValues = result.sldProfiles{i}(:,1);
+        sldXValues = sldProfiles{i}(:,1);
 
         min = limits(vals(1),:);
         max = limits(vals(2),:);
@@ -145,7 +146,7 @@ function bayesShadedPlot(project, result, options)
 
         sld = sldValues(i,:);
         limits = sldValues(i,:);
-        sldXValues = result.sldProfiles(i,:);
+        sldXValues = sldProfiles(i,:);
 
         for j = 1:2
             min = limits{j}(vals(1),:);
diff --git a/utilities/plotting/plotRefSLD.m b/utilities/plotting/plotRefSLD.m
index f3920ac30..383d8250f 100644
--- a/utilities/plotting/plotRefSLD.m
+++ b/utilities/plotting/plotRefSLD.m
@@ -37,72 +37,14 @@ function plotRefSLD(project, result, options)
     
     data.reflectivity = result.reflectivity;
     data.shiftedData = result.shiftedData;
-    data.sldProfiles = result.sldProfiles;
-    data.resampledLayers = result.resampledLayers;
     data.dataPresent = projectStruct.dataPresent;
     data.subRoughs = result.contrastParams.subRoughs;
     data.resample = projectStruct.resample;
     data.contrastNames = projectStruct.names.contrasts;
 
-    % If we have air/substrate geometry, modify the SLD profiles slightly
-    % so that the substrates line up (for custom XY the user does this
-    % themselves)...
-    if strcmpi(projectStruct.geometry,'air/substrate') && ~strcmpi(projectStruct.modelType,'custom xy')
-        data = alignALProfiles(data);
-    end
-    
+    [slds, resampledLayers, ~] = alignALProfiles(projectStruct.geometry, projectStruct.modelType, result.sldProfiles, result.resampledLayers, {});
+    data.sldProfiles = slds;
+    data.resampledLayers = resampledLayers;
     plotRefSLDHelper(data, false, options.linearX, options.q4, options.showErrorBar, ...
                      options.showGrid, options.showLegend, options.shiftValue);
 end
-
-
-function data = alignALProfiles(data)
-% Aligns the A/L SLD profiles so that the substrates line up by padding the
-% start of any shorter than the longest profile..
-
-% Get the sld profiles out of data
-slds = data.sldProfiles;
-resamLays = data.resampledLayers;
-
-% Find the length of the longest profile...
-f = @(x)size(x{:},1);
-lengths = arrayfun(f,slds);
-maxPos = find(lengths == max(lengths));
-
-% If maxPos is an array we have many of equal (leng) length.
-% We can just pick one of them...
-if length(maxPos) > 1
-    maxPos = maxPos(1);
-end
-
-maxLen = lengths(maxPos);
-max_XValue = slds{maxPos}(end,1);
-
-% Get the longest profile...
-max_X = slds{maxPos}(:,1);
-
-% Pad the start of any profiles that are shorter than this
-for i = 1:length(slds)
-    thisSLD = slds{i};
-    thisLen = size(thisSLD,1);
-    if thisLen < maxLen
-        diffLen = maxLen - thisLen;
-        pad = zeros(diffLen,1);
-        newY = [pad ; thisSLD(:,2)];
-        slds{i} = [max_X(:,1) newY(:)];
-        
-        % For resampled layers, the pad is just one big layer at the start
-        thisResam = resamLays{i};
-        if ~all(thisResam,'All')      % not all zeros
-            totLength = sum(thisResam(:,1));
-            padLength = max_XValue - totLength;
-            resamPad = [padLength 0 0];
-            resamLays{i} = [resamPad ; thisResam]; 
-        end
-    end
-end
-
-data.sldProfiles = slds;
-data.resampledLayers = resamLays;
-
-end
\ No newline at end of file

From 89c191690638370db6f37c2eb04228ca50162c07 Mon Sep 17 00:00:00 2001
From: Stephen Nneji <steve.nneji@gmail.com>
Date: Fri, 10 Jul 2026 10:03:57 +0100
Subject: [PATCH 3/3] Address review comment

---
 utilities/plotting/alignALProfiles.m | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/utilities/plotting/alignALProfiles.m b/utilities/plotting/alignALProfiles.m
index 3b1511bb1..7ef91d992 100644
--- a/utilities/plotting/alignALProfiles.m
+++ b/utilities/plotting/alignALProfiles.m
@@ -34,11 +34,9 @@
 for i = 1:numel(sldProfiles)
     lengths(i) = size(sldProfiles{i}, 1);
 end
-% Get max length and its index
-[maxLen, maxPos] = max(lengths);
-maxPos = maxPos(1);
-maxLen  = maxLen (1);
 
+% Get max length and its index
+[maxLen, maxPos] = max(lengths, [], "all");
 maxXValue = sldProfiles{maxPos}(end,1);
 
 % Get the longest profile...