t-nissie/00anatase.en.md

## 00anatase.en.md

      
    Raw
  

              00anatase.en.md
            
          
    Plot band structure and DOS of TiO2 anatase

Original files are in https://gist.github.com/t-nissie/ad99810ddf1bceb602f6 .
Preparation


Clone files in the gist as git clone https://gist.github.com/ad99810ddf1bceb602f6.git anatase08-k6x6x4-band-dos-gist.
cd anatase08-k6x6x4-band-dos-gist.
Get O.pw-mt_fhi.UPF and Ti.pw-mt_fhi.UPF form http://www.quantum-espresso.org/pseudopotentials/ .
Make symlinks to bands.x, dos.x, plotband.x and pw.x in the
current directory, i.e. ln -s /SOMEWHERE/espresso-5.1.2/bin/bands.x.

relaxation of cell and atomic positions

Using an input file of
anatase.vc-relax.in,
we perform optimization of cell parameters and atomic positions.
$ mpirun -np 12 ./pw.x -in anatase.vc-relax.in | tee anatase.vc-relax.out
$ grep -B13 'End final coordinates' anatase.vc-relax.out

CELL_PARAMETERS (alat=  7.14000000)
   0.496771433  -0.496771433   1.216801080
   0.496771433   0.496771433   1.216801080
  -0.496771433  -0.496771433   1.216801080

ATOMIC_POSITIONS (crystal)
Ti      -0.000000000   0.000000000   0.000000000
Ti       0.500000000   0.750000000   0.250000000
O        0.500000000   0.539268418   0.039268418
O        0.000000000   0.789268418   0.789268418
O        0.000000000   0.210731582   0.210731582
O        0.500000000   0.960731582   0.460731582
End final coordinates

SCF calculation

Although the last calculation with
anatase.vc-relax.in gives
SCF results in its end, we perform an SCF calculation
with anatase.scf.in.
Optimized cell parameters and atom positions were copied from anatase.vc-relax.out
into anatase.scf.in.
$ mpirun -np 12 ./pw.x -in anatase.scf.in | tee anatase.scf.out

Confirm that stress and forces are small enough.
Plot band structure

In anatase.bands.in, crystal_b is used.
How to write input files of
anatase.bands.in and
bands.in is described around

http://www.stat.phys.titech.ac.jp/SATL_qe_tutorial/graphene_banddos.html (in Japanese)
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idm6080432
http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_BANDS.html .

Anyway, we do non-SCF calculations at each k-point along Z-Gamma-X-P with pw.x,
and then we execute bands.x with bands.sh as
$ ./bands.sh
$ gv anatase.bands.ps &

If you do not have gv(1), you can use evince(1) instead for preview of generated anatase.bands.ps.
Plot DOS

$ ./dos.sh
$ gnuplot
plot [0:12] [-6:10] 'anatase.dos' u 2:($1-5.0) w l


Plotted electronic dispersion and DOS of anatase TiO2.
Spikes in the band plot may be due to a bug in pw.x.
ToDo


6 6 4 1 1 1 or 6 6 4 0 0 0 for K_POINTS AUTOMATIC
To check convergence w.r.t. k-points
To check convergence w.r.t. kinetic energy cutoff
Two 5.0 in bands.sh should be
adjusted to the valence band maximum (VBM) according to the calculated KS-levels in anatase.scf.out.

Refereces


Adisak Boonchun, Naoto Umezawa, Takahisa Ohno, Shuxin Ouyanga and Jinhua Ye: J. Mater. Chem. A 1, 6664-6669 (2013).


## anatase.bands.in
&control
calculation = 'bands'
prefix = 'anatase'
pseudo_dir = './'
outdir = './'
/

&system
ibrav = 7
celldm(1) = 7.093904
celldm(3) = 2.4494134129942915
space_group = 141
nat = 2
ntyp = 2
ecutwfc = 100.0
ecutrho = 1000.0
nbnd=40
/

&electrons
/

ATOMIC_SPECIES
 Ti 47.867 Ti.pw-mt_fhi.UPF
 O  16.00  O.pw-mt_fhi.UPF
ATOMIC_POSITIONS (crystal_sg)
Ti       0.0   0.0   0.00
O        0.0   0.0   0.21073169670146766
K_POINTS (crystal_b)
 4
  0.5000  0.5000  0.5000  50
  0.0000  0.0000  0.0000  50
  0.0000  0.5000 -0.5000  50
  0.2500  0.7500 -0.2500  50

## anatase.dos.in
&control
calculation = 'nscf'
prefix = 'anatase'
pseudo_dir = './'
outdir = './'
wf_collect=.false.
forc_conv_thr = 1d-4
!disk_io = 'none'
/

&system
ibrav = 7
celldm(1) = 7.093904
celldm(3) = 2.4494134129942915
space_group = 141
nat = 2
ntyp = 2
ecutwfc = 100.0
ecutrho = 1000.0
nbnd=40
/

&electrons
conv_thr = 1.0d-8
/

&IONS
/

&cell
cell_factor = 3.0d0
/
ATOMIC_SPECIES
 Ti 47.867 Ti.pw-mt_fhi.UPF
 O  16.00  O.pw-mt_fhi.UPF
K_POINTS AUTOMATIC
10 10 6 1 1 1
ATOMIC_POSITIONS (crystal_sg)
Ti       0.0   0.0   0.00
O        0.0   0.0   0.21073169670146766

## anatase.scf.in
&control
calculation = 'scf'
restart_mode = 'from_scratch'
prefix = 'anatase'
tstress = .true.
tprnfor = .true.
pseudo_dir = './'
outdir = './'
wf_collect=.true.
forc_conv_thr = 1d-4
!disk_io = 'none'
/

&system
ibrav = 7
celldm(1) = 7.093904
celldm(3) = 2.4494134129942915
space_group = 141
nat = 2
ntyp = 2
!occupations = 'fixed'
ecutwfc = 100.0
ecutrho = 1000.0
!input_dft = 'vdW-DF-C09'
!nosym = .TRUE.
/

&electrons
conv_thr = 1.0d-8
/

&IONS
/

&cell
cell_factor = 3.0d0
/
ATOMIC_SPECIES
 Ti 47.867 Ti.pw-mt_fhi.UPF
 O  16.00  O.pw-mt_fhi.UPF
K_POINTS AUTOMATIC
6 6 4 1 1 1
ATOMIC_POSITIONS (crystal_sg)
Ti       0.0   0.0   0.00
O        0.0   0.0   0.21073169670146766

## anatase.vc-relax.in
&control
calculation = 'vc-relax'
restart_mode = 'from_scratch'
prefix = 'anatase.vc-relax'
tstress = .true.
tprnfor = .true.
pseudo_dir = './'
outdir = './'
wf_collect=.true.
forc_conv_thr = 1d-4
disk_io = 'none'
/

&system
ibrav = 7
celldm(1) = 7.14
celldm(3) = 2.5
space_group = 141
nat = 2
ntyp = 2
ecutwfc = 100.0
ecutrho = 1000.0
/

&electrons
conv_thr = 1.0d-8
/

&IONS
/

&cell
cell_factor = 3.0d0
/
ATOMIC_SPECIES
 Ti 47.867 Ti.pw-mt_fhi.UPF
 O  16.00  O.pw-mt_fhi.UPF
K_POINTS AUTOMATIC
6 6 4 1 1 1
ATOMIC_POSITIONS (crystal_sg)
Ti       0.0   0.0   0.00
O        0.0   0.0   0.21

## band-dos.png

      
    Raw
  

              band-dos.png
            
          
## bands.in
 &bands
    prefix  = 'anatase'
    outdir='./'
    filband = 'bands.dat'
 /

## bands.sh
#!/bin/sh
##
mpirun -np 12 ./pw.x -in anatase.bands.in | tee anatase.bands.out
mpirun -np 12 ./bands.x < bands.in | tee bands.out

./plotband.x <<EOF
bands.dat
-1, 15
anatase.bands.xmgr
anatase.bands.ps
5.0
2.0, 5.0
EOF

rm -f anatase.wfc*

## dos.in
&dos
   outdir = './',
   prefix='anatase',
   fildos='anatase.dos',
   DeltaE=0.1
   ngauss=0,
   degauss=0.01
/

## dos.sh
#!/bin/sh
##
mpiexec -np 12 ./pw.x -in anatase.dos.in | tee anatase.dos.out
mpiexec -np 12 ./dos.x < dos.in | tee dos.out

## ZGXP.rb
#!/bin/sh
# -*- ruby -*-  We do not need this k-points generator ZGXP.rb anymore, because we can use crystal_b in anatase.bands.in.
exec ruby -x "$0" "$@"
#!ruby
i=0
N_Z=50
N_X=50
N_P=50

N_Z.step(0, -1).each do |j|
  x = j / (2.0 * N_Z)
 printf("%8.4f%8.4f%8.4f%4d\n", x, x, x, i+=1)
end

(1..N_X).each do |j|
  x = j / (2.0 * N_X)
 printf("%8.4f%8.4f%8.4f%4d\n", 0, x, -x, i+=1)
end

(1..N_P).each do |j|
  x = j / (4.0 * N_P)
 printf("%8.4f%8.4f%8.4f%4d\n", x, 0.5+x, -0.5+x, i+=1)
end
	&control
	calculation = 'bands'
	prefix = 'anatase'
	pseudo_dir = './'
	outdir = './'
	/

	&system
	ibrav = 7
	celldm(1) = 7.093904
	celldm(3) = 2.4494134129942915
	space_group = 141
	nat = 2
	ntyp = 2
	ecutwfc = 100.0
	ecutrho = 1000.0
	nbnd=40
	/

	&electrons
	/

	ATOMIC_SPECIES
	Ti 47.867 Ti.pw-mt_fhi.UPF
	O 16.00 O.pw-mt_fhi.UPF
	ATOMIC_POSITIONS (crystal_sg)
	Ti 0.0 0.0 0.00
	O 0.0 0.0 0.21073169670146766
	K_POINTS (crystal_b)
	4
	0.5000 0.5000 0.5000 50
	0.0000 0.0000 0.0000 50
	0.0000 0.5000 -0.5000 50
	0.2500 0.7500 -0.2500 50
	&control
	calculation = 'nscf'
	prefix = 'anatase'
	pseudo_dir = './'
	outdir = './'
	wf_collect=.false.
	forc_conv_thr = 1d-4
	!disk_io = 'none'
	/

	&system
	ibrav = 7
	celldm(1) = 7.093904
	celldm(3) = 2.4494134129942915
	space_group = 141
	nat = 2
	ntyp = 2
	ecutwfc = 100.0
	ecutrho = 1000.0
	nbnd=40
	/

	&electrons
	conv_thr = 1.0d-8
	/

	&IONS
	/

	&cell
	cell_factor = 3.0d0
	/
	ATOMIC_SPECIES
	Ti 47.867 Ti.pw-mt_fhi.UPF
	O 16.00 O.pw-mt_fhi.UPF
	K_POINTS AUTOMATIC
	10 10 6 1 1 1
	ATOMIC_POSITIONS (crystal_sg)
	Ti 0.0 0.0 0.00
	O 0.0 0.0 0.21073169670146766
	&control
	calculation = 'scf'
	restart_mode = 'from_scratch'
	prefix = 'anatase'
	tstress = .true.
	tprnfor = .true.
	pseudo_dir = './'
	outdir = './'
	wf_collect=.true.
	forc_conv_thr = 1d-4
	!disk_io = 'none'
	/

	&system
	ibrav = 7
	celldm(1) = 7.093904
	celldm(3) = 2.4494134129942915
	space_group = 141
	nat = 2
	ntyp = 2
	!occupations = 'fixed'
	ecutwfc = 100.0
	ecutrho = 1000.0
	!input_dft = 'vdW-DF-C09'
	!nosym = .TRUE.
	/

	&electrons
	conv_thr = 1.0d-8
	/

	&IONS
	/

	&cell
	cell_factor = 3.0d0
	/
	ATOMIC_SPECIES
	Ti 47.867 Ti.pw-mt_fhi.UPF
	O 16.00 O.pw-mt_fhi.UPF
	K_POINTS AUTOMATIC
	6 6 4 1 1 1
	ATOMIC_POSITIONS (crystal_sg)
	Ti 0.0 0.0 0.00
	O 0.0 0.0 0.21073169670146766
	&control
	calculation = 'vc-relax'
	restart_mode = 'from_scratch'
	prefix = 'anatase.vc-relax'
	tstress = .true.
	tprnfor = .true.
	pseudo_dir = './'
	outdir = './'
	wf_collect=.true.
	forc_conv_thr = 1d-4
	disk_io = 'none'
	/

	&system
	ibrav = 7
	celldm(1) = 7.14
	celldm(3) = 2.5
	space_group = 141
	nat = 2
	ntyp = 2
	ecutwfc = 100.0
	ecutrho = 1000.0
	/

	&electrons
	conv_thr = 1.0d-8
	/

	&IONS
	/

	&cell
	cell_factor = 3.0d0
	/
	ATOMIC_SPECIES
	Ti 47.867 Ti.pw-mt_fhi.UPF
	O 16.00 O.pw-mt_fhi.UPF
	K_POINTS AUTOMATIC
	6 6 4 1 1 1
	ATOMIC_POSITIONS (crystal_sg)
	Ti 0.0 0.0 0.00
	O 0.0 0.0 0.21
	#!/bin/sh
	##
	mpirun -np 12 ./pw.x -in anatase.bands.in \| tee anatase.bands.out
	mpirun -np 12 ./bands.x < bands.in \| tee bands.out

	./plotband.x <<EOF
	bands.dat
	-1, 15
	anatase.bands.xmgr
	anatase.bands.ps
	5.0
	2.0, 5.0
	EOF

	rm -f anatase.wfc*
	&dos
	outdir = './',
	prefix='anatase',
	fildos='anatase.dos',
	DeltaE=0.1
	ngauss=0,
	degauss=0.01
	/
	#!/bin/sh
	##
	mpiexec -np 12 ./pw.x -in anatase.dos.in \| tee anatase.dos.out
	mpiexec -np 12 ./dos.x < dos.in \| tee dos.out
	#!/bin/sh
	# -- ruby -- We do not need this k-points generator ZGXP.rb anymore, because we can use crystal_b in anatase.bands.in.
	exec ruby -x "$0" "$@"
	#!ruby
	i=0
	N_Z=50
	N_X=50
	N_P=50

	N_Z.step(0, -1).each do \|j\|
	x = j / (2.0 * N_Z)
	printf("%8.4f%8.4f%8.4f%4d\n", x, x, x, i+=1)
	end

	(1..N_X).each do \|j\|
	x = j / (2.0 * N_X)
	printf("%8.4f%8.4f%8.4f%4d\n", 0, x, -x, i+=1)
	end

	(1..N_P).each do \|j\|
	x = j / (4.0 * N_P)
	printf("%8.4f%8.4f%8.4f%4d\n", x, 0.5+x, -0.5+x, i+=1)
	end