Difficulty: how to deal accurately with both the core and valence electrons

1
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
2
Download the last versions of both codes, Siesta
and Abinit
Regarding the Abinit code, you can download the
required version from http//personales.unican.e
s/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
3
A few modifications to be done before
runningSiesta
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
X. Gonze et al., Phys. Rev. B 44, 8503 (1991)
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
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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)
6
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
7
A few modifications to be done before
runningAbinit
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
2. Remember to compile the code enabling the FOX
library
./configure --with-trio-flavornetcdfetsf_iofox

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Examples to run Siesta and Abinit with the same
pseudos
1. Visit the web page http//personales.unican.es
/junqueraj and follow the links Teaching Métod
os 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)
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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)
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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 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
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Running the energy versus cutoff energy in Abinit
To check the equivalent cutoff energy in Abinit

• 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)

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Diamond structure at the lattice constant that
minimizes the energy in Siesta
6 6 6 Monkhorst-Pack mesh
Ceperley-Alder (LDA) functional
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Running the energy versus cutoff energy in Abinit
To check the equivalent cutoff energy in Abinit

• 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)

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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
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Running the energy versus lattice constant curve
in Abinit
setting the plane wave cutoff to the equivalent
one to a DZP basis set
and changing the lattice constant embracing the
minimum
17
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
18
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.
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Comparing the energy versus lattice constant in
Siesta and Abinit bulk Si (covalent
semiconductor)
20
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
21
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
22
Running the energy versus cutoff energy in
Abinit bulk Al (a sp metal)
Lattice constant 3.97 Å
23
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
24
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
25
Running the energy versus cutoff energy in
Abinit bulk Au (a noble metal)
Lattice constant 4.08 Å
26
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
27
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
28
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
29
Running the energy versus cutoff energy in
Abinit bulk Fe (a magnetic transition metal)
Lattice constant 2.87 Å
30
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