Buckling paper analyses

analysis/Buckling Paper Analyses/BucklingModes.m

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+classdef BucklingModes < Analysis
+
+	% This analysis compares buckling due to weak membrane adhesion,
+	% buckling due to weak membrane tension
+
+	properties
+
+		% STATIC: DO NOT CHANGE
+		% IF CHANGE IS NEEDED, MAKE A NEW OBJECT
+
+		w = 10;
+
+		p = 10;
+		g = 5;
+
+		f = 0;
+
+		b = 1:20;
+
+		sae = 10;
+		spe = 1:20;
+
+		seed = 1:50;
+
+		targetTime = 500;
+
+		analysisName = 'BucklingModes';
+
+		parameterSet = []
+		missingParameterSet = []
+
+		simulationRuns = 50
+		slurmTimeNeeded = 12
+		simulationDriverName = 'ManageDynamicLayer'
+		simulationInputCount = 7
+
+
+	end
+
+	methods
+
+		function obj = BucklingModes()
+
+			obj.seedIsInParameterSet = false; % The seed not given in MakeParameterSet, it is set in properties
+			obj.seedHandledByScript = false; % The seed will be in the parameter file, not the job script
+			obj.usingHPC = true;
+
+		end
+
+		function MakeParameterSet(obj)
+
+			% n, p, g, b, f, sae, spe
+
+			params = [];
+
+			for w = obj.w
+				for p = obj.p
+					for g = obj.g
+						for b = obj.b
+							for f = obj.f
+								for sae = obj.sae
+									for spe = obj.spe
+
+										params(end+1,:) = [w,p,g,b,f,sae,spe];
+
+									end
+								end
+							end
+						end
+					end
+				end
+			end
+
+
+
+			obj.parameterSet = params;
+
+		end
+
+
+
+		function BuildSimulation(obj)
+
+			obj.MakeParameterSet();
+			obj.ProduceSimulationFiles();
+
+		end
+
+		function AssembleData(obj)
+
+			buckleThreshold = 1.1;
+
+			MakeParameterSet(obj);
+
+			buckleOutcome = [];
+			buckleTime = [];
+			stromaRatioAtBuckle = [];
+
+			for i = 1:length(obj.parameterSet)
+				s = obj.parameterSet(i,:);
+				% w, p, g, b, f, sae, spe, seed
+				w = s(1);
+				p = s(2);
+				g = s(3);
+				b = s(4);
+				f = s(5);
+				sae = s(6);
+				spe = s(7);
+
+
+				bottom = [];
+				for j = obj.seed
+
+					a = ManageDynamicLayer(w,p,g,b,f,sae,spe,j);
+					a.LoadSimulationData();
+
+					if ~isnan(a.data.bottomWiggleData)
+						if max(a.data.bottomWiggleData) >= buckleThreshold
+							buckleOutcome(i,j) = true;
+							buckleTime(i,j) = find(a.data.bottomWiggleData >= buckleThreshold,1) * 20 * a.dt;
+							if ~isnan(a.data.stromaWiggleData)
+								% This should always be at the same index when finding the buckleTime
+								% But there might be a difference if the data was generated separately to
+								% buckleWiggleData. Not sure how this will impact the analysis, but it should
+								% not be much unless there are major problems
+								stromaRatioAtBuckle(i,j) = a.data.stromaWiggleData(end);
+							else
+								stromaRatioAtBuckle(i,j) = nan;
+								obj.missingParameterSet(end + 1,:) =[w,p,g,b,f,sae,spe,j];
+							end
+						else
+							buckleOutcome(i,j) = false;
+							buckleTime(i,j) = obj.targetTime;
+							stromaRatioAtBuckle(i,j) = nan;
+						end
+					else
+						% In case the simulation fails for some reason
+						buckleOutcome(i,j) = nan;
+						buckleTime(i,j) = nan;
+						stromaRatioAtBuckle(i,j) = nan;
+
+						obj.missingParameterSet(end + 1,:) =[w,p,g,b,f,sae,spe,j];
+					end
+
+				end
+
+				fprintf('Completed %3.2f%%\n', 100*i/length(obj.parameterSet));
+
+			end
+
+
+			obj.result = {buckleOutcome, buckleTime, stromaRatioAtBuckle};
+
+			if ~isempty(obj.missingParameterSet)
+
+				obj.ProduceMissingDataSimulationFiles();
+			end
+
+
+		end
+
+		function PlotData(obj)
+
+			buckleOutcome = obj.result{1};
+			buckleTime = obj.result{2};
+
+			titleFontSize = 20;
+			labelFontSize = 20;
+			axisFontSize = 15;
+
+			h = figure;
+
+			% data = nansum(buckleOutcome,2)./sum(~isnan(buckleOutcome),2);
+			data = nanmean(buckleOutcome,2);
+
+			scatter(obj.parameterSet(:,7), obj.parameterSet(:,4), 250, data,'filled');
+            ax = gca;
+            ax.Color = 'black';
+			ax.FontSize = axisFontSize;
+			ylabel('Adhesion ($\kappa_{\textrm{Attract}}$)','Interpreter', 'latex', 'FontSize', labelFontSize);
+			xlabel('Perimeter energy ($\beta_S$)','Interpreter', 'latex', 'FontSize', labelFontSize);
+			% title(sprintf('Proportion buckled'),'Interpreter', 'latex', 'FontSize', 28);
+			axis equal;
+            ylim([min(obj.b)-1, max(obj.b)+1]);
+			xlim([min(obj.spe)-1, max(obj.spe)+1]);
+			set(ax, 'XTick', 0:2:max(obj.spe));
+			set(ax, 'XTickLabel', 0:2:max(obj.spe));
+			c = colorbar;
+			c.Label.String = 'Proportion buckled';
+			c.Label.Interpreter = 'latex';
+			c.Label.FontSize = titleFontSize;
+            c.TickLabelInterpreter = 'latex';
+            ax.TickLabelInterpreter = 'latex';
+            caxis([0 1]);
+			colormap jet;
+
+			c = ax.Color;
+
+			set(h, 'InvertHardcopy', 'off')
+			set(h,'color','w');
+
+			SavePlot(obj, h, sprintf('PerimVSAdhesion'));
+
+
+			stromaRatioAtBuckle = obj.result{3};
+
+			h = figure;
+
+			data = nanmean(stromaRatioAtBuckle,2);
+
+			scatter(obj.parameterSet(:,7), obj.parameterSet(:,4), 250, [0.125,0.125,0.125], 'filled');
+			hold on
+			scatter(obj.parameterSet(:,7), obj.parameterSet(:,4), 250, data,'filled');
+			ax = gca;
+            ax.Color = 'black';
+			ax.FontSize = axisFontSize;
+            ylabel('Adhesion ($\kappa_{\textrm{Attract}}$)','Interpreter', 'latex', 'FontSize', labelFontSize);
+			xlabel('Perimeter energy ($\beta_S$)','Interpreter', 'latex', 'FontSize', labelFontSize);
+			% title(sprintf('Average $r_s$ at buckle'),'Interpreter', 'latex', 'FontSize', titleFontSize);
+			axis equal;
+            ylim([min(obj.b)-1, max(obj.b)+1]);
+			xlim([min(obj.spe)-1, max(obj.spe)+1]);
+			set(ax, 'XTick', 0:2:max(obj.spe));
+			set(ax, 'XTickLabel', 0:2:max(obj.spe));
+			c = colorbar;
+			c.Label.String = 'Average $r_s$ at buckle';
+			c.Label.Interpreter = 'latex';
+			c.Label.FontSize = titleFontSize;
+            c.TickLabelInterpreter = 'latex';
+            ax.TickLabelInterpreter = 'latex'; 
+            caxis([1 1.05]);
+			colormap jet;
+			c = ax.Color;
+
+			set(h, 'InvertHardcopy', 'off')
+			set(h,'color','w');
+
+			SavePlot(obj, h, sprintf('BucklingMode'));
+
+
+
+		end
+
+	end
+
+end