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cosmo ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceOrca log
idcosmo
nameCosmo section
pattern\s*-{10,}$\s*COSMO\sINITIALIZATION.*
endPattern\s*-{10,}$\s*\w.*
repeat*
xml:basejob/cosmo/cosmo.xml

Input ​

--------------------
COSMO INITIALIZATION
--------------------

Epsilon                                      ...   80.4000
Refractive Index                             ...    1.3300
Potential Evaluation                         ...  ANALYTIC
Technical COSMO parameters:
  rsolv                                      ...    1.3000
  routf                                      ...    0.8500
  disex                                      ...   10.0000
  nppa                                       ... 1082   
  nspa                                       ...   92   
Radii:
 Radius for O  used is    3.2503 Bohr (=   1.7200 Ang.)
 Radius for C  used is    3.7795 Bohr (=   2.0000 Ang.)
 Radius for H  used is    2.4566 Bohr (=   1.3000 Ang.)
Initializing COSMO package            ... done
Setting COSMO radii                   ... done
Setting atoms and making cavity       ...  USING 1082 GRID
done
Cholesky decomposition of A           ... done
--------------

Output text ​

xml
<comment class="example.output" id="cosmo">
        <module cmlx:templateRef="cosmo" dictRef="cc:userDefinedModule">
           <list cmlx:templateRef="technical">
              <list>
                 <scalar dataType="xsd:string" dictRef="cc:parameter">rsolv</scalar>
                 <scalar dataType="xsd:string" dictRef="cc:value">1.3000</scalar>
              </list>
              <list>
                 <scalar dataType="xsd:string" dictRef="cc:parameter">routf</scalar>
                 <scalar dataType="xsd:string" dictRef="cc:value">0.8500</scalar>
              </list>
              <list>
                 <scalar dataType="xsd:string" dictRef="cc:parameter">disex</scalar>
                 <scalar dataType="xsd:string" dictRef="cc:value">10.0000</scalar>
              </list>
              <list>
                 <scalar dataType="xsd:string" dictRef="cc:parameter">nppa</scalar>
                 <scalar dataType="xsd:string" dictRef="cc:value">1082</scalar>
              </list>
              <list>
                 <scalar dataType="xsd:string" dictRef="cc:parameter">nspa</scalar>
                 <scalar dataType="xsd:string" dictRef="cc:value">92</scalar>
              </list>
           </list>
           <list cmlx:templateRef="radii">
              <array dataType="xsd:string" dictRef="cc:elementType" size="3">O C H</array>
              <array dataType="xsd:double" dictRef="o:radius" size="3" units="nonsi:angstrom">1.7200 2.0000 1.3000</array>
           </list>
           <list cmlx:templateRef="parameters" dictRef="parameters">
              <list>
                 <scalar dataType="xsd:string" dictRef="cc:parameter">Epsilon</scalar>
                 <scalar dataType="xsd:string" dictRef="cc:value">80.4000</scalar>
              </list>
              <list>
                 <scalar dataType="xsd:string" dictRef="cc:parameter">Refractive Index</scalar>
                 <scalar dataType="xsd:string" dictRef="cc:value">1.3300</scalar>
              </list>
              <list>
                 <scalar dataType="xsd:string" dictRef="cc:parameter">Potential Evaluation</scalar>
                 <scalar dataType="xsd:string" dictRef="cc:value">ANALYTIC</scalar>
              </list>
              <list>
                 <scalar dataType="xsd:string" dictRef="cc:parameter">Initializing COSMO package</scalar>
                 <scalar dataType="xsd:string" dictRef="cc:value">done</scalar>
              </list>
              <list>
                 <scalar dataType="xsd:string" dictRef="cc:parameter">Setting COSMO radii</scalar>
                 <scalar dataType="xsd:string" dictRef="cc:value">done</scalar>
              </list>
              <list>
                 <scalar dataType="xsd:string" dictRef="cc:parameter">Setting atoms and making cavity</scalar>
                 <scalar dataType="xsd:string" dictRef="cc:value">USING 1082 GRID</scalar>
              </list>
              <list>
                 <scalar dataType="xsd:string" dictRef="cc:parameter">Cholesky decomposition of A</scalar>
                 <scalar dataType="xsd:string" dictRef="cc:value">done</scalar>
              </list>
           </list>
        </module>
    </comment>

Template definition ​

xml
<templateList>  <template pattern="\s*Technical\sCOSMO\sparameters.*" endPattern="\s*Radii.*" endPattern2="\w.*" endPattern3="~" repeat="*">    <record />    <record id="technical" repeat="*">&#123;X,cc:parameter&#125;\.\.\.&#123;X,cc:value&#125;</record>
        </template>  <template pattern="\s*Radii:\s*" endPattern="\s*(?!.*Radius).+" endPattern2="~" repeat="*">    <record />    <record id="radii" repeat="*" makeArray="true">\s*Radius\sfor&#123;A,cc:elementType&#125;used\sis.*\(=&#123;F,o:radius&#125;.*</record>
        </template>  <template id="parameter" pattern=".*\.\.\..*" endPattern=".*" endPattern2="~" repeat="*">    <record>&#123;X,cc:parameter&#125;\.\.\.&#123;X,cc:value&#125;</record>
        </template>
    </templateList>
<transform process="move" xpath=".//cml:module[@cmlx:templateRef='parameter']/cml:list/cml:list" to="." />
<transform process="pullup" xpath=".//cml:list[@cmlx:templateRef='radii']" />
<transform process="pullup" xpath=".//cml:list[@cmlx:templateRef='technical']" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:module[count(*)=0]" />
<transform process="delete" xpath=".//cml:module" />
<transform process="addUnits" xpath=".//cml:array[@dictRef='o:radius']" value="nonsi:angstrom" />
<transform process="addChild" elementName="cml:list" xpath="." dictRef="parameters" />
<transform process="addAttribute" xpath=".//cml:list[@dictRef='parameters']" name="cmlx:templateRef" value="parameters" />
<transform process="move" xpath="./cml:list[not(@cmlx:templateRef)]" to="./cml:list[@cmlx:templateRef='parameters']" />