.TH "sc::SymmMolecularCoor" 3 "Sun Oct 4 2020" "Version 2.3.1" "MPQC" \" -*- nroff -*-
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.SH NAME
sc::SymmMolecularCoor \- The \fBSymmMolecularCoor\fP class derives from \fBIntMolecularCoor\fP\&.  

.SH SYNOPSIS
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\fC#include <coor\&.h>\fP
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Inherits \fBsc::IntMolecularCoor\fP\&.
.SS "Public Member Functions"

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.RI "\fBSymmMolecularCoor\fP (\fBRef\fP< \fBMolecule\fP > &mol)"
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.RI "\fBSymmMolecularCoor\fP (\fBStateIn\fP &)"
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.RI "\fBSymmMolecularCoor\fP (const \fBRef\fP< \fBKeyVal\fP > &)"
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.RI "The \fBKeyVal\fP constructor\&. "
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.RI "void \fBsave_data_state\fP (\fBStateOut\fP &)"
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.RI "Save the base classes (with save_data_state) and the members in the same order that the \fBStateIn\fP CTOR initializes them\&. "
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.RI "void \fBform_coordinates\fP (int keep_variable=0)"
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.RI "Actually form the variable and constant internal coordinates from simple internal coordinates\&. "
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.RI "void \fBguess_hessian\fP (\fBRefSymmSCMatrix\fP &hessian)"
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.RI "Form the approximate hessian\&. "
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.RI "\fBRefSymmSCMatrix\fP \fBinverse_hessian\fP (\fBRefSymmSCMatrix\fP &)"
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.RI "Invert the hessian\&. "
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.RI "\fBRef\fP< \fBNonlinearTransform\fP > \fBchange_coordinates\fP ()"
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.RI "This overrides MoleculeCoor's change_coordinates and might transform to a new set of coordinates\&. "
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.RI "void \fBprint\fP (std::ostream &=\fBExEnv::out0\fP()) const"
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.RI "Print the coordinate\&. "
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.SS "Protected Member Functions"

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.RI "void \fBinit\fP ()"
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.RI "This is called by the constructors of classes derived from \fBIntMolecularCoor\fP\&. "
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.SS "Protected Attributes"

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.RI "int \fBchange_coordinates_\fP"
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.RI "int \fBtransform_hessian_\fP"
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.RI "double \fBmax_kappa2_\fP"
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.SS "Additional Inherited Members"
.SH "Detailed Description"
.PP 
The \fBSymmMolecularCoor\fP class derives from \fBIntMolecularCoor\fP\&. 

It provides a unique set of totally symmetric internal coordinates\&. Giving an \fBMolecularEnergy\fP object a coor is usually the best way to optimize a molecular structure\&. However, for some classes of molecules \fBSymmMolecularCoor\fP doesn't work very well\&. For example, enediyne can cause problems\&. In these cases, cartesian coordinates (obtained by not giving the \fBMolecularEnergy\fP object the coor keyword) might be better or you can manually specify the coordinates that the \fBSymmMolecularCoor\fP object uses with the variable keyword (see the \fBIntMolecularCoor\fP class description)\&. 
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.SH "Constructor & Destructor Documentation"
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.SS "sc::SymmMolecularCoor::SymmMolecularCoor (const \fBRef\fP< \fBKeyVal\fP > &)"

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The \fBKeyVal\fP constructor\&. 
.IP "\fB\fCchange_coordinates\fP\fP" 1c
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\&.
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.IP "\fB\fCmax_kappa2\fP\fP" 1c
A measure of the quality of the internal coordinates\&. Values of the 2-norm condition, $\kappa_2$, larger than max_kappa2 are considered linearly dependent\&. The default is 10\&.0\&.
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.IP "\fB\fCtransform_hessian\fP\fP" 1c
If true, the hessian will be transformed every time the internal coordinates are formed\&. The default is true\&.
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.SH "Member Function Documentation"
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.SS "void sc::SymmMolecularCoor::init ()\fC [protected]\fP, \fC [virtual]\fP"

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This is called by the constructors of classes derived from \fBIntMolecularCoor\fP\&. It initialized the lists of simple internal coordinates, and then calls the \fBform_coordinates()\fP member\&. 
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Reimplemented from \fBsc::IntMolecularCoor\fP\&.
.SS "void sc::SymmMolecularCoor::save_data_state (\fBStateOut\fP &)\fC [virtual]\fP"

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Save the base classes (with save_data_state) and the members in the same order that the \fBStateIn\fP CTOR initializes them\&. This must be implemented by the derived class if the class has data\&. 
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Reimplemented from \fBsc::IntMolecularCoor\fP\&.

.SH "Author"
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Generated automatically by Doxygen for MPQC from the source code\&.