Public Member Functions | Private Attributes | Friends | List of all members
PLMD::ReferenceValuePack Class Reference

#include <ReferenceValuePack.h>

Public Member Functions

 ReferenceValuePack (const unsigned &nargs, const unsigned &natoms, MultiValue &vals)
 
void resize (const unsigned &nargs, const unsigned &natoms)
 
void clear ()
 
unsigned getNumberOfDerivatives () const
 
unsigned getNumberOfArguments () const
 
unsigned getNumberOfAtoms () const
 
void setAtomIndex (const unsigned &iatom, const unsigned &jindex)
 
unsigned getAtomIndex (const unsigned &iatom) const
 
void copyScaledDerivatives (const unsigned &from, const double &scalef, const MultiValue &tvals)
 
void addArgumentDerivatives (const unsigned &iarg, const double &der)
 
void setArgumentDerivatives (const unsigned &iarg, const double &der)
 
void setAtomDerivatives (const unsigned &jder, const Vector &der)
 
void addAtomDerivatives (const unsigned &iatom, const Vector &der)
 
void addBoxDerivatives (const Tensor &vir)
 
bool updateComplete () const
 
void updateDynamicLists ()
 
void scaleAllDerivatives (const double &scalef)
 
void setValIndex (const unsigned &ind)
 
void moveDerivatives (const unsigned &from, const unsigned &to)
 
bool virialWasSet () const
 
Vector getAtomDerivative (const unsigned &iatom) const
 
double getArgumentDerivative (const unsigned &ival) const
 
Tensor getBoxDerivatives () const
 
bool calcUsingPCAOption () const
 
void switchOnPCAOption ()
 
std::vector< Vector > & getAtomVector ()
 
std::vector< Vector > & getAtomsDisplacementVector ()
 

Private Attributes

bool boxWasSet
 Was the virial set. More...
 
unsigned numberOfArgs
 
bool oind_set
 
unsigned oind
 
MultiValuemyvals
 Copy of the values that we are adding to. More...
 
std::vector< unsigned > & atom_indices
 Ths list of atom indices. More...
 
bool pca
 Are we using pca. More...
 
std::vector< Vectorcenteredpos
 A vector of vectors to save us some overhead for vector resizes. More...
 
std::vector< Vectordisplacement
 
std::vector< Tensorrot
 
Matrix< std::vector< Vector > > DRotDPos
 

Friends

class MultiDomainRMSD
 
class OptimalRMSD
 

Constructor & Destructor Documentation

◆ ReferenceValuePack()

PLMD::ReferenceValuePack::ReferenceValuePack ( const unsigned &  nargs,
const unsigned &  natoms,
MultiValue vals 
)

Member Function Documentation

◆ addArgumentDerivatives()

void PLMD::ReferenceValuePack::addArgumentDerivatives ( const unsigned &  iarg,
const double &  der 
)
inline

◆ addAtomDerivatives()

void PLMD::ReferenceValuePack::addAtomDerivatives ( const unsigned &  iatom,
const Vector der 
)
inline

◆ addBoxDerivatives()

void PLMD::ReferenceValuePack::addBoxDerivatives ( const Tensor vir)
inline

◆ calcUsingPCAOption()

bool PLMD::ReferenceValuePack::calcUsingPCAOption ( ) const
inline

◆ clear()

void PLMD::ReferenceValuePack::clear ( )

◆ copyScaledDerivatives()

void PLMD::ReferenceValuePack::copyScaledDerivatives ( const unsigned &  from,
const double &  scalef,
const MultiValue tvals 
)

◆ getArgumentDerivative()

double PLMD::ReferenceValuePack::getArgumentDerivative ( const unsigned &  ival) const
inline

◆ getAtomDerivative()

Vector PLMD::ReferenceValuePack::getAtomDerivative ( const unsigned &  iatom) const
inline

◆ getAtomIndex()

unsigned PLMD::ReferenceValuePack::getAtomIndex ( const unsigned &  iatom) const
inline

◆ getAtomsDisplacementVector()

std::vector< Vector > & PLMD::ReferenceValuePack::getAtomsDisplacementVector ( )
inline

◆ getAtomVector()

std::vector< Vector > & PLMD::ReferenceValuePack::getAtomVector ( )
inline

◆ getBoxDerivatives()

Tensor PLMD::ReferenceValuePack::getBoxDerivatives ( ) const
inline

◆ getNumberOfArguments()

unsigned PLMD::ReferenceValuePack::getNumberOfArguments ( ) const
inline

◆ getNumberOfAtoms()

unsigned PLMD::ReferenceValuePack::getNumberOfAtoms ( ) const
inline

◆ getNumberOfDerivatives()

unsigned PLMD::ReferenceValuePack::getNumberOfDerivatives ( ) const
inline

◆ moveDerivatives()

void PLMD::ReferenceValuePack::moveDerivatives ( const unsigned &  from,
const unsigned &  to 
)

◆ resize()

void PLMD::ReferenceValuePack::resize ( const unsigned &  nargs,
const unsigned &  natoms 
)

◆ scaleAllDerivatives()

void PLMD::ReferenceValuePack::scaleAllDerivatives ( const double &  scalef)

◆ setArgumentDerivatives()

void PLMD::ReferenceValuePack::setArgumentDerivatives ( const unsigned &  iarg,
const double &  der 
)
inline

◆ setAtomDerivatives()

void PLMD::ReferenceValuePack::setAtomDerivatives ( const unsigned &  jder,
const Vector der 
)
inline

◆ setAtomIndex()

void PLMD::ReferenceValuePack::setAtomIndex ( const unsigned &  iatom,
const unsigned &  jindex 
)
inline

◆ setValIndex()

void PLMD::ReferenceValuePack::setValIndex ( const unsigned &  ind)
inline

◆ switchOnPCAOption()

void PLMD::ReferenceValuePack::switchOnPCAOption ( )
inline

◆ updateComplete()

bool PLMD::ReferenceValuePack::updateComplete ( ) const
inline

◆ updateDynamicLists()

void PLMD::ReferenceValuePack::updateDynamicLists ( )

◆ virialWasSet()

bool PLMD::ReferenceValuePack::virialWasSet ( ) const
inline

Friends And Related Function Documentation

◆ MultiDomainRMSD

friend class MultiDomainRMSD
friend

◆ OptimalRMSD

friend class OptimalRMSD
friend

Member Data Documentation

◆ atom_indices

std::vector<unsigned>& PLMD::ReferenceValuePack::atom_indices
private

Ths list of atom indices.

◆ boxWasSet

bool PLMD::ReferenceValuePack::boxWasSet
private

Was the virial set.

◆ centeredpos

std::vector<Vector> PLMD::ReferenceValuePack::centeredpos
private

A vector of vectors to save us some overhead for vector resizes.

◆ displacement

std::vector<Vector> PLMD::ReferenceValuePack::displacement
private

◆ DRotDPos

Matrix< std::vector<Vector> > PLMD::ReferenceValuePack::DRotDPos
private

◆ myvals

MultiValue& PLMD::ReferenceValuePack::myvals
private

Copy of the values that we are adding to.

◆ numberOfArgs

unsigned PLMD::ReferenceValuePack::numberOfArgs
private

◆ oind

unsigned PLMD::ReferenceValuePack::oind
private

◆ oind_set

bool PLMD::ReferenceValuePack::oind_set
private

◆ pca

bool PLMD::ReferenceValuePack::pca
private

Are we using pca.

◆ rot

std::vector<Tensor> PLMD::ReferenceValuePack::rot
private

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