Construct ternary grid, evaluate a function on the grid and contour plot in Matlab - matlab

I need to evaluate a function (say)
Fxy = 2*x.^2 +3 *y.^2;
on a ternary grid x-range (0 - 1), y-range (0-1) and 1-x-y (0 - 1).
I am unable to construct the ternary grid on which I need to evaluate the above function. Also, once evaluated I need to plot the function in a ternary contour plot. Ideally, I need the axes to go counter clockwise in the sense (x -> y--> (1-x-y)).
I have tried the function
function tg = triangle_grid ( n, t )
ng = ( ( n + 1 ) * ( n + 2 ) ) / 2;
tg = zeros ( 2, ng );
p = 0;
for i = 0 : n
for j = 0 : n - i
k = n - i - j;
p = p + 1;
tg(1:2,p) = ( i * t(1:2,1) + j * t(1:2,2) + k * t(1:2,3) ) / n;
end
end
return
end
for the number of sub intervals between the triangle edge coordinates
n = 10 (say)
and for the edge coordinates of an equilateral triangle
t = tcoord = [0.0, 0.5, 1.0;
0.0, 1.0*sqrt(3)/2, 0.0];
This generated a triangular grid with the x-axis from 0-1 but the other two are not from 0-1.
I need something like this:
... with the axes range 0-1 (0-100 would also do).
In addition, I need to know the coordinate points for all intersections within the triangular grid. Once I have this I can proceed to evaluate the function in this grid.
My final aim is to get something like this. This is a better representation of what I need to achieve (as compared to the previous plot which I have now removed)
Note that the two ternary plots have iso-value contours which are different in in magnitude. In my case the difference is an order of magnitude, two very different Fxy's.
If I can plot the two ternary plots on top of each other then and evaluate the compositions at the intersection of two iso-value contours on the ternary plane. The compositions should be as read from the ternary plot and not the rectangular grid on which triangle is defined.
Currently there are issues (as highlighted in the comments section, will update this once the problem is closer to solution).

I am the author of ternplot. As you have correctly surmised, ternpcolor does not do what you want, as it is built to grid data automatically. In retrospect, this was not a particularly wise decision, I've made a note to change the design. In the mean time this code should do what you want:
EDIT: I've changed the code to find the intersection of two curves rather than just one.
N = 10;
x = linspace(0, 1, N);
y = x;
% The grid intersections on your diagram are actually rectangularly arranged,
% so meshgrid will build the intersections for us
[xx, yy] = meshgrid(x, y);
zz = 1 - (xx + yy);
% now that we've got the intersections, we can evaluate the function
f1 = #(x, y) 2*x.^2 + 3*y.^2 + 0.1;
Fxy1 = f1(xx, yy);
Fxy1(xx + yy > 1) = nan;
f2 = #(x, y) 3*x.^2 + 2*y.^2;
Fxy2 = f2(xx, yy);
Fxy2(xx + yy > 1) = nan;
f3 = #(x, y) (3*x.^2 + 2*y.^2) * 1000; % different order of magnitude
Fxy3 = f3(xx, yy);
Fxy3(xx + yy > 1) = nan;
subplot(1, 2, 1)
% This constructs the ternary axes
ternaxes(5);
% These are the coordinates of the compositions mapped to plot coordinates
[xg, yg] = terncoords(xx, yy);
% simpletri constructs the correct triangles
tri = simpletri(N);
hold on
% and now we can plot
trisurf(tri, xg, yg, Fxy1);
trisurf(tri, xg, yg, Fxy2);
hold off
view([137.5, 30]);
subplot(1, 2, 2);
ternaxes(5)
% Here we plot the line of intersection of the two functions
contour(xg, yg, Fxy1 - Fxy2, [0 0], 'r')
axis equal
EDIT 2: If you want to find the point of intersection between two contours, you are effectively solving two simultaneous equations. This bit of extra code will solve that for you (notice I've used some anonymous functions in the code above now, as well):
f1level = 1;
f3level = 1000;
intersection = fsolve(#(v) [f1(v(1), v(2)) - f1level; f3(v(1), v(2)) - f3level], [0.5, 0.4]);
% if you don't have the optimization toolbox, this command works almost as well
intersection = fminsearch(#(v) sum([f1(v(1), v(2)) - f1level; f3(v(1), v(2)) - f3level].^2), [0.5, 0.4]);
ternaxes(5)
hold on
contour(xg, yg, Fxy1, [f1level f1level]);
contour(xg, yg, Fxy3, [f3level f3level]);
ternplot(intersection(1), intersection(2), 1 - sum(intersection), 'r.');
hold off

I have played a bit with the file exchange submission https://www.mathworks.com/matlabcentral/fileexchange/2299-alchemyst-ternplot.
if you just do this:
[x,y]=meshgrid(0:0.1:1);
Fxy = 2*x.^2 +3 *y.^2;
ternpcolor(x(:),y(:),Fxy(:))
You get:
The thirds axis is created exactly as you say (1-x-y) inside the ternpcolor function. There are lots of things to "tune" here but I hope it is enough to get you started.

Here is a solution using R and my package ggtern. I have also included the points within proximity underneath, for the purpose of comparison.
library(ggtern)
Fxy = function(x,y){ 2*x^2 + 3*y^2 }
x = y = seq(0,1,length.out = 100)
df = expand.grid(x=x,y=y);
df$z = 1 - df$x - df$y
df = subset(df,z >= 0)
df$value = Fxy(df$x,df$y)
#The Intended Breaks
breaks = pretty(df$value,n=10)
#Create subset of the data, within close proximity to the breaks
df.sub = ldply(breaks,function(b,proximity = 0.02){
s = b - abs(proximity)/2; f = b + abs(proximity)/2
subset(df,value >= s & value <= f)
})
#Plot the ternary diagram
ggtern(df,aes(x,y,z)) +
theme_bw() +
geom_point(data=df.sub,alpha=0.5,color='red',shape=21) +
geom_interpolate_tern(aes(value = value,color=..level..), size = 1, n = 200,
breaks = c(breaks,max(df$value) - 0.01,min(df$value) + 0.01),
base = 'identity',
formula = value ~ poly(x,y,degree=2)) +
labs(title = "Contour Plot on Modelled Surface", x = "Left",y="Top",z="Right")
Which produces the following:

Related

Matlab: Extract values that I plot but which has not been stored

I have a mathematical function E which I want to minimize. I get from solving this 16 possible solutions x1, x2, ..., x16, only two of which that actually minimize the function (located at a minimum). Using a for loop, I can then plug all of these 16 solutions into the original function, and select the solutions I need by applying some criteria via if statements (plotting E vs E(x) if x is real and positive, if first derivative of E is below a threshold, and if the second derivative of E is positive).
That way I only plot the solutions I'm interested in. However, I would now like to extract the relevant x that I plot. Here's a sample MATLAB code that plots the way I just described. I want to extract the thetas that I actually end up plotting. How to do that?
format long
theta_s = 0.77944100;
sigma = 0.50659500;
Delta = 0.52687700;
%% Defining the coefficients of the 4th degree polynomial
alpha = cos(2*theta_s);
beta = sin(2*theta_s);
gamma = 2*Delta^2/sigma^2;
a = -gamma^2 - beta^2*Delta^2 - alpha^2*Delta^2 + 2*alpha*Delta*gamma;
b = 2*alpha*gamma - 2*Delta*gamma - 2*alpha^2*Delta + 2*alpha*Delta^2 -...
2*beta^2*Delta;
c = 2*gamma^2 - 2*alpha*Delta*gamma - 2*gamma - alpha^2 + 4*alpha*Delta +...
beta^2*Delta^2 - beta^2 - Delta^2;
d = -2*alpha*gamma + 2*Delta*gamma + 2*alpha + 2*beta^2*Delta - 2*Delta;
e = beta^2 - gamma^2 + 2*gamma - 1;
%% Solve the polynomial numerically.
P = [a b c d e];
R = roots(P);
%% Solve r = cos(2x) for x: x = n*pi +- 1/2 * acos(r). Using n = 0 and 1.
theta = [1/2.*acos(R) -1/2.*acos(R) pi+1/2.*acos(R) pi-1/2.*acos(R)];
figure;
hold on;
x = 0:1/1000:2*pi;
y_1 = sigma*cos(x - theta_s) + sqrt(1 + Delta*cos(2*x));
y_2 = sigma*cos(x - theta_s) - sqrt(1 + Delta*cos(2*x));
plot(x,y_1,'black');
plot(x,y_2,'black');
grid on;
%% Plot theta if real, if positive, if 1st derivative is ~zero, and if 2nd derivative is positive
for j=1:numel(theta);
A = isreal(theta(j));
x_j = theta(j);
y_j = sigma*cos(x_j - theta_s) + sqrt(1 + Delta*cos(2*x_j));
FirstDer = sigma* sin(theta(j) - theta_s) + Delta*sin(2*theta(j))/...
sqrt(1 + Delta*cos(2*theta(j)));
SecDer = -sigma*cos(theta(j)-theta_s) - 2*Delta*cos(2*theta(j))/...
(1 + Delta*cos(2*theta(j)))^(1/2) - Delta^2 * (sin(2*theta(j)))^2/...
(1 + Delta*cos(2*theta(j)))^(3/2);
if A == 1 && x_j>=0 && FirstDer < 1E-7 && SecDer > 0
plot(x_j,y_j,['o','blue'])
end
end
After you finish all plotting, get the axes handle:
ax = gca;
then write:
X = get(ax.Children,{'XData'});
And X will be cell array of all the x-axis values from all lines in the graph. One cell for each line.
For the code above:
X =
[1.961054062875753]
[4.514533853417446]
[1x6284 double]
[1x6284 double]
(First, the code all worked. Thanks for the effort there.)
There are options here. A are couple below
Record the values as you generate them
Within the "success" if statement, simply record the values. See edits to your code below.
This would always be the preferred option for me, it just seems much more efficient.
xyResults = zeros(0,2); %%% INITIALIZE HERE
for j=1:numel(theta);
A = isreal(theta(j));
x_j = theta(j);
y_j = sigma*cos(x_j - theta_s) + sqrt(1 + Delta*cos(2*x_j));
FirstDer = sigma* sin(theta(j) - theta_s) + Delta*sin(2*theta(j))/...
sqrt(1 + Delta*cos(2*theta(j)));
SecDer = -sigma*cos(theta(j)-theta_s) - 2*Delta*cos(2*theta(j))/...
(1 + Delta*cos(2*theta(j)))^(1/2) - Delta^2 * (sin(2*theta(j)))^2/...
(1 + Delta*cos(2*theta(j)))^(3/2);
if A == 1 && x_j>=0 && FirstDer < 1E-7 && SecDer > 0
xyResults(end+1,:) = [x_j y_j]; %%%% RECORD HERE
plot(x_j,y_j,['o','blue'])
end
end
Get the result from the graphics objects
You can get the data you want from the actual graphics objects. This would be the option if there was just no way to capture the data as it was generated.
%First find the objects witht the data you want
% (Ideally you could record handles to the lines as you generated
% them above. But then you could also simply record the answer, so
% let's assume that direct record is not possible.)
% (BTW, 'findobj' is an underused, powerful function.)
h = findobj(0,'Marker','o','Color','b','type','line')
%Then get the `xdata` filed from each
capturedXdata = get(h,'XData');
capturedXdata =
2×1 cell array
[1.96105406287575]
[4.51453385341745]
%Then get the `ydata` filed from each
capturedYdata = get(h,'YData');
capturedYdata =
2×1 cell array
[1.96105406287575]
[4.51453385341745]

Plotting a 2d vector on 3d axes in matlab

I have three vectors x,y,t. For each combination x,y,t there is a (u,v) value associated with it. How to plot this in matlab? Actually I'm trying to plot the solution of 2d hyperbolic equation
vt = A1vx + A2vy where A1 and A2 are 2*2 matrices and v is a 2*1 vector. I was trying scatter3 and quiver3 but being new to matlab I'm not able to represent the solution correctly.
In the below code I have plot at only a particular time-level. How to show the complete solution in just one plot? Any help?
A1 = [5/3 2/3; 1/3 4/3];
A2 = [-1 -2; -1 0];
M = 10;
N = 40;
delta_x = 1/M;
delta_y = delta_x;
delta_t = 1/N;
x_points = 0:delta_x:1;
y_points = 0:delta_y:1;
t_points = 0:delta_t:1;
u = zeros(M+1,M+1,N+1,2);
for i=1:M+1,
for j=1:M+1,
u(i,j,1,1) = (sin(pi*x_points(i)))*sin(2*pi*y_points(j)) ;
u(i,j,1,2) = cos(2*pi*x_points(i));
end
end
for j=1:M+1,
for t=1:N+1,
u(M+1,j,t,1) = sin(2*t);
u(M+1,j,t,2) = cos(2*t);
end
end
for i=1:M+1
for t=1:N+1
u(i,1,t,1) = sin(2*t);
u(i,M+1,t,2) = sin(5*t) ;
end
end
Rx = delta_t/delta_x;
Ry = delta_t/delta_y;
for t=2:N+1
v = zeros(M+1,M+1,2);
for i=2:M,
for j=2:M,
A = [(u(i+1,j,t-1,1) - u(i-1,j,t-1,1)) ; (u(i+1,j,t-1,2) - u(i-1,j,t-1,2))];
B = [(u(i+1,j,t-1,1) -2*u(i,j,t-1,1) +u(i-1,j,t-1,1)) ; (u(i+1,j,t-1,2) -2*u(i,j,t-1,2) +u(i-1,j,t-1,2))];
C = [u(i,j,t-1,1) ; u(i,j,t-1,2)];
v(i,j,:) = C + Rx*A1*A/2 + Rx*Rx*A1*A1*B/2;
end
end
for i=2:M,
for j=2:M,
A = [(v(i,j+1,1) - v(i,j-1,1)) ; (v(i,j+1,2) - v(i,j-1,2)) ];
B = [(v(i,j+1,1) - 2*v(i,j,1) +v(i,j-1,1)) ; (v(i,j+1,2) - 2*v(i,j,2) +v(i,j-1,2))];
C = [v(i,j,1) ; v(i,j,2)];
u(i,j,t,:) = C + Ry*A2*A/2 + Ry*Ry*A2*A2*B/2;
end
end
if j==2
u(i,1,t,2) = u(i,2,t,2);
end
if j==M
u(i,M+1,t,1) = u(i,M,t,1);
end
if i==2
u(1,j,t,:) = u(2,j,t,:) ;
end
end
time_level = 2;
quiver(x_points, y_points, u(:,:,time_level,1), u(:,:,time_level,2))
You can plot it in 3D, but personally I think it would be hard to make sense of.
There's a quiver3 equivalent for your plotting function. z-axis in this case would be time (say, equally spaced), and z components of the vectors would be zero. Unlike 2D version of this function, it does not support passing in coordinate vectors, so you need to create the grid explicitly using meshgrid:
sz = size(u);
[X, Y, Z] = meshgrid(x_points, y_points, 1:sz(3));
quiver3(X, Y, Z, u(:,:,:,1), u(:,:,:,2), zeros(sz(1:3)));
You may also color each timescale differently by plotting them one at a time, but it's still hard to make sense of the results:
figure(); hold('all');
for z = 1:sz(3)
[X, Y, Z] = meshgrid(x_points, y_points, z);
quiver3(X, Y, Z, u(:,:,z,1), u(:,:,z,2), zeros([sz(1:2),1]));
end

Non overlapping randomly located circles

I need to generate a fixed number of non-overlapping circles located randomly. I can display circles, in this case 20, located randomly with this piece of code,
for i =1:20
x=0 + (5+5)*rand(1)
y=0 + (5+5)*rand(1)
r=0.5
circle3(x,y,r)
hold on
end
however circles overlap and I would like to avoid this. This was achieved by previous users with Mathematica https://mathematica.stackexchange.com/questions/69649/generate-nonoverlapping-random-circles , but I am using MATLAB and I would like to stick to it.
For reproducibility, this is the function, circle3, I am using to draw the circles
function h = circle3(x,y,r)
d = r*2;
px = x-r;
py = y-r;
h = rectangle('Position',[px py d d],'Curvature',[1,1]);
daspect([1,1,1])
Thank you.
you can save a list of all the previously drawn circles. After
randomizing a new circle check that it doesn't intersects the previously drawn circles.
code example:
nCircles = 20;
circles = zeros(nCircles ,2);
r = 0.5;
for i=1:nCircles
%Flag which holds true whenever a new circle was found
newCircleFound = false;
%loop iteration which runs until finding a circle which doesnt intersect with previous ones
while ~newCircleFound
x = 0 + (5+5)*rand(1);
y = 0 + (5+5)*rand(1);
%calculates distances from previous drawn circles
prevCirclesY = circles(1:i-1,1);
prevCirclesX = circles(1:i-1,2);
distFromPrevCircles = ((prevCirclesX-x).^2+(prevCirclesY-y).^2).^0.5;
%if the distance is not to small - adds the new circle to the list
if i==1 || sum(distFromPrevCircles<=2*r)==0
newCircleFound = true;
circles(i,:) = [y x];
circle3(x,y,r)
end
end
hold on
end
*notice that if the amount of circles is too big relatively to the range in which the x and y coordinates are drawn from, the loop may run infinitely.
in order to avoid it - define this range accordingly (it can be defined as a function of nCircles).
If you're happy with brute-forcing, consider this solution:
N = 60; % number of circles
r = 0.5; % radius
newpt = #() rand([1,2]) * 10; % function to generate a new candidate point
xy = newpt(); % matrix to store XY coordinates
fails = 0; % to avoid looping forever
while size(xy,1) < N
% generate new point and test distance
pt = newpt();
if all(pdist2(xy, pt) > 2*r)
xy = [xy; pt]; % add it
fails = 0; % reset failure counter
else
% increase failure counter,
fails = fails + 1;
% give up if exceeded some threshold
if fails > 1000
error('this is taking too long...');
end
end
end
% plot
plot(xy(:,1), xy(:,2), 'x'), hold on
for i=1:size(xy,1)
circle3(xy(i,1), xy(i,2), r);
end
hold off
Slightly amended code #drorco to make sure exact number of circles I want are drawn
nCircles = 20;
circles = zeros(nCircles ,2);
r = 0.5;
c=0;
for i=1:nCircles
%Flag which holds true whenever a new circle was found
newCircleFound = false;
%loop iteration which runs until finding a circle which doesnt intersect with previous ones
while ~newCircleFound & c<=nCircles
x = 0 + (5+5)*rand(1);
y = 0 + (5+5)*rand(1);
%calculates distances from previous drawn circles
prevCirclesY = circles(1:i-1,1);
prevCirclesX = circles(1:i-1,2);
distFromPrevCircles = ((prevCirclesX-x).^2+(prevCirclesY-y).^2).^0.5;
%if the distance is not to small - adds the new circle to the list
if i==1 || sum(distFromPrevCircles<=2*r)==0
newCircleFound = true;
c=c+1
circles(i,:) = [y x];
circle3(x,y,r)
end
end
hold on
end
Although this is an old post, and because I faced the same problem before I would like to share my solution, which uses anonymous functions: https://github.com/davidnsousa/mcsd/blob/master/mcsd/cells.m . This code allows to create 1, 2 or 3-D cell environments from user-defined cell radii distributions. The purpose was to create a complex environment for monte-carlo simulations of diffusion in biological tissues: https://www.mathworks.com/matlabcentral/fileexchange/67903-davidnsousa-mcsd
A simpler but less flexible version of this code would be the simple case of a 2-D environment. The following creates a space distribution of N randomly positioned and non-overlapping circles with radius R and with minimum distance D from other cells. All packed in a square region of length S.
function C = cells(N, R, D, S)
C = #(x, y, r) 0;
for n=1:N
o = randi(S-R,1,2);
while C(o(1),o(2),2 * R + D) ~= 0
o = randi(S-R,1,2);
end
f = #(x, y) sqrt ((x - o(1)) ^ 2 + (y - o(2)) ^ 2);
c = #(x, y, r) f(x, y) .* (f(x, y) < r);
C = #(x, y, r) + C(x, y, r) + c(x, y, r);
end
C = #(x, y) + C(x, y, R);
end
where the return C is the combined anonymous functions of all circles. Although it is a brute force solution it is fast and elegant, I believe.

Matlab/CUDA: ocean wave simulation

I've studied "Simulating Ocean Water" article by Jerry Tessendorf and tried to program the Statistical Wave Model but I didn't get correct result and I don't understand why.
In my program I tried only to create a wave height field at time t = 0 without any further changes in time. After execution of my program I got not what I was expecting:
Here's my source code:
clear all; close all; clc;
rng(11); % setting seed for random numbers
meshSize = 64; % field size
windDir = [1, 0]; % ||windDir|| = 1
patchSize = 64;
A = 1e+4;
g = 9.81; % gravitational constant
windSpeed = 1e+2;
x1 = linspace(-10, 10, meshSize+1); x = x1(1:meshSize);
y1 = linspace(-10, 10, meshSize+1); y = y1(1:meshSize);
[X,Y] = meshgrid(x, y);
H0 = zeros(size(X)); % height field at time t = 0
for i = 1:meshSize
for j = 1:meshSize
kx = 2.0 * pi / patchSize * (-meshSize / 2.0 + x(i)); % = 2*pi*n / Lx
ky = 2.0 * pi / patchSize * (-meshSize / 2.0 + y(j)); % = 2*pi*m / Ly
P = phillips(kx, ky, windDir, windSpeed, A, g); % phillips spectrum
H0(i,j) = 1/sqrt(2) * (randn(1) + 1i * randn(1)) * sqrt(P);
end
end
H0 = H0 + conj(H0);
surf(X,Y,abs(ifft(H0)));
axis([-10 10 -10 10 -10 10]);
And the phillips function:
function P = phillips(kx, ky, windDir, windSpeed, A, g)
k_sq = kx^2 + ky^2;
L = windSpeed^2 / g;
k = [kx, ky] / sqrt(k_sq);
wk = k(1) * windDir(1) + k(2) * windDir(2);
P = A / k_sq^2 * exp(-1.0 / (k_sq * L^2)) * wk^2;
end
Is there any matlab ocean simulation source code which could help me to understand my mistakes? Fast google search didn't get any results.
Here's a "correct" result I got from "CUDA FFT Ocean Simulation". I didn't achieve this behavior in Matlab yet but I've ploted "surf" in matlab using data from "CUDA FFT Ocean Simulation". Here's what it looks like:
I've made an experiment and got an interesting result:
I've taken generated h0 from "CUDA FFT Ocean Simulation". So I have to do ifft to transform from frequency domain to spatial domain to plot the graph. I've done it for the same h0 using matlab ifft and using cufftExecC2C from CUDA library. Here's the result:
CUDA ifft:
Matlab ifft:
Either I don't understand some aspects of realization of cufftExecC2C or cufftExecC2C and matlab ifft are different algorithms with different results.
By the way parameters for generating such surface are:
meshSize = 32
A = 1e-7
patchSize = 80
windSpeed = 10
Well that was definitely a funny exercise. This is a completely rewritten answer since you found the issues you were asking about by yourself.
Instead of deleting my answer, there is still merit in posting to help you vectorize and/or explain a few bits of code.
I completely rewrote the GUI I gave in my former answer in order to incorporate your changes and add a couple of options. It started to grew arms and legs so I won't put the listing here but you can find the full file there:
ocean_simulator.m.
This is completely self contained and it includes all the calculating functions I vectorized and list separately below.
The GUI will allow you to play with the parameters, animate the waves, export GIF file (and a few other options like the "preset", but they are not too ironed out yet). A few examples of what you can achieve:
Basic
This is what you get with the quick default settings, and a couple of rendering options. This uses a small grid size and a fast time step, so it runs pretty quickly on any machine.
I am quite limited at home (Pentium E2200 32bit), so I could only practice with limited settings. The gui will run even with the settings maxed but it will become to slow to really enjoy.
However, with a quick run of ocean_simulator at work (I7 64 bit, 8 cores, 16GB ram, 2xSSD in Raid), it makes it much more fun! Here are a few examples:
Although done on a much better machine, I didn't use any parallel functionality nor any GPU calculations, so Matlab was only using a portion of these specs, which means it could probably run just as good on any 64bit system with decent RAM
Windy lake
This is a rather flat water surface like a lake. Even high winds do not produce high amplitude waves (but still a lot of mini wavelets). If you're a wind surfer looking at that from your window on top of the hill, your heart is going to skip a beat and your next move is to call Dave "Man! gear up. Meet you in five on the water!"
Swell
This is you looking from the bridge of your boat on the morning, after having battled with the storm all night. The storm has dissipated and the long large waves are the last witness of what was definitely a shaky night (people with sailing experience will know ...).
T-Storm
And this was what you were up to the night before...
second gif done at home, hence the lack of detail ... sorry
To the bottom:
Finally, the gui will let you add a patch around the water domain. In the gui it is transparent so you could add objects underwater or a nice ocean bottom. Unfortunately, the GIF format cannot include an alpha channel so no transparency here (but if you export in a video then you should be ok).
Moreover, the export to GIF degrade the image, the joint between the domain border and the water surface is flawless if you run that in Matlab. In some case it also make Matlab degrade the rendering of the lighting, so this is definitely not the best option for export, but it allows more things to play within matlab.
Now onto the code:
Instead of listing the full GUI, which would be super long (this post is long enough already), I will just list here the re-written version of your code, and explain the changes.
You should notice a massive increase of speed execution (orders of magnitude), thanks to the remaining vectorization, but mostly for two reasons:
(i) A lot of calculations were repeated. Caching values and reusing them is much faster than recalculating full matrices in loops (during the animation part).
(ii) Note how I defined the surface graphic object. It is defined only once (empty even), then all the further calls (in the loop) only update the underlying ZData of the surface object (instead of re-creating a surface object at each iteration.
Here goes:
%% // clear workspace
clear all; close all; clc;
%% // Default parameters
param.meshsize = 128 ; %// main grid size
param.patchsize = 200 ;
param.windSpeed = 100 ; %// what unit ? [m/s] ??
param.winddir = 90 ; %// Azimuth
param.rng = 13 ; %// setting seed for random numbers
param.A = 1e-7 ; %// Scaling factor
param.g = 9.81 ; %// gravitational constant
param.xLim = [-10 10] ; %// domain limits X
param.yLim = [-10 10] ; %// domain limits Y
param.zLim = [-1e-4 1e-4]*2 ;
gridSize = param.meshsize * [1 1] ;
%% // Define the grid X-Y domain
x = linspace( param.xLim(1) , param.xLim(2) , param.meshsize ) ;
y = linspace( param.yLim(1) , param.yLim(2) , param.meshsize ) ;
[X,Y] = meshgrid(x, y);
%% // get the grid parameters which remain constants (not time dependent)
[H0, W, Grid_Sign] = initialize_wave( param ) ;
%% // calculate wave at t0
t0 = 0 ;
Z = calc_wave( H0 , W , t0 , Grid_Sign ) ;
%% // populate the display panel
h.fig = figure('Color','w') ;
h.ax = handle(axes) ; %// create an empty axes that fills the figure
h.surf = handle( surf( NaN(2) ) ) ; %// create an empty "surface" object
%% // Display the initial wave surface
set( h.surf , 'XData',X , 'YData',Y , 'ZData',Z )
set( h.ax , 'XLim',param.xLim , 'YLim',param.yLim , 'ZLim',param.zLim )
%% // Change some rendering options
axis off %// make the axis grid and border invisible
shading interp %// improve shading (remove "faceted" effect)
blue = linspace(0.4, 1.0, 25).' ; cmap = [blue*0, blue*0, blue]; %'// create blue colormap
colormap(cmap)
%// configure lighting
h.light_handle = lightangle(-45,30) ; %// add a light source
set(h.surf,'FaceLighting','phong','AmbientStrength',.3,'DiffuseStrength',.8,'SpecularStrength',.9,'SpecularExponent',25,'BackFaceLighting','unlit')
%% // Animate
view(75,55) %// no need to reset the view inside the loop ;)
timeStep = 1./25 ;
nSteps = 2000 ;
for time = (1:nSteps)*timeStep
%// update wave surface
Z = calc_wave( H0,W,time,Grid_Sign ) ;
h.surf.ZData = Z ;
pause(0.001);
end
%% // This block of code is only if you want to generate a GIF file
%// be carefull on how many frames you put there, the size of the GIF can
%// quickly grow out of proportion ;)
nFrame = 55 ;
gifFileName = 'MyDancingWaves.gif' ;
view(-70,40)
clear im
f = getframe;
[im,map] = rgb2ind(f.cdata,256,'nodither');
im(1,1,1,20) = 0;
iframe = 0 ;
for time = (1:nFrame)*.5
%// update wave surface
Z = calc_wave( H0,W,time,Grid_Sign ) ;
h.surf.ZData = Z ;
pause(0.001);
f = getframe;
iframe= iframe+1 ;
im(:,:,1,iframe) = rgb2ind(f.cdata,map,'nodither');
end
imwrite(im,map,gifFileName,'DelayTime',0,'LoopCount',inf)
disp([num2str(nFrame) ' frames written in file: ' gifFileName])
You'll notice that I changed a few things, but I can assure you the calculations are exactly the same. This code calls a few subfunctions but they are all vectorized so if you want you can just copy/paste them here and run everything inline.
The first function called is initialize_wave.m
Everything calculated here will be constant later (it does not vary with time when you later animate the waves), so it made sense to put that into a block on it's own.
function [H0, W, Grid_Sign] = initialize_wave( param )
% function [H0, W, Grid_Sign] = initialize_wave( param )
%
% This function return the wave height coefficients H0 and W for the
% parameters given in input. These coefficients are constants for a given
% set of input parameters.
% Third output parameter is optional (easy to recalculate anyway)
rng(param.rng); %// setting seed for random numbers
gridSize = param.meshsize * [1 1] ;
meshLim = pi * param.meshsize / param.patchsize ;
N = linspace(-meshLim , meshLim , param.meshsize ) ;
M = linspace(-meshLim , meshLim , param.meshsize ) ;
[Kx,Ky] = meshgrid(N,M) ;
K = sqrt(Kx.^2 + Ky.^2); %// ||K||
W = sqrt(K .* param.g); %// deep water frequencies (empirical parameter)
[windx , windy] = pol2cart( deg2rad(param.winddir) , 1) ;
P = phillips(Kx, Ky, [windx , windy], param.windSpeed, param.A, param.g) ;
H0 = 1/sqrt(2) .* (randn(gridSize) + 1i .* randn(gridSize)) .* sqrt(P); % height field at time t = 0
if nargout == 3
Grid_Sign = signGrid( param.meshsize ) ;
end
Note that the initial winDir parameter is now expressed with a single scalar value representing the "azimuth" (in degrees) of the wind (anything from 0 to 360). It is later translated to its X and Y components thanks to the function pol2cart.
[windx , windy] = pol2cart( deg2rad(param.winddir) , 1) ;
This insure that the norm is always 1.
The function calls your problematic phillips.m separately, but as said before it works even fully vectorized so you can copy it back inline if you like. (don't worry I checked the results against your versions => strictly identical). Note that this function does not output complex numbers so there was no need to compare the imaginary parts.
function P = phillips(Kx, Ky, windDir, windSpeed, A, g)
%// The function now accept scalar, vector or full 2D grid matrix as input
K_sq = Kx.^2 + Ky.^2;
L = windSpeed.^2 ./ g;
k_norm = sqrt(K_sq) ;
WK = Kx./k_norm * windDir(1) + Ky./k_norm * windDir(2);
P = A ./ K_sq.^2 .* exp(-1.0 ./ (K_sq * L^2)) .* WK.^2 ;
P( K_sq==0 | WK<0 ) = 0 ;
end
The next function called by the main program is calc_wave.m. This function finishes the calculations of the wave field for a given time. It is definitely worth having that on its own because this is the mimimun set of calculations which will have to be repeated for each given time when you want to animate the waves.
function Z = calc_wave( H0,W,time,Grid_Sign )
% Z = calc_wave( H0,W,time,Grid_Sign )
%
% This function calculate the wave height based on the wave coefficients H0
% and W, for a given "time". Default time=0 if not supplied.
% Fourth output parameter is optional (easy to recalculate anyway)
% recalculate the grid sign if not supplied in input
if nargin < 4
Grid_Sign = signGrid( param.meshsize ) ;
end
% Assign time=0 if not specified in input
if nargin < 3 ; time = 0 ; end
wt = exp(1i .* W .* time ) ;
Ht = H0 .* wt + conj(rot90(H0,2)) .* conj(wt) ;
Z = real( ifft2(Ht) .* Grid_Sign ) ;
end
The last 3 lines of calculations require a bit of explanation as they received the biggest changes (all for the same result but a much better speed).
Your original line:
Ht = H0 .* exp(1i .* W .* (t * timeStep)) + conj(flip(flip(H0,1),2)) .* exp(-1i .* W .* (t * timeStep));
recalculate the same thing too many times to be efficient:
(t * timeStep) is calculated twice on the line, at each loop, while it is easy to get the proper time value for each line when time is initialised at the beginning of the loop for time = (1:nSteps)*timeStep.
Also note that exp(-1i .* W .* time) is the same than conj(exp(1i .* W .* time)). Instead of doing 2*m*n multiplications to calculate them each, it is faster to calculate one once, then use the conj() operation which is much faster.
So your single line would become:
wt = exp(1i .* W .* time ) ;
Ht = H0 .* wt + conj(flip(flip(H0,1),2)) .* conj(wt) ;
Last minor touch, flip(flip(H0,1),2)) can be replaced by rot90(H0,2) (also marginally faster).
Note that because the function calc_wave is going to be repeated extensively, it is definitely worth reducing the number of calculations (as we did above), but also by sending it the Grid_Sign parameter (instead of letting the function recalculate it every iteration). This is why:
Your mysterious function signCor(ifft2(Ht),meshSize)), simply reverse the sign of every other element of Ht. There is a faster way of achieving that: simply multiply Ht by a matrix the same size (Grid_Sign) which is a matrix of alternated +1 -1 ... and so on.
so signCor(ifft2(Ht),meshSize) becomes ifft2(Ht) .* Grid_Sign.
Since Grid_Sign is only dependent on the matrix size, it does not change for each time in the loop, you only calculate it once (before the loop) then use it as it is for every other iteration. It is calculated as follow (vectorized, so you can also put it inline in your code):
function sgn = signGrid(n)
% return a matrix the size of n with alternate sign for every indice
% ex: sgn = signGrid(3) ;
% sgn =
% -1 1 -1
% 1 -1 1
% -1 1 -1
[x,y] = meshgrid(1:n,1:n) ;
sgn = ones( n ) ;
sgn(mod(x+y,2)==0) = -1 ;
end
Lastly, you will notice a difference in how the grids [Kx,Ky] are defined between your version and this one. They do produce slightly different result, it's just a matter of choice.
To explain with a simple example, let's consider a small meshsize=5. Your way of doing things will split that into 5 values, equally spaced, like so:
Kx(first line)=[-1.5 -0.5 0.5 1.5 2.5] * 2 * pi / patchSize
while my way of producing the grid will produce equally spaced values, but also centered on the domain limits, like so:
Kx(first line)=[-2.50 -1.25 0.0 1.25 2.50] * 2 * pi / patchSize
It seems to respect more your comment % = 2*pi*n / Lx, -N/2 <= n < N/2 on the line where you define it.
I tend to prefer symmetric solutions (plus it is also slightly faster but it is only calculated once so it is not a big deal), so I used my vectorized way, but it is purely a matter of choice, you can definitely keep your way, it only ever so slightly "offset" the whole result matrix, but it doesn't perturbate the calculations per se.
last remains of the first answer
Side programming notes:
I detect you come from the C/C++ world or family. In Matlab you do not need to define decimal number with a coma (like 2.0, you used that for most of your numbers). Unless specifically defined otherwise, Matlab by default cast any number to double, which is a 64 bit floating point type. So writing 2 * pi is enough to get the maximum precision (Matlab won't cast pi as an integer ;-)), you do not need to write 2.0 * pi. Although it will still work if you don't want to change your habits.
Also, (one of the great benefit of Matlab), adding . before an operator usually mean "element-wise" operation. You can add (.+), substract (.-), multiply (.*), divide (./) full matrix element wise this way. This is how I got rid of all the loops in your code. This also work for the power operator: A.^2 will return a matrix the same size as A with every element squared.
Here's the working program.
First of all - source code:
clear all; close all; clc;
rng(13); % setting seed for random numbers
meshSize = 128; % field size
windDir = [0.1,1];
patchSize = 200;
A = 1e-7;
g = 9.81; % gravitational constant
windSpeed = 100;
timeStep = 1/25;
x1 = linspace(-10, 10, meshSize+1); x = x1(1:meshSize);
y1 = linspace(-10, 10, meshSize+1); y = y1(1:meshSize);
[X,Y] = meshgrid(x,y); % wave field
i = 1:meshSize; j = 1:meshSize; % indecies
[I,J] = meshgrid(i,j); % field of indecies
Kx = 2.0 * pi / patchSize * (-meshSize / 2.0 + I); % = 2*pi*n / Lx, -N/2 <= n < N/2
Ky = 2.0 * pi / patchSize * (-meshSize / 2.0 + J); % = 2*pi*m / Ly, -M/2 <= m < M/2
K = sqrt(Kx.^2 + Ky.^2); % ||K||
W = sqrt(K .* g); % deep water frequencies (empirical parameter)
P = zeros(size(X)); % Cant compute P without loops
for i = 1:meshSize
for j = 1:meshSize
P(i,j) = phillips(Kx(i,j), Ky(i,j), windDir, windSpeed, A, g); % phillips spectrum
end
end
H0 = 1/sqrt(2) .* (randn(size(X)) + 1i .* randn(size(X))) .* sqrt(P); % height field at time t = 0
rotate3d on;
for t = 1:10000 % 10000 * timeStep (sec)
Ht = H0 .* exp(1i .* W .* (t * timeStep)) + ...
conj(flip(flip(H0,1),2)) .* exp(-1i .* W .* (t * timeStep));
[az,el] = view;
surf(X,Y,real(signCor(ifft2(Ht),meshSize)));
axis([-10 10 -10 10 -1e-4 1e-4]); view(az,el);
blue = linspace(0.4, 1.0, 25)'; map = [blue*0, blue*0, blue];
%shading interp; % improve shading (remove "faceted" effect)
colormap(map);
pause(1/60);
end
phillips.m: (I've tried to vectorize the computation of Phillips spectrum but I faced with a difficulty which I'll show further)
function P = phillips(kx, ky, windDir, windSpeed, A, g)
k_sq = kx^2 + ky^2;
if k_sq == 0
P = 0;
else
L = windSpeed^2 / g;
k = [kx, ky] / sqrt(k_sq);
wk = k(1) * windDir(1) + k(2) * windDir(2);
P = A / k_sq^2 * exp(-1.0 / (k_sq * L^2)) * wk^2;
if wk < 0
P = 0;
end
end
end
signCor.m: (This function is an absolutely mystery for me... I've copied it from "CUDA FFT Ocean Simulation" realization. Simulation works much worse without it. And again I don't know how to vectorize this function.)
function H = signCor(H1, meshSize)
H = H1;
for i = 1:meshSize
for j = 1:meshSize
if mod(i+j,2) == 0
sign = -1; % works fine if we change signs vice versa
else
sign = 1;
end
H(i,j) = H1(i,j) * sign;
end
end
end
The biggest mistake that I've done is that I used ifft instead of using ifft2, that's why CUDA ifft and Matlab ifft didn't match.
My second mistake was in this lines of code:
kx = 2.0 * pi / patchSize * (-meshSize / 2.0 + x(i)); % = 2*pi*n / Lx
ky = 2.0 * pi / patchSize * (-meshSize / 2.0 + y(j)); % = 2*pi*m / Ly
I should've write:
kx = 2.0 * pi / patchSize * (-meshSize / 2.0 + i); % = 2*pi*n / Lx
ky = 2.0 * pi / patchSize * (-meshSize / 2.0 + j); % = 2*pi*m / Ly
I've played a bit with parameters A, meshSize, patchSize and I came to the conclusion that:
Somehow plausible parameter of wave amplitude is A * (patchSize / meshSize), where A is nothing but a scaling factor.
For 'calm' patchSize / meshSize <= 0.5.
For 'tsunami' patchSize / meshSize >= 3.0.
Difficulty with a vectorization of Phillips spectrum:
I have 2 functions:
% non-vectorized spectrum
function P = phillips1(kx, ky, windDir, windSpeed, A, g)
k_sq = kx^2 + ky^2;
if k_sq == 0
P = 0;
else
L = windSpeed^2 / g;
k = [kx, ky] / sqrt(k_sq);
wk = k(1) * windDir(1) + k(2) * windDir(2);
P = A / k_sq^2 * exp(-1.0 / (k_sq * L^2)) * wk^2;
if wk < 0
P = 0;
end
end
end
% vectorized spectrum
function P = phillips2(Kx, Ky, windDir, windSpeed, A, g)
K_sq = Kx .^ 2 + Ky .^ 2;
L = -g^2 / windSpeed^4;
WK = (Kx ./ K_sq) .* windDir(1) + (Ky ./ K_sq) .* windDir(2);
P = (A ./ (K_sq .^ 2)) .* ( exp(L ./ K_sq) .* (WK .^ 2) );
P(K_sq == 0) = 0;
P(WK < 0) = 0;
P(isinf(P)) = 0;
end
After I compute P1 using phillips1 and P2 using phillips2 I plot their difference:
subplot(2,1,1); surf(X,Y,real(P2-P1)); title('Difference in real part');
subplot(2,1,2); surf(X,Y,imag(P2-P1)); title('Difference in imaginary part');
It perfectly illustrates that there's a huge difference between this 2 spectrums in real part.

Matlab function that does (0:N-1)/N * M

I'd like to generate 20 uniformly spaced angles. Here are two not-so-neat solutions:
n = 20;
% unnecessary line
angles = linspace(0,2*pi,n+1);
angles = angles(1:end-1)
% intention unclear
angles = (0:n-1)/n * 2*pi
Is there a linspace-like function that does this in a better way?
linspace is written in Matlab (i.e. it's not a built-in function). You could easily modify its code so as not to generate the last element, and save that as another function.
In fact, if you see linspace's code you'll notice that the last element has to be appended specifically. So your hunch was right: it's more "natural" not to include the last element.
In the code below I include the modified three lines and the original ones to compare.
function y = linspace2(d1, d2, n)
if nargin == 2
n = 100;
end
n = double(n+1); %// modified line
%// Originally: n = double(n);
n1 = floor(n)-1;
vec = 0:n-2;
if isinf(d2 - d1)
y = d1 + (d2/n1).*vec - (d1/n1).*vec; %// modified line
%// Originally: y = [d1 + (d2/n1).*vec - (d1/n1).*vec, d2];
else
y = d1 + (vec.*(d2-d1)/n1); %// modified line
%// Originally: y = [d1 + (vec.*(d2-d1)/n1), d2];
end