Deformation gradient from points coordinates

Hello, I'm trying to evaluate the deformation gradient of a trasformation, as input I have only the points coordinates of the initial configuration and the final configuration. I tried to manually build the deformation gradient tensor evaluating the partial derivatives, but since I know only the value of the coordinates it's like if I try to derivate a costant so every partial derivative is zero. How can I do? I tried to use the function gradient, but right now it's not working cause maybe I'm making some mistakes. Thanks everybody.