castep.geom¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
| Attribute | Value |
|---|---|
| source | CASTEP geom file |
| id | castep.geom |
| name | CASTEP geom file |
| xml:base | topTemplate.xml |
Input
BEGIN header
CASTEP calculation from Materials Studio
END header
0 F F F F &-- c
-5.0078005415924089E+001 -5.0078005415924089E+001 &-- E
1.0262214418141220E+001 0.0000000000000000E+000 0.0000000000000000E+000 &-- h
0.0000000000000000E+000 1.0262214418141220E+001 0.0000000000000000E+000 &-- h
0.0000000000000000E+000 0.0000000000000000E+000 1.0262214418141220E+001 &-- h
-1.2285877876718027E-004 4.2351647362715017E-022 -4.2351647362715017E-022 &-- S
4.2351647362715017E-022 -1.2285877876718040E-004 0.0000000000000000E+000 &-- S
-4.2351647362715017E-022 0.0000000000000000E+000 -1.2285877876718019E-004 &-- S
Si 1 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- R
Si 2 0.0000000000000000E+000 5.1311072090706089E+000 5.1311072090706089E+000 &-- R
Si 3 5.1311072090706089E+000 0.0000000000000000E+000 5.1311072090706089E+000 &-- R
Si 4 5.1311072090706089E+000 5.1311072090706089E+000 0.0000000000000000E+000 &-- R
Si 5 7.6966608136059138E+000 2.5655536045353049E+000 7.6966608136059138E+000 &-- R
Si 6 2.5655536045353049E+000 2.5655536045353049E+000 2.5655536045353049E+000 &-- R
Si 7 2.5655536045353049E+000 7.6966608136059138E+000 7.6966608136059138E+000 &-- R
Si 8 7.6966608136059138E+000 7.6966608136059138E+000 2.5655536045353049E+000 &-- R
Si 1 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 2 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 3 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 4 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 5 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 6 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 7 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 8 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
3 T T T T &-- c
-5.0080304782430773E+001 -5.0080304782430773E+001 &-- E
1.0405743066368817E+001 3.8200054405598108E-037 2.6136879330146068E-037 &-- h
3.8200054405598108E-037 1.0405743066368817E+001 3.2168466867872084E-037 &-- h
2.6136879330146068E-037 3.2168466867872084E-037 1.0405743066368817E+001 &-- h
1.1138356651379254E-007 0.0000000000000000E+000 2.1175823681357508E-022 &-- S
0.0000000000000000E+000 1.1138356651379600E-007 0.0000000000000000E+000 &-- S
2.1175823681357508E-022 0.0000000000000000E+000 1.1138356651380637E-007 &-- S
Si 1 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- R
Si 2 3.2168466867872079E-037 5.2028715331844078E+000 5.2028715331844078E+000 &-- R
Si 3 5.2028715331844078E+000 3.5184260636735089E-037 5.2028715331844078E+000 &-- R
Si 4 5.2028715331844078E+000 5.2028715331844078E+000 2.9152673099009069E-037 &-- R
Si 5 7.8043072997766121E+000 2.6014357665922043E+000 7.8043072997766121E+000 &-- R
Si 6 2.6014357665922043E+000 2.6014357665922043E+000 2.6014357665922043E+000 &-- R
Si 7 2.6014357665922043E+000 7.8043072997766121E+000 7.8043072997766121E+000 &-- R
Si 8 7.8043072997766121E+000 7.8043072997766121E+000 2.6014357665922043E+000 &-- R
Si 1 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 2 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 3 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 4 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 5 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 6 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 7 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
Si 8 0.0000000000000000E+000 0.0000000000000000E+000 0.0000000000000000E+000 &-- F
BEGIN footer
Hirshfeld analysis of final structure
Si 1 H charge= 0.00 H spin= -0.00 &-- HQS
Si 2 H charge= 0.00 H spin= -0.00 &-- HQS
Si 3 H charge= 0.00 H spin= -0.00 &-- HQS
Si 4 H charge= 0.00 H spin= -0.00 &-- HQS
Si 5 H charge= 0.00 H spin= -0.00 &-- HQS
Si 6 H charge= 0.00 H spin= -0.00 &-- HQS
Si 7 H charge= 0.00 H spin= -0.00 &-- HQS
Si 8 H charge= 0.00 H spin= -0.00 &-- HQS
END footer
Output text
<comment class="example.output" id="castep.geom">
<module id="castep.geom">
<module cmlx:templateRef="header">
<scalar dataType="xsd:string" dictRef="cc:title">BEGIN header</scalar>
</module>
<module cmlx:templateRef="section">
<molecule id="initial">
<crystal>
<scalar id="sc1" title="a" units="nonsi:angstrom">5.4305303944401055</scalar>
<scalar id="sc2" title="b" units="nonsi:angstrom">5.4305303944401055</scalar>
<scalar id="sc3" title="c" units="nonsi:angstrom">5.4305303944401055</scalar>
<scalar id="sc4" title="alpha" units="nonsi:degree">90.0</scalar>
<scalar id="sc5" title="beta" units="nonsi:degree">90.0</scalar>
<scalar id="sc6" title="gamma" units="nonsi:degree">90.0</scalar>
</crystal>
<atomArray>
<atom elementType="Si" id="a1" x3="0.0000" xFract="0.0000" y3="0.0000" yFract="0.0000" z3="0.0000" zFract="0.0000" />
<atom elementType="Si" id="a2" x3="0.0000" xFract="0.0000" y3="2.7152652" yFract="0.5000" z3="2.7152652" zFract="0.5000" />
<atom elementType="Si" id="a3" x3="2.7152652" xFract="0.5000" y3="0.0000" yFract="0.0000" z3="2.7152652" zFract="0.5000" />
<atom elementType="Si" id="a4" x3="2.7152652" xFract="0.5000" y3="2.7152652" yFract="0.5000" z3="0.0000" zFract="0.0000" />
<atom elementType="Si" id="a5" x3="4.0728978" xFract="0.7500" y3="1.3576326" yFract="0.2500" z3="4.0728978" zFract="0.7500" />
<atom elementType="Si" id="a6" x3="1.3576326" xFract="0.2500" y3="1.3576326" yFract="0.2500" z3="1.3576326" zFract="0.2500" />
<atom elementType="Si" id="a7" x3="1.3576326" xFract="0.2500" y3="4.0728978" yFract="0.7500" z3="4.0728978" zFract="0.7500" />
<atom elementType="Si" id="a8" x3="4.0728978" xFract="0.7500" y3="4.0728978" yFract="0.7500" z3="1.3576326" zFract="0.2500" />
</atomArray>
<bondArray />
<formula concise="Si8">
<atomArray count="8" elementType="Si" />
</formula>
<property dictRef="cml:molmass">
<scalar units="unit:dalton">224.684</scalar>
</property>
</molecule>
<list dictRef="ca:axis" id="axis">
<array dataType="xsd:double" dictRef="cc:latticeA" size="3">5.4305303944401055 0.0 0.0</array>
<array dataType="xsd:double" dictRef="cc:latticeB" size="3">0.0 5.4305303944401055 0.0</array>
<array dataType="xsd:double" dictRef="cc:latticeC" size="3">0.0 0.0 5.4305303944401055</array>
</list>
<scalar dataType="xsd:integer" dictRef="ca:niter">0</scalar>
<scalar dataType="xsd:string" dictRef="ca:convergence">F F F F</scalar>
<scalar dataType="xsd:double" dictRef="cc:finalEnergy">-1362.6918613673529</scalar>
<scalar dataType="xsd:double" dictRef="ca:enthalpy">-1362.6918613673529</scalar>
</module>
<module cmlx:templateRef="section">
<molecule id="final">
<crystal>
<scalar id="sc1" title="a" units="nonsi:angstrom">5.506482489661875</scalar>
<scalar id="sc2" title="b" units="nonsi:angstrom">5.506482489661875</scalar>
<scalar id="sc3" title="c" units="nonsi:angstrom">5.506482489661875</scalar>
<scalar id="sc4" title="alpha" units="nonsi:degree">90.0</scalar>
<scalar id="sc5" title="beta" units="nonsi:degree">90.0</scalar>
<scalar id="sc6" title="gamma" units="nonsi:degree">90.0</scalar>
</crystal>
<atomArray>
<atom elementType="Si" id="a9" x3="0.0000" xFract="0.0000" y3="0.0000" yFract="0.0000" z3="0.0000" zFract="0.0000" />
<atom elementType="Si" id="a10" x3="0.0000" xFract="-0.0000" y3="2.75324124" yFract="0.5000" z3="2.75324124" zFract="0.5000" />
<atom elementType="Si" id="a11" x3="2.75324124" xFract="0.5000" y3="0.0000" yFract="-0.0000" z3="2.75324124" zFract="0.5000" />
<atom elementType="Si" id="a12" x3="2.75324124" xFract="0.5000" y3="2.75324124" yFract="0.5000" z3="0.0000" zFract="-0.0000" />
<atom elementType="Si" id="a13" x3="4.12986187" xFract="0.7500" y3="1.37662062" yFract="0.2500" z3="4.12986187" zFract="0.7500" />
<atom elementType="Si" id="a14" x3="1.37662062" xFract="0.2500" y3="1.37662062" yFract="0.2500" z3="1.37662062" zFract="0.2500" />
<atom elementType="Si" id="a15" x3="1.37662062" xFract="0.2500" y3="4.12986187" yFract="0.7500" z3="4.12986187" zFract="0.7500" />
<atom elementType="Si" id="a16" x3="4.12986187" xFract="0.7500" y3="4.12986187" yFract="0.7500" z3="1.37662062" zFract="0.2500" />
</atomArray>
<bondArray />
<formula concise="Si8">
<atomArray count="8" elementType="Si" />
</formula>
<property dictRef="cml:molmass">
<scalar units="unit:dalton">224.684</scalar>
</property>
</molecule>
<list dictRef="ca:axis" id="axis">
<array dataType="xsd:double" dictRef="cc:latticeA" size="3">5.506482489661875 2.0214599702004734E-37 1.3831041901371658E-37</array>
<array dataType="xsd:double" dictRef="cc:latticeB" size="3">2.0214599702004734E-37 5.506482489661875 1.7022820801688194E-37</array>
<array dataType="xsd:double" dictRef="cc:latticeC" size="3">1.3831041901371658E-37 1.7022820801688194E-37 5.506482489661875</array>
</list>
<scalar dataType="xsd:integer" dictRef="ca:niter">3</scalar>
<scalar dataType="xsd:string" dictRef="ca:convergence">T T T T</scalar>
<scalar dataType="xsd:double" dictRef="cc:finalEnergy">-1362.7544303135187</scalar>
<scalar dataType="xsd:double" dictRef="ca:enthalpy">-1362.7544303135187</scalar>
</module>
</module>
</comment>
Template definition
<templateList> <template id="header" pattern="\s*BEGIN\sheader.*" endPattern="\s*END\sheader.*"> <record repeat="*">\s*</record> <record>{X,cc:title}</record> <transform process="pullup" xpath=".//cml:scalar" /> <transform process="delete" xpath=".//cml:list" />
</template> <template id="section" pattern="\s{20,}[0-9].*" endPattern="\s*" endPattern2="~" repeat="*" keep="firstandlast"> <record>{I,ca:niter}{X,ca:convergence}.--\s*c</record> <record>{E,cc:finalEnergy}{E,ca:enthalpy}.*--\s*E</record> <record>{3E,cc:latticeA}.*--\s*h</record> <record>{3E,cc:latticeB}.*--\s*h</record> <record>{3E,cc:latticeC}.*--\s*h</record> <record repeat="*">.*--\s*S</record> <record repeat="*" id="atom">\s*{A,cc:elementType}{I,cc:serial}{E,cc:x3}{E,cc:y3}{E,cc:z3}.*--\s*R</record> <transform process="operateScalar" xpath=".//cml:scalar[@dictRef='cc:finalEnergy' or @dictRef='ca:enthalpy']" args="operator=multiply operand=27.21139" /> <transform process="operateArray" xpath=".//cml:array[@dictRef='cc:latticeA' or @dictRef='cc:latticeB' or @dictRef='cc:latticeC']" args="operator=multiply operand=0.529177249" /> <transform process="operateScalar" xpath=".//cml:scalar[@dictRef='cc:x3' or @dictRef='cc:y3' or @dictRef='cc:z3']" args="operator=multiply operand=0.529177249" /> <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="x3" value="$string(preceding-sibling::cml:scalar[@dictRef='cc:x3']/text())" /> <transform process="addAttribute" xpath=".//cml:atom" name="y3" value="$string(preceding-sibling::cml:scalar[@dictRef='cc:y3']/text())" /> <transform process="addAttribute" xpath=".//cml:atom" name="z3" value="$string(preceding-sibling::cml:scalar[@dictRef='cc:z3']/text())" /> <transform process="setValue" xpath=".//cml:atom" value="$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" /> <transform process="addChild" xpath="." elementName="cml:list" id="axis" /> <transform process="addAttribute" xpath=".//cml:list[@id='axis']" name="dictRef" value="ca:axis" /> <transform process="move" xpath=".//cml:array[@dictRef='cc:latticeA']" to=".//cml:list[@id='axis']" /> <transform process="move" xpath=".//cml:array[@dictRef='cc:latticeB']" to=".//cml:list[@id='axis']" /> <transform process="move" xpath=".//cml:array[@dictRef='cc:latticeC']" to=".//cml:list[@id='axis']" /> <transform process="createCrystal" xpath=".//cml:atomArray" lattice=".//cml:list[@dictRef='ca:axis']" id="coordinates" connect="no" /> <transform process="delete" xpath="./cml:atomArray" /> <transform process="delete" xpath=".//cml:list[@cmlx:templateRef='atom']" /> <transform process="move" xpath=".//cml:scalar[@dictRef='ca:niter' or @dictRef='ca:convergence' or @dictRef='cc:finalEnergy' or @dictRef='ca:enthalpy']" to="." /> <transform process="delete" xpath=".//cml:list[count(*) = 0]" /> <transform process="delete" xpath=".//cml:list[count(*) = 0]" />
</template> <transform process="addAttribute" xpath="(.//cml:molecule)[1]" name="id" value="initial" /> <transform process="addAttribute" xpath="(.//cml:molecule)[last()]" name="id" value="final" />
</templateList>