structure¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation |  |
| Attribute | Value |
|---|---|
| source | GRRM log |
| id | structure |
| pattern | # Geometry of.* |
| pattern2 | INITIAL STRUCTURE.* |
| pattern3 | INPUT ORIENTATION.* |
| endPattern | # Geometry of.* |
| endPattern2 | ^\s*$ |
| endPattern3 | CONNECTION.* |
| repeat | * |
| xml:base | singleStruc.xml |
Input
# Geometry of EQ 0, 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 = -114.415498155970 (-114.415498155970 : 0.000000000000)
Spin(**2) = 0.000000000000
ZPVE = 0.026536542348
Normal mode eigenvalues : nmode = 6
0.053871195 0.060584067 0.088631469 0.131480115 0.311308040
0.324295946
Input
INITIAL STRUCTURE
C -0.064198235583 -0.007930187832 -0.000000000000
O 1.233143761809 0.016481892179 0.000000000000
H 0.644724226899 1.031280651044 0.000000000000
H -0.513669753124 -1.039832355389 0.000000000000
ENERGY = -114.276451735641
Spin(**2) = 0.000000000000
GRADIENT VECTOR
-0.000015411633
-0.000011833303
0.000000000000
0.000003349007
0.000007583517
0.000000000000
0.000015586121
0.000009500992
-0.000000000000
-0.000003523494
-0.000005251206
-0.000000000000
HESSIAN MATRIX
0.483870417
0.021477761 0.399410092
0.000000000 0.000000000 0.031760643
-0.572059444 -0.025014466 0.000000000 0.573554180
0.167659525 0.037218727 -0.000000000 0.009670607 0.026493405
-0.000000000 -0.000000000 0.003555306 -0.000000000 0.000000000
0.133879425 0.029603924 -0.000000000 0.019884615 -0.110041445
-0.112346200 -0.161842890 0.000000000 0.044034835 -0.092936388
0.000000000 0.000000000 -0.017647961 -0.000000000 -0.000000000
-0.045690398 -0.026067220 -0.000000000 -0.021379351 -0.067288687
-0.076791086 -0.274785929 -0.000000000 -0.028690976 0.029224256
-0.000000000 0.000000000 -0.017667987 0.000000000 0.000000000
0.000306969
0.000000000 -0.129079016
-0.000000000 0.061067209 0.252234827
-0.001910541 -0.000000000 0.000000000 0.009768881
0.000000000 -0.024685024 0.007244156 -0.000000000 0.091754773
0.000000000 0.019370312 0.002544451 -0.000000000 0.086111750
-0.001951734 0.000000000 -0.000000000 0.009789622 0.000000000
0.243017222
0.000000000 0.009830099
NORMAL MODE EIGENVALUE : N_MODE = 6
-0.160200511 0.022117307 0.066664995 0.082519618 0.263111301
0.313383199
Output text
<comment class="example.output" id="structure2">
<module cmlx:templateRef="structure">
<module cmlx:templateRef="molecule">
<molecule cmlx:templateRef="atom" id="molecule">
<atomArray>
<atom elementType="C" id="a1" x3="-0.97636194" y3="0.11153149" z3="-0.33793524">
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
</atom>
<atom elementType="O" id="a2" x3="0.74275724" y3="-0.10033779" z3="-0.23073234">
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
</atom>
<atom elementType="H" id="a3" x3="0.46752383" y3="0.73164846" z3="0.26582554">
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
</atom>
<atom elementType="H" id="a4" x3="0.93150704" y3="-0.88276953" z3="0.31747787">
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
</atom>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="S" />
<bond atomRefs2="a2 a3" order="S" />
<bond atomRefs2="a2 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">-114.136991357592</scalar>
<scalar cmlx:templateRef="spinsqr" dataType="xsd:double" dictRef="cc:s2">0.000000000000</scalar>
<array cmlx:templateRef="gradient-vector" dataType="xsd:double" dictRef="cc:grad" size="12">0.000015914887 0.000012610186 0.000002846427 -0.000035628051 0.000081501872 0.000040350355 -0.000005755657 -0.000022336099 -0.000053681663 0.000025468820 -0.000071775959 0.000010484881</array>
<array cmlx:templateRef="hess" dataType="xsd:double" dictRef="cc:hessianmatrix" size="78">0.044205190 -0.006412971 0.007027217 0.004417132 -0.003502960 0.000597432 -0.049966196 -0.010052197 -0.011353132 0.059532869 0.043423072 0.014713894 0.028617102 -0.120888805 0.552367836 -0.003207739 0.011718116 0.009895864 0.033795717 -0.080345449 0.016720679 0.007300593 0.010504324 0.005664706 0.014638871 -0.060855490 -0.028184625 -0.024077536 0.078496524 -0.226600098 -0.011371698 -0.010415119
-0.012679097 0.033258263 -0.165062130 -0.010959674 0.009164575 -0.003568324 -0.015231379 0.062826862 0.023845389 0.006443513 -0.001036606 0.052444478 -0.340481633 0.010162306 0.002199962 0.002185801 -0.055700848 0.216790477 0.303129498 0.014871439 -0.019199307 -0.117471227 -0.014454998 0.256478752 -0.126730439 -0.021143154 0.151945345 0.124634197 -0.045459417 -0.003186079 -0.003186035 -0.000743410 0.029377132 0.186098559 -0.007484466 -0.001694029 0.023531903 -0.068805401 -0.186294923
-0.004232610 -0.010396582 0.014775339 0.049771151 0.335732149 -0.208593856 0.169333782</array>
<array cmlx:templateRef="normal-mode-eigvals" dataType="xsd:double" dictRef="cc:eigenval" size="6">-0.024704258 0.002537847 0.016029896 0.061744645 0.372987694 0.522395019</array>
</module>
</comment>
Template definition
<template id="label-symmetry" pattern="# Geometry of.*" endPattern=".*"> <record id="label-symmetry"># Geometry of {X,cc:label},\s*SYMMETRY ={X,cc:pointgroup}</record>
</template>
<template id="initial-structure" pattern="INITIAL STRUCTURE.*" endPattern=".*"> <record id="null" />
</template>
<template id="initial-structure" pattern="INPUT ORIENTATION.*" endPattern=".*"> <record id="null" />
</template>
<template id="molecule" pattern=".*" endPattern="ENERGY\s*=.*" endPattern2="Energy.*"> <record makeArray="true" repeat="*" id="atom">\s*{A,compchem:elementType}\s*{F,compchem:x3}\s*{F,compchem:y3}\s*{F,compchem:z3}\s*
</record> <transform process="createMolecule" xpath="./cml:list[@cmlx:templateRef='atom']/cml:array" id="molecule" /> <transform process="pullupSingleton" xpath="./cml:list" />
</template>
<template id="energy" pattern="(ENERGY|Energy)\s*=.*\(.*" endPattern=".*"> <record id="energy">(ENERGY|Energy)\s*=\s*{F,cc:energy}\s*\(.*\)</record> <transform process="pullupSingleton" xpath="./cml:list" />
</template>
<template id="energy" pattern="(ENERGY|Energy)\s*=.*[^\(\n]*$" endPattern=".*"> <record id="energy">(ENERGY|Energy)\s*=\s*{F,cc:energy}</record> <transform process="pullupSingleton" xpath="./cml:list" />
</template>
<template id="spin" pattern="Spin\(\*\*2\).*" endPattern=".*"> <record id="spinsqr">\s*Spin\(\*\*2\)\s*=\s*{F,cc:s2}</record> <transform process="pullupSingleton" xpath="./cml:list" />
</template>
<template id="zpve" pattern="ZPVE\s*=.*" endPattern=".*"> <record id="zpve">ZPVE\s*=\s*{F,cc:zpe.correction}</record> <transform process="pullupSingleton" xpath="./cml:list" />
</template>
<template id="gradient" pattern="GRADIENT VECTOR" endPattern="HESSIAN MATRIX\s*"> <record id="null" /> <record id="gradient-vector" repeat="*" makeArray="true">\s+{F,cc:grad}</record> <transform process="pullupSingleton" xpath="./cml:list" />
</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" />
</template>
<template id="eigenvals" pattern="NORMAL MODE EIGENVALUE.*" endPattern="~"> <record id="null" repeat="1" /> <record id="normal-mode-eigvals" makeArray="true" repeat="*">\s*{1_5F,cc:eigenval}</record> <transform process="pullupSingleton" xpath="./cml:list" />
</template>
<template id="eigenvals" pattern="Normal mode eigenvalues.*" endPattern="~"> <record id="null" repeat="1" /> <record id="normal-mode-eigvals" makeArray="true" repeat="*">\s*{1_5F,cc:eigenval}</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" />