ENM::VSA Class Reference

Vibrational subsystem analysis ENM. More...

#include <vsa-lib.hpp>

Inheritance diagram for ENM::VSA:

Collaboration diagram for ENM::VSA:

Public Member Functions
	VSA (SuperBlock *blocker, const uint subn)
	Constructor for VSA without masses.
	VSA (SuperBlock *blocker, const uint subn, const loos::DoubleMatrix &M)
	Constructor for VSA with masses.
void	solve ()
	Computes the hessian and solves for the eigenpairs.
void	setMasses (const loos::DoubleMatrix &M)
	Sets the mass matrix and determines what kind of VSA calc to use.
void	free ()
	Free up internal storage...
Public Member Functions inherited from ENM::ElasticNetworkModel
	ElasticNetworkModel (SuperBlock *blocker)
	Base constructor for all ENMs.
void	setSuperBlockFunction (SuperBlock *p)
void	prefix (const std::string &s)
	Filename prefix when we have to write something out.
std::string	prefix () const
void	meta (const std::string &s)
	Any metadata that gets added to matrices written out.
std::string	meta () const
void	debugging (const bool b)
	Debugging flag (generally means write out all intermediate matrices)
bool	debugging () const
void	verbosity (const int i)
	How wordy are we?
int	verbosity () const
SpringFunction::Params	setParams (const SpringFunction::Params &v)
	Forwards to contained superblock.
bool	validParams () const
	Forwards to contained superblock.
uint	paramSize () const
	Forwards to contained superblock.
const loos::DoubleMatrix &	eigenvectors () const
	Accessors for eigenpairs and hessian.
const loos::DoubleMatrix &	eigenvalues () const
	Accessors for eigenpairs and hessian.
const loos::DoubleMatrix &	hessian () const
	Accessors for eigenpairs and hessian.

Additional Inherited Members
Protected Member Functions inherited from ENM::ElasticNetworkModel
void	buildHessian ()
	Construct the hessian using the contained SuperBlock.
Protected Attributes inherited from ENM::ElasticNetworkModel
SuperBlock *	blocker_
std::string	name_
std::string	prefix_
std::string	meta_
bool	debugging_
int	verbosity_
loos::DoubleMatrix	eigenvecs_
loos::DoubleMatrix	eigenvals_
loos::DoubleMatrix	hessian_

Detailed Description

Vibrational subsystem analysis ENM.

References:

• Woodcock et al, J Chem Phys (2008) 129:214109
• Haffner & Zheng, J Chem Phys (2009) 130:194111

The VSA class expects that the list of nodes contained in the passed SuperBlock instance represents the combined system, i.e. subsystem and environment. The first subn nodes are the subsystem.

Constructor & Destructor Documentation

VSA() [1/2]

ENM::VSA::VSA ( SuperBlock * blocker, const uint subn )

inline

Constructor for VSA without masses.

Arguments:

• blocker Determines how the Hessian is built
• subn The number of nodes in the subsystem

VSA() [2/2]

ENM::VSA::VSA ( SuperBlock * blocker, const uint subn, const loos::DoubleMatrix & M )

inline

Constructor for VSA with masses.

Arguments:

• c blocker Determines how the Hessian is built
• c subn The number of nodes in the subsystem
• c M Diagonal 3N x 3N matrix of node masses

Member Function Documentation

setMasses()

void ENM::VSA::setMasses ( const loos::DoubleMatrix & M )

inline

Sets the mass matrix and determines what kind of VSA calc to use.

Setting the mass matrix to an initialized matrix implies that VSA will use the mass-VSA version. On the other hand, setting the matrix to a default, uninitialized matrix will switch to the mass-less VSA:

vsa.setMasses(DoubleMatrix());

solve()

void ENM::VSA::solve ( )

virtual

Computes the hessian and solves for the eigenpairs.

Implements ENM::ElasticNetworkModel.

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The documentation for this class was generated from the following files:

• Packages/ElasticNetworks/vsa-lib.hpp
• Packages/ElasticNetworks/vsa-lib.cpp