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l103 ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceGaussian log
idl103
nameBerny optimizations to minima and TS, STQN transition state searches
repeat*
pattern\s*\(Enter.*l103\..*
pattern2\s*(Grad){2,}
endPattern\s*Leave\sLink\s+103\s.*
endOffset1
endPattern2\s*(Grad){2,}
xml:basel103.xml

Input ​

 (Enter /opt/G09/g09/l103.exe)
 
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
 Berny optimization.
 Initialization pass.
                           ----------------------------
                           !    Initial Parameters    !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)                  1.113          estimate D2E/DX2                !
 ! R2    R(1,3)                  1.113          estimate D2E/DX2                !
 ! R3    R(1,4)                  1.113          estimate D2E/DX2                !
 ! R4    R(1,5)                  1.113          estimate D2E/DX2                !
 ! A1    A(2,1,3)              109.4712         estimate D2E/DX2                !
 ! A2    A(2,1,4)              109.4712         estimate D2E/DX2                !
 ! A3    A(2,1,5)              109.4712         estimate D2E/DX2                !
 ! A4    A(3,1,4)              109.4712         estimate D2E/DX2                !
 ! A5    A(3,1,5)              109.4712         estimate D2E/DX2                !
 ! A6    A(4,1,5)              109.4712         estimate D2E/DX2                !
 --------------------------------------------------------------------------------
 Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-06
 Number of steps in this run=  20 maximum allowed number of steps= 100.
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
 
  Leave Link  103 at Fri Sep 13 17:06:50 2013, MaxMem=  419430400 cpu:       0.0

Input ​

 (Enter /opt/G09/g09/l103.exe)
 
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
 Berny optimization.
 Internal  Forces:  Max     0.002386724 RMS     0.000538609
 Search for a saddle point.
 Step number   1 out of a maximum of  137
 All quantities printed in internal units (Hartrees-Bohrs-Radians)
 Swaping is turned off.
 Second derivative matrix not updated -- analytic derivatives used.
     Eigenvalues ---   -0.03403   0.00144   0.00463   0.00759   0.00906
     Eigenvalues ---    0.01177   0.01317   0.01431   0.01623   0.01839
     Eigenvalues ---    0.40148   0.40211   0.40329   0.46257   0.48142
     Eigenvalues ---    0.51910   1.01166   1.025821000.000001000.00000
     Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000
     Eigenvalues --- 1000.000001000.00000
 Eigenvectors required to have negative eigenvalues:
                          R25       R14       R27       R16       D47
   1                    0.36641   0.36640   0.22975   0.22974  -0.19160
                          D48       D8        D11       D6        D9
   1                    0.19153   0.16306  -0.16304   0.15371  -0.15366
 RFO step:  Lambda0=9.155600927D-04 Lambda=-1.51225227D-04.
 Linear search not attempted -- option 19 set.
 Iteration  1 RMS(Cart)=  0.01149217 RMS(Int)=  0.00020982
 Iteration  2 RMS(Cart)=  0.00019717 RMS(Int)=  0.00012443
 Iteration  3 RMS(Cart)=  0.00000003 RMS(Int)=  0.00012443
 Variable       Old X    -DE/DX   Delta X   Delta X   Delta X     New X
                                 (Linear)    (Quad)   (Total)
    R1        2.63420   0.00003   0.00000   0.00038   0.00026   2.63446
    R2        2.63420   0.00004   0.00000   0.00037   0.00026   2.63446
   R41        2.01442   0.00057   0.00000  -0.00167  -0.00165   2.01277
    A1        1.93497   0.00006   0.00000  -0.00261  -0.00267   1.93230
    A2        2.13721  -0.00006   0.00000   0.00116   0.00111   2.13833
   A37        2.20391  -0.00012   0.00000   0.01113   0.01057   2.21448
    D1        3.00181  -0.00035   0.00000   0.00163   0.00163   3.00344
    D2       -0.15405  -0.00021   0.00000   0.00583   0.00583  -0.14822
   D49        0.00020   0.00000   0.00000  -0.00022  -0.00022  -0.00002
         Item               Value     Threshold  Converged?
 Maximum Force            0.002387     0.000450     NO 
 RMS     Force            0.000539     0.000300     NO 
 Maximum Displacement     0.044296     0.001800     NO 
 RMS     Displacement     0.011477     0.001200     NO 
 Predicted change in Energy= 3.932148D-04
 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad
 
 Leave Link  103 at Fri Sep 13 17:06:50 2013, MaxMem=  419430400 cpu:       0.0

Output text ​

xml
<comment class="example.output" id="l103">  
    <module cmlx:templateRef="l103">
         <list cmlx:templateRef="berny">
            <scalar dataType="xsd:string" dictRef="g:optimization">Berny optimization.</scalar>
         </list>
         <module cmlx:templateRef="l103.init">
            <list cmlx:templateRef="length">
               <array dataType="xsd:string" dictRef="g:symbol" size="4">R1 R2 R3 R4</array>
               <array dataType="xsd:integer" dictRef="g:atom1" size="4">1 1 1 1</array>
               <array dataType="xsd:integer" dictRef="g:atom2" size="4">2 3 4 5</array>
               <array dataType="xsd:double" dictRef="cc:distance" size="4">1.113 1.113 1.113 1.113</array>
               <array dataType="xsd:string" delimiter="|" dictRef="g:deriv" size="4">estimate D2E/DX2|estimate D2E/DX2|estimate D2E/DX2|estimate D2E/DX2</array>
            </list>
            <list cmlx:templateRef="angle">
               <array dataType="xsd:string" dictRef="g:symbol" size="6">A1 A2 A3 A4 A5 A6</array>
               <array dataType="xsd:integer" dictRef="g:atom1" size="6">2 2 2 3 3 4</array>
               <array dataType="xsd:integer" dictRef="g:atom2" size="6">1 1 1 1 1 1</array>
               <array dataType="xsd:integer" dictRef="g:atom3" size="6">3 4 5 4 5 5</array>
               <array dataType="xsd:double" dictRef="cc:angle" size="6">109.4712 109.4712 109.4712 109.4712 109.4712 109.4712</array>
               <array dataType="xsd:string" delimiter="|" dictRef="g:deriv" size="6">estimate D2E/DX2|estimate D2E/DX2|estimate D2E/DX2|estimate D2E/DX2|estimate D2E/DX2|estimate D2E/DX2</array>
            </list>
         </module>
         <module cmlx:templateRef="l103.trust">
            <scalar dataType="xsd:double" dictRef="g:trustrad">3.00e-01</scalar>
            <scalar dataType="xsd:double" dictRef="g:fncerr">1.00e-07</scalar>
            <scalar dataType="xsd:double" dictRef="g:grderr">1.00e-06</scalar>
            <scalar dataType="xsd:integer" dictRef="g:nstep">20</scalar>
            <scalar dataType="xsd:integer" dictRef="g:allowedstep">100</scalar>
         </module>
         <module cmlx:templateRef="l103.catchall">
            <list cmlx:templateRef="l103.discard">
               <scalar dataType="xsd:string" dictRef="x:discard" />
            </list>
         </module>
      </module>
  </comment>

Output text ​

xml
<comment class="example.output" id="l103.1">
    <module cmlx:templateRef="l103">
       <list cmlx:templateRef="berny">
          <scalar dataType="xsd:string" dictRef="g:optimization">Berny optimization.</scalar>
       </list>
       <module cmlx:templateRef="l103.localminsaddle">
          <scalar cmlx:templateRef="r" dataType="xsd:string" dictRef="cc:minmaxts">saddle point</scalar>
          <array cmlx:templateRef="junk" dataType="xsd:string" dictRef="x:junk1" size="9">Step number 1 out of a maximum of 137</array>
          <array cmlx:templateRef="junk" dataType="xsd:string" dictRef="x:junk1" size="7">All quantities printed in internal units (Hartrees-Bohrs-Radians)</array>
          <array cmlx:templateRef="junk" dataType="xsd:string" dictRef="x:junk1" size="4">Swaping is turned off.</array>
          <array cmlx:templateRef="eigenvaluelist" dataType="xsd:double" dictRef="" size="27">-0.03403 0.00144 0.00463 0.00759 0.00906 0.01177 0.01317 0.01431 0.01623 0.01839 0.40148 0.40211 0.40329 0.46257 0.48142 0.51910 1.01166 1.02582 1000.00000 1000.00000 1000.00000 1000.00000 1000.00000 1000.00000 1000.00000 1000.00000 1000.00000</array>
       </module>
       <module cmlx:templateRef="rfo">
          <list cmlx:templateRef="rfo">
             <scalar dataType="xsd:double" dictRef="g:lambda0">9.155600927e-04</scalar>
             <scalar dataType="xsd:double" dictRef="g:lambda">-1.51225227e-04</scalar>
          </list>
          <list cmlx:templateRef="nolinear">
             <scalar dataType="xsd:string" dictRef="g:linear">Linear search</scalar>
          </list>
          <list cmlx:templateRef="iteration">
             <array dataType="xsd:integer" dictRef="cc:serial" size="3">1 2 3</array>
             <array dataType="xsd:double" dictRef="g:rmscart" size="3">0.01149217 0.00019717 0.00000003</array>
             <array dataType="xsd:double" dictRef="g:rmsint" size="3">0.00020982 0.00012443 0.00012443</array>
          </list>
       </module>
       <module cmlx:templateRef="l103.deltas">
          <list cmlx:templateRef="delta">
             <array dataType="xsd:string" dictRef="cc:variable" size="9">R1 R2 R41 A1 A2 A37 D1 D2 D49</array>
             <array dataType="xsd:double" dictRef="g:lastval" size="9">2.63420 2.63420 2.01442 1.93497 2.13721 2.20391 3.00181 -0.15405 0.00020</array>
             <array dataType="xsd:double" dictRef="cc:deriv" size="9">0.00003 0.00004 0.00057 0.00006 -0.00006 -0.00012 -0.00035 -0.00021 0.00000</array>
             <array dataType="xsd:double" dictRef="cc:delta.linear" size="9">0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000</array>
             <array dataType="xsd:double" dictRef="cc:delta.quad" size="9">0.00038 0.00037 -0.00167 -0.00261 0.00116 0.01113 0.00163 0.00583 -0.00022</array>
             <array dataType="xsd:double" dictRef="cc:delta.total" size="9">0.00026 0.00026 -0.00165 -0.00267 0.00111 0.01057 0.00163 0.00583 -0.00022</array>
             <array dataType="xsd:double" dictRef="cc:newval" size="9">2.63446 2.63446 2.01277 1.93230 2.13833 2.21448 3.00344 -0.14822 -0.00002</array>
          </list>
       </module>
       <module cmlx:templateRef="l103.itemconverge">
          <list cmlx:templateRef="row">
             <array dataType="xsd:string" delimiter="|" dictRef="g:item" size="4">|Maximum Force|RMS Force|Maximum Displacement|RMS Displacement|</array>
             <array dataType="xsd:double" dictRef="g:value" size="4">0.002387 0.000539 0.044296 0.011477</array>
             <array dataType="xsd:double" dictRef="g:threshold" size="4">0.000450 0.000300 0.001800 0.001200</array>
             <array dataType="xsd:string" dictRef="g:converged" size="4">NO NO NO NO</array>
          </list>
       </module>
       <module cmlx:templateRef="preddelta">
          <list cmlx:templateRef="predicted">
             <scalar dataType="xsd:double" dictRef="g:predchange">3.932148e-04</scalar>
          </list>
       </module>
       <module cmlx:templateRef="l103.catchall">
          <list cmlx:templateRef="l103.discard">
             <scalar dataType="xsd:string" dictRef="x:discard" />
          </list>
       </module>
    </module>
  </comment>

Template definition ​

xml
<record id="tmp" repeat="*">(\s+\(Enter.*|\s*GradGradGrad.*|\s+)</record>
<record id="berny">&#123;X,g:optimization&#125;</record>
<templateList>  <xi:include href="l103/l103.catchall.xml" />  <xi:include href="l103/l103.trust.xml" />  <xi:include href="l103/l103.init.xml" />  <xi:include href="l103/l103.rfo.xml" />  <xi:include href="l103/l103.localmin.xml" />  <xi:include href="l103/l103.deltas.xml" />  <xi:include href="l103/l103.itemconverge.xml" />  <xi:include href="l103/l103.optimizedparam.xml" />  <xi:include href="l103/l103.preddelta.xml" />
  </templateList>
<transform process="delete" xpath=".//cml:scalar[empty(text())]" />
<transform process="delete" xpath="./text()[starts-with(normalize-space(.),'GradGrad')]" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />