Others

OpenMX useful commands:

• 1. scf.restart on

  2. scf.fixed.grid  x  y  z  ( e.g. scf.fixed.grid 0 0 0 )

  3. scf.Kgrid  kx ky kz

  4. scf.energycutoff  500 # Ryd  /   scf.Ngrid nx ny nz

  5. HS.fileout on (for printing out *.scfout file)

  6. scf.SpinPolarization  NC  # On|Off|NC

  7. scf.SpinOrbit.Coupling  On  # On|Off, default=off

  8. level.of.stdout    1 # default=1 (1-3)

  9. level.of.fileout    0 # default=1 (0-2), no printing *.cube file -> 0

  10. DATA.PATH  /home/***/openmx/openmx3.9/DFT_DATA19

  11. Constraint for cell vectors

Quantum Espresso:

• Band structure calculation

• Phonon calculation:

  • Si example: (1) scf.in, (2) ph.in, (3) q2r.in, (4) matdyn.in - a, b, c, (5) *.plotband, (6) *.xmgr.gnuplot. 

  • Force constants for reference:

    • si.666.fc, diamond.101010.fc, graphene.999.fc.

    • with LO-TO splitting: sic.666.fc, gaas.444.fc.

• EPW

My Notes:

• Phonons: The unit of phonon frequency in phonopy code (or use --factor=xxx)

• BoltzTraP for OpenMX: Si example.

• OpenMX Modified Codes (3.8.5):

  1. Output accurate cell vectors: MD_pac.c (for 3.8.5) / MD_pac_PrintAccurateCoordinates.c (for 3.9.9), e.g. MD_pac.txt .

  2. Output accurate atomic fractional coordinates: Make_FracCoord.c, e.g. Make_FracCoord.txt .

  3. Output final atomic coordinates with 15 digits in *.md2 file: iterout.c .

  4. 1 Hartree = 27.2113845 eV in bandgnu13.c.

  5. Shift_K_Point = 0.000001 (i.e. 1e-6). A k-point is shifted about (+1e-6, -1e-6, +2e-6) automatically at each calculation.

  6. Overlap matrix in electric polarization expanded with high-order terms of Taylor series

  7. Phonon dispersion with LO-TO splitting (v3.7.10/v3.8.1/v3.8.3)

  8. Example - Band structure by DC-LNO method: (1) Si2-normal.dat, (2) Si2-LNO.dat, (3) Figure.

  9. Modify " bandgnu_20250217_YTLee.c " for plotting electronic band structure:

• OpenMX input files: ( YTL's Optimized Structure Database (*.dat) , GitHub )

  • Nomd calculation : Graphene.dat

  • Optimization : Graphene_opt.dat

  • Band structures : Graphene.dat

  • Density of States : Graphene.dat

  • Optical properties : Graphene_cddf.dat

  • Unfolding optical conductivity : Si2_1x1x1.dat, Si2_2x2x2.dat

• Codes for output files of unfolding optical conductivity in OpenMX:

  • Add column along k-paths: Add.c

    • Commands: (1) gcc Add.c -o Add , (2) ./add input_name output_name distance

  • Remove N-th rows whose value is below a criterion: Remove.c

    • Commands: (1) gcc Remove.c -o Remove , (2) ./remove input_name output_name criterion

  • GNUPLOT for an unfolded data

• Density Reader for OpenMX cube file or *.cube:

  • Example: Code, example.

  • Commands: (1) gcc DensityReader.c -o DensityReader , (2) ./DensityReader graphene.tden.cube 21 21 189

  • Unit of Density (*.cube) = electrons / a small unit cell, i.e. summation of density * volume / (x-grid*y-grid*z-grid) .

• Obtain STM images along a direction from  a *.cube file.

  • Example:

    1. Read a *.cube file to get 3D data, i.e. data[# of x-grid][# of y-grid][# of z-grid], and then print out data into a file.

    2. Draw a simulated STM image by using Gnuplot to plot 2D data[x-grid][y-grid] at a selected z-grid.

  • How to project parts of charge density of specific orbital(s) in selected atom(s) in the Tersoff-Hamann scheme in OpenMX-3.9.9 code?

• How to use "zheev" in LAPACK library for diagonalization? ( Example , Reference )

  • Command: gcc abc.c -o abc -lm -llapack  or  gcc ex_zheev.c -o ex_zheev -L/home/ytl/software/lapack-3.9.0 -llapack -lrefblas -ltmglib -lm -lgfortran

• How to use FFTW3 library: Example .

  • Command: gcc *.c -o * -lfftw3 -lm

• Anaconda Installation in macOS

Gnuplot sample:

set size ratio 1.5

set zeroaxis

set grid

set ylabel "Energy (eV)"

set xtics ("{/Symbol G}" 0, "M" 0.5774, "K" 0.9107, "{/Symbol G}" 1.5773, "A" 1.7145) out

set ytics 1 out

set mytics 2

set xrange [0:1.7145]

set yrange [-6:3]

FermiL = 9.1221

p '*.dat' u 1:($2-FermiL) w l lw 1 lc rgb "#0000ff" notitle

pause -1

# {/:Italic xxx} = make 'xxx' italic

Calculus and Technical Notes:

• • 1. Derivative of the Fermi-Dirac distribution

    2. Units of Thermal Electric Conductivity

    3. The sum rule of optical conductivity and its unit

    4. How to calculate distances of band dispersions in a crystal?

    5. Transform Cartesian to fractional coordinates in a unit cell , Example in  C

Simple Tools:

1. K to eV: KtoeV.py

2. Output strings: command lines ( by online python )

An  example:

for i in range(41,85,1):

    print("mpirun -np 8 /home/username/openmx/openmx3.9/source/openmx phonon_0"+(str)(i)+" > phonon_0"+(str)(i)+".log")