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species ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceQuantumEspresso log
idspecies
nameAtomic species
pattern^\s*atomic\s+species.*
endPattern\s*
endOffset1
xml:baseinitialization/atomic-species.xml

Input ​

     atomic species   valence    mass     pseudopotential
        Fe1           16.00    55.84500     Fe( 1.00)
        Fe2           16.00    55.84500     Fe( 1.00)
        O              6.00    15.99990     O ( 1.00)
        H              1.00     1.00790     H ( 1.00)

Output text ​

xml
<comment class="example.output" id="species">
    <module cmlx:templateRef="species">
        <list cmlx:templateRef="species">
            <array dataType="xsd:string" dictRef="qex:specie" size="4">Fe1 Fe2 O H</array>
            <array dataType="xsd:double" dictRef="x:valelectrons" size="4">16.00 16.00 6.00 1.00</array>
            <array dataType="xsd:double" dictRef="cc:mass" size="4">55.84500 55.84500 15.99990 1.00790</array>
            <array dataType="xsd:string" dictRef="cc:elementType" size="4">Fe Fe O H</array>
            <array dataType="xsd:double" dictRef="qex:pseudopot" size="4">1.00 1.00 1.00 1.00</array>
        </list>
        <map id="speciesToAtomTypeMap">
            <link from="Fe1" to="Fe" />
            <link from="Fe2" to="Fe" />
            <link from="O" to="O" />
            <link from="H" to="H" />
        </map>        
    </module>
   </comment>

Template definition ​

xml
<record repeat="1" />
<record id="species" repeat="*">&#123;A,qex:specie&#125;&#123;F,x:valelectrons&#125;&#123;F,cc:mass&#125;&#123;A,cc:elementType&#125;\(&#123;F,qex:pseudopot&#125;\).*</record>
<transform process="addMap" xpath="." id="speciesToAtomTypeMap" from=".//cml:scalar[@dictRef='qex:specie']" to=".//cml:scalar[@dictRef='cc:elementType']" />
<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='qex:specie']" />
<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='x:valelectrons']" />
<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:mass']" />
<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:elementType']" />
<transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='qex:pseudopot']" />
<transform process="pullup" xpath=".//cml:array" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />