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Table of Contents

SIESTA at a glance

Purpose: ab initio electronic structure, molecular dynamics
Latest version: 4.0b2
Availability: all machines
Licence: mixed licence
Documentation: User's Guide

Description

SIESTA is a program for ab initio electronic structure and molecular dynamics of solids and molecules.

SIESTA applies DFT hamiltonians (LDA, GGA) to strictly localized numerical basis sets and non-local pseudopotentials to obtain electronic structures. From these it can compute solid properties (band structure, DOS, k-space sampling, dielectric polarisation, phonons), perform Born-Oppenheimer molecular dynamics (NVT and NPT), and, in recent versions, Van der Waals potentials and ballistic electron transport properties (TranSIESTA).

A more detailed description can be found in this manifest.

Licence

SIESTA is provided free of charge to academic users only.

For more information please visit this page.

Available Versions

The currently available versions of SIESTA in our facilities are:

  • 2.0.2 (prades, pirineus)
  • 3.0-rc2 (pirineus)
  • TranSIESTA-3.0b (prades)
  • 3.1 (pirineus)
  • 3.2 (all machines)
  • 4.0b2 (pirineus, collserola)

To load a version, call it in a script via 

module load siesta/4.0b2

Benchmark


SIESTA 3.2 benchmark at collserola: actual speed-up (green) and ideal speed-up (blue) vs. number of cores for the conjugated gradient optimisation of a hydrogen atom in solid silicon using the SIESTA methodology.

LSF example script (collserola)

#!/bin/bash
##
# IMPORTANT NOTICE: replace the email address
# and the working directories with your own info
##
# BSUB -J gromacs
# BSUB -o gromacs.log # send standard output here
# BSUB -e gromacs.err # send error output here
#
# Pick a queue
# BSUB -q short
#
# Send an email notice once the job is finished
# BSUB -N -u youremail@wherever
#
# Indicate the number of cores
# BSUB -n 4
#
# Pick the machine
# BSUB -R collserola

date

# Set up the environment
. /opt/modules/default/init/bash
module load siesta/3.2-new

# Run SIESTA with MPI
mpijob siesta < input.inp > output.out

date

LSF example script (pirineus)

#!/bin/bash
##
# IMPORTANT NOTICE: replace the email address
# and the working directories with your own info
##
# BSUB -J gromacs
# BSUB -o gromacs.log # send standard output here
# BSUB -e gromacs.err # send error output here
#
# Pick a queue
# BSUB -q short
#
# Send an email notice once the job is finished
# BSUB -N -u youremail@wherever
#
# Indicate the number of cores
# BSUB -n 4
#
# BSUB -R collserola


date

# Set up the environment
. /opt/modules/default/init/bash
module load siesta/3.2

# Run SIESTA with MPI
mpijob siesta < input.inp > output.out

date
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