I am not sure if you tried typing your code in, or pasted your code. The format of your For statement is wrong and in the second statement you are using j and i both which if it worked would be incrementing j until i is = 9 which would cause your stackoverflow. something like this simple console program example should work. Also the only way your above code will compile is if you have Option Strict Off, do yourself a favor and place Option Strict On at the top of your Class, it will prevent implicit narrowing conversions and save you a lot of grief.
Option Strict On
Module Module1
Dim atomcode(,) As Integer
Sub Main()
ReDim atomcode(12, 9)
For i As Integer = 0 To 12
For j As Integer = 0 To 9
atomcode(i, j) = (i * 10000 + j * 1000 + 99)
Next j
Next i
End Sub
End Module