PhonoKit

Phononic transmission calculation for different model configurations of electrodes and the scattering region.

Configuration

Input is YAML. The main config is plot/config_dat.yaml.

The CALCULATION block:

CALCULATION:
  
  sys_descr: &descr "SystemDescription"
  data_path: "PathToSave"

  full_output_path: !join ["C:/Users/sevke/Desktop/Dev/MA/phonokit/plot/new_paper_results/periodic", *descr]

  M_E: "Au"
  M_C: "Au"
  E: [0.001, 25]
  N: 7000
  T_min: 0.001
  T_max: 300
  kappa_grid_points: 1000
  T_kappa_c: 77

Behavior in code:

1. full_output_path is used as output directory if present.
2. Otherwise data_path is used.
3. !join is supported by a custom YAML loader in src/main.py.

Set up the system (example): Left electrode | Scattering region | Right electrode:

ELECTRODE_L:
  DebyeModel:
    enabled: false
    E_D: 80
    k_coupl_x: 900
    k_coupl_xy: 0
  Chain1D:
    enabled: false
    k_el_x: 14400
    k_coupl_x: 14400
    interaction_range: 1
    interact_potential: reciproke_squared
    atom_type: Au
    lattice_constant: 3.0
  Ribbon2D:
    enabled: false
    N_y: 3
    k_el_x: 900
    k_el_y: 900
    k_el_xy: 90
    k_coupl_x: 900
    k_coupl_xy: 90
    interaction_range: 1
    interact_potential: reciproke_squared
    atom_type: Au
    lattice_constant: 3.0
  AnalyticalFourier:
    enabled: false
    N_q: 50
    k_el_x: 900
    k_el_y: 18
    k_el_xy: 0
    k_coupl_x: 180
    k_coupl_xy: 0
    interaction_range: 1
    interact_potential: reciproke_squared
    atom_type: Au
    lattice_constant: 3.0
  DecimationFourier:
    enabled: true
    N_y: 101
    N_q: 50
    k_el_x: 900
    k_el_y: 900
    k_el_xy: 90
    k_coupl_x: 900
    k_coupl_xy: 90
    interaction_range: 1
    interact_potential: reciproke_squared
    atom_type: Au
    lattice_constant: 3.0

ELECTRODE_R:
  DebyeModel:
    enabled: false
    E_D: 80
    k_coupl_x: 900
    k_coupl_xy: 0
  Chain1D:
    enabled: false
    k_el_x: 14400
    k_coupl_x: 14400
    interaction_range: 1
    interact_potential: reciproke_squared
    atom_type: Au
    lattice_constant: 3.0
  Ribbon2D:
    enabled: false
    N_y: 3
    k_el_x: 900
    k_el_y: 900
    k_el_xy: 90
    k_coupl_x: 900
    k_coupl_xy: 90
    interaction_range: 1
    interact_potential: reciproke_squared
    atom_type: Au
    lattice_constant: 3.0
  AnalyticalFourier:
    enabled: false
    N_q: 50
    k_el_x: 900
    k_el_y: 18
    k_el_xy: 0
    k_coupl_x: 180
    k_coupl_xy: 0
    interaction_range: 1
    interact_potential: reciproke_squared
    atom_type: Au
    lattice_constant: 3.0
  DecimationFourier:
    enabled: true
    N_y: 101
    N_q: 50
    k_el_x: 900
    k_el_y: 900
    k_el_xy: 90
    k_coupl_x: 900
    k_coupl_xy: 90
    interaction_range: 1
    interact_potential: reciproke_squared
    atom_type: Au
    lattice_constant: 3.0

SCATTER:
  Chain1D:
    enabled: false
    N: 2
    k_c_x: 180
    lattice_constant: 3.0
    interaction_range: 1
    interact_potential: reciproke_squared
    atom_type: Au
  FiniteLattice2D:
    enabled: true
    N_y: 1
    N_x: 2
    k_c_x: 900
    k_c_y: 900
    k_c_xy: 90
    lattice_constant: 3.0
    interaction_range: 1
    interact_potential: reciproke_squared
    atom_type: Au

Run

python src/main.py plot/config_dat.yaml

Output Defaults

By default, only these outputs are written:

1. trans
2. trans_prob_matrices

All other outputs are default false and can be enabled via data_output.

Supported data_output keys:

1. write_trans (default true)
2. write_trans_prob_matrices (default true)
3. write_dos (default false)
4. write_trans_dos (default false)
5. write_kappa (default false)
6. write_greensf (default false)
7. write_bandstructure (default false)
8. plot_transmission (default false)
9. plot_dos (default false)

Compatibility:

1. calculate_bandstructure is still accepted and mapped to write_bandstructure.

Dependency installation

pip install -r requirements.txt

References

• "Highly efficient schemes for the calculation of bulk and surface Green functions", M P Lopez Sancho etal 1985 J.Phys.F:Met.Phys. 15 851
  DOI: 10.1088/0305-4608/15/4/009
• M. Bürkle, Thomas J. Hellmuth, F. Pauly, Y. Asai, First-principles calculation of the thermoelectric figure of merit for [2,2]paracyclophane-based single-molecule junctions, PHYSICAL REVIEW B 91, 165419 (2015)
  DOI: 10.1103/PhysRevB.91.165419
• Troels Markussen, Phonon interference effects in molecular junctions, J. Chem. Phys. 139, 244101 (2013)
  DOI: 10.1063/1.4849178