SIESTA

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SIESTA

Description

From the NERSC website: “SIESTA is an O (N) DFT code for electronic structure calculations and ab initio molecular dynamics simulations for molecules and solids. It uses norm-conserving pseudopotentials and linear combination of numerical atomic orbitals (LCAO) basis set.”

Version

  • 3.1

Authorized Users

  • CIRCE account holders

Platforms

  • CIRCE cluster

Running SIESTA Jobs on CIRCE

Modules

Before running a job, you must first set up your environment properly. Below is the required module file.

  • apps/siesta/3.1
    See Modules for more information.

Submitting Jobs

The SIESTA manual is essential to understanding the application and making the most of it. Please refer to the Additional Documentation section for a link to the guide.

If, for example, you have an SIESTA input file named input.in, you would set up a submit script like this:

The script below (for testing, name it “siesta-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. For help on submitting jobs to the queue, see our SLURM User’s Guide. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.

#!/bin/bash
#
#SBATCH --comment=siesta-test
#SBATCH --ntasks=4
#SBATCH --job-name=siesta-test
#SBATCH --output=output.%j.siesta-test
#SBATCH --time=01:00:00

#### Slurm 4 processor SIESTA test to run for 1 hour.

module purge
module load apps/siesta/3.1

mpirun siesta < input.in

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./siesta-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Tutorials and Tests

The following contain input parameters for known SIESTA Examples:

Additional Documentation

  • SIESTA Manual
    • /apps/siesta/3.1/Docs/siesta-3.1-manual.pdf

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with SIESTA to the IT Help Desk: rc-help@usf.edu