SIESTA

Description

From the SIESTA website: 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. SIESTA's efficiency stems from the use of strictly localized basis sets and from the implementation of linear-scaling algorithms which can be applied to suitable systems. A very important feature of the code is that its accuracy and cost can be tuned in a wide range, from quick exploratory calculations to highly accurate simulations matching the quality of other approaches, such as plane-wave and all-electron methods.

Version

  • 4.0.1

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

SIESTA requires the following module file to run:

  • apps/siesta/4.0.1

Running SIESTA on CIRCE/SC

The SIESTA user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting Jobs

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.

#!/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

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

  • SIESTA Tutorials
    • /apps/siesta/4.0.1/Tutorials
  • SIESTA Known Tests
    • /apps/siesta/4.0.1/Obj/Tests

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