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PLMD::ActionAtomistic Class Referenceabstract

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:
Inheritance graph
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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 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...
 
 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 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 Attributes

Atomsatoms
 

Private Attributes

std::vector< AtomNumberindexes
 
std::set< AtomNumberunique
 
std::vector< Vectorpositions
 
double energy
 
Pbcpbc
 
Tensor virial
 
std::vector< double > masses
 
bool chargesWereSet
 
std::vector< double > charges
 
std::vector< Vectorforces
 
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
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
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: