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Revision as of 08:09, 2 November 2017
This page is flagged as an 'ancient wiki page' and is under review in ticket [28755]. |
Contents
Note: Some of the information on this page is for our legacy systems only. The page is scheduled for an update to make it applicable to Graham. |
Introduction
SIESTA |
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Description: Linear-scaling DFT based on Numerical Atomic Orbitals |
SHARCNET Package information: see SIESTA software page in web portal |
Full list of SHARCNET supported software |
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