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MAJOR corrections to scripts to extract densities

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This commit is contained in:
Karthik 2025-06-03 16:48:11 +02:00
parent 4416bc58b6
commit 63904f2a95
3 changed files with 293 additions and 111 deletions
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10
Dipolar-Gas-Simulator/+Scripts/extractAveragePeakColumnDensity.m
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@ -5,7 +5,15 @@ function [AveragePCD] = extractAveragePeakColumnDensity(folder_path, run_index,
format long format long
% Load data % Load data
Data = load(sprintf(horzcat(folder_path, '/Run_%03i/psi_gs.mat'),run_index),'psi','Params','Transf','Observ'); filePath = sprintf(horzcat(folder_path, '/Run_%03i/psi_gs.mat'), run_index);
try
Data = load(filePath, 'psi', 'Params', 'Transf', 'Observ');
catch ME
warning('Failed to load file: %s\n%s', filePath, ME.message);
AveragePCD = NaN;
return;
end
Params = Data.Params; Params = Data.Params;
Transf = Data.Transf; Transf = Data.Transf;

241
Dipolar-Gas-Simulator/+Scripts/extractAverageUnitCellDensity.m
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@ -1,96 +1,177 @@
function [UCD] = extractAverageUnitCellDensity(folder_path, run_index, radius, minPeakHeight, SuppressPlotFlag) function [UCD] = extractAverageUnitCellDensity(folder_path, run_index, radius, minPeakHeight, SuppressPlotFlag)
set(0,'defaulttextInterpreter','latex') set(0,'defaulttextInterpreter','latex')
set(groot, 'defaultAxesTickLabelInterpreter','latex'); set(groot, 'defaultLegendInterpreter','latex'); set(groot, 'defaultAxesTickLabelInterpreter','latex');
set(groot, 'defaultLegendInterpreter','latex');
format long
% Load data % Load data
Data = load(sprintf(horzcat(folder_path, '/Run_%03i/psi_gs.mat'),run_index),'psi','Params','Transf','Observ'); filePath = sprintf(horzcat(folder_path, '/Run_%03i/psi_gs.mat'), run_index);
try
Data = load(filePath, 'psi', 'Params', 'Transf', 'Observ');
catch ME
warning('Failed to load file: %s\n%s', filePath, ME.message);
UCD = NaN;
return;
end
Params = Data.Params; Params = Data.Params;
Transf = Data.Transf; Transf = Data.Transf;
Observ = Data.Observ; psi = gather(Data.psi);
if isgpuarray(Data.psi)
psi = gather(Data.psi);
else
psi = Data.psi;
end
if isgpuarray(Data.Observ.residual)
Observ.residual = gather(Data.Observ.residual);
else
Observ.residual = Data.Observ.residual;
end
% Axes scaling and coordinates in micrometers
x = Transf.x * Params.l0 * 1e6;
y = Transf.y * Params.l0 * 1e6;
z = Transf.z * Params.l0 * 1e6;
dz = z(2)-z(1);
% Compute probability density |psi|^2
n = abs(psi).^2;
nxy = squeeze(trapz(n*dz,3));
state = nxy';
peaks = extractPeaks(state, radius, minPeakHeight);
peakHeights = state(peaks);
[row, col] = find(peaks);
[~, maxIdx] = max(peakHeights);
MaxPeakLocation = [row(maxIdx), col(maxIdx)];
% Voronoi diagram of peak positions
points = [col, row]; % Voronoi uses [x, y]
[V, C] = voronoin(points);
% Voronoi cell of the max peak % Axes in micrometers
Vcell_indices = C{maxIdx}; x = Transf.x * Params.l0 * 1e6;
y = Transf.y * Params.l0 * 1e6;
% Plot the Voronoi cell z = Transf.z * Params.l0 * 1e6;
if all(Vcell_indices > 0) && all(Vcell_indices <= size(V, 1)) && ~any(isinf(V(Vcell_indices, 1))) dz = z(2) - z(1);
vx = interp1(1:numel(x), x, V(Vcell_indices,1), 'linear', 'extrap');
vy = interp1(1:numel(y), y, V(Vcell_indices,2), 'linear', 'extrap'); % Compute integrated density
% Close the polygon by repeating the first vertex n = abs(psi).^2;
vx(end+1) = vx(1); nxy = squeeze(trapz(n * dz, 3));
vy(end+1) = vy(1); state = nxy';
% Compute area of the Voronoi cell polygon using the shoelace formula
AreaOfVoronoiCell = polyarea(vx, vy); % Area of Voronoi cell around max peak in um^2 % Fourier spectrum for orientation detection
else F = fftshift(abs(fft2(state - mean(state(:)))));
warning('Voronoi cell for max peak is unbounded or invalid.'); [nx, ny] = size(state);
kx = linspace(-pi / (x(2) - x(1)), pi / (x(2) - x(1)), nx);
ky = linspace(-pi / (y(2) - y(1)), pi / (y(2) - y(1)), ny);
[KX, KY] = meshgrid(kx, ky);
theta = atan2(KY, KX);
% Remove center/DC
R = sqrt(KX.^2 + KY.^2);
F(R < 0.1 * max(kx(:))) = 0;
% Angular histogram of power spectrum
nbins = 180;
angles = linspace(-pi, pi, nbins);
powerAngular = zeros(1, nbins);
for k = 1:nbins-1
mask = theta >= angles(k) & theta < angles(k+1);
powerAngular(k) = sum(F(mask), 'all');
end end
powerAngular(end) = powerAngular(1); % wrap around
% Create grid points mesh
[X, Y] = meshgrid(x, y); % Note: size(X) and size(Y) match size(state)
% Determine points inside Voronoi polygon
inCellMask = inpolygon(X, Y, vx, vy);
% Sum all state values inside the Voronoi cell polygon
NumberOfParticlesInVoronoiCell = sum(state(inCellMask));
UCD = NumberOfParticlesInVoronoiCell / AreaOfVoronoiCell; % Anisotropy measure
peakRatio = max(powerAngular) / mean(powerAngular);
% Threshold to distinguish stripe vs droplet
isStripe = peakRatio > 20;
if ~isStripe
% === DROPLET MODE: Voronoi cell ===
peaks = extractPeaks(state, radius, minPeakHeight);
[row, col] = find(peaks);
peakHeights = state(peaks);
[~, maxIdx] = max(peakHeights);
MaxPeakLocation = [row(maxIdx), col(maxIdx)];
points = [col, row];
[V, C] = voronoin(points);
Vcell_indices = C{maxIdx};
if all(Vcell_indices > 0) && all(Vcell_indices <= size(V,1)) && ~any(isinf(V(Vcell_indices, 1)))
vx = interp1(1:numel(x), x, V(Vcell_indices,1), 'linear', 'extrap');
vy = interp1(1:numel(y), y, V(Vcell_indices,2), 'linear', 'extrap');
vx(end+1) = vx(1);
vy(end+1) = vy(1);
AreaOfVoronoiCell = polyarea(vx, vy);
[X, Y] = meshgrid(x, y);
inCellMask = inpolygon(X, Y, vx, vy);
NumberOfParticles = sum(state(inCellMask));
UCD = NumberOfParticles / AreaOfVoronoiCell;
else
warning('Voronoi cell for max peak is invalid.');
UCD = NaN;
end
else
% === STRIPE MODE: Use rectangular unit cell aligned with stripe direction ===
[~, idxMax] = max(F(:));
stripeAngle = theta(idxMax); % radians
% Rotate image to align stripes horizontally
rotatedState = imrotate(state, -rad2deg(stripeAngle), 'bilinear', 'crop');
% Estimate vertical stripe spacing (stripe-normal direction)
stripeProfileY = mean(rotatedState, 2) - mean(rotatedState(:));
fftY = abs(fft(stripeProfileY));
fftY(1:3) = 0;
[~, fyIdx] = max(fftY(1:floor(end/2)));
spacingY = round(numel(stripeProfileY) / fyIdx);
% Estimate horizontal spacing (along-stripe periodicity)
stripeProfileX = mean(rotatedState, 1) - mean(rotatedState(:));
fftX = abs(fft(stripeProfileX));
fftX(1:3) = 0;
[~, fxIdx] = max(fftX(1:floor(end/2)));
spacingX = round(numel(stripeProfileX) / fxIdx);
% Find stripe center (vertical)
[~, centerY] = max(stripeProfileY);
rowRange = max(1, centerY - round(0.5 * spacingY)) : ...
min(size(rotatedState,1), centerY + round(0.5 * spacingY));
% Find repeat center along stripe direction (horizontal)
[~, centerX] = max(stripeProfileX);
colRange = max(1, centerX - round(0.5 * spacingX)) : ...
min(size(rotatedState,2), centerX + round(0.5 * spacingX));
% Extract unit cell region
unitCellRegion = rotatedState(rowRange, colRange);
NumberOfParticles = sum(unitCellRegion(:));
AreaOfUnitCell = numel(unitCellRegion) * abs(x(2)-x(1)) * abs(y(2)-y(1));
UCD = NumberOfParticles / AreaOfUnitCell;
end
% Optional plot
if ~SuppressPlotFlag if ~SuppressPlotFlag
figure(1); figure(1);
clf clf
set(gcf,'Position', [100, 100, 900, 900]) set(gcf,'Position', [100, 100, 900, 900])
plotxy = pcolor(x,y,state); if ~isStripe
set(plotxy, 'EdgeColor', 'none'); plotxy = pcolor(x,y,state);
hold on; set(plotxy, 'EdgeColor', 'none');
plot(x(MaxPeakLocation(2)), y(MaxPeakLocation(1)), 'w+', 'MarkerSize', 8, 'LineWidth', 1.5); hold on;
plot(vx, vy, 'w-', 'LineWidth', 1.5); plot(vx, vy, 'w-', 'LineWidth', 2);
cbar1 = colorbar; cbar1 = colorbar;
cbar1.Label.Interpreter = 'latex'; cbar1.Label.Interpreter = 'latex';
% cbar1.Ticks = []; % Disable the ticks % cbar1.Ticks = []; % Disable the ticks
colormap(gca, Helper.Colormaps.plasma()) colormap(gca, Helper.Colormaps.plasma())
xlabel('$x$ ($\mu$m)', 'Interpreter', 'latex', 'FontSize', 16) xlabel('$x$ ($\mu$m)', 'Interpreter', 'latex', 'FontSize', 16)
ylabel('$y$ ($\mu$m)', 'Interpreter', 'latex', 'FontSize', 16) ylabel('$y$ ($\mu$m)', 'Interpreter', 'latex', 'FontSize', 16)
title(['UCD = ' num2str(UCD) ' \mum^{-2}'], ... title(['UCD = ' num2str(UCD) ' \mum^{-2}'], ...
'Interpreter', 'tex', 'FontSize', 16) 'Interpreter', 'tex', 'FontSize', 16)
set(gca, 'FontSize', 16); % For tick labels only set(gca, 'FontSize', 16); % For tick labels only
else
imagesc(rotatedState);
axis image;
cbar1 = colorbar;
cbar1.Label.Interpreter = 'latex';
colormap(gca, Helper.Colormaps.plasma())
xlabel('$y$ ($\mu$m)', 'Interpreter', 'latex', 'FontSize', 16)
ylabel('$x$ ($\mu$m)', 'Interpreter', 'latex', 'FontSize', 16)
% Title with UCD
title(['UCD = ' num2str(UCD, '%.3f') ' $\mu$m$^{-2}$'], ...
'Interpreter', 'latex', 'FontSize', 16)
% Highlight unit cell region
rectX = colRange(1) - 0.5;
rectY = rowRange(1) - 0.5;
rectW = length(colRange);
rectH = length(rowRange);
rectangle('Position', [rectX, rectY, rectW, rectH], ...
'EdgeColor', 'w', 'LineWidth', 2);
title(sprintf('UCD = %.4f $\\mu$m$^{-2}$', UCD), ...
'Interpreter', 'latex', 'FontSize', 16);
end
end end
end end
function [peaks_mask] = extractPeaks(image, radius, minPeakHeight) function [peaks_mask] = extractPeaks(image, radius, minPeakHeight)
peaks = imregionalmax(image); peaks = imregionalmax(image);

153
Dipolar-Gas-Simulator/+Scripts/run_locally.m
View File

@ -593,7 +593,7 @@ JobNumber = 0;
SuppressPlotFlag = false; SuppressPlotFlag = false;
AveragePCD = Scripts.extractAveragePeakColumnDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag); AveragePCD = Scripts.extractAveragePeakColumnDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
%% Extract average unit cell density %% Extract average unit cell density - Droplets
Radius = 2; % The radius within which peaks will be considered duplicates Radius = 2; % The radius within which peaks will be considered duplicates
PeakThreshold = 3E3; PeakThreshold = 3E3;
SaveDirectory = 'D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/HighN/aS_9.562000e+01_theta_000_phi_000_N_712500'; SaveDirectory = 'D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/HighN/aS_9.562000e+01_theta_000_phi_000_N_712500';
@ -601,6 +601,19 @@ JobNumber = 0;
SuppressPlotFlag = false; SuppressPlotFlag = false;
UCD = Scripts.extractAverageUnitCellDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag); UCD = Scripts.extractAverageUnitCellDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
%% Extract average unit cell density - Stripes
Radius = 2; % The radius within which peaks will be considered duplicates
PeakThreshold = 3E3;
SaveDirectory = 'D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/HighN/aS_9.562000e+01_theta_000_phi_000_N_1529167';
JobNumber = 0;
SuppressPlotFlag = false;
UCD = Scripts.extractAverageUnitCellDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
NUM_ATOMS_LIST = [100000 304167 508333 712500 916667 1120833 1325000 ...
1529167 1733333 1937500 2141667 2345833 2550000 2754167 ...
2958333 3162500 3366667 3570833 3775000 3979167 4183333 ...
4387500 4591667 4795833 5000000];
%% Plot number of droplets %% Plot number of droplets
% Parameters % Parameters
Radius = 2; Radius = 2;
@ -676,60 +689,140 @@ SuppressPlotFlag = true;
SCATTERING_LENGTH_RANGE = [95.62]; SCATTERING_LENGTH_RANGE = [95.62];
NUM_ATOMS_LIST = [50000 54545 59091 63636 68182 72727 77273 81818 86364 90909 95455 100000 304167 508333 712500 916667 1120833 1325000 ... NUM_ATOMS_LIST_FULL = [100000 304167 508333 712500 916667 1120833 1325000 1529167 1733333 1937500 2141667 2345833 2550000 2754167 2958333 3162500 3366667 3570833 3775000 3979167 4183333 4387500 4591667 4795833 5000000];
1529167 1733333 1937500 2141667 2345833 2550000 2754167 2958333 3162500 3366667 3570833 3775000 3979167 4183333 4387500 ...
4591667 4795833 5000000]; NUM_ATOMS_LIST_INSET = [50000 54545 59091 63636 68182 72727 77273 81818 86364 90909 95455];
% Prepare figure % Prepare figure
figure(1); figure(1);
clf; clf;
set(gcf,'Position', [100, 100, 1000, 700]); set(gcf,'Position', [100, 100, 1000, 700]);
hold on;
% Color order for better visibility % Color order
colors = lines(length(SCATTERING_LENGTH_RANGE)); colors = lines(length(SCATTERING_LENGTH_RANGE));
% Store legend labels % Store data for both sets
legendEntries = cell(1, length(SCATTERING_LENGTH_RANGE)); AverageCDs_full = zeros(length(SCATTERING_LENGTH_RANGE), length(NUM_ATOMS_LIST_FULL));
AverageCDs_inset = zeros(length(SCATTERING_LENGTH_RANGE), length(NUM_ATOMS_LIST_INSET));
% Main plot
main_ax = axes;
hold(main_ax, 'on');
% Loop over scattering lengths
for j = 1:length(SCATTERING_LENGTH_RANGE) for j = 1:length(SCATTERING_LENGTH_RANGE)
aS = SCATTERING_LENGTH_RANGE(j); aS = SCATTERING_LENGTH_RANGE(j);
% Format scattering length in scientific notation with 6 decimal places
aS_string = sprintf('%.6e', aS); aS_string = sprintf('%.6e', aS);
% Construct base directory for this aS baseDir = ['D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/HighN/aS_' ...
baseDir = ['D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/aS_' ...
aS_string '_theta_000_phi_000_N_']; aS_string '_theta_000_phi_000_N_'];
% Preallocate results for this curve % Full list
AverageCDs = zeros(size(NUM_ATOMS_LIST)); for i = 1:length(NUM_ATOMS_LIST_FULL)
N = NUM_ATOMS_LIST_FULL(i);
% Loop over all atom numbers
for i = 1:length(NUM_ATOMS_LIST)
N = NUM_ATOMS_LIST(i);
SaveDirectory = [baseDir num2str(N)]; SaveDirectory = [baseDir num2str(N)];
AverageCDs_full(j,i) = Scripts.extractAveragePeakColumnDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
% Call your droplet counting function
AverageCDs(i) = Scripts.extractAveragePeakColumnDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
end end
% Plot curve baseDir = ['D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/LowN/aS_' ...
plot(NUM_ATOMS_LIST, AverageCDs, 'o-', ... aS_string '_theta_000_phi_000_N_'];
'Color', colors(j, :), 'LineWidth', 1.5);
% Inset list
for i = 1:length(NUM_ATOMS_LIST_INSET)
N = NUM_ATOMS_LIST_INSET(i);
SaveDirectory = [baseDir num2str(N)];
AverageCDs_inset(j,i) = Scripts.extractAveragePeakColumnDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
end
% Store legend entry % Plot main curve
legendEntries{j} = ['a_s = ' num2str(aS) 'a_o']; x = NUM_ATOMS_LIST_FULL;
y = AverageCDs_full(j,:);
valid = ~isnan(y); % logical index of valid points
plot(main_ax,x(valid), y(valid), 'o-', ...
'Color', colors(j,:), 'LineWidth', 1.5);
end end
% Finalize plot
xlabel('Number of Atoms', 'Interpreter', 'tex', 'FontSize', 16); xlabel('Number of Atoms', 'Interpreter', 'tex', 'FontSize', 16);
ylabel('Average Peak Column Density', 'Interpreter', 'tex', 'FontSize', 16); ylabel('Average Peak Column Density', 'Interpreter', 'tex', 'FontSize', 16);
title(TitleString, 'Interpreter', 'tex', 'FontSize', 18); title(TitleString, 'Interpreter', 'tex', 'FontSize', 18);
legend(legendEntries, 'Interpreter', 'tex', 'FontSize', 12, 'Location', 'bestoutside'); legend(arrayfun(@(aS) sprintf('a_s = %.2f a_0', aS), SCATTERING_LENGTH_RANGE, ...
'UniformOutput', false), ...
'Interpreter', 'tex', 'FontSize', 12, 'Location', 'bestoutside');
grid(main_ax, 'on');
% Inset plot
inset_ax = axes('Position', [0.45 0.18 0.28 0.28]); % Normalized position [x y w h]
box(inset_ax, 'on');
hold(inset_ax, 'on');
for j = 1:length(SCATTERING_LENGTH_RANGE)
plot(inset_ax, NUM_ATOMS_LIST_INSET, AverageCDs_inset(j,:), 'o-', ...
'Color', colors(j,:), 'LineWidth', 1.2);
end
set(inset_ax, 'FontSize', 8);
title(inset_ax, 'Low-N', 'FontSize', 9);
grid(inset_ax, 'on');
xlabel(inset_ax, 'N', 'FontSize', 9);
ylabel(inset_ax, 'CD', 'FontSize', 9);
%% Plot average unit cell density
Radius = 2;
PeakThreshold = 3E3;
JobNumber = 0;
SuppressPlotFlag = true; % Suppress plots during batch processing
TitleString = "[ \omega_x, \omega_y, \omega_z ] = 2 \pi \times [ 50, 20, 150 ] Hz; \theta = 0^\circ";
SCATTERING_LENGTH_RANGE = [95.62];
NUM_ATOMS_LIST = [712500 916667 1120833 1325000 1529167 1733333 1937500 2141667 2345833 2550000 2754167 2958333 3162500 3366667 3570833];
UCD_values = zeros(length(SCATTERING_LENGTH_RANGE), length(NUM_ATOMS_LIST));
% Prepare figure
figure(1);
clf;
set(gcf,'Position', [100, 100, 1000, 700]);
hold on
% Color order
colors = lines(length(SCATTERING_LENGTH_RANGE));
for j = 1:length(SCATTERING_LENGTH_RANGE)
aS = SCATTERING_LENGTH_RANGE(j);
aS_string = sprintf('%.6e', aS);
baseDir = ['D:/Results - Numerics/Data_Full3D/PhaseDiagram/ImagTimePropagation/Theta0/HighN/aS_' ...
aS_string '_theta_000_phi_000_N_'];
for i = 1:length(NUM_ATOMS_LIST)
N = NUM_ATOMS_LIST(i);
% Construct folder path for this N
SaveDirectory = sprintf('%s%d', baseDir, N);
try
UCD_values(j,i) = Scripts.extractAverageUnitCellDensity(SaveDirectory, JobNumber, Radius, PeakThreshold, SuppressPlotFlag);
catch ME
warning('Error processing N=%d: %s', N, ME.message);
UCD_values(j,i) = NaN; % mark as NaN on error
end
end
x = NUM_ATOMS_LIST;
y = UCD_values(j,:);
valid = ~isnan(y); % logical index of valid points
plot(x(valid), y(valid), 'o-', 'Color', colors(j,:), 'LineWidth', 1.5);
end
xlabel('Number of Atoms', 'Interpreter', 'latex', 'FontSize', 16);
ylabel('Unit Cell Density (UCD) [$\mu m^{-2}$]', 'Interpreter', 'latex', 'FontSize', 16);
title(TitleString, 'Interpreter', 'tex', 'FontSize', 18);
legend(arrayfun(@(aS) sprintf('a_s = %.2f a_0', aS), SCATTERING_LENGTH_RANGE, ...
'UniformOutput', false), ...
'Interpreter', 'tex', 'FontSize', 12, 'Location', 'bestoutside');
set(gca, 'FontSize', 14);
grid on; grid on;
hold off;
%% Plot TF radii of unmodulated states %% Plot TF radii of unmodulated states
% Parameters % Parameters