Applications/Siesta - Revision history

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2017-04-11T09:07:23Z

Pysdlb: Pysdlb moved page Siesta to Applications/Siesta without leaving a redirect

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Pysdlb moved page Siesta to Applications/Siesta without leaving a redirect

Pysdlb at 08:58, 11 April 2017

2017-04-11T08:58:00Z

Pysdlb: Created page with "==Application Details== * Description: SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio m..."

2017-04-11T08:56:44Z

Created page with "==Application Details== * Description: SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio m..."

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==Application Details==

* Description: 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.
* Version: 3.2p5 (compiled with gcc and intel)
* Modules: siesta/gcc/3.2p5 and siesta/intel/3.2p5
* Licence: Free, open-source

==Usage Examples==

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.

The possibility of treating large systems with some first-principles electronic-structure methods has opened up new opportunities in many disciplines. The SIESTA program is distributed freely to academics and has become quite popular, being increasingly used by researchers in geosciences, biology, and engineering (apart from those in its natural habitat of materials physics and chemistry).

=== Interactive Jobs===

This example shows an interactive job running on one of the high memory nodes, with input file input.in.

<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">

[username@c232] module load siesta/gcc/3.2p5
[username@c232] siesta < input.in

</pre>

===Non-interactive Jobs===

With a SIESTA input file named inputs.in, you would set up a submit script like this:

The script below (called '''siesta.job''') and then can be submitted to SLURM:

<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">

#!/bin/bash
#
#SBATCH --comment=siesta-test
#SBATCH -p highmem
#SBATCH -N 2
#SBATCH --ntasks-per-node=40
#SBATCH -o %N.%j.%a.out
#SBATCH -e %N.%j.%a.err
#SBATCH --exclusive
#SBATCH -t 03:00:00

module purge
module add openmpi/gcc/1.10.5
module add siesta/gcc/3.2p5

mpirun siesta < input.in

</pre>

Running the job with the scheduler '''SLURM''' as below:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

[username@login01 ~]$ sbatch siesta.job
Submitted Job 432783

</pre>

==Further Information==

* [https://departments.icmab.es/leem/siesta/ https://departments.icmab.es/leem/siesta/]

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

← Older revision		Revision as of 10:58, 16 November 2022
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	* [https://departments.icmab.es/leem/siesta/ https://departments.icmab.es/leem/siesta/]		* [https://departments.icmab.es/leem/siesta/ https://departments.icmab.es/leem/siesta/]

−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

← Older revision		Revision as of 09:07, 11 April 2017
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	==Usage Examples==		==Usage Examples==
		+
		+	''From the NERSC website'': SIESTA is an O (N) DFT code for electronic structure calculations and ''ab initio'' molecular dynamics simulations for molecules and solids. It uses norm-conserving pseudo potentials and linear combination of numerical atomic orbitals (LCAO) basis set.

	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.		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.

@@ Line 67: / Line 67: @@
 * [https://departments.icmab.es/leem/siesta/ https://departments.icmab.es/leem/siesta/]
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 20: / Line 20: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[username@c232] module load siesta/gcc/3.2p5
+[username@c232] module add siesta/gcc/3.2p5
 [username@c232] siesta < input.in

← Older revision	Revision as of 09:00, 11 April 2017
(No difference)

@@ Line 16: / Line 16: @@
 This example shows an interactive job running on one of the high memory nodes, with input file input.in.
-<pre style="background-color: #f5f5dc; color: black; font-family: monospace, sans-serif;">
+<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 [username@c232] module load siesta/gcc/3.2p5