SIESTA

SIESTA

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	https://www.iochem-bd.org/handle/10/123456
Program	<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

---

1. 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:choose>
                   <xsl:when test="matches($type,'BROYDEN') or 
                                   matches($type,'CG') or 
                                   matches($type,'FIRE')">
                       <xsl:value-of select="'Geometry optimization'"/>
                   </xsl:when>
                   <xsl:when test="matches($type, 'VERLET') or 
                                   matches($type, 'NOSE') or 
                                   matches($type, 'PARRINELLORAHMAN') or 
                                   matches($type, 'NOSEPARRINELLORAHMAN') or 
                                   matches($type, 'ANNEAL') or 
                                   matches($type, 'LUA')">
                       <xsl:value-of select="'Molecular Dynamics'"/>
                   </xsl:when>
                   <xsl:when test="matches($type, 'FC')">
                       <xsl:value-of select="'Phonon'"/>
                   </xsl:when>
                   <xsl:when test="matches($type, 'SINGLE-POINT')">
                       <xsl:value-of select="'Single point'"/>
                   </xsl:when>
                   <xsl:when test="matches($type, 'MASTER') or 
                                   matches($type, 'FORCES')">
                       <xsl:value-of select="''"/>
                   </xsl:when>
                   <xsl:otherwise>
                           <xsl:value-of select="''"/>
                   </xsl:otherwise>
           </xsl:choose>
                           
                                               

   ↩︎

Settings

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>

Modules

Energies

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

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

Pressure

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'>

Timing

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'>