Output files

Taking the previously mentioned Option_file example and POSCAR example of Cu(111) surface, examples of the InterPhon output are shown below.

Outputs of Pre-process

Usage:

$ interphon -enlarge "4 4 1" -pbc "1 1 0"

pre_process.yaml (Pre-process record file)

- unit_cell_file: POSCAR  # This is input file of Pre-process
- supercell_file: SUPERCELL  # This is output file of Pre-process
- displaced_supercell_files: POSCAR-{0001..}  # This is output file of Pre-process
- dft_code: vasp
- point_group: 3m
- user_arguments:
  - displacement: 0.02
  - enlargement: 4 4 1
  - periodicity: 1 1 0
- unit_cell:
  - lattice_matrix:
      a1: 2.5712952614000000,   0.0000000000000000,   0.0000000000000000
      a2: 1.2856476307000000,   2.2268070170000001,   0.0000000000000000
      a3: 0.0000000000000000,   0.0000000000000000,  27.7901687622000004
  - num_atom: 7
  - selected_atom_index: 4, 5, 6
  - atoms:
    - index: 0
      position: 0.0000000000000000,   0.0000000000000000,   6.2983610850000522
      selection: false
      type: Cu
    - index: 1
      position: 2.5712951080000064,   1.4845379229999942,   8.3978147800000702
      selection: false
      type: Cu
    - index: 2
      position: 1.2856475539999939,   0.7422689609999932,  10.4987696089513474
      selection: false
      type: Cu
    - index: 3
      position: 0.0000000000000000,   0.0000000000000000,  12.6063618648222011
      selection: false
      type: Cu
    - index: 4
      position: 2.5712951080000064,   1.4845379229999942,  14.7139551036653078
      selection: true
      type: Cu
    - index: 5
      position: 1.2856475539999939,   0.7422689609999932,  16.8159162965492293
      selection: true
      type: Cu
    - index: 6
      position: 0.0000000000000000,   0.0000000000000000,  18.9003445564971102
      selection: true
      type: Cu

Outputs of Post-process

Usage:

$ interphon FORCE-0*/vasprun.xml -kdos KPOINTS_dos -thermal -kband KPOINTS_band -mode -option Option_file

Note

In the Post-process, the first 4 lines of the Option_file example are not needed, since the Basic option tags are automatically read from pre_process.yaml.

1. post_process.yaml (Post-process record file)

- files:
  - unit_cell_file: POSCAR
  - super_cell_file: SUPERCELL
  - k_point_file_dos: KPOINTS_dos
  - k_point_file_band: KPOINTS_band
  - force_file:
    - FORCE-0001\vasprun.xml
    - FORCE-0002\vasprun.xml
    - FORCE-0003\vasprun.xml
    - FORCE-0004\vasprun.xml
    - FORCE-0005\vasprun.xml
    - FORCE-0006\vasprun.xml
- dft_code: vasp
- user_arguments:
  - displacement: 0.02
  - enlargement: 4 4 1
  - periodicity: 1 1 0
- dos_arguments:
  - flag: true
  - sigma: 0.1
  - num_dos: 1000
  - color: black
  - option: stack
  - orientation: horizontal
  - legend_loc: best
  - atom:
    - - 6
    - - 5
      - 4
  - legend:
    - 1st layer
    - 2nd + 3rd layer
  - elimit:
    - -1
    - 8
- thermal_arguments:
  - flag: true
  - temp: range(0, 1000, 10)
  - legend_loc: best
- band_arguments:
  - flag: true
  - color: tab:orange
  - option: projection
  - bar_loc: right
  - bar_label: 1st layer
  - k_label:
    - G
    - M
    - K
    - G
  - atom:
    - 6
  - elimit:
- mode_arguments:
    flag: true
    index:
    - 0
    k_point:
    - 0.0
    - 0.0
    - 0.0

2. dos.png along with total_dos.dat and projected_dos.dat

2.1. OPTION_DOS = stack:

2.2. OPTION_DOS = line:

2.3. OPTION_DOS = plain:

3. thermal_properties.png along with thermal_properties.dat

4. band.png along with band.dat

4.1. OPTION_BAND = projection:

4.2. OPTION_BAND = plain:

5. band_dos.png

6. ASE Visualization of Trajectory along with XDATCAR

XDATCAR file is the general output of molecular dynamics and the file format can be visualized directly by VMD.