Don't forget to change the file run_script.sh
SIESTA=$HOME/bin/siestayou have to change for the path where are your siesta
are!
In my case is SIESTA=/home/guilherme/Programas/siesta-3.2/Obj/siestaI don't
know if this what's happening wrong if your simulation...
_______________________Guilherme Maia Santos
Doutorando (PhD student)
Multifunctional Devices Development Lab - MDDL
Departamento de Física - DF(Departament of physics)
Universidade Estadual de Maringá - UEM
(State University of Maringá)
University of Texas at San Antonio - UTSA
Em Quinta-feira, 11 de Junho de 2015 13:19, Abraham Hmiel
<[email protected]> escreveu:
My guess regarding the compilation errors: there's no need to use sudo for
this install, and your compiler in the makefile is pointing to f77, is it that
the same compiler you used to install SIESTA? It doesn't have to be, but if
SIESTA compiles you should use what works there. Your FC line should be
pointing to f90, or whatever fortran compiler (pg90, ifort, ifc, gfortran,
etc.) you used in the SIESTA install. Check your Obj/ folder in the SIESTA
source tree for the arch.make.
I could not reproduce your error when I used my own f77 compiler or f90 or
gfortran so that's strange. Try using gfortran, perhaps? You should not have to
edit the source code to get this utility to work. Just try a different compiler
until you can get it to work. My gfortran is: GNU Fortran 95 (GCC) 4.1.2
20070115 and it compiles without error. Swarm is Open-MP enabled, so you could
compile it in parallel as well.
On Thu, Jun 11, 2015 at 6:29 AM, Ludwig, Stephan
<[email protected]> wrote:
Hello Abraham,
thank you for your suggestion. Unfortunately I have proplems to install the
optimization programm.typing 'make swarm simplex' I receive the error message
i1@QuanQal2:/home/siesta-3.2-pl-5/Util/Optimizer$ sudo make swarm simplexf77
-c io.f
io_assign:
Error on line 2: syntax error
Warning on line 13: ignoring text after "end".
Warning on line 13: local variable out never used
Warning on line 13: local variable intend never used
Error on line 13: Declaration error for intend: adjustable dimension on
non-argument
/usr/bin/f77: aborting compilation
make: *** [io.o] Fehler 25
The io.f file looks like this
SUBROUTINE io_assign(lun)
integer intend(out) :: lun
logical used
integer iostat
c
c Looks for a free unit and assigns it to lun
c
do lun= 10, 99
inquire(unit=lun, opened=used, iostat=iostat)
if (iostat .ne. 0) used = .true.
if (.not. used) return
enddo
end SUBROUTINE io_assign
Can you help me to find the syntax error?
Best regards
Stephan
-----Original message-----
From: Abraham Hmiel <[email protected]>
Sent: Wednesday 10th June 2015 17:42
To: Siesta, Self-Consistent DFT LCAO program, http://www.uam.es/siesta
<[email protected]>
Subject: Re: [SIESTA-L] PAO-basis block for As
Stephan,
Creating a PAO basis set from scratch is a nontrivial exercise even for
experts. The way I usually use involves the simplex tetrahedral method, which
allows you to vary several parameters at a time and find their optimized
values. There is an implementation included with SIESTA.
Look in the Util/Optimizer folder of the siesta source tree. There are some
examples there which will allow you to use the simplex method code in a basic
manner for a water molecule to optimize basis set parameters. Take a look at
the files and study them and run the example calculations. They're pretty
quick. From there, it's not a big stretch to apply the principles to arsenic.
You will still have to figure out the format of the PAO basis block
corresponding to your pseudopotential and desired size of the basis set. You
might try using As2S3 or solid arsenic as input, and optimize for bond length
and total energy minimization. I'd offer that you might learn more doing it
this way.
Kind regards,
On Wed, Jun 10, 2015 at 7:27 AM, Nick Papior Andersen <[email protected]>
wrote:
I would suggest you ask your supervisor/professor (I suspect you have one?).
2015-06-10 16:24 GMT+02:00 Ludwig, Stephan
<[email protected]>:
Hello everybody,
I'm an absolute beginner in DFT calculations (I'm a Master student) and now I
have to cope with a material containing Arsenid.
The pseudopotential of As in the database has a semicore state so I have to
implement the PAO-basis block in the fdf-file.
I have no idea how to choose the parameters of this block to obtain reasonable
results.
I was able to start siesta by using a PAO-basis block which was originally
designed for iron:
%block PAO.Basis # Define Basis set
As 1 # Species label, number of
l-shells
n=3 2 2 # n, l, Nzeta
6.000 0.000
1.000 1.000
%endblock PAO.Basis
Can anybody please deliver a suitable PAO-basis and a pseudopotential for As.
Or can anybody help me to find a suitable PAO-basis for the pseudopotential I
use. You can find it in the attachment
It would be a great help and I would learn a lot through it
Thanks and regards
Stephan Ludwig
--
Kind regards Nick
--
Abraham Hmiel, Ph. D.http://abehmiel.net/about
-----Original message-----
From: Abraham Hmiel <[email protected]>
Sent: Wednesday 10th June 2015 17:42
To: Siesta, Self-Consistent DFT LCAO program, http://www.uam.es/siesta
<[email protected]>
Subject: Re: [SIESTA-L] PAO-basis block for As
Stephan,
Creating a PAO basis set from scratch is a nontrivial exercise even for
experts. The way I usually use involves the simplex tetrahedral method, which
allows you to vary several parameters at a time and find their optimized
values. There is an implementation included with SIESTA.
Look in the Util/Optimizer folder of the siesta source tree. There are some
examples there which will allow you to use the simplex method code in a basic
manner for a water molecule to optimize basis set parameters. Take a look at
the files and study them and run the example calculations. They're pretty
quick. From there, it's not a big stretch to apply the principles to arsenic.
You will still have to figure out the format of the PAO basis block
corresponding to your pseudopotential and desired size of the basis set. You
might try using As2S3 or solid arsenic as input, and optimize for bond length
and total energy minimization. I'd offer that you might learn more doing it
this way.
Kind regards,
On Wed, Jun 10, 2015 at 7:27 AM, Nick Papior Andersen <[email protected]>
wrote:
I would suggest you ask your supervisor/professor (I suspect you have one?).
2015-06-10 16:24 GMT+02:00 Ludwig, Stephan
<[email protected]>:
Hello everybody,
I'm an absolute beginner in DFT calculations (I'm a Master student) and now I
have to cope with a material containing Arsenid.
The pseudopotential of As in the database has a semicore state so I have to
implement the PAO-basis block in the fdf-file.
I have no idea how to choose the parameters of this block to obtain reasonable
results.
I was able to start siesta by using a PAO-basis block which was originally
designed for iron:
%block PAO.Basis # Define Basis set
As 1 # Species label, number of
l-shells
n=3 2 2 # n, l, Nzeta
6.000 0.000
1.000 1.000
%endblock PAO.Basis
Can anybody please deliver a suitable PAO-basis and a pseudopotential for As.
Or can anybody help me to find a suitable PAO-basis for the pseudopotential I
use. You can find it in the attachment
It would be a great help and I would learn a lot through it
Thanks and regards
Stephan Ludwig
--
Kind regards Nick
--
Abraham Hmiel, Ph. D.http://abehmiel.net/about
--
Abraham Hmiel, Ph. D.http://abehmiel.net/about
