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<hr><h1>sc::SetIntCoor Class Reference</h1>The <a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a> class describes a set of internal coordinates.
<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::SetIntCoor<p><center><img src="class_sc__SetIntCoor_inherit_graph.gif" border="0" usemap="#sc::SetIntCoor_inherit_map" alt="Inheritance graph"></center>
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<center><font size="2">[<a href="graph_legend.html">legend</a>]</font></center>Collaboration diagram for sc::SetIntCoor:<p><center><img src="class_sc__SetIntCoor_coll_graph.gif" border="0" usemap="#sc::SetIntCoor_coll_map" alt="Collaboration graph"></center>
<map name="sc::SetIntCoor_coll_map">
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<center><font size="2">[<a href="graph_legend.html">legend</a>]</font></center><a href="class_sc__SetIntCoor-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::SetIntCoor::SetIntCoor"></a>
</td><td valign=bottom><b>SetIntCoor</b> ()</td></tr>
<tr><td nowrap align=right valign=top><a name="a1" doxytag="sc::SetIntCoor::SetIntCoor"></a>
</td><td valign=bottom><b>SetIntCoor</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__SetIntCoor.html#a2">SetIntCoor</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::SetIntCoor::~SetIntCoor"></a>
virtual </td><td valign=bottom><b>~SetIntCoor</b> ()</td></tr>
<tr><td nowrap align=right valign=top>void </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.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::SetIntCoor::add"></a>
void </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.html#a5">add</a> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__IntCoor.html">IntCoor</a> > &)</td></tr>
<tr><td> </td><td><font size=-1><em>Adds an internal coordinate to the set.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a6" doxytag="sc::SetIntCoor::add"></a>
void </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.html#a6">add</a> (const <a class="el" href="class_sc__Ref.html">Ref</a>< SetIntCoor > &)</td></tr>
<tr><td> </td><td><font size=-1><em>Adds all the elements of another set to this one.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a7" doxytag="sc::SetIntCoor::pop"></a>
void </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.html#a7">pop</a> ()</td></tr>
<tr><td> </td><td><font size=-1><em>Removes the last coordinate from this set.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a8" doxytag="sc::SetIntCoor::clear"></a>
void </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.html#a8">clear</a> ()</td></tr>
<tr><td> </td><td><font size=-1><em>Removes all coordinates from the set.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a9" doxytag="sc::SetIntCoor::n"></a>
int </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.html#a9">n</a> () const</td></tr>
<tr><td> </td><td><font size=-1><em>Returns the number of coordinates in the set.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a10" doxytag="sc::SetIntCoor::coor"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__IntCoor.html">IntCoor</a>> </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.html#a10">coor</a> (int i) const</td></tr>
<tr><td> </td><td><font size=-1><em>Returns a reference to the i'th coordinate in the set.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a11" doxytag="sc::SetIntCoor::fd_bmat"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.html#a11">fd_bmat</a> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__Molecule.html">Molecule</a> > &,<a class="el" href="class_sc__RefSCMatrix.html">RefSCMatrix</a> &)</td></tr>
<tr><td> </td><td><font size=-1><em><a class="el" href="class_sc__Compute.html">Compute</a> the B matrix by finite displacements.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a12" doxytag="sc::SetIntCoor::bmat"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.html#a12">bmat</a> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__Molecule.html">Molecule</a> > &, <a class="el" href="class_sc__RefSCMatrix.html">RefSCMatrix</a> &)</td></tr>
<tr><td> </td><td><font size=-1><em><a class="el" href="class_sc__Compute.html">Compute</a> the B matrix the old-fashioned way.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top>virtual void </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.html#a13">guess_hessian</a> (<a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__Molecule.html">Molecule</a> > &,<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &)</td></tr>
<tr><td> </td><td><font size=-1><em>Create an approximate Hessian for this set of coordinates.</em> <a href="#a13">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a14" doxytag="sc::SetIntCoor::print_details"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.html#a14">print_details</a> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__Molecule.html">Molecule</a> > &,std::ostream &=ExEnv::out0()) const</td></tr>
<tr><td> </td><td><font size=-1><em>Print the coordinates in the set.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a15" doxytag="sc::SetIntCoor::update_values"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.html#a15">update_values</a> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__Molecule.html">Molecule</a> > &)</td></tr>
<tr><td> </td><td><font size=-1><em>Recalculate the values of the internal coordinates in the set.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a16" doxytag="sc::SetIntCoor::values_to_vector"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__SetIntCoor.html#a16">values_to_vector</a> (const <a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> &)</td></tr>
<tr><td> </td><td><font size=-1><em>Copy the values of the internal coordinates to a vector.</em></font><br><br></td></tr>
</table>
<hr><a name="_details"></a><h2>Detailed Description</h2>
The <a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a> class describes a set of internal coordinates.
<p>
It can automatically generate these coordinates using a integral coordinate generator object (see the <a class="el" href="class_sc__IntCoorGen.html">IntCoorGen</a> class) or the internal coordinates can be explicity given.
<p>
The following is a sample <a class="el" href="class_sc__ParsedKeyVal.html">ParsedKeyVal</a> input for a <a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a> object. <pre>
setintcoor<<a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a>>: [
<<a class="el" href="class_sc__SumIntCoor.html">SumIntCoor</a>>: (
coor: [
<<a class="el" href="class_sc__StreSimpleCo.html">StreSimpleCo</a>>:( atoms = [ 1 2 ] )
<<a class="el" href="class_sc__StreSimpleCo.html">StreSimpleCo</a>>:( atoms = [ 2 3 ] )
]
coef = [ 1.0 1.0 ]
)
<<a class="el" href="class_sc__BendSimpleCo.html">BendSimpleCo</a>>:( atoms = [ 1 2 3 ] )
]
</pre>
<p>
<hr><h2>Constructor & Destructor Documentation</h2>
<a name="a2" doxytag="sc::SetIntCoor::SetIntCoor"></a><p>
<table width="100%" cellpadding="2" cellspacing="0" border="0">
<tr>
<td class="md">
<table cellpadding="0" cellspacing="0" border="0">
<tr>
<td nowrap valign="top"><b>
sc::SetIntCoor::SetIntCoor (
</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>
</tr>
</table>
</td>
</tr>
</table>
<table cellspacing=5 cellpadding=0 border=0>
<tr>
<td>
</td>
<td>
<p>
The <a class="el" href="class_sc__KeyVal.html">KeyVal</a> constructor.
<p>
<dl compact>
<p>
<dt><code>generator</code><dd> A <a class="el" href="class_sc__IntCoorGen.html">IntCoorGen</a> object that will be used to generate the internal coordinates.
<p>
<dt><code>i</code><dd> A sequence of integer keywords, all <img align="top" src="form-7.gif">
for <img align="top" src="form-8.gif">
, can be assigned to <a class="el" href="class_sc__IntCoor.html">IntCoor</a> objects.
<p>
</dl>
</td>
</tr>
</table>
<hr><h2>Member Function Documentation</h2>
<a name="a13" doxytag="sc::SetIntCoor::guess_hessian"></a><p>
<table width="100%" cellpadding="2" cellspacing="0" border="0">
<tr>
<td class="md">
<table cellpadding="0" cellspacing="0" border="0">
<tr>
<td nowrap valign="top"><b>
void sc::SetIntCoor::guess_hessian (
</b></td>
<td valign="bottom"><b>
<a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__Molecule.html">Molecule</a> > &,
</b></td>
</tr>
<tr>
<td></td>
<td><b>
<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> & )<code> [virtual]</code>
</b></td>
</tr>
</table>
</td>
</tr>
</table>
<table cellspacing=5 cellpadding=0 border=0>
<tr>
<td>
</td>
<td>
<p>
Create an approximate Hessian for this set of coordinates.
<p>
This Hessian is a symmetric matrix whose i'th diagonal is the force constant for the i'th coordinate in the set. </td>
</tr>
</table>
<a name="a4" doxytag="sc::SetIntCoor::save_data_state"></a><p>
<table width="100%" cellpadding="2" cellspacing="0" border="0">
<tr>
<td class="md">
<table cellpadding="0" cellspacing="0" border="0">
<tr>
<td nowrap valign="top"><b>
void sc::SetIntCoor::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>
</tr>
</table>
</td>
</tr>
</table>
<table cellspacing=5 cellpadding=0 border=0>
<tr>
<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__SavableState.html#a5">sc::SavableState</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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