Siesta

Software name: 
Siesta
Policy 

Siesta is made available for academic users.

General 

SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

Description 

SIESTA's main characteristics are:

  • It uses the standard Kohn-Sham self-consistent density functional method in the local density (LDA-LSD) or generalized gradient (GGA) approximations. Recent versions implement a functional capable of describing van der Waals interactions.
  • It employs norm-conserving pseudopotentials in their fully nonlocal (Kleinman-Bylander) form.
  • It uses atomic orbitals with finite support as a basis set, allowing unlimited multiple-zeta and angular momenta, polarization and off-site orbitals. Finite-support basis sets are the key for calculating the Hamiltonian and overlap matrices in O(N) operations.
  • 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.
Availability 

HPC2N has a site installation on Abisko and Kebnekaise.

Usage at HPC2N 

To use Siesta, you need to load the module. Use:

module spider siesta

to see which versions are available and how to load the module and the needed prerequisites.

Example, loading Siesta version 4.0

ml icc/2017.1.132-GCC-5.4.0-2.26
ml ifort/2017.1.132-GCC-5.4.0-2.26
ml OpenMPI/2.0.1
ml Siesta/4.0

You can read more about loading modules on our Accessing software with Lmod page and our Using modules (Lmod) page.

Example Submit Script

Change number of cores needed (n) and time to what suits your program. Note that Abisko has 48 cores per node and Kebnekaise has 28 cores per node on the regular compute nodes (see the "Kebnekaise Hardware page" for information about the other types of nodes). Change "--ntasks-per-node=XX" accordingly.

#!/bin/bash
# Change to your own project number
#SBATCH -A <SNICXXXX-YY-ZZZ>
#SBATCH -J <jobname>
#SBATCH -n 48
#SBATCH --ntasks-per-node=12
#SBATCH --time=24:00:00
#SBATCH --error=job.%J.err
#SBATCH --output=job.%J.out

ml purge
ml icc/2017.1.132-GCC-5.4.0-2.26
ml ifort/2017.1.132-GCC-5.4.0-2.26
ml OpenMPI/2.0.1
ml Siesta/4.0

# Always use srun to start siesta programs
srun siesta < <input>.fdf > <filename>.out

Denchar should NOT be run with srun, it may fail with en internal error if done so.

Additional info 

More documentation is available on http://www.icmab.es/siesta/

Updated: 2017-12-06, 15:21