![Page 1: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/1.jpg)
How to run with the same pseudos in Siesta and Abinit
Objectives
Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander projectors) in Siesta and Abinit.
Compare total energies
![Page 2: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/2.jpg)
Download the last versions of both codes, Siesta and Abinit
Regarding the Abinit code, you can download the required version from:
http://personales.unican.es/junqueraj/Abinit.tar.gz
But the merge of the relevant subroutines into the main trunk will be done soon
Regarding Siesta, the code is available at the usual web site:
http://www.icmab.es/siesta
![Page 3: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/3.jpg)
A few modifications to be done before running:Siesta
Edit the file atom.F in the Src directory
1. Replace “nrval” by “nrwf” in the call to schro_eq inside the subroutine KBgen (file atom.F)
2. Replace “nrval” by “nrwf” in the call to ghost inside the subroutine KBgen (file atom.F)
3. Increase the default of Rmax_kb_default to 60.0 bohrs (file atom.F)
![Page 4: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/4.jpg)
Definition of the Kleinman-Bylander projectors
The normalized Kleinman-Bylander projectors are given by
where
For the sake of simplicity, we assume here only one projector per angular momentum shell. If more than one is used, they must be orthogonalized
and are the eigenstates of the semilocal pseudopotential (screened by the pseudovalence charge density).
X. Gonze et al., Phys. Rev. B 44, 8503 (1991)
Note that these are the radial part of the wave function multiplied by ,
![Page 5: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/5.jpg)
Definition of the Kleinman-Bylander projectors (old choice in Siesta for the atomic eigenstates)
In the standard version of Siesta, the Schrödinger equation for the isolated
atom while generating the KB projectors is solved inside a box
whose size is determined by nrval.This is usually a very large radius (of
the order of 120 bohrs)
Then, this wave functions is normalized inside a sphere of a much
smaller radius, determined by Rmax_KB (default value = 6.0 bohr)
![Page 6: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/6.jpg)
Definition of the Kleinman-Bylander projectors (new choice in Siesta for the atomic eigenstates)
In the new version of Siesta, everything is consistent, and the Schrödinger equation and the normalization are
solved with respect the same boundary conditions
Almost no change in total energies observed, but the Kleinman-Bylander energies might be very different, specially for unbounded orbitals
![Page 7: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/7.jpg)
A few modifications to be done before running:Abinit
Edit the file src/65_psp/psp5nl.F90
1. Uncomment the last two lines for the sake of comparing Kleinman-Bylander energies and cosines with the ones obtained with Siesta
./configure --with-trio-flavor=netcdf+etsf_io+fox
2. Remember to compile the code enabling the FOX library
![Page 8: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/8.jpg)
Examples to run Siesta and Abinit with the same pseudos
1. Visit the web page:http://personales.unican.es/junqueraj
and follow the links:TeachingMétodos Computacionales en Estructura de la MateriaHand-on sessionsPseudos
2. Download the Pseudos and input files for both codes
3. Untar the ball file$ tar –xvf Siesta-Abinit.tar
This will generate a directory called Comparison-Siesta-Abinit with 4 directories:$ cd Comparison-Siesta-Abinit$ ls -ltr$ Si (example for a covalent semiconductor, LDA)$ Al (example for a sp-metal, LDA)$ Au (example for a noble metal, includes d-orbital, LDA)$ Fe (example for a transition metal, includes NLCC, GGA)
![Page 9: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/9.jpg)
Examples to run Siesta and Abinit with the same pseudos
In every subdirectory it can be found:$ cd Si$ ls –ltr$ Pseudo (files to generate and test the pseudopotential)$ Optimized-Basis (files to optimize the basis set)$ Runsiesta (files to run Siesta)$ Runabinit (files to run Abinit)
![Page 10: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/10.jpg)
How to generate and test a norm-conserving pseudopotential
Generate the pseudopotential using the ATM code as usual, following the notes in the Tutorial
“How to generate a norm conserving pseudopotential”
Copy the input file in the corresponding atom/Tutorial/PS_Generation directory and run
The pseudopotentials will be on the same parent directory: .vps (unformatted) (required to test the pseudopotential) .psf (formatted) .xml (in XML format) (required to run Abinit)
Remember to test the pseudopotential using the ATM code as usual, following the notes in the Tutorial
“How to test the transferability of a norm conserving pseudopotential”
![Page 11: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/11.jpg)
Running the energy versus lattice constant curve in Siesta
Run the energy versus lattice constant curve in Siesta as usual. You can use both the .psf or the .xml pseudopotential.
Follow the rules given in the tutorial“Lattice constant, bulk modulus, and equilibrium energy of solids”
The input file has been prepared for you (file Si.fdf).Since we are interested in compare the performance of the basis set, it is
important to converge all the rest of approximations (Mesh Cutoff, k-point grid, etc.) as much as possible
At the end, we would be able to write a file (here called Si.siesta.latcon.dat) that looks like this:
These data have been obtained with a double-zeta plus polarization basis
set, optimized at the theoretical lattice constant with a pressure of 0.05 GPa
![Page 12: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/12.jpg)
Running the energy versus cutoff energy in Abinit
To check the equivalent cutoff energy in Abinit:
1. We run the same system (same lattice vectors and internal coordinates) at the same level of approximations (same exchange and correlation functional, Monkhorst-Pack mesh etc.) at a given lattice constant.
Here it has been written for you (file Si.input.convergence)
![Page 13: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/13.jpg)
Diamond structure at the lattice constant that minimizes the energy in Siesta
6 × 6 × 6 Monkhorst-Pack mesh
Ceperley-Alder (LDA) functional
![Page 14: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/14.jpg)
Running the energy versus cutoff energy in Abinit
To check the equivalent cutoff energy in Abinit:
1. We run the same system (same lattice vectors and internal coordinates) at the same level of approximations (same exchange and correlation functional, Monkhorst-Pack mesh etc.) at a given lattice constant.
Here it has been written for you (file Si.input.convergence)
2. Change the cutoff energy for the plane waves
4. Run the code
3. Edit the .files file and select the input file and the pseudo file (in XML format)
![Page 15: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/15.jpg)
Running the energy versus cutoff energy in Abinit: bulk Si (covalent semiconductor)
Write the total energy as a function of the cutoff energy and edit the corresponding file that should look like this
Equivalent PW cutoff a DZP basis set at 5.38 Å
![Page 16: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/16.jpg)
Running the energy versus lattice constant curve in Abinit
1. Same input as before but…
… setting the plane wave cutoff to the equivalent one to a DZP basis set
… and changing the lattice constant embracing the minimum
2. Change in the .files the name of the input file
3. Run the code
![Page 17: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/17.jpg)
Running the energy versus lattice constant curve in Abinit
Write the total energy as a function of the lattice constant and edit the corresponding file that should look like this
![Page 18: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/18.jpg)
Comparing the pseudopotential in Siesta and Abinit: bulk Si (covalent semiconductor)
To be totally sure that we have run Siesta and Abinit with the same peudopotential operator, i.e. with the same decomposition in local part and
Kleinman-Bylander projectors:
1. Edit one of the output files in Siesta and search for the following lines:
2. Edit the log file in Abinit and search for the following lines:
The Kleinman-Bylander energies and cosines should be the same upto numerical
roundoff errors
Note: In Siesta they are written in Ry and in
Abinit they are in Ha.
![Page 19: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/19.jpg)
Comparing the energy versus lattice constant in Siesta and Abinit: bulk Si (covalent semiconductor)
![Page 20: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/20.jpg)
Comparing the pseudopotential in Siesta and Abinit: bulk Al (sp metal)
To be totally sure that we have run Siesta and Abinit with the same peudopotential operator, i.e. with the same decomposition in local part and
Kleinman-Bylander projectors:
![Page 21: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/21.jpg)
Comparing the pseudopotential in Siesta and Abinit: bulk Al (sp metal)
For the case of metallic system, besides the k-point sampling we have to pay particular attention to the occupation option
Siesta Abinit
Default: Fermi-Dirac
Also, as explained in the Tutorial“Convergence of electronic and structural properties of a metal with respect to
the k-point sampling: bulk Al”we should look at the Free Energy and not to the Kohn-Sham energy
![Page 22: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/22.jpg)
Lattice constant 3.97 Å
Running the energy versus cutoff energy in Abinit: bulk Al (a sp metal)
![Page 23: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/23.jpg)
Comparing the energy versus lattice constant in Siesta and Abinit: bulk Al (sp metal)Basis set of Siesta: DZP optimized with a pressure of 0.001 GPa at the theoretical
lattice constant of 3.97 Å)Plane wave cutoff in Abinit: 8.97 Ha
![Page 24: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/24.jpg)
Comparing the pseudopotential in Siesta and Abinit: bulk Au (a noble metal)
To be totally sure that we have run Siesta and Abinit with the same peudopotential operator, i.e. with the same decomposition in local part and
Kleinman-Bylander projectors:
![Page 25: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/25.jpg)
Lattice constant 4.08 Å
Running the energy versus cutoff energy in Abinit: bulk Au (a noble metal)
![Page 26: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/26.jpg)
Comparing the energy versus lattice constant in Siesta and Abinit: bulk Au (a noble metal)
Basis set of Siesta: DZP optimized with a pressure of 0.02 GPa at the theoretical lattice constant of 4.08 Å
Plane wave cutoff in Abinit: 17.432 Ha
![Page 27: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/27.jpg)
Comparing the pseudopotential in Siesta and Abinit: bulk Fe (a magnetic transition metal)
To be totally sure that we have run Siesta and Abinit with the same peudopotential operator, i.e. with the same decomposition in local part and
Kleinman-Bylander projectors:
![Page 28: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/28.jpg)
Comparing the pseudopotential in Siesta and Abinit: bulk Fe (a magnetic transition metal)
For the case of metallic system, besides the k-point sampling we have to pay particular attention to the occupation option.
Now, besides:-The system is spin polarized-We use a GGA functional-We include non-linear partial core corrections in the pseudo
Siesta Abinit
![Page 29: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/29.jpg)
Lattice constant 2.87 Å
Running the energy versus cutoff energy in Abinit: bulk Fe (a magnetic transition metal)
![Page 30: How to run with the same pseudos in S IESTA and A BINIT Objectives Run examples with the same pseudos (same decomposition in local part and Kleinman-Bylander](https://reader036.vdocuments.site/reader036/viewer/2022062511/55164507550346b2068b54b7/html5/thumbnails/30.jpg)
Comparing the energy versus lattice constant in Siesta and Abinit: bulk Fe(magnetic transition metal)
Basis set of Siesta: DZP optimized without pressure at the experimental lattice constant of 2.87 Å
Plane wave cutoff in Abinit: 34.82 Ha