Analysis, post-processing and visualization tools

Javier Junquera Andrei Postnikov

Summary of different tools for post-processing and visualization

DENCHAR PLRHO DOS, PDOS

DOS and PDOS

total Fe, d

MACROAVE

SIESTAs output with XCRYSDEN

Summary of different tools for post-processing and visualization

DENCHAR PLRHO DOS, PDOS

DOS and PDOS

total Fe, d

MACROAVE

SIESTAs output with XCRYSDEN

DENCHAR plots the charge density and wave functions in real space
Wave functions

Coefficients of the eigenvector with eigenvalue

atomic orbitals

Charge density

density matrix

DENCHAR operates in two different modes: 2D and 3D

2D
Charge density and/or electronic wave functions are printed on a regular grid of points contained in a 2D plane specified by the user. Used to plot contour maps by means of 2D graphics packages.

3D
Charge density and/or electronic wave functions are printed on a regular grid of points in 3D. Results printed in Gaussian Cube format. Can be visualized by means of standard programs (Moldel, Molekel, Xcrysden)

How to compile DENCHAR

Use the same arch.make file as for the compilation of serial SIESTA
Versions before 2.0.1, please check for patches in http://fisica.ehu.es/ag/siesta-extra/issues.html

and where to find the Users Guide and some Examples

How to run DENCHAR

SIESTA WriteDenchar WriteWaveFunctions %block WaveFuncKPoints 0.0 0.0 0.0 %endblock WaveFuncKPoints .true. .true.
Only if you want to plot wave functions

Output of SIESTA required by DENCHAR SystemLabel.PLD SystemLabel.DIM SystemLabel.DM SystemLabel.WFS (only if wave functions) ChemicalSpecies.ion (one for each chemical species) DENCHAR $ ln s ~/siesta/Src/denchar . $ denchar < dencharinput.fdf

You do not need to rerun SIESTA to run DENCHAR as many times as you want

Input of DENCHAR General issues

Written in fdf (Flexible Data Format), as in SIESTA It shares some input variables with SIESTA
SystemLabel NumberOfSpecies ChemicalSpeciesLabel

Some other input variables are specific of DENCHAR (all of them start with Denchar.)
To specify the mode of usage To define the plane or 3D grid where the charge/wave functions are plotted To specify the units of the input/output

Input of DENCHAR can be attached at the end of the input file

of SIESTA

Input of DENCHAR How to specify the mode of run

Denchar.TypeOfRun Denchar.PlotCharge Denchar.PlotWaveFunctions

(string) (logical) (logical)

2D or 3D .TRUE. or .FALSE. .TRUE. or .FALSE.

If .true. SystemLabel.DM must be present

If .true. SystemLabel.WFS must be present

Either one or the other (or both of them) must be .true.

Input of DENCHAR How to specify the plane

Denchar.PlaneGeneration
NormalVector TwoLines ThreePoints ThreeAtomicIndices

Plane of the plot in 2D mode x-y plane in 3D mode

(string)

+ more variables to define the

generation object (the normal vector, lines, points or atoms) origin of the plane x-axis size of the plane number of points in the grid

Different variables described in the User Guide (take a look to the Examples)

Output of DENCHAR 2D mode

Charge density
Spin unpolarized:
self-consistent charge (.CON.SCF) deformation charge (.CON.DEL)

Wave functions
Wave function for different bands (each wavefunction in a different file)
.CON.WF#, where # is the number of the wf (If spin polarized, suffix .UP or .DOWN)

Spin polarized:
density spin up (.CON.UP) density spin down (.CON.DOWN) deformation charge (.CON.DEL) magnetization (.CON.MAG)

Format

Output of DENCHAR 3D mode

Charge density
Spin unpolarized:
self-consistent charge (.RHO.cube) deformation charge (.DRHO.cube)

Wave functions
Wave function for different bands (each wavefunction in a different file)
.WF#.cube, where # is the number of the wf (If spin polarized, suffix .UP or .DOWN)

Spin polarized:
density spin up (.RHO.UP.cube) density spin down (.RHO.DOWN.cube) deformation charge (.DRHO.cube)

Format
Gaussian Cube format Atomic coordinates and grid points in the reference frame given in the input Reference frame orthogonal

Summary of different tools for post-processing and visualization

DENCHAR PLRHO DOS, PDOS

DOS and PDOS

total Fe, d

MACROAVE

SIESTAs output with XCRYSDEN

PLRHO plots a 3D isosurface of the charge density and colours it with a second function

LDOS integrated in a given energy interval + electrostatic potential + total potential + spin density

Plrho reads the values of the functions in the real space grid and Interpolates to plot the 3D surface.

How to compile PLRHO

First you need to install the PGPLOT library, available from

http://www.astro.caltech.edu/~tjp/pgplot

You can find plrho at

~/siesta/Utils/Plrho

Then compile PLRHO with

$ f90 plrho.f lX11 lpgplot o plrho

Check plrho_guide.txt for extra information.

How to run PLRHO

SIESTA SaveRho .true. SaveElectrostaticPotential .true. SaveTotalPotential .true. %block LocalDensityOfStates %block AtomicCoordinatesOrigin
Depending on what you want to plot If you want to center the system

Output of SIESTA required by PLRHO SystemLabel.RHO SystemLabel.VH SystemLabel.VT SystemLabel.LDOS

PLRHO Prepare the input file plrho.dat $ plrho

You do not need to rerun SIESTA to run PLRHO as many times as you want

Input of PLRHO: plrho.dat

Input of PLRHO: plrho.dat

rho ldos vh vt spin LDOS integrated in a given energy interval + electrostatic potential + total potential + spin density

Input of PLRHO: plrho.dat

Viewpoint is always from above (positive z axis) y

To view the system from a different angle, rotate it with the Euler angles

Input of PLRHO: plrho.dat

Example: view from y (Euler angles = 90 -90 -90) y z

Input of PLRHO: plrho.dat

Example: view from y (Euler angles = 90 -90 -90) Reference axes y System axes y

Input of PLRHO: plrho.dat

Example: view from y (Euler angles = 90 -90 -90) Reference axes y System axes y x

Alpha: first rotation around z

Input of PLRHO: plrho.dat

Example: view from y (Euler angles = 90 -90 -90) Reference axes y System axes y x x

Beta: rotation around y

Input of PLRHO: plrho.dat

Example: view from y (Euler angles = 90 -90 -90) Reference axes y System axes y x x z

Gamma: second rotation around z

Input of PLRHO: plrho.dat

Input of PLRHO: plrho.dat

Value of colouring function Potential or Spin

Pure blue Third value: maximum saturation range blue Interpolation white/blue Second value: mean saturation range white Interpolation red/white First value: minimum saturation range red Pure red

Output of PLRHO

screen

grey-scale postscrip

colour postscrip

Output of PLRHO

H2O molecule

Summary of different tools for post-processing and visualization

DENCHAR PLRHO DOS, PDOS

DOS and PDOS

total Fe, d

MACROAVE

SIESTAs output with XCRYSDEN

Density Of States (DOS)

the number of one-electron levels between E and E + dE

Si bulk

Density Of States (DOS)

the number of one-electron levels between E and E + dE

Si bulk

Units: (Energy)-1

Projected Density Of States (PDOS)

the number of one-electron levels with weight on orbital between E and E + dE

Coefficients of the eigenvector with eigenvalue

Overlap matrix of the atomic basis

Units: (Energy)-1

Relation between the DOS and PDOS:

The eigenvalues are broadening by a gaussian to smooth the shape of the DOS and PDOS

related with
the FWHM

Two step procedure to produce smooth DOS and PDOS

First:
Run a simulation with a sensible (converged) number of k-points kgrid_cutoff %block kgrid_Monkhorst_Pack Get converged geometry and density matrix

Second:
Starting from the previously converged geometry and density matrix, run a single SCF step with fixed geometry, with many more k-points DM.UseSaveDM MaxSCFIterations MD.NumCGsteps (or equivalent) Increase number of k-points (see above) %block ProjectedDensityOfStates .true. 1 0

How to compute the DOS and PDOS

%block ProjectedDensityOfStates -20.0 10.0 0.200 500 eV %endblock ProjectedDensityOfStates

-20.0 10.0 : Energy window where the DOS and PDOS will be computed

How to compute the DOS and PDOS

%block ProjectedDensityOfStates -20.0 10.0 0.200 500 eV %endblock ProjectedDensityOfStates

-20.0 10.0 : Energy window where the DOS and PDOS will be computed 0.200 : Peak width of the gaussian used to broad the eigenvalues (energy)

How to compute the DOS and PDOS

%block ProjectedDensityOfStates -20.0 10.0 0.200 500 eV %endblock ProjectedDensityOfStates

-20.0 10.0 : Energy window where the DOS and PDOS will be computed 0.200 : Peak width of the gaussian used to broad the eigenvalues (energy)

500 : Number of points in the histogram

How to compute the DOS and PDOS

%block ProjectedDensityOfStates -20.0 10.0 0.200 500 eV %endblock ProjectedDensityOfStates

-20.0 10.0 : Energy window where the DOS and PDOS will be computed 0.200 : Peak width of the gaussian used to broad the eigenvalues (energy)

500 : Number of points in the histogram

eV : Units in which the previous energies are introduced

Output for the Density Of States

SystemLabel.DOS Format
Energy (eV) DOS Spin Up (eV-1) DOS Spin Down (eV-1)

Output for the Projected Density Of States

SystemLabel.PDOS
Written in XML

Energy Window

One element <orbital> for every atomic orbital in the basis set

How to digest the SystemLabel.PDOS file

During the compilation of SIESTA
For some compilers, the libwxml.a library needs to be compiled with -DWXML_INIT_FIX (see known issues in http://fisica.ehu.es/ag/siesta-extra/issues.html)

pdosxml (by Alberto Garca)

Siesta/Util/pdosxml Edit the readme file to: Learn how to select the orbitals whose PDOS will be accumulated How to compile the code How to run the code

fmpdos (by Andrei Postnikov)

Download from http://www.home.uni-osnabrueck.de/apostnik/download.html Compile and follow the instructions at run-time

Normalization of the DOS and PDOS

Number of bands per k-point

Number of atomic orbitals in the unit cell

Number of electrons in the unit cell

Occupation factor at energy E

Example of DOS and PDOS

total Fe, d

J. Junquera et al. Surf. Sci. 482-485, 625 (2001) SIESTA, single-zeta polarized basis

K. A. Mder et al. Phys. Rev. B 48, 4364 (1998) All electron calculation

Summary of different tools for post-processing and visualization

DENCHAR PLRHO DOS, PDOS

DOS and PDOS

total Fe, d

MACROAVE

SIESTAs output with XCRYSDEN

How to extract from the immense detail provided by firstprinciples calculations on surfaces reliable values of the physical quantities of interest

Physical quantities of interest in surfaces and interfaces

Charge densities at the surface/interface Dipole moment densities at the surface/interface Work functions (surfaces) and band offsets (interfaces)

: the band structure term

Difference of the top of the valence bands From two independent bulk band structure calculations of the bulk material

: jump of the average electrostatic potential

Contains all the intrinsic interface effects Obtained by nanosmoothing the electrostatic potential

<VA>

<VB>

First step: average in the plane

vacuum

BaTiO3

vacuum

Second step: nanosmooth the planar average on the z-direction

vacuum

BaTiO3

vacuum

Atomic scale fluctuations are washed out by filtering the magnitudes via convolution with smooth functions

is readily obtained from the nanosmoothed potential

vacuum

BaTiO3

vacuum

How to compile MACROAVE

Use the same arch.make file as for the compilation of serial SIESTA

and where to find the Users Guide and some Examples

How to run MACROAVE

SIESTA SaveRho SaveTotalCharge SaveIonicCharge SaveDeltaRho SaveElectrostaticPotential SaveTotalPotential .true. .true. .true. .true. .true. .true.

Depending on what you want to nanosmooth

Output of SIESTA required by MACROAVE SystemLabel.RHO SystemLabel.TOCH SystemLabel.IOCH SystemLabel.DRHO SystemLabel.VH SystemLabel.VT MACROAVE Prepare the input file macroave.in $ ~/siesta/Util/Macroave/Src/macroave.x
You do not need to rerun SIESTA to run MACROAVE as many times as you want

Input of MACROAVE: macroave.in

The same code with the same input runs with information provided by

Siesta

or

Abinit

(indeed it should be quite straight forward to generalize to any other code)

Input of MACROAVE: macroave.in

Name of the magnitude that will be nanosmoothed Potential: Charge: TotalCharge: SystemLabel.VH SystemLabel.RHO SystemLabel.TOCH

Input of MACROAVE: macroave.in

SystemLabel

Input of MACROAVE: macroave.in

Number of square filter functions used for nanosmoothing 1 2 Surfaces Interfaces and superlattices

Input of MACROAVE: macroave.in

Length of the different square filter functions (in bohrs)

Input of MACROAVE: macroave.in

Total number of electrons

(used only to renormalize if we nanosmooth the electronic charge)

Input of MACROAVE: macroave.in

Type of interpolation from the SIESTA mesh to a FFT mesh

Spline

or

Linear

Output of MACROAVE
Planar average Nanosmoothed

SystemLabel.PAV

SystemLabel.MAV

Format

Units
Coordinates: bohr Potential: eV Charge density: electrons/bohr3

To learn more on nanosmoothing and how to compute work functions and band offsets with SIESTA