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geometry.cycle ​

Implementation level ​

TypeStatus
CML extraction template
HTML5 representation

Template attributes ​

AttributeValue
sourceADF log
idgeometry.cycle
nameGeometry optimization cycle
pattern\sGeometry\sCYCLE.*
pattern2\s*G\sE\sO\sM\sE\sT\sR\sY\s*U\sP\sD\sA\sT\sE.*
endPattern.*$\s*Number\sof\selements\sof\sthe\sdensity\smatrix.*
endPattern2(\s*\S+\s*){11}+\s*$\s*\-{20,}+\s*
endOffset2
repeat*
xml:basecomputation/geometry.cycle.xml

Input ​

 =============================
 G E O M E T R Y   U P D A T E  ***  1  ***
 =============================
 ...

--------------------------------------
Geometry Convergence after Step   4
--------------------------------------
current energy                              -27.14895237 Hartree
abs of energy change                0.00034166     0.00100000    T
constrained gradient max            0.00178229     0.00100000    F
constrained gradient rms            0.00030637     0.00066667    T
gradient max                        0.00178229
gradient rms                        0.00030637
cart. step max                      0.00450423     0.01000000    T
cart. step rms                      0.00098385     0.00666667    T  
...
    
 Coordinates (Cartesian)
 =======================

     Atom                    bohr                                 angstrom
                   X           Y           Z              X           Y           Z
 -------------------------------------------------------------------------------------
     1 Mo      0.000000   -4.459974    0.000318       0.000000   -2.360117    0.000169
     2 Mo      4.459974    0.000000    0.000318       2.360117    0.000000    0.000169
     3 Mo     -4.459974    0.000000    0.000318      -2.360117    0.000000    0.000169
     4 Mo      0.000000    4.459974    0.000318       0.000000    2.360117    0.000169
     5 Mo      0.000000    0.000000   -4.460768       0.000000    0.000000   -2.360537
     6 W       0.000000    0.000000    4.459603       0.000000    0.000000    2.359920
     7 O       0.000000    0.000000    0.001640       0.000000    0.000000    0.000868
 -------------------------------------------------------------------------------------


 Coordinates (Cartesian, in Input Orientation)
 =======================

     Atom                    bohr                                 angstrom                 Geometric Variables
                   X           Y           Z              X           Y           Z       (0:frozen, *:LT par.)
 --------------------------------------------------------------------------------------------------------------
     1 Mo     -0.000318   -4.459974    0.000000      -0.000169   -2.360117    0.000000      1       2       3
     2 Mo     -0.000318    0.000000    4.459974      -0.000169    0.000000    2.360117      4       5       6
     3 Mo     -0.000318    0.000000   -4.459974      -0.000169    0.000000   -2.360117      7       8       9
     4 Mo     -0.000318    4.459974    0.000000      -0.000169    2.360117    0.000000     10      11      12
     5 Mo      4.460768    0.000000    0.000000       2.360537    0.000000    0.000000     13      14      15
     6 W      -4.459603    0.000000    0.000000      -2.359920    0.000000    0.000000     16      17      18
     7 O      -0.001640    0.000000    0.000000      -0.000868    0.000000    0.000000     19      20      21
 --------------------------------------------------------------------------------------------------------------
 
  Number of elements of the density matrix on this node (used, total):     25057    246753

Input ​

 Geometry CYCLE 1
 ==============

 Energy gradients wrt nuclear displacements
 ==========================================
 ...

 Coordinates (Cartesian)
 =======================

     Atom                    bohr                                 angstrom                 Geometric Variables
                   X           Y           Z              X           Y           Z       (0:frozen, *:LT par.)
 --------------------------------------------------------------------------------------------------------------
     1 C      -4.748701   -1.104688   -6.013399      -2.512904   -0.584576   -3.182154      1       2       3
     2 C      -4.518962    1.637904   -6.075522      -2.391332    0.866742   -3.215028      4       5       6
     3 C      -5.816176    3.015449   -4.125306      -3.077788    1.595707   -2.183018      7       8       9
     4 C       0.196292   -0.913573    7.712840       0.103873   -0.483442    4.081459     10      11      12
     5 C      -2.773029   -2.909791   -6.786550      -1.467424   -1.539795   -3.591288     13      14      15
     6 C       1.783334   -3.265805   -6.963282       0.943700   -1.728190   -3.684810     16      17      18
     7 C      -0.495078   -2.421894   -8.180332      -0.261984   -1.281611   -4.328845     19      20      21
 --------------------------------------------------------------------------------------------------------------

Output text ​

xml
<comment class="example.output" id="geometry.cyle">
        <module cmlx:lineCount="161" cmlx:templateRef="geometry.cycle">
            <scalar dataType="xsd:integer" dictRef="cc:cycleNumber">1</scalar>
            <module cmlx:lineCount="10" cmlx:templateRef="convergence">
               <list cmlx:templateRef="energy">
                  <scalar dataType="xsd:double" dictRef="cc:energy">-27.14895237</scalar>
               </list>
               <list cmlx:templateRef="change">
                  <scalar dataType="xsd:double" dictRef="cc:current">3.4166E-4</scalar>
                  <scalar dataType="xsd:double" dictRef="cc:threshold">0.001</scalar>
                  <scalar dataType="xsd:string" dictRef="cc:valid">T</scalar>
               </list>
               <list cmlx:templateRef="cgradmax">
                  <scalar dataType="xsd:double" dictRef="cc:current">0.00178229</scalar>
                  <scalar dataType="xsd:double" dictRef="cc:threshold">0.001</scalar>
                  <scalar dataType="xsd:string" dictRef="cc:valid">F</scalar>
               </list>
               <list cmlx:templateRef="cgradrms">
                  <scalar dataType="xsd:double" dictRef="cc:current">3.0637E-4</scalar>
                  <scalar dataType="xsd:double" dictRef="cc:threshold">6.6667E-4</scalar>
                  <scalar dataType="xsd:string" dictRef="cc:valid">T</scalar>
               </list>
               <list cmlx:templateRef="gradmax">
                  <scalar dataType="xsd:double" dictRef="cc:current">0.00178229</scalar>
               </list>
               <list cmlx:templateRef="gradrms">
                  <scalar dataType="xsd:double" dictRef="cc:current">3.0637E-4</scalar>
               </list>
               <list cmlx:templateRef="cstepmax">
                  <scalar dataType="xsd:double" dictRef="cc:current">0.00450423</scalar>
                  <scalar dataType="xsd:double" dictRef="cc:threshold">0.01</scalar>
                  <scalar dataType="xsd:string" dictRef="cc:valid">T</scalar>
               </list>
               <list cmlx:templateRef="csteprms">
                  <scalar dataType="xsd:double" dictRef="cc:current">9.8385E-4</scalar>
                  <scalar dataType="xsd:double" dictRef="cc:threshold">0.00666667</scalar>
                  <scalar dataType="xsd:string" dictRef="cc:valid">T</scalar>
               </list>
            </module>             
            <module cmlx:lineCount="30" cmlx:templateRef="coordinates">
                <scalar dataType="xsd:string" dictRef="cc:label">Cartesian</scalar>
                <molecule id="a99">
                    <atomArray>
                        <atom id="a1" elementType="Mo" x3="0.0" y3="-2.360117" z3="1.69E-4">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">1</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">42</scalar>
                        </atom>
                        <atom id="a2" elementType="Mo" x3="2.360117" y3="0.0" z3="1.69E-4">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">2</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">42</scalar>
                        </atom>
                        <atom id="a3" elementType="Mo" x3="-2.360117" y3="0.0" z3="1.69E-4">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">3</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">42</scalar>
                        </atom>
                        <atom id="a4" elementType="Mo" x3="0.0" y3="2.360117" z3="1.69E-4">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">4</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">42</scalar>
                        </atom>
                        <atom id="a5" elementType="Mo" x3="0.0" y3="0.0" z3="-2.360537">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">5</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">42</scalar>
                        </atom>
                        <atom id="a6" elementType="W" x3="0.0" y3="0.0" z3="2.35992">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">6</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">74</scalar>
                        </atom>
                        <atom id="a7" elementType="O" x3="0.0" y3="0.0" z3="8.68E-4">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">7</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
                        </atom>
                    </atomArray>
                </molecule>
            </module>
            <module cmlx:lineCount="31" cmlx:templateRef="coordinates">
                <scalar dataType="xsd:string" dictRef="cc:label">Cartesian, in Input Orientation</scalar>
                <molecule id="a24">
                    <atomArray>
                        <atom id="a1" elementType="Mo" x3="-1.69E-4" y3="-2.360117" z3="0.0">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">1</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">42</scalar>
                        </atom>
                        <atom id="a2" elementType="Mo" x3="-1.69E-4" y3="0.0" z3="2.360117">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">2</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">42</scalar>
                        </atom>
                        <atom id="a3" elementType="Mo" x3="-1.69E-4" y3="0.0" z3="-2.360117">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">3</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">42</scalar>
                        </atom>
                        <atom id="a4" elementType="Mo" x3="-1.69E-4" y3="2.360117" z3="0.0">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">4</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">42</scalar>
                        </atom>
                        <atom id="a5" elementType="Mo" x3="2.360537" y3="0.0" z3="0.0">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">5</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">42</scalar>
                        </atom>
                        <atom id="a6" elementType="W" x3="-2.35992" y3="0.0" z3="0.0">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">6</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">74</scalar>
                        </atom>
                        <atom id="a7" elementType="O" x3="-8.68E-4" y3="0.0" z3="0.0">
                            <scalar dataType="xsd:integer" dictRef="cc:serial">7</scalar>
                            <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
                        </atom>                   
                    </atomArray>
                </molecule>
            </module>
        </module>
        </comment>

Output text ​

xml
<comment class="example.output" id="geometry.cycle2">
     <module cmlx:lineCount="1911" cmlx:templateRef="geometry.cycle">
        <scalar dataType="xsd:integer" dictRef="cc:cycleNumber">1</scalar>
        <module cmlx:lineCount="105" cmlx:templateRef="coordinates">
              <scalar dataType="xsd:string" dictRef="cc:label">Cartesian</scalar>
              <molecule id="geometry.cycle">
               <atomArray>
                <atom id="a1" elementType="C" x3="-2.512904" y3="-0.584576" z3="-3.182154">
                 <scalar dataType="xsd:integer" dictRef="cc:serial">1</scalar>
                 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                </atom>
                <atom id="a2" elementType="C" x3="-2.391332" y3="0.866742" z3="-3.215028">
                 <scalar dataType="xsd:integer" dictRef="cc:serial">2</scalar>
                 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                </atom>
                <atom id="a3" elementType="C" x3="-3.077788" y3="1.595707" z3="-2.183018">
                 <scalar dataType="xsd:integer" dictRef="cc:serial">3</scalar>
                 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                </atom>
                <atom id="a4" elementType="C" x3="0.103873" y3="-0.483442" z3="4.081459">
                 <scalar dataType="xsd:integer" dictRef="cc:serial">4</scalar>
                 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                </atom>
                <atom id="a5" elementType="C" x3="-1.467424" y3="-1.539795" z3="-3.591288">
                 <scalar dataType="xsd:integer" dictRef="cc:serial">5</scalar>
                 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                </atom>
                <atom id="a6" elementType="C" x3="0.9437" y3="-1.72819" z3="-3.68481">
                 <scalar dataType="xsd:integer" dictRef="cc:serial">6</scalar>
                 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                </atom>
                <atom id="a7" elementType="C" x3="-0.261984" y3="-1.281611" z3="-4.328845">
                 <scalar dataType="xsd:integer" dictRef="cc:serial">7</scalar>
                 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
                </atom>
                </atomArray>
            </molecule>
            </module>
        </module>
    </comment>

Template definition ​

xml
<templateList>  <template id="cycle" pattern="\s*Geometry\sCYCLE.*" endPattern=".*" endOffset="0">    <record id="cycle">\s*Geometry\sCYCLE&#123;I,cc:cycleNumber&#125;</record>
        </template>  <template id="cycle" pattern="\s*G\sE\sO\sM\sE\sT\sR\sY\s*U\sP\sD\sA\sT\sE.*" endPattern=".*" endOffset="0">    <record id="cycle">\s*G\sE\sO\sM\sE\sT\sR\sY\s*U\sP\sD\sA\sT\sE\s*\*\*\*&#123;I,cc:cycleNumber&#125;\s*\*\*\*.*
            </record>
        </template>  <template id="convergence" name="Geometry convergence" pattern="\s*Geometry\sConvergence\safter.*" endPattern="\s*cart\.\sstep\srms.*" endOffset="1" repeat="*">    <record id="step">\s*Geometry\sConvergence\safter\sStep&#123;I,a:nstep&#125;\s*\**\**&#123;A,x:converged&#125;.*</record>    <record repeat="1" />    <record id="energy">\s*current\senergy&#123;F,cc:energy&#125;Hartree.*</record>    <record id="change">\s*abs\sof\senergy\schange&#123;F,cc:current&#125;&#123;F,cc:threshold&#125;&#123;A,cc:valid&#125;</record>    <record id="cgradmax">\s*constrained\sgradient\smax&#123;F,cc:current&#125;&#123;F,cc:threshold&#125;&#123;A,cc:valid&#125;</record>    <record id="cgradrms">\s*constrained\sgradient\srms&#123;F,cc:current&#125;&#123;F,cc:threshold&#125;&#123;A,cc:valid&#125;</record>    <record id="gradmax">\s*gradient\smax&#123;F,cc:current&#125;</record>    <record id="gradrms">\s*gradient\srms&#123;F,cc:current&#125;</record>    <record id="cstepmax">\s*cart.\sstep\smax&#123;F,cc:current&#125;&#123;F,cc:threshold&#125;&#123;A,cc:valid&#125;</record>    <record id="csteprms">\s*cart.\sstep\srms&#123;F,cc:current&#125;&#123;F,cc:threshold&#125;&#123;A,cc:valid&#125;</record>    <transform process="pullup" xpath=".//cml:list/cml:list/cml:scalar" />
        </template>  <template id="coordinates" name="Cycle coordinates" pattern="\s*Coordinates\s\(.*" endPattern="(\s*\S+\s*)&#123;11&#125;+\s*$\s*\-&#123;20,&#125;+\s*" endPattern2="(\s*\S+\s*)&#123;8&#125;+$\s*\-&#123;20,&#125;+\s*" endPattern3="~" endOffset="1" repeat="*">    <record id="label">\s*Coordinates\s\(&#123;X,cc:label&#125;\).*</record>    <templateList>      <template pattern="(\s*\S+\s*)&#123;8&#125;+" endPattern="~">        <record id="atom" repeat="*" makeArray="true">&#123;I,cc:serial&#125;&#123;A,cc:elementType&#125;\s+\S+\s+\S+\s+\S+\s+&#123;F,cc:x3&#125;&#123;F,cc:y3&#125;&#123;F,cc:z3&#125;
                    </record>
                </template>
            </templateList>    <templateList>      <template pattern="(\s*\S+\s*)&#123;11&#125;+" endPattern="~">        <record id="atom" repeat="*" makeArray="true">&#123;I,cc:serial&#125;&#123;A,cc:elementType&#125;\s+\S+\s+\S+\s+\S+\s+&#123;F,cc:x3&#125;&#123;F,cc:y3&#125;&#123;F,cc:z3&#125;.*
                    </record>
                </template>
            </templateList>    <transform process="createMolecule" id="geometry.cycle" xpath=".//cml:list[@cmlx:templateRef='atom']/cml:array" />    <transform process="pullup" xpath=".//cml:molecule" />    <transform process="pullup" xpath=".//cml:scalar[@dictRef='cc:label']" />
        </template>       
    </templateList>
<transform process="pullup" xpath=".//cml:scalar[@dictRef='cc:cycleNumber']" repeat="2" />
<transform process="pullup" xpath=".//cml:molecule" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:list[count(*)=0]" />
<transform process="delete" xpath=".//cml:module[count(*)=0]" />