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Purpose: Ab initio electronic structure, Molecular Dynamics
Latest version: 4.1
License: Free of use for academics users
Mixed
Website: https://departments.icmab.es/_ext-link

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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).

SLURM Submit script example

For more information use the Job Script Generator [old].

Code Block

language	bash
theme	Emacs
title	siesta_example.slm

#!/bin/bash
#SBATCH -J siesta_example
#SBATCH -e siesta_example.%j.err
#SBATCH -o siesta_example.%j.out
#SBATCH -p std
#SBATCH -n 1
#SBATCH -t 0-02:00

module load apps/siesta/4.1

##
#  Modify the input and output files!
INPUT_FILE=siesta_example.inp
OUTPUT_FILE=siesta_example.out
 
##
#  You don't need to modify nothing more
cp -r ${SLURM_SUBMIT_DIR}/${INPUT_FILE} ${SCRATCH}
cd ${SCRATCH}
 
srun siesta < ${INPUT_FILE} > ${OUTPUT_FILE}
 
cp ./${OUTPUT_FILE} ${SLURM_SUBMIT_DIR}

Sbatch options:

The options shown in the example are detailed below. For more information and a more comprehensive list of available options, see the sbatch command page.

-J: Name for the job's allocation.

-e: Name of the stderr redirection filename.

-o: Name of the stdout redirection filename.

-p: Name of the partition (queue) where the job will be submitted.

-n: Number of tasks.

-c: Number of cores per task.

-t: Set the job's time limit. If the job don't finish before the time runs out, it will be killed.

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SLURM Submit script example

Sbatch options: