/usr/share/doc/gausssum/html/ch06s03.html is in gausssum 3.0.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 | <?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>How to find the nature of the overlap between different groups of atoms (COOP)</title><link rel="stylesheet" type="text/css" href="style.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.78.1" /><link rel="home" href="index.html" title="GaussSum Version 3.0" /><link rel="up" href="ch06.html" title="Chapter 6. How do I extract molecular orbital information?" /><link rel="prev" href="ch06s02.html" title="How to find the % contribution of a group to each molecular orbital (PDOS)" /><link rel="next" href="ch07.html" title="Chapter 7. How do I get the UV-Vis or circular dichroism spectrum of a molecule?" /></head><body><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">How to find the nature of the overlap between different groups of atoms (COOP)</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="ch06s02.html">Prev</a> </td><th width="60%" align="center">Chapter 6. How do I extract molecular orbital information?</th><td width="20%" align="right"> <a accesskey="n" href="ch07.html">Next</a></td></tr></table><hr /></div><div class="section"><div class="titlepage"><div><div><h2 class="title" style="clear: both"><a id="idp43106656"></a>How to find the nature of the overlap between different groups of atoms (COOP)</h2></div></div></div><p>
Crystal Orbital Overlap Population (COOP) diagrams were first developed by Huckel. They are especially used in the area of extended solids. They are equivalent to a multiplication of the DOS spectrum and the overlap population (positive or negative) between two groups. In this way, the bond between two groups can be described as bonding or antibonding with respect to each of the molecular orbitals.
</p><p>
Exactly the same information as for creating a PDOS diagram is needed for creating a COOP diagram. That is, you need a log file which is the result of a single-point calculation containing the same keywords as described in "How to find the % contribution of a group to each molecular orbital". You also need a file <code class="filename">Groups.txt</code> describing the groups of interest in the molecule (see "How to find the % contribution of a group to each molecular orbital"). The rules for <code class="filename">Groups.txt</code> are not as strict in this case: no atom can be listed twice, but not every atom needs to be listed.
</p><p>
Choose COOP after picking <span class="command"><strong>Orbitals</strong></span>. The options for creating a COOP diagram are the same as for creating a DOS or PDOS diagram.
</p><p>
Click on the <span class="application">GaussSum</span> logo to calculate the COOP. Information on the overlap is written to <code class="filename">gausssum3.0/COOP_data.txt</code> and <code class="filename">gausssum3.0/COOP_spectrum.txt</code>.
</p></div><div class="navfooter"><hr /><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="ch06s02.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="ch06.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="ch07.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">How to find the % contribution of a group to each molecular orbital (PDOS) </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> Chapter 7. How do I get the UV-Vis or circular dichroism spectrum of a molecule?</td></tr></table></div></body></html>
|