MATLAB Programming/Debugging M Files
This section explains things you can do if you fix all the syntax errors (the ones that give you actual error messages), the program runs... but it gives you some result you don't want. Maybe it goes into an infinite loop, maybe it goes through the loop one too few or one too many times, maybe one of your "if" statements doesn't work, maybe the program is giving you "infinity" or "NaN" as an answer (which usually isn't very useful!)... there's as many things that can go wrong as there are lines in the code. Thankfully there are techniques for both fixing and improving on working MATLAB code.
Using MATLAB's Debugging tool
Using the Debugging Tool will let you stop your program in mid-execution to examine the contents of variables and other things which can help you find mistakes in your program.
M-file programs are stopped at "breakpoints". To create a breakpoint, simply press F12 and a red dot will appear next to the line where your cursor is. You can also click on the dash next to the line number on the left side of the M-file window to achieve the same result.
Then press F5 or Debug->Run from the menu to run the program. It will stop at the breakpoint with a green arrow next to it. You can then examine the contents of variables in the workspace, step, continue or stop your program using the Debug menu. To examine contents of a variable, simply type its name into the workspace, but be warned: you can only look at the values of variables in the file you stop in, so this means that you'll probably need multiple breakpoints to find the source of your problem.
There are several different ways you can move through the program from a breakpoint. One way is to go through the whole program, line by line, entering every function that is called. This is effective if you don't know where the problem is, but since it enters every function (including MATLAB functions like ode45), you may not desire to use it all the time. Thankfully, there's also a way to simply step through the function you're currently stopped in, one line at a time, and instead of going through the child functions line by line MATLAB will simply give you the results of those functions.
Finally, note that you cannot set a breakpoint until you save the M-file. If you change something, you must save before the breakpoint "notices" your changes. This situation is depicted in MATLAB by changing the dots from red to gray. Sometimes, you'll save but the dots will still be gray; this occurs when you have more than one breakpoint in multiple files. To get around this (which is really annoying), you have to keep going to "exit debug mode" until it turns gray. Once you're completely out of debug mode, your file will save and you'll be ready to start another round of debugging.
Using comments to help you debug code
If you want to test the effects of leaving out certain lines of code (to see, for example, if the program still returns Inf if you take them out), you can comment out the code. To do this, highlight it and then go to:
Text -> Comment
Or press CTRL+R. This will simply put a '%' in front of every line; if the line is already commented out it will put another '%' there so when you uncomment them the pattern of comment lines will not change. Commented lines will be ignored by the compiler, so the effect will be that the program is run without them.
To uncomment a line go to
Text -> Uncomment
Or press CTRL+T.
Another use of commenting is to test the difference between two different possible sets of code to do something (for example, you may want to test the effect of using ODE113 as opposed to ODE45 to solve a differential equation, so you'd have one line calling each). You can test the difference by commenting one out and running the program, then uncommenting that one and commenting the other one out, and calling the program again.
How to escape infinite loops
If your program is doing nothing for a long time, it may just be slow (MATLAB creates a lot of overhead and if you don't use arrays wisely it will go very, very slow) but if you are testing a small module, it is more likely that you have an infinite loop. Though MATLAB can't directly tell you you have an infinite loop, it does attempt to give you some hints. The first comes when you terminate the program. Terminate it by pressing CTRL+C and MATLAB will give you a message telling you exactly what line you stopped on. If your program is running a long time, it is likely the line you stopped in is in the middle of an infinite loop (though be warned, if the loop calls a sub-function, it is likely that you will stop in the sub-function and not the parent. Nevertheless, MATLAB also will tell you the lines of the parents too so you can track down the loop easily enough).
However, sometimes MATLAB won't even let you return to the main window to press CTRL-C. In this case you probably have to kill the whole MATLAB process. After this, add a "pause (0.001)" or a similarly small value in the loop you suspect to be the infinite one. Whenever MATLAB passes this instruction you will be able to interact with MATLAB for a (very) short time, e.g. go to the main window and press CTRL-C with MATLAB being able to respond to your command.