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Can you explain the difference between indices and coordinates? They are usually the same thing.

If you set one of the dimensions (z) to a constant value (5), there would be 40X40 values in the other two dimemsions

Once the data is loaded into the array, what does the program use it for?

Your code says that there are 3 two dim arrays in the three dim array. The first dim is for x,y,z
x,y and z each have a 2 dim array to hold their data.
What data is stored in those two dim...