Difference between revisions of "SIESTA"

Revision as of 08:09, 2 November 2017

Introduction

SIESTA performs self-consistent DFT employing order-N techniques developed for tight-binding, founded on using Numerical Atomic Orbitals (NAOs) as a basis set.

Version Selection

The latest stable version of Siesta is 3.2 (patch) 4 and users are strongly encouraged to use it.

To load the siesta module, execute:

module load siesta/3.2

You can add this line to your startup script (.bashrc) to avoid executing it every time you log in.

Both serial and mpi compiled executables are available, named siesta-serial and siesta-mpi respectively.

Siesta 3.1 is still available, but will be removed soon.

Examples

To try the examples, first download the source code from Siesta website, using this link

To get the file directly to SHARCNET, just execute:

wget http://departments.icmab.es/leem/siesta/CodeAccess/Code/siesta-3.2-pl-5.tgz

then unpack the files with

tar xvfz siesta-3.2-pl-5.tgz

There is a comprehensive set of examples in the tests directory. To try them, first log into a development node. On orca, you can do this by doing:

ssh orc-dev1

On the development node it is possible to run short test programs without using sqsub. Next do:

cd siesta-3.2-pl-4/Tests

In that directory, edit the file

test.mk

so it has the line:

SIESTA=siesta-serial

Then to make sure you can find Siesta, execute:

module load siesta

Now you can cd into any of the directories in the tests directory and run :

make

This will copy the necessary pseudopotentials and then run the serial version of Siesta.

If you want to run again, without using make, then just:

cd work

then run

siesta-serial < ../FILE.fdf

where you would replace FILE with the actual name of the .fdf file in the example you are trying.

Job Submission

Example of starting an mpi job (after module is loaded):

sqsub -q mpi -r 40m -n 4 -o example.out -i example.fdf siesta-mpi

Example of starting a serial job (after module is loaded):

sqsub -q serial -r 40m -o example.out -i example.fdf siesta-serial

Example Job

General Notes

Note: sometimes Siesta crashes when trying to generate xml output. You can disable this output by adding

WriteXML F

to your .fdf input file.

References

o Siesta homepage
http://www.icmab.es/siesta