QE_tutorial/Au のバックアップ(No.3) - 第一原理分子動力学プログラム STATE Senri Wiki

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QE_tutorial/Au へ行く。
- 1 (2019-01-09 (水) 09:25:18)
- 2 (2019-01-09 (水) 11:58:46)
- 3 (2019-01-31 (木) 00:00:08)
- 4 (2019-02-04 (月) 13:06:33)
- 5 (2019-11-28 (木) 12:19:14)
- 6 (2019-12-03 (火) 17:20:49)
- 7 (2023-01-23 (月) 11:56:57)

Gold †

In this tutorial how to draw a band structure is described by taking gold (Au) in the face centered cubic structure as an example

↑

SCF calculation †

First, perform an SCF calculation to get the charge density.

Input file: au_scf.in

&control
   calculation='scf'
   restart_mode='from_scratch',
   pseudo_dir = '/home/ikutaro/QE/pseudo/'
   outdir='./tmp'
   prefix='au'
   tprnfor = .true.
   tstress = .true.
   forc_conv_thr = 1.d-4
   nstep=10000
/
&system
   ibrav = 2
   A     = 4.00
   !A     = 4.079
   nat   = 1
   ntyp  = 1
   ecutwfc = 40.0
   ecutrho = 400.0
   occupations='smearing'
   smearing='mp'
   degauss=0.01
   nbnd=24
   !input_dft='vdW-DF2-B86R'
   !assume_isolated = 'esm', esm_bc='bc1'
/
&electrons
   diagonalization='cg'
   conv_thr = 1.0e-12
   mixing_beta = 0.1
/
&ions
 ion_dynamics='bfgs'
/
&cell
 cell_dynamics='bfgs'
/
ATOMIC_SPECIES
 Au 0.0000 au_pbe_v1.uspp.F.UPF
ATOMIC_POSITIONS (crystal)
Au      0.000000000000      0.000000000000      0.00000000000
K_POINTS (automatic)
16 16 16 0 0 0

Execution
```
mpirun -np 8 < au_scf.in > au_scf.out
```

↑

Cell optimization †

For the cell optimization, use the input file like follows

Input file: au_scf.in

&control
   calculation='vc-relax'
   restart_mode='from_scratch',
   pseudo_dir = '/home/ikutaro/QE/pseudo/'
   outdir='./tmp'
   prefix='au'
   tprnfor = .true.
   tstress = .true.
   forc_conv_thr = 1.d-4
   nstep=10000
/
&system
   ibrav = 2
   A     = 4.00
   !A     = 4.079
   nat   = 1
   ntyp  = 1
   ecutwfc = 40.0
   ecutrho = 400.0
   occupations='smearing'
   smearing='mp'
   degauss=0.01
   nbnd=24
   !input_dft='vdW-DF2-B86R'
   !assume_isolated = 'esm', esm_bc='bc1'
/
&electrons
   diagonalization='cg'
   conv_thr = 1.0e-12
   mixing_beta = 0.1
/
&ions
 ion_dynamics='bfgs'
/
&cell
 cell_dynamics='bfgs'
/
ATOMIC_SPECIES
 Au 0.0000 au_pbe_v1.uspp.F.UPF
ATOMIC_POSITIONS (crystal)
Au      0.000000000000      0.000000000000      0.00000000000
K_POINTS (automatic)
16 16 16 0 0 0

Here we use default values for the pressure tolerance.

Execution
```
mpirun -np 8 < au_scf.in > au_scf.out
```

↑

Band structure calculation †

Having connfirmed the convergence of the SCF calculation, we are ready to perform the band structure calculation. Here is an input file for the band structure calculation.

Input file: au_bands.in

&control
   calculation='bands'
   restart_mode='from_scratch',
   pseudo_dir = '/home/ikutaro/QE/pseudo/'
   outdir='./tmp'
   prefix='au'
   tprnfor = .true.
   tstress = .true.
   forc_conv_thr = 1.d-4
   nstep=10000
/
&system
   ibrav = 2
   A     = 4.00
   !A     = 4.079
   nat   = 1
   ntyp  = 1
   ecutwfc = 40.0
   ecutrho = 400.0
   occupations='smearing'
   smearing='mp'
   degauss=0.01
   nbnd=24
   !input_dft='vdW-DF2-B86R'
   !assume_isolated = 'esm', esm_bc='bc1'
/
&electrons
   diagonalization='cg'
   conv_thr = 1.0e-12
   mixing_beta = 0.1
/
&ions
 ion_dynamics='bfgs'
/
&cell
 cell_dynamics='bfgs'
/
ATOMIC_SPECIES
 Au 0.0000 au_pbe_v1.uspp.F.UPF
ATOMIC_POSITIONS (crystal)
Au      0.000000000000      0.000000000000      0.00000000000
K_POINTS tpiba_b
5
 0.0 0.0 0.0 50.0
 1.0 0.0 0.0 50.0
 1.0 0.5 0.0 50.0
 0.5 0.5 0.5 50.0
 0.0 0.0 0.0  0.0

In this example, we draw a band structure along

Gamma (0, 0, 0)
X 2pi/a (1, 0, 0)
W 2pi/a (1, 1/2, 0)
L 2pi/a (1/2, 1/2, 1/2) In the cartesian coordinate, and in the following how to specify the k-points along the symmetry points. The KPOINTS card starts like
```
K_POINTS tpiba_b
```
If you want to use the k-points in the unit of the reciprocal lattice vector, use
```
K_POINTS crystal_b
```
Then set the number of high symmetry points. In this case
```
5
```
The number is followed by the k-points and the mesh (number of intervals)
```
 0.0 0.0 0.0 50.0
 1.0 0.0 0.0 50.0
 1.0 0.5 0.0 50.0
 0.5 0.5 0.5 50.0
 0.0 0.0 0.0  0.0
```
which define the segments of the high symmetry line in the Brillouin zone. In this example, total number of k-points is 50+50+50+50+1=201. In general, something like
```
K_POINTS tpiba_b | crystal_b
NKSEG
K1X K1Y K1Z NKMESH1
K2X K2Y K2Z NKMESH2
...
KNX KNY KNZ NKMESHN
```
and the i-th k-point in the first segment (for instance) is determined by
kx(i) = (K2X -K1X) * (i-1) / NKMESH1
ky(i) = (K2Y - K1Y) * (i-1) / NKMESH1
kz(i) = (K2Z - K1Z) * (i-1) / NKMESH1
Execution
```
mpirun -np 8 < au_bands.in > au_bands.out
```
NOTE: Make sure you use the same number of cores/cpus as that for the SCF calculation.
In order to plot the band structure, we need to convert the data in such a way that your favorite graphic software such as gnuplot can read. The simplest way is to use "bands.x." Here is an input file for the bands.x

Input file: bands.in

&bands
   outdir='./tmp'
   prefix='au'
   filband='au_band'
   lsym=.true.
/

Execution

mpirun -np 8 bands.x < bands.in > bands.out

You will obtain

au_band.gnu
au_band.rap The latter will be an input file for other program, and the former, just Kohn-Sham eigenvalues in an XY data, which can be plotted by gnuplot, for e.g.
```
$ gnuplot
$ > plot 'au_band.gnu'
```
If you want to set the energy origin to the Fermi level, it may be like
```
$ > plot 'au_and.gnu' using ($1):($2-17.1096)
```
The value "17.1096" is the the Fermi level, taken from the previsou SCF calculation.