cpcm¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation |  |
| Attribute | Value |
|---|---|
| source | Orca log |
| id | cpcm |
| name | CPCM section |
| pattern | \s*-{10,}$\s*CPCM\sSOLVATION\sMODEL.* |
| endPattern | \s*Overall\stime\sfor\sCPCM\sinitialization.* |
| repeat | * |
| endOffset | 1 |
| xml:base | job/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
<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
<templateList> <template pattern="\s*CPCM\sparameters.*" endPattern="\s*Radii.*" endPattern2="\w.*" endPattern3="~" repeat="*"> <record /> <record id="technical" repeat="*">{X,cc:parameter}\.\.\.{X,cc:value}</record>
</template> <template pattern="\s*Radii:\s*" endPattern="\s*(?!.*Radius).+" endPattern2="~" repeat="*"> <record /> <record id="radii" repeat="*" makeArray="true">\s*Radius\sfor{A,cc:elementType}used\sis.*\(={F,o:radius}.*</record>
</template> <template id="parameter" pattern=".*\.\.\..*" endPattern=".*" endPattern2="~" repeat="*"> <record>{X,cc:parameter}\.\.\.{X,cc:value}</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']" />