cosmo¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
| Attribute | Value |
|---|---|
| source | Orca log |
| id | cosmo |
| name | Cosmo section |
| pattern | \s*-{10,}$\s*COSMO\sINITIALIZATION.* |
| endPattern | \s*-{10,}$\s*\w.* |
| repeat | * |
| xml:base | job/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
<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
<templateList> <template pattern="\s*Technical\sCOSMO\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']" />