PLMD::adjmat::OutputCluster Class Reference

Provides the keyword OUTPUT_CLUSTER More...

Inheritance diagram for PLMD::adjmat::OutputCluster:

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

Public Member Functions
	OutputCluster (const ActionOptions &)
virtual void	activate ()
	Set action to active. More...
void	addDependency (Action *)
	Specify that this Action depends on another one. More...
void	apply () override
	Apply an Action. More...
virtual void	beforeUpdate ()
	Before Update. More...
void	calculate () override
	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 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...
const Dependencies &	getDependencies () const
	Return dependencies. More...
virtual std::string	getDocumentation () const
bool	getExchangeStep () const
	Check if we are on an exchange step. 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 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...
virtual void	unlockRequests ()
void	update () override
	Update. More...
void	warning (const std::string &msg)
	Issue a warning. 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...

Private Member Functions
void	explore (const unsigned &index, const unsigned &depth)
bool	explore_dfs (const unsigned &index)

Private Attributes
Matrix< unsigned >	adj_list
std::vector< Vector >	atomsin
std::vector< std::pair< unsigned, unsigned > >	cluster_sizes
unsigned	clustr
bool	makewhole
unsigned	maxdepth
unsigned	maxgoes
std::vector< unsigned >	myatoms
ClusteringBase *	myclusters
std::vector< unsigned >	nneigh
int	number_of_cluster
OFile	ofile
bool	output_xyz
double	rcut2
std::vector< bool >	visited
std::vector< unsigned >	which_cluster

Detailed Description

Provides the keyword OUTPUT_CLUSTER

Member Typedef Documentation

Dependencies

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

inherited

Constructor & Destructor Documentation

OutputCluster()

PLMD::adjmat::OutputCluster::OutputCluster ( const ActionOptions &  ao )

explicit

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::adjmat::OutputCluster::apply ( )

inlineoverridevirtual

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.

calculate()

void PLMD::adjmat::OutputCluster::calculate ( )

inlineoverridevirtual

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::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::multicolvar::MultiColvarBase, PLMD::analysis::AnalysisBase, PLMD::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, PLMD::multicolvar::DumpMultiColvar, PLMD::ActionWithArguments, PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::vesselbase::ActionWithInputVessel.

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

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.

explore()

void PLMD::adjmat::OutputCluster::explore ( const unsigned &  index, const unsigned &  depth  )

private

explore_dfs()

bool PLMD::adjmat::OutputCluster::explore_dfs ( const unsigned &  index )

private

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.

getDependencies()

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

inlineinherited

Return dependencies.

getDocumentation()

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

virtualinherited

getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

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 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.

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::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::mapping::Mapping, PLMD::vesselbase::ActionWithAveraging, PLMD::ActionWithArguments, and PLMD::analysis::AnalysisBase.

onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtualinherited

Check if the action is active on this step.

Reimplemented in PLMD::gridtools::ConvertToFES.

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::multicolvar::MultiColvarBase, PLMD::generic::DumpMassCharge, PLMD::generic::Read, PLMD::maze::Optimizer, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::colvar::Energy, PLMD::SetupMolInfo, PLMD::gridtools::ConvertToFES, PLMD::colvar::ExtraCV, and PLMD::colvar::CoordinationBase.

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::adjmat::OutputCluster::registerKeywords ( Keywords &  keys )

static

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.

Reimplemented in PLMD::vesselbase::ActionWithAveraging, PLMD::analysis::AnalysisBase, PLMD::gridtools::ConvertToFES, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::gridtools::GridPrintingBase.

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.

unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::mapping::Mapping, PLMD::vesselbase::ActionWithAveraging, PLMD::ActionWithArguments, and PLMD::analysis::AnalysisBase.

update()

void PLMD::adjmat::OutputCluster::update ( )

overridevirtual

Update.

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

Reimplemented from PLMD::Action.

warning()

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

inherited

Issue a warning.

Member Data Documentation

adj_list

Matrix<unsigned> PLMD::adjmat::OutputCluster::adj_list

private

atomsin

std::vector<Vector> PLMD::adjmat::OutputCluster::atomsin

private

cluster_sizes

std::vector< std::pair<unsigned,unsigned> > PLMD::adjmat::OutputCluster::cluster_sizes

private

clustr

unsigned PLMD::adjmat::OutputCluster::clustr

private

comm

Communicator& PLMD::Action::comm

inherited

files

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

inherited

keywords

const Keywords& PLMD::Action::keywords

inherited

log

Log& PLMD::Action::log

inherited

Reference to the log stream.

makewhole

bool PLMD::adjmat::OutputCluster::makewhole

private

maxdepth

unsigned PLMD::adjmat::OutputCluster::maxdepth

private

maxgoes

unsigned PLMD::adjmat::OutputCluster::maxgoes

private

multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

myatoms

std::vector<unsigned> PLMD::adjmat::OutputCluster::myatoms

private

myclusters

ClusteringBase* PLMD::adjmat::OutputCluster::myclusters

private

nneigh

std::vector<unsigned> PLMD::adjmat::OutputCluster::nneigh

private

number_of_cluster

int PLMD::adjmat::OutputCluster::number_of_cluster

private

ofile

OFile PLMD::adjmat::OutputCluster::ofile

private

output_xyz

bool PLMD::adjmat::OutputCluster::output_xyz

private

plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

rcut2

double PLMD::adjmat::OutputCluster::rcut2

private

visited

std::vector<bool> PLMD::adjmat::OutputCluster::visited

private

which_cluster

std::vector<unsigned> PLMD::adjmat::OutputCluster::which_cluster

private

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

• adjmat/OutputCluster.cpp