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It’s not directly possible to draw a Gaussian shape. Since it’s driven by an equation, what you can do is define a script that would place “atom” objects at the points defined by your shape. If you have enough objects, the approximation by this discretization is in the same order of magnitude of the approximation of the FDTD algorithm and so there is no loss of information.
We can give you hand if needed in defining your geometry if you use our trial version (OptiFDTD 12) or if you are under active subscription.