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Setting up the input files Post Processing Structural Relaxations Molecular Dynamics
S. Fabris and C. Sbraccia
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:
&system ibrav= 2,
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
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)
Tetragonal supercell
a a
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
Al1
ATOMIC_POSITIONS (alat)
c a
Al2
Al1
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
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
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
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/
Pseudopotentials
Where to get the psudopotential files? 3. Generate your own PP see Paolo Giannozzi Lecture
Cc Linear mixing
BAD CHOICE
It is more flexible to mix the density instead of the potential PWscf mix the density by default
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=$TMP/DIR' prefix='ni' fildos='ni.dos' Emin=5.0, Emax=25.0, DeltaE=0.1 / and run the DOS calculation: run-ni.dos
in eV!
Exercise 9: DOS
Have a look at the output file containing the DOS: ni.dos more ni.dos # E (eV) dosup(E) 5.749 0.0000E+00 5.849 0.9326E-03 5.949 0.3730E-02 6.049 0.1327E-01 6.149 0.1422E-01 6.249 0.1686E-01 6.349 0.1969E-01 dosdw(E) Int dos(E) 0.0000E+00 0.0000E+00 0.4531E-03 0.1386E-03 0.2685E-02 0.7801E-03 0.6781E-02 0.2785E-02 0.1859E-01 0.6066E-02 0.1600E-01 0.9352E-02 0.1876E-01 0.1320E-01
Exercise 9: DOS
Plot the density of states and notice the difference in the spin up and spin down components:
Run the scf calculation for the AlAs (110) surface run-alas.scf Run the non scf calculation for the AlAs (110) surface: run-alas.nscf
Set up the input file for the post processing (see run-AlAs.ppstm): &inputpp prefix = 'AlAs110' outdir='$TMP_DIR/', filplot = 'AlAs-1.0' sample_bias=-0.0735d0, stm_wfc_matching=.false., plot_num= 5 / see O-sesame/pwdocs/INPUT_PP
Run the post processing simulation: run-AlAs.ppstm Redo the STM simulation, imaging empty states
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
gradient versor