frequencies¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
| Attribute | Value |
|---|---|
| source | GRRM log |
| id | frequencies |
| pattern | FREQFREQFREQ.* |
| endPattern | FREQFREQFREQ.* |
| xml:base | freq.xml |
Input
FREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQF
Geometry (Origin = Center of Mass, Axes = Principal Axis), SYMMETRY = Cs
C 0.695923922878 -0.078083657444 0.000000000000
O -0.593539542416 0.066747898232 0.000000000000
H -0.142357946467 -1.016067523497 0.000000000000
H 1.276014279045 0.886458672976 0.000000000000
0 1 2
Freq. : -2057.48295026 764.48759088 1327.25145851
Red. M : 1.11011042 1.13331104 1.48466990
C - x : 0.0736577931 -0.0000000000 0.1016741031
C - y : 0.0269522857 -0.0000000000 0.0816479203
C - z : 0.0000000000 0.1063487433 -0.0000000000
O - x : 0.0110603025 0.0000000000 -0.1322915082
O - y : -0.0468028304 0.0000000000 -0.0429480082
O - z : -0.0000000000 0.0088125096 -0.0000000000
H - x : -0.9362476713 -0.0000000000 -0.0003848867
H - y : 0.2898534479 -0.0000000000 0.1101947651
H - z : 0.0000000000 -0.7022360951 -0.0000000000
H - x : -0.1163180795 -0.0000000000 0.8893309965
H - y : 0.1320251858 -0.0000000000 -0.4007465080
H - z : 0.0000000000 -0.7039010948 -0.0000000000
3 4 5
Freq. : 1476.66812187 2636.78083809 2877.67762880
Red. M : 3.78641458 1.02616200 1.11714936
C - x : 0.3645796096 -0.0205570543 -0.0500408456
C - y : -0.1541243024 -0.0022958180 -0.0851005576
C - z : 0.0000000000 0.0000000000 -0.0000000000
O - x : -0.2519313691 0.0156845601 0.0017538140
O - y : 0.0837797969 -0.0257623597 -0.0119672876
O - z : 0.0000000000 0.0000000000 0.0000000000
H - x : 0.3509961657 0.2374991109 0.1221460329
H - y : 0.1100310570 0.8460836173 0.4395017979
H - z : 0.0000000000 0.0000000000 0.0000000000
H - x : -0.6936494699 -0.2416551384 0.4458474423
H - y : 0.3954544344 -0.4098803618 0.7637055005
H - z : 0.0000000000 -0.0000000000 0.0000000000
Thermochemistry (use all positive eigenvalues) at 298.15 K, 1.00 Atm
E(el) = -114.276451735640
ZPVE = 0.020692289810
Enthalpie(0K) = -114.255759445830
E(tr) = 0.001416276854
E(rot) = 0.001416276854
E(vib) = 0.020797050421
H-E(el) = 0.024573788698
Enthalpie = -114.251877946942
S(el) = 0.000000000000
S(tr) = 0.000057576784
S(rot) = 0.000027931273 (Symmetry number = 1)
S(vib) = 0.000000439335
G-E(el) = -0.001051426350
Free Energy = -114.277503161990
Small eigenvalues are replaced by MinEigenValue = 0.0000946088 u
Thermochemistry (after the above replacements) at 298.15 K, 1.00 Atm
E(el) = -114.276451735640
ZPVE = 0.020692289810
Enthalpie(0K) = -114.255759445830
E(rot) = 0.001416276854
E(vib) = 0.020797050421
H-E(el) = 0.024573788698
Enthalpie = -114.251877946942
S(el) = 0.000000000000
S(tr) = 0.000057576784
S(rot) = 0.000027931273 (Symmetry number = 1)
S(vib) = 0.000000439335
G-E(el) = -0.001051426350
Free Energy = -114.277503161990
FREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQFREQF
Output text
<comment class="example.output" id="frequencies">
<module cmlx:templateRef="frequencies">
<module cmlx:templateRef="molecule">
<molecule cmlx:templateRef="atom" id="molecule-rot">
<atomArray>
<atom elementType="C" id="a1" x3="0.69592392" y3="-0.07808366" z3="0.0000">
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">6</scalar>
</atom>
<atom elementType="O" id="a2" x3="-0.59353954" y3="0.0667479" z3="0.0000">
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">8</scalar>
</atom>
<atom elementType="H" id="a3" x3="-0.14235795" y3="-1.01606752" z3="0.0000">
<scalar dataType="xsd:integer" dictRef="cc:atomicNumber">1</scalar>
</atom>
<atom elementType="H" id="a4" x3="1.27601428" y3="0.88645867" 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" />
<bond atomRefs2="a2 a3" 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>
<module cmlx:templateRef="freq-block">
<array dataType="xsd:integer" dictRef="x:serial" size="6">0 1 2 3 4 5</array>
<array dataType="xsd:double" dictRef="cc:frequency" size="6">-2057.48295026 764.48759088 1327.25145851 1476.66812187 2636.78083809 2877.67762880</array>
<array dataType="xsd:double" dictRef="cc:redmass" size="6">1.11011042 1.13331104 1.48466990 3.78641458 1.02616200 1.11714936</array>
<array dataType="xsd:double" dictRef="cc:displacement" size="72">0.0736577931 0.0269522857 0.0000000000 0.0110603025 -0.0468028304 -0.0000000000 -0.9362476713 0.2898534479 0.0000000000 -0.1163180795 0.1320251858 0.0000000000 -0.0000000000 -0.0000000000 0.1063487433 0.0000000000 0.0000000000 0.0088125096 -0.0000000000 -0.0000000000 -0.7022360951 -0.0000000000 -0.0000000000 -0.7039010948 0.1016741031 0.0816479203 -0.0000000000 -0.1322915082 -0.0429480082 -0.0000000000 -0.0003848867
0.1101947651 -0.0000000000 0.8893309965 -0.4007465080 -0.0000000000 0.3645796096 -0.1541243024 0.0000000000 -0.2519313691 0.0837797969 0.0000000000 0.3509961657 0.1100310570 0.0000000000 -0.6936494699 0.3954544344 0.0000000000 -0.0205570543 -0.0022958180 0.0000000000 0.0156845601 -0.0257623597 0.0000000000 0.2374991109 0.8460836173 0.0000000000 -0.2416551384 -0.4098803618 -0.0000000000 -0.0500408456 -0.0851005576 -0.0000000000 0.0017538140 -0.0119672876 0.0000000000 0.1221460329
0.4395017979 0.0000000000 0.4458474423 0.7637055005 0.0000000000</array>
</module>
<module cmlx:templateRef="thermo">
<scalar dataType="xsd:double" dictRef="cc:temp" units="si:k">298.15</scalar>
<scalar dataType="xsd:double" dictRef="cc:press" units="nonsi:atm">1.00</scalar>
<list cmlx:templateRef="state" />
<scalar cmlx:templateRef="energy" dataType="xsd:double" dictRef="cc:energy" units="nonsi:hartree">-114.276451735640</scalar>
<scalar cmlx:templateRef="zpe" dataType="xsd:double" dictRef="cc:zpe.correction" units="nonsi:hartree">0.020692289810</scalar>
<scalar cmlx:templateRef="elec-zpe" dataType="xsd:double" dictRef="cc:zpe.sumelectzpe" units="nonsi:hartree">-114.255759445830</scalar>
<scalar cmlx:templateRef="thermal-tr" dataType="xsd:double" dictRef="cc:ethermo.trans" units="nonsi:hartree">0.001416276854</scalar>
<scalar cmlx:templateRef="thermal-rot" dataType="xsd:double" dictRef="cc:ethermo.rot" units="nonsi:hartree">0.001416276854</scalar>
<scalar cmlx:templateRef="thermal-vib" dataType="xsd:double" dictRef="cc:ethermo.vib" units="nonsi:hartree">0.020797050421</scalar>
<scalar cmlx:templateRef="enthalpy-corr" dataType="xsd:double" dictRef="cc:zpe.thermalcorrenthalpy" units="nonsi:hartree">0.024573788698</scalar>
<scalar cmlx:templateRef="enthalpy" dataType="xsd:double" dictRef="cc:zpe.sumelectthermalent" units="nonsi:hartree">-114.251877946942</scalar>
<scalar cmlx:templateRef="entropy-el" dataType="xsd:double" dictRef="cc:s.elect" units="nonsi2:hartree.K-1">0.000000000000</scalar>
<scalar cmlx:templateRef="entropy-tr" dataType="xsd:double" dictRef="cc:s.trans" units="nonsi2:hartree.K-1">0.000057576784</scalar>
<scalar cmlx:templateRef="entropy-rot" dataType="xsd:double" dictRef="cc:s.rot" units="nonsi2:hartree.K-1">0.000027931273</scalar>
<scalar dataType="xsd:integer" dictRef="cc:symmnumber" units="nonsi2:hartree.K-1">1</scalar>
<list cmlx:templateRef="entropy-rot" />
<scalar cmlx:templateRef="entropy-vib" dataType="xsd:double" dictRef="cc:s.vib" units="nonsi2:hartree.K-1">0.000000439335</scalar>
<scalar cmlx:templateRef="gibbs-corr" dataType="xsd:double" dictRef="cc:zpe.thermalcorrgfe" units="nonsi:hartree">-0.001051426350</scalar>
<scalar cmlx:templateRef="gibbs" dataType="xsd:double" dictRef="cc:zpe.sumelectthermalfe" units="nonsi:hartree">-114.277503161990</scalar>
</module>
</module>
</comment>
Template definition
<record id="null" repeat="2" />
<template id="molecule" pattern="[A-Za-z]{1,2}\s+.*" endPattern="Freq\..*" endOffset="-2"> <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-rot" /> <transform process="pullupSingleton" xpath="./cml:list" />
</template>
<record id="null" repeat="1" />
<template id="freq-block" pattern="Freq\..*" endPattern="Freq\..*" endPattern2="Thermochemistry.*" repeat="*" offset="-1"> <record makeArray="true" id="serial">{1_3I,x:serial}</record> <record makeArray="true" id="freq">Freq\.\s+:\s+{1_3F,cc:frequency}</record> <record makeArray="true" id="redmass">Red\. M :\s+{1_3F,cc:redmass}</record> <transform process="pullupSingleton" xpath="./cml:list" /> <templateList> <template id="displs-3" pattern="[A-Z].*\- [xyz]\s+:\s+{3}.*"> <record makeArray="true" id="displ-all" repeat="*">[A-Z].*\- [xyz]\s+:\s*{F,cc:displace1}\s*{F,cc:displace2}\s*{F,cc:displace3}\s*</record>
</template> <template id="displs-2" pattern="[A-Z].*\- [xyz]\s+:\s+{2}.*"> <record makeArray="true" id="displ-all" repeat="*">[A-Z].*\- [xyz]\s+:\s*{F,cc:displace1}\s*{F,cc:displace2}\s*</record>
</template> <template id="displs-1" pattern="[A-Z].*\- [xyz]\s+:\s+{1}.*"> <record makeArray="true" id="displ-all" repeat="*">[A-Z].*\- [xyz]\s+:\s*{F,cc:displace1}\s*</record>
</template>
</templateList> <transform process="joinArrays" xpath=".//cml:array[starts-with(@dictRef,'cc:displace')]" /> <transform process="pullupSingleton" xpath="./cml:list" /> <record id="null" repeat="1" />
</template>
<transform process="joinArrays" xpath=".//cml:array[starts-with(@dictRef,'cc:displace')]" />
<transform process="joinArrays" xpath=".//cml:array[@dictRef='x:serial']" />
<transform process="joinArrays" xpath=".//cml:array[@dictRef='cc:frequency']" />
<transform process="joinArrays" xpath=".//cml:array[@dictRef='cc:redmass']" />
<transform process="addUnits" xpath="./cml:array[@dictRef='cc:frequency']" value="nonsi:cm-1" />
<template id="thermo" pattern="Thermochemistry.*after.*" endPattern="~"> <record id="state">Thermochemistry.*at\s*{F,cc:temp}\s*K,\s*{F,cc:press}\s*Atm\s*</record> <record id="energy">E\(el\)\s+=\s+{F,cc:energy}</record> <record id="zpe">ZPVE\s+=\s+{F,cc:zpe.correction}</record> <record id="elec-zpe">Enthalpie\(0K\)\s+=\s+{F,cc:zpe.sumelectzpe}</record> <record id="thermal-tr">E\(tr\)\s+=\s+{F,cc:ethermo.trans}</record> <record id="thermal-rot">E\(rot\)\s+=\s+{F,cc:ethermo.rot}</record> <record id="thermal-vib">E\(vib\)\s+=\s+{F,cc:ethermo.vib}</record> <record id="enthalpy-corr">H-E\(el\)\s+=\s+{F,cc:zpe.thermalcorrenthalpy}</record> <record id="enthalpy">Enthalpie\s+=\s+{F,cc:zpe.sumelectthermalent}</record> <record id="entropy-el">S\(el\)\s+=\s+{F,cc:s.elect}</record> <record id="entropy-tr">S\(tr\)\s+=\s+{F,cc:s.trans}</record> <record id="entropy-rot">S\(rot\)\s+=\s+{F,cc:s.rot}\s+\(Symmetry number\s+={I,cc:symmnumber}.*</record> <record id="entropy-vib">S\(vib\)\s+=\s+{F,cc:s.vib}</record> <record id="gibbs-corr">G-E\(el\)\s+=\s+{F,cc:zpe.thermalcorrgfe}</record> <record id="gibbs">Free Energy\s+=\s+{F,cc:zpe.sumelectthermalfe}</record> <transform process="pullupSingleton" xpath="./cml:list" /> <transform process="pullup" xpath="./cml:list/cml:scalar" /> <transform process="addAttribute" xpath="./cml:scalar[@dictRef='cc:s.rot']" name="cmlx:templateRef" value="entropy-rot" /> <transform process="addUnits" xpath="./cml:scalar[@dictRef='cc:energy']" value="nonsi:hartree" /> <transform process="addUnits" xpath="./cml:scalar[starts-with(@dictRef,'cc:zpe')]" value="nonsi:hartree" /> <transform process="addUnits" xpath="./cml:scalar[starts-with(@dictRef,'cc:ethermo')]" value="nonsi:hartree" /> <transform process="addUnits" xpath="./cml:scalar[starts-with(@dictRef,'cc:s')]" value="nonsi2:hartree.K-1" /> <transform process="addUnits" xpath="./cml:scalar[@dictRef='cc:temp']" value="si:k" /> <transform process="addUnits" xpath="./cml:scalar[@dictRef='cc:press']" value="nonsi:atm" />
</template>
<transform process="delete" xpath="(//cml:list[@cmlx:templateRef='null'])" />
<transform process="pullupSingleton" xpath="./cml:list" />
<transform process="move" xpath="./cml:module//cml:array[@dictRef='cc:displace1']" to="(./cml:module[@cmlx:templateRef='freq-block'])[1]" />
<transform process="delete" xpath="(.//cml:module[@cmlx:templateRef='displs-3'])" />
<transform process="delete" xpath="(.//cml:module[@cmlx:templateRef='freq-block'])[count(*)=0]" />
<transform process="createArray" from=".//cml:module[@cmlx:templateRef='freq-block']/cml:array[@dictRef='cc:displace1']" xpath="." dictRef="cc:displacement" dataType="xsd:double" />