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<h4></h4>
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<h2>2.2 Quantum-Mechanical Modelling</h2>
The alternative "Quantum Mechanics" project is for quantum-mechanical
models.
<p>Currently we have no QM code of our own, but we use code "borrowed" from
external programs MOPAC7 and MPQC instead. The code from MOPAC7 is included
in the package, but the MPQC code is external (at the moment, at least).
In order to use the features from MPQC program, you have to compile and
install the MQPC program (both version 1.2.5 and newer versions 2.0 are
supported) to your system, and recompile the Ghemical program with the MPQC
front-end feature enabled. This brings the working MPQC engine available,
in addition to the default MOPAC7 engine. </p>
<p>Select "Compute/Setup..." from the popup menu to check the settings for
your calculation; hamiltonian / basis set to be used and total charge of
the system. Only singlet states with even number of electrons are supported
at the moment. </p>
<p>The MOPAC7 engine runs MOPAC7 code in cartesian coordinate (XYZ) mode.
User can select one of the following hamiltonians: MNDO, MINDO/3, AM1,
PM3. When using MOPAC7 engine please note the following: </p>
<p></p>
<ol>
<li>MOPAC7 code relies heavily on use of global variables, so it is
not possible to run multiple instances of MOPAC7 at the same time in
a same program; you have to start multiple programs at different working
directories instead.</li>
<li>The MOPAC7 engine creates intermediate files like FOR005 and SHUTDOWN
to the working directory when run. In normal operation these files are
removed when not needed anymore, <b><u>but if something goes wrong you have
to manually remove these files!</u></b> </li>
<li>Due to a bug in MOPAC7, the first three atoms should not be linearly
arranged; this might affect for example carbon dioxide molecule O=C=O.
When studying cases like this, draw the molecule in a sequence 1-3-2 instead
of sequence 1-2-3 to avoid the problem. </li>
<li>The hamiltonians in MOPAC7 support (at least?) the following elements:
H, C, N, O, F, P, S, Cl, Br, I. If you try to use elements not supported
by MOPAC7, the program will stop. </li>
</ol>
<p>The MPQC engine runs the MPQC closed-shell hartree-fock code with no symmetry.
User can select any of the standard ab initio basis sets from STO-3G to
6-31G**. </p>
<p>Both QM engines can run geometry optimization, and draw ESP, MO, and MO
density plots. Also a specific energy-level diagram view is available that
shows molecular orbital indices, energies (in eV) and occupation (you
can use mouse tools Zoom and Translate XY to manipulate the diagram): </p>
<center>
<p><img src="images/enlevdiag.png" height="379" width="463"
alt="an energy-level diagram">
</p>
</center>
<p>It is possible to convert MM models to QM models and vice versa. Therefore
you are adviced to draw your molecule as a MM model, optimize it to get
a good starting structure, and then to convert it into a QM model for further
refinement and inspection. To save your QM model, you are adviced to
convert it into MM model and then save it (currently there is no file
format specified for QM models). </p>
<p>The popup menu in a "Quantum Mechanics" project currently has the following
features:<br>
</p>
<p> </p>
<p></p>
<ul>
<li>File : Open and save project files, Close the project.</li>
<li>Settings : Change the current element. </li>
<li>Render : Add/remove views/lights. Change the rendering mode and projection.
Add an energy-level diagram view. </li>
<li>Objects : Add visualization objects (planes, surfaces etc) and remove
them. </li>
<li>Compute : Select the engine and other settings, compute energy, geometry
optimization. </li>
<li>Set Current Orbital : Here you can set the orbital index for visualization. </li>
<li>Convert to MM project : Copies the contents of this project into
a new MM project, and optionally closes this project. </li>
</ul>
<p> </p>
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<h3> </h3>
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