HANDS-ON TUTORIAL ON THE PWscf/FPMD/CP PACKAGE

Setting up the input files Post Processing Structural Relaxations Molecular Dynamics
S. Fabris and C. Sbraccia

CINECA March 3rd 2004

 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

bulk Al:

cubic fcc and sc bravais lattice

defective Al: sc bravais lattice

Al surfaces t bravais lattice

&system ibrav= 2,

celldm(1) =7.50, nat= 1, ntyp=1,

ecutwfc =15.0,

ibrav
0 1 2 3 4 5 6 7

structure
"free", see above cubic P (sc) cubic F (fcc) cubic I (bcc)

celldm(2)-celldm(6)
not used not used not used not used celldm(3)=c/a celldm(4)=cos(aalpha) celldm(3)=c/a celldm(3)=c/a

Hexagonal and Trigonal P Trigonal R Tetragonal P (st) Tetragonal I (bct)

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

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.in and producing the output file al.fcc.out Write down the total energy: it will be used in the following as reference Edit the script file run-al.sc modifying the variables IBRAV and NAT so that to obtain a simple cubic supercell with 4 atoms IBRAV=?, , NAT=?

Exercise 1: cubic supercell

Add the atomic coordinates in the ATOMIC_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 in file al.fcc.out: do they differ? Why?

ATOMIC_POSITIONS
Atomic positions in the supercell can be defined in 4 ways: 1. in units of ALAT (this is the default) 2. in crystal coordinates 3. In bohr 4. In Angstrom (alat) (crystal) (bohr) (angstrom)

The unit is defined by specifying the right flag as ATOMIC_POSITIONS (crystal)

Tetragonal supercell

a a

Exercise 2: tetragonal supercell

Have a look at the script file run-al.tet Modify the variables IBRAV and NAT so that to obtain a tetragonal 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 ?? ?? ??

ATOMIC_POSITIONS (alat)

c a

Al2

celldm(3)= 1.41421356237 Al 0.0 0.0 0.0 Al 0.5 0.5 0.707107

Al1

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

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 the reference one calculated in Example1 (al.fcc.out) grep ! ../Ex1/al.fcc.out grep ! al.tet.out why do they differ? What can you learn from the energy difference between the two?

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 ??? ??? ???

ATOMIC_POSITIONS (alat)

c a

Al2

Al1

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

Al 0.0 0.0 0.0 Al 0.5 0.5 0.5

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 one calculated in Example2 (al.tet.out) grep ! ../Ex2/al.tet.out grep ! al.tet2.out Do they differ? Why (or why not)?

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 repeated unit cells N With periodic boundaries conditions N infinity & Nk 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

K-POINT SAMPLING
The choice of the k-point mesh is system dependent. Examples: 1. Non-cubic supercells 2. Surfaces 3. Molecules isloated in vacuum

Exercise 4: elongated supercell

Have a look at the script file run-al.tet3 Modify the variables IBRAV, NAT, celldm(3), so that to double the size of the tetragonal supercell in the z direction (double the c/a ratio and double the number of atoms).

Exercise 4: elongated supercell

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 Run the scf calculation again (be careful not to overwrite the files ). Fill up the following table. Comment the difference in the total energies (per atom) of the 4 set of calculations: al.fcc.out -4.18739 al.tet.out al.tet3.out (12 12 10) al.tet3.out (12 12 5) ????? ????? -4.187028 -4.186958 ????? -4.187028

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 ?? 0.0 0.0 0.0 Al ?? ?? .. 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 withcalculation: Xcrysden: Run the self-consistent xcrysden pwi al.001.in ./run-al001

Exercise 6: isolated molecule

Simulation 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

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?

Exercise 7: energy-volume

Exercise 7: energy-volume
Calculation of an energy-volume curve for bulk Si Working input file: run-si.scf

Set the energy cutoff to 20 Ry: ecut=20 Set 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.out Repeat the procedure for the lattice parameters: Lattice parameter Energy 9.8 ??? 10.0 ??? 10.2 ??? 10.4 ???

Exercise 7: energy-volume
Write table on file: envol-ecut20.dat 9.8 ??? 10.0 ??? 10.2 ??? 10.4 ??? Plot the results:

Exercise 7: energy-volume
Recalculate the energy-volume curve with a larger cutoff: ecut=40 Collect the results in file envol-ecut40.dat 9.8 ??? 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?

Exercise 7: energy-volume

Pseudopotentials
Where to get the psudopotential files? 1. From the PWscf web site: http://www.pwscf.org

Pseudopotentials

You get psudopotential files ready-to-use with PWscf

Pseudopotentials
Where to get the psudopotential files? 2. From other databases: i.e. Vanderbilt ultra-soft pseudopotential site http://www.physics.rutgers.edu/~dhv/uspp/

Pseudopotentials
! Different xc functionals !

Pseudopotentials
Where to get the psudopotential files? 2. From other databases: i.e. Vanderbilt ultra-soft pseudopotential site http://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

Pseudopotentials
Where to get the psudopotential files? 3. Generate your own PP see Paolo Giannozzi Lecture

Self consistency: mixing

Cc Linear mixing

BAD CHOICE

Advanced mixing schemes

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

Example 8: improving convergency

Run the scf calculation for an elongated supercell of 16 Fe atoms run-fe16.scf & During the run check the convergency of the total energy grep e scf e total energy fe16.scf.out

What do you notice?? SUGGESTION Try to decrease the mixing parameter: mixing_beta = 0.1

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

Exercise 9: DOS
Run the scf calculation for bulk Ni run-ni.scf What happens? Why does the program stop? 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 9: DOS
Run the nscf calculation for bulk Ni: increase the number of bands to 8: nbnd=8 and 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 &inputpp outdir=$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!

Exercise 9: DOS
Have a look at the output file containing the DOS: ni.dos more ni.dos # E (eV) dosup(E) 5.749 0.0000E+00 5.849 0.9326E-03 5.949 0.3730E-02 6.049 0.1327E-01 6.149 0.1422E-01 6.249 0.1686E-01 6.349 0.1969E-01 dosdw(E) Int dos(E) 0.0000E+00 0.0000E+00 0.4531E-03 0.1386E-03 0.2685E-02 0.7801E-03 0.6781E-02 0.2785E-02 0.1859E-01 0.6066E-02 0.1600E-01 0.9352E-02 0.1876E-01 0.1320E-01

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

Exercise 10: PDOS

Have a look at the input file for the PDOS calculation: more run-pdos.in &inputpp outdir=$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

Exercise 10: 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) 4.249 4.349 4.449 4.549 4.649 4.749 4.849 dosup(E) 0.151E-13 0.379E-12 0.761E-11 0.122E-09 0.158E-08 0.163E-07 0.136E-06 dosdw(E) 0.545E-14 0.146E-12 0.314E-11 0.541E-10 0.746E-09 0.824E-08 0.731E-07

Exercise 10: PDOS

Plot the s and d components of the density of states : interpret the total density of states.

Simulating the STM image of the AlAs (110) surface

Exercise 11: STM images

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

 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?

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

Exercise 11: STM images

Producing a 3D file comptatible with the XCrysDen package: more run-AlAs.chdens &input nfile=1 filepp(1)='AlAsresm-1.0' weight(1)=1.0 iflag=3 3D plot plot_out=1 output_format=5 XCrysDen format e1(1)=7.0, e1(2)=0.0, e1(3)=0.0 e2(1)=0.0, e2(2)=7.07107, e2(3)=0.0 x0(1)=0.0, x0(2)=-0.18, x0(3)=3.25 nx=36 ,ny=56 fileout='AlAs110-1.0.xsf' /

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

Exercise 11: STM images

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

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[XI3N,(XI3N)] 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.

Ionic relaxation
Steepest Descent minimization :

discretization

gradient versor

Ionic relaxation
Steepest Descent minimization :

discretization

gradient versor

Ionic relaxation
Steepest Descent minimization :

discretization

gradient versor

Ionic relaxation
Steepest Descent minimization :

discretization

gradient versor

Ionic relaxation
Steepest Descent minimization :

discretization

gradient versor

Ionic relaxation
Steepest Descent minimization :

discretization

gradient versor

Ionic relaxation
Steepest Descent minimization :

discretization

gradient versor

Ionic relaxation
Steepest Descent minimization :

discretization

The minimum is reached !!!

gradient versor

Exercise 12: surface relaxation

Structural 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: what do 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 /

Exercise 12: surface relaxation

Analyze the output file: how are the forces evolving during the relaxation? 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 the 3 k points)

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 equilibrium C-O bond length.

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?

Exercise 14: molecular dinamics