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<hr><h1>sc::MolecularCoor Class Reference</h1>The <a class="el" href="class_sc__MolecularCoor.html">MolecularCoor</a> abstract class describes the coordinate system used to describe a molecule.
<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::MolecularCoor<p><center><img src="class_sc__MolecularCoor_inherit_graph.gif" border="0" usemap="#sc::MolecularCoor_inherit_map" alt="Inheritance graph"></center>
<map name="sc::MolecularCoor_inherit_map">
<area href="class_sc__CartMolecularCoor.html" shape="rect" coords="14,347,150,366">
<area href="class_sc__IntMolecularCoor.html" shape="rect" coords="174,347,302,366">
<area href="class_sc__SavableState.html" shape="rect" coords="109,214,210,232">
<area href="class_sc__DescribedClass.html" shape="rect" coords="102,147,217,166">
<area href="class_sc__RefCount.html" shape="rect" coords="118,80,201,99">
<area href="class_sc__Identity.html" shape="rect" coords="123,14,195,32">
<area href="class_sc__RedundMolecularCoor.html" shape="rect" coords="73,414,227,432">
<area href="class_sc__SymmMolecularCoor.html" shape="rect" coords="251,414,398,432">
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<center><font size="2">[<a href="graph_legend.html">legend</a>]</font></center>Collaboration diagram for sc::MolecularCoor:<p><center><img src="class_sc__MolecularCoor_coll_graph.gif" border="0" usemap="#sc::MolecularCoor_coll_map" alt="Collaboration graph"></center>
<map name="sc::MolecularCoor_coll_map">
<area href="class_sc__SavableState.html" shape="rect" coords="21,238,122,257">
<area href="class_sc__DescribedClass.html" shape="rect" coords="14,153,129,171">
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<center><font size="2">[<a href="graph_legend.html">legend</a>]</font></center><a href="class_sc__MolecularCoor-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::MolecularCoor::MolecularCoor"></a>
</td><td valign=bottom><b>MolecularCoor</b> (<a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__Molecule.html">Molecule</a> > &)</td></tr>
<tr><td nowrap align=right valign=top><a name="a1" doxytag="sc::MolecularCoor::MolecularCoor"></a>
</td><td valign=bottom><b>MolecularCoor</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__MolecularCoor.html#a2">MolecularCoor</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::MolecularCoor::~MolecularCoor"></a>
virtual </td><td valign=bottom><b>~MolecularCoor</b> ()</td></tr>
<tr><td nowrap align=right valign=top>void </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.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::MolecularCoor::dim_natom3"></a>
<a class="el" href="class_sc__RefSCDimension.html">RefSCDimension</a> </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a5">dim_natom3</a> ()</td></tr>
<tr><td> </td><td><font size=-1><em>Returns a smart reference to an <a class="el" href="class_sc__SCDimension.html">SCDimension</a> equal to the number of atoms in the molecule times 3.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a6" doxytag="sc::MolecularCoor::molecule"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__Molecule.html">Molecule</a>> </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a6">molecule</a> () const</td></tr>
<tr><td> </td><td><font size=-1><em>Returns the molecule.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a7" doxytag="sc::MolecularCoor::print"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a7">print</a> (std::ostream &=ExEnv::out0()) const=0</td></tr>
<tr><td> </td><td><font size=-1><em>Print the coordinate.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a8" doxytag="sc::MolecularCoor::print_simples"></a>
virtual void </td><td valign=bottom><b>print_simples</b> (std::ostream &=ExEnv::out0()) const=0</td></tr>
<tr><td nowrap align=right valign=top><a name="a9" doxytag="sc::MolecularCoor::dim"></a>
virtual <a class="el" href="class_sc__RefSCDimension.html">RefSCDimension</a> </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a9">dim</a> ()=0</td></tr>
<tr><td> </td><td><font size=-1><em>Returns a smart reference to an <a class="el" href="class_sc__SCDimension.html">SCDimension</a> equal to the number of coordinates (be they Cartesian, internal, or whatever) that are being optimized.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top>int </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a10">to_cartesian</a> (const <a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> &internal)</td></tr>
<tr><td> </td><td><font size=-1><em>Given a set of displaced internal coordinates, update the cartesian coordinates of the <a class="el" href="class_sc__Molecule.html">Molecule</a> contained herein.</em> <a href="#a10">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a11" doxytag="sc::MolecularCoor::to_cartesian"></a>
virtual int </td><td valign=bottom><b>to_cartesian</b> (const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__Molecule.html">Molecule</a> > &mol, const <a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> &internal)=0</td></tr>
<tr><td nowrap align=right valign=top>virtual int </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a12">to_internal</a> (<a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> &internal)=0</td></tr>
<tr><td> </td><td><font size=-1><em>Fill in the vector ``internal'' with the current internal coordinates.</em> <a href="#a12">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top>virtual int </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a13">to_cartesian</a> (<a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> &cartesian, <a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> &internal)=0</td></tr>
<tr><td> </td><td><font size=-1><em>Convert the internal coordinate gradients in ``internal'' to Cartesian coordinates and copy these Cartesian coordinate gradients to ``cartesian''.</em> <a href="#a13">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top>virtual int </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a14">to_internal</a> (<a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> &internal, <a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> &cartesian)=0</td></tr>
<tr><td> </td><td><font size=-1><em>Convert the Cartesian coordinate gradients in ``cartesian'' to internal coordinates and copy these internal coordinate gradients to ``internal''.</em> <a href="#a14">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top>virtual int </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a15">to_cartesian</a> (<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &cartesian, <a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &internal)=0</td></tr>
<tr><td> </td><td><font size=-1><em>Convert the internal coordinate Hessian ``internal'' to Cartesian coordinates and copy the result to ``cartesian''.</em> <a href="#a15">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top>virtual int </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a16">to_internal</a> (<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &internal, <a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &cartesian)=0</td></tr>
<tr><td> </td><td><font size=-1><em>Convert the Cartesian coordinate Hessian ``cartesian'' to internal coordinates and copy the result to ``internal''.</em> <a href="#a16">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a17" doxytag="sc::MolecularCoor::guess_hessian"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a17">guess_hessian</a> (<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &hessian)=0</td></tr>
<tr><td> </td><td><font size=-1><em>Calculate an approximate hessian and place the result in ``hessian''.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top>virtual <a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a18">inverse_hessian</a> (<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &)=0</td></tr>
<tr><td> </td><td><font size=-1><em>Given an Hessian, return the inverse of that hessian.</em> <a href="#a18">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a19" doxytag="sc::MolecularCoor::nconstrained"></a>
virtual int </td><td valign=bottom><a class="el" href="class_sc__MolecularCoor.html#a19">nconstrained</a> ()</td></tr>
<tr><td> </td><td><font size=-1><em>Returns the number of constrained coordinates.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top>virtual <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__MolecularCoor.html#a20">change_coordinates</a> ()</td></tr>
<tr><td> </td><td><font size=-1><em>When this is called, MoleculeCoor may select a new internal coordinate system and return a transform to it.</em> <a href="#a20">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a21" doxytag="sc::MolecularCoor::matrixkit"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__SCMatrixKit.html">SCMatrixKit</a>> </td><td valign=bottom><b>matrixkit</b> () const</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::MolecularCoor::molecule_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__Molecule.html">Molecule</a>> </td><td valign=bottom><b>molecule_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n1" doxytag="sc::MolecularCoor::dnatom3_"></a>
<a class="el" href="class_sc__RefSCDimension.html">RefSCDimension</a> </td><td valign=bottom><b>dnatom3_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n2" doxytag="sc::MolecularCoor::matrixkit_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__SCMatrixKit.html">SCMatrixKit</a>> </td><td valign=bottom><b>matrixkit_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n3" doxytag="sc::MolecularCoor::debug_"></a>
int </td><td valign=bottom><b>debug_</b></td></tr>
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<hr><a name="_details"></a><h2>Detailed Description</h2>
The <a class="el" href="class_sc__MolecularCoor.html">MolecularCoor</a> abstract class describes the coordinate system used to describe a molecule.
<p>
It is used to convert a molecule's cartesian coordinates to and from this coordinate system.
<p>
<hr><h2>Constructor & Destructor Documentation</h2>
<a name="a2" doxytag="sc::MolecularCoor::MolecularCoor"></a><p>
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sc::MolecularCoor::MolecularCoor (
</b></td>
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const <a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__KeyVal.html">KeyVal</a> > & )
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<p>
The <a class="el" href="class_sc__KeyVal.html">KeyVal</a> constructor.
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<dl compact>
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<dt><code>molecule</code><dd> A <a class="el" href="class_sc__Molecule.html">Molecule</a> object. There is no default.
<p>
<dt><code>debug</code><dd> An integer which, if nonzero, will cause extra output.
<p>
<dt><code>matrixkit</code><dd> A <a class="el" href="class_sc__SCMatrixKit.html">SCMatrixKit</a> object. It is usually unnecessary to give this keyword.
<p>
<dt><code>natom3</code><dd> An <a class="el" href="class_sc__SCDimension.html">SCDimension</a> object for the dimension of the vector of cartesian coordinates. It is usually unnecessary to give this keyword.
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<hr><h2>Member Function Documentation</h2>
<a name="a20" doxytag="sc::MolecularCoor::change_coordinates"></a><p>
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<a class="el" href="class_sc__Ref.html">Ref</a>< <a class="el" href="class_sc__NonlinearTransform.html">NonlinearTransform</a> > sc::MolecularCoor::change_coordinates (
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<p>
When this is called, MoleculeCoor may select a new internal coordinate system and return a transform to it.
<p>
The default action is to not change anything and return an <a class="el" href="class_sc__IdentityTransform.html">IdentityTransform</a>.
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Reimplemented in <a class="el" href="class_sc__SymmMolecularCoor.html#a8">sc::SymmMolecularCoor</a>. </td>
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<a name="a18" doxytag="sc::MolecularCoor::inverse_hessian"></a><p>
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<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> sc::MolecularCoor::inverse_hessian (
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<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> & )<code> [pure virtual]</code>
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Given an Hessian, return the inverse of that hessian.
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For singular matrices this should return the generalized inverse.
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Reimplemented in <a class="el" href="class_sc__SymmMolecularCoor.html#a7">sc::SymmMolecularCoor</a>, <a class="el" href="class_sc__RedundMolecularCoor.html#a7">sc::RedundMolecularCoor</a>, and <a class="el" href="class_sc__CartMolecularCoor.html#a15">sc::CartMolecularCoor</a>. </td>
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<a name="a4" doxytag="sc::MolecularCoor::save_data_state"></a><p>
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void sc::MolecularCoor::save_data_state (
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<a class="el" href="class_sc__StateOut.html">StateOut</a> & <em>s</em> )<code> [virtual]</code>
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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.
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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>.
<p>
Reimplemented in <a class="el" href="class_sc__IntMolecularCoor.html#a4">sc::IntMolecularCoor</a>, <a class="el" href="class_sc__SymmMolecularCoor.html#a4">sc::SymmMolecularCoor</a>, <a class="el" href="class_sc__RedundMolecularCoor.html#a4">sc::RedundMolecularCoor</a>, and <a class="el" href="class_sc__CartMolecularCoor.html#a4">sc::CartMolecularCoor</a>. </td>
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<a name="a15" doxytag="sc::MolecularCoor::to_cartesian"></a><p>
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int sc::MolecularCoor::to_cartesian (
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<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> & <em>cart</em>,
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<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> & <em>internal</em> )<code> [pure virtual]</code>
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Convert the internal coordinate Hessian ``internal'' to Cartesian coordinates and copy the result to ``cartesian''.
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Only the variable internal coordinate force constants are transformed.
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Reimplemented in <a class="el" href="class_sc__IntMolecularCoor.html#a13">sc::IntMolecularCoor</a>, and <a class="el" href="class_sc__CartMolecularCoor.html#a10">sc::CartMolecularCoor</a>. </td>
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<a name="a13" doxytag="sc::MolecularCoor::to_cartesian"></a><p>
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int sc::MolecularCoor::to_cartesian (
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<a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> & <em>cartesian</em>,
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<a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> & <em>internal</em> )<code> [pure virtual]</code>
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Convert the internal coordinate gradients in ``internal'' to Cartesian coordinates and copy these Cartesian coordinate gradients to ``cartesian''.
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Only the variable internal coordinate gradients are transformed.
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Reimplemented in <a class="el" href="class_sc__IntMolecularCoor.html#a11">sc::IntMolecularCoor</a>, and <a class="el" href="class_sc__CartMolecularCoor.html#a8">sc::CartMolecularCoor</a>. </td>
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<a name="a10" doxytag="sc::MolecularCoor::to_cartesian"></a><p>
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int sc::MolecularCoor::to_cartesian (
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const <a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> & <em>internal</em> )
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Given a set of displaced internal coordinates, update the cartesian coordinates of the <a class="el" href="class_sc__Molecule.html">Molecule</a> contained herein.
<p>
This function does not change the vector ``internal''. </td>
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<a name="a16" doxytag="sc::MolecularCoor::to_internal"></a><p>
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int sc::MolecularCoor::to_internal (
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<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> & <em>internal</em>,
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<td></td>
<td><b>
<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> & <em>cart</em> )<code> [pure virtual]</code>
</b></td>
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</td>
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<table cellspacing=5 cellpadding=0 border=0>
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<td>
</td>
<td>
<p>
Convert the Cartesian coordinate Hessian ``cartesian'' to internal coordinates and copy the result to ``internal''.
<p>
Only the variable internal coordinate force constants are calculated.
<p>
Reimplemented in <a class="el" href="class_sc__IntMolecularCoor.html#a14">sc::IntMolecularCoor</a>, and <a class="el" href="class_sc__CartMolecularCoor.html#a11">sc::CartMolecularCoor</a>. </td>
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<a name="a14" doxytag="sc::MolecularCoor::to_internal"></a><p>
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<td nowrap valign="top"><b>
int sc::MolecularCoor::to_internal (
</b></td>
<td valign="bottom"><b>
<a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> & <em>internal</em>,
</b></td>
</tr>
<tr>
<td></td>
<td><b>
<a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> & <em>cartesian</em> )<code> [pure virtual]</code>
</b></td>
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</td>
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<table cellspacing=5 cellpadding=0 border=0>
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<td>
</td>
<td>
<p>
Convert the Cartesian coordinate gradients in ``cartesian'' to internal coordinates and copy these internal coordinate gradients to ``internal''.
<p>
Only the variable internal coordinate gradients are calculated.
<p>
Reimplemented in <a class="el" href="class_sc__IntMolecularCoor.html#a12">sc::IntMolecularCoor</a>, and <a class="el" href="class_sc__CartMolecularCoor.html#a9">sc::CartMolecularCoor</a>. </td>
</tr>
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<a name="a12" doxytag="sc::MolecularCoor::to_internal"></a><p>
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<td class="md">
<table cellpadding="0" cellspacing="0" border="0">
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<td nowrap valign="top"><b>
int sc::MolecularCoor::to_internal (
</b></td>
<td valign="bottom"><b>
<a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> & <em>internal</em> )<code> [pure virtual]</code>
</b></td>
</tr>
</table>
</td>
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<table cellspacing=5 cellpadding=0 border=0>
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<td>
</td>
<td>
<p>
Fill in the vector ``internal'' with the current internal coordinates.
<p>
Note that this member will update the values of the variable internal coordinates.
<p>
Reimplemented in <a class="el" href="class_sc__IntMolecularCoor.html#a10">sc::IntMolecularCoor</a>, and <a class="el" href="class_sc__CartMolecularCoor.html#a7">sc::CartMolecularCoor</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>
<address>
<small>
Generated at Mon Oct 14 14:17:09 2002 for <a
href="http://aros.ca.sandia.gov/~cljanss/mpqc">MPQC</a>
2.1.2 using the documentation package <a
href="http://www.stack.nl/~dimitri/doxygen/index.html">Doxygen</a>
1.2.5.
</small>
</address>
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