Molecular orbital association

Example 1.


<molecule xmlns="http://www.xml-cml.org/schema/cml2/comp" id="mol1">
<atomArray>
<atom id="a1" elementType="C" xyz3="0.0003482 0.9443707 0.0000000" />
<atom id="a2" elementType="C" xyz3="-1.7820833 1.5720639 0.0000000" />
<atom id="a3" elementType="C" xyz3="0.0003482 -0.9453544 0.0000000" />
<atom id="a4" elementType="C" xyz3="0.8884300 1.5764903 -1.5436310" />
<atom id="a5" elementType="C" xyz3="0.8884300 1.5764903 1.5436310" />
<atom id="a6" elementType="C" xyz3="-1.7820833 -1.5730476 0.0000000" />
<atom id="a7" elementType="C" xyz3="0.8915640 -1.5730476 -1.5436310" />
<atom id="a8" elementType="C" xyz3="0.8915640 -1.5730476 1.5436310" />
</atomArray>
</molecule>

<atomicBasisSet xmlns="http://grids.ac.uk/eccp/ns" name="6-31G" angular="spherical" type="gaussian" elementType="C">
<basisGroup minL="0" maxL="0">
<exponents>
3047.524880
457.369518
103.948685
29.210155
9.286663
 3.163927
</exponents>
<contraction>
0.001835
0.014037
0.068843
0.232184
0.467941
0.362312
</contraction>
</basisGroup>
<basisGroup minL="0" maxL="1">
<exponents>
7.868272
1.881289
0.544249
</exponents>
<contraction>
-0.119332
-0.160854
1.143456
</contraction>
<contraction>
0.068999
0.316424
0.744308
</contraction>
</basisGroup>
<basisGroup minL="0" maxL="0">
<exponents>
0.168714
</exponents>
<contraction>
1.000000
</contraction>
</basisGroup>
<basisGroup>
<exponents>
0.168714
</exponents>
<contraction>
1.000000
</contraction>
</basisGroup>
</atomicBasisSet>

<atomicBasisSet xmlns="http://grids.ac.uk/eccp/ns" name="6-31G" angular="spherical" type="gaussian" elementType="H">
<basisGroup minL="0" maxL="0">
<exponents>
5.447178
0.824547
</exponents>
<contraction>
0.156285
0.904691
</contraction>
</basisGroup>
<basisGroup minL="1" maxL="1">
<exponents>
0.183192
</exponents>
<contraction>
1.000000
</contraction>
</basisGroup>
</atomicBasisSet>

<eccpns:associate role="eccp:molecular_orbital">
<cml:array dictRef="eccp:density_matrix" id="array1">
 0.848220   0.021731  -0.000014  -0.000116   0.000014  -0.013404
 0.000056   0.000586  -0.000056   0.522335   0.013073  -0.000003
 0.000123   0.000003  -0.005840   0.000004  -0.001584  -0.000004
-0.000052   0.002821  -0.000069   0.002782  -0.000069   0.002782
-0.000128   0.001707  -0.000136   0.001730  -0.000136   0.001730
</cml:array>
<cml:scalar dictRef="eccp:occupation">2</cml:scalar>
</eccpns:associate>

<link xmlns="http://grids.ac.uk/eccp/ns" xlink:role="http://grids.ac.uk/eccp/association/basisAssignment">
<locator xlink:label="atom1" xlink:href="#xpointer(//cml:molecule[@id='mol1']/cml:atom[@elementType='C'])"/>
<locator xlink:label="atom2" xlink:href="#xpointer(//cml:molecule[@id='mol1']/cml:atom[@elementType='H'])"/>
<locator xlink:label="basis1" xlink:href="#xpointer(//eccpns:atomicBasisSet[@elementType='C'])"/>
<locator xlink:label="basis2" xlink:href="#xpointer(//eccpns:atomicBasisSet[@elementType='H'])"/>
<arc xlink:from="atom1" xlink:to="basis1"/>
<arc xlink:from="atom2" xlink:to="basis2"/>
</link>

<link xlink:role="http://grids.ac.uk/eccp/association/molecular_orbital">
<locator xlink:href="#xpointer(//eccpns:link[@xlink:role='http://grids.ac.uk/eccp/association/basisAssignment'])"/>
<locator xlink:href="#xpointer(//eccpns:associate[@dictRef='eccp:molecular_orbital'][1])"/>
</link>

-- PhilipCouch - 10 Nov 2004

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Topic revision: r2 - 10 Nov 2004 - PhilipCouch
 
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