input.file

Implementation level
Type Status
CML extraction template image0
HTML5 representation image1
Template attributes
Attribute Value
source MOPAC log
id input.file
name Input file section
pattern \s**+ s*$s**s*CALCULATIONsDONE:.*
endPattern \s*$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.

<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.

<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>