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<hr><h1>sc::SymmMolecularCoor Class Reference</h1>The <a class="el" href="class_sc__SymmMolecularCoor.html">SymmMolecularCoor</a> class derives from <a class="el" href="class_sc__IntMolecularCoor.html">IntMolecularCoor</a>.
<a href="#_details">More...</a>
<p>
<code>#include <<a class="el" href="coor_h-source.html">coor.h</a>></code>
<p>
Inheritance diagram for sc::SymmMolecularCoor<p><center><img src="class_sc__SymmMolecularCoor_inherit_graph.gif" border="0" usemap="#sc::SymmMolecularCoor_inherit_map" alt="Inheritance graph"></center>
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<area href="class_sc__MolecularCoor.html" shape="rect" coords="31,280,143,299">
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<center><font size="2">[<a href="graph_legend.html">legend</a>]</font></center>Collaboration diagram for sc::SymmMolecularCoor:<p><center><img src="class_sc__SymmMolecularCoor_coll_graph.gif" border="0" usemap="#sc::SymmMolecularCoor_coll_map" alt="Collaboration graph"></center>
<map name="sc::SymmMolecularCoor_coll_map">
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<area href="class_sc__MolecularCoor.html" shape="rect" coords="226,330,338,349">
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<center><font size="2">[<a href="graph_legend.html">legend</a>]</font></center><a href="class_sc__SymmMolecularCoor-members.html">List of all members.</a><table border=0 cellpadding=0 cellspacing=0>
<tr><td colspan=2><br><h2>Public Methods</h2></td></tr>
<tr><td nowrap align=right valign=top><a name="a0" doxytag="sc::SymmMolecularCoor::SymmMolecularCoor"></a>
</td><td valign=bottom><b>SymmMolecularCoor</b> (<a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__Molecule.html">Molecule</a> > &mol)</td></tr>
<tr><td nowrap align=right valign=top><a name="a1" doxytag="sc::SymmMolecularCoor::SymmMolecularCoor"></a>
</td><td valign=bottom><b>SymmMolecularCoor</b> (<a class="el" href="class_sc__StateIn.html">StateIn</a> &)</td></tr>
<tr><td nowrap align=right valign=top> </td><td valign=bottom><a class="el" href="class_sc__SymmMolecularCoor.html#a2">SymmMolecularCoor</a> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__KeyVal.html">KeyVal</a> > &)</td></tr>
<tr><td> </td><td><font size=-1><em>The <a class="el" href="class_sc__KeyVal.html">KeyVal</a> constructor.</em> <a href="#a2">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a3" doxytag="sc::SymmMolecularCoor::~SymmMolecularCoor"></a>
virtual </td><td valign=bottom><b>~SymmMolecularCoor</b> ()</td></tr>
<tr><td nowrap align=right valign=top>void </td><td valign=bottom><a class="el" href="class_sc__SymmMolecularCoor.html#a4">save_data_state</a> (<a class="el" href="class_sc__StateOut.html">StateOut</a> &)</td></tr>
<tr><td> </td><td><font size=-1><em>Save the base classes (with save_data_state) and the members in the same order that the <a class="el" href="class_sc__StateIn.html">StateIn</a> CTOR initializes them.</em> <a href="#a4">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a5" doxytag="sc::SymmMolecularCoor::form_coordinates"></a>
void </td><td valign=bottom><a class="el" href="class_sc__SymmMolecularCoor.html#a5">form_coordinates</a> (int keep_variable=0)</td></tr>
<tr><td> </td><td><font size=-1><em>Actually form the variable and constant internal coordinates from simple internal coordinates.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a6" doxytag="sc::SymmMolecularCoor::guess_hessian"></a>
void </td><td valign=bottom><a class="el" href="class_sc__SymmMolecularCoor.html#a6">guess_hessian</a> (<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &hessian)</td></tr>
<tr><td> </td><td><font size=-1><em>Form the approximate hessian.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a7" doxytag="sc::SymmMolecularCoor::inverse_hessian"></a>
<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> </td><td valign=bottom><a class="el" href="class_sc__SymmMolecularCoor.html#a7">inverse_hessian</a> (<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &)</td></tr>
<tr><td> </td><td><font size=-1><em>Invert the hessian.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a8" doxytag="sc::SymmMolecularCoor::change_coordinates"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__NonlinearTransform.html">NonlinearTransform</a>> </td><td valign=bottom><a class="el" href="class_sc__SymmMolecularCoor.html#a8">change_coordinates</a> ()</td></tr>
<tr><td> </td><td><font size=-1><em>This overrides MoleculeCoor's change_coordinates and might transform to a new set of coordinates.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a9" doxytag="sc::SymmMolecularCoor::print"></a>
void </td><td valign=bottom><a class="el" href="class_sc__SymmMolecularCoor.html#a9">print</a> (std::ostream &=ExEnv::out0()) const</td></tr>
<tr><td> </td><td><font size=-1><em>Print the coordinate.</em></font><br><br></td></tr>
<tr><td colspan=2><br><h2>Protected Methods</h2></td></tr>
<tr><td nowrap align=right valign=top>void </td><td valign=bottom><a class="el" href="class_sc__SymmMolecularCoor.html#b0">init</a> ()</td></tr>
<tr><td> </td><td><font size=-1><em>This is called by the constructors of classes derived from <a class="el" href="class_sc__IntMolecularCoor.html">IntMolecularCoor</a>.</em> <a href="#b0">More...</a><em></em></font><br><br></td></tr>
<tr><td colspan=2><br><h2>Protected Attributes</h2></td></tr>
<tr><td nowrap align=right valign=top><a name="n0" doxytag="sc::SymmMolecularCoor::change_coordinates_"></a>
int </td><td valign=bottom><b>change_coordinates_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n1" doxytag="sc::SymmMolecularCoor::transform_hessian_"></a>
int </td><td valign=bottom><b>transform_hessian_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n2" doxytag="sc::SymmMolecularCoor::max_kappa2_"></a>
double </td><td valign=bottom><b>max_kappa2_</b></td></tr>
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<hr><a name="_details"></a><h2>Detailed Description</h2>
The <a class="el" href="class_sc__SymmMolecularCoor.html">SymmMolecularCoor</a> class derives from <a class="el" href="class_sc__IntMolecularCoor.html">IntMolecularCoor</a>.
<p>
It provides a unique set of totally symmetric internal coordinates. Giving an <a class="el" href="class_sc__MolecularEnergy.html">MolecularEnergy</a> object a coor is usually the best way to optimize a molecular structure. However, for some classes of molecules <a class="el" href="class_sc__SymmMolecularCoor.html">SymmMolecularCoor</a> doesn't work very well. For example, enediyne can cause problems. In these cases, cartesian coordinates (obtained by not giving the <a class="el" href="class_sc__MolecularEnergy.html">MolecularEnergy</a> object the coor keyword) might be better or you can manually specify the coordinates that the <a class="el" href="class_sc__SymmMolecularCoor.html">SymmMolecularCoor</a> object uses with the variable keyword (see the <a class="el" href="class_sc__IntMolecularCoor.html">IntMolecularCoor</a> class description).
<p>
<hr><h2>Constructor & Destructor Documentation</h2>
<a name="a2" doxytag="sc::SymmMolecularCoor::SymmMolecularCoor"></a><p>
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sc::SymmMolecularCoor::SymmMolecularCoor (
</b></td>
<td valign="bottom"><b>
const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__KeyVal.html">KeyVal</a> > & )
</b></td>
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<p>
The <a class="el" href="class_sc__KeyVal.html">KeyVal</a> constructor.
<p>
<dl compact>
<p>
<dt><code>change_coordinates</code><dd> If true, the quality of the internal coordinates will be checked periodically and if they are beginning to become linearly dependent a new set of internal coordinates will be computed. The default is false.
<p>
<dt><code>max_kappa2</code><dd> A measure of the quality of the internal coordinates. Values of the 2-norm condition, <img align="top" src="form-14.gif">
, larger than max_kappa2 are considered linearly dependent. The default is 10.0.
<p>
<dt><code>transform_hessian</code><dd> If true, the hessian will be transformed every time the internal coordinates are formed. The default is true.
<p>
</dl>
</td>
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<hr><h2>Member Function Documentation</h2>
<a name="b0" doxytag="sc::SymmMolecularCoor::init"></a><p>
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void sc::SymmMolecularCoor::init (
</b></td>
<td valign="bottom"><b>
)<code> [protected, virtual]</code>
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<p>
This is called by the constructors of classes derived from <a class="el" href="class_sc__IntMolecularCoor.html">IntMolecularCoor</a>.
<p>
It initialized the lists of simple internal coordinates, and then calls the <a class="el" href="class_sc__SymmMolecularCoor.html#a5">form_coordinates</a>() member.
<p>
Reimplemented from <a class="el" href="class_sc__IntMolecularCoor.html#b1">sc::IntMolecularCoor</a>. </td>
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<a name="a4" doxytag="sc::SymmMolecularCoor::save_data_state"></a><p>
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void sc::SymmMolecularCoor::save_data_state (
</b></td>
<td valign="bottom"><b>
<a class="el" href="class_sc__StateOut.html">StateOut</a> & <em>s</em> )<code> [virtual]</code>
</b></td>
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<td>
</td>
<td>
<p>
Save the base classes (with save_data_state) and the members in the same order that the <a class="el" href="class_sc__StateIn.html">StateIn</a> CTOR initializes them.
<p>
This must be implemented by the derived class if the class has data.
<p>
Reimplemented from <a class="el" href="class_sc__IntMolecularCoor.html#a4">sc::IntMolecularCoor</a>. </td>
</tr>
</table>
<hr>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="coor_h-source.html">coor.h</a></ul>
<hr>
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