CASTEP¶

For this specific format, the minimum required files are:

A user defined input file (.param).
A cell file (.cell), with the atomic cooordinates, cell dimensions and kpoints used in the calculation.
The generated resume output file (.castep).

Note

CASTEP allows to change the default units used inside the calculation and printed in its output file. The current ioChem-BD release supports the default units only.

The geometry optimization method used must be BFGS, the default one. Damped molecular dynamics optimizations are not supported.

Geometry optimization calculations generate a .geom file that must be also appended when uploading it to ioChem-BD, otherwise the optimized geometry won’t be available in the final resume.

All generated CASTEP graph files .xcd can be attached to the upload process and its content will be rendered in the final resume.

General Info¶

CASTEP - General Info - Main fields¶
Field	Source	Sample value
Title	Set on Browse calculation publication	Sample calculation
Browse Item	URL pointing Browse published item	https://iochem-bd.iciq.es/browse/handle/100/5672
Program	program.header template	CASTEP 2021 HF1
Author	Username fullname	Doe, John
Calculation type	Custom logic [1]	Geometry optimization

Settings¶

This section captures initialization settings like units used, geometry optimization parameters, exchange correlation parameters, etc.

Data source: <module cmlx:templateRef=’parameters’>

Atomic coordinates¶

After settings, our HTML resume will output cell dimensions and an xyz coordinates table with current molecule atoms.

For every atom, we will output it’s serial number, atom type, coordinates in angstroms in cartesian and fractional types.

Information is read from geometry steps file or from atoms section.

On geometry optimization calculations it will indicate if it converged along with the initial and final geometries.

Molecular Info¶

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

Molecular Info - Main fields¶
Field	Source	Description
Point group	<scalar dictRef=”cc:pointgroup”>	Variable found inside Symmetry and Constraints section
Space group	<scalar dictRef=”ca:spacegroup”>	Variable found inside Symmetry and Constraints section
k-point	Read from castep.cell	K-point list and its weight, defined inside .cell file

Modules¶

Energies¶

Data source:

<module cmlx:templateRef=’step’>
<module cmlx:templateRef=’enthalpy’>

Mulliken Atomic Charges¶

Data source:

<module cmlx:templateRef=’mulliken’>

Graphs¶

Data source:

.xcd files attached to the calculation during its upload.

It can contain geometry optimization step parameters, density of states or band gap graphs.

Timing¶

Data sources:

<module cmlx:templateRef=’timing’>

[1]

string ca:getCalcType string setup

$setup          Refers to all read elements from <module cmlx:templateRef="parameters">

<xsl:variable name="ca:minimize">Geometry optimization</xsl:variable>
<xsl:variable name="ca:spectroscopy">Electronic spectroscopy</xsl:variable>

<xsl:function name="ca:getCalcType">
    <xsl:param name="setup"  />

    <xsl:variable name="type" select="ca:getParameter($setup, 'type of calculation')" />
    <xsl:choose>
        <xsl:when test="matches($type, 'geometry optimization')">
            <xsl:value-of select="$ca:minimize"/>
        </xsl:when>
        <xsl:when test="matches($type, 'Electronic Spectroscopy')">
            <xsl:value-of select="$ca:spectroscopy"/>
        </xsl:when>
        <xsl:otherwise><xsl:text>N/A</xsl:text></xsl:otherwise>
    </xsl:choose>
</xsl:function>

<xsl:function name="ca:getParameter">
    <xsl:param name="setup" />
    <xsl:param name="name" />
    <xsl:copy-of select="$setup/cml:parameter/cml:scalar[@dictRef='x:label'][text()=$name]/following-sibling::cml:scalar[@dictRef='x:value']"/>
</xsl:function>