HANDS-ON TUTORIAL ON THE

QUANTUM-ESPRESSO PACKAGE
POST PROCESSING OF DATA:
Density of states: DOS and PDOS
Charge density and bonding charge
STM image simulation

Cagliari September 2005

Guido Fratesi and Stefano Fabris

 Getting started
Move to your own scratch directory:
cd /scratch/XXX/
Download this tutorial and the examples from:
http://[ESPRESSO-TUTORIAL-SITE]/
tutorial_postproc.pdf
http://[ESPRESSO-TUTORIAL-SITE]/
examples_postproc.tgz

Untar the example file and enter in the resulting directory:

tar zxvf examples_postproc.tgz
cd PostProcessing
Edit the environment_variables file:
e.g., TMP_DIR=/scratch/XXX/tmp/
Create the output directory as specified above:
mkdir /scratch/XXX/tmp/
 Exercise 1: DOS of bulk Ni
Run the scf calculation for bulk Ni
run-ni.scf
What happens? Why does the program stop? See the output file:
more ni.scf.out
Add the required input
starting_magnetization(1)=0.0
run again the simulation. Copy the output file:
cp ni.scf.out ni.scf.out-0magn
Modify the starting magnetization in run-ni.scf
starting_magnetization(1)=0.7
run again the simulation.
run-ni.scf
Compare the total energies of the two simulations: do they
differ? Why? What about the magnetization?
 Exercise 1: DOS
Edit the file run-ni.nscf:
increase the number of bands to 8: nbnd=8
and the set a denser k-point mesh: 12 12 12 0 0 0
Run the nscf calculation for bulk Ni: run-ni.nscf
Have a look at the input file for the DOS calculation:
more run-ni.dos
&inputpp
outdir=$TMP/DIR'
prefix='ni'
fildos='ni.dos'
Emin=5.0, Emax=25.0, DeltaE=0.1 in eV!
/
and run the DOS calculation:
run-ni.dos
 Exercise 1: DOS
Have a look at the output file containing the DOS: ni.dos
more ni.dos

# E (eV) dosup(E) dosdw(E) Int dos(E)

5.000 -0.3790E-05 -0.2225E-05 -0.6015E-06
5.100 -0.1772E-04 -0.1149E-04 -0.3523E-05
5.200 -0.5902E-04 -0.4251E-04 -0.1368E-04
5.300 -0.1373E-03 -0.1105E-03 -0.3846E-04
5.400 -0.2211E-03 -0.1989E-03 -0.8046E-04
5.500 -0.2479E-03 -0.2498E-03 -0.1302E-03
5.600 -0.8376E-04 -0.1768E-03 -0.1563E-03
5.700 0.1017E-02 0.4889E-03 -0.5688E-05

 Exercise 1: DOS
Plot the total density of states: gnuplot dos.gnu
 Exercise 1: DOS
Plot the total density of states: gnuplot dos.gnu
Note difference between spin up and spin down components.

Plot the integrated charge

 Exercise 1: DOS
Plot the integrated charge
 Exercise 1: DOS
More input variables:
&inputpp
outdir=$TMP/DIR'
prefix='ni
ngauss= 0,1,-1,99
degauss= xx in Ry!
fildos='ni.dos'
Emin=5.0, Emax=25.0, DeltaE=0.1 in eV!
/
 Exercise 2: PDOS of bulk Ni
Have a look at the input file for the PDOS calculation:
more run-pdos.in

&inputpp
outdir=$TMP_DIR/'
prefix='ni'
io_choice='both
Emin=5.0, Emax=25.0, DeltaE=0.1
ngauss=1, degauss=0.02
/
and run the PDOS calculation (projwfc.x):
run-ni.pdos
 Exercise 2: PDOS
Have a look at the output file ni.pdos.out:
more ni.pdos.out

Lowdin Charges:

Atom # 1: total charge = 9.881

spin up = 5.239
spin down = 4.6426
polarization = 0.5965
Spilling Parameter: 0.0118
 Exercise 2: PDOS
Have a look at the output files containing the s and d
components of the PDOS:
more ni.pdos_atm#1(Ni)_wfc#1(s)
more ni.pdos_atm#1(Ni)_wfc#2(d)

# E (eV) ldosup(E) ldosdw(E) pdosup(E) pdosdw(E)

5.000 -0.378E-05 -0.222E-05 -0.378E-05 -0.222E-05
5.100 -0.177E-04 -0.115E-04 -0.177E-04 -0.115E-04
5.200 -0.589E-04 -0.425E-04 -0.589E-04 -0.425E-04
5.300 -0.137E-03 -0.110E-03 -0.137E-03 -0.110E-03
5.400 -0.221E-03 -0.199E-03 -0.221E-03 -0.199E-03
5.500 -0.247E-03 -0.249E-03 -0.247E-03 -0.249E-03
5.600 -0.831E-04 -0.176E-03 -0.831E-04 -0.176E-03
5.700 0.102E-02 0.489E-03 0.102E-02 0.489E-03
5.800 0.491E-02 0.331E-02 0.491E-02 0.331E-02
5.900 0.126E-01 0.996E-02 0.126E-01 0.996E-02
 Exercise 2: PDOS
Plot the s and d components of the DOS: gnuplot
dos.gnu
 Exercise 3: Charge density of Si
Run the scf calculation for bulk Si:
run-si.scf
Modify the input file for the post processing run-si.pp for
calculating the total charge density. First modify the inputpp
namelist:
&inputpp
prefix = 'si'
outdir = '/tmp/',
filplot = 'si.charge'
plot_num= XXX
/
see espresso/Docs/INPUT_PP for the value of plot_num
corresponding to the charge density.
 Exercise 3: Charge density of Si
Then modify the plot namelist to convert data in a format
compatible with the selected visualization packages (plotrho,
gnuplot, XCrysDen... Now use plotrho):
vi run-si.pp
&plot
nfile=1
filepp(1)='si.charge'
iflag=XXX 2D plot
output_format=XXX plotrho format
e1(1)=1.0, e1(2)=0.0, e1(3)=0.0,
e2(1)=0.0, e2(2)=1.0, e2(3)=0.0,
x0(1)=0.0, x0(2)=0.0, x0(3)=0.0,
nx=40, ny=40
fileout='si.charge001.dat'
/ 001 plane
Run the calculation: run-si.pp
 Exercise 3: Charge density of Si
Then modify the plot namelist to convert data in a format
compatible with the selected visualization packages (plotrho,
gnuplot, XCrysDen... Now use plotrho):
vi run-si.pp
&plot
nfile=1
filepp(1)='si.charge'
iflag=2 2D plot
output_format=2 plotrho format
e1(1)=1.0, e1(2)=0.0, e1(3)=0.0,
e2(1)=0.0, e2(2)=1.0, e2(3)=0.0,
x0(1)=0.0, x0(2)=0.0, x0(3)=0.0,
nx=40, ny=40
fileout='si.charge001.dat'
/ 001 plane
Run the calculation: run-si.pp
 Exercise 3: Charge density of Si
Visualize the charge on the (001) plane by using the program
plotrho.x (included in espresso):
run-si.plot
input file > si.charge001.dat
output file > si.charge001.ps
Logarithmic scale (y/n)? > n
min, max, # of levels > 0.01 0.08 8
gv si.charge001.ps
 Exercise 3: Charge density of Si
Calculate and plot the charge density of Si on the (110) plane:
cp run-si.pp to run-si.pp110
Modify the input file so that to define the (110) plane
e1(1)=?, e1(2)=?, e1(3)=?,
e2(1)=?, e2(2)=?, e2(3)=?,

fileout='si.charge110.dat'
Run the pp.x calculation: run-si.pp110
Run the plotrho.x program and visualize the result: run-si.plot
 Exercise 4: Bonding charge density
Bonding charge density of an O atom on the Al (001) surface

Run the following script: run-Al-O-OAl-scf-pp &

It follows the step seen in Ex 3 to calculate the charge densities of:
1) an O atom adsorbed on an Al(001) slab,
2) an Al(001) slab,
3) an O atom.

Compare the atomic coordinates

of the O atom in the file
O.scf.out with those in
OAl.scf.out. What do you
notice? Why are they so?
 Exercise 4: Bonding charge density
Use the program chdens.x to subtract the charge densities of the Al
(001) slab and of the O atom from the that one of the complete
system O/Al(001): (file: run-OAl.chdiff)
&input
nfile=3
filepp(1)='???', weight(1)=??? The first file is
filepp(2)='???', weight(2)=??? the one for the
filepp(3)='???', weight(3)=??? O/Al(001) system
iflag=?? 3D
output_format=?? XCrySDen
fileout='OAl.chdensDIFF.xsf'
/
Run the calculation: run-chdens.diff
 Exercise 4: Bonding charge density
Visualizing the output file with XCrysDen:
xcrysden --xsf OAl.chdensDIFF.xsf

Hint: see the isosurfaces by selecting: tools - datagrid - ok

- isovalue=0.003 - render+/-isovalue - submit
 Exercise 5: STM simulation
Simulating the STM image of the AlAs (110) surface

Run the scf calculation for the AlAs (110) surface

run-AlAs.scf
Run the non scf calculation for the AlAs (110) surface:
run-AlAs.nscf
 Exercise 5: STM simulation
Set up the input file for the post processing; inputpp namelist
(see run-AlAs.stm):
&inputpp
prefix = 'AlAs110'
outdir='$TMP_DIR/',
filplot = 'AlAs-1.0'
sample_bias=-0.0735d0, in Ry!
stm_wfc_matching=.false.,
plot_num= XXX
/
see O-sesame/pwdocs/INPUT_PP

How to choose the sample_bias?

 Exercise 5: STM simulation

How to choose the sample_bias? What is the DOS?

Fermi energy

Exercise: image empty states

 Exercise 5: STM simulation
Set plot namelist to produce a 3D file comptatible with the
XCrySDen package:
vi run-AlAs.stm
...
&plot
nfile=1
filepp(1)='AlAs-1.0'
weight(1)=1.0
iflag=3 3D plot
output_format=5 XCrysDen format
fileout='AlAs110-1.0.xsf'
/
 Exercise 5: STM simulation
Run the post-processing simulation:
run-AlAs.stm

Visualize the output file with the XCrysDen package:

xcrysden xsf AlAs110-1.0.xsf
 Exercise 6: Si charge (using PWgui)

from SCF calculation of Si bulk to visualization of its charge

density with xcrysden. Use pwgui to construct
appropriate input files and run the necessary calculations:
SCF calculation: use pw.x program
post-processing: use pp.x program (select the charge-
density, and transform the charge-density to XSF format,
suitable for xcrysden)
visualize the calculated charge density stored in file.xsf
with xcrysden
Input for pw.x: SCF calculation
Input for pp.x: extract the charge density
Input for pp.x: generate file for XCrySDen