Updated the phonopy parser to the right commit-tmk

The heat capacity was erroneously reported for the smaller base system cell size. Now it is correctly reported per the supercell that is referenced by the section_single_configuration_calculation.

Wrapped reference resolution with exception catching to  avoid issues when running in test environment which does not have access to referenced calculations.

Automatized changes to license and copyright information

See merge request !1

program_name
program_version
configuration_periodic_dimensions
single_configuration_calculation_to_system_ref
single_configuration_to_calculation_method_ref

And free energy is now given per atom not per cell