The code translated by Crop2ML in file layer_temp.f90 at layer_thickness2depth subroutine, produced an invalid statement for the layer_depth indexes. The index in Fortran should start in 1 and the math done creates always an index of 0.
Note that the Loop always starts count at 1 for z. See the code below.
layer_depth(z - 1+1) = sum(layer_thick(1 - 1:z))
New code:
layer_depth(z - 1+1) = sum(layer_thick(1:z))