For this specific format, the uploaded output file is the original XML generated by SIESTA.

General Info

SIESTA - General Info - Main fields
Field Source Sample value
Title Set on Browse calculation publication Benzene molecule
Browse Item URL pointing Browse published item

<cml><metadataList><metadata name='siesta:Program'>

<cml><metadataList><metadata name='siesta:Version'>

Siesta v4.1-b4
Author Username fullname Doe, John
Formula Atom count from final geometry C6H6
Calculation type Custom logic [1] Geometry optimization
Method Method used (fixed) DFT
Functional N/A  


Most relevant calculation input parameters.

All fields come from the <cml><parameterList><parameter> entries.


Atoms and lattice vectors

After settings section, our HTML resume will output lattice vectors and a coordinates table with molecule atoms.

Geometry is read from the final geometry at <cml><module[@title='Finalization']> or else from <cml><module[@title='Initial System']>

For every atom, we will output it’s serial number, atom type, cartesian coordinates (in angstroms).


Molecular Info

This section captures molecule additional information not captured on previous section.

Volume data source: <cml><module title='Finalization'><propertyList title='Final Pressure'><property dictRef='siesta:cellvol'>

Kpoint cell data source: <cml><property dictRef='siesta:kscell'>

Kpoint list data source: <cml><propertyList title='k-points']><kpoint>




Data source: <cml><module title='Finalization'><propertyList title='Final Energy'>

On geometry optimizations, a graph will depict Kohn-Sham energy progress.

../_images/SIESTA_module_energies.png ../_images/SIESTA_module_energies_graph.png


Data source: <cml><module title='Finalization'><propertyList title='Final Pressure'><property dictRef='siesta:pressSol'>

Data source: <cml><module title='Finalization'><propertyList title='Final Pressure'><property dictRef='siesta:pressMol'>



Data source <cml><metadataList><metadata name='siesta:Mode'>

Data source <cml><metadataList><metadata name='siesta:Nodes'>

Data source <cml><metadataList><metadata name='siesta:StartTime'>

Data source <cml><metadataList><metadata name='siesta:EndTime'>


string siesta:normalizeRunType string type

$type  Value of the parameter <parameter name='MD.TypeOfRun'>

<!-- Calculation type related constants -->
<xsl:param name="type" as="xs:string"/>
             <xsl:when test="matches($type,'BROYDEN') or
                             matches($type,'CG') or
                 <xsl:value-of select="'Geometry optimization'"/>
             <xsl:when test="matches($type, 'VERLET') or
                             matches($type, 'NOSE') or
                             matches($type, 'PARRINELLORAHMAN') or
                             matches($type, 'NOSEPARRINELLORAHMAN') or
                             matches($type, 'ANNEAL') or
                             matches($type, 'LUA')">
                 <xsl:value-of select="'Molecular Dynamics'"/>
             <xsl:when test="matches($type, 'FC')">
                 <xsl:value-of select="'Phonon'"/>
             <xsl:when test="matches($type, 'SINGLE-POINT')">
                 <xsl:value-of select="'Single point'"/>
             <xsl:when test="matches($type, 'MASTER') or
                             matches($type, 'FORCES')">
                 <xsl:value-of select="''"/>
                     <xsl:value-of select="''"/>