[Phonopy-users] RV: Nanoribbon primitive axis (--pa)
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From: Pablo Á. Z. <pab...@ho...> - 2017-08-28 11:47:48
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Hello everyone, I am trying to compute the thermal conductivity using pwscf interface of a graphene nanoribbon. Thus, i have calculated the forces using phono3py propperly, replicating periodicaly the system in the x direction, while setting a vaccum space along y and z directions. My input system is a 80 atoms slab with the width I want in the y direction, while as i said, it is replicated along the x axis in the calculation in QE, so i selected the 1x1x1 supercell, since the system is a supercell itself. The problem I would like to ask is when calculating the thermal conductivity using this command: phono3py --pwscf --dim="1 1 1" -c input.in --pa="..." \ --mesh="3 1 1" --fc3 --fc2 --br which --pa option (primitive axis) should i set? As i understand from this debate: https://sourceforge.net/p/phonopy/mailman/message/32790661/ , and from every example in <https://github.com/atztogo/phono3py/> https://github.com/atztogo/phono3py/, this numbers represent the matrix (Mp) which link the vectors used in the unit cell (set by POSCAR), with those of the primitive cell: u_primitive=u_poscar·Mp (https://atztogo.github.io/phonopy/setting-tags.html). Since the primitive cell of graphene is already know : a( sqrt(3)/2, 1/2 ,0 ); a( sqrt(3)/2, -1/2,0 ), a=2.46 Angs, I can easily calculate Mp values. However, if i use phonopy -c --pwscf input.in --symmetry the primitive axis in the pposcar output file which phonopy seems to find for my system are completely different!: (4.2614 0 0 ; 0 10.0033 0 ; 0 0 35.01172) Thus, the question is, which primitive axis (--pa option) should i use? These are the cell parameters used in input.in which provide a vaccum space between y and z replicated slabs: CELL_PARAMETERS {bohr} 16.10586 0.000 0.000 0.000 66.16257 0.000 0.000 0.000 18.90359 Thank you for your patience! |