SIESTA

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. More information can be found from here.

Availability and Restrictions

Versions

SIESTA is available on the Owens and Oakley clusters. A serial and a parallel build were created in order to meet users' computational needs.

You can use module spider siesta to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

SIESTA newer than version 4.0 is under GPL license. Therefore, any users can access SIESTA on Owens. If you have any questions, please contact OSC Help for further information.

Publisher/Vendor/Repository and License Type

https://departments.icmab.es/leem/siesta/, Open source

Usage

Batch Usage

When you log into oakley.osc.edu or owens.osc.edu, you are actually logged into a linux box referred to as the login node. To gain access to the 4000+ processors in the computing environment, you must submit your SIESTA job to the batch system for execution.

Assume that you have a test case in your work directory (where you submit your job, represented by $PBS_O_WORKDIR), with the input file 32_h2o.fdf. A batch script can be created and submitted for a serial or parallel run. The following are the sample batch scripts for running serial and parallel SIESTA jobs.  Sample batch scripts and input files are also available here:

~srb/workshops/compchem/siesta/

Sample Batch Script for Serial Jobs

#!/bin/bash
#SBATCH --time=0:30:00
#SBATCH --nodes=1 --ntasks-per-node=28
#SBATCH --job-name=siesta
#SBATCH --account <project-account>
#
# Set up the package environment
module load siesta
#
# Execute the serial solver (nodes=1, ppn<=12)
siesta <32_h2o.fdf> output
exit

Sample Batch Script for Parallel Jobs

#!/bin/bash
#SBATCH --time=0:30:00
#SBATCH --nodes=2 --ntasks-per-node=28
#SBATCH --job-name=siesta
#SBATCH --account <project-account> 
#
# Set up the package environment
module swap intel/12.1.4.319 intel/13.1.3.192
module load siesta_par
#
# Execute the parallel solver (nodes>1, ppn=28)
srun siesta <32_h2o.fdf> output
exit

Usage on Pitzer

#!/bin/bash
#SBATCH --time=0:30:00 
#SBATCH --nodes=1 --ntasks-per-node=48
#SBATCH --job-name=siesta
#SBATCH --account <project-account> 
#
# Set up the package environment
module load siesta
#
# Execute the serial solver (nodes=1, ppn<=48)
siesta <32_h2o.fdf> output
exit

Further Reading

Online documentation is available at the SIESTA homepage.

Citations

This is required for the versions older than 4.0.

1. “Self-consistent order-N density-functional calculations for very large systems”, P. Ordejón, E. Artacho and J. M. Soler, Phys. Rev. B (Rapid Comm.) 53, R10441-10443 (1996).

2. “The SIESTA method for ab initio order-N materials simulation”, J. M. Soler, E. Artacho,J. D. Gale, A. García, J. Junquera, P. Ordejón, and D. Sánchez-Portal, J. Phys.: Condens. Matt. 14, 2745-2779 (2002).