#include <ActionAtomistic.h>

Inheritance diagram for PLMD::ActionAtomistic:

[legend]

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

Public Member Functions
	ActionAtomistic (const ActionOptions &ao)

	~ActionAtomistic ()

virtual bool	actionHasForces ()

virtual void	activate ()
	Set action to active. More...

void	addDependency (Action *)
	Specify that this Action depends on another one. More...

void	addForce (const std::pair< std::size_t, std::size_t > &a, const Vector &f)
	Add force to an atom. More...

virtual void	apply ()=0
	Apply an Action. More...

virtual void	beforeUpdate ()
	Before Update. More...

virtual void	calculate ()=0
	Calculate an Action. 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	calculateFromPDB (const PDB &)
	Calculate the action given a pdb file as input. More...

void	calculateNumericalDerivatives (ActionWithValue *a=NULL) override
	N.B. More...

ActionAtomistic *	castToActionAtomistic () noexcept final

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

void	changeBox (const Tensor &newbox)
	Change the box shape. More...

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	doNotForce ()
	Skip atom forces - use with care. More...

void	doNotRetrieve ()
	Skip atom retrieval - use with care. 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...

AtomNumber	getAbsoluteIndex (int i) const
	Get the absolute index of an atom. More...

virtual const std::vector< AtomNumber > &	getAbsoluteIndexes () const
	Get the vector of absolute indexes. More...

const Tensor &	getBox () const
	Get box shape. More...

double	getCharge (int i) const
	Get charge of i-th atom. 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...

const double &	getEnergy () const
	Get energy. More...

bool	getExchangeStep () const
	Check if we are on an exchange step. More...

Vector	getForce (const std::pair< std::size_t, std::size_t > &a) const
	Get the force acting on a particular atom. More...

Vector	getGlobalPosition (const std::pair< std::size_t, std::size_t > &) const
	Get position of i-th atom (access by absolute AtomNumber). More...

void	getGradient (const unsigned &ind, Vector &deriv, std::map< AtomNumber, Vector > &gradients) const
	Transfer the gradients. 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...

double	getMass (int i) const
	Get mass of i-th atom. More...

const std::string &	getName () const
	Returns the name. More...

unsigned	getNumberOfAtoms () const
	Get number of available atoms. More...

const Pbc &	getPbc () const
	Get reference to Pbc. More...

const Vector &	getPosition (int) const
	Get position of i-th atom (access by relative index) More...

const std::vector< Vector > &	getPositions () const
	Get the array of all positions. More...

bool	getRestart () const
	Return true if we are doing a restart. More...

long long int	getStep () const
	Return the present timestep. More...

double	getTime () const
	Return the present time. More...

double	getTimeStep () const
	Return the timestep. More...

unsigned	getTotAtoms () const
	Get total number of atoms, including virtual ones. More...

const std::vector< AtomNumber > &	getUnique () const

const std::vector< AtomNumber > &	getUniqueLocal () const

Tensor	getVirial () const
	Get the virial that is acting. More...

void	interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t)
	Interpret the atom selection. Just a wrapper to the static function with four arguments called interpretAtomList that passes xpos and this. More...

bool	isActive () const
	Check if action is active. More...

bool	isOptionOn (const std::string &s) const
	Check if an option is on. More...

void	lockRequests () override

void	makeWhole ()
	Make atoms whole, assuming they are in the proper order. More...

double &	modifyForceOnEnergy ()
	Get a reference to force on energy. More...

template<class T >
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type. 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	parseAtomList (const std::string &key, std::vector< AtomNumber > &t)
	Parse a list of atoms without a numbered keyword. 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...

void	pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const
	Applies PBCs to a seriens of positions or distances. More...

Vector	pbcDistance (const Vector &, const Vector &) const
	Compute the pbc distance between two positions. More...

virtual void	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...

void	readAtomsFromPDB (const PDB &pdb) override
	Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...

void	requestAtoms (const std::vector< AtomNumber > &a, const bool clearDep=true)
	Request an array of atoms. More...

void	resetStoredTimestep ()
	Set the timestep that is stored in the action to the correct value. More...

virtual void	retrieveAtoms (const bool &force=false)

virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation. More...

void	setForcesOnAtoms (const std::vector< double > &forcesToApply, unsigned &ind)
	Add the forces to the atoms. More...

void	setForcesOnCell (const double *forcesToApply, std::size_t size, unsigned &ind)
	Add the virial forces (span-like syntax) More...

void	setForcesOnCell (const std::vector< double > &forcesToApply, unsigned &ind)
	Add the virial forces. More...

void	setGlobalPosition (const std::pair< std::size_t, std::size_t > &, const Vector &pos)
	Modify position of i-th atom (access by absolute AtomNumber). More...

virtual void	setOption (const std::string &s)

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...

void	unlockRequests () override

virtual 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	getAtomValuesFromPlumedObject (const PlumedMain &plumed, std::vector< Value * > &xpos, std::vector< Value * > &ypos, std::vector< Value * > &zpos, std::vector< Value * > &masv, std::vector< Value * > &chargev)
	This gets std::vector that contain the PLMD::Value objects that contain xpositions, ypositions, zpositions, masses and charges. More...

static void	interpretAtomList (std::vector< std::string > &strings, const std::vector< Value * > &xpos, Action *action, std::vector< AtomNumber > &t)
	Convert a set of read in strings into an atom list (this is used in parseAtomList) More...

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...

std::pair< std::size_t, std::size_t >	getValueIndices (const AtomNumber &i) const
	Used to interpret whether this index is a virtual atom or a real atom. More...

void	setExtraCV (const std::string &name)

bool	usingNaturalUnits () const
	Are we using natural units. More...

Protected Attributes
bool	chargesWereSet

bool	massesWereSet

Private Member Functions
void	updateUniqueLocal (const bool &useunique, const std::vector< int > &g2l)

Private Attributes
bool	active
	Switch to activate Action on this step. More...

Dependencies	after
	Actions on which this Action depends. More...

std::vector< std::pair< std::size_t, std::size_t > >	atom_value_ind

std::vector< std::pair< std::size_t, std::vector< std::size_t > > >	atom_value_ind_grouped

Value *	boxValue

std::vector< double >	charges

std::vector< Value * >	chargev

std::string	defaults
	The set of default arguments that we are using. More...

bool	doCheckPoint

bool	donotforce

bool	donotretrieve

double	energy

double	forceOnEnergy

double	forceOnExtraCV

std::vector< Vector >	forces

std::vector< AtomNumber >	indexes

std::string	label
	Label of the Action, as set with LABEL= in the plumed.dat file. More...

std::vector< std::string >	line
	Directive line. More...

bool	lockRequestAtoms

std::vector< double >	masses

std::vector< Value * >	masv

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...

Pbc &	pbc =*pbc_fwd

ForwardDecl< Pbc >	pbc_fwd

std::vector< Vector >	positions

int	replica_index

bool	restart

double	timestep
	Save the timestep here. More...

std::vector< AtomNumber >	unique
	unique should be an ordered set since we later create a vector containing the corresponding indexes More...

std::vector< AtomNumber >	unique_local

bool	unique_local_needs_update
	unique_local should be an ordered set since we later create a vector containing the corresponding indexes More...

double	update_from
	Update only after this time. More...

double	update_until
	Update only until this time. More...

std::vector< std::size_t >	value_depends

std::vector< Value * >	xpos
	Values that hold information about atom positions and charges. More...

std::vector< Value * >	ypos

std::vector< Value * >	zpos

Friends
class	ActionWithVirtualAtom

class	colvar::SelectMassCharge

class	DomainDecomposition

class	Group

Detailed Description

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

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ ActionAtomistic()

PLMD::ActionAtomistic::ActionAtomistic ( const ActionOptions & ao )

explicit

◆ ~ActionAtomistic()

PLMD::ActionAtomistic::~ActionAtomistic ( )

Member Function Documentation

◆ actionHasForces()

bool PLMD::ActionAtomistic::actionHasForces ( )

virtual

Reimplemented in PLMD::generic::FitToTemplate, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::DumpAtoms, PLMD::generic::WholeMolecules, PLMD::generic::DumpMassCharge, and PLMD::generic::PrintNDX.

◆ 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.

◆ addForce()

void PLMD::ActionAtomistic::addForce	(	const std::pair< std::size_t, std::size_t > &	a,
		const Vector &	f
	)

inline

Add force to an atom.

◆ apply()

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::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::FitToTemplate, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::Include, PLMD::generic::DumpAtoms, PLMD::metatensor::MetatensorPlumedAction, PLMD::generic::EffectiveEnergyDrift, PLMD::generic::WholeMolecules, PLMD::generic::ResetCell, PLMD::ves::OutputFesBias, PLMD::generic::Read, PLMD::DomainDecomposition, PLMD::clusters::ClusterDistribution, PLMD::generic::UpdateIf, PLMD::generic::DumpMassCharge, PLMD::wham::Wham, PLMD::generic::Print, PLMD::ves::OutputBasisFunctions, PLMD::ves::OutputTargetDistribution, PLMD::ActionToPutData, PLMD::generic::RandomExchanges, PLMD::colvar::Energy, PLMD::generic::Committor, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::GenericMolInfo, PLMD::generic::Constant, PLMD::dimred::ArrangePoints, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::generic::DumpPDB, PLMD::generic::DumpProjections, PLMD::clusters::ClusterWeights, PLMD::generic::Debug, PLMD::bias::Bias, PLMD::valtools::SelectWithMask, PLMD::ActionShortcut, PLMD::Colvar, PLMD::dimred::ProjectPoints, PLMD::generic::PrintNDX, PLMD::vatom::ArgsToVatom, PLMD::generic::Accumulate, PLMD::generic::Collect, PLMD::gridtools::FunctionOfGrid< T >, PLMD::clusters::ClusteringBase, PLMD::generic::DumpVector, PLMD::colvar::RMSDVector, PLMD::generic::CreateMask, PLMD::matrixtools::InvertMatrix, PLMD::opes::ExpansionCVs, PLMD::contour::DumpContour, PLMD::valtools::Flatten, PLMD::function::Function, PLMD::generic::Time, PLMD::matrixtools::TransposeMatrix, PLMD::bias::ReweightBase, PLMD::landmarks::FarthestPointSampling, PLMD::matrixtools::MatrixOperationBase, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::Group, PLMD::ActionWithVector, PLMD::ActionWithVirtualAtom, PLMD::mapping::PathReparameterization, PLMD::contour::DistanceFromContourBase, PLMD::mapping::PathDisplacements, PLMD::valtools::Concatenate, PLMD::ActionToGetData, and PLMD::generic::GatherReplicas.

◆ 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()

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::isdb::CS2Backbone, PLMD::isdb::SAXS, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::EMMI, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::function::FuncPathMSD, PLMD::generic::FitToTemplate, PLMD::function::FuncSumHills, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::opes::OPESexpanded, PLMD::ves::VesDeltaF, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::Include, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::vatom::Center, PLMD::colvar::Distance, PLMD::metatensor::MetatensorPlumedAction, PLMD::colvar::Dimer, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::ExtendedLagrangian, PLMD::colvar::Torsion, PLMD::bias::MovingRestraint, PLMD::bias::External, PLMD::colvar::ContactMap, PLMD::generic::WholeMolecules, PLMD::colvar::ERMSD, PLMD::colvar::Angle, PLMD::crystdistrib::Quaternion, PLMD::isdb::Shadow, PLMD::colvar::Position, PLMD::generic::ResetCell, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::colvar::EEFSolv, PLMD::generic::Read, PLMD::sizeshape::position_linear_proj, PLMD::colvar::Dipole, PLMD::vatom::FixedAtom, PLMD::colvar::PathMSDBase, PLMD::colvar::SelectMassCharge, PLMD::ActionWithMatrix, PLMD::bias::ABMD, PLMD::clusters::ClusterDistribution, PLMD::generic::DumpMassCharge, PLMD::wham::Wham, PLMD::colvar::Gyration, PLMD::isdb::FretEfficiency, PLMD::ves::OutputBasisFunctions, PLMD::generic::UpdateIf, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::generic::Print, PLMD::ves::OutputTargetDistribution, PLMD::isdb::PRE, PLMD::membranefusion::memFusionP, PLMD::sizeshape::position_maha_dist, PLMD::fourier::FourierTransform, PLMD::membranefusion::fusionPoreNucleationP, PLMD::function::LocalEnsemble, PLMD::membranefusion::fusionPoreExpansionP, PLMD::generic::RandomExchanges, PLMD::bias::BiasValue, PLMD::contour::DistanceFromContour, PLMD::isdb::NOE, PLMD::maze::Loss, PLMD::bias::Restraint, PLMD::colvar::DihedralCorrelation, PLMD::colvar::Puckering, PLMD::colvar::Plane, PLMD::ActionForInterface, PLMD::generic::Committor, PLMD::vatom::Ghost, PLMD::function::FunctionOfVector< T >, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::function::Ensemble, PLMD::GenericMolInfo, PLMD::generic::Constant, PLMD::function::Stats, PLMD::dimred::ArrangePoints, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::generic::DumpPDB, PLMD::generic::Debug, PLMD::gridtools::FindGridOptimum, PLMD::clusters::ClusterWeights, PLMD::generic::DumpProjections, PLMD::dimred::ProjectPoints, PLMD::valtools::SelectWithMask, PLMD::colvar::Template, PLMD::ActionShortcut, PLMD::generic::Accumulate, PLMD::generic::Collect, PLMD::vatom::ArgsToVatom, PLMD::generic::DumpVector, PLMD::colvar::Cell, PLMD::opes::ExpansionCVs, PLMD::matrixtools::DiagonalizeMatrix, PLMD::valtools::Concatenate, PLMD::clusters::ClusteringBase, PLMD::generic::CreateMask, PLMD::colvar::RMSDVector, PLMD::contour::DumpContour, PLMD::function::FunctionOfScalar< T >, PLMD::matrixtools::InvertMatrix, PLMD::colvar::MultiColvarTemplate< T >, PLMD::colvar::Volume, PLMD::generic::PrintNDX, PLMD::generic::Time, PLMD::valtools::Flatten, PLMD::colvar::ColvarFake, PLMD::landmarks::FarthestPointSampling, PLMD::matrixtools::TransposeMatrix, PLMD::mapping::GeometricPath, PLMD::symfunc::ThreeBodyGFunctions, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::refdist::MatrixProductDiagonal, PLMD::colvar::PCARMSD, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::colvar::RMSD, PLMD::gridtools::ActionWithGrid, PLMD::Group, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::piv::PIV, PLMD::sasa::SASA_HASEL, PLMD::sasa::SASA_LCPO, PLMD::fisst::FISST, PLMD::isdb::Rescale, PLMD::maze::OptimizerBias, PLMD::funnel::Funnel, PLMD::function::FuncPathGeneral, PLMD::funnel::FUNNEL_PS, PLMD::function::annfunc::ANN, PLMD::isdb::Caliber, PLMD::maze::Optimizer, PLMD::s2cm::S2ContactModel, PLMD::colvar::ProjectionOnAxis, PLMD::isdb::Select, PLMD::mapping::PathReparameterization, PLMD::volumes::ActionVolume, PLMD::mapping::PathDisplacements, PLMD::ActionToGetData, PLMD::generic::GatherReplicas, and PLMD::contour::DistanceFromSphericalContour.

◆ calculateAtomicNumericalDerivatives()

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

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

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

overridevirtual

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::ActionWithVector, PLMD::generic::DumpAtoms, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, and PLMD::isdb::MetainferenceBase.

◆ castToActionAtomistic()

ActionAtomistic* PLMD::ActionAtomistic::castToActionAtomistic ( )

inlinefinalvirtualnoexcept

Reimplemented from PLMD::Action.