[SIESTA-L] Unit of length for atomic positions

[Soumaia Djaadi]

Hi User !

 What is the unit of length for atomic positions the atoms stored in the
siesta .DIM output file ?
ThanksSoumaia Djaadi

Re: [SIESTA-L] Problem siesta 4 + openmpi

[Soumaia Djaadi]

Hello Jonathan! You can compile your code siesta-4.0 by intel fortran 
parallel studio compiler.Best regard Soumaia.
 

Le Lundi 27 février 2017 22h13, Gee Ufpi  a écrit :
 

 This message is eligible for Automatic Cleanup! (geeu...@gmail.com) Add 
cleanup rule | More info
 
Hi everyone,

I am compiling siesta 4.0 and 4.1  with openmpi, lapack, blas and scalapack, it 
worked. 
However, when I run siesta, the job finish with the message below


** End of input data file *
*
ERROR
 
FDF module: fdf_read:  Bad %endblock found in INPUT_TMP.14000
 
 File: fdf.F90
 Line:   934
*
STOP Stopping Program

It is confuse, because if I compile siesta 3.2 with similar arch.make, it 
works. There is similar behavior 
in serial or parallel mode. 

I would appreciate if you could help me on this issue.
Thanks

Jonathan



   

[SIESTA-L] install siesta-4.0 with intel fortran

[Soumaia Djaadi]

Hi allHow to compile siesta-4.0 by intel fortran 
parallel_studio_xe_2017_update1,
 can any one help me please ? 

[SIESTA-L] siesta-4.0

[Soumaia Djaadi]

Hello usersi want compile siesta-4.0 by intel fortran not by gnu fortran can 
any one help me ?  

[SIESTA-L] siestaxc

[Soumaia Djaadi]

Hello Users 
Where i can find the SiestaXC in siesta-3.2-pl-5 ?

[SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

[Soumaia Djaadi]

Hello Users 
I' m trying to install FAST TDDFT code but I have some problams, can you help 
me ?
Djaadi Soumaia.
.
Generators

The following generators are available on this platform:
  Ninja   = Generates build.ninja files (experimental).
  Unix Makefiles  = Generates standard UNIX makefiles.
  CodeBlocks - Unix Makefiles = Generates CodeBlocks project files.
  Eclipse CDT4 - Unix Makefiles
  = Generates Eclipse CDT 4.0 project files.
  KDevelop3   = Generates KDevelop 3 project files.
  KDevelop3 - Unix Makefiles  = Generates KDevelop 3 project files.

[ilaf@localhost build]$ 
-DSIESTA_XC_DIR=/ABSOLUTEPATH/home/siesta-3.2-pl-5/Obj/SiestaXC ../
bash: -DSIESTA_XC_DIR=/ABSOLUTEPATH/home/siesta-3.2-pl-5/Obj/SiestaXC: No such 
file or directory
[ilaf@localhost build]$ -DSIESTA_XC_DIR=/ABSOLUTEPATH//Obj/SiestaXC ../
bash: -DSIESTA_XC_DIR=/ABSOLUTEPATH//Obj/SiestaXC: No such file or directory
[ilaf@localhost build]$ 
..

Re: [SIESTA-L] Fast TDDFT

[Soumaia Djaadi]

 Hello Pr. Ross Brown!
   Thank you very much to help me.
   

   Djaadi Soumaia

[SIESTA-L] Fast TDDFT

[Soumaia Djaadi]

Hi all
I'm trying calculate the optical properties of clusters   by siesta.3 code but 
this latter is based in DFT method. After the search, l found Fast code, this 
version is designed to work with data produced by the siesta dft code. But I do 
not know anything for him. Where possible, it is found ?and how they are 
installed? and how the process works with siesta3 code ?Can any one help me.
With Best rogards Soumaia Djaadi.

[SIESTA-L] GGA pseudopotential non local

[Soumaia Djaadi]

Hi all

does anybody have a GGA (Pb) pseudopotential non local norme conserving 
factorized in the kleinman bylander form for Ge and Si?

With best regared

[SIESTA-L] GGA pseudopotential relativistic

[Soumaia Djaadi]

Hi all

does anybody have a GGA (Pb) pseudopotential relativistic for Ge and Si?

With best regared

[SIESTA-L] beta siesta4

[Soumaia Djaadi]

Hi Alberto GarciaThis is what I found at the site siesta
.
Siesta downloads

Stable version
   
   - Siesta 3.2 (patch level 5) (ChangeLog) (Manual)
   - Siesta 3.2 (Mar 28, 2013)
   - Older version: Siesta 3.1

Development version
It might be unstable, as new features are added at a faster pace. See the 
Docs/CHANGES file for more information.This version includes the van der Waals 
functional, the new load-balancing code for real-space grid operations, and 
other improvements and bug fixes.Recent development snapshots include 
significant enhancements to TranSiesta/TBTrans. TranSiesta users are encouraged 
to test the recent snapshots. Please read the file Docs/TranSiestaUpdate.pdf, 
as well as the manual, to get a primer on the new features and things to watch 
out for and explore in the new code.We welcome bug reports (see the file 
Docs/REPORTING_BUGS).   
   - Most recent development snapshot: siesta-trunk-462 (May 29, 2014). 
(ChangeLog from 458) (Reference Manual)(Includes new functionals and other 
fixes.)
   - Older development snapshot: siesta-trunk-458 (March 13, 2014). (ChangeLog 
from 454)(Includes an experimental charge-density-mixing scheme and other 
fixes.)
   - Older development snapshot: siesta-trunk-454 (January 31, 2014). 
(ChangeLog)(Includes an experimental orbital-minimization method without 
localization as an alternative to diagonalization, new mixing options, and 
other fixes.)NOTE: The grid functions (charge densities, potentials, etc) are 
in double precision by default in the development version (as of trunk-322). 
The 'phi' array that holds the values of the basis orbitals on the real-space 
grid is kept in single precision. Please take this into account if you compare 
the results of development-version runs with those of siesta-3.X runs. See the 
manual in both versions for more information.For more information on the 
load-balancing changes, see: C. F. Sanz-Navarro, R. Grima, A. Garcia, E. A. 
Bea, A. Soba, J.M. Cela, and P. Ordejon, Theoretical Chemistry Accounts 128, 
825-833 (2011). DOI: 10.1007/s00214-010-0816-5

Older 2.X version (not maintained any more)
   
   - Siesta 2.0.2

Other versions of Siesta
   
   - SIESTA-PEXSI (Dec. 2014)
   - Development version which includes the DFT+U functionality: 
siesta-ldau-308 (Feb. 2010)(Note that this version is several patches behind 
the main development. We are working towards merging the DFT+U code into the 
main version.)
   - Older version compatible with the Smeagol program: siesta-1.3f1 (Feb. 2004)
.All
 the bestDJAADI Soumaia

[SIESTA-L] siesta-trunk-462

[Soumaia Djaadi]

hi alli want to install siesta -trunk -462 but i have this problam 
m_zminim.F90:(.text+0x1bb71): undefined reference to `zhetri_'
m_svd.o: In function `__m_svd_MOD_solve_with_svd':
m_svd.F90:(.text+0x3d9): undefined reference to `dgelss_'
collect2: error: ld returned 1 exit status
make: *** [siesta] Error 1
[dell-inspiron@localhost Obj]$ 
what i do ?

[SIESTA-L] [***Posible SPAM***]

[Soumaia Djaadi]

Hi all, I want  calculate the optics properties of the clusters atomic but the 
results illogical for example the refrax-index in area 0.98-1.001. Do we have 
to change DFT to TDDFT and How to use TDDFT in siesta 3 cod?

[SIESTA-L] cobalt

[Soumaia Djaadi]

Hi all,I went caculate the electronic properties of germanium doped cobalt but 
i have a problem  as it is in output 
fileSiesta
 Version:    siesta-3.1
Architecture  : x86_64-unknown-linux-gnu--unknown
Compiler flags: mpif90 -g -O2
PARALLEL version

* Running in serial mode with MPI
>> Start of run:  10-OCT-2015  20:00:19

   ***   
   *  WELCOME TO SIESTA  *   
   ***   

reinit: Reading from standard input
** Dump of input data file 
SystemName   Ge1Co    # Descriptive name of the system
SystemLabel  Ge1Co   # Short name for naming files
# Output options
WriteCoorStep
WriteMullikenPop   1
LongOutput
WriteCoorXmol
# Species and atoms
NumberOfSpecies    2
NumberOfAtoms  2
%block ChemicalSpeciesLabel
  1  32  Ge
  2  27  Co
%endblock ChemicalSpeciesLabel
# Basis
PAO.EnergyShift   50 meV
%block PAO.BasisSizes
   Ge SZ
   Co DZP
%endblock PAO.BasisSizes
LatticeConstant    5.65 Ang
%block LatticeVectors
 7.    0.0    0.0
 0.    7.0    0.0
 0.    0.0    7.0
%endblock LatticeVectors
%block BandLines
  1  0.0   0.00  0.00  \Gamma
 40  2.0   0.00  0.00  H
 28  1.0   1.00  0.00  N
 28  0.0   0.00  0.00  \Gamma
 34  1.0   1.00  1.00  P
%endblock BandLines
xc.functional GGA   # Exchange-correlation functional
xc.authors    PBE   # Exchange-correlation version
SpinPolarized true  # Logical parameters are: yes or no
MeshCutoff  40. Ry    # Mesh cutoff. real space mesh
# SCF options
MaxSCFIterations   200   # Maximum number of SCF iter
DM.MixingWeight   0.1   # New DM amount for next SCF cycle
DM.Tolerance  1.d-4 # Tolerance in maximum difference
    # between input and output DM
DM.UseSaveDM  .true.  # to use continuation files
MD.UseSaveXV  .true.
WriteMDhistory    .true.
DM.NumberPulay 3
SolutionMethod    diagon    # OrderN or Diagon
ElectronicTemperature  25 meV   # Temp. for Fermi smearing
# MD options
MD.TypeOfRun   cg   # Type of dynamics:
MD.NumCGsteps  300   # Number of CG steps for
    #   coordinate optimization
MD.MaxCGDispl  0.1 Ang  # Maximum atomic displacement
    #   in one CG step (Bohr)
MD.MaxForceTol 0.01 eV/Ang  # Tolerance in the maximum
    #   atomic force (Ry/Bohr)
UseSaveData .true.
%block ProjectedDensityOfStates
   -100.00 +100.00    0.500   500    eV
%endblock ProjectedDensityOfStates
# Atomic coordinates
AtomicCoordinatesFormat  Ang
%block AtomicCoordinatesAndAtomicSpecies
 0.475613    2.393742    0.223623  1  #  Ge 1
-0.47    0.013820   -0.232985  2  #  Co 2
%endblock AtomicCoordinatesAndAtomicSpecies
OpticalCalculation .true.
%block  Optical.Mesh
  20 20 20
%endblock  Optical.Mesh
Optical.OffsetMesh .true.
Optical.PolarizationType polarized
%block  Optical.Vector
  1.0 0.0 0.0
%endblock  Optical.Vector
Optical.Broaden 0.2 eV
Optical.EnergyMaximum  30.0 eV
Optical.EnergyMinimum  0.0 eV
** End of input data file *

reinit: ---
reinit: System Name: Ge1Co
reinit: ---
reinit: System Label: Ge1Co 
  
reinit: ---

initatom: Reading input for the pseudopotentials and atomic orbitals --
 Species number:    1  Label: Ge Atomic number:  32
 Species number:    2  Label: Co Atomic number:  27
Ground state valence configuration:   4s02  4p02
Reading pseudopotential information in formatted form from Ge.psf

Valence configuration for pseudopotential generation:
4s( 2.00) rc: 2.06
4p( 2.00) rc: 2.85
4d( 0.00) rc: 2.58
4f( 0.00) rc: 2.58
Ground state valence configuration:   4s02  3d07
Reading pseudopotential information in formatted form from Co.psf

Valence configuration for pseudopotential generation:
Semicore shell(s) with -9 electrons included in the valence for
Co
resizes: Read basis size for species Ge = sz  
resizes: Read basis size for species Co = dzp 
Co   must be in PAO.Basis (it has semicore states)
ERROR STOP from Node:    0
what
 is the 

Re: [SIESTA-L] optic

[Soumaia Djaadi]

 
  Hi Younnas khan
Can i calculate the optical properties  for  Germanium clusters using siesta ? 
How ?
  
  
  Regards
  
   Soumaia DJAADI
  
  
  
  

Re : [SIESTA-L] fedora 20

[Soumaia Djaadi]

Hi Younnas khan
 no results, this is erreur message and fortran compiler installed in my system

[dell-inspiron@localhost Optical]$ gfortran  optical.f -o optical
bash: gfortran: command not found...
[dell-inspiron@localhost Optical]$ man -k fortran
ctags (1p)   - create a tags file (DEVELOPMENT, FORTRAN)
fort77 (1p)  - FORTRAN compiler (FORTRAN)
[dell-inspiron@localhost Optical]$ 
Regards
 Soumaia DJAADI 

Re: [SIESTA-L] fedora 20

[Soumaia Djaadi]

 Hi Younnas khan
I used the command: which fortran 
[dell-inspiron@localhost ~]$ which fortran
/usr/bin/which: no fortran in 
(/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/home/dell-inspiron/.local/bin:/home/dell-inspiron/bin)
[dell-inspiron@localhost ~]$ 
Do  must install the Fortran my system

 
 
 Regards
 
  Soumaia DJAADI
 
 
 
 

[SIESTA-L] fedora 20

[Soumaia Djaadi]

This is error message :
[dell-inspiron@localhost Optical]$ f77  optical.f -o optical
bash: f77: command not found...

[SIESTA-L] linux fedora 20

[Soumaia Djaadi]

Thanks for help me Younas Khan
I have tried but without result. What to do ?
Soumaia DJAADI

[SIESTA-L] linux fedora 20

[Soumaia Djaadi]

     hi, how to compile
input.f and optical.f in linux fedora 20 ?
  
  
     can any one help me?
    
     soumaia djaadi

[SIESTA-L] Fw : optical properties

[Soumaia Djaadi]

  hi,  i would calculate the optical properties of Gen (n= 2,8) clusters using 
annealing simulated method. for this reason i have instaled the  siesta-3.1 and 
linux
  fedora 20. i have tried to run the optical properties of the  Gen (n= 2,8) 
clusters. the optical properties was calculated in normal manner with:
  
 
..
   OpticalCalculation .true.
  
 
   %block  Optical.Mesh
  
    
    20 20 20
  
 %endblock  Optical.Mesh
   
   Optical.OffsetMesh .true.
  
 
   Optical.PolarizationType unpolarized
   %block Optical.Vector
             1.0 0.0 0.0
  
  %endblock Optical.Vector
   
  
 Optical.Broaden 0.2 eV
   
   Optical.EnergyMaximum  30.0 eV
  
   Optical.EnergyMinimum 0.0 eV
  
 
 

   I obtained Gen.EPSIMG file for each clusters but the problem is  the file 
Ge2..EPSIMG   is generated to the file e2.dat and the rest of the files
 (Ge3.EPSIMG, Ge4.EPSIMG,) have not generated with the next error 
message:
  
 
 
..
    ##    0.   
         136.039899    
     ##            1
 
  
  
  
 ##   0.63892    
    
 ##   
  
 
 0.    
     Fsum rule is not  fulfilled by more than a  20% 
 The dielectric function will be extended to higher
   energies by enforcing the Fsum rule This will increase the
   quality of the quantities calculated via the Kramers-Kroning relation
   
 
 
..
   
    soumaia djaadi
    department of physic
    university of ouargla  
         algeria

[SIESTA-L] Fw : Re : optical properties

[Soumaia Djaadi]

--- En date de : Mer 26.8.15, Soumaia Djaadi soumaia_...@yahoo.fr a écrit :

 De: Soumaia Djaadi soumaia_...@yahoo.fr
 Objet: Re : optical properties
 À: siesta-l@uam.es
 Date: Mercredi 26 août 2015, 22h35
 
 
  
  Hi Dear siesta user
  I
 calculeted optical properties of Gen (n =
 
 2,8)clusters with siesta by annealing simulated method.
  I obtained Gen.EPSIMG file for each
 clusters
  but the the problem is Ge2.EPSIMG
 file has been generated to
  e2.dat this last
 has been generated to  optical properties
 
 (epsilon_real.out, epsilon_img.out,  )but the rest
 of
  the clusters Ge3, Ge4 , are not
 being generated to
  e2.dat and the terminal
 is print:
 
 ..
    ##    0.       
  136.039899    
  ## 
          
  1
 
 ##   0.63892   
  
  ##    0.    
  Fsum rule is not fulfilled by more than a 
  20%
  The dielectric function
 will be
  extended
  to higher
 energies by enforcing the
  Fsum rule
  This will increase the quality of
  the quantities
  calculated via
 the
  Kramers-Kroning relation
 
 .
  and the part of optical properties
 calculation
  in fdf is:
 
 OpticalCalculation .true.
  
 
 %block  Optical.Mesh
        20 20 20
  %endblock 
  Optical.Mesh
  
  Optical.OffsetMesh .true.
  
  Optical.PolarizationType
 unpolarized
  %block  Optical.Vector
     
        1.0 0.0 0.0
  %endblock 
  Optical.Vector
  
  Optical.Broaden 0.2 eV
  
  Optical.EnergyMaximum  30.0
 eV
  
 
 Optical.EnergyMinimum  0.0
  eV
  
  Can any one help me?
  soumaia
  
  
       

Re : [SIESTA-L] SUBSCRIBE SIESTA-L soumaia DJAADI

[Soumaia Djaadi]