atoms¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
| Attribute | Value |
|---|---|
| source | CASTEP log |
| id | atoms |
| pattern | \s*\-{10,}.*$\s*Cell\sContents.* |
| endPattern | \s*$\s*\-{10,} |
| endOffset | 0 |
| xml:base | setup/atoms.xml |
Input
-------------------------------
Cell Contents
-------------------------------
Total number of ions in cell = 8
Total number of species in cell = 1
Max number of any one species = 8
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
x Element Atom Fractional coordinates of atoms x
x Number u v w x
x----------------------------------------------------------x
x Si 1 0.000000 0.000000 0.000000 x
x Si 2 0.000000 0.500000 0.500000 x
x Si 3 0.500000 0.000000 0.500000 x
x Si 4 0.500000 0.500000 0.000000 x
x Si 5 0.750000 0.250000 0.750000 x
x Si 6 0.250000 0.250000 0.250000 x
x Si 7 0.250000 0.750000 0.750000 x
x Si 8 0.750000 0.750000 0.250000 x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
No user defined ionic velocities
-------------------------------
Output text
<comment class="example.output" id="atoms">
<module cmlx:templateRef="atoms">
<module cmlx:templateRef="atomtable">
<list cmlx:templateRef="atom">
<list>
<scalar dataType="xsd:string" dictRef="cc:elementType">Si</scalar>
<scalar dataType="xsd:integer" dictRef="cc:serial">1</scalar>
<scalar dataType="xsd:double" dictRef="cc:xFract">0.000000</scalar>
<scalar dataType="xsd:double" dictRef="cc:yFract">0.000000</scalar>
<scalar dataType="xsd:double" dictRef="cc:zFract">0.000000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="cc:elementType">Si</scalar>
<scalar dataType="xsd:integer" dictRef="cc:serial">2</scalar>
<scalar dataType="xsd:double" dictRef="cc:xFract">0.000000</scalar>
<scalar dataType="xsd:double" dictRef="cc:yFract">0.500000</scalar>
<scalar dataType="xsd:double" dictRef="cc:zFract">0.500000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="cc:elementType">Si</scalar>
<scalar dataType="xsd:integer" dictRef="cc:serial">3</scalar>
<scalar dataType="xsd:double" dictRef="cc:xFract">0.500000</scalar>
<scalar dataType="xsd:double" dictRef="cc:yFract">0.000000</scalar>
<scalar dataType="xsd:double" dictRef="cc:zFract">0.500000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="cc:elementType">Si</scalar>
<scalar dataType="xsd:integer" dictRef="cc:serial">4</scalar>
<scalar dataType="xsd:double" dictRef="cc:xFract">0.500000</scalar>
<scalar dataType="xsd:double" dictRef="cc:yFract">0.500000</scalar>
<scalar dataType="xsd:double" dictRef="cc:zFract">0.000000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="cc:elementType">Si</scalar>
<scalar dataType="xsd:integer" dictRef="cc:serial">5</scalar>
<scalar dataType="xsd:double" dictRef="cc:xFract">0.750000</scalar>
<scalar dataType="xsd:double" dictRef="cc:yFract">0.250000</scalar>
<scalar dataType="xsd:double" dictRef="cc:zFract">0.750000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="cc:elementType">Si</scalar>
<scalar dataType="xsd:integer" dictRef="cc:serial">6</scalar>
<scalar dataType="xsd:double" dictRef="cc:xFract">0.250000</scalar>
<scalar dataType="xsd:double" dictRef="cc:yFract">0.250000</scalar>
<scalar dataType="xsd:double" dictRef="cc:zFract">0.250000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="cc:elementType">Si</scalar>
<scalar dataType="xsd:integer" dictRef="cc:serial">7</scalar>
<scalar dataType="xsd:double" dictRef="cc:xFract">0.250000</scalar>
<scalar dataType="xsd:double" dictRef="cc:yFract">0.750000</scalar>
<scalar dataType="xsd:double" dictRef="cc:zFract">0.750000</scalar>
</list>
<list>
<scalar dataType="xsd:string" dictRef="cc:elementType">Si</scalar>
<scalar dataType="xsd:integer" dictRef="cc:serial">8</scalar>
<scalar dataType="xsd:double" dictRef="cc:xFract">0.750000</scalar>
<scalar dataType="xsd:double" dictRef="cc:yFract">0.750000</scalar>
<scalar dataType="xsd:double" dictRef="cc:zFract">0.250000</scalar>
</list>
</list>
<atomArray>
<atom elementType="Si" id="a1" xFract="0.000000" yFract="0.000000" zFract="0.000000">Si</atom>
<atom elementType="Si" id="a2" xFract="0.000000" yFract="0.500000" zFract="0.500000">Si</atom>
<atom elementType="Si" id="a3" xFract="0.500000" yFract="0.000000" zFract="0.500000">Si</atom>
<atom elementType="Si" id="a4" xFract="0.500000" yFract="0.500000" zFract="0.000000">Si</atom>
<atom elementType="Si" id="a5" xFract="0.750000" yFract="0.250000" zFract="0.750000">Si</atom>
<atom elementType="Si" id="a6" xFract="0.250000" yFract="0.250000" zFract="0.250000">Si</atom>
<atom elementType="Si" id="a7" xFract="0.250000" yFract="0.750000" zFract="0.750000">Si</atom>
<atom elementType="Si" id="a8" xFract="0.750000" yFract="0.750000" zFract="0.250000">Si</atom>
</atomArray>
</module>
</module>
</comment>
Template definition
<templateList> <template id="atomtable" pattern="\s+x{20,}x.*" endPattern="\s+x{20,}x.*"> <record repeat="4" /> <record repeat="*" id="atom">\s*x{A,cc:elementType}{I,cc:serial}{F,cc:xFract}{F,cc:yFract}{F,cc:zFract}\s*x.*</record> <transform process="addChild" xpath=".//cml:list[@cmlx:templateRef='atom']/cml:list" elementName="cml:atom" id="atom" /> <transform process="addAttribute" xpath=".//cml:atom" name="id" value="$string(concat('a', count(preceding::cml:atom)+1))" /> <transform process="addAttribute" xpath=".//cml:atom" name="elementType" value="$string(preceding-sibling::cml:scalar[@dictRef='cc:elementType']/text())" /> <transform process="addAttribute" xpath=".//cml:atom" name="xFract" value="$string(preceding-sibling::cml:scalar[@dictRef='cc:xFract']/text())" /> <transform process="addAttribute" xpath=".//cml:atom" name="yFract" value="$string(preceding-sibling::cml:scalar[@dictRef='cc:yFract']/text())" /> <transform process="addAttribute" xpath=".//cml:atom" name="zFract" value="$string(preceding-sibling::cml:scalar[@dictRef='cc:zFract']/text())" /> <transform process="setValue" xpath=".//cml:atom" value="$string(preceding-sibling::cml:scalar[@dictRef='cc:elementType']/text())" /> <transform process="addChild" xpath="." elementName="cml:atomArray" /> <transform process="move" xpath=".//cml:atom" to="./cml:atomArray" />
</template>
</templateList>
<transform process="delete" xpath=".//cml:list[count(*) = 0]" />
<transform process="delete" xpath=".//cml:list[count(*) = 0]" />