opt

Implementation level

Type	Status
CML extraction template
HTML5 representation

Template attributes

Attribute	Value
source	GRRM log
id	opt
pattern	OPTOPTOPT.*
endPattern	=====.*
xml:base	opt.xml

Input

    OPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTO

    # ITR. 0
    C      0.000000000000      0.000000000000      0.000000000000
    O      1.200000000000      0.000000000000      0.000000000000
    H     -0.500000000000      1.000000000000      0.000000000000
    H     -0.500000000000     -1.000000000000      0.000000000000
            Item                       Value            Threshold
            ENERGY          -114.411340148425                             (   0.000000000000 :    0.000000000000)
            Spin(**2)          0.000000000000
            LAMDA             -0.044086028537
            TRUST RADII        0.100000000000
            STEP RADII         0.099999772863
    Maximum  Force             0.060160801264      0.000060000000
    RMS      Force             0.027342505434      0.000040000000
    Maximum  Displacement      0.041995124706      0.000300000000
    RMS      Displacement      0.028867447891      0.000200000000
    NORMAL MODE EIGENVALUE : N_MODE = 6
    0.127182496   0.172800300   0.222172473   0.382188000   0.873986295
    1.804155953

    # ITR. 1
    C      0.041995124706     -0.000000000000      0.000000000000
    O      1.240611085149     -0.000000000000      0.000000000000
    H     -0.541303104928      0.960155233197      0.000000000000
    H     -0.541303104928     -0.960155233197      0.000000000000
            Item                       Value            Threshold
            ENERGY          -114.415281650643                             (   0.000000000000 :    0.000000000000)
            Spin(**2)          0.000000000000
            LAMDA             -0.000438194998
            TRUST RADII        0.299999318587
            STEP RADII         0.030670409747
    Maximum  Force             0.014223663897      0.000060000000
    RMS      Force             0.005975118658      0.000040000000
    Maximum  Displacement      0.015360034330      0.000300000000
    RMS      Displacement      0.008853784662      0.000200000000
    NORMAL MODE EIGENVALUE : N_MODE = 6
    0.129460642   0.172928531   0.222530463   0.389774177   0.873454815
    1.815713072

    # ITR. 2
    C      0.052372084277     -0.000000000000     -0.000000000000
    O      1.251877081287     -0.000000000000     -0.000000000000
    H     -0.552124582782      0.944795198867      0.000000000000
    H     -0.552124582782     -0.944795198867     -0.000000000000
            Item                       Value            Threshold
            ENERGY          -114.415497750428                             (   0.000000000000 :    0.000000000000)
            Spin(**2)          0.000000000000
            LAMDA             -0.000000942648
            TRUST RADII        0.092011229241
            STEP RADII         0.000763328126
    Maximum  Force             0.001085693332      0.000060000000
    RMS      Force             0.000579095912      0.000040000000
    Maximum  Displacement      0.000460488138      0.000300000000
    RMS      Displacement      0.000220353850      0.000200000000
    NORMAL MODE EIGENVALUE : N_MODE = 6
    0.131638656   0.172870054   0.222531346   0.396090889   0.872938732
    1.819986160

    # ITR. 3
    C      0.051911596139     -0.000000000000      0.000000000000
    O      1.251598064141      0.000000000000     -0.000000000000
    H     -0.551754830140      0.944696873126     -0.000000000000
    H     -0.551754830140     -0.944696873126     -0.000000000000
            Item                       Value            Threshold
            ENERGY          -114.415498155971                             (   0.000000000000 :    0.000000000000)
            Spin(**2)          0.000000000000
            LAMDA             -0.000000317202
            TRUST RADII        0.010000000000
            STEP RADII         0.000010525342
    Maximum  Force             0.000038304881      0.000060000000
    RMS      Force             0.000015729923      0.000040000000
    Maximum  Displacement      0.000007220466      0.000469913999
    RMS      Displacement      0.000003038404      0.000313276000
    NORMAL MODE EIGENVALUE : N_MODE = 6
    0.132095091   0.172870422   0.222531963   0.394282898   0.872956860
    1.851748547

    =========================================================================

Output text

xml

<comment class="example.output" id="opt">
        <module cmlx:templateRef="opt">    
            <module cmlx:templateRef="geometry.cycle">
                <scalar cmlx:templateRef="iter" dataType="xsd:integer" dictRef="cc:cycleNumber">0</scalar>
                <module cmlx:templateRef="molecule">
                   <molecule cmlx:templateRef="atom" id="molecule">
                      <atomArray>
                         <atom elementType="C" id="a1" x3="0.0000" y3="0.0000" z3="0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                         </atom>
                         <atom elementType="O" id="a2" x3="1.2000" y3="0.0000" z3="0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
                         </atom>
                         <atom elementType="H" id="a3" x3="-0.5000" y3="1.0000" z3="0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
                         </atom>
                         <atom elementType="H" id="a4" x3="-0.5000" y3="-1.0000" z3="0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
                         </atom>
                      </atomArray>
                      <bondArray>
                         <bond atomRefs2="a1 a2" order="S" />
                         <bond atomRefs2="a1 a3" order="S" />
                         <bond atomRefs2="a1 a4" order="S" />
                      </bondArray>
                      <formula concise="CH2O">
                         <atomArray count="1 2 1" elementType="C H O" />
                      </formula>
                      <property dictRef="cml:molmass">
                         <scalar units="unit:dalton">28.0101</scalar>
                      </property>
                   </molecule>
                </module>
                <scalar cmlx:templateRef="energy" dataType="xsd:double" dictRef="cc:energy" units="nonsi:hartree">-114.411340148425</scalar>
                <scalar cmlx:templateRef="spinsqr" dataType="xsd:double" dictRef="cc:s2">0.000000000000</scalar>
                <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">0.060160801264 0.027342505434 0.041995124706 0.028867447891</array>
                <array dataType="xsd:double" dictRef="g:threshold" size="4">0.000060000000 0.000040000000 0.000300000000 0.000200000000</array>
                <array cmlx:templateRef="normal-mode-eigvals" dataType="xsd:double" dictRef="cc:eigenval" size="6">0.127182496 0.172800300 0.222172473 0.382188000 0.873986295 1.804155953</array>
             </module>
             <module cmlx:templateRef="geometry.cycle">
                <scalar cmlx:templateRef="iter" dataType="xsd:integer" dictRef="cc:cycleNumber">1</scalar>
                <module cmlx:templateRef="molecule">
                   <molecule cmlx:templateRef="atom" id="molecule">
                      <atomArray>
                         <atom elementType="C" id="a1" x3="0.04199512" y3="-0.0000" z3="0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                         </atom>
                         <atom elementType="O" id="a2" x3="1.24061109" y3="-0.0000" z3="0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
                         </atom>
                         <atom elementType="H" id="a3" x3="-0.5413031" y3="0.96015523" z3="0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
                         </atom>
                         <atom elementType="H" id="a4" x3="-0.5413031" y3="-0.96015523" z3="0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
                         </atom>
                      </atomArray>
                      <bondArray>
                         <bond atomRefs2="a1 a2" order="S" />
                         <bond atomRefs2="a1 a3" order="S" />
                         <bond atomRefs2="a1 a4" order="S" />
                      </bondArray>
                      <formula concise="CH2O">
                         <atomArray count="1 2 1" elementType="C H O" />
                      </formula>
                      <property dictRef="cml:molmass">
                         <scalar units="unit:dalton">28.0101</scalar>
                      </property>
                   </molecule>
                </module>
                <scalar cmlx:templateRef="energy" dataType="xsd:double" dictRef="cc:energy" units="nonsi:hartree">-114.415281650643</scalar>
                <scalar cmlx:templateRef="spinsqr" dataType="xsd:double" dictRef="cc:s2">0.000000000000</scalar>
                <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">0.014223663897 0.005975118658 0.015360034330 0.008853784662</array>
                <array dataType="xsd:double" dictRef="g:threshold" size="4">0.000060000000 0.000040000000 0.000300000000 0.000200000000</array>
                <array cmlx:templateRef="normal-mode-eigvals" dataType="xsd:double" dictRef="cc:eigenval" size="6">0.129460642 0.172928531 0.222530463 0.389774177 0.873454815 1.815713072</array>
             </module>
             <module cmlx:templateRef="geometry.cycle">
                <scalar cmlx:templateRef="iter" dataType="xsd:integer" dictRef="cc:cycleNumber">2</scalar>
                <module cmlx:templateRef="molecule">
                   <molecule cmlx:templateRef="atom" id="molecule">
                      <atomArray>
                         <atom elementType="C" id="a1" x3="0.05237208" y3="-0.0000" z3="-0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                         </atom>
                         <atom elementType="O" id="a2" x3="1.25187708" y3="-0.0000" z3="-0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
                         </atom>
                         <atom elementType="H" id="a3" x3="-0.55212458" y3="0.9447952" z3="0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
                         </atom>
                         <atom elementType="H" id="a4" x3="-0.55212458" y3="-0.9447952" z3="-0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
                         </atom>
                      </atomArray>
                      <bondArray>
                         <bond atomRefs2="a1 a2" order="S" />
                         <bond atomRefs2="a1 a3" order="S" />
                         <bond atomRefs2="a1 a4" order="S" />
                      </bondArray>
                      <formula concise="CH2O">
                         <atomArray count="1 2 1" elementType="C H O" />
                      </formula>
                      <property dictRef="cml:molmass">
                         <scalar units="unit:dalton">28.0101</scalar>
                      </property>
                   </molecule>
                </module>
                <scalar cmlx:templateRef="energy" dataType="xsd:double" dictRef="cc:energy" units="nonsi:hartree">-114.415497750428</scalar>
                <scalar cmlx:templateRef="spinsqr" dataType="xsd:double" dictRef="cc:s2">0.000000000000</scalar>
                <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">0.001085693332 0.000579095912 0.000460488138 0.000220353850</array>
                <array dataType="xsd:double" dictRef="g:threshold" size="4">0.000060000000 0.000040000000 0.000300000000 0.000200000000</array>
                <array cmlx:templateRef="normal-mode-eigvals" dataType="xsd:double" dictRef="cc:eigenval" size="6">0.131638656 0.172870054 0.222531346 0.396090889 0.872938732 1.819986160</array>
             </module>
             <module cmlx:templateRef="geometry.cycle">
                <scalar cmlx:templateRef="iter" dataType="xsd:integer" dictRef="cc:cycleNumber">3</scalar>
                <module cmlx:templateRef="molecule">
                   <molecule cmlx:templateRef="atom" id="molecule">
                      <atomArray>
                         <atom elementType="C" id="a1" x3="0.0519116" y3="-0.0000" z3="0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                         </atom>
                         <atom elementType="O" id="a2" x3="1.25159806" y3="0.0000" z3="-0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
                         </atom>
                         <atom elementType="H" id="a3" x3="-0.55175483" y3="0.94469687" z3="-0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
                         </atom>
                         <atom elementType="H" id="a4" x3="-0.55175483" y3="-0.94469687" z3="-0.0000">
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
                         </atom>
                      </atomArray>
                      <bondArray>
                         <bond atomRefs2="a1 a2" order="S" />
                         <bond atomRefs2="a1 a3" order="S" />
                         <bond atomRefs2="a1 a4" order="S" />
                      </bondArray>
                      <formula concise="CH2O">
                         <atomArray count="1 2 1" elementType="C H O" />
                      </formula>
                      <property dictRef="cml:molmass">
                         <scalar units="unit:dalton">28.0101</scalar>
                      </property>
                   </molecule>
                </module>
                <scalar cmlx:templateRef="energy" dataType="xsd:double" dictRef="cc:energy" units="nonsi:hartree">-114.415498155971</scalar>
                <scalar cmlx:templateRef="spinsqr" dataType="xsd:double" dictRef="cc:s2">0.000000000000</scalar>
                <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">0.000038304881 0.000015729923 0.000007220466 0.000003038404</array>
                <array dataType="xsd:double" dictRef="g:threshold" size="4">0.000060000000 0.000040000000 0.000469913999 0.000313276000</array>
                <array cmlx:templateRef="normal-mode-eigvals" dataType="xsd:double" dictRef="cc:eigenval" size="6">0.132095091 0.172870422 0.222531963 0.394282898 0.872956860 1.851748547</array>
             </module>
         </module>
    </comment>

Template definition

xml

<templateList>  <template id="geometry.cycle" pattern="# ITR.*" endPattern="# ITR.*" endPattern2="==========.*" endPattern3="~" repeat="*">    <template id="iter" pattern=".*" endPattern=".*">      <record id="iter"># ITR.\s+&#123;I,cc:cycleNumber&#125;</record>      <transform process="pullupSingleton" xpath="./cml:list" />
            </template>    <template id="molecule" pattern="[A-Za-z]&#123;1,2&#125;\s+.*" endPattern="\s+Item\s+Value\s+Threshold.*" repeat="*">      <record makeArray="true" repeat="*" id="atom">\s*&#123;A,compchem:elementType&#125;\s*&#123;F,compchem:x3&#125;\s*&#123;F,compchem:y3&#125;\s*&#123;F,compchem:z3&#125;\s*
                </record>      <transform process="createMolecule" xpath="./cml:list[@cmlx:templateRef='atom']/cml:array" id="molecule" />      <transform process="pullupSingleton" xpath="./cml:list" />      <record id="null" repeat="1" />
            </template>    <template id="energy" pattern="\s*ENERGY.*" endPattern=".*">      <record id="energy">\s+ENERGY\s+&#123;F,cc:energy&#125;\s+\(.*\)</record>      <transform process="pullupSingleton" xpath="./cml:list" />
            </template>    <template id="spinsqr" pattern="\s*Spin\(\*\*2\).*" endPattern=".*">      <record id="spinsqr">\s*Spin\(\*\*2\)\s*&#123;F,cc:s2&#125;\s*</record>      <transform process="pullupSingleton" xpath="./cml:list" />
            </template>    <template id="convergence" pattern="\s+Maximum\s+Force.*" endPattern="\s+RMS\s+Displacement.*" endOffset="1">      <record id="row" repeat="*" makeArray="true">\s*&#123;X,g:item&#125;\s+&#123;F,g:value&#125;&#123;F,g:threshold&#125;\s*
                </record>      <transform process="moveRelative" xpath="./cml:list/cml:array[@dictRef]" to="./ancestor::cml:module[@cmlx:templateRef='convergence']" />      <transform process="delete" xpath="(./cml:list[@cmlx:templateRef='row'])" />      <transform process="pullupSingleton" xpath="./cml:list" />      <transform process="setValue" xpath=".//cml:array[@dictRef='g:item']" value="$string(replace(replace(./text(), '^\||\|$', ''), '\s+', ' '))" />
            </template>    <template id="eigenvals" pattern="NORMAL MODE EIGENVALUE.*" offset="1" endPattern="~">      <record id="normal-mode-eigvals" makeArray="true" repeat="*">\s+&#123;1_5F,cc:eigenval&#125;</record>      <transform process="pullupSingleton" xpath="./cml:list" />
            </template>    <transform process="pullup" xpath="./cml:module/cml:scalar" />    <transform process="pullup" xpath="./cml:module/cml:array" />    <transform process="delete" xpath="(//cml:list[@cmlx:templateRef='null'])" />    <transform process="delete" xpath=".//cml:module[count(*)=0]" />    <transform process="pullupSingleton" xpath="./cml:list" />    <transform process="addUnits" xpath=".//cml:scalar[@dictRef='cc:energy']" value="nonsi:hartree" />
        </template>
    </templateList>

ADF

nmr

dirac

adf

model.parameters

adf.runtype

adf.computation

adf.results

adf.frequencyanalysis

quild.module

statistics

quild.iteration

AMS

nmr

dirac

adf

model.parameters

adf.results

Amber

amber.parm

CASTEP

setup

final

Gaussian

l1

l1.end

l101

l601.popanal

mulliken

link1a

l103

preddelta

l202

l301

l302

l401

l401.orbsym

l401.alphabeta

l502

l716

l716.forcematrix

l716.thermochemistry

l914

l301

l401

l401.orbsym

l401.alphabeta

GROMACS

times

GronOR

GRRM

LAMMPS

MOLCAS

mulliken

properties

spin.orbit

spin.free

thermochemistry

MOPAC

optimization

Orca

mullikenpopulation

loewdin

mayer

electricproperties

ci

tddft

QuantumEspresso

Turbomole

module

population.analysis

orbitalenergies

turbomole.control

vibrations

orbitals.control

turbomole.coord

VASP

incar

potcar

eigenvalues

opt

Implementation level

Template attributes

Input

Output text

Template definition