How to run with the same pseudos
in SIESTA and ABINIT
-215.78
Siesta (DZP)
Abinit (13.005 Ha)
Free Energy (eV)
-215.79
-215.80
-215.81
-215.82
5.30
5.35
5.40
5.45
Lattice constant (Ang)
5.50
Objectives
Run examples with the same pseudos (same decomposition in
local part and Kleinman-Bylander projectors) in SIESTA and ABINIT.
Compare total energies
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
A few modifications to be done before running:
SIESTA
Edit the file atom.F in the Src directory
I.
E N E R G Y F U N C T I ON A L F OR A D I E L E C T R I C I N SI D E A N E L E C T R I C
1. Replace “nrval”I 1.byEN
“nrwf”
KBgen
ER G Yin Fthe
U Ncall
C T I to
ONschro_eq
A L FOR Ainside
D I EL the
EC Tsubroutine
R I C I N SI D E
A N EL
Cit e .
(file atom.F)
I . E N E R G Y F U N C T I ON A L F OR A D I E L E C T R I C I N SI D E A N E L E C T R
1
i
f
( er ef kb( i kb, l ) . ge. 1. 0d3) t hen
Cit e .
nnodes=i kb
+1
i f ( er efnpr
kb(i n=l
i kb,
l ) . ge. 1. 0d3) t hen
cal
l
schr
, r 1.
of 0d3)
i , vps(
1, l ) , ve, s, dr di ,
i f ( er ef
kb(o_eq(
i kb, lZval
) . ge.
t hen
nnodes=i
kb
.
nnodes=i kb nr wf , l , a, b, nnodes, npr i n,
npr
i
n=l
+1
.
npr i n=l +1 er ef kb( i kb, l ) , r phi ( 1, i kb) )
Cit e1 .
cal l schr
Zval Zval
, r of, ri of, vps(
1,1,l l) ),,ve,
s,drdrdidi, ,
cal lo_eq(
schr o_eq(
i , vps(
ve, s,
i f ( nkbl ( l ) . eq. 1) t hen
.
nr, wf
, lwf
, a,
n,
.
nr
, l ,b,
a, nnodes,
b, nnodes,npr
npr i n,
cal l in
ghost
( Zval
rto
of i ghost
, vps( : , inside
l ) , vl ocal
, subroutine KBgen (file
2. Replace “nrval”
by
“nrwf”
the
call
the
.
er
ef ikb(
i kb, l ) , r phi ( 1, i kb) )
.
er, ef
kb(
.
ve, s, dr di , nr wf
l , a,
b, nrkb,
wf ,l ) , r phi ( 1, i kb) )
atom.F)
.
eri ef
kb( i (kb,
) , r 1)
phi t(hen
: , i kb) , i ghost )
f ( nkbl
l ) .l eq.
el se(cal
i f ( nkbl
l ) l. eq.
1)( Zval
t hen
ghost
, r of i , vps( : , l ) , vl ocal ,
( Zval
r of
: ,wfl ,) , vl ocal ,
.cal l ghost
ve, s,
dr di ,,nr
wf ,i l ,, vps(
a, b, nr
r eal ( dp) , par amet er : : Rmax_kb_def aul t = 60. 0d0
. ve, s, drerdief,kb(
( : ,w
i fkb)
.
nr iwkb,
f , ll ,) ,a,r phi
b, nr
, , i ghost )
el se
.
er ef kb(
i kb, l ) , r phi ( : , i kb) , i ghost )
el se
( dp) , par amet er : : to
Rmax_kb_def
aul t (file
= 60.atom.F)
0d0
3. Increase the default
ofr eal
Rmax_kb_default
60.0 bohrs
1
2
ealY(.-H.
dp)Shin,
, par
am
: :J. R
max_kb_def
= 60.
0d0
G. rLee,
and
J.etYer
. Son,
Am.
Ceram. Soc.,aul
95,t 2773
(2012).
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
and
Note that these
are the eigenstates of the semilocal pseudopotential
(screened by the pseudovalence charge density).
are the radial part of the wave function multiplied by
,
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
Definition of the Kleinman-Bylander projectors
(old choice in SIESTA for the atomic eigenstates)
s - shell
p - shell
d - shell
f - shell
ul
PS
(r)
1,0
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)
0,5
0,0
0
10
Rmax_KB
20
30
radius (bohr)
40
Then, this wave functions is
normalized inside a sphere of a much
smaller radius, determined by
50
Rmax_KB (default value = 6.0 bohr)
Definition of the Kleinman-Bylander projectors
(new choice in SIESTA for the atomic eigenstates)
0,8
s - shell
p - shell
d - shell
f - shell
0,6
0,4
ul
PS
(r)
In the new version of Siesta, everything
is consistent, and the Schrödinger
equation and the normalization are
solved with respect the same boundary
conditions
0,2
0,0
0
10
20
30
40
radius (bohr)
50
60
Rmax_KB
Almost no change in total energies observed, but the Kleinman-Bylander
energies might be very different, specially for unbounded orbitals
A few modifications to be done before running:
ABINIT
Edit the file src/65_psp/psp5nl.F90
1. Uncomment the last two lines
ofT comparing
I . E for
N E Rthe
G Y sake
FU N C
I ON A L F OR Kleinman-Bylander
A D I E L E C T R I C I N SI D E
energies and cosines with the ones obtained with SIESTA
Cit e1 .
! DEBUG
wr i t e( st d_out , * ) ’ EKB=’ , ( ekb( i q) , i q=1, 4)
wr i t e( st d_out , * ) ’ COSKB=’ , ( ckb( i q) , i q=1, 4)
! ENDDEBUG
i f ( nkbl ( l ) . eq. 1) t hen
cal enabling
l ghost ( Zval
of i , vps(
: , l ) , vl ocal ,
2. Remember to compile the code
the, rFOX
library
.
ve, s, dr di , nr wf , l , a, b, nr wf ,
.
er ef kb( i kb, l ) , r phi ( : , i kb) , i ghost )
el se
./configure --with-trio-flavor=netcdf+etsf_io+fox
r eal ( dp) , par amet er : : Rmax_kb_def aul t = 60. 0d0
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
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)
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)
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
directory
I . Ein
N Ethe
R G Ycorresponding
F U N C T I ON A L F atom/Tutorial/PS_Generation
OR A D I E L E C T R I C I N SI D E A N E L E
CT R I C FI EL D
and run
Cit e1 .
$ . . / . . / Ut i l s/ pg. sh Si . t m2. i np
==> Out put dat a i n di r ect or y Si . t m2
==> Pseudopot ent i al i n Si . t m2. vps and Si . t m2. psf ( and maybe i n Si . t m2. xml )
i f ( nkbl ( l ) . eq. 1) t hen
cal l ghost ( Zval , r of i , vps( : , l ) , vl ocal ,
The pseudopotentials
will be on the same parent directory:
.
ve, s, dr di , nr wf , l , a, b, nr wf ,
.vps
test )the pseudopotential)
. (unformatted)
er ef kb( i kb, l ) ,(required
r phi ( : , i kb)to
, i ghost
el se
.psf (formatted)
.xml (inr eal
XML
format) (required to run Abinit)
( dp) , par amet er : : Rmax_kb_def aul t = 60. 0d0
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”
1
G. Lee, Y .-H. Shin, and J. Y . Son, J. A m. Ceram. Soc., 95, 2773 (2012).
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
2
I . E N Ewe
R G Ywould
F U N C T I be
ON Aable
L F O R to
A Dwrite
I EL EC Ta
RIC
I N SI
D E A N called
E L E C T R I Si.siesta.latcon.dat)
C FI EL D .
At the end,
file
(here
that looks like this:
Cit e1 .
# Lat t i ce Const ant ( Ang)
5. 30
5. 32
5. 34
5. 36
5. 38
5. 40
5. 42
5. 44
5. 46
5. 48
Fr ee Ener gy ( eV)
- 215. 790381
- 215. 802337
- 215. 811082
- 215. 816643
- 215. 819095
- 215. 818374
- 215. 814586
- 215. 808022
- 215. 798710
- 215. 786727
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
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)
Diamond structure at the lattice
constant that minimizes the energy
in SIESTA
6 × 6 × 6 Monkhorst-Pack mesh
Ceperley-Alder (LDA) functional
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
$ mor e Si . f i l es $ mor e Si . f i l es
Si . i nput . conver gence
Si . i nput . conver gence
Si . out
3. Edit the .files file and
select
Si . out
Si i
Si o
i
the input file and theSipseudo
t 1x
file (in XML format) Si o
Si . xml
t 1x
Si . xml
$ abi ni t < Si . f i l es > Si . l og &
4. Run the code
$ abi ni t < Si . f i l es > Si . l og &
1
G. Lee, Y .-H. Shin, and J. Y . Son, J. A m. Ceram. Soc., 95, 2773 (2012).
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
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
$ mor e Si . f i l es
Si . i nput . conver gence
Si . out
Si i
Si o
t 1x
Si . xml
3. Run the code
$ abi ni t < Si . f i l es > Si . l og &
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
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.
Comparing the energy versus lattice constant in
SIESTA and ABINIT: bulk Si (covalent semiconductor)
-215.78
Siesta (DZP)
Abinit (13.005 Ha)
Free Energy (eV)
-215.79
-215.80
-215.81
-215.82
5.30
5.35
5.40
5.45
Lattice constant (Ang)
5.50
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:
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
Running the energy versus cutoff energy in ABINIT:
bulk Al (a sp metal)
Lattice constant 3.97 Å
-56,9
Free Energy (eV)
-57,0
-57,1
DZP
-57,2
0
5
10
20
15
Cutoff energy (Ha)
25
30
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
-57.14
Siesta (DZP)
Abinit (8.97 Ha)
Free Energy (eV)
-57.15
-57.16
-57.17
-57.18
3.85
3.90
4.00
3.95
4.05
Lattice constant (Ang)
4.10
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:
Running the energy versus cutoff energy in ABINIT:
bulk Au (a noble metal)
Lattice constant 4.08 Å
-903.6
-903.8
Free Energy (eV)
-904.0
-904.2
-904.4
DZP
-904.6
-904.8
-905.0
20
30
40
Cutoff energy (Ha)
50
60
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
-904.66
Siesta (DZP)
Abinit (17.432 Ha)
Free Energy (eV)
-904.67
-904.68
-904.69
-904.70
4.00
4.10
4.05
Lattice constant (Ang)
4.15
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:
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
Running the energy versus cutoff energy in ABINIT:
bulk Fe (a magnetic transition metal)
Lattice constant 2.87 Å
-765.0
Free Energy (eV)
-770.0
-775.0
-780.0
20
DZP
30
40
50
Cutoff energy (Ha)
60
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
-782.48
Siesta (DZP)
Abinit (34.82 Ha)
Free Energy (eV)
-782.50
-782.52
-782.54
-782.56
-782.58
-782.60
2.75
2.80
2.90
2.85
2.95
Lattice constant (Ang)
3,00