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PLMD::ActionWithVirtualAtom Class Referenceabstract

Inherit from here if you are calculating the position of a virtual atom (eg a center of mass) More...

#include <ActionWithVirtualAtom.h>

Inheritance diagram for PLMD::ActionWithVirtualAtom:
Inheritance graph
[legend]

Public Types

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

Public Member Functions

void setGradients ()
 
const std::map< AtomNumber,
Tensor > & 
getGradients () const
 
AtomNumber getIndex () const
 Return the atom id of the corresponding virtual atom. More...
 
 ActionWithVirtualAtom (const ActionOptions &ao)
 
 ~ActionWithVirtualAtom ()
 
void setGradientsIfNeeded ()
 
const VectorgetPosition (int) const
 Get position of i-th atom (access by relative index) More...
 
const VectorgetPosition (AtomNumber) const
 Get position of i-th atom (access by absolute AtomNumber). More...
 
VectormodifyPosition (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...
 
VectormodifyGlobalForce (AtomNumber)
 Get modifiable force of i-th atom (access by absolute AtomNumber). More...
 
TensormodifyGlobalVirial ()
 Get modifiable virial Should be used by action that need to modify the stored virial. More...
 
const TensorgetBox () 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...
 
TensormodifyVirial ()
 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 PbcgetPbc () 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...
 
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 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 DependenciesgetDependencies () 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

PlumedMainplumed
 Reference to main plumed object. More...
 
Loglog
 Reference to the log stream. More...
 
std::set< FILE * > files
 
Communicatorcomm
 
Communicatormulti_sim_comm
 
const Keywordskeywords
 

Protected Member Functions

void setPosition (const Vector &)
 Set position of the virtual atom. More...
 
void setMass (double)
 Set its mass. More...
 
void setCharge (double)
 Set its charge. More...
 
void requestAtoms (const std::vector< AtomNumber > &a)
 Request atoms on which the calculation depends. More...
 
void setAtomsDerivatives (const std::vector< Tensor > &d)
 Set the derivatives of virtual atom coordinate wrt atoms on which it dependes. More...
 
void setBoxDerivatives (const std::vector< Tensor > &d)
 Set the box derivatives. More...
 

Protected Attributes

Atomsatoms
 

Private Member Functions

void apply ()
 Apply an Action. More...
 

Private Attributes

AtomNumber index
 
std::vector< Tensorderivatives
 
std::vector< TensorboxDerivatives
 
std::map< AtomNumber, Tensorgradients
 

Detailed Description

Inherit from here if you are calculating the position of a virtual atom (eg a center of mass)

Class to add a single virtual atom to the system. (it might be extended to add multiple virtual atoms).

Member Typedef Documentation

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

Constructor & Destructor Documentation

PLMD::ActionWithVirtualAtom::ActionWithVirtualAtom ( const ActionOptions ao)
PLMD::ActionWithVirtualAtom::~ActionWithVirtualAtom ( )

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.

void PLMD::ActionWithVirtualAtom::apply ( )
privatevirtual

Apply an Action.

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

Implements PLMD::Action.

void ActionAtomistic::applyForces ( )
inherited
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 
)
inherited

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)
virtualinherited

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)
inherited

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 ( )
inherited
void PLMD::Action::deactivate ( )
inlinevirtualinherited

Set action to inactive.

void PLMD::ActionAtomistic::doNotForce ( )
inlineinherited

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 ( )
inlineinherited

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
inlineinherited

Get the absolute index of an atom.

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

Get the vector of absolute indexes.

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

Get box shape.

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

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
inlineinherited

Get energy.

bool PLMD::Action::getExchangeStep ( ) const
inherited

Check if we are on an exchange step.

const std::map< AtomNumber, Tensor > & PLMD::ActionWithVirtualAtom::getGradients ( ) const
inline
AtomNumber PLMD::ActionWithVirtualAtom::getIndex ( ) const
inline

Return the atom id of the corresponding virtual atom.

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

Returns the label.

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

Get mass of i-th atom.

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

Returns the name.

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const
inlineinherited

Get number of available atoms.

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

Get reference to Pbc.

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

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

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

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
inlineinherited

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
inlineinherited

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
inlineinherited
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 ( )
inlinevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::Mapping.

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )
inlineinherited

Get a reference to force on energy.

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

Get a reference to forces array.

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

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 ( )
inlineinherited

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

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

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 ( )
inlineinherited

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 
)
inherited

Parse a list of atoms without a numbered keyword.

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

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
inherited

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)
virtualinherited

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

Reimplemented from PLMD::Action.

void PLMD::ActionWithVirtualAtom::registerKeywords ( Keywords keys)
static
void PLMD::ActionWithVirtualAtom::requestAtoms ( const std::vector< AtomNumber > &  a)
protected

Request atoms on which the calculation depends.

void ActionAtomistic::retrieveAtoms ( )
inherited
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 PLMD::ActionWithVirtualAtom::setAtomsDerivatives ( const std::vector< Tensor > &  d)
inlineprotected

Set the derivatives of virtual atom coordinate wrt atoms on which it dependes.

void PLMD::ActionWithVirtualAtom::setBoxDerivatives ( const std::vector< Tensor > &  d)
protected

Set the box derivatives.

This should be a vector of size 3. First index corresponds to the components of the virtual atom. Notice that this routine subtract the trivial term coming from cell deformation since this term is already implicitly included. Indeed, if the vatom position is a linear function of atomic coordinates it is not necessary to call this function (implicit term is fine) (e.g. vatom::COM and vatom::Center). On the other hand if the vatom position is a non-linear function of atomic coordinates this should be called (see vatom::Ghost).

void PLMD::ActionWithVirtualAtom::setCharge ( double  c)
inlineprotected

Set its charge.

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

Add the forces to the atoms.

void PLMD::ActionWithVirtualAtom::setGradients ( )
void PLMD::ActionWithVirtualAtom::setGradientsIfNeeded ( )
void PLMD::ActionWithVirtualAtom::setMass ( double  m)
inlineprotected

Set its mass.

void PLMD::Action::setOption ( const std::string &  s)
virtualinherited
void PLMD::ActionWithVirtualAtom::setPosition ( const Vector pos)
inlineprotected

Set position of the virtual atom.

void PLMD::ActionAtomistic::unlockRequests ( )
inlinevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::Mapping.

virtual void PLMD::Action::update ( )
inlinevirtualinherited
void PLMD::Action::warning ( const std::string &  msg)
inherited

Issue a warning.

Member Data Documentation

Atoms& PLMD::ActionAtomistic::atoms
protectedinherited
std::vector<Tensor> PLMD::ActionWithVirtualAtom::boxDerivatives
private
Communicator& PLMD::Action::comm
inherited
std::vector<Tensor> PLMD::ActionWithVirtualAtom::derivatives
private
std::set<FILE*> PLMD::Action::files
inherited
std::map<AtomNumber,Tensor> PLMD::ActionWithVirtualAtom::gradients
private
AtomNumber PLMD::ActionWithVirtualAtom::index
private
const Keywords& PLMD::Action::keywords
inherited
Log& PLMD::Action::log
inherited

Reference to the log stream.

Communicator& PLMD::Action::multi_sim_comm
inherited
PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.


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