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cosmo ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceTurbomole log
idcosmo
nameCosmo results
pattern\s*=+\s*$\s*COSMO\sRESULTS\s*$\s*=+\s*
endPattern\s*=+\s*$\s*
endOffset1
repeat*
xml:basecosmo.xml

Input ​

 ============================================================================== 
                                  COSMO RESULTS
 ============================================================================== 
  PARAMETER:
    nppa:      1082
    nspa:        92
    nsph:        32
    nps:        712
    npspher:    224
    disex:   10.0000    
    disex2:  4128.15    
    rsolv [A]: 3.5400
    routf:     0.8500
    phsran:   0.00    
    ampran:   0.10E-04
    cavity:  closed
    epsilon:  9.800
    fepsi:      0.8543689
  CAVITY VOLUME/AREA [a.u.]:
    surface: V1.0, A matrix: V1.0
    area:   654.69
    volume:  1389.84
  SCREENING CHARGE:
    cosmo      :  -0.024349
    correction :   0.024631
    total      :   0.000282
  ENERGIES [a.u.]:
    Total energy            =    -1650.4710944278
    Total energy + OC corr. =    -1650.4709392488
    Dielectric energy       =       -0.0050408508
    Diel. energy + OC corr. =       -0.0048856718
    The following value is included for downward compatibility
    Total energy corrected  =    -1650.4710168383
  RADII [Angstroem]:
    atom       1     2     3     4     5     6     7     8     9    10    11  
    radius  2.00  2.00  2.00  2.00  2.00  1.06  2.00  2.00  2.00  2.00  2.00 
    atom      12    13    14    15    16    17    18    19    20    21  
    radius  1.30  1.30  1.30  1.30  1.30  1.30  1.30  1.30  1.30  1.30 
 ==============================================================================

Input ​

Output text ​

xml
<comment class="example.output" id="cosmo">
       <module cmlx:lineCount="39" cmlx:templateRef="cosmo">
          <list cmlx:templateRef="parameters">
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">nppa</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">1082</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">nspa</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">92</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">nsph</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">32</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">nps</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">712</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">npspher</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">224</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">disex</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">10.0000</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">disex2</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">4128.15</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">rsolv [A]</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">3.5400</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">routf</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">0.8500</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">phsran</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">0.00</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">ampran</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">0.10E-04</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">cavity</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">closed</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">epsilon</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">9.800</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">fepsi</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">0.8543689</scalar>
              </list>
          </list>
          <list cmlx:templateRef="cavityVolumeArea">
              <list>
                  <scalar dataType="xsd:string" dictRef="t:surface">V1.0</scalar>
                  <scalar dataType="xsd:string" dictRef="t:matrix">V1.0</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">area</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">654.69</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">volume</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">1389.84</scalar>
              </list>
          </list>
          <list cmlx:templateRef="screeningCharge">
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">cosmo</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">-0.024349</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">correction</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">0.024631</scalar>
              </list>
              <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">total</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">0.000282</scalar>
              </list>
          </list>
          <list id="energies" cmlx:templateRef="energies">
              <scalar dataType="xsd:double" dictRef="cc:energy">-1650.4710944278</scalar>
              <scalar dataType="xsd:double" dictRef="t:energyOcCorr">-1650.4709392488</scalar>
              <scalar dataType="xsd:double" dictRef="t:dielectricEnergy">-0.0050408508</scalar>
              <scalar dataType="xsd:double" dictRef="t:dielectricEnergyOcCorr">-0.0048856718</scalar>
              <scalar dataType="xsd:double" dictRef="t:energyCorrected">-1650.4710168383</scalar>
          </list>
          <list id="radii" cmlx:templateRef="radii">
              <array dataType="xsd:integer" size="21" dictRef="cc:serial">1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21</array>
              <array dataType="xsd:double" size="21" dictRef="t:radius">2.0 2.0 2.0 2.0 2.0 1.06 2.0 2.0 2.0 2.0 2.0 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3</array>
          </list>
      </module>   
    </comment>

Output text ​

xml
<comment class="example.output" id="cosmo2">
        <module cmlx:templateRef="cosmo">
            <list cmlx:templateRef="parameters">
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">nppa</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">1082</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">nspa</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">92</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">nsph</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">32</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">nps</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">351</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">npspher</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">197</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">disex</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">10.0000</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">disex2</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">4473.83</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">rsolv [A]</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">1.3000</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">routf</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">0.8500</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">phsran</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">0.0</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">ampran</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">0.10E-04</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">cavity</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">closed</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">epsilon</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">infinity</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">refind</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">1.300</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">fepsi</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">1.0000000</scalar>
               </list>
            </list>
            <list cmlx:templateRef="cavityVolumeArea">
               <list>
                  <scalar dataType="xsd:string" dictRef="t:surface">V1.0</scalar>
                  <scalar dataType="xsd:string" dictRef="t:matrix">V1.0</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">area</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">349.52</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">volume</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">542.84</scalar>
               </list>
            </list>
            <list cmlx:templateRef="screeningCharge">
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">cosmo</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">-0.019014</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">correction</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">0.018692</scalar>
               </list>
               <list>
                  <scalar dataType="xsd:string" dictRef="t:parameter">total</scalar>
                  <scalar dataType="xsd:string" dictRef="t:value">-0.000323</scalar>
               </list>
            </list>
            <list cmlx:templateRef="energies" id="energies">
               <scalar dataType="xsd:double" dictRef="cc:energy">-190.8500889093</scalar>
               <scalar dataType="xsd:double" dictRef="t:energyOcCorr">-190.8501078686</scalar>
               <scalar dataType="xsd:double" dictRef="t:dielectricEnergy">-0.0158822461</scalar>
               <scalar dataType="xsd:double" dictRef="t:dielectricEnergyOcCorr">-0.0159012054</scalar>
            </list>
            <list cmlx:templateRef="radii" id="radii">
               <array dataType="xsd:string" dictRef="cc:elementType" size="3">o c h</array>
               <array dataType="xsd:double" dictRef="t:atomicradii" size="3">1.72 2.00 1.30</array>
               <array dataType="xsd:string" dictRef="t:atomrange" size="3">1 2-4 5-8</array>
            </list>
         </module>
    </comment>

Template definition ​

xml
<templateList>  <template pattern="\s*PARAMETER:.*" endPattern="\s*[A-Z]+.*" endOffset="0">    <record repeat="1" />    <record id="parameters" repeat="*">&#123;X,t:parameter&#125;\:&#123;A,t:value&#125;</record>      
        </template>  <template pattern="\s*CAVITY\sVOLUME/AREA\s\[a\.u\.\].*" endPattern="\s*[A-Z]+.*" endOffset="0">    <record repeat="1" />    <record id="tmp">\s*surface:&#123;A,t:surface&#125;,.*:&#123;A,t:matrix&#125;</record>    <record id="cavityVolumeArea" repeat="*">&#123;X,t:parameter&#125;\:&#123;A,t:value&#125;</record>    <transform process="move" xpath=".//cml:list[@cmlx:templateRef='tmp']/cml:list" to=".//cml:list[@cmlx:templateRef='cavityVolumeArea']" position="1" />
        </template>  <template pattern="\s*SCREENING\sCHARGE:.*" endPattern="\s*[A-Z]&#123;2,&#125;.*" endOffset="0">    <record repeat="1" />    <record id="screeningCharge" repeat="*">&#123;X,t:parameter&#125;\:&#123;A,t:value&#125;</record>     
        </template>  <template pattern="\s*ENERGIES.*:.*" endPattern="\s*[A-Z]&#123;2,&#125;.*" endPattern2="~" endOffset="0">    <record repeat="1" />    <record>\s*Total\senergy\s*=&#123;F,cc:energy&#125;</record>    <record>\s*Total\senergy\s\+\sOC\scorr\.\s*=&#123;F,t:energyOcCorr&#125;</record>    <record>\s*Dielectric\senergy\s*=&#123;F,t:dielectricEnergy&#125;</record>    <record>\s*Diel\.\senergy\s\+\sOC\scorr\.\s*=&#123;F,t:dielectricEnergyOcCorr&#125;</record>    <record repeat="1" />    <record>\s*Total\senergy\scorrected\s*=&#123;F,t:energyCorrected&#125;</record>    <transform process="addChild" xpath="." elementName="cml:list" id="energies" />    <transform process="addAttribute" xpath=".//cml:list[@id='energies']" name="cmlx:templateRef" value="energies" />    <transform process="move" xpath=".//cml:scalar" to=".//cml:list[@id='energies']" />     
        </template>  <template pattern="\s*RADII.*" endPattern="\s*=+\s*" endPattern2="\s*[A-Z]&#123;2,&#125;.*" endPattern3="~" endOffset="0">    <record repeat="1" />    <templateList>      <template id="atom" pattern="\s*atom.*" endPattern=".*" endPattern2="~" endOffset="0" repeat="*">        <record>\s*atom&#123;1_11I,cc:serial&#125;</record>
                </template>      <template id="radius" pattern="\s*radius.*" endPattern=".*" endPattern2="~" endOffset="0" repeat="*">        <record>\s*radius&#123;1_11F,t:radius&#125;</record>
                </template>
            </templateList>    <transform process="joinArrays" xpath=".//cml:array[@dictRef='cc:serial']" />    <transform process="joinArrays" xpath=".//cml:array[@dictRef='t:radius']" />    <transform process="addChild" xpath="." elementName="cml:list" id="radii" />    <transform process="addAttribute" xpath=".//cml:list[@id='radii']" name="cmlx:templateRef" value="radii" />    <transform process="move" xpath=".//cml:array" to=".//cml:list[@id='radii']" />      
        </template>  <template id="" pattern="\s*ELEMENT\sRADIUS\s\[A\]:\sATOM\sLIST\s*" endPattern2="\s*[A-Z]&#123;2,&#125;.*" endPattern3="~" endOffset="0">    <record repeat="1" />    <record repeat="*" makeArray="true">&#123;A,cc:elementType&#125;&#123;F,t:atomicradii&#125;:&#123;A,t:atomrange&#125;</record>    <transform process="addChild" xpath="." elementName="cml:list" id="radii" />    <transform process="addAttribute" xpath=".//cml:list[@id='radii']" name="cmlx:templateRef" value="radii" />    <transform process="move" xpath=".//cml:array" to=".//cml:list[@id='radii']" />
        </template>                       
    </templateList>
<transform process="move" xpath=".//cml:module/cml:list" to="." />
<transform process="move" xpath=".//cml:module/cml:list" to="." />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:module[count(*)=0]" />
<transform process="delete" xpath=".//cml:module[count(*)=0]" />