PLMD::ActionAtomistic Class Reference

Action used to create objects that access the positions of the atoms from the MD code. More...

#include <ActionAtomistic.h>

Inheritance diagram for PLMD::ActionAtomistic:

Public Types
typedef std::vector< Action * >	Dependencies
typedef std::set< FILE * > ::iterator	files_iterator

Public Member Functions
void	requestAtoms (const std::vector< AtomNumber > &a)
	Request an array of atoms. More...
const Vector &	getPosition (int) const
	Get position of i-th atom (access by relative index) More...
const Vector &	getPosition (AtomNumber) const
	Get position of i-th atom (access by absolute AtomNumber). More...
Vector &	modifyPosition (AtomNumber)
	Get modifiable position of i-th atom (access by absolute AtomNumber). More...
unsigned	getTotAtoms () const
	Get total number of atoms, including virtual ones. More...
Vector &	modifyGlobalForce (AtomNumber)
	Get modifiable force of i-th atom (access by absolute AtomNumber). More...
Tensor &	modifyGlobalVirial ()
	Get modifiable virial Should be used by action that need to modify the stored virial. More...
const Tensor &	getBox () const
	Get box shape. More...
const std::vector< Vector > &	getPositions () const
	Get the array of all positions. More...
const double &	getEnergy () const
	Get energy. More...
double	getMass (int i) const
	Get mass of i-th atom. More...
double	getCharge (int i) const
	Get charge of i-th atom. More...
std::vector< Vector > &	modifyForces ()
	Get a reference to forces array. More...
Tensor &	modifyVirial ()
	Get a reference to virial array. More...
double &	modifyForceOnEnergy ()
	Get a reference to force on energy. More...
unsigned	getNumberOfAtoms () const
	Get number of available atoms. More...
Vector	pbcDistance (const Vector &, const Vector &) const
	Compute the pbc distance between two positions. More...
const std::vector< AtomNumber > &	getAbsoluteIndexes () const
	Get the vector of absolute indexes. More...
AtomNumber	getAbsoluteIndex (int i) const
	Get the absolute index of an atom. More...
void	parseAtomList (const std::string &key, std::vector< AtomNumber > &t)
	Parse a list of atoms without a numbered keyword. More...
void	parseAtomList (const std::string &key, const int num, std::vector< AtomNumber > &t)
	Parse an list of atom with a numbred keyword. More...
void	changeBox (const Tensor &newbox)
	Change the box shape. More...
const Pbc &	getPbc () const
	Get reference to Pbc. More...
void	setForcesOnAtoms (const std::vector< double > &forcesToApply, unsigned ind=0)
	Add the forces to the atoms. More...
void	doNotRetrieve ()
	Skip atom retrieval - use with care. More...
void	doNotForce ()
	Skip atom forces - use with care. More...
	ActionAtomistic (const ActionOptions &ao)
	~ActionAtomistic ()
void	clearOutputForces ()
virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	N.B. More...
void	calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
	Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...
void	retrieveAtoms ()
void	applyForces ()
void	lockRequests ()
void	unlockRequests ()
const std::set< AtomNumber > &	getUnique () const
void	readAtomsFromPDB (const PDB &pdb)
	Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...
void	addDependency (Action *)
	Specify that this Action depends on another one. More...
void	clearDependencies ()
	Clear the dependence list for this Action. More...
long int	getStep () const
	Return the present timestep. More...
double	getTime () const
	Return the present time. More...
double	getTimeStep () const
	Return the timestep. More...
template<class T >
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type. 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 >
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector. More...
template<class T >
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number. More...
void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...
void	error (const std::string &msg) const
	Crash calculation and print documentation. More...
void	warning (const std::string &msg)
	Issue a warning. More...
void	exit (int c=0)
	Exit with error code c. More...
void	checkRead ()
	Check if Action was properly read. 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	calculate ()=0
	Calculate an Action. More...
virtual void	apply ()=0
	Apply an Action. More...
virtual void	update ()
	Update. More...
virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation. More...
void	fflush ()
	Tell to the Action to flush open files. More...
virtual std::string	getDocumentation () const
const std::string &	getLabel () const
	Returns the label. More...
const std::string &	getName () const
	Returns the name. More...
virtual void	activate ()
	Set action to active. More...
virtual void	setOption (const std::string &s)
virtual void	clearOptions ()
virtual void	deactivate ()
	Set action to inactive. More...
bool	isActive () const
	Check if action is active. More...
bool	isOptionOn (const std::string &s) const
	Check if an option is on. More...
const Dependencies &	getDependencies () const
	Return dependencies. More...
virtual bool	checkNumericalDerivatives () const
	Check if numerical derivatives should be performed. More...
virtual bool	checkNeedsGradients () const
	Check if the action needs gradient. More...
FILE *	fopen (const char *path, const char *mode)
	Opens a file. More...
int	fclose (FILE *fp)
	Closes a file opened with Action::fclose(). More...
void	calculateFromPDB (const PDB &)
	Calculate the action given a pdb file as input. More...
bool	getExchangeStep () const
	Check if we are on an exchange step. More...
std::string	cite (const std::string &s)
	Cite a paper see PlumedMain::cite. More...

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

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

Protected Attributes
Atoms &	atoms

Private Attributes
std::vector< AtomNumber >	indexes
std::set< AtomNumber >	unique
std::vector< Vector >	positions
double	energy
Pbc &	pbc
Tensor	virial
std::vector< double >	masses
bool	chargesWereSet
std::vector< double >	charges
std::vector< Vector >	forces
double	forceOnEnergy
bool	lockRequestAtoms
bool	donotretrieve
bool	donotforce

Detailed Description

Action used to create objects that access the positions of the atoms from the MD code.

Member Typedef Documentation

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

inherited

typedef std::set<FILE*>::iterator PLMD::Action::files_iterator

inherited

Constructor & Destructor Documentation

ActionAtomistic::ActionAtomistic

(

const ActionOptions &

ao

)

ActionAtomistic::~ActionAtomistic

(

)

Member Function Documentation

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

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

inherited

Specify that this Action depends on another one.

virtual void PLMD::Action::apply ( )

pure virtualinherited

Apply an Action.

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

Implemented in PLMD::analysis::Analysis, PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, PLMD::generic::WholeMolecules, PLMD::generic::Group, PLMD::generic::DumpAtoms, PLMD::generic::FitToTemplate, PLMD::multicolvar::Sprint, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::IMD, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::generic::Print, PLMD::generic::Include, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::manyrestraints::ManyRestraintsBase, PLMD::generic::Debug, PLMD::Colvar, PLMD::generic::Time, PLMD::bias::Bias, PLMD::generic::DumpProjections, PLMD::function::Function, PLMD::ActionWithVirtualAtom, and PLMD::ActionSetup.

void ActionAtomistic::applyForces

(

)

virtual void PLMD::Action::calculate ( )

pure virtualinherited

Calculate an Action.

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

Implemented in PLMD::bias::MetaD, PLMD::function::FuncSumHills, PLMD::function::Matheval, PLMD::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::RDC, PLMD::colvar::Distance, PLMD::bias::MovingRestraint, PLMD::generic::WholeMolecules, PLMD::multicolvar::ActionVolume, PLMD::generic::Group, PLMD::bias::External, PLMD::generic::DumpAtoms, PLMD::generic::FitToTemplate, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::multicolvar::MultiColvarFunction, PLMD::colvar::ContactMap, PLMD::function::Combine, PLMD::bias::BiasValue, PLMD::colvar::DRMSD, PLMD::colvar::Gyration, PLMD::colvar::NOE, PLMD::IMD, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::colvar::PathMSDBase, PLMD::function::Piecewise, PLMD::colvar::Position, PLMD::vatom::Center, PLMD::colvar::Torsion, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::MultiColvar, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::generic::Include, PLMD::generic::Print, PLMD::bias::Restraint, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::vatom::COM, PLMD::colvar::Energy, PLMD::function::Sort, PLMD::generic::DumpDerivatives, PLMD::colvar::Constant, PLMD::generic::DumpForces, PLMD::manyrestraints::ManyRestraintsBase, PLMD::function::Ensemble, PLMD::generic::Debug, PLMD::vatom::Ghost, PLMD::colvar::Dipole, PLMD::colvar::Cell, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::colvar::Template, PLMD::function::Target, PLMD::generic::Time, PLMD::generic::DumpProjections, PLMD::colvar::MultiRMSD, PLMD::colvar::RMSD, PLMD::colvar::CoordinationBase, PLMD::ActionSetup, and PLMD::mapping::PathBase.

void ActionAtomistic::calculateAtomicNumericalDerivatives	(	ActionWithValue *	a,
		const unsigned &	startnum
	)

Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic.

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

void ActionAtomistic::calculateNumericalDerivatives ( ActionWithValue *  a = NULL )

virtual

N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases

Reimplemented from PLMD::Action.

Reimplemented in PLMD::analysis::Analysis, PLMD::multicolvar::ActionVolume, PLMD::multicolvar::MultiColvarFunction, and PLMD::mapping::Mapping.

void ActionAtomistic::changeBox

(

const Tensor &

newbox

)

Change the box shape.

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

inlinevirtualinherited

Check if the action needs gradient.

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

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

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

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

inherited

Cite a paper see PlumedMain::cite.

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

void PLMD::Action::clearOptions ( )

virtualinherited

void ActionAtomistic::clearOutputForces

(

)

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

void PLMD::ActionAtomistic::doNotForce ( )

inline

Skip atom forces - use with care.

If this function is called during initialization, then forces are not going to be propagated. Can be used for optimization.

void PLMD::ActionAtomistic::doNotRetrieve ( )

inline

Skip atom retrieval - use with care.

If this function is called during initialization, then atoms are not going to be retrieved. Can be used for optimization. Notice that calling getPosition(int) in an Action where DoNotRetrieve() was called might lead to undefined behavior.

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

inherited

Crash calculation and print documentation.

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

inherited

Exit with error code c.

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

inherited

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

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

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)

AtomNumber PLMD::ActionAtomistic::getAbsoluteIndex ( int  i ) const

inline

Get the absolute index of an atom.

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

inline

Get the vector of absolute indexes.

const Tensor & PLMD::ActionAtomistic::getBox ( ) const

inline

Get box shape.

double PLMD::ActionAtomistic::getCharge ( int  i ) const

inline

Get charge of i-th atom.

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

inlineinherited

Return dependencies.

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

virtualinherited

const double & PLMD::ActionAtomistic::getEnergy ( ) const

inline

Get energy.

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

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

inlineinherited

Returns the label.

double PLMD::ActionAtomistic::getMass ( int  i ) const

inline

Get mass of i-th atom.

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

inlineinherited

Returns the name.

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const

inline

Get number of available atoms.

const Pbc & PLMD::ActionAtomistic::getPbc ( ) const

inline

Get reference to Pbc.

const Vector & PLMD::ActionAtomistic::getPosition ( int  i ) const

inline

Get position of i-th atom (access by relative index)

const Vector & PLMD::ActionAtomistic::getPosition ( AtomNumber  i ) const

inline

Get position of i-th atom (access by absolute AtomNumber).

With direct access to the global atom array

const std::vector< Vector > & PLMD::ActionAtomistic::getPositions ( ) const

inline

Get the array of all positions.

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

inherited

Return the present timestep.

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

unsigned PLMD::ActionAtomistic::getTotAtoms ( ) const

inline

Get total number of atoms, including virtual ones.

Can be used to make a loop on modifyPosition or getPosition(AtomNumber)

const std::set< AtomNumber > & PLMD::ActionAtomistic::getUnique ( ) const

inline

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

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

inlineinherited

Check if an option is on.

void PLMD::ActionAtomistic::lockRequests ( )

inlinevirtual

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::Mapping.

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )

inline

Get a reference to force on energy.

std::vector< Vector > & PLMD::ActionAtomistic::modifyForces ( )

inline

Get a reference to forces array.

Vector & PLMD::ActionAtomistic::modifyGlobalForce ( AtomNumber  i )

inline

Get modifiable force of i-th atom (access by absolute AtomNumber).

Should be used by action that need to modify the stored atomic forces

Tensor & PLMD::ActionAtomistic::modifyGlobalVirial ( )

inline

Get modifiable virial Should be used by action that need to modify the stored virial.

Vector & PLMD::ActionAtomistic::modifyPosition ( AtomNumber  i )

inline

Get modifiable position of i-th atom (access by absolute AtomNumber).

Should be used by action that need to modify the stored atomic coordinates

Tensor & PLMD::ActionAtomistic::modifyVirial ( )

inline

Get a reference to virial array.

template<class T >

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

inherited

Parse one keyword as generic type.

void ActionAtomistic::parseAtomList	(	const std::string &	key,
		std::vector< AtomNumber > &	t
	)

Parse a list of atoms without a numbered keyword.

void ActionAtomistic::parseAtomList	(	const std::string &	key,
		const int	num,
		std::vector< AtomNumber > &	t
	)

Parse an list of atom with a numbred keyword.

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

inherited

Parse one keyword as boolean flag.

template<class T >

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

inherited

Parse one numbered keyword as generic type.

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.

template<class T >

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

inherited

Parse one keyword as std::vector.

Vector ActionAtomistic::pbcDistance	(	const Vector &	v1,
		const Vector &	v2
	)		const

Compute the pbc distance between two positions.

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::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Read, PLMD::generic::Print, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.

void ActionAtomistic::readAtomsFromPDB ( const PDB &  pdb )

virtual

Read in an input file containing atom positions and calculate the action for the atomic configuration therin.

Reimplemented from PLMD::Action.

void ActionAtomistic::registerKeywords ( Keywords &  keys )

static

void ActionAtomistic::requestAtoms

(

const std::vector< AtomNumber > &

a

)

Request an array of atoms.

This method is used to ask for a list of atoms. Atoms should be asked for by number. If this routine is called during the simulation, atoms will be available at the next step MAYBE WE HAVE TO FIND SOMETHING MORE CLEAR FOR DYNAMIC LISTS OF ATOMS

void ActionAtomistic::retrieveAtoms

(

)

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::analysis::Analysis.

void ActionAtomistic::setForcesOnAtoms	(	const std::vector< double > &	forcesToApply,
		unsigned	ind = 0
	)

Add the forces to the atoms.

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

virtualinherited

void PLMD::ActionAtomistic::unlockRequests ( )

inlinevirtual

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::Mapping.

virtual void PLMD::Action::update ( )

inlinevirtualinherited

Update.

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

Reimplemented in PLMD::bias::MetaD, PLMD::analysis::Analysis, PLMD::generic::DumpAtoms, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::generic::Print, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, and PLMD::generic::DumpProjections.

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

inherited

Issue a warning.

Member Data Documentation

Atoms& PLMD::ActionAtomistic::atoms

protected

std::vector<double> PLMD::ActionAtomistic::charges

private

bool PLMD::ActionAtomistic::chargesWereSet

private

Communicator& PLMD::Action::comm

inherited

bool PLMD::ActionAtomistic::donotforce

private

bool PLMD::ActionAtomistic::donotretrieve

private

double PLMD::ActionAtomistic::energy

private

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

inherited

double PLMD::ActionAtomistic::forceOnEnergy

private

std::vector<Vector> PLMD::ActionAtomistic::forces

private

std::vector<AtomNumber> PLMD::ActionAtomistic::indexes

private

const Keywords& PLMD::Action::keywords

inherited

bool PLMD::ActionAtomistic::lockRequestAtoms

private

Log& PLMD::Action::log

inherited

Reference to the log stream.

std::vector<double> PLMD::ActionAtomistic::masses

private

Communicator& PLMD::Action::multi_sim_comm

inherited

Pbc& PLMD::ActionAtomistic::pbc

private

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

std::vector<Vector> PLMD::ActionAtomistic::positions

private

std::set<AtomNumber> PLMD::ActionAtomistic::unique

private

Tensor PLMD::ActionAtomistic::virial

private

---

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

• core/ActionAtomistic.h
• core/ActionAtomistic.cpp