How can one calculate the index of a Fredholm operator numerically ?
In numerically calculations one uses always finte dimensional spaces. But linear operators on finite dimensional spaces have always index zero.
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The two key properties of the Fredholm index are
So you will now need to do something smarter. This is possible in many particular cases, for example for Toeplitz operators. The first property allows one to reduce the computation of the index to the computation of the winding number of a polynomial. Or the Atiyah--Singer index theorems reduces computing the index to some topological information ...
So to get a more meaningful answer, you will need to be more specific about the problem.