ioChem-BD

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logfile ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceADF log
idlogfile
nameFinal log file resume
pattern\s*\(LOGFILE\).*
endPattern.*END.*$(.(?!😃)*
endPattern2~
endOffset1
repeat*
xml:baselogfile.xml

Input ​

            (LOGFILE)
         <May04-2010> <06:12:25>  END
         <May04-2010> <06:12:26>  ADF 2009.01  RunTime: May04-2010 06:12:26
         <May04-2010> <06:12:26>  OPT C80BUTPROD69 CONT 12
         <May04-2010> <06:12:27>  RunType   : SINGLE POINT
         <May04-2010> <06:12:27>  Net Charge: 0 (Nuclei minus Electrons)
         <May04-2010> <06:12:27>  Symmetry  : NOSYM
         <May04-2010> <06:12:27>  >>>> FRAGM
         <May04-2010> <06:12:28>  >>>> CORORT
         <May04-2010> <06:12:29>  >>>> FITINT
         <May04-2010> <06:12:35>  >>>> CLSMAT
         <May04-2010> <06:12:35>  >>>> ORTHON
         <May04-2010> <06:12:40>  >>>> GENPT
         <May04-2010> <06:12:41>  Acc.Num.Int.=   6.000
         <May04-2010> <06:12:42>  Block Length= 128
         <May04-2010> <06:12:48>  >>>> PTBAS
         <May04-2010> <06:15:28>  >>>> CYCLE
         <May04-2010> <06:15:50>    1
         <May04-2010> <06:16:33>    2  ErrMat   2.79814121  MaxEl  0.48176486
         <May04-2010> <06:17:06>    3  ErrMat   1.51224955  MaxEl  0.09978819
         <May04-2010> <06:17:39>    4  ErrMat   0.94765889  MaxEl -0.04486329
         <May04-2010> <06:18:25>    5  ErrMat   0.61366968  MaxEl  0.04137339
         <May04-2010> <06:18:59>    6  ErrMat   0.63098527  MaxEl  0.09804162
         <May04-2010> <06:19:32>    7  ErrMat   0.22216777  MaxEl  0.03069437
         <May04-2010> <06:20:05>    8  ErrMat   0.09119102  MaxEl -0.01194218
         <May04-2010> <06:20:37>    9  ErrMat   0.08555816  MaxEl  0.00727754
         <May04-2010> <06:21:10>   10  ErrMat   0.03727656  MaxEl -0.00234168
         <May04-2010> <06:21:44>   11  ErrMat   0.01712033  MaxEl  0.00302702
         <May04-2010> <06:22:17>   12  ErrMat   0.00478966  MaxEl -0.00038518
         <May04-2010> <06:22:49>   13  ErrMat   0.00736128  MaxEl -0.00097317
         <May04-2010> <06:23:22>   14  ErrMat   0.00303646  MaxEl  0.00049233
         <May04-2010> <06:23:55>   15  ErrMat   0.00100783  MaxEl -0.00014174
         <May04-2010> <06:24:27>   16  ErrMat   0.00043373  MaxEl  0.00006704
         <May04-2010> <06:25:01>   17  ErrMat   0.00027019  MaxEl -0.00002004
         <May04-2010> <06:25:35>   18  ErrMat   0.00007548  MaxEl -0.00000797
         <May04-2010> <06:26:08>   19  ErrMat   0.00008791  MaxEl -0.00001188
         <May04-2010> <06:26:41>   20  ErrMat   0.00002641  MaxEl  0.00000333
         <May04-2010> <06:27:14>   21  ErrMat   0.00000780  MaxEl -0.00000057
         <May04-2010> <06:27:20>  SCF converged
         <May04-2010> <06:27:47>   22  ErrMat   0.00001758  MaxEl -0.00000151
         <May04-2010> <06:28:12>  >>>> TOTEN
         <May04-2010> <06:36:34>  >>>> POPAN
         <May04-2010> <06:36:34>  >>>> DEBYE
         <May04-2010> <06:36:37>  >>>> AMETS
         <May04-2010> <06:36:43>   Bond Energy LDA     -31.82018839 a.u.
         <May04-2010> <06:36:43>   Bond Energy LDA    -865.87138203 eV
         <May04-2010> <06:36:43>           + GGA-X     -25.93787799 a.u.
         <May04-2010> <06:36:43>           + GGA-X    -705.80557174 eV
         <May04-2010> <06:36:43>          + GGA-XC     -28.47073192 a.u.
         <May04-2010> <06:36:43>          + GGA-XC    -774.72803397 eV
         <May04-2010> <06:36:43>  >>>> POPUL
         <May04-2010> <06:36:49>  NORMAL TERMINATION
         <May04-2010> <06:36:51>  END

Output text ​

xml
<comment class="example.output" id="logfile">
        <module cmlx:lineCount="53" cmlx:templateRef="logfile">
            <scalar dataType="xsd:string" dictRef="cc:runDate">May04-2010 06:12:26</scalar>
            <scalar dataType="xsd:integer" dictRef="a:charge">0</scalar>
            <scalar dataType="xsd:double" dictRef="cc:potentialEnergy" units="nonsi:electronvolt">-774.72803397</scalar>
        </module>
    </comment>

Template definition ​

xml
<templateList>  <template pattern=".*ADF.*RunTime:.*" endPattern=".*" endOffset="1" repeat="*">    <record id="runtime">.*RunTime:&#123;X,cc:runDate&#125;</record>    <record id="title">.*:\d\d:\d\d.?\s*&#123;X,cc:title&#125;\s*</record>
        </template>  <template pattern=".*RunTime:.*" endPattern=".*" repeat="*">    <record id="runtime">.*RunTime:&#123;X,cc:runDate&#125;</record>
        </template>  <template pattern=".*current energy.*" endPattern=".*" repeat="*">    <record id="potential.energy">.*current energy&#123;F,cc:potentialEnergy&#125;Hartree.*</record>    <transform process="addUnits" xpath=".//cml:scalar" value="nonsi:hartree" />                 
        </template>  <template pattern=".*GGA-XC.*eV.*" endPattern=".*" repeat="*">    <record id="potential.energy">.*GGA-XC.&#123;F,cc:potentialEnergy&#125;eV.*</record>    <transform process="addUnits" xpath=".//cml:scalar" value="nonsi:electronvolt" />            
        </template>  <template pattern=".*ERROR: GEOMETRY DID NOT CONVERGE.*" endPattern=".*" repeat="*">    <record id="converged">.*ERROR:&#123;X,a:converged&#125;</record>
        </template>  <template pattern=".*(Geometry\sConverged|GEOMETRY\sCONVERGED).*" endPattern=".*" repeat="*">    <record id="converged">.*:\d\d:\d\d.&#123;X,a:converged&#125;</record>      
        </template>  <template pattern=".*Net\sCharge:.*\(Nuclei\sminus\sElectrons\).*" endPattern=".*" repeat="*">    <record id="charge">.*Net\sCharge:&#123;I,a:charge&#125;\(Nuclei\sminus\sElectrons\).*</record>        
        </template>  <template pattern=".*Spin\spolar:.*\(Spin_A\sminus\sSpin_B\selectrons\).*" endPattern=".*" repeat="*">    <record id="spin.polarization">.*Spin\spolar:&#123;A,a:spinPolarization&#125;\(Spin_A\sminus\sSpin_B\selectrons\).*</record>       
        </template>
    </templateList>
<transform process="pullup" repeat="2" xpath=".//cml:scalar" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:module[count(*)=0]" />