cosmo

Implementation level
Type Status
CML extraction template image0
HTML5 representation image1
Template attributes
Attribute Value
source Turbomole log
id cosmo
name Cosmo results
pattern \s*=+s*$s*COSMOsRESULTSs*$s*=+s*
endPattern \s*=+s*$s*
endOffset 1
repeat *
xml:base cosmo.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.**
<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.

<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.

<templateList>  <template pattern="\s*PARAMETER:.*" endPattern="\s*[A-Z]+.*" endOffset="0">    <record repeat="1" />    <record id="parameters" repeat="*">{X,t:parameter}\:{A,t:value}</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:{A,t:surface},.*:{A,t:matrix}</record>    <record id="cavityVolumeArea" repeat="*">{X,t:parameter}\:{A,t:value}</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]{2,}.*" endOffset="0">    <record repeat="1" />    <record id="screeningCharge" repeat="*">{X,t:parameter}\:{A,t:value}</record>
        </template>  <template pattern="\s*ENERGIES.*:.*" endPattern="\s*[A-Z]{2,}.*" endPattern2="~" endOffset="0">    <record repeat="1" />    <record>\s*Total\senergy\s*={F,cc:energy}</record>    <record>\s*Total\senergy\s\+\sOC\scorr\.\s*={F,t:energyOcCorr}</record>    <record>\s*Dielectric\senergy\s*={F,t:dielectricEnergy}</record>    <record>\s*Diel\.\senergy\s\+\sOC\scorr\.\s*={F,t:dielectricEnergyOcCorr}</record>    <record repeat="1" />    <record>\s*Total\senergy\scorrected\s*={F,t:energyCorrected}</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]{2,}.*" endPattern3="~" endOffset="0">    <record repeat="1" />    <templateList>      <template id="atom" pattern="\s*atom.*" endPattern=".*" endPattern2="~" endOffset="0" repeat="*">        <record>\s*atom{1_11I,cc:serial}</record>
                </template>      <template id="radius" pattern="\s*radius.*" endPattern=".*" endPattern2="~" endOffset="0" repeat="*">        <record>\s*radius{1_11F,t:radius}</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]{2,}.*" endPattern3="~" endOffset="0">    <record repeat="1" />    <record repeat="*" makeArray="true">{A,cc:elementType}{F,t:atomicradii}:{A,t:atomrange}</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]" />