geometry.cycle¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation |  |
| Attribute | Value |
|---|---|
| source | ADF log |
| id | geometry.cycle |
| name | Geometry 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* |
| endOffset | 2 |
| repeat | * |
| xml:base | computation/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
<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
<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
<templateList> <template id="cycle" pattern="\s*Geometry\sCYCLE.*" endPattern=".*" endOffset="0"> <record id="cycle">\s*Geometry\sCYCLE{I,cc:cycleNumber}</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*\*\*\*{I,cc:cycleNumber}\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{I,a:nstep}\s*\**\**{A,x:converged}.*</record> <record repeat="1" /> <record id="energy">\s*current\senergy{F,cc:energy}Hartree.*</record> <record id="change">\s*abs\sof\senergy\schange{F,cc:current}{F,cc:threshold}{A,cc:valid}</record> <record id="cgradmax">\s*constrained\sgradient\smax{F,cc:current}{F,cc:threshold}{A,cc:valid}</record> <record id="cgradrms">\s*constrained\sgradient\srms{F,cc:current}{F,cc:threshold}{A,cc:valid}</record> <record id="gradmax">\s*gradient\smax{F,cc:current}</record> <record id="gradrms">\s*gradient\srms{F,cc:current}</record> <record id="cstepmax">\s*cart.\sstep\smax{F,cc:current}{F,cc:threshold}{A,cc:valid}</record> <record id="csteprms">\s*cart.\sstep\srms{F,cc:current}{F,cc:threshold}{A,cc:valid}</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*){11}+\s*$\s*\-{20,}+\s*" endPattern2="(\s*\S+\s*){8}+$\s*\-{20,}+\s*" endPattern3="~" endOffset="1" repeat="*"> <record id="label">\s*Coordinates\s\({X,cc:label}\).*</record> <templateList> <template pattern="(\s*\S+\s*){8}+" endPattern="~"> <record id="atom" repeat="*" makeArray="true">{I,cc:serial}{A,cc:elementType}\s+\S+\s+\S+\s+\S+\s+{F,cc:x3}{F,cc:y3}{F,cc:z3}
</record>
</template>
</templateList> <templateList> <template pattern="(\s*\S+\s*){11}+" endPattern="~"> <record id="atom" repeat="*" makeArray="true">{I,cc:serial}{A,cc:elementType}\s+\S+\s+\S+\s+\S+\s+{F,cc:x3}{F,cc:y3}{F,cc:z3}.*
</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]" />