Pw Tutorial

7/28/2019 Pw Tutorial

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HANDS-ON TUTORIAL ON THE

PWscf/FPMD/CP PACKAGE

CINECA March 3 rd 2004

S. Fabris and C. Sbraccia

Setting up the input files

Post Processing Structural Relaxations Molecular Dynamics


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Select the appropriate unit-cell

Input the atomic coordinates

Choose and download the pseudopotentials Determine a suitable k-point sampling & smearing

Select the size of the basis set


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bulk Al: cubic fcc and sc bravais lattice


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defective Al:

sc bravais lattice


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Al surfaces

t bravais lattice


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&system ibrav= 2,

celldm(1) =7.50,

nat= 1, ntyp=1,

ecutwfc =15.0,


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ibrav structure celldm(2)-celldm(6)

0 "free", see above not used

1 cubic P (sc) not used

2 cubic F (fcc) not used

3 cubic I (bcc) not used4 Hexagonal and Trigonal P celldm(3)=c/a

5 Trigonal R celldm(4)=cos(aalpha)

6 Tetragonal P (st) celldm(3)=c/a

7 Tetragonal I (bct) celldm(3)=c/a

(see file INPUT_PW in O-sesame/pwdocs/)


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Edit the script file

run-al.sc

modifying the variables IBRAV and NAT so that to obtain asimple cubic supercell with 4 atoms

IBRAV=?, , NAT=?

Exercise 1: cubic supercell Run a self-consistent calculation for bulk Al (al.fcc.in)

run-al.fcc

run-al.fcc is a script containing the input file al.fcc.inand producing the output file al.fcc.out Write down the total energy: it will be used in the following as

reference


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Exercise 1: cubic supercellAdd the atomic coordinates in theATOMIC_POSITION field

Al 0.0 0.0 0.0

Al ?? ?? ??

Al ?? ?? ?? Al ?? ?? ??

Run a self-consistent calculation (input= al.sc.in)run-al.sc

Compare the total energy (file al.sc.out) with the reference one infile al.fcc.out: do they differ? Why?


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ATOMIC_POSITIONSAtomic positions in the supercell can be defined in 4 ways:

1. in units of ALAT (this is the default) (alat)2. in crystal coordinates (crystal)

3. In bohr (bohr)

4. In Angstrom (angstrom)

The unit is defined by specifying the right flag as

ATOMIC_POSITIONS (crystal)


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aa

c

Tetragonal supercell


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Exercise 2: tetragonal supercell Have a look at the script file run-al.tet

Modify the variables IBRAV and NAT so that to obtain atetragonal supercell with 2 atoms

IBRAV=??, celldm(1) =5.3033,

celldm(3) = ??, NAT=?? Specify the (alat) instruction

ATOMIC_POSITIONS (alat)

Add the coordinates of the second atom in units of alat

Al ?? ?? ??


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aa

c

a= sqrt(2)/2 * ac= ac/a= sqrt(2)

Al1

Al2

celldm(3)= 1.41421356237

Al 0.0 0.0 0.0

Al 0.5 0.5 0.707107



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Exercise 2: tetragonal supercell Run the self consistent calculation (input= al.tet.in)

run-al.tet

Compare the total energy (output in al.tet.out) with thereference one calculated in Example1 (al.fcc.out)

grep ! ../Ex1/al.fcc.outgrep ! al.tet.out

why do they differ? What can you learn from the energy

difference between the two?


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Exercise 3: crystal coordinates Have a look at the script

run-al.tet2

Specify the (crystal) instruction

ATOMIC_POSITIONS (crystal)

Add the coordinates of the second atom in crystal units: Al ??? ??? ???


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aa

c

a= sqrt(2)/2 * ac= ac/a= sqrt(2)

Al1

Al2

Al 0.0 0.0 0.0 Al 0.5 0.5 0.5



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Exercise 3: tetragonal supercells Run the self consistent calculation (input= al.tet.in)

run-al.tet2

Compare the total energy in al.tet2.out with the onecalculated in Example2 (al.tet.out)

grep ! ../Ex2/al.tet.outgrep ! al.tet2.out

Do they differ? Why (or why not)?


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K-POINTS Periodic system Wave function and Hamiltonian expanded in PW

The electron states in the BZ are naturally classified by the points k in the Brillouin Zone

The number of the k points is proportional to the number of repeatedunit cells N With periodic boundaries conditions N infinity & N k infinity

!!WF and H can not be calculated at each k point!!

SOLUTION:WF and H are sampled on a suitable set of representable k points

in the BZ


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K-POINT SAMPLINGThe choice of the k-point mesh is system dependent.

Examples:1. Non-cubic supercells2. Surfaces3. Molecules isloated in vacuum


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Exercise 4: elongated supercell Have a look at the script file

run-al.tet3

Modify the variables IBRAV , NAT, celldm(3), so that todouble the size of the tetragonal supercell in the z direction (doublethe c/a ratio and double the number of atoms).


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Exercise 4: elongated supercell

Run the scf calculation again (be careful not to overwrite thefiles ). Fill up the following table. Comment the difference in

the total energies (per atom) of the 4 set of calculations:al.fcc.out al.tet.out al.tet3.out (12 12 10) al.tet3.out (12 12 5)

-4.18739 ????? ????? ?????

Run the scf calculation (input=al.tet3.in) and check the total energy

run-al.tet3

Reduce the size of the k-point mesh along k_z:

K_POINTS (automatic)

12 12 5 1 1 1

-4.18739 -4.187028 -4.186958 -4.187028


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Exercise 5: Al (001) surface Working input file: run-al001 Modify the variables IBRAV and NAT so that to obtain

a tetragonal supercell with 7 atoms

Specify the (alat) instruction ATOMIC_POSITIONS (alat)

Add the coordinates of the other 7 atoms in units of alat: Al ?? ?? ?? .. Al 0.0 0.0 0.0

Al 0.5 0.5 0.707107 Al 0.0 0.0 1.414213 Al 0.5 0.5 2.121320

. And symmetric with respect to xy plane Check the structure with Xcrysden:

xcrysden pwi al.001.in

Run the self-consistent calculation:

./run-al001


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Exercise 6: isolated moleculeSimulation of a CO molecule isolated in vacuum

How many k-points are needed? Why? Have a look at the script file run-co.scf and run the calculation:

run-co.scf


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Energy cut-off WF is expanded on a finite basis of plane waves. The size of the basis is controlled by the energy cut off ecut

Checking convergence of results towards the basis size

WHICH RESULTS? Total energy? Structural parameters?


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Exercise 7: energy-volume


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Exercise 7: energy-volumeCalculation of an energy-volume curve for bulk Si

Working input file: run-si.scf

Set the energy cutoff to 20 Ry: ecut=20Set the lattice parameter to 9.8 a.u.: celldm(1)=9.8

Run the scf calculation:run-si.scf Save the output file: cp si.scf.out si-e20-a9.8.outRepeat the procedure for the lattice parameters:

Lattice parameter Energy9.8 ???10.0 ???10.2 ???10.4 ???


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Write table on file: envol-ecut20.dat9.8 ???10.0 ???10.2 ???10.4 ???

Plot the results:


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Recalculate the energy-volume curve with a larger cutoff:ecut=40

Collect the results in file envol-ecut40.dat9.8 ???10.0 ???10.2 ???10.4 ???

Plot the two files together: what do you learn?Is the total energy converged?Are the structural parameter converged?Which cutoff would you choose for scientific production?


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Pseudopotentials Where to get the psudopotential files?

1. From the PWscf web site: http://www.pwscf.org


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Pseudopotentials

You get psudopotential files ready-to-use with PWscf


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2. From other databases:

i.e. Vanderbilt ultra-soft pseudopotential sitehttp://www.physics.rutgers.edu/~dhv/uspp/


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Pseudopotentials! Different xc functionals !


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2. From other databases:

i.e. Vanderbilt ultra-soft pseudopotential sitehttp://www.physics.rutgers.edu/~dhv/uspp/

You get psudopotential files not compatible with PWscf

Convert them in the UPF format:

O-sesame/upftools/uspp2upf xxx.uspp


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3. Generate your own PP see Paolo Giannozzi Lecture


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Cc BAD CHOICE

Linear mixing

Self consistency: mixing

Advanced mixing schemes

It is more flexible to mix the density instead of the potentialPWscf mix the density by default


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Example 8: improving convergency

Run the scf calculation for an elongated supercell of 16 Fe atomsrun-fe16.scf &

During the run check the convergency of the total energygrep e scf e total energy fe16.scf.out

What do you notice??

SUGGESTION Try to decrease the mixing parameter: mixing_beta = 0.1


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Exercise 8

OTHER SUGGESTIONS FOR DIFFICOULT CASES: Increase the number of calculated bands: nbnd=80 Change the mixing method mixing_mode or the size of history mixing_ndim


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Exercise 9: DOS Run the scf calculation for bulk Nirun-ni.scf

What happens? Why does the program stop? Add the required inputstarting_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 theydiffer? Why? What about the magnetization?


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Exercise 9: DOS Run the nscf calculation for bulk Ni:

increase the number of bands to 8: nbnd=8and the set a denser k-point mesh: 12 12 12 0 0 0

Have a look at the input file for the DOS calculation: more run-ni.dos

&inputppoutdir=$TMP/DIR'

prefix='ni'fildos='ni.dos'Emin=5.0, Emax=25.0, DeltaE=0.1

/ and run the DOS calculation:

run-ni.dos

in eV!


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Exercise 9: DOS

# E (eV) dosup(E) dosdw(E) Int dos(E)5.749 0.0000E+00 0.0000E+00 0.0000E+005.849 0.9326E-03 0.4531E-03 0.1386E-03

5.949 0.3730E-02 0.2685E-02 0.7801E-036.049 0.1327E-01 0.6781E-02 0.2785E-026.149 0.1422E-01 0.1859E-01 0.6066E-026.249 0.1686E-01 0.1600E-01 0.9352E-02

6.349 0.1969E-01 0.1876E-01 0.1320E-01

Have a look at the output file containing the DOS: ni.dos more ni.dos


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Exercise 9: DOS Plot the density of states and notice the difference in the spinup and spin down components:


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Exercise 10: PDOS Have a look at the input file for the PDOS calculation:

more run-pdos.in

&inputppoutdir=$TMP_DIR/'

prefix='ni'io_choice='both'Emax=25.0, DeltaE=0.1, smoothing=0.3

/

and run the PDOS calculation ( projwfc.x) :run-ni.pdos


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Exercise 10: PDOS Have a look at the output files containing the s and dcomponents of the PDOS: more ni.pdos_atm#1(Ni)_wfc#1(s) more ni.pdos_atm#1(Ni)_wfc#2(d)

# E (eV) dosup(E) dosdw(E)

4.249 0.151E-13 0.545E-144.349 0.379E-12 0.146E-124.449 0.761E-11 0.314E-114.549 0.122E-09 0.541E-10

4.649 0.158E-08 0.746E-094.749 0.163E-07 0.824E-084.849 0.136E-06 0.731E-07


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Exercise 10: PDOS Plot the s and d components of the density of states : interpretthe total density of states.


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Exercise 11: STM imagesSimulating the STM image of the AlAs (110) surface

Run the scf calculation for the AlAs (110) surfacerun-alas.scf

Run the non scf calculation for the AlAs (110) surface:

run-alas.nscf


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Set up the input file for the post processing(see run-AlAs.ppstm ):&inputpp

prefix = 'AlAs110'outdir='$TMP_DIR/',filplot = 'AlAs-1.0'sample_bias=-0.0735d0,

stm_wfc_matching=.false., plot_num= 5/ see O-sesame/pwdocs/INPUT_PP

How to choose the sample_bias ?


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Exercise 11: STM images How to choose the sample_bias?

Run the post processing simulation:run-AlAs.ppstm

Redo the STM simulation, imaging empty states


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Exercise 11: STM images Producing a 3D file comptatible with the XCrysDen package: more run-AlAs.chdens&input

nfile=1filepp(1)='AlAsresm-1.0'

weight(1)=1.0iflag=3

plot_out=1output_format=5e1(1)=7.0, e1(2)=0.0, e1(3)=0.0e2(1)=0.0, e2(2)=7.07107, e2(3)=0.0

x0(1)=0.0, x0(2)=-0.18, x0(3)=3.25nx=36 ,ny=56fileout='AlAs110-1.0.xsf'

/

3D plot

XCrysDen format


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Exercise 11: STM images Producing a 3D file comptatible with the XCrysDen package:

run-AlAs.chdens

Visualizing the output file with the XCrysDen package:xcrysdens xsf AlAs110-1.0.xsf

E i 11 STM i


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Exercise 11: STM images Visualizing the output file with the XCrysDen package:

xcrysdens xsf AlAs110-1.0.xsf

S l l i


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Structural relaxation

The Potential Energy Surface

Given the ionic configuration, the total energy of the system is

obtained with the Density Functional Theory.

Total Energy E[X I 3N , (X I 3N )] is a function of ionic configurations and

defines a 3N-dim surface called Potential Energy Surface.

The problem of identifing stable ionic configurations (where forces

are zero) is thus equivalent to the identification of the minima on the

PES.


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Ionic relaxationSteepest Descent minimization :

X

discretization

gradient versor


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discretization

gradient versor


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discretization

gradient versor


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discretization

gradient versor


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discretization

gradient versor


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discretization

gradient versor


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discretization

gradient versor


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The minimum is reached !!!

discretization

gradient versor

E i 12 f l ti


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Exercise 12: surface relaxationStructural relaxation of the Al(001) surface

Run the self-consistent calculation for the Al (001) slab:

run-al001.scf Scroll to the end of the output file and analyze the forces: whatdo you notice? Are the atomic forces pointing outward or inward?more al.scf.out

Modify the input file so that to perform a structural relaxation:(see O-sesame/pwdocs/INPUT_PW)&control

calculation=???.&ions/

E i 12 f l i


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Exercise 12: surface relaxation Analyze the output file: how are the forces evolving during therelaxation?

How are the atoms relaxing? How much does the interlayer distances change with respect to the bulk value?

Xcrysden does not work!!

( eventually rerun the calculation in parallel distributing over the3 k points)

Exercise 13: molecular relaxation


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Exercise 13: molecular relaxation Finding the equilibrium structure of the CO molecule

Run the self consistent calculation for an isolated CO molecule:run-co.scf

Check the output file: what is the direction of the forces?

Modify the input file, relax the structure and find the equilibriumC-O bond length.

Exercise 14: molecular dinamics


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Exercise 14: molecular dinamics Molecular dynamics for bulk Si

Run the self consistent calculation for bulk Si:run-si.md

During the run, check the evolution of the total energy: md_analizer.sh

what do you notice? How does it change?



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