update for transport branch

[whzhangg]

Summary of main changes

parsephonon.cpp

• conductivity->fph_rta is removed, since it is now a internal variable of conductivity class
• accept len_boundary in &general, which take length in meter and give the value to conductivity->len_boundary

conductivity.cpp

• a new function define in conductivity to take the inverse from gamma to lifetime Conductivity::lifetime_from_gamma (double **lifetime, double **gamma)
• Gamma due to boundary scattering is given by Gamma_{total} = Gamma' + |v|/d, which is consistent with analyze_phonon.cpp
• the workflow of summing Gamma is changed, now isotope and boundary is summed with three-phonon first, if four-phonon is included, we take lifetime before summing the four-phonon contribution using lifetime_from_gamma and calculate kappa_3only. Then we sum the four-phonon contribution and calculate kappa

write_phonon.cpp

• write_kappa() is changed so that it write prefix.kl3 and prefix.kl4 if (conductivity→fph_rta > 0). The len_boundary is written to prefix.kl just as the case in analyze_phonon.cpp
• as a small fix, the kappa_coherent now write the whole thermal conductivity tensor, instead of just xx, yy and zz

[ttadano]

Thank you @whzhangg. Did you remove Makefile in the tools directory? If yes, can you add it again?

[whzhangg]

Hi, @ttadano, sorry, I modified the makefile when I compile, I have added it back