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PLMD::ReferenceAtoms Class Referenceabstract

In many applications (e.g. More...

#include <ReferenceAtoms.h>

Inheritance diagram for PLMD::ReferenceAtoms:
Inheritance graph
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Public Member Functions

 ReferenceAtoms (const ReferenceConfigurationOptions &ro)
 
unsigned getNumberOfReferencePositions () const
 This returns the number of reference atom positions. More...
 
const std::vector< Vector > & getReferencePositions () const
 Get the reference positions. More...
 
unsigned getAtomIndex (const unsigned &) const
 This allows us to use a single pos array with RMSD objects using different atom indexes. More...
 
virtual void getAtomRequests (std::vector< AtomNumber > &, bool disable_checks=false)
 Get the atoms required (additional checks are required when we have multiple domains) More...
 
void setAtomNumbers (const std::vector< AtomNumber > &numbers)
 Set the indices of the reference atoms. More...
 
virtual void setReferenceAtoms (const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in)=0
 Set the positions of the reference atoms. More...
 
void printAtoms (OFile &ofile, const double &lunits) const
 Print the atomic positions. More...
 
const std::vector< AtomNumber > & getAbsoluteIndexes ()
 Return all atom indexes. More...
 
unsigned getNumberOfAtoms () const
 This returns how many atoms there should be. More...
 
void displaceReferenceAtoms (const double &weight, const std::vector< Vector > &dir)
 Displace the positions of the reference atoms a bit. More...
 
virtual void extractAtomicDisplacement (const std::vector< Vector > &pos, std::vector< Vector > &direction) const
 Extract a displacement from a position in space. More...
 
virtual double projectAtomicDisplacementOnVector (const bool &normalized, const std::vector< Vector > &eigv, ReferenceValuePack &mypack) const
 Project the displacement on a vector. More...
 
const std::vector< double > & getAlign () const
 Get the vector of alignment weights. More...
 
const std::vector< double > & getDisplace () const
 Get the vector of displacement weights. More...
 
std::string getName () const
 Return the name of this metric. More...
 
virtual unsigned getNumberOfReferenceArguments () const
 
virtual void getArgumentRequests (std::vector< std::string > &, bool disable_checks=false)
 Retrieve the arguments that are required for this guy. More...
 
virtual void set (const PDB &)
 Set the final number of arguments. More...
 
virtual void read (const PDB &)=0
 Do all local business for setting the configuration. More...
 
void setWeight (const double &ww)
 Set the weight for this frame. More...
 
double getWeight () const
 Return the weight for this frame. More...
 
double calculate (const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value *> &vals, ReferenceValuePack &myder, const bool &squared=false) const
 Calculate the distance from the reference configuration. More...
 
virtual double calc (const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value *> &vals, const std::vector< double > &args, ReferenceValuePack &myder, const bool &squared) const =0
 Calculate the distance from the reference configuration. More...
 
template<class T >
bool parse (const std::string &key, T &t, bool ignore_missing=false)
 Return the derivatives of the distance wrt the cell vectors. More...
 
template<class T >
bool parseVector (const std::string &key, std::vector< T > &t, bool ignore_missing=false)
 Parse vector from the pdb remarks. More...
 
void parseFlag (const std::string &key, bool &t)
 Parse a flag. More...
 
void checkRead ()
 Check that all the remarks in the pdb have been read in. More...
 
void copyDerivatives (const ReferenceConfiguration *)
 Copy derivatives from one frame to this frame. More...
 
void setNamesAndAtomNumbers (const std::vector< AtomNumber > &numbers, const std::vector< std::string > &arg)
 Set the atom numbers and the argument names. More...
 
void setReferenceConfig (const std::vector< Vector > &pos, const std::vector< double > &arg, const std::vector< double > &metric)
 Set the reference structure (perhaps should also pass the pbc and align and displace ) More...
 
void print (OFile &ofile, const double &time, const double &weight, const double &lunits, const double &old_norm)
 Print a pdb file containing the reference configuration. More...
 
void print (OFile &ofile, const std::string &fmt, const double &lunits)
 
virtual double getReferenceArgument (const unsigned &i) const
 Get one of the referene arguments. More...
 
virtual const std::vector< double > & getReferenceArguments () const
 
virtual const std::vector< double > & getReferenceMetric ()
 
virtual const std::vector< std::string > & getArgumentNames ()
 
void extractDisplacementVector (const std::vector< Vector > &pos, const std::vector< Value *> &vals, const std::vector< double > &arg, const bool &nflag, Direction &mydir) const
 Extract a Direction giving you the displacement from some position. More...
 
virtual bool pcaIsEnabledForThisReference ()
 Stuff for pca. More...
 
double projectDisplacementOnVector (const Direction &mydir, const std::vector< Value *> &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const
 
virtual void setupPCAStorage (ReferenceValuePack &mypack)
 Stuff to setup pca. More...
 
void displaceReferenceConfiguration (const double &weight, Direction &dir)
 Move the reference configuration by an ammount specified using a Direction. More...
 

Protected Member Functions

void readAtomsFromPDB (const PDB &, const bool allowblocks=false)
 Read in the atoms from the pdb file. More...
 
void setAtomIndices (const std::vector< AtomNumber > &atomnumbers)
 Add atom indices to list. More...
 
bool parseAtomList (const std::string &, std::vector< unsigned > &)
 Read a list of atoms from the pdb input file. More...
 
Vector getReferencePosition (const unsigned &iatom) const
 Get the position of the ith atom. More...
 
void singleDomainRequests (std::vector< AtomNumber > &, bool disable_checks)
 Add derivatives to iatom th atom in list. More...
 
void error (const std::string &msg)
 Derivatives wrt to the arguments. More...
 

Private Attributes

bool checks_were_disabled
 This flag tells us if the user has disabled checking of the input in order to do fancy paths with weird inputs. More...
 
std::vector< double > align
 The atoms to be used to align the instantaneous atomic positions to the reference configuration. More...
 
std::vector< double > displace
 The atoms to be used to calculate the distance the atoms have moved from the reference configuration. More...
 
std::vector< Vectorreference_atoms
 The positions of the atoms in the reference configuration. More...
 
std::vector< AtomNumberindices
 The indices of the atoms in the pdb file. More...
 
std::vector< unsigned > atom_der_index
 The indeces for setting derivatives. More...
 

Friends

class Direction
 
class SingleDomainRMSD
 
class ReferenceConfiguration
 

Detailed Description

In many applications (e.g.

paths, fields, property maps) it is necessary to calculate the distance between two configurations. These distances can be calculated in a variety of different ways. For instance, one can assert that the distance between the two configuration is the distance one would have to move all the atoms to transform configuration 1 into configuration

  1. Alternatively, one could calculate the values of a large set of collective coordinates in the two configurations and then calculate the Euclidean distances between these two points in the resulting high-dimensional vector space. Lastly, one can combine these two forms of distance calculation to calculate a hybrid distance. Plumed allows one to use all these forms of distance calculations and also to implement new forms of distance. You should inherit from this class if your distance involves reference atomic positions. This class and PLMD::ReferenceArguments mirror the functionalities in and PLMD::ActionAtomistic and PLMD::ActionWithArguments respectively but for distances.

Constructor & Destructor Documentation

◆ ReferenceAtoms()

PLMD::ReferenceAtoms::ReferenceAtoms ( const ReferenceConfigurationOptions ro)
explicit

Member Function Documentation

◆ calc()

virtual double PLMD::ReferenceConfiguration::calc ( const std::vector< Vector > &  pos,
const Pbc pbc,
const std::vector< Value *> &  vals,
const std::vector< double > &  args,
ReferenceValuePack myder,
const bool &  squared 
) const
pure virtualinherited

Calculate the distance from the reference configuration.

Implemented in PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::SingleDomainRMSD, PLMD::Direction, and PLMD::FakeFrame.

◆ calculate()

double PLMD::ReferenceConfiguration::calculate ( const std::vector< Vector > &  pos,
const Pbc pbc,
const std::vector< Value *> &  vals,
ReferenceValuePack myder,
const bool &  squared = false 
) const
inherited

Calculate the distance from the reference configuration.

◆ checkRead()

void PLMD::ReferenceConfiguration::checkRead ( )
inherited

Check that all the remarks in the pdb have been read in.

◆ copyDerivatives()

void PLMD::ReferenceConfiguration::copyDerivatives ( const ReferenceConfiguration )
inherited

Copy derivatives from one frame to this frame.

◆ displaceReferenceAtoms()

void PLMD::ReferenceAtoms::displaceReferenceAtoms ( const double &  weight,
const std::vector< Vector > &  dir 
)

Displace the positions of the reference atoms a bit.

◆ displaceReferenceConfiguration()

void PLMD::ReferenceConfiguration::displaceReferenceConfiguration ( const double &  weight,
Direction dir 
)
inherited

Move the reference configuration by an ammount specified using a Direction.

◆ error()

void PLMD::ReferenceConfiguration::error ( const std::string &  msg)
protectedinherited

Derivatives wrt to the arguments.

The virial contribution has to be stored Derivatives wrt to the atoms Crash with an error

◆ extractAtomicDisplacement()

virtual void PLMD::ReferenceAtoms::extractAtomicDisplacement ( const std::vector< Vector > &  pos,
std::vector< Vector > &  direction 
) const
inlinevirtual

Extract a displacement from a position in space.

Reimplemented in PLMD::MultiDomainRMSD, PLMD::Direction, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.

◆ extractDisplacementVector()

void PLMD::ReferenceConfiguration::extractDisplacementVector ( const std::vector< Vector > &  pos,
const std::vector< Value *> &  vals,
const std::vector< double > &  arg,
const bool &  nflag,
Direction mydir 
) const
inherited

Extract a Direction giving you the displacement from some position.

◆ getAbsoluteIndexes()

const std::vector< AtomNumber > & PLMD::ReferenceAtoms::getAbsoluteIndexes ( )
inlinevirtual

Return all atom indexes.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getAlign()

const std::vector< double > & PLMD::ReferenceAtoms::getAlign ( ) const
inline

Get the vector of alignment weights.

◆ getArgumentNames()

const std::vector< std::string > & PLMD::ReferenceConfiguration::getArgumentNames ( )
inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getArgumentRequests()

virtual void PLMD::ReferenceConfiguration::getArgumentRequests ( std::vector< std::string > &  ,
bool  disable_checks = false 
)
inlinevirtualinherited

Retrieve the arguments that are required for this guy.

Reimplemented in PLMD::ReferenceArguments.

◆ getAtomIndex()

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

This allows us to use a single pos array with RMSD objects using different atom indexes.

◆ getAtomRequests()

void PLMD::ReferenceAtoms::getAtomRequests ( std::vector< AtomNumber > &  numbers,
bool  disable_checks = false 
)
virtual

Get the atoms required (additional checks are required when we have multiple domains)

Reimplemented from PLMD::ReferenceConfiguration.

◆ getDisplace()

const std::vector< double > & PLMD::ReferenceAtoms::getDisplace ( ) const
inline

Get the vector of displacement weights.

◆ getName()

std::string PLMD::ReferenceConfiguration::getName ( ) const
inherited

Return the name of this metric.

◆ getNumberOfAtoms()

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

This returns how many atoms there should be.

◆ getNumberOfReferenceArguments()

unsigned PLMD::ReferenceConfiguration::getNumberOfReferenceArguments ( ) const
inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getNumberOfReferencePositions()

unsigned PLMD::ReferenceAtoms::getNumberOfReferencePositions ( ) const
inlinevirtual

This returns the number of reference atom positions.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArgument()

virtual double PLMD::ReferenceConfiguration::getReferenceArgument ( const unsigned &  i) const
inlinevirtualinherited

Get one of the referene arguments.

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceArguments()

const std::vector< double > & PLMD::ReferenceConfiguration::getReferenceArguments ( ) const
inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceMetric()

const std::vector< double > & PLMD::ReferenceConfiguration::getReferenceMetric ( )
inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getReferencePosition()

Vector PLMD::ReferenceAtoms::getReferencePosition ( const unsigned &  iatom) const
inlineprotected

Get the position of the ith atom.

◆ getReferencePositions()

const std::vector< Vector > & PLMD::ReferenceAtoms::getReferencePositions ( ) const
inlinevirtual

Get the reference positions.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getWeight()

double PLMD::ReferenceConfiguration::getWeight ( ) const
inlineinherited

Return the weight for this frame.

◆ parse()

template<class T >
bool PLMD::ReferenceConfiguration::parse ( const std::string &  key,
T &  t,
bool  ignore_missing = false 
)
inherited

Return the derivatives of the distance wrt the cell vectors.

This returns false for everything other than DRMSD as these sort of calculations have to be done separately when you use RMSD Parse something from the pdb remarks

◆ parseAtomList()

bool PLMD::ReferenceAtoms::parseAtomList ( const std::string &  key,
std::vector< unsigned > &  numbers 
)
protected

Read a list of atoms from the pdb input file.

◆ parseFlag()

void PLMD::ReferenceConfiguration::parseFlag ( const std::string &  key,
bool &  t 
)
inherited

Parse a flag.

◆ parseVector()

template<class T >
bool PLMD::ReferenceConfiguration::parseVector ( const std::string &  key,
std::vector< T > &  t,
bool  ignore_missing = false 
)
inherited

Parse vector from the pdb remarks.

◆ pcaIsEnabledForThisReference()

virtual bool PLMD::ReferenceConfiguration::pcaIsEnabledForThisReference ( )
inlinevirtualinherited

◆ print() [1/2]

void PLMD::ReferenceConfiguration::print ( OFile ofile,
const double &  time,
const double &  weight,
const double &  lunits,
const double &  old_norm 
)
inherited

Print a pdb file containing the reference configuration.

◆ print() [2/2]

void PLMD::ReferenceConfiguration::print ( OFile ofile,
const std::string &  fmt,
const double &  lunits 
)
inherited

◆ printAtoms()

void PLMD::ReferenceAtoms::printAtoms ( OFile ofile,
const double &  lunits 
) const

Print the atomic positions.

◆ projectAtomicDisplacementOnVector()

virtual double PLMD::ReferenceAtoms::projectAtomicDisplacementOnVector ( const bool &  normalized,
const std::vector< Vector > &  eigv,
ReferenceValuePack mypack 
) const
inlinevirtual

Project the displacement on a vector.

Reimplemented in PLMD::MultiDomainRMSD, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.

◆ projectDisplacementOnVector()

double PLMD::ReferenceConfiguration::projectDisplacementOnVector ( const Direction mydir,
const std::vector< Value *> &  vals,
const std::vector< double > &  arg,
ReferenceValuePack mypack 
) const
inherited

◆ read()

virtual void PLMD::ReferenceConfiguration::read ( const PDB )
pure virtualinherited

◆ readAtomsFromPDB()

void PLMD::ReferenceAtoms::readAtomsFromPDB ( const PDB pdb,
const bool  allowblocks = false 
)
protected

Read in the atoms from the pdb file.

◆ set()

void PLMD::ReferenceConfiguration::set ( const PDB pdb)
virtualinherited

Set the final number of arguments.

Set the final number of atoms Set the reference configuration using a PDB

◆ setAtomIndices()

void PLMD::ReferenceAtoms::setAtomIndices ( const std::vector< AtomNumber > &  atomnumbers)
protected

Add atom indices to list.

◆ setAtomNumbers()

void PLMD::ReferenceAtoms::setAtomNumbers ( const std::vector< AtomNumber > &  numbers)

Set the indices of the reference atoms.

◆ setNamesAndAtomNumbers()

void PLMD::ReferenceConfiguration::setNamesAndAtomNumbers ( const std::vector< AtomNumber > &  numbers,
const std::vector< std::string > &  arg 
)
inherited

Set the atom numbers and the argument names.

◆ setReferenceAtoms()

virtual void PLMD::ReferenceAtoms::setReferenceAtoms ( const std::vector< Vector > &  conf,
const std::vector< double > &  align_in,
const std::vector< double > &  displace_in 
)
pure virtual

Set the positions of the reference atoms.

Implemented in PLMD::DRMSD, PLMD::MultiDomainRMSD, PLMD::Direction, and PLMD::SingleDomainRMSD.

◆ setReferenceConfig()

void PLMD::ReferenceConfiguration::setReferenceConfig ( const std::vector< Vector > &  pos,
const std::vector< double > &  arg,
const std::vector< double > &  metric 
)
inherited

Set the reference structure (perhaps should also pass the pbc and align and displace )

◆ setupPCAStorage()

virtual void PLMD::ReferenceConfiguration::setupPCAStorage ( ReferenceValuePack mypack)
inlinevirtualinherited

◆ setWeight()

void PLMD::ReferenceConfiguration::setWeight ( const double &  ww)
inlineinherited

Set the weight for this frame.

◆ singleDomainRequests()

void PLMD::ReferenceAtoms::singleDomainRequests ( std::vector< AtomNumber > &  numbers,
bool  disable_checks 
)
protected

Add derivatives to iatom th atom in list.

Get the atomic derivatives on the ith atom in the list Add derivatives to the viral This does the checks that are always required

Friends And Related Function Documentation

◆ Direction

friend class Direction
friend

◆ ReferenceConfiguration

friend class ReferenceConfiguration
friend

◆ SingleDomainRMSD

friend class SingleDomainRMSD
friend

Member Data Documentation

◆ align

std::vector<double> PLMD::ReferenceAtoms::align
private

The atoms to be used to align the instantaneous atomic positions to the reference configuration.

◆ atom_der_index

std::vector<unsigned> PLMD::ReferenceAtoms::atom_der_index
private

The indeces for setting derivatives.

◆ checks_were_disabled

bool PLMD::ReferenceAtoms::checks_were_disabled
private

This flag tells us if the user has disabled checking of the input in order to do fancy paths with weird inputs.

◆ displace

std::vector<double> PLMD::ReferenceAtoms::displace
private

The atoms to be used to calculate the distance the atoms have moved from the reference configuration.

◆ indices

std::vector<AtomNumber> PLMD::ReferenceAtoms::indices
private

The indices of the atoms in the pdb file.

◆ reference_atoms

std::vector<Vector> PLMD::ReferenceAtoms::reference_atoms
private

The positions of the atoms in the reference configuration.


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