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Aplicacións

SIESTA

Versións dispoñibles:

SVG

  • 2.0.2
  • 3.1
  • 3.2-pl3
  • trunk-462

FinisTerraeII

  • trunk-462
  • 4.0b-458
  • 3.2-pl-5

Descrición


Siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. Its main characteristics are: 

  • It uses the standard Kohn-Sham selfconsistent density functional method in the local density (LDA-LSD) or generalized gradient (GGA) approximations. 
  • Uses norm-conserving pseudopotentials in its fully nonlocal (Kleinman-Bylander) form. 
  • The basis set is a very general and flexible linear combination of numerical atomic orbitals (LCAO). It allows arbitrary angular momenta, multiple-zeta, polarized and off-site orbitals. 
  • Projects the electron wavefunctions and density onto a real-space grid in order to calculate the Hartree and exchange-correlation potentials and their matrix elements. 
  • Besides the standard Rayleigh-Ritz eigenstate method, it allows the use of localized linear combinations of the occupied orbitals (valence-bond or Wannier-like functions), making the computer time and memory scale linearly with the number of atoms. Simulations with several hundred atoms are feasible with modest workstations. 
  • It is written in Fortran90. In particular, memory is allocated dynamically, so there is no need to recompile the program when the problem size changes. 
  • It may be compiled for serial or parallel execution (under MPI). (Note: This feature might not be available in all distributions) It routinely provides: 
  • Total and partial energies. 
  • Atomic forces. 
  • Stress tensor. 
  • Electric dipole moment. 
  • Atomic, orbital and bond populations (Mulliken). 
  • Electron density. And also (though not all options are compatible): 
  • Geometry relaxation, fixed or variable cell. 
  • Constant-temperature molecular dynamics (Nose thermostat). 
  • Variable cell dynamics (Parrinello-Rahman). 
  • Spin polarized calculations (collinear or not).
  • k-sampling of the Brillouin zone. 
  • Local and orbital-projected density of states. 
  • Band structure.

Guía de uso


SVG

Please use the following module commands:

module av siesta

Check the SIESTA available versions

module help siesta

Get a brief server specific user guide

module load siesta

Load default version environment

module load siesta/<version>

Load specific version environment

 

 

FinisTerrae

The sequetial and parallel version of SIESTA 2.0.1 e 2.0.2 are installed in Finistarre. Then two module files can be loaded:

$ module load siesta/2.0.1

or

$ module load siesta/2.0.2

You can execute the following binaries of the application

  • siesta: sequential version of the program
  • siesta_mpi: paralell HP-MPI version of the program
  • siesta_mpich: paralell version compilled with mpich support

For the MPI version must use the mpirun command, and the -np option for set the number of processors to be used.

 

MPI Script to run SIESTA

#!/bin/bash
module load siesta/2.0.2
mpirun -np $NSLOTS siesta_mpi < input.fdf > output.out

These parameters would be:
 siesta_mpi: the program to execute
 input.fdf: your input data file (It can be another name)
 output.out: This is the output associated to the program (siesta_mpi) and your input data file (input.fdf)

Run the previous script (lanzar.sh)

qsub -l num_proc=1,s_rt=60:00:00,s_vmem=2G,h_fsize=20G -pe mpi 4 lanzar.sh 

Asking for 60 CPU hours, with 2 GB of RAM and 20 GB of harddisk. 4 MPI processes will be created.

The value of the variable $NSLOTS is the same number of the MPI threads show in the qsub sentence, in this case 4 (-pe mpi 4).

 

Bug XML for version 2.0.1

The PDOS output in SystemLabel.PDOS (and pdos.xml) sometimes exhibits wrongly formatted attributes: http://fisica.ehu.es/ag/siesta-extra/issues.html

 

URL Manual

Soporte


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