vibrations ​
Implementation level ​
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
Template attributes ​
| Attribute | Value |
|---|---|
| source | MOLCAS log |
| id | vibrations |
| name | Vibrational frequencies |
| pattern | \s*Harmonic\sfrequencies\sin\scm-1\s* |
| endPattern | .*[0-9]$\s*$\s*$\s* |
| endPattern2 | ~ |
| endOffset | 1 |
| xml:base | modules/vibrations.xml |
Input ​
Harmonic frequencies in cm-1
IR Intensities in km/mol
1 2 3 4 5 6
Frequency: 72.78 409.43 524.37 555.29 641.43 819.00
Intensity: 0.445E+00 0.572E+01 0.237E+02 0.288E+02 0.780E+02 0.863E+01
C1 x -0.00036 0.01676 0.00922 -0.06545 0.00611 0.05350
C1 y -0.00523 0.07362 0.09809 0.00999 0.06763 0.04613
C1 z 0.00689 0.05104 -0.14429 0.00319 -0.09816 0.03567
C2 x -0.00002 0.03023 -0.00153 -0.12629 0.00073 -0.15937
C2 y -0.00224 -0.09438 -0.00662 -0.01401 0.01571 0.00571
C2 z 0.00320 -0.06215 0.00953 -0.01755 -0.02267 -0.00570
O3 x -0.00252 -0.12904 -0.00019 0.05095 -0.00413 0.06342
O3 y -0.02547 0.02459 -0.00523 0.07938 -0.05042 -0.09906
O3 z 0.03868 0.00851 0.00809 0.05714 0.07168 -0.06361
O4 x 0.00245 0.09257 -0.00201 0.11575 -0.00280 0.04433
O4 y 0.02740 0.03252 -0.02736 -0.08837 -0.03097 0.07418
O4 z -0.04100 0.02797 0.03992 -0.05271 0.04666 0.05258
H5 x 0.02513 0.17571 -0.29537 -0.09568 -0.19678 -0.14680
H5 y 0.57220 -0.18407 -0.03671 -0.02754 -0.03884 0.00077
H5 z 0.02154 -0.10646 0.09122 -0.02678 0.03233 -0.01062
H6 x 0.00722 0.17940 0.27979 -0.09828 0.19062 -0.15174
H6 y -0.22416 -0.17779 -0.08828 -0.02842 -0.02814 -0.00167
H6 z -0.52660 -0.11702 0.09331 -0.02441 0.06543 -0.01336
H7 x -0.02637 -0.23134 -0.01011 -0.18570 -0.00470 -0.23333
H7 y -0.28924 -0.17912 -0.11195 -0.03104 -0.05092 -0.01249
H7 z 0.42173 -0.13572 0.16413 -0.03427 0.07502 -0.02470
H8 x -0.00025 -0.10455 -0.03102 0.01698 0.03944 0.08236
H8 y -0.00064 -0.11830 -0.33493 0.27766 0.41734 -0.20899
H8 z 0.00002 -0.08736 0.49400 0.18610 -0.61223 -0.13314
7 8 9 10 11 12
Frequency: 955.57 1025.37 1147.68 1285.43 1355.42 1430.75
Intensity: 0.902E+02 0.679E+01 0.198E+03 0.259E+02 0.388E+02 0.172E+02
C1 x -0.07860 0.00786 -0.10180 0.13030 0.05985 -0.02575
C1 y 0.03725 0.08146 0.07349 -0.09468 -0.04594 0.00412
C1 z 0.01875 -0.11933 0.04463 -0.05641 -0.02724 -0.00228
C2 x 0.03713 -0.00639 0.04075 0.00691 -0.13520 -0.01591
C2 y 0.09647 -0.07200 -0.06547 0.01920 0.00204 0.04256
C2 z 0.06960 0.10288 -0.04263 0.01368 -0.00745 0.02086
O3 x 0.03922 -0.00157 -0.00212 -0.05821 -0.02097 0.00316
O3 y -0.06986 -0.01001 -0.08437 -0.01030 0.00113 -0.00077
O3 z -0.04498 0.01584 -0.05779 -0.01061 -0.00070 0.00004
O4 x -0.02185 -0.00139 0.04106 0.00154 0.00059 0.01517
O4 y -0.02093 -0.01600 0.03639 0.04481 0.01898 0.01172
O4 z -0.01556 0.02370 0.02683 0.03059 0.01284 0.00920
H5 x 0.34006 0.45804 -0.08066 -0.17891 0.46626 -0.07424
H5 y -0.17098 0.12508 0.13493 -0.09940 0.05872 -0.63483
H5 z -0.03094 -0.03073 0.00672 0.04833 -0.15737 -0.00778
H6 x 0.33869 -0.44893 -0.08829 -0.17054 0.44497 -0.11599
H6 y -0.11074 0.01223 0.05987 0.02101 -0.15205 -0.17133
H6 z -0.12236 -0.16478 0.11582 -0.12468 0.15222 -0.54171
H7 x -0.45218 0.02054 0.36221 -0.25858 0.34749 0.38907
H7 y -0.06737 0.16150 0.03989 -0.06661 0.14714 0.10335
H7 z -0.07564 -0.23312 0.05396 -0.06050 0.12522 0.19764
H8 x -0.00837 -0.00011 -0.08437 -0.12635 -0.03808 0.00630
H8 y 0.19783 0.00140 0.43133 0.49610 0.14971 -0.02689
H8 z 0.13778 -0.00320 0.29106 0.32856 0.10034 -0.01604
13 14 15 16 17 18
Frequency: 1435.27 1744.19 2963.96 3037.74 3088.44 3581.48
Intensity: 0.909E+01 0.339E+03 0.258E+01 0.425E+01 0.496E+01 0.533E+02
C1 x 0.00390 0.14546 0.00044 0.00012 -0.00127 -0.00321
C1 y 0.01340 0.14143 -0.00093 0.00070 -0.00215 0.00081
C1 z -0.02054 0.10564 -0.00068 -0.00090 -0.00154 0.00044
C2 x 0.00471 -0.02052 -0.04457 0.00493 0.01344 0.00098
C2 y 0.02404 -0.00807 -0.01302 0.04854 -0.07260 0.00025
C2 z -0.04496 -0.00713 -0.01247 -0.07136 -0.04836 0.00026
O3 x -0.00034 -0.01160 -0.00004 -0.00001 -0.00029 -0.05873
O3 y -0.00112 -0.01204 -0.00006 -0.00005 0.00022 -0.00447
O3 z 0.00227 -0.00901 -0.00003 0.00007 0.00013 -0.00680
O4 x -0.00171 -0.07941 0.00037 -0.00003 0.00036 0.00003
O4 y -0.00246 -0.09461 0.00056 0.00006 0.00078 -0.00066
O4 z 0.00083 -0.06939 0.00043 -0.00017 0.00056 -0.00050
H5 x 0.34077 -0.04373 0.15371 0.17901 0.07687 0.00001
H5 y -0.24732 -0.04180 -0.03692 -0.01811 -0.03251 -0.00001
H5 z -0.12853 0.00253 0.60621 0.64483 0.27478 -0.00148
H6 x -0.32574 -0.04162 0.20486 -0.23672 0.10514 0.00010
H6 y 0.27805 -0.00828 0.53407 -0.58716 0.24645 -0.00173
H6 z 0.29037 -0.04246 -0.23307 0.23165 -0.12375 0.00001
H7 x -0.08463 0.07209 0.15961 -0.00179 -0.32938 -0.00084
H7 y -0.41348 0.02633 -0.33961 0.01943 0.65951 -0.00087
H7 z 0.56004 0.02545 -0.22331 -0.01526 0.43167 -0.00085
H8 x -0.00021 -0.02996 0.00203 -0.00006 0.00140 0.95871
H8 y -0.00628 0.12849 0.00051 -0.00059 0.00062 0.07150
H8 z 0.00892 0.08584 0.00049 0.00078 0.00046 0.10974
Output text ​
xml
<comment class="example.output" id="vibrations">
<module cmlx:templateRef="vibrations">
<array dataType="xsd:string" dictRef="m:label" size="8">C1 C2 O3 O4 H5 H6 H7 H8</array>
<array dataType="xsd:string" dictRef="cc:frequency" size="18">72.78 409.43 524.37 555.29 641.43 819.00 955.57 1025.37 1147.68 1285.43 1355.42 1430.75 1435.27 1744.19 2963.96 3037.74 3088.44 3581.48</array>
<array dataType="xsd:double" dictRef="cc:irintensity" size="18">0.445E+00 0.572E+01 0.237E+02 0.288E+02 0.780E+02 0.863E+01 0.902E+02 0.679E+01 0.198E+03 0.259E+02 0.388E+02 0.172E+02 0.909E+01 0.339E+03 0.258E+01 0.425E+01 0.496E+01 0.533E+02</array>
<matrix cols="24" dataType="xsd:double" dictRef="cc:displacement" rows="18">-0.00036 -0.00523 0.00689 -0.00002 -0.00224 0.00320 -0.00252 -0.02547 0.03868 0.00245 0.02740 -0.04100 0.02513 0.57220 0.02154 0.00722 -0.22416 -0.52660 -0.02637 -0.28924 0.42173 -0.00025 -0.00064 0.00002 0.01676 0.07362 0.05104 0.03023 -0.09438 -0.06215 -0.12904 0.02459 0.00851 0.09257 0.03252 0.02797 0.17571 -0.18407 -0.10646 0.17940 -0.17779 -0.11702 -0.23134 -0.17912 -0.13572 -0.10455 -0.11830 -0.08736 0.00922 0.09809 -0.14429 -0.00153 -0.00662 0.00953 -0.00019 -0.00523 0.00809 -0.00201 -0.02736 0.03992 -0.29537 -0.03671 0.09122 0.27979 -0.08828 0.09331 -0.01011 -0.11195 0.16413 -0.03102 -0.33493 0.49400 -0.06545 0.00999 0.00319 -0.12629 -0.01401 -0.01755 0.05095 0.07938 0.05714 0.11575 -0.08837 -0.05271 -0.09568 -0.02754 -0.02678 -0.09828 -0.02842 -0.02441 -0.18570 -0.03104 -0.03427 0.01698 0.27766 0.18610 0.00611 0.06763 -0.09816 0.00073 0.01571 -0.02267 -0.00413 -0.05042 0.07168 -0.00280 -0.03097 0.04666 -0.19678 -0.03884 0.03233 0.19062 -0.02814 0.06543 -0.00470 -0.05092 0.07502 0.03944 0.41734 -0.61223 0.05350 0.04613 0.03567 -0.15937 0.00571 -0.00570 0.06342 -0.09906 -0.06361 0.04433 0.07418 0.05258 -0.14680 0.00077 -0.01062 -0.15174 -0.00167 -0.01336 -0.23333 -0.01249 -0.02470 0.08236 -0.20899 -0.13314 -0.07860 0.03725 0.01875 0.03713 0.09647 0.06960 0.03922 -0.06986 -0.04498 -0.02185 -0.02093 -0.01556 0.34006 -0.17098 -0.03094 0.33869 -0.11074 -0.12236 -0.45218 -0.06737 -0.07564 -0.00837 0.19783 0.13778 0.00786 0.08146 -0.11933 -0.00639 -0.07200 0.10288 -0.00157 -0.01001 0.01584 -0.00139 -0.01600 0.02370 0.45804 0.12508 -0.03073 -0.44893 0.01223 -0.16478 0.02054 0.16150 -0.23312 -0.00011 0.00140 -0.00320 -0.10180 0.07349 0.04463 0.04075 -0.06547 -0.04263 -0.00212 -0.08437 -0.05779 0.04106 0.03639 0.02683 -0.08066 0.13493 0.00672 -0.08829 0.05987 0.11582 0.36221 0.03989 0.05396 -0.08437 0.43133 0.29106 0.13030 -0.09468 -0.05641 0.00691 0.01920 0.01368 -0.05821 -0.01030 -0.01061 0.00154 0.04481 0.03059 -0.17891 -0.09940 0.04833 -0.17054 0.02101 -0.12468 -0.25858 -0.06661 -0.06050 -0.12635 0.49610 0.32856 0.05985 -0.04594 -0.02724 -0.13520 0.00204 -0.00745 -0.02097 0.00113 -0.00070 0.00059 0.01898 0.01284 0.46626 0.05872 -0.15737 0.44497 -0.15205 0.15222 0.34749 0.14714 0.12522 -0.03808 0.14971 0.10034 -0.02575 0.00412 -0.00228 -0.01591 0.04256 0.02086 0.00316 -0.00077 0.00004 0.01517 0.01172 0.00920 -0.07424 -0.63483 -0.00778 -0.11599 -0.17133 -0.54171 0.38907 0.10335 0.19764 0.00630 -0.02689 -0.01604 0.00390 0.01340 -0.02054 0.00471 0.02404 -0.04496 -0.00034 -0.00112 0.00227 -0.00171 -0.00246 0.00083 0.34077 -0.24732 -0.12853 -0.32574 0.27805 0.29037 -0.08463 -0.41348 0.56004 -0.00021 -0.00628 0.00892 0.14546 0.14143 0.10564 -0.02052 -0.00807 -0.00713 -0.01160 -0.01204 -0.00901 -0.07941 -0.09461 -0.06939 -0.04373 -0.04180 0.00253 -0.04162 -0.00828 -0.04246 0.07209 0.02633 0.02545 -0.02996 0.12849 0.08584 0.00044 -0.00093 -0.00068 -0.04457 -0.01302 -0.01247 -0.00004 -0.00006 -0.00003 0.00037 0.00056 0.00043 0.15371 -0.03692 0.60621 0.20486 0.53407 -0.23307 0.15961 -0.33961 -0.22331 0.00203 0.00051 0.00049 0.00012 0.00070 -0.00090 0.00493 0.04854 -0.07136 -0.00001 -0.00005 0.00007 -0.00003 0.00006 -0.00017 0.17901 -0.01811 0.64483 -0.23672 -0.58716 0.23165 -0.00179 0.01943 -0.01526 -0.00006 -0.00059 0.00078 -0.00127 -0.00215 -0.00154 0.01344 -0.07260 -0.04836 -0.00029 0.00022 0.00013 0.00036 0.00078 0.00056 0.07687 -0.03251 0.27478 0.10514 0.24645 -0.12375 -0.32938 0.65951 0.43167 0.00140 0.00062 0.00046 -0.00321 0.00081 0.00044 0.00098 0.00025 0.00026 -0.05873 -0.00447 -0.00680 0.00003 -0.00066 -0.00050 0.00001 -0.00001 -0.00148 0.00010 -0.00173 0.00001 -0.00084 -0.00087 -0.00085 0.95871 0.07150 0.10974</matrix>
</module>
</comment>Template definition ​
xml
<template id="section" pattern="\s{20,}[0-9].*" endPattern="\s*$\s*" endPattern2="~" repeat="*"> <record>{1_6I,m:serial}</record> <record /> <record>\s*(Frequency:|Freq\.){1_6A,cc:frequency}</record> <templateList> <template pattern=".*Intensity:.*" endPattern=".*" endOffset="0" repeat="*"> <record>\s*Intensity:{1_6E,cc:irintensity}</record>
</template> <template pattern="\s*\S+\s+x(\s+\S+){6}\s*" endPattern="\s*\S+\s+z.*" endPattern2="~" endOffset="1" repeat="*"> <record>{A,m:label}x{F,x:valuex1}{F,x:valuex2}{F,x:valuex3}{F,x:valuex4}{F,x:valuex5}{F,x:valuex6}</record> <record>.*y{F,y:valuey1}{F,y:valuey2}{F,y:valuey3}{F,y:valuey4}{F,y:valuey5}{F,y:valuey6}</record> <record>.*z{F,z:valuez1}{F,z:valuez2}{F,z:valuez3}{F,z:valuez4}{F,z:valuez5}{F,z:valuez6}</record> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'1')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'2')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'3')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'4')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'5')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'6')]" />
</template> <template pattern="\s*\S+\s+x(\s+\S+){5}\s*" endPattern="\s*\S+\s+z.*" endPattern2="~" endOffset="1" repeat="*"> <record>{A,m:label}x{F,x:valuex1}{F,x:valuex2}{F,x:valuex3}{F,x:valuex4}{F,x:valuex5}</record> <record>.*y{F,y:valuey1}{F,y:valuey2}{F,y:valuey3}{F,y:valuey4}{F,y:valuey5}</record> <record>.*z{F,z:valuez1}{F,z:valuez2}{F,z:valuez3}{F,z:valuez4}{F,z:valuez5}</record> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'1')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'2')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'3')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'4')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'5')]" />
</template> <template pattern="\s*\S+\s+x(\s+\S+){4}\s*" endPattern="\s*\S+\s+z.*" endPattern2="~" endOffset="1" repeat="*"> <record>{A,m:label}x{F,x:valuex1}{F,x:valuex2}{F,x:valuex3}{F,x:valuex4}</record> <record>.*y{F,y:valuey1}{F,y:valuey2}{F,y:valuey3}{F,y:valuey4}</record> <record>.*z{F,z:valuez1}{F,z:valuez2}{F,z:valuez3}{F,z:valuez4}</record> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'1')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'2')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'3')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'4')]" />
</template> <template pattern="\s*\S+\s+x(\s+\S+){3}\s*" endPattern="\s*\S+\s+z.*" endPattern2="~" endOffset="1" repeat="*"> <record>{A,m:label}x{F,x:valuex1}{F,x:valuex2}{F,x:valuex3}</record> <record>.*y{F,y:valuey1}{F,y:valuey2}{F,y:valuey3}</record> <record>.*z{F,z:valuez1}{F,z:valuez2}{F,z:valuez3}</record> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'1')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'2')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'3')]" />
</template> <template pattern="\s*\S+\s+x(\s+\S+){2}\s*" endPattern="\s*\S+\s+z.*" endPattern2="~" endOffset="1" repeat="*"> <record>{A,m:label}x{F,x:valuex1}{F,x:valuex2}</record> <record>.*y{F,y:valuey1}{F,y:valuey2}</record> <record>.*z{F,z:valuez1}{F,z:valuez2}</record> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'1')]" /> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'2')]" />
</template> <template pattern="\s*\S+\s+x(\s+\S+)\s*" endPattern="\s*\S+\s+z.*" endPattern2="~" endOffset="1" repeat="*"> <record>{A,m:label}x{F,x:valuex1}</record> <record>.*y{F,y:valuey1}</record> <record>.*z{F,z:valuez1}</record> <transform process="createArray" xpath="." from=".//cml:scalar[ends-with(@dictRef,'1')]" />
</template> <transform process="createArray" xpath="." from=".//cml:scalar[@dictRef='m:label']" />
</templateList> <transform process="joinArrays" xpath=".//cml:array[@dictRef='x:valuex1']" dictRef="x:value1" /> <transform process="joinArrays" xpath=".//cml:array[@dictRef='x:valuex2']" dictRef="x:value2" /> <transform process="joinArrays" xpath=".//cml:array[@dictRef='x:valuex3']" dictRef="x:value3" /> <transform process="joinArrays" xpath=".//cml:array[@dictRef='x:valuex4']" dictRef="x:value4" /> <transform process="joinArrays" xpath=".//cml:array[@dictRef='x:valuex5']" dictRef="x:value5" /> <transform process="joinArrays" xpath=".//cml:array[@dictRef='x:valuex6']" dictRef="x:value6" />
</template>
<transform process="joinArrays" xpath=".//cml:array[@dictRef='m:serial']" dictRef="m:serial" />
<transform process="joinArrays" xpath=".//cml:array[@dictRef='cc:frequency']" dictRef="cc:frequency" />
<transform process="joinArrays" xpath=".//cml:array[@dictRef='cc:irintensity']" dictRef="cc:irintensity" />
<transform process="createMatrix" xpath="." from=".//cml:array[starts-with(@dictRef, 'x:value')]" dictRef="cc:displacement" />
<transform process="move" xpath="(.//cml:array[@dictRef='m:label'])[1]" to="." />
<transform process="move" xpath=".//cml:array[@dictRef='cc:frequency']" to="." />
<transform process="move" xpath=".//cml:array[@dictRef='cc:irintensity']" to="." />
<transform process="move" xpath=".//cml:matrix" to="." />
<transform process="delete" xpath=".//cml:module" />