input.file ​
Implementation level ​
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation |  |
Template attributes ​
| Attribute | Value |
|---|---|
| source | MOPAC log |
| id | input.file |
| name | Input file section |
| pattern | \s*\*+\s*$\s*\*\s*CALCULATION\sDONE:.* |
| endPattern | \s*$\s*$\s* |
| startOffset | 2 |
| endOffset | 0 |
| xml:base | job/input.xml |
Input ​
*******************************************************************************
* CALCULATION DONE: Fri Jan 6 19:51:47 2017 *
* PM6 - The PM6 Hamiltonian to be used
* MOZYME - USE LOCALIZED M.O.s IN SOLVING THE SCF EQUATIONS
* PRECISE - CRITERIA TO BE INCREASED BY 100 TIMES
* T= - A TIME OF 172800.0 SECONDS REQUESTED
* DUMP=N - RESTART FILE WRITTEN EVERY 7200.000 SECONDS
* AUX - OUTPUT AUXILIARY INFORMATION
* PRTXYZ - PRINT CARTESIAN COORDINATES
* PRNT - EXTRA PRINTING IN EF ROUTINE
* DISP - PRINT DISPERSION AND HYDROGEN BOND ENERGIES
* PL - MONITOR CONVERGENCE IN DENSITY MATRIX
*******************************************************************************
PM6 MOZYME PRECISE PRTXYZ PRNT=5 DISP(1.0) PL AUX
AI
PM6 optimization
ATOM CHEMICAL X Y Z
NUMBER SYMBOL (ANGSTROMS) (ANGSTROMS) (ANGSTROMS)
1 C -4.19184475 * 2.56171882 * 1.35180722 *
2 C -4.85437358 * 3.57297417 * 0.50049748 *
3 C -6.22952321 * 3.62747474 * 0.39522324 *
4 C -7.13930258 * 2.80943244 * 1.25599220 *
5 C -6.41595323 * 1.70580884 * 2.18557431 *
6 C -4.92595752 * 1.63926235 * 2.06986776 *
Output text ​
xml
<comment class="example.output" id="input.file">
<module cmlx:templateRef="input.file">
<module cmlx:templateRef="inputlines">
<list cmlx:templateRef="lines">
<scalar dataType="xsd:string" dictRef="mp:inputline">*******************************************************************************</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">* CALCULATION DONE: Fri Jan 6 19:51:47 2017 *</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">* PM6 - The PM6 Hamiltonian to be used</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">* MOZYME - USE LOCALIZED M.O.s IN SOLVING THE SCF EQUATIONS</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">* PRECISE - CRITERIA TO BE INCREASED BY 100 TIMES</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">* T= - A TIME OF 172800.0 SECONDS REQUESTED</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">* DUMP=N - RESTART FILE WRITTEN EVERY 7200.000 SECONDS</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">* AUX - OUTPUT AUXILIARY INFORMATION</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">* PRTXYZ - PRINT CARTESIAN COORDINATES</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">* PRNT - EXTRA PRINTING IN EF ROUTINE</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">* DISP - PRINT DISPERSION AND HYDROGEN BOND ENERGIES</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">* PL - MONITOR CONVERGENCE IN DENSITY MATRIX</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">*******************************************************************************</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">PM6 MOZYME PRECISE PRTXYZ PRNT=5 DISP(1.0) PL AUX</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">AI</scalar>
<scalar dataType="xsd:string" dictRef="mp:inputline">PM6 optimization</scalar>
</list>
</module>
<module cmlx:templateRef="geometry">
<molecule id="initial">
<atomArray>
<atom elementType="C" id="a1" x3="0.19184475" y3="2.56171882" z3="1.35180722">
<scalar dataType="xsd:integer" dictRef="cc:serial">1</scalar>
<scalar dataType="xsd:integer" dictRef="g:atomicType">-4</scalar>
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
</atom>
<atom elementType="C" id="a2" x3="0.85437358" y3="3.57297417" z3="0.50049748">
<scalar dataType="xsd:integer" dictRef="cc:serial">2</scalar>
<scalar dataType="xsd:integer" dictRef="g:atomicType">-4</scalar>
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
</atom>
<atom elementType="C" id="a3" x3="0.22952321" y3="3.62747474" z3="0.39522324">
<scalar dataType="xsd:integer" dictRef="cc:serial">3</scalar>
<scalar dataType="xsd:integer" dictRef="g:atomicType">-6</scalar>
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
</atom>
<atom elementType="C" id="a4" x3="0.13930258" y3="2.80943244" z3="1.2559922">
<scalar dataType="xsd:integer" dictRef="cc:serial">4</scalar>
<scalar dataType="xsd:integer" dictRef="g:atomicType">-7</scalar>
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
</atom>
<atom elementType="C" id="a5" x3="0.41595323" y3="1.70580884" z3="2.18557431">
<scalar dataType="xsd:integer" dictRef="cc:serial">5</scalar>
<scalar dataType="xsd:integer" dictRef="g:atomicType">-6</scalar>
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
</atom>
<atom elementType="C" id="a6" x3="0.92595752" y3="1.63926235" z3="2.06986776">
<scalar dataType="xsd:integer" dictRef="cc:serial">6</scalar>
<scalar dataType="xsd:integer" dictRef="g:atomicType">-4</scalar>
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
</atom>
</atomArray>
</molecule>
</module>
</module>
</comment>Template definition ​
xml
<templateList> <template id="inputlines" pattern="\s*\*+\s*$\s*\*\s*CALCULATION\sDONE:.*" endPattern="\s*ATOM\s*CHEMICAL\s*X\s*Y\s*Z\s*"> <record id="lines" repeat="*">{X,mp:inputline}</record>
</template> <template id="geometry" pattern="\s*ATOM\s*CHEMICAL\s*X\s*Y\s*Z\s*" endPattern="~"> <record repeat="3" /> <record id="atom" repeat="*">{I,cc:serial}{A,cc:elementType}{F,cc:x3}\*?{F,cc:y3}\*?{F,cc:z3}\*?</record> <transform process="delete" xpath="//cml:list[child::cml:scalar[@dictRef='cc:elementType' and text() = 'Tv']]" /> <transform id="atom" process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:serial']" dictRef="cc:serial" dataType="xsd:integer" /> <transform id="atom" process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:elementType']" dictRef="cc:elementType" dataType="xsd:string" /> <transform id="atom" process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:x3']" dictRef="cc:x3" dataType="xsd:double" /> <transform id="atom" process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:y3']" dictRef="cc:y3" dataType="xsd:double" /> <transform id="atom" process="createArray" xpath="." from=".//cml:scalar[@dictRef='cc:z3']" dictRef="cc:z3" dataType="xsd:double" /> <transform process="pullup" xpath=".//cml:list/cml:array" /> <transform process="delete" xpath=".//cml:list[count(*)=0]" /> <transform process="createMolecule" xpath=".//cml:list[@cmlx:templateRef='atom']/cml:array" id="initial" /> <transform process="delete" xpath=".//cml:molecule//cml:scalar[@dictRef='cc:serial']" /> <transform process="delete" xpath=".//cml:molecule//cml:scalar[@dictRef='cc:atomicNumber']" /> <transform process="pullup" xpath=".//cml:molecule" /> <transform process="delete" xpath=".//cml:list[count(*)=0]" /> <transform process="delete" xpath=".//cml:list[count(*)=0]" />
</template>
</templateList>