phonon transport

This is the phonon transport part in SMEAGOL. --- Mar. 8, 2018 --- --- by Hao Wang ---

compile

The DFT part of SMEAGOL was written with Fortran. To reduce the coupling to the initial code and better encapsule , C++ was used to encode this part. Some characteristic of Fortran2003 and C++11 were used, especially in building the interface. The following compile labels are necessary in arch.make,

• CXX = g++ #(newer than 4.8)
• CCFLAGS = -Wall -Wextra -std=c++11
• LDFLAGS = $(FFLAGS) libstdc++.so.6.0.17 #(must newer than 17)

execute

• run script "run_phononTrans.sh slabel.fdf" to construct a huge non-peiordic super cell for lead

  • no further label is needed, the script will add them automatically
  • systemlabel.LeadInfo will be generate to contain calculating information
  • slabelFC.fdf then can be used as input file for smeagol

• run "pathforsmeagol/smeagol < slabelFC.fdf >slabelFc.out" for lead calculations

  • bulksgf.lft, bulksgf.rt will be generated. Copy them to the transport calculation directory.

• in transport directory,

  • MD.FCfirst 14
  • MD.FClast 28 should be added to boundary the central scattering region,

• run "run_phononTrans.sh slabel.fdf E" to construct supercell for transport calculation

  • generate systemlabel.EMInfo, slabelFC.fdf

• run "pathforsmeagol/smeagol < slabelFC.fdf >slabelFc.out" for transport calculations

  • generate:
    • systemlabel.PhTrc // transmission
    • systemlabel.THERMPH // thermal conductance
    • systemlabel.BulkDOS // system DOS before and after connecting molecules to leads
    • systemlabel.EigenMode // eigenmode and eigenvectors of local vibration
    • systemlabel.EigenChannel // Eigen conduction channel

• calulate decay rate of local vibration

  • copy systemlabel.EigenMode to lead directory and add vibDecayRate T to slabelFc.fdf and run smeagol
  • copy bulksgf.lft, bulksgf.rt to transport directory and add vibDecayRate T to slabelFc.fdf in transport directory and run smeagol
  • generate
    • systemlabel.EigenModeRate // decay rate of local vibration

• also, the demanding FC matrix calculations could also be performed with siesta, the label

  • MD.FCRead T
  • MD.FCAtomRestart 10000 should be added into the fdf file.

end