Hi Nicola,
try to change following statement in the script '(16,0) CNT STD.py':
# Repeat the configuration 3 times in each direction
bulk_configuration = configuration.repeat(1, 1, 3)
to
# Repeat the configuration 3 times in each direction
bulk_configuration = configuration.repeat(1, 1, 1)
the bulk configuration used in the SpecialThermalDisplacement class should be consistent with the that used in the script '(16,0) Carbon Nanotube DynMat.py', not with the number of repetitions used in the dynamical matrix class.
Best,
Daniele