<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><meta name="robots" content="noindex">
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>sc::IntMolecularCoor class Reference</title>
<link href="doxygen.css" rel="stylesheet" type="text/css">
</head><body bgcolor="#ffffff">
<!-- Generated by Doxygen 1.2.5 on Mon Oct 14 14:17:03 2002 -->
<center>
<a class="qindex" href="index.html">Main Page</a> <a class="qindex" href="hierarchy.html">Class Hierarchy</a> <a class="qindex" href="annotated.html">Compound List</a> <a class="qindex" href="files.html">File List</a> <a class="qindex" href="functions.html">Compound Members</a> <a class="qindex" href="pages.html">Related Pages</a> </center>
<hr><h1>sc::IntMolecularCoor Class Reference</h1>The <a class="el" href="class_sc__IntMolecularCoor.html">IntMolecularCoor</a> abstract class describes a molecule's coordinates in terms 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::IntMolecularCoor<p><center><img src="class_sc__IntMolecularCoor_inherit_graph.gif" border="0" usemap="#sc::IntMolecularCoor_inherit_map" alt="Inheritance graph"></center>
<map name="sc::IntMolecularCoor_inherit_map">
<area href="class_sc__RedundMolecularCoor.html" shape="rect" coords="14,414,169,432">
<area href="class_sc__SymmMolecularCoor.html" shape="rect" coords="193,414,339,432">
<area href="class_sc__MolecularCoor.html" shape="rect" coords="122,280,234,299">
<area href="class_sc__SavableState.html" shape="rect" coords="127,214,229,232">
<area href="class_sc__DescribedClass.html" shape="rect" coords="121,147,235,166">
<area href="class_sc__RefCount.html" shape="rect" coords="137,80,219,99">
<area href="class_sc__Identity.html" shape="rect" coords="142,14,214,32">
</map>
<center><font size="2">[<a href="graph_legend.html">legend</a>]</font></center>Collaboration diagram for sc::IntMolecularCoor:<p><center><img src="class_sc__IntMolecularCoor_coll_graph.gif" border="0" usemap="#sc::IntMolecularCoor_coll_map" alt="Collaboration graph"></center>
<map name="sc::IntMolecularCoor_coll_map">
<area href="class_sc__MolecularCoor.html" shape="rect" coords="226,329,338,348">
<area href="class_sc__SavableState.html" shape="rect" coords="21,237,122,256">
<area href="class_sc__DescribedClass.html" shape="rect" coords="14,152,129,171">
<area href="class_sc__RefCount.html" shape="rect" coords="30,83,113,101">
<area href="class_sc__Identity.html" shape="rect" coords="35,13,107,32">
<area href="class_sc__Ref.html" shape="rect" coords="114,195,237,213">
<area href="class_sc__RefBase.html" shape="rect" coords="487,83,565,101">
<area href="class_sc__Ref.html" shape="rect" coords="266,195,407,213">
<area href="class_sc__Ref.html" shape="rect" coords="381,152,527,171">
<area href="class_sc__Ref.html" shape="rect" coords="511,329,642,348">
<area href="class_sc__Ref.html" shape="rect" coords="613,280,749,299">
<area href="class_sc__Ref.html" shape="rect" coords="777,280,891,299">
<area href="class_sc__RefSCDimension.html" shape="rect" coords="385,237,510,256">
</map>
<center><font size="2">[<a href="graph_legend.html">legend</a>]</font></center><a href="class_sc__IntMolecularCoor-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::IntMolecularCoor::IntMolecularCoor"></a>
</td><td valign=bottom><b>IntMolecularCoor</b> (<a class="el" href="class_sc__StateIn.html">StateIn</a> &)</td></tr>
<tr><td nowrap align=right valign=top><a name="a1" doxytag="sc::IntMolecularCoor::IntMolecularCoor"></a>
</td><td valign=bottom><b>IntMolecularCoor</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> </td><td valign=bottom><a class="el" href="class_sc__IntMolecularCoor.html#a2">IntMolecularCoor</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::IntMolecularCoor::~IntMolecularCoor"></a>
virtual </td><td valign=bottom><b>~IntMolecularCoor</b> ()</td></tr>
<tr><td nowrap align=right valign=top>void </td><td valign=bottom><a class="el" href="class_sc__IntMolecularCoor.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::IntMolecularCoor::form_coordinates"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__IntMolecularCoor.html#a5">form_coordinates</a> (int keep_variable=0)=0</td></tr>
<tr><td> </td><td><font size=-1><em>Actually form the variable and constant internal coordinates from the simple internal coordinates.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a6" doxytag="sc::IntMolecularCoor::all_to_cartesian"></a>
virtual int </td><td valign=bottom><a class="el" href="class_sc__IntMolecularCoor.html#a6">all_to_cartesian</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__RefSCVector.html">RefSCVector</a> &internal)</td></tr>
<tr><td> </td><td><font size=-1><em>Like to_cartesians(), except all internal coordinates are considered, not just the variable ones.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a7" doxytag="sc::IntMolecularCoor::all_to_internal"></a>
virtual int </td><td valign=bottom><a class="el" href="class_sc__IntMolecularCoor.html#a7">all_to_internal</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__RefSCVector.html">RefSCVector</a> &internal)</td></tr>
<tr><td> </td><td><font size=-1><em>Like <a class="el" href="class_sc__IntMolecularCoor.html#a10">to_internal</a>(), except all internal coordinates are considered, not just the variable ones.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a8" doxytag="sc::IntMolecularCoor::dim"></a>
virtual <a class="el" href="class_sc__RefSCDimension.html">RefSCDimension</a> </td><td valign=bottom><a class="el" href="class_sc__IntMolecularCoor.html#a8">dim</a> ()</td></tr>
<tr><td> </td><td><font size=-1><em>These implement the virtual functions inherited from <a class="el" href="class_sc__MolecularCoor.html">MolecularCoor</a>.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a9" doxytag="sc::IntMolecularCoor::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> > &,const <a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> &internal)</td></tr>
<tr><td nowrap align=right valign=top>virtual int </td><td valign=bottom><a class="el" href="class_sc__IntMolecularCoor.html#a10">to_internal</a> (<a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> &internal)</td></tr>
<tr><td> </td><td><font size=-1><em>Fill in the vector ``internal'' with the current internal coordinates.</em> <a href="#a10">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__IntMolecularCoor.html#a11">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)</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="#a11">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__IntMolecularCoor.html#a12">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)</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="#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__IntMolecularCoor.html#a13">to_cartesian</a> (<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &cart, <a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &internal)</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="#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__IntMolecularCoor.html#a14">to_internal</a> (<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &internal, <a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> &cart)</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="#a14">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="a15" doxytag="sc::IntMolecularCoor::print"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__IntMolecularCoor.html#a15">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 nowrap align=right valign=top><a name="a16" doxytag="sc::IntMolecularCoor::print_simples"></a>
virtual void </td><td valign=bottom><b>print_simples</b> (std::ostream &=ExEnv::out0()) const</td></tr>
<tr><td nowrap align=right valign=top><a name="a17" doxytag="sc::IntMolecularCoor::print_variable"></a>
virtual void </td><td valign=bottom><b>print_variable</b> (std::ostream &=ExEnv::out0()) const</td></tr>
<tr><td nowrap align=right valign=top><a name="a18" doxytag="sc::IntMolecularCoor::print_constant"></a>
virtual void </td><td valign=bottom><b>print_constant</b> (std::ostream &=ExEnv::out0()) const</td></tr>
<tr><td nowrap align=right valign=top><a name="a19" doxytag="sc::IntMolecularCoor::nconstrained"></a>
int </td><td valign=bottom><a class="el" href="class_sc__IntMolecularCoor.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 colspan=2><br><h2>Protected Methods</h2></td></tr>
<tr><td nowrap align=right valign=top><a name="b0" doxytag="sc::IntMolecularCoor::form_K_matrix"></a>
void </td><td valign=bottom><b>form_K_matrix</b> (<a class="el" href="class_sc__RefSCDimension.html">RefSCDimension</a> &dredundant, <a class="el" href="class_sc__RefSCDimension.html">RefSCDimension</a> &dfixed, <a class="el" href="class_sc__RefSCMatrix.html">RefSCMatrix</a> &K, int *&is_totally_symmetric)</td></tr>
<tr><td nowrap align=right valign=top>virtual void </td><td valign=bottom><a class="el" href="class_sc__IntMolecularCoor.html#b1">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="#b1">More...</a><em></em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="b2" doxytag="sc::IntMolecularCoor::new_coords"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__IntMolecularCoor.html#b2">new_coords</a> ()</td></tr>
<tr><td> </td><td><font size=-1><em>Allocates memory for the <a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a>'s used to store the simple and internal coordinates.</em></font><br><br></td></tr>
<tr><td nowrap align=right valign=top><a name="b3" doxytag="sc::IntMolecularCoor::read_keyval"></a>
virtual void </td><td valign=bottom><a class="el" href="class_sc__IntMolecularCoor.html#b3">read_keyval</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>Reads the <a class="el" href="class_sc__KeyVal.html">KeyVal</a> input.</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::IntMolecularCoor::generator_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__IntCoorGen.html">IntCoorGen</a>> </td><td valign=bottom><b>generator_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n1" doxytag="sc::IntMolecularCoor::dim_"></a>
<a class="el" href="class_sc__RefSCDimension.html">RefSCDimension</a> </td><td valign=bottom><b>dim_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n2" doxytag="sc::IntMolecularCoor::dvc_"></a>
<a class="el" href="class_sc__RefSCDimension.html">RefSCDimension</a> </td><td valign=bottom><b>dvc_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n3" doxytag="sc::IntMolecularCoor::variable_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a>> </td><td valign=bottom><b>variable_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n4" doxytag="sc::IntMolecularCoor::constant_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a>> </td><td valign=bottom><b>constant_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n5" doxytag="sc::IntMolecularCoor::fixed_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a>> </td><td valign=bottom><b>fixed_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n6" doxytag="sc::IntMolecularCoor::watched_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a>> </td><td valign=bottom><b>watched_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n7" doxytag="sc::IntMolecularCoor::followed_"></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><b>followed_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n8" doxytag="sc::IntMolecularCoor::bonds_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a>> </td><td valign=bottom><b>bonds_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n9" doxytag="sc::IntMolecularCoor::bends_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a>> </td><td valign=bottom><b>bends_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n10" doxytag="sc::IntMolecularCoor::tors_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a>> </td><td valign=bottom><b>tors_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n11" doxytag="sc::IntMolecularCoor::outs_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a>> </td><td valign=bottom><b>outs_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n12" doxytag="sc::IntMolecularCoor::extras_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a>> </td><td valign=bottom><b>extras_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n13" doxytag="sc::IntMolecularCoor::all_"></a>
<a class="el" href="class_sc__Ref.html">Ref</a><<a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a>> </td><td valign=bottom><b>all_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n14" doxytag="sc::IntMolecularCoor::update_bmat_"></a>
int </td><td valign=bottom><b>update_bmat_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n15" doxytag="sc::IntMolecularCoor::only_totally_symmetric_"></a>
int </td><td valign=bottom><b>only_totally_symmetric_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n16" doxytag="sc::IntMolecularCoor::symmetry_tolerance_"></a>
double </td><td valign=bottom><b>symmetry_tolerance_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n17" doxytag="sc::IntMolecularCoor::simple_tolerance_"></a>
double </td><td valign=bottom><b>simple_tolerance_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n18" doxytag="sc::IntMolecularCoor::coordinate_tolerance_"></a>
double </td><td valign=bottom><b>coordinate_tolerance_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n19" doxytag="sc::IntMolecularCoor::cartesian_tolerance_"></a>
double </td><td valign=bottom><b>cartesian_tolerance_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n20" doxytag="sc::IntMolecularCoor::scale_bonds_"></a>
double </td><td valign=bottom><b>scale_bonds_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n21" doxytag="sc::IntMolecularCoor::scale_bends_"></a>
double </td><td valign=bottom><b>scale_bends_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n22" doxytag="sc::IntMolecularCoor::scale_tors_"></a>
double </td><td valign=bottom><b>scale_tors_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n23" doxytag="sc::IntMolecularCoor::scale_outs_"></a>
double </td><td valign=bottom><b>scale_outs_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n24" doxytag="sc::IntMolecularCoor::nextra_bonds_"></a>
int </td><td valign=bottom><b>nextra_bonds_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n25" doxytag="sc::IntMolecularCoor::extra_bonds_"></a>
int* </td><td valign=bottom><b>extra_bonds_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n26" doxytag="sc::IntMolecularCoor::given_fixed_values_"></a>
int </td><td valign=bottom><b>given_fixed_values_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n27" doxytag="sc::IntMolecularCoor::decouple_bonds_"></a>
int </td><td valign=bottom><b>decouple_bonds_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n28" doxytag="sc::IntMolecularCoor::decouple_bends_"></a>
int </td><td valign=bottom><b>decouple_bends_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n29" doxytag="sc::IntMolecularCoor::max_update_steps_"></a>
int </td><td valign=bottom><b>max_update_steps_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n30" doxytag="sc::IntMolecularCoor::max_update_disp_"></a>
double </td><td valign=bottom><b>max_update_disp_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n31" doxytag="sc::IntMolecularCoor::form_print_simples_"></a>
int </td><td valign=bottom><b>form_print_simples_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n32" doxytag="sc::IntMolecularCoor::form_print_variable_"></a>
int </td><td valign=bottom><b>form_print_variable_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n33" doxytag="sc::IntMolecularCoor::form_print_constant_"></a>
int </td><td valign=bottom><b>form_print_constant_</b></td></tr>
<tr><td nowrap align=right valign=top><a name="n34" doxytag="sc::IntMolecularCoor::form_print_molecule_"></a>
int </td><td valign=bottom><b>form_print_molecule_</b></td></tr>
</table>
<hr><a name="_details"></a><h2>Detailed Description</h2>
The <a class="el" href="class_sc__IntMolecularCoor.html">IntMolecularCoor</a> abstract class describes a molecule's coordinates in terms of internal coordinates.
<p>
<hr><h2>Constructor & Destructor Documentation</h2>
<a name="a2" doxytag="sc::IntMolecularCoor::IntMolecularCoor"></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::IntMolecularCoor::IntMolecularCoor (
</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>variable</code><dd> Gives a <a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a> object that specifies the internal coordinates that can be varied. If this is not given, the variable coordinates will be generated.
<p>
<dt><code>followed</code><dd> Gives a <a class="el" href="class_sc__IntCoor.html">IntCoor</a> object that specifies a coordinate to used as the first coordinate in the variable coordinate list. The remaining coordinates will be automatically generated. The default is no followed coordinate. This option is usually used to set the initial search direction for a transition state optimization, where it is used in conjunction with the mode_following keyword read by the <a class="el" href="class_sc__EFCOpt.html">EFCOpt</a> class.
<p>
<dt><code>fixed</code><dd> Gives a <a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a> object that specifies the internal coordinates that will be fixed. The default is no fixed coordinates.
<p>
<dt><code>watched</code><dd> Gives a <a class="el" href="class_sc__SetIntCoor.html">SetIntCoor</a> object that specifies internal coordinates that will be printed out whenever the coordinates are changed. The default is none.
<p>
<dt><code>have_fixed_values</code><dd> If true, then values for the fixed coordinates must be given in fixed and an attempt will be made to displace the initial geometry to the given fixed values. The default is false.
<p>
<dt><code>extra_bonds</code><dd> This is only read if the generator keyword is not given. It is a vector of atom numbers, where elements <img align="top" src="form-11.gif">
and <img align="top" src="form-12.gif">
specify the atoms which are bound in extra bond <img align="top" src="form-7.gif">
. The extra_bonds keyword should only be needed for weakly interacting fragments, otherwise all the needed bonds will be found.
<p>
<dt><code>generator</code><dd> Specifies an <a class="el" href="class_sc__IntCoorGen.html">IntCoorGen</a> object that creates simple, redundant internal coordinates. If this keyword is not given, then a vector giving extra bonds to be added is read from extra_bonds and this is used to create an <a class="el" href="class_sc__IntCoorGen.html">IntCoorGen</a> object.
<p>
<dt><code>decouple_bonds</code><dd> Automatically generated internal coordinates are linear combinations of possibly any mix of simple internal coordinates. If decouple_bonds is true, an attempt will be made to form some of the internal coordinates from just stretch simple coordinates. The default is false.
<p>
<dt><code>decouple_bends</code><dd> This is like decouple_bonds except it applies to the bend-like coordinates. The default is false.
<p>
<dt><code>max_update_disp</code><dd> The maximum displacement to be used in the displacement to fixed internal coordinates values. Larger displacements will be broken into several smaller displacements and new coordinates will be formed for each of these displacments. This is only used when fixed and have_fixed_values are given. The default is 0.5.
<p>
<dt><code>max_update_steps</code><dd> The maximum number of steps permitted to convert internal coordinate displacements to cartesian coordinate displacements. The default is 100.
<p>
<dt><code>update_bmat</code><dd> Displacements in internal coordinates are converted to a cartesian displacements interatively. If there are large changes in the cartesian coordinates during conversion, then recompute the <img align="top" src="form-13.gif">
matrix, which is using to do the conversion. The default is false.
<p>
<dt><code>only_totally_symmetric</code><dd> If a simple test reveals that an internal coordinate is not totally symmetric, then it will not be added to the internal coordinate list. The default is true.
<p>
<dt><code>simple_tolerance</code><dd> The internal coordinates are formed as linear combinations of simple, redundant internal coordinates. Coordinates with coefficients smaller then simple_tolerance will be omitted. The default is 1.0e-3.
<p>
<dt><code>cartesian_tolerance</code><dd> The tolerance for conversion of internal coordinate displacements to cartesian displacements. The default is 1.0e-12.
<p>
<dt><code>form:print_simple</code><dd> Print the simple internal coordinates. The default is false.
<p>
<dt><code>form:print_variable</code><dd> Print the variable internal coordinates. The default is false.
<p>
<dt><code>form:print_constant</code><dd> Print the constant internal coordinates. The default is false.
<p>
<dt><code>form:print_molecule</code><dd> Print the molecule when forming coordinates. The default is false.
<p>
<dt><code>scale_bonds</code><dd> Obsolete. The default value is 1.0.
<p>
<dt><code>scale_bends</code><dd> Obsolete. The default value is 1.0.
<p>
<dt><code>scale_tors</code><dd> Obsolete. The default value is 1.0.
<p>
<dt><code>scale_outs</code><dd> Obsolete. The default value is 1.0.
<p>
<dt><code>symmetry_tolerance</code><dd> Obsolete. The default is 1.0e-5.
<p>
<dt><code>coordinate_tolerance</code><dd> Obsolete. The default is 1.0e-7.
<p>
</dl>
</td>
</tr>
</table>
<hr><h2>Member Function Documentation</h2>
<a name="b1" doxytag="sc::IntMolecularCoor::init"></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::IntMolecularCoor::init (
</b></td>
<td valign="bottom"><b>
)<code> [protected, virtual]</code>
</b></td>
</tr>
</table>
</td>
</tr>
</table>
<table cellspacing=5 cellpadding=0 border=0>
<tr>
<td>
</td>
<td>
<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__IntMolecularCoor.html#a5">form_coordinates</a>() member.
<p>
Reimplemented in <a class="el" href="class_sc__SymmMolecularCoor.html#b0">sc::SymmMolecularCoor</a>. </td>
</tr>
</table>
<a name="a4" doxytag="sc::IntMolecularCoor::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::IntMolecularCoor::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__MolecularCoor.html#a4">sc::MolecularCoor</a>.
<p>
Reimplemented in <a class="el" href="class_sc__SymmMolecularCoor.html#a4">sc::SymmMolecularCoor</a>, and <a class="el" href="class_sc__RedundMolecularCoor.html#a4">sc::RedundMolecularCoor</a>. </td>
</tr>
</table>
<a name="a13" doxytag="sc::IntMolecularCoor::to_cartesian"></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>
virtual int sc::IntMolecularCoor::to_cartesian (
</b></td>
<td valign="bottom"><b>
<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> & <em>cart</em>,
</b></td>
</tr>
<tr>
<td></td>
<td><b>
<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> & <em>internal</em> )<code> [virtual]</code>
</b></td>
</tr>
</table>
</td>
</tr>
</table>
<table cellspacing=5 cellpadding=0 border=0>
<tr>
<td>
</td>
<td>
<p>
Convert the internal coordinate Hessian ``internal'' to Cartesian coordinates and copy the result to ``cartesian''.
<p>
Only the variable internal coordinate force constants are transformed.
<p>
Reimplemented from <a class="el" href="class_sc__MolecularCoor.html#a15">sc::MolecularCoor</a>. </td>
</tr>
</table>
<a name="a11" doxytag="sc::IntMolecularCoor::to_cartesian"></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>
virtual int sc::IntMolecularCoor::to_cartesian (
</b></td>
<td valign="bottom"><b>
<a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> & <em>cartesian</em>,
</b></td>
</tr>
<tr>
<td></td>
<td><b>
<a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> & <em>internal</em> )<code> [virtual]</code>
</b></td>
</tr>
</table>
</td>
</tr>
</table>
<table cellspacing=5 cellpadding=0 border=0>
<tr>
<td>
</td>
<td>
<p>
Convert the internal coordinate gradients in ``internal'' to Cartesian coordinates and copy these Cartesian coordinate gradients to ``cartesian''.
<p>
Only the variable internal coordinate gradients are transformed.
<p>
Reimplemented from <a class="el" href="class_sc__MolecularCoor.html#a13">sc::MolecularCoor</a>. </td>
</tr>
</table>
<a name="a14" doxytag="sc::IntMolecularCoor::to_internal"></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>
virtual int sc::IntMolecularCoor::to_internal (
</b></td>
<td valign="bottom"><b>
<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> & <em>internal</em>,
</b></td>
</tr>
<tr>
<td></td>
<td><b>
<a class="el" href="class_sc__RefSymmSCMatrix.html">RefSymmSCMatrix</a> & <em>cart</em> )<code> [virtual]</code>
</b></td>
</tr>
</table>
</td>
</tr>
</table>
<table cellspacing=5 cellpadding=0 border=0>
<tr>
<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 from <a class="el" href="class_sc__MolecularCoor.html#a16">sc::MolecularCoor</a>. </td>
</tr>
</table>
<a name="a12" doxytag="sc::IntMolecularCoor::to_internal"></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>
virtual int sc::IntMolecularCoor::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> [virtual]</code>
</b></td>
</tr>
</table>
</td>
</tr>
</table>
<table cellspacing=5 cellpadding=0 border=0>
<tr>
<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 from <a class="el" href="class_sc__MolecularCoor.html#a14">sc::MolecularCoor</a>. </td>
</tr>
</table>
<a name="a10" doxytag="sc::IntMolecularCoor::to_internal"></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>
virtual int sc::IntMolecularCoor::to_internal (
</b></td>
<td valign="bottom"><b>
<a class="el" href="class_sc__RefSCVector.html">RefSCVector</a> & <em>internal</em> )<code> [virtual]</code>
</b></td>
</tr>
</table>
</td>
</tr>
</table>
<table cellspacing=5 cellpadding=0 border=0>
<tr>
<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 from <a class="el" href="class_sc__MolecularCoor.html#a12">sc::MolecularCoor</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 14:17:04 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>
</body>
</html>
distrib
>
Mandriva
>
9.1
>
ppc
>
media
>
contrib
>
by-pkgid
>
263386785cefb9ae5d63b926d214d809
>
files
>
266
