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<div class="navpath"><b>sc</b>::<a class="el" href="classsc_1_1SymmMolecularCoor.html">SymmMolecularCoor</a>
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<h1>sc::SymmMolecularCoor Class Reference</h1><!-- doxytag: class="sc::SymmMolecularCoor" --><!-- doxytag: inherits="sc::IntMolecularCoor" -->The <a class="el" href="classsc_1_1SymmMolecularCoor.html" title="The SymmMolecularCoor class derives from IntMolecularCoor.">SymmMolecularCoor</a> class derives from <a class="el" href="classsc_1_1IntMolecularCoor.html" title="The IntMolecularCoor abstract class describes a molecule's coordinates in terms...">IntMolecularCoor</a>.
<a href="#_details">More...</a>
<p>
<code>#include <<a class="el" href="coor_8h_source.html">coor.h</a>></code>
<p>
<div class="dynheader">
Inheritance diagram for sc::SymmMolecularCoor:</div>
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<p><center><img src="classsc_1_1SymmMolecularCoor.png" usemap="#sc::SymmMolecularCoor_map" border="0" alt=""></center>
<map name="sc::SymmMolecularCoor_map">
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<area href="classsc_1_1SavableState.html" alt="sc::SavableState" shape="rect" coords="0,168,149,192">
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<p>
<a href="classsc_1_1SymmMolecularCoor-members.html">List of all members.</a><table border="0" cellpadding="0" cellspacing="0">
<tr><td></td></tr>
<tr><td colspan="2"><br><h2>Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="e26a0277e3e815e7d024fb5b847d22b3"></a><!-- doxytag: member="sc::SymmMolecularCoor::SymmMolecularCoor" ref="e26a0277e3e815e7d024fb5b847d22b3" args="(Ref< Molecule > &mol)" -->
</td><td class="memItemRight" valign="bottom"><b>SymmMolecularCoor</b> (<a class="el" href="classsc_1_1Ref.html">Ref</a>< <a class="el" href="classsc_1_1Molecule.html">Molecule</a> > &mol)</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="2b98340ebd8f6623117b0dcd00e46bc5"></a><!-- doxytag: member="sc::SymmMolecularCoor::SymmMolecularCoor" ref="2b98340ebd8f6623117b0dcd00e46bc5" args="(StateIn &)" -->
</td><td class="memItemRight" valign="bottom"><b>SymmMolecularCoor</b> (<a class="el" href="classsc_1_1StateIn.html">StateIn</a> &)</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SymmMolecularCoor.html#86c25018a4c4e2484eee7ff116516dcf">SymmMolecularCoor</a> (const <a class="el" href="classsc_1_1Ref.html">Ref</a>< <a class="el" href="classsc_1_1KeyVal.html">KeyVal</a> > &)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">The <a class="el" href="classsc_1_1KeyVal.html" title="The KeyVal class is designed to simplify the process of allowing a user to specify...">KeyVal</a> constructor. <a href="#86c25018a4c4e2484eee7ff116516dcf"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SymmMolecularCoor.html#745a15439fab967060259ed08a8fdf91">save_data_state</a> (<a class="el" href="classsc_1_1StateOut.html">StateOut</a> &)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Save the base classes (with save_data_state) and the members in the same order that the <a class="el" href="classsc_1_1StateIn.html" title="Restores objects that derive from SavableState.">StateIn</a> CTOR initializes them. <a href="#745a15439fab967060259ed08a8fdf91"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SymmMolecularCoor.html#1ea9e5291c26430b81a10ebf0b57692b">form_coordinates</a> (int keep_variable=0)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Actually form the variable and constant internal coordinates from simple internal coordinates. <a href="#1ea9e5291c26430b81a10ebf0b57692b"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="8cae52410dfbe5938c5140d19cab3f9e"></a><!-- doxytag: member="sc::SymmMolecularCoor::guess_hessian" ref="8cae52410dfbe5938c5140d19cab3f9e" args="(RefSymmSCMatrix &hessian)" -->
void </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SymmMolecularCoor.html#8cae52410dfbe5938c5140d19cab3f9e">guess_hessian</a> (<a class="el" href="classsc_1_1RefSymmSCMatrix.html">RefSymmSCMatrix</a> &hessian)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Form the approximate hessian. <br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="a4ec750e3f4f0639e9258c17069aa617"></a><!-- doxytag: member="sc::SymmMolecularCoor::inverse_hessian" ref="a4ec750e3f4f0639e9258c17069aa617" args="(RefSymmSCMatrix &)" -->
<a class="el" href="classsc_1_1RefSymmSCMatrix.html">RefSymmSCMatrix</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SymmMolecularCoor.html#a4ec750e3f4f0639e9258c17069aa617">inverse_hessian</a> (<a class="el" href="classsc_1_1RefSymmSCMatrix.html">RefSymmSCMatrix</a> &)</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Invert the hessian. <br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="el" href="classsc_1_1Ref.html">Ref</a>< <a class="el" href="classsc_1_1NonlinearTransform.html">NonlinearTransform</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SymmMolecularCoor.html#725dbd9d25fe74220e1c7c62fa5c6ed9">change_coordinates</a> ()</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">This overrides MoleculeCoor's change_coordinates and might transform to a new set of coordinates. <a href="#725dbd9d25fe74220e1c7c62fa5c6ed9"></a><br></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="2027da3ddc7dff5ce186cd02de7e18ed"></a><!-- doxytag: member="sc::SymmMolecularCoor::print" ref="2027da3ddc7dff5ce186cd02de7e18ed" args="(std::ostream &=ExEnv::out0()) const " -->
void </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SymmMolecularCoor.html#2027da3ddc7dff5ce186cd02de7e18ed">print</a> (std::ostream &=ExEnv::out0()) const </td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">Print the coordinate. <br></td></tr>
<tr><td colspan="2"><br><h2>Protected Member Functions</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classsc_1_1SymmMolecularCoor.html#180608a2f1f2ffc8b94a9de8c8fc8c9c">init</a> ()</td></tr>
<tr><td class="mdescLeft"> </td><td class="mdescRight">This is called by the constructors of classes derived from <a class="el" href="classsc_1_1IntMolecularCoor.html" title="The IntMolecularCoor abstract class describes a molecule's coordinates in terms...">IntMolecularCoor</a>. <a href="#180608a2f1f2ffc8b94a9de8c8fc8c9c"></a><br></td></tr>
<tr><td colspan="2"><br><h2>Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="dc1f7e6056e08b4ddb628fdf74482295"></a><!-- doxytag: member="sc::SymmMolecularCoor::change_coordinates_" ref="dc1f7e6056e08b4ddb628fdf74482295" args="" -->
int </td><td class="memItemRight" valign="bottom"><b>change_coordinates_</b></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="4b5e4dfe5c2548694495ac42e002d125"></a><!-- doxytag: member="sc::SymmMolecularCoor::transform_hessian_" ref="4b5e4dfe5c2548694495ac42e002d125" args="" -->
int </td><td class="memItemRight" valign="bottom"><b>transform_hessian_</b></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="anchor" name="582a5c711810670ccee8ec55636de910"></a><!-- doxytag: member="sc::SymmMolecularCoor::max_kappa2_" ref="582a5c711810670ccee8ec55636de910" args="" -->
double </td><td class="memItemRight" valign="bottom"><b>max_kappa2_</b></td></tr>
</table>
<hr><a name="_details"></a><h2>Detailed Description</h2>
The <a class="el" href="classsc_1_1SymmMolecularCoor.html" title="The SymmMolecularCoor class derives from IntMolecularCoor.">SymmMolecularCoor</a> class derives from <a class="el" href="classsc_1_1IntMolecularCoor.html" title="The IntMolecularCoor abstract class describes a molecule's coordinates in terms...">IntMolecularCoor</a>.
<p>
It provides a unique set of totally symmetric internal coordinates. Giving an <a class="el" href="classsc_1_1MolecularEnergy.html" title="The MolecularEnergy abstract class inherits from the Function class.">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="classsc_1_1SymmMolecularCoor.html" title="The SymmMolecularCoor class derives from IntMolecularCoor.">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="classsc_1_1MolecularEnergy.html" title="The MolecularEnergy abstract class inherits from the Function class.">MolecularEnergy</a> object the coor keyword) might be better or you can manually specify the coordinates that the <a class="el" href="classsc_1_1SymmMolecularCoor.html" title="The SymmMolecularCoor class derives from IntMolecularCoor.">SymmMolecularCoor</a> object uses with the variable keyword (see the <a class="el" href="classsc_1_1IntMolecularCoor.html" title="The IntMolecularCoor abstract class describes a molecule's coordinates in terms...">IntMolecularCoor</a> class description). <hr><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" name="86c25018a4c4e2484eee7ff116516dcf"></a><!-- doxytag: member="sc::SymmMolecularCoor::SymmMolecularCoor" ref="86c25018a4c4e2484eee7ff116516dcf" args="(const Ref< KeyVal > &)" -->
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<td class="memname">sc::SymmMolecularCoor::SymmMolecularCoor </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classsc_1_1Ref.html">Ref</a>< <a class="el" href="classsc_1_1KeyVal.html">KeyVal</a> > & </td>
<td class="paramname"> </td>
<td> ) </td>
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<p>
The <a class="el" href="classsc_1_1KeyVal.html" title="The KeyVal class is designed to simplify the process of allowing a user to specify...">KeyVal</a> constructor.
<p>
<dl>
<dt><code>change_coordinates</code></dt>
<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>
</dd>
<dt><code>max_kappa2</code></dt>
<dd>A measure of the quality of the internal coordinates. Values of the 2-norm condition, <img class="formulaInl" alt="$\kappa_2$" src="form_8.png">, larger than max_kappa2 are considered linearly dependent. The default is 10.0.<p>
</dd>
<dt><code>transform_hessian</code></dt>
<dd>If true, the hessian will be transformed every time the internal coordinates are formed. The default is true.<p>
</dd>
</dl>
</div>
</div><p>
<hr><h2>Member Function Documentation</h2>
<a class="anchor" name="725dbd9d25fe74220e1c7c62fa5c6ed9"></a><!-- doxytag: member="sc::SymmMolecularCoor::change_coordinates" ref="725dbd9d25fe74220e1c7c62fa5c6ed9" args="()" -->
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<td class="memname"><a class="el" href="classsc_1_1Ref.html">Ref</a><<a class="el" href="classsc_1_1NonlinearTransform.html">NonlinearTransform</a>> sc::SymmMolecularCoor::change_coordinates </td>
<td>(</td>
<td class="paramname"> </td>
<td> ) </td>
<td><code> [virtual]</code></td>
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<p>
This overrides MoleculeCoor's change_coordinates and might transform to a new set of coordinates.
<p>
<p>Reimplemented from <a class="el" href="classsc_1_1MolecularCoor.html#873e195bb693f0a273c747faab9efac8">sc::MolecularCoor</a>.</p>
</div>
</div><p>
<a class="anchor" name="1ea9e5291c26430b81a10ebf0b57692b"></a><!-- doxytag: member="sc::SymmMolecularCoor::form_coordinates" ref="1ea9e5291c26430b81a10ebf0b57692b" args="(int keep_variable=0)" -->
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<td class="memname">void sc::SymmMolecularCoor::form_coordinates </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"> <em>keep_variable</em> = <code>0</code> </td>
<td> ) </td>
<td><code> [virtual]</code></td>
</tr>
</table>
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<div class="memdoc">
<p>
Actually form the variable and constant internal coordinates from simple internal coordinates.
<p>
<p>Implements <a class="el" href="classsc_1_1IntMolecularCoor.html#a91a3c2ee20174f9926ab1b630ff3659">sc::IntMolecularCoor</a>.</p>
</div>
</div><p>
<a class="anchor" name="180608a2f1f2ffc8b94a9de8c8fc8c9c"></a><!-- doxytag: member="sc::SymmMolecularCoor::init" ref="180608a2f1f2ffc8b94a9de8c8fc8c9c" args="()" -->
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<td class="memname">void sc::SymmMolecularCoor::init </td>
<td>(</td>
<td class="paramname"> </td>
<td> ) </td>
<td><code> [protected, virtual]</code></td>
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<p>
This is called by the constructors of classes derived from <a class="el" href="classsc_1_1IntMolecularCoor.html" title="The IntMolecularCoor abstract class describes a molecule's coordinates in terms...">IntMolecularCoor</a>.
<p>
It initialized the lists of simple internal coordinates, and then calls the <a class="el" href="classsc_1_1SymmMolecularCoor.html#1ea9e5291c26430b81a10ebf0b57692b" title="Actually form the variable and constant internal coordinates from simple internal...">form_coordinates()</a> member.
<p>Reimplemented from <a class="el" href="classsc_1_1IntMolecularCoor.html#c25a7d52a9947c349a59dbbc6f0db475">sc::IntMolecularCoor</a>.</p>
</div>
</div><p>
<a class="anchor" name="745a15439fab967060259ed08a8fdf91"></a><!-- doxytag: member="sc::SymmMolecularCoor::save_data_state" ref="745a15439fab967060259ed08a8fdf91" args="(StateOut &)" -->
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<td class="memname">void sc::SymmMolecularCoor::save_data_state </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classsc_1_1StateOut.html">StateOut</a> & </td>
<td class="paramname"> </td>
<td> ) </td>
<td><code> [virtual]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>
Save the base classes (with save_data_state) and the members in the same order that the <a class="el" href="classsc_1_1StateIn.html" title="Restores objects that derive from SavableState.">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="classsc_1_1IntMolecularCoor.html#ba8a0db96971237aad839520e8efeb0b">sc::IntMolecularCoor</a>.</p>
</div>
</div><p>
<hr>The documentation for this class was generated from the following file:<ul>
<li><a class="el" href="coor_8h_source.html">coor.h</a></ul>
</div>
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