vibrations¶
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
| Attribute | Value |
|---|---|
| source | Orca log |
| id | vibrations |
| name | Vibrational frequencies |
| pattern | \s*\-+\s*$\s*VIBRATIONAL\sFREQUENCIES.* |
| endPattern | \s*\-+\s*$(?!(NORMAL|VIBRATIONAL)).*$\s*\-+\s* |
| repeat | * |
| xml:base | job/vibrations.xml |
Input
-----------------------
VIBRATIONAL FREQUENCIES
-----------------------
0: 0.00 cm**-1
1: 0.00 cm**-1
2: 0.00 cm**-1
3: 0.00 cm**-1
4: 0.00 cm**-1
5: 0.00 cm**-1
6: -434.84 cm**-1 ***imaginary mode***
7: -419.45 cm**-1 ***imaginary mode***
8: -289.83 cm**-1 ***imaginary mode***
9: -272.32 cm**-1 ***imaginary mode***
10: -168.02 cm**-1 ***imaginary mode***
11: -122.97 cm**-1 ***imaginary mode***
12: -114.81 cm**-1 ***imaginary mode***
13: -110.33 cm**-1 ***imaginary mode***
14: -68.54 cm**-1 ***imaginary mode***
15: -51.59 cm**-1 ***imaginary mode***
16: -30.16 cm**-1
17: 12.43 cm**-1
18: 48.29 cm**-1
19: 56.20 cm**-1
20: 76.33 cm**-1
...
119: 3560.03 cm**-1
120: 3687.73 cm**-1
121: 3905.08 cm**-1
122: 3910.12 cm**-1
------------
NORMAL MODES
------------
These modes are the cartesian displacements weighted by the diagonal matrix
M(i,i)=1/sqrt(m[i]) where m[i] is the mass of the displaced atom
Thus, these vectors are normalized but *not* orthogonal
0 1 2 3 4 5
0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
5 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
6 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
7 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
8 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
...
120 0.158785 0.002231 -0.004623
121 -0.160155 -0.002115 0.004968
122 -0.035114 -0.000336 0.001664
Output text
<comment class="example.output" id="vibrations">
<module cmlx:templateRef="vibrations">
<array dataType="xsd:double" dictRef="cc:frequency" size="123">0.00 0.00 0.00 0.00 0.00 0.00 -434.84 -419.45 -289.83 -272.32 -168.02 -122.97 -114.81 -110.33 -68.54 -51.59 -30.16 12.43 48.29 56.20 76.33 ... 3560.03 3687.73 3905.08 3910.12</array>
<matrix cols="123" dataType="xsd:double" dictRef="cc:displacement" rows="123">0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 ... -0.000121 -0.000040 -0.000235 -0.000016 0.000051 0.000049 -0.000072 0.000062 0.000277 0.000188 0.000023 -0.000067 0.000039 0.000005 -0.000052 0.000067 0.000027 0.000108 -0.000026 -0.000007 0.000011 0.000079 -0.000014 0.000017 0.000008 -0.000181 0.000019 0.000405 -0.000100 0.001416 -0.004623 0.004968 0.001664</matrix>
</module>
</comment>
Template definition
<templateList> <template id="frequencies" pattern="\s*VIBRATIONAL\sFREQUENCIES\s*" endPattern=".*cm\*\*-1$\s*" endPattern2="~" endOffset="1"> <templateList> <template pattern="\s*[0-9].*" endPattern2="~" endOffset="1"> <record repeat="*" makeArray="true">{I,cc:index}:{F,cc:frequency}cm\*\*-1.*</record>
</template>
</templateList>
</template> <template id="normal" pattern="\s*NORMAL\sMODES\s*" endPattern=".*[0-9]$\s*" endPattern2="~" endOffset="1"> <record repeat="7" /> <templateList> <template id="section" pattern="[^\.]*" endPattern="[^\.]*" endPattern2="\s*" endPattern3="~" endOffset="0" repeat="*"> <record repeat="1" /> <record repeat="*" makeArray="false">{I,cc:index}{1_6F,cc:value}</record> <transform process="addAttribute" name="index" xpath=".//cml:array" value="$number(..//cml:scalar[@dictRef='cc:index']/text())" />
</template>
</templateList>
</template> <transform process="joinArrays" xpath=".//cml:array[@dictRef='cc:value']" key="$number(@index)" /> <transform process="createMatrix" xpath="." from=".//cml:array[@dictRef='cc:value']" dictRef="cc:displacement" /> <transform process="operateMatrix" xpath=".//cml:matrix[@dictRef='cc:displacement']" args="operator=transpose" />
</templateList>
<transform process="move" xpath=".//cml:array[@dictRef='cc:frequency']" to="." />
<transform process="move" xpath=".//cml:matrix" to="." />
<transform process="delete" xpath=".//cml:module[@cmlx:templateRef='frequencies']" />
<transform process="delete" xpath=".//cml:module[@cmlx:templateRef='normal']" />