final-geometry
Type |
Status |
|---|---|
CML extraction template |
|
HTML5 representation |
|
Attribute |
Value |
|---|---|
source |
GRRM log |
id |
final-geometry |
pattern |
\s*Optimized structure.* |
endPattern |
OPTOPTOPT.* |
xml:base |
optiStruc.xml |
Input
Optimized structure, SYMMETRY = C2v
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
ENERGY = -114.415498155971
Spin(**2) = 0.000000000000
GRADIENT VECTOR
-0.000015613036
0.000000000000
-0.000000000000
0.000012953701
-0.000000000000
0.000000000000
0.000001329667
0.000000558707
0.000000000000
0.000001329667
-0.000000558707
-0.000000000000
Stationary point was found
OPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTOPTO
Output text
1<comment class="example.output" id="">
2 <module cmlx:templateRef="final-geometry">
3 <scalar cmlx:templateRef="symmetry-group" dataType="xsd:string" dictRef="cc:pointgroup">C2v</scalar>
4 <module cmlx:templateRef="molecule">
5 <molecule cmlx:templateRef="atom" id="molecule">
6 <atomArray>
7 <atom elementType="C" id="a1" x3="0.0519116" y3="-0.0000" z3="0.0000">
8 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
9 </atom>
10 <atom elementType="O" id="a2" x3="1.25159806" y3="0.0000" z3="-0.0000">
11 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
12 </atom>
13 <atom elementType="H" id="a3" x3="-0.55175483" y3="0.94469687" z3="-0.0000">
14 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
15 </atom>
16 <atom elementType="H" id="a4" x3="-0.55175483" y3="-0.94469687" z3="-0.0000">
17 <scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
18 </atom>
19 </atomArray>
20 <bondArray>
21 <bond atomRefs2="a1 a2" order="S" />
22 <bond atomRefs2="a1 a3" order="S" />
23 <bond atomRefs2="a1 a4" order="S" />
24 </bondArray>
25 <formula concise="CH2O">
26 <atomArray count="1 2 1" elementType="C H O" />
27 </formula>
28 <property dictRef="cml:molmass">
29 <scalar units="unit:dalton">28.0101</scalar>
30 </property>
31 </molecule>
32 </module>
33 <scalar cmlx:templateRef="energy" dataType="xsd:double" dictRef="cc:energy" units="nonsi:hartree">-114.415498155971</scalar>
34 <scalar cmlx:templateRef="spinsqr" dataType="xsd:double" dictRef="cc:s2">0.000000000000</scalar>
35 </module>
36 </comment>
Template definition
1<templateList> <record id="symmetry-group">\s*Optimized structure,\s*SYMMETRY ={X,cc:pointgroup}</record> <template id="molecule" pattern=".*" endPattern="ENERGY\s+=.*"> <record makeArray="true" repeat="*" id="atom">\s*{A,compchem:elementType}\s*{F,compchem:x3}\s*{F,compchem:y3}\s*{F,compchem:z3}\s*
2 </record> <transform process="createMolecule" xpath="./cml:list[@cmlx:templateRef='atom']/cml:array" id="molecule" /> <transform process="pullupSingleton" xpath="./cml:list" />
3 </template> <template id="energy-par" pattern="ENERGY\s+=.*\(.*" endPattern=".*"> <record id="energy">ENERGY\s*=\s*{F,cc:energy}\s*\(.*\)</record> <transform process="pullupSingleton" xpath="./cml:list" />
4 </template> <template id="energy" pattern="ENERGY\s*=.*" endPattern=".*"> <record id="energy">ENERGY\s*=\s*{F,cc:energy}</record> <transform process="pullupSingleton" xpath="./cml:list" />
5 </template> <template id="spinsqr" pattern="\s*Spin\(\*\*2\)\s*=.*" endPattern=".*"> <record id="spinsqr">\s*Spin\(\*\*2\)\s*=\s*{F,cc:s2}</record> <transform process="pullupSingleton" xpath="./cml:list" />
6 </template> <template id="zpve" pattern="\s*Spin\(\*\*2\)\s*=.*" endPattern=".*"> <record id="zpve">ZPVE\s*=\s*{F,cc:zpe.correction}</record> <transform process="pullupSingleton" xpath="./cml:list" />
7 </template> <template id="gradient" pattern="GRADIENT VECTOR" endPattern="HESSIAN MATRIX"> <record id="null" /> <record id="gradient-vector" repeat="*" makeArray="true">\s+{F,cc:grad}</record> <transform process="pullupSingleton" xpath="./cml:list" />
8 </template> <template id="hessian" pattern="HESSIAN MATRIX\s*" endPattern="NORMAL MODE EIGENVALUE.*" endPattern2="Normal mode eigenvalues.*"> <record id="null" /> <record id="hess" makeArray="true" repeat="*">\s*{1_5F,cc:hessianmatrix}</record> <transform process="pullupSingleton" xpath="./cml:list" />
9 </template> <template id="eigenvals" pattern="NORMAL MODE EIGENVALUE.*" endPattern="~"> <record id="null" /> <record id="normal-mode-eigvals" makeArray="true" repeat="*">\s+{1_5F,cc:eigenval}</record> <transform process="pullupSingleton" xpath="./cml:list" />
10 </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" />
11 </templateList>