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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.

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Presentation on theme: "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."— Presentation transcript:

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 projectors) in S IESTA and A BINIT. Compare total energies

2 Download the last versions of both codes, S IESTA and A BINIT Regarding the A BINIT code, you can download the required version from: 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:

3 A few modifications to be done before running: S IESTA 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)

4 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,

5 Definition of the Kleinman-Bylander projectors (old choice in S IESTA 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)

6 Definition of the Kleinman-Bylander projectors (new choice in S IESTA 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

7 A few modifications to be done before running: A BINIT 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 S IESTA./configure --with-trio-flavor=netcdf+etsf_io+fox 2. Remember to compile the code enabling the FOX library

8 Examples to run S IESTA and A BINIT with the same pseudos 1. Visit the web page: and follow the links: Teaching Métodos Computacionales en Estructura de la Materia Hand-on sessions Pseudos 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)

9 Examples to run S IESTA and A BINIT 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)

10 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

11 Running the energy versus lattice constant curve in S IESTA 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

12 Running the energy versus cutoff energy in A BINIT 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)

13 Diamond structure at the lattice constant that minimizes the energy in S IESTA 6 × 6 × 6 Monkhorst-Pack mesh Ceperley-Alder (LDA) functional

14 Running the energy versus cutoff energy in A BINIT 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)

15 Running the energy versus cutoff energy in A BINIT : 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

16 Running the energy versus lattice constant curve in A BINIT 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

17 Running the energy versus lattice constant curve in A BINIT Write the total energy as a function of the lattice constant and edit the corresponding file that should look like this

18 Comparing the pseudopotential in S IESTA and A BINIT : bulk Si (covalent semiconductor) To be totally sure that we have run S IESTA and A BINIT 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 S IESTA and search for the following lines: 2. Edit the log file in A BINIT and search for the following lines: The Kleinman-Bylander energies and cosines should be the same upto numerical roundoff errors Note: In S IESTA they are written in Ry and in A BINIT they are in Ha.

19 Comparing the energy versus lattice constant in S IESTA and A BINIT : bulk Si (covalent semiconductor)

20 Comparing the pseudopotential in S IESTA and A BINIT : bulk Al (sp metal) To be totally sure that we have run S IESTA and A BINIT with the same peudopotential operator, i.e. with the same decomposition in local part and Kleinman-Bylander projectors:

21 Comparing the pseudopotential in S IESTA and A BINIT : 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 S IESTA A BINIT 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

22 Lattice constant 3.97 Å Running the energy versus cutoff energy in A BINIT : bulk Al (a sp metal)

23 Comparing the energy versus lattice constant in S IESTA and A BINIT : bulk Al (sp metal) Basis set of Siesta: DZP optimized with a pressure of GPa at the theoretical lattice constant of 3.97 Å) Plane wave cutoff in Abinit: 8.97 Ha

24 Comparing the pseudopotential in S IESTA and A BINIT : bulk Au (a noble metal) To be totally sure that we have run S IESTA and A BINIT with the same peudopotential operator, i.e. with the same decomposition in local part and Kleinman-Bylander projectors:

25 Lattice constant 4.08 Å Running the energy versus cutoff energy in A BINIT : bulk Au (a noble metal)

26 Comparing the energy versus lattice constant in S IESTA and A BINIT : 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: Ha

27 Comparing the pseudopotential in S IESTA and A BINIT : bulk Fe (a magnetic transition metal) To be totally sure that we have run S IESTA and A BINIT with the same peudopotential operator, i.e. with the same decomposition in local part and Kleinman-Bylander projectors:

28 Comparing the pseudopotential in S IESTA and A BINIT : 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 S IESTA A BINIT

29 Lattice constant 2.87 Å Running the energy versus cutoff energy in A BINIT : bulk Fe (a magnetic transition metal)

30 Comparing the energy versus lattice constant in S IESTA and A BINIT : 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: Ha


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