A short introduction to SIESTAA short introduction to SIESTA

***************************** * WELCOME TO SIESTA *

*****************************

What Do you need?What Do you need?The code

 

The main input file

The pseudopotentials

 

The manual:

Tutorials, lectures, talks:

https://launchpadlibrarian.net/326725678/siesta.pdf

http://google.com

 https://launchpad.net/siesta

https://departments.icmab.es/leem/siesta/Databases/Pseudopotentials/periodictable-intro.html

The main input fileThe main input file1. Data can be given by any order

2. Omitted data -> default values

3.  Syntax: 'data label' followed by its value

Character string:          SystemLabel    water

Integer number:            NumberOfAtoms    42

Physical magnitude:    LatticeConstant    1.37 Ang

Logical:                                SpinOrbit    true

4. Labels are case insensitive and characters -_. are ignored LatticeConstant is

eq.ui-val_en_t to lattice_constant

Mandatory variables: GeneralMandatory variables: Generalsystem descriptors system descriptors 

SystemName: descriptive name of the system  

SystemLabel: nickname of the system to name output files

SystemLabel Si (After a successful run, you should have files like

Si.DM : Density matrix

Si.XV: Final positions and velocities

Si.bands: Electronic band structure

Si.DOS: Total density of states ...and many more, depending on your requests)

Mandatory variables: StructuralMandatory variables: Structuraland geometrical variablesand geometrical variables

NumberOfAtoms:  2     #number of atoms in the simulation box       

NumberOfSpecies:  1   #number of different atomic species

#ChemicalSpeciesLabel: specify the different chemical species

%block ChemicalSpeciesLabel

1 14 Si

2 42 Mo

%endblock ChemicalSpeciesLabel

Control the convergenceControl the convergenceFunctionals and authors:

GGA (PBE, revPBE, PBEsol, WC, BLYP)

LDA (CA, PZ)

VDW (DRSLL)

Basis-size: PAO.BasisSize: SZ

                                                           DZ

                                                           SZP

                                                           DZP

K-sampling: Monkhorst-Pack

Eggbox effectEggbox effectReal space grid is used to calculate the 3 center integrals

grid points

orbital

Forces are more affected than energy

Important for very precise relaxations andphonon calculations

Solution: MeshCutOff 

Convergence rarely achievable under 200 Ry

In case of spin-orbit interaction > 1000 Ry 

How to run SIESTA?How to run SIESTA?

[path_to_siesta]/siesta < myinput.fdf > myoutput

1st Example: dimers1st Example: dimers“ Your mission, should you choose to accept it...

1. Choose an element from the periodic table

2. Find out the bond length

 

http://www.kayelaby.npl.co.uk/chemistry/3_7/3_7_2.html

2nd Example: Al bulk2nd Example: Al bulk“ Your mission, should you choose to accept it...

Study the convergence of the structural and electronic properties of ametal with respect the first Brillouin zone sampling

1. Find out the stable, relaxed configure

2. Calculate the band structure

3. Calculate the DOS

Task: Fermi velocity of grapheneTask: Fermi velocity of graphene“ Your mission, should you choose to accept it...

Figure out the Fermi velocity for graphene!

v =F ℏ1

∂k∂E

a 1

a 2

142pm

1. Graphene is a hexagon formed by carbon atoms

2. Two atoms in the unit cell

3. Find out the optimized structure from SIESTA

4. Calculate the band structure near K point

5. Evaluate the Fermi velocity