By default, atomic masses are those that represent the normal isotopic mixture, so, for example, the atomic weight of chlorine is 35.45. If specific isotopes are needed, the isotopic mass would be given immediately after the atomic symbol. Thus if an atom in a molecule was a labeled C-13, then the symbol for the atom would be: C13.0034.
Because the three isotopes of hydrogen are so important, they have been given special symbols. If "heavy hydrogen" - deuterium - is wanted, then use the symbol "D", if tritium is wanted, use the symbol "T"
For example, the geometry specification for heavy water could be written as:
D
O 1.0 1
D 1.0 1 120 1 0 0 2 1
or as
H2.01355
O 1.0 1
H2.01355 1.0 1 120 1 0 0 2 1