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SIESTA

Introduction

From the code's Web page: "SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids." It is a periodic Density Functional Code that uses strictly localized, numerical atomic orbitals (PAOs) with effective core potentials and features fast linear-scaling computational methods.

Licensing and access

Starting from version 4.0, SIESTA is an open software licensed with GNU General Public License version 3. So for 4.0 and newer versions, no special action should be needed by researchers to access the software.

Earlier versions of SIESTA were distributed free of charge to academics, however it was not public-domain software in the sense that it could not be redistributed. If you need a pre-4.0 version of SIESTA, please review the Academic license for the older versions of SIESTA here. Then send an email to support@westgrid.ca with the subject line "SIESTA access requested for your_user_name" and indicate that you have read and can abide by the SIESTA license. Your user name will then be added to the wg-siest UNIX group that is used to control access to the software on WestGrid systems.

Runnning SIESTA on Grex

On Grex we have installed the current stable version, SIESTA 3.2 patch level 5, as well as beta-version of SIESTA 4.1.  The codes were compiled with Intel compilers, Open MPI and the Intel Math Kernel Library (MKL) and include NetCDF file format support. There is also an intermediate trunk version build.  An experimental GUI program GDIS available on Grex can be used to prepare SIESTA inputs and visualize outputs.

The command PATH to the executables (siesta and transiesta, tbtrans) and shared libraries required to run the code are initialized using module commands for an appropriate SIESTA version:

module load siesta/3.2p5

or

module load siesta/4.1b

On Grex there is no SIESTA in the default PATH, so it is recommended to use one of the above mentioned module commands in your scripts. Note that these SIESTA modules automatically load compiler and MPI modules, as well as the Tcl module that is required for the GUI. This automatic load might in some cases, especially for older SIESTA versions, confict with other modules if they are already loaded.  Therefore, we recommend to do the module purge command before loading the SIESTA module, as shown below. For more information on using modules on WestGrid systems, click here. An example SIESTA batch script is provided below (the input file, MgO.fdf, and pseudopotentials for it can be found on Grex in /global/software/siesta-4.1b-rh6/Examples/MgO and /global/software/siesta-4.1b-rh6/Tests/Pseudos, respectively):

#!/bin/bash
#PBS -S /bin/bash
#PBS -l procs=16,pmem=1000mb,walltime=8:00:00
#PBS -r n
#PBS -N MgO-test
#PBS -m bea
##PBS -M my_email_user_name@my_email_service_provider
# Adjust the pmem and procs above to match the requirements of your job.
# Remove the -m and -M lines if you don't want notification of job starts and finishes.
# If you do want notifications, remove one of the # characters on the -M line
# and replace my_email_user_name@my_email_service_provider with your real email address.

cd $PBS_O_WORKDIR
echo "Current working directory is `pwd`"

# Provide some diagnostic information
echo "Nodes I am on:"
cat $PBS_NODEFILE
echo "Running on `hostname`"

# Initialize the environment for the chosen version of SIESTA.
module purge
module load siesta/4.1b
which siesta

# Run SIESTA
echo "Starting run at: `date`"

mpiexec siesta < MgO.fdf > MgO.${PBS_JOBID}.log

echo "Finished run at: `date`"

 

2016-02-22 - Grex section added.
2017-04-19 - Updated licensing conditions.