ioChem-BD

Appearance

final-geometry ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceGRRM log
idfinal-geometry
pattern\s*Optimized structure.*
endPatternOPTOPTOPT.*
xml:baseoptiStruc.xml

Input ​

    Optimized structure, SYMMETRY = C2v 
    C      0.051911596139     -0.000000000000      0.000000000000
    O      1.251598064141      0.000000000000     -0.000000000000
    H     -0.551754830140      0.944696873126     -0.000000000000
    H     -0.551754830140     -0.944696873126     -0.000000000000
    ENERGY    = -114.415498155971
    Spin(**2) =    0.000000000000
    GRADIENT VECTOR
    -0.000015613036
    0.000000000000
    -0.000000000000
    0.000012953701
    -0.000000000000
    0.000000000000
    0.000001329667
    0.000000558707
    0.000000000000
    0.000001329667
    -0.000000558707
    -0.000000000000

    Stationary point was found
    OPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTO

Output text ​

xml
<comment class="example.output" id="">
      <module cmlx:templateRef="final-geometry">
         <scalar cmlx:templateRef="symmetry-group" dataType="xsd:string" dictRef="cc:pointgroup">C2v</scalar>
         <module cmlx:templateRef="molecule">
            <molecule cmlx:templateRef="atom" id="molecule">
               <atomArray>
                  <atom elementType="C" id="a1" x3="0.0519116" y3="-0.0000" z3="0.0000">
                     <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                  </atom>
                  <atom elementType="O" id="a2" x3="1.25159806" y3="0.0000" z3="-0.0000">
                     <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
                  </atom>
                  <atom elementType="H" id="a3" x3="-0.55175483" y3="0.94469687" z3="-0.0000">
                     <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
                  </atom>
                  <atom elementType="H" id="a4" x3="-0.55175483" y3="-0.94469687" z3="-0.0000">
                     <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
                  </atom>
               </atomArray>
               <bondArray>
                  <bond atomRefs2="a1 a2" order="S" />
                  <bond atomRefs2="a1 a3" order="S" />
                  <bond atomRefs2="a1 a4" order="S" />
               </bondArray>
               <formula concise="CH2O">
                  <atomArray count="1 2 1" elementType="C H O" />
               </formula>
               <property dictRef="cml:molmass">
                  <scalar units="unit:dalton">28.0101</scalar>
               </property>
            </molecule>
         </module>
         <scalar cmlx:templateRef="energy" dataType="xsd:double" dictRef="cc:energy" units="nonsi:hartree">-114.415498155971</scalar>
         <scalar cmlx:templateRef="spinsqr" dataType="xsd:double" dictRef="cc:s2">0.000000000000</scalar>
      </module>
    </comment>

Template definition ​

xml
<templateList>  <record id="symmetry-group">\s*Optimized structure,\s*SYMMETRY =&#123;X,cc:pointgroup&#125;</record>  <template id="molecule" pattern=".*" endPattern="ENERGY\s+=.*">    <record makeArray="true" repeat="*" id="atom">\s*&#123;A,compchem:elementType&#125;\s*&#123;F,compchem:x3&#125;\s*&#123;F,compchem:y3&#125;\s*&#123;F,compchem:z3&#125;\s*
            </record>    <transform process="createMolecule" xpath="./cml:list[@cmlx:templateRef='atom']/cml:array" id="molecule" />    <transform process="pullupSingleton" xpath="./cml:list" />
        </template>  <template id="energy-par" pattern="ENERGY\s+=.*\(.*" endPattern=".*">    <record id="energy">ENERGY\s*=\s*&#123;F,cc:energy&#125;\s*\(.*\)</record>    <transform process="pullupSingleton" xpath="./cml:list" />
        </template>  <template id="energy" pattern="ENERGY\s*=.*" endPattern=".*">    <record id="energy">ENERGY\s*=\s*&#123;F,cc:energy&#125;</record>    <transform process="pullupSingleton" xpath="./cml:list" />
        </template>  <template id="spinsqr" pattern="\s*Spin\(\*\*2\)\s*=.*" endPattern=".*">    <record id="spinsqr">\s*Spin\(\*\*2\)\s*=\s*&#123;F,cc:s2&#125;</record>    <transform process="pullupSingleton" xpath="./cml:list" />
        </template>  <template id="zpve" pattern="\s*Spin\(\*\*2\)\s*=.*" endPattern=".*">    <record id="zpve">ZPVE\s*=\s*&#123;F,cc:zpe.correction&#125;</record>    <transform process="pullupSingleton" xpath="./cml:list" />
        </template>  <template id="gradient" pattern="GRADIENT VECTOR" endPattern="HESSIAN MATRIX">    <record id="null" />    <record id="gradient-vector" repeat="*" makeArray="true">\s+&#123;F,cc:grad&#125;</record>    <transform process="pullupSingleton" xpath="./cml:list" />
        </template>  <template id="hessian" pattern="HESSIAN MATRIX\s*" endPattern="NORMAL MODE EIGENVALUE.*" endPattern2="Normal mode eigenvalues.*">    <record id="null" />    <record id="hess" makeArray="true" repeat="*">\s*&#123;1_5F,cc:hessianmatrix&#125;</record>    <transform process="pullupSingleton" xpath="./cml:list" />
        </template>  <template id="eigenvals" pattern="NORMAL MODE EIGENVALUE.*" endPattern="~">    <record id="null" />    <record id="normal-mode-eigvals" makeArray="true" repeat="*">\s+&#123;1_5F,cc:eigenval&#125;</record>    <transform process="pullupSingleton" xpath="./cml:list" />
        </template>  <transform process="pullup" xpath="./cml:module/cml:scalar" />  <transform process="pullup" xpath="./cml:module/cml:array" />  <transform process="delete" xpath="(//cml:list[@cmlx:templateRef='null'])" />  <transform process="delete" xpath=".//cml:module[count(*)=0]" />  <transform process="pullupSingleton" xpath="./cml:list" />  <transform process="addUnits" xpath=".//cml:scalar[@dictRef='cc:energy']" value="nonsi:hartree" />
    </templateList>