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cpcm ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceOrca log
idcpcm
nameCPCM section
pattern\s*-{10,}$\s*CPCM\sSOLVATION\sMODEL.*
endPattern\s*Overall\stime\sfor\sCPCM\sinitialization.*
repeat*
endOffset1
xml:basejob/cpcm/cpcm.xml

Input ​

------------------------------------------------------------------------------
                           CPCM SOLVATION MODEL                               
------------------------------------------------------------------------------


CPCM parameters:
  Epsilon                                         ...      80.4000
  Refrac                                          ...       1.3300
  Rsolv                                           ...       1.3000
  Surface type                                    ...    GEPOL SES
  Epsilon function type                           ...         CPCM
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.)
 
Calculating surface                               ...        done! (  0.0s)
GEPOL surface points                              ...          281
GEPOL Volume                                      ...     538.7664
GEPOL Surface-area                                ...     353.6151
Calculating surface distance matrix               ...        done! (  0.0s)
Performing Cholesky decomposition & store         ...        done! (  0.0s)
Overall time for CPCM initialization              ...                 0.0s

Output text ​

xml
<comment class="example.output" id="cpcm">    
      <module dictRef="cc:userDefinedModule" id="otherComponents">       
          <list cmlx:templateRef="technical">
             <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">Refrac</scalar>
                <scalar dataType="xsd:string" dictRef="cc:value">1.3300</scalar>
             </list>
             <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">Surface type</scalar>
                <scalar dataType="xsd:string" dictRef="cc:value">GEPOL SES</scalar>
             </list>
             <list>
                <scalar dataType="xsd:string" dictRef="cc:parameter">Epsilon function type</scalar>
                <scalar dataType="xsd:string" dictRef="cc:value">CPCM</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">Calculating surface</scalar>
                <scalar dataType="xsd:string" dictRef="cc:value">done! (  0.0s)</scalar>
             </list>
             <list>
                <scalar dataType="xsd:string" dictRef="cc:parameter">GEPOL surface points</scalar>
                <scalar dataType="xsd:string" dictRef="cc:value">281</scalar>
             </list>
             <list>
                <scalar dataType="xsd:string" dictRef="cc:parameter">GEPOL Volume</scalar>
                <scalar dataType="xsd:string" dictRef="cc:value">538.7664</scalar>
             </list>
             <list>
                <scalar dataType="xsd:string" dictRef="cc:parameter">GEPOL Surface-area</scalar>
                <scalar dataType="xsd:string" dictRef="cc:value">353.6151</scalar>
             </list>
             <list>
                <scalar dataType="xsd:string" dictRef="cc:parameter">Calculating surface distance matrix</scalar>
                <scalar dataType="xsd:string" dictRef="cc:value">done! (  0.0s)</scalar>
             </list>
             <list>
                <scalar dataType="xsd:string" dictRef="cc:parameter">Performing Cholesky decomposition & store</scalar>
                <scalar dataType="xsd:string" dictRef="cc:value">done! (  0.0s)</scalar>
             </list>
             <list>
                <scalar dataType="xsd:string" dictRef="cc:parameter">Overall time for CPCM initialization</scalar>
                <scalar dataType="xsd:string" dictRef="cc:value">0.0s</scalar>
             </list>
          </list>
       </module>
    </comment>

Template definition ​

xml
<templateList>  <template pattern="\s*CPCM\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']" />