PLMD::mapping::PathReparameterization Class Reference

Provides the keyword REPARAMETERIZE_PATH More...

Inheritance diagram for PLMD::mapping::PathReparameterization:

Public Types
typedef std::vector< Action * >	Dependencies

Public Member Functions
	PathReparameterization (const ActionOptions &)
virtual void	activate ()
	Set action to active. More...
void	addDependency (Action *)
	Specify that this Action depends on another one. More...
void	apply ()
	Apply an Action. More...
virtual void	beforeUpdate ()
	Before Update. More...
void	calculate ()
	Calculate an Action. More...
void	calculateFromPDB (const PDB &)
	Calculate the action given a pdb file as input. More...
virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Perform calculation using numerical derivatives N.B. More...
virtual ActionAtomistic *	castToActionAtomistic () noexcept
virtual ActionForInterface *	castToActionForInterface () noexcept
virtual ActionShortcut *	castToActionShortcut () noexcept
virtual ActionToGetData *	castToActionToGetData () noexcept
virtual ActionToPutData *	castToActionToPutData () noexcept
virtual ActionWithArguments *	castToActionWithArguments () noexcept
virtual ActionWithValue *	castToActionWithValue () noexcept
	Specialized casts, to make PlumedMain run faster. More...
virtual ActionWithVirtualAtom *	castToActionWithVirtualAtom () noexcept
virtual DomainDecomposition *	castToDomainDecomposition () noexcept
virtual PbcAction *	castToPbcAction () noexcept
bool	checkForDependency (Action *)
	Check that this action does not depend on the action in the argument. More...
virtual bool	checkNeedsGradients () const
	Check if the action needs gradient. More...
virtual bool	checkNumericalDerivatives () const
	Check if numerical derivatives should be performed. More...
void	checkRead ()
	Check if Action was properly read. More...
bool	checkUpdate () const
	Check if action should be updated. More...
std::string	cite (const std::string &s)
	Cite a paper see PlumedMain::cite. More...
void	clearDependencies ()
	Clear the dependence list for this Action. More...
virtual void	clearOptions ()
virtual void	deactivate ()
	Set action to inactive. More...
void	error (const std::string &msg) const
	Crash calculation and print documentation. More...
void	exit (int c=0)
	Exit with error code c. More...
int	fclose (FILE *fp)
	Closes a file opened with Action::fclose(). More...
void	fflush ()
	Tell to the Action to flush open files. More...
FILE *	fopen (const char *path, const char *mode)
	Opens a file. More...
bool	getCPT () const
	Return true if we are doing at a checkpoint step. More...
std::string	getDefaultString () const
	Get the defaults. More...
const Dependencies &	getDependencies () const
	Return dependencies. More...
bool	getExchangeStep () const
	Check if we are on an exchange step. More...
double	getkBT ()
	Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code. More...
std::string	getKeyword (const std::string &key)
	Just read one of the keywords and return the whole thing as a string. More...
const std::string &	getLabel () const
	Returns the label. More...
const std::string &	getName () const
	Returns the name. More...
bool	getRestart () const
	Return true if we are doing a restart. More...
long long int	getStep () const
	Return the present timestep. More...
int	getStride () const
	Get the stride. More...
double	getTime () const
	Return the present time. More...
double	getTimeStep () const
	Return the timestep. More...
bool	isActive () const
	Check if action is active. More...
bool	isOptionOn (const std::string &s) const
	Check if an option is on. More...
virtual void	lockRequests ()
virtual bool	onStep () const
	Check if the action is active on this step. More...
template<class T >
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type. More...
void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...
template<class T >
bool	parseNumbered (const std::string &key, const int no, T &t)
	Parse one numbered keyword as generic type. More...
template<class T >
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number. More...
template<class T >
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector. More...
virtual void	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...
virtual void	readAtomsFromPDB (const PDB &)
	This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code. More...
virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation. More...
virtual void	setOption (const std::string &s)
void	setStride (const int &n)
	Set the value of the stride. More...
void	setupConstantValues (const bool &have_atoms)
	This calculates any values that are constant and ensures that we don't calculate these actions on every timestep. More...
virtual void	unlockRequests ()
void	update ()
	Update. More...
void	warning (const std::string &msg)
	Issue a warning. More...
virtual std::string	writeInGraph () const
	Get the info on what to calculate. More...

Static Public Member Functions
static void	registerKeywords (Keywords &keys)

Public Attributes
Communicator &	comm
std::set< FILE * >	files
const Keywords &	keywords
Log &	log
	Reference to the log stream. More...
Communicator &	multi_sim_comm
PlumedMain &	plumed
	Reference to main plumed object. More...

Protected Member Functions
double	getKBoltzmann () const
	Get the value of Boltzmann's constant. More...
const Units &	getUnits () const
	Get the units that we are operating in. More...
bool	usingNaturalUnits () const
	Are we using natural units. More...

Private Member Functions
void	calcCurrentPathSpacings (const int &istart, const int &iend)
double	computeSpacing (const unsigned &ifrom, const unsigned &ito)
bool	loopEnd (const int &index, const int &end, const int &inc) const
void	reparameterizePart (const int &istart, const int &iend, const double &target)

Private Attributes
bool	active
	Switch to activate Action on this step. More...
Dependencies	after
	Actions on which this Action depends. More...
std::vector< double >	data
	Used to store current spacing between frames in path. More...
std::string	defaults
	The set of default arguments that we are using. More...
Value *	displace_value
	Value containing ammount to displace each reference configuration by. More...
bool	doCheckPoint
unsigned	ifix1
	The points on the path to fix. More...
unsigned	ifix2
std::string	label
	Label of the Action, as set with LABEL= in the plumed.dat file. More...
std::vector< double >	len
std::vector< std::string >	line
	Directive line. More...
unsigned	maxcycles
	Number of cycles of the optimization algorithm to run. More...
const std::string	name
	Name of the directive in the plumed.dat file. More...
bool	never_activate
std::set< std::string >	options
	Option that you might have enabled. More...
PathProjectionCalculator	path_projector
	The action for calculating the distances between the frames. More...
int	replica_index
bool	restart
std::vector< double >	sfrac
int	stride
std::vector< double >	sumlen
double	timestep
	Save the timestep here. More...
double	TOL
	Tolerance for the minimization algorithm. More...
double	update_from
	Update only after this time. More...
double	update_until
	Update only until this time. More...

Detailed Description

Provides the keyword REPARAMETERIZE_PATH

Member Typedef Documentation

Dependencies

typedef std::vector<Action*> PLMD::Action::Dependencies

inherited

Constructor & Destructor Documentation

PathReparameterization()

PLMD::mapping::PathReparameterization::PathReparameterization

(

const ActionOptions &

ao

)

Member Function Documentation

activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

addDependency()

void PLMD::Action::addDependency ( Action *  action )

inherited

Specify that this Action depends on another one.

apply()

void PLMD::mapping::PathReparameterization::apply ( )

inlinevirtual

Apply an Action.

This method is called one time per step. The set of all Actions is applied in backward order.

Implements PLMD::Action.

beforeUpdate()

virtual void PLMD::Action::beforeUpdate ( )

inlinevirtualinherited

Before Update.

This is a special method that is called just before the update() method. It can be used by actions that want to do something irrespectively of the fact that update() is active or not. In other words, this is always called, even when action is not active.

Reimplemented in PLMD::generic::UpdateIf.

calcCurrentPathSpacings()

void PLMD::mapping::PathReparameterization::calcCurrentPathSpacings ( const int &  istart, const int &  iend  )

private

calculate()

void PLMD::mapping::PathReparameterization::calculate ( )

inlinevirtual

Calculate an Action.

This method is called one or more times per step. The set of all Actions is calculated in forward order.

Implements PLMD::Action.

calculateFromPDB()

void PLMD::Action::calculateFromPDB ( const PDB &  pdb )

inherited

Calculate the action given a pdb file as input.

This is used to initialize things like distance from a point in CV map space given a pdb as an input file

calculateNumericalDerivatives()

void PLMD::Action::calculateNumericalDerivatives ( ActionWithValue *  a = NULL )

virtualinherited

Perform calculation using numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing.

Reimplemented in PLMD::ActionWithVector, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::contour::DistanceFromContourBase.

castToActionAtomistic()

virtual ActionAtomistic* PLMD::Action::castToActionAtomistic ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionAtomistic.

castToActionForInterface()

virtual ActionForInterface* PLMD::Action::castToActionForInterface ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionForInterface.

castToActionShortcut()

virtual ActionShortcut* PLMD::Action::castToActionShortcut ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionShortcut.

castToActionToGetData()

virtual ActionToGetData* PLMD::Action::castToActionToGetData ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToGetData.

castToActionToPutData()

virtual ActionToPutData* PLMD::Action::castToActionToPutData ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToPutData.

castToActionWithArguments()

virtual ActionWithArguments* PLMD::Action::castToActionWithArguments ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithArguments.

castToActionWithValue()

virtual ActionWithValue* PLMD::Action::castToActionWithValue ( )

inlinevirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented in PLMD::ActionWithValue.

castToActionWithVirtualAtom()

virtual ActionWithVirtualAtom* PLMD::Action::castToActionWithVirtualAtom ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithVirtualAtom.

castToDomainDecomposition()

virtual DomainDecomposition* PLMD::Action::castToDomainDecomposition ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::DomainDecomposition.

castToPbcAction()

virtual PbcAction* PLMD::Action::castToPbcAction ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::PbcAction.

checkForDependency()

bool PLMD::Action::checkForDependency ( Action *  action )

inherited

Check that this action does not depend on the action in the argument.

checkNeedsGradients()

virtual bool PLMD::Action::checkNeedsGradients ( ) const

inlinevirtualinherited

Check if the action needs gradient.

Reimplemented in PLMD::bias::MetaD, PLMD::bias::PBMetaD, and PLMD::generic::DumpProjections.

checkNumericalDerivatives()

virtual bool PLMD::Action::checkNumericalDerivatives ( ) const

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

This checks if Action::line is empty. It must be called after a final Action has been initialized

checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

cite()

std::string PLMD::Action::cite ( const std::string &  s )

inherited

Cite a paper see PlumedMain::cite.

clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

computeSpacing()

double PLMD::mapping::PathReparameterization::computeSpacing ( const unsigned &  ifrom, const unsigned &  ito  )

private

deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

error()

void PLMD::Action::error ( const std::string &  msg ) const

inherited

Crash calculation and print documentation.

exit()

void PLMD::Action::exit ( int  c = 0 )

inherited

Exit with error code c.

fclose()

int PLMD::Action::fclose ( FILE *  fp )

inherited

Closes a file opened with Action::fclose().

fflush()

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

fopen()

FILE * PLMD::Action::fopen ( const char *  path, const char *  mode  )

inherited

Opens a file.

This is similar to plain fopen, but with some extra functionality.

• When opened for writing, processors other than the one with rank 0 just open /dev/null
• PlumedMain::fopen is used, so that other tricks may appear (see PlumedMain::fopen)

getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

getDefaultString()

std::string PLMD::Action::getDefaultString ( ) const

inlineinherited

Get the defaults.

getDependencies()

const Dependencies& PLMD::Action::getDependencies ( ) const

inlineinherited

Return dependencies.

getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

getKBoltzmann()

double PLMD::Action::getKBoltzmann ( ) const

protectedinherited

Get the value of Boltzmann's constant.

getkBT()

double PLMD::Action::getkBT ( )

inherited

Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code.

getKeyword()

std::string PLMD::Action::getKeyword ( const std::string &  key )

inherited

Just read one of the keywords and return the whole thing as a string.

getLabel()

const std::string & PLMD::Action::getLabel ( ) const

inlineinherited

Returns the label.

getName()

const std::string & PLMD::Action::getName ( ) const

inlineinherited

Returns the name.

getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

getStep()

long long int PLMD::Action::getStep ( ) const

inherited

Return the present timestep.

getStride()

int PLMD::ActionPilot::getStride ( ) const

inherited

Get the stride.

getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

getUnits()

const Units & PLMD::Action::getUnits ( ) const

protectedinherited

Get the units that we are operating in.

isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

isOptionOn()

bool PLMD::Action::isOptionOn ( const std::string &  s ) const

inlineinherited

Check if an option is on.

lockRequests()

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, and PLMD::contour::DistanceFromContourBase.

loopEnd()

bool PLMD::mapping::PathReparameterization::loopEnd ( const int &  index, const int &  end, const int &  inc  ) const

private

onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtualinherited

Check if the action is active on this step.

parse()

template<class T >

void PLMD::Action::parse ( const std::string &  key, T &  t  )

inherited

Parse one keyword as generic type.

parseFlag()

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

inherited

Parse one keyword as boolean flag.

parseNumbered()

template<class T >

bool PLMD::Action::parseNumbered ( const std::string &  key, const int  no, T &  t  )

inherited

Parse one numbered keyword as generic type.

parseNumberedVector()

template<class T >

bool PLMD::Action::parseNumberedVector ( const std::string &  key, const int  no, std::vector< T > &  t  )

inherited

Parse a vector with a number.

parseVector()

template<class T >

void PLMD::Action::parseVector ( const std::string &  key, std::vector< T > &  t  )

inherited

Parse one keyword as std::vector.

prepare()

void PLMD::Action::prepare ( )

virtualinherited

Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.

Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.

Reimplemented in PLMD::isdb::EMMI, PLMD::function::FuncPathMSD, PLMD::generic::Plumed, PLMD::ActionWithVector, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::adjmat::FunctionOfMatrix< T >, PLMD::function::FunctionOfVector< T >, PLMD::adjmat::AdjacencyMatrixBase, PLMD::adjmat::MatrixTimesMatrix, PLMD::valtools::SelectWithMask, PLMD::dimred::ProjectPoints, PLMD::adjmat::DiagonalizeMatrix, PLMD::analysis::CreateMask, PLMD::adjmat::OuterProduct, PLMD::adjmat::VStack, PLMD::adjmat::MatrixTimesVector, PLMD::analysis::FarthestPointSampling, PLMD::adjmat::TransposeMatrix, PLMD::colvar::CoordinationBase, PLMD::adjmat::Voronoi, PLMD::function::FuncPathGeneral, PLMD::maze::Optimizer, and PLMD::s2cm::S2ContactModel.

readAtomsFromPDB()

virtual void PLMD::Action::readAtomsFromPDB ( const PDB &  )

inlinevirtualinherited

This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code.

Reimplemented in PLMD::ActionAtomistic.

registerKeywords()

void PLMD::mapping::PathReparameterization::registerKeywords ( Keywords &  keys )

static

reparameterizePart()

void PLMD::mapping::PathReparameterization::reparameterizePart ( const int &  istart, const int &  iend, const double &  target  )

private

runFinalJobs()

virtual void PLMD::Action::runFinalJobs ( )

inlinevirtualinherited

RunFinalJobs This method is called once at the very end of the calculation.

The set of all Actions in run for the final time in forward order.

setOption()

void PLMD::Action::setOption ( const std::string &  s )

virtualinherited

setStride()

void PLMD::ActionPilot::setStride ( const int &  n )

inherited

Set the value of the stride.

setupConstantValues()

void PLMD::Action::setupConstantValues ( const bool &  have_atoms )

inherited

This calculates any values that are constant and ensures that we don't calculate these actions on every timestep.

unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, and PLMD::contour::DistanceFromContourBase.

update()

void PLMD::mapping::PathReparameterization::update ( )

virtual

Update.

This method is called one time per step. The set of all Actions is updated in forward order.

Reimplemented from PLMD::Action.

usingNaturalUnits()

bool PLMD::Action::usingNaturalUnits ( ) const

protectedinherited

Are we using natural units.

warning()

void PLMD::Action::warning ( const std::string &  msg )

inherited

Issue a warning.

writeInGraph()

std::string PLMD::Action::writeInGraph ( ) const

virtualinherited

Get the info on what to calculate.

Reimplemented in PLMD::generic::Print, PLMD::adjmat::ContactMatrix, PLMD::function::FunctionOfVector< T >, PLMD::adjmat::FunctionOfMatrix< T >, PLMD::generic::PrintNDX, PLMD::function::FunctionOfScalar< T >, and PLMD::gridtools::FunctionOfGrid< T >.

Member Data Documentation

active

bool PLMD::Action::active

privateinherited

Switch to activate Action on this step.

after

Dependencies PLMD::Action::after

privateinherited

Actions on which this Action depends.

comm

Communicator& PLMD::Action::comm

inherited

data

std::vector<double> PLMD::mapping::PathReparameterization::data

private

Used to store current spacing between frames in path.

defaults

std::string PLMD::Action::defaults

privateinherited

The set of default arguments that we are using.

displace_value

Value* PLMD::mapping::PathReparameterization::displace_value

private

Value containing ammount to displace each reference configuration by.

doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

files

std::set<FILE*> PLMD::Action::files

inherited

ifix1

unsigned PLMD::mapping::PathReparameterization::ifix1

private

The points on the path to fix.

ifix2

unsigned PLMD::mapping::PathReparameterization::ifix2

private

keywords

const Keywords& PLMD::Action::keywords

inherited

label

std::string PLMD::Action::label

privateinherited

Label of the Action, as set with LABEL= in the plumed.dat file.

len

std::vector<double> PLMD::mapping::PathReparameterization::len

private

line

std::vector<std::string> PLMD::Action::line

privateinherited

Directive line.

This line is progressively erased during Action construction so as to check if all the present keywords are correct.

log

Log& PLMD::Action::log

inherited

Reference to the log stream.

maxcycles

unsigned PLMD::mapping::PathReparameterization::maxcycles

private

Number of cycles of the optimization algorithm to run.

multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

name

const std::string PLMD::Action::name

privateinherited

Name of the directive in the plumed.dat file.

never_activate

bool PLMD::Action::never_activate

privateinherited

options

std::set<std::string> PLMD::Action::options

privateinherited

Option that you might have enabled.

path_projector

PathProjectionCalculator PLMD::mapping::PathReparameterization::path_projector

private

The action for calculating the distances between the frames.

plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

replica_index

int PLMD::Action::replica_index

privateinherited

restart

bool PLMD::Action::restart

privateinherited

sfrac

std::vector<double> PLMD::mapping::PathReparameterization::sfrac

private

stride

int PLMD::ActionPilot::stride

privateinherited

sumlen

std::vector<double> PLMD::mapping::PathReparameterization::sumlen

private

timestep

double PLMD::Action::timestep

privateinherited

Save the timestep here.

TOL

double PLMD::mapping::PathReparameterization::TOL

private

Tolerance for the minimization algorithm.

update_from

double PLMD::Action::update_from

privateinherited

Update only after this time.

update_until

double PLMD::Action::update_until

privateinherited

Update only until this time.

---

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

• mapping/PathReparameterization.cpp