New App Added

-> Added N-Layer PES Intensity Modelling App.

MatBase-v1.0.1/N Layer PES Intensity Modelling/2-layer model/overlayer_calc.m

@@ -0,0 +1,25 @@
+function d_o = overlayer_calc(theta, C_m, imfp_m, I_m, C_o, imfp_o, I_o)
+% d_o = overlayer_calc(C_m, imfp_m, I_m, C_o, imfp_o, I_o)
+%   Function that determines the thickness of a uniform oxide-film on an
+%   oxidised metal surface. This is calculated from the relative
+%   photoelectron intensity of the oxidic or the metallic component, with
+%   respect to that of the corresponding oxide or clean metal, respectively.
+%   This model assumes that the underlying metallic layer is an infinitely
+%   thick slab, with a uniform oxide layer of thickness d_o on top.
+%
+%   IN:
+%   -   theta:      scalar of the photoelectron take-off angle.
+%   -   C_m:        scalar of the volume density of metal atoms in the metal [mole / cc].
+%   -   imfp_m:  	scalar of the imfp of electrons in the metal [nm].
+%   -   I_m:        scalar of the total peak area of the metal photoelectron peak.
+%   -   C_o:        scalar of the volume density of metal atoms in the oxide [mole / cc].
+%   -   imfp_o:   	scalar of the imfp of electrons in the oxide [nm].
+%   -   I_o:        scalar of the total peak area of the oxide photoelectron peak.
+%
+%   OUT:
+%   -   d_o:      	thickness of the oxide in nm.
+
+%% 1 : Determination of the oxide thickness
+d_o = imfp_o .* sin(deg2rad(theta)) .* log(1 + (C_m.*imfp_m.*I_o) ./ (C_o.*imfp_o.*I_m));
+
+end

MatBase-v1.0.1/N Layer PES Intensity Modelling/n-layer model/view_nlayer_pes_model.m

@@ -0,0 +1,36 @@
+function fig = view_nlayer_pes_model(pes_model, lyr_cols)
+% fig = view_nlayer_pes_model(pes_model)
+%   This function plots the solutions to the 'nlayer_pes_model()' function;
+%   the n-layered sample stack and the corresponding photoelectron
+%   contribution from each one of the layers. The user can input the colors
+%   for each one of the layers using the 'lyr_cols' argument; this is
+%   convenient when you want to color-match the schematic to your own
+%   drawings.
+%
+%   IN:
+%   -   pes_model:      data structure that contains all the pes model parameters and variables (from 'nlayer_pes_model()').
+%   -   lyr_cols:       Mx1 cell-vector of the [R,G,B] color of each independent layer.
+%
+%   OUT:
+%   -   fig:            MATLAB figure object with the ARPES data plotted.
+
+%% Default parameters
+def_cols = flipud(num2cell([0.25,0.25,0.25;lines(length(pes_model.lyr_mat)-1)], 2));
+% -- Defining the default parameters
+if nargin < 2; lyr_cols = def_cols; end
+if isempty(lyr_cols); lyr_cols = def_cols; end
+
+%% 1 - Plotting the the model solutions
+% -- Range of photon energies, but a single angle
+if length(pes_model.hv) > 1 && length(pes_model.theta) == 1
+    fig{1} = view_nlayer_pes_model_vs_hv(pes_model, lyr_cols);
+% -- Single photon energy, but a range of angles
+elseif length(pes_model.hv) == 1 && length(pes_model.theta) > 1
+    fig{1} = view_nlayer_pes_model_vs_theta(pes_model, lyr_cols);
+% -- Range of photon energies and angles
+elseif length(pes_model.hv) > 1 && length(pes_model.theta) > 1
+    fig{1} = view_nlayer_pes_model_vs_hv(pes_model, lyr_cols);
+    fig{2} = view_nlayer_pes_model_vs_theta(pes_model, lyr_cols);
+% -- Single values only
+else; fig{1} = view_nlayer_pes_model_vs_hv(pes_model, lyr_cols);
+end

MatBase-v1.0.1/N Layer PES Intensity Modelling/n-layer model/view_nlayer_pes_model_vs_hv.m

@@ -0,0 +1,124 @@
+function fig = view_nlayer_pes_model_vs_hv(pes_model, lyr_cols)
+% fig = view_nlayer_pes_model_vs_hv(pes_model, lyr_cols)
+%   This function plots the solutions to the 'nlayer_pes_model()' function;
+%   the n-layered sample stack and the corresponding photoelectron
+%   contribution from each one of the layers. The user can input the colors
+%   for each one of the layers using the 'lyr_cols' argument; this is
+%   convenient when you want to color-match the schematic to your own
+%   drawings.
+%
+%   IN:
+%   -   pes_model:      data structure that contains all the pes model parameters and variables (from 'nlayer_pes_model()').
+%   -   lyr_cols:       Mx1 cell-vector of the [R,G,B] color of each independent layer.
+%
+%   OUT:
+%   -   fig:            MATLAB figure object with the ARPES data plotted.
+
+%% Default parameters
+def_cols = flipud(num2cell([0.25,0.25,0.25;lines(length(pes_model.lyr_mat)-1)], 2));
+% -- Defining the default parameters
+if nargin < 2; lyr_cols = def_cols; end
+if isempty(lyr_cols); lyr_cols = def_cols; end
+
+%% 1 - Plotting the the model solutions
+fig = figure();
+fig.Position(3) = 900; 
+fig.Position(4) = 450;
+%% 1.1 - Plotting the intensity profiles for each layer
+subplot(1,3,1); hold on;
+x_width	= 5;
+bulk_thickness = 5;
+if pes_model.Nlyrs == 1
+    y_cum   = cell2mat(pes_model.lyr_thick);
+else
+    y_cum   = cumsum(cell2mat(pes_model.lyr_thick));
+    y_cum(isinf(y_cum)) = y_cum(end-1) + bulk_thickness;
+end
+% -- Plotting each layer from bottom-up
+for i = pes_model.Nlyrs:-1:1
+    patch([-1, -1, 1, 1, -1].*x_width, [0, y_cum(i), y_cum(i), 0, 0].*-1,...
+        lyr_cols{i}, 'edgecolor', [0 0 0]);
+end
+% -- Adding text for each material type
+for i = 1:pes_model.Nlyrs
+    if i == 1;  y_loc = 0 - 0.5*(y_cum(i) - 0);
+    else;       y_loc = -y_cum(i-1) - 0.5*(y_cum(i) - y_cum(i-1));
+    end
+    if i == pes_model.Nlyrs
+        text(0, y_loc, "(Bulk) "+string(pes_model.lyr_mat{i}),...
+        'color', 'k', 'horizontalalignment', 'center', 'verticalalignment', 'middle', 'FontWeight','bold', 'FontSize',10);
+    else
+        text(0, y_loc, sprintf("(Layer %i) ",i)+string(pes_model.lyr_mat{i}),...
+        'color', 'k', 'horizontalalignment', 'center', 'verticalalignment', 'middle', 'FontWeight','bold', 'FontSize',10);
+    end
+end
+% - Box Styling and Axis properties
+ylabel('Depth From Surface [nm]', 'fontweight', 'bold');
+title('Sample model stack');
+axis([-x_width, x_width, -1*max(y_cum(:)), 0]);
+% - Formatting the axes
+ax = gca;
+% Font properties
+ax.FontName         = 'Segoe UI'; 
+ax.FontWeight       = 'normal'; 
+ax.FontSize         = 10;
+% Tick properties
+ax.XMinorTick       = 'off'; 
+ax.YMinorTick       = 'off';
+ax.TickDir          = 'both';
+ax.XColor           = [0 0 0]; 
+ax.YColor           = [0 0 0];
+% Ruler properties
+ax.XAxisLocation    = 'bottom';             % 'bottom' | 'top' | 'origin'
+ax.YAxisLocation    = 'left';               % 'left' | 'right' | 'origin'
+% Box Styling properties
+ax.Color            = [1 1 1];
+ax.Box              = 'off';                % 'on' | 'off'
+ax.LineWidth        = 0.75;     
+ax.Layer            = 'Top';
+%% 4.2 - Plotting the intensity profiles for each layer
+subplot(1,3,[2,3]); hold on;
+% - Filing through each layer
+for i = 1:pes_model.Nlyrs
+    % -- If only one angle is given
+    if length(pes_model.theta) == 1
+        plot(pes_model.hv, pes_model.lyr_ints0{i}, 'k.-', 'color', lyr_cols{i}, 'markerfacecolor', lyr_cols{i}, 'linewidth', 2.5);
+    % -- If a range of angles are to be plotted
+    else
+        num_cols    = length(pes_model.theta);
+        start_col   = lyr_cols{i};
+        end_col     = lyr_cols{i} + 0.50*(1-lyr_cols{i});
+        colors_p = [linspace(start_col(1),end_col(1),num_cols)', linspace(start_col(2),end_col(2),num_cols)', linspace(start_col(3),end_col(3),num_cols)'];
+        for j = 1:length(pes_model.theta)
+            plot(pes_model.hv, pes_model.lyr_ints0{i}(j,:), 'k.-', 'color', colors_p(j,:), 'markerfacecolor', colors_p(j,:), 'linewidth', 2.5);
+        end
+    end
+    leg_labels{i}   = string(pes_model.lyr_mat{i})+"("+string(pes_model.lyr_cls{i})+")";
+    leg_cols{i}     = plot(nan, 'k.-', 'color', lyr_cols{i}, 'markerfacecolor', lyr_cols{i}, 'linewidth', 2.5);
+end
+% -- Formatting the axes
+legend([leg_cols{:}], leg_labels, 'location', 'best');
+title('Photoelectron intensities vs photon energy');
+xlabel('Photon energy [eV]', 'Interpreter', 'none', 'FontWeight', 'bold');
+ylabel('Relative Contribution', 'Interpreter', 'none', 'FontWeight', 'bold');
+ylim([0, 1.00]);
+% - Formatting the axes
+ax = gca;
+% Font properties
+ax.FontName         = 'Segoe UI'; 
+ax.FontWeight       = 'normal'; 
+ax.FontSize         = 10;
+% Tick properties
+ax.XMinorTick       = 'off'; 
+ax.YMinorTick       = 'off';
+ax.TickDir          = 'both';
+ax.XColor           = [0 0 0]; 
+ax.YColor           = [0 0 0];
+% Ruler properties
+ax.XAxisLocation    = 'bottom';             % 'bottom' | 'top' | 'origin'
+ax.YAxisLocation    = 'right';               % 'left' | 'right' | 'origin'
+% Box Styling properties
+ax.Color            = [1 1 1];
+ax.Box              = 'off';                % 'on' | 'off'
+ax.LineWidth        = 0.75;     
+ax.Layer            = 'Top';

MatBase-v1.0.1/N Layer PES Intensity Modelling/n-layer model/view_nlayer_pes_model_vs_theta.m

@@ -0,0 +1,125 @@
+function fig = view_nlayer_pes_model_vs_theta(pes_model, lyr_cols)
+% fig = view_nlayer_pes_model_vs_theta(pes_model, lyr_cols)
+%   This function plots the solutions to the 'nlayer_pes_model()' function;
+%   the n-layered sample stack and the corresponding photoelectron
+%   contribution from each one of the layers. The user can input the colors
+%   for each one of the layers using the 'lyr_cols' argument; this is
+%   convenient when you want to color-match the schematic to your own
+%   drawings.
+%
+%   IN:
+%   -   pes_model:      data structure that contains all the pes model parameters and variables (from 'nlayer_pes_model()').
+%   -   lyr_cols:       Mx1 cell-vector of the [R,G,B] color of each independent layer.
+%
+%   OUT:
+%   -   fig:            MATLAB figure object with the ARPES data plotted.
+
+%% Default parameters
+def_cols = flipud(num2cell([0.25,0.25,0.25;lines(length(pes_model.lyr_mat)-1)], 2));
+% -- Defining the default parameters
+if nargin < 2; lyr_cols = def_cols; end
+if isempty(lyr_cols); lyr_cols = def_cols; end
+
+%% 1 - Plotting the the model solutions
+fig = figure();
+fig.Position(3) = 900; 
+fig.Position(4) = 450;
+%% 1.1 - Plotting the intensity profiles for each layer
+subplot(1,3,1); hold on;
+x_width	= 5;
+bulk_thickness = 5;
+if pes_model.Nlyrs == 1
+    y_cum   = cell2mat(pes_model.lyr_thick);
+else
+    y_cum   = cumsum(cell2mat(pes_model.lyr_thick));
+    y_cum(isinf(y_cum)) = y_cum(end-1) + bulk_thickness;
+end
+% -- Plotting each layer from bottom-up
+for i = pes_model.Nlyrs:-1:1
+    patch([-1, -1, 1, 1, -1].*x_width, [0, y_cum(i), y_cum(i), 0, 0].*-1,...
+        lyr_cols{i}, 'edgecolor', [0 0 0]);
+end
+% -- Adding text for each material type
+for i = 1:pes_model.Nlyrs
+    if i == 1;  y_loc = 0 - 0.5*(y_cum(i) - 0);
+    else;       y_loc = -y_cum(i-1) - 0.5*(y_cum(i) - y_cum(i-1));
+    end
+    if i == pes_model.Nlyrs
+        text(0, y_loc, "(Bulk) "+string(pes_model.lyr_mat{i}),...
+        'color', 'k', 'horizontalalignment', 'center', 'verticalalignment', 'middle', 'FontWeight','bold', 'FontSize',10);
+    else
+        text(0, y_loc, sprintf("(Layer %i) ",i)+string(pes_model.lyr_mat{i}),...
+        'color', 'k', 'horizontalalignment', 'center', 'verticalalignment', 'middle', 'FontWeight','bold', 'FontSize',10);
+    end
+end
+% - Box Styling and Axis properties
+ylabel('Depth From Surface [nm]', 'fontweight', 'bold');
+title('Sample model stack');
+axis([-x_width, x_width, -1*max(y_cum(:)), 0]);
+% - Formatting the axes
+ax = gca;
+% Font properties
+ax.FontName         = 'Segoe UI'; 
+ax.FontWeight       = 'normal'; 
+ax.FontSize         = 10;
+% Tick properties
+ax.XMinorTick       = 'off'; 
+ax.YMinorTick       = 'off';
+ax.TickDir          = 'both';
+ax.XColor           = [0 0 0]; 
+ax.YColor           = [0 0 0];
+% Ruler properties
+ax.XAxisLocation    = 'bottom';             % 'bottom' | 'top' | 'origin'
+ax.YAxisLocation    = 'left';               % 'left' | 'right' | 'origin'
+% Box Styling properties
+ax.Color            = [1 1 1];
+ax.Box              = 'off';                % 'on' | 'off'
+ax.LineWidth        = 0.75;     
+ax.Layer            = 'Top';
+%% 4.2 - Plotting the intensity profiles for each layer
+subplot(1,3,[2,3]); hold on;
+% - Filing through each layer
+for i = 1:pes_model.Nlyrs
+    % -- If only one photon energy is given
+    if length(pes_model.hv) == 1
+        plot(pes_model.theta, pes_model.lyr_ints0{i}, 'k.-', 'color', lyr_cols{i}, 'markerfacecolor', lyr_cols{i}, 'linewidth', 2.5);
+    % -- If a range of angles are to be plotted
+    else
+        num_cols    = length(pes_model.hv);
+        start_col   = lyr_cols{i};
+        end_col     = lyr_cols{i} + 0.50*(1-lyr_cols{i});
+        colors_p = [linspace(start_col(1),end_col(1),num_cols)', linspace(start_col(2),end_col(2),num_cols)', linspace(start_col(3),end_col(3),num_cols)'];
+        for j = 1:length(pes_model.hv)
+            plot(pes_model.theta, pes_model.lyr_ints0{i}(:,j), 'k.-', 'color', colors_p(j,:), 'markerfacecolor', colors_p(j,:), 'linewidth', 2.5);
+        end
+    end
+    leg_labels{i}   = string(pes_model.lyr_mat{i})+"("+string(pes_model.lyr_cls{i})+")";
+    leg_cols{i}     = plot(nan, 'k.-', 'color', lyr_cols{i}, 'markerfacecolor', lyr_cols{i}, 'linewidth', 2.5);
+end
+% -- Formatting the axes
+legend([leg_cols{:}], leg_labels, 'location', 'best');
+title('Photoelectron intensities vs theta');
+xlabel('Emission Angle [deg.]', 'Interpreter', 'none', 'FontWeight', 'bold');
+ylabel('Relative Contribution', 'Interpreter', 'none', 'FontWeight', 'bold');
+xlim([0, 90]);
+ylim([0, 1.00]);
+% - Formatting the axes
+ax = gca;
+% Font properties
+ax.FontName         = 'Segoe UI'; 
+ax.FontWeight       = 'normal'; 
+ax.FontSize         = 10;
+% Tick properties
+ax.XMinorTick       = 'off'; 
+ax.YMinorTick       = 'off';
+ax.TickDir          = 'both';
+ax.XColor           = [0 0 0]; 
+ax.YColor           = [0 0 0];
+% Ruler properties
+ax.XAxisLocation    = 'bottom';             % 'bottom' | 'top' | 'origin'
+ax.YAxisLocation    = 'right';               % 'left' | 'right' | 'origin'
+% Box Styling properties
+ax.Color            = [1 1 1];
+ax.Box              = 'off';                % 'on' | 'off'
+ax.LineWidth        = 0.75;     
+ax.Layer            = 'Top';