Phono3py

- A new option of `--cutoff_mfp` for including effective boundary mean free
path.
- The option name `--cutfc3` is changed to `--cutoff_fc3`.
- The option name `--cutpair` is changed to `--cutoff_pair`.
- A new option `--ga` is created.
- Fix spectrum plot of joint dos and imaginary part of self energy

- Different supercell size of fc2 from fc3 can be specified using `--dim_fc2`
option.
- `--isotope` option is implemented. This is used instead of `--mass_variances`
option without specifying the values. Mass variance parameters are read from
database.

- Phono3py python interface is rewritten and a lot of changes are introduced.
- `FORCES_SECOND` and `FORCES_THIRD` are no more used. Instead just one file of
`FORCES_FC3` is used. Now `FORCES_FC3` is generated by `--cf3` option and the
backward compatibility is simple:
`cat FORCES_SECOND FORCES_THIRD > FORCES_FC3`.
- `--multiple_sigmas` is removed. The same behavior is achieved by `--sigma`.

- `--q_direction` didn't work. Fix it.
- Implementation of tetrahedron method whcih is activated by `--thm`.
- Grid addresses are written out by `--wgp` option.

- Cut-off distance for fc3 is implemented. This is activated by `--cutfc3`
option. FC3 elements where any atomic pair has larger distance than cut-off
distance are set zero.
- `--cutpair` works only when creating displacements. The cut-off pair distance
is written into `disp_fc3.yaml` and FC3 is created from `FORCES_THIRD` with
this information. Usually sets of pair displacements are more redundant than
that needed for creating fc3 if index permutation symmetry is considered.
Therefore using index permutation symmetry, some elements of fc3 can be
recovered even if some of supercell force calculations are missing. In
paticular, all pair distances among triplet atoms are larger than cutoff pair
distance, any fc3 elements are not recovered, i.e., the element will be zero.

- Default displacement distance is changed to 0.03.
- Files names of displacement supercells now have 5 digits numbering,
`POSCAR-xxxxx`.
- Cutoff distance between pair displacements is implemented. This is triggered
by `--cutpair` option. This option works only for calculating atomic forces in
supercells with configurations of pairs of displacements.