k-Wave User Forum » Topic: error with kWaveDiffusion

k-Wave User Forum » Topic: error with kWaveDiffusion http://www.k-wave.org/forum/topic/error-with-kwavediffusion Support for the k-Wave MATLAB toolbox en-US Wed, 13 May 2026 08:12:04 +0000 http://bbpress.org/?v=1.0.2 <![CDATA[Search]]> q http://www.k-wave.org/forum/search.php Bradley Treeby on "error with kWaveDiffusion" http://www.k-wave.org/forum/topic/error-with-kwavediffusion#post-6830 Tue, 09 Apr 2019 09:21:59 +0000 Bradley Treeby 6830@http://www.k-wave.org/forum/ Hi cgenes, There seems to be two issues here. The first is a bug in k-Wave for plotting in 3D when the grid size has an odd number of grid points. To fix this, under the <code>plotTemp</code> method in <code>kWaveDiffusion</code> for <code>case 3</code>, replace with the following code: <pre><code>% plot temperature distribution in x-y plane subplot(2, 2, 1), if isnumeric(obj.plot_scale) imagesc(obj.y_vec .* obj.plot_axes_scale, obj.x_vec .* obj.plot_axes_scale, squeeze(obj.T(:, :, ceil(obj.Nz/2))), obj.plot_scale); else imagesc(obj.y_vec .* obj.plot_axes_scale, obj.x_vec .* obj.plot_axes_scale, squeeze(obj.T(:, :, ceil(obj.Nz/2)))); end axis image; % add plot labels title('x-y plane'); % plot temperature distribution in x-z plane subplot(2, 2, 2) if isnumeric(obj.plot_scale) imagesc(obj.z_vec .* obj.plot_axes_scale, obj.x_vec .* obj.plot_axes_scale, squeeze(obj.T(:, ceil(obj.Ny/2), :)), obj.plot_scale); else imagesc(obj.z_vec .* obj.plot_axes_scale, obj.x_vec .* obj.plot_axes_scale, squeeze(obj.T(:, ceil(obj.Ny/2), :))); end axis image; % add plot labels title('x-z plane'); xlabel(['(All axes in ' obj.plot_axes_prefix 'm)']); % plot temperature distribution in y-z plane subplot(2, 2, 3) if isnumeric(obj.plot_scale) imagesc(obj.z_vec .* obj.plot_axes_scale, obj.y_vec .* obj.plot_axes_scale, squeeze(obj.T(ceil(obj.Nx/2), :, :)), obj.plot_scale); else imagesc(obj.z_vec .* obj.plot_axes_scale, obj.y_vec .* obj.plot_axes_scale, squeeze(obj.T(ceil(obj.Nx/2), :, :))); end axis image; % add plot labels title('y-z plane'); % set colormap colormap(obj.color_map);</code></pre> The second issue is the error you see. I don't know what <code>absorbCube</code> is (or what it's dimensions are), but if I replace this line with: <code>source.Q = 1e7 * makeBall(201, 201, 201, 100, 100, 100, 20);</code> The code seems to run correctly (with the fix above). As a final note, it's generally advisable to chose grid sizes with small prime factors - the simulations will run much faster. If you run <code>factor(201)</code> you can see the largest prime factor is 67. If you run <code>checkFactors(200, 250)</code>, you can see that 192 or 216 are good numbers to choose. Hope that helps, Brad. cgenes on "error with kWaveDiffusion" http://www.k-wave.org/forum/topic/error-with-kwavediffusion#post-6826 Mon, 08 Apr 2019 14:27:08 +0000 cgenes 6826@http://www.k-wave.org/forum/ HI I'm not quite understudying something basic here as I'm getting this error (see below) I have a 201x201x201 matrix of values in W/m3 which I am trying to get it to calculate on. is I something wrong with my kgrid? Running k-Wave thermal simulation... start time: 08-Apr-2019 14:22:38 dt: 500ms, t_end: 150s, time steps: 300 input grid size: 202 by 202 by 202 grid points (20.2 by 20.2 by 20.2mm) Array dimensions must match for binary array op. Error in kWaveDiffusion/takeTimeStep (line 689) q_term = obj.diffusion_p1 .* obj.IT( kappa .* obj.FT( obj.Q ) ); Error in k_wave (line 61) kdiff.takeTimeStep(Nt, dt); the code I am running is here: % create the computational grid Nx = 201; % number of grid points in the x (row) direction Ny = 201; % number of grid points in the y (column) direction Nz = 201; dx = 1e-4; % grid point spacing in the x direction [m] dy = 1e-4; % grid point spacing in the y direction [m] dz = 1e-4; kgrid = kWaveGrid(Nx, dx, Ny, dy, Nz, dz); % define medium properties medium.density = 1079; % [kg/m^3] medium.thermal_conductivity = 0.52; % [W/(m.K)] medium.specific_heat = 3540; % [J/(kg.K)] % set Gaussian initial temperature distribution [degC] % width = 4 * dx; % source.T0 = 37 + 5 .* exp( -(kgrid.x ./ width).^2 - (kgrid.y ./width).^2 ); T0 = 37 .* ones(201, 201, 201); T0(:, 120:201, :) = 20 ; source.T0 = T0; source.Q = absorbCube; % set input args input_args = {'PlotScale', [37, 50]}; % create kWaveDiffusion object kdiff = kWaveDiffusion(kgrid, medium, source, [], input_args{:}); % % take time steps (temperature can be accessed as kdiff.T) Nt = 300; dt = 0.5; kdiff.takeTimeStep(Nt, dt); % % % % plot the current temperature field figure; kdiff.plotTemp;