Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
PLMD::colvar::Distance Class Reference

Provides the keyword DISTANCE More...

Inheritance diagram for PLMD::colvar::Distance:
Inheritance graph
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Public Types

typedef std::vector< Action * > Dependencies
 

Public Member Functions

 Distance (const ActionOptions &)
 
virtual void calculate ()
 Calculate an Action. More...
 
bool checkIsEnergy ()
 
virtual unsigned getNumberOfDerivatives ()
 
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...
 
PbcmodifyGlobalPbc ()
 Get modifiable PBC Should be used by action that need to modify the stored box. 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...
 
void pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const
 Applies PBCs to a seriens of positions or distances. More...
 
virtual 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 interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t)
 Convert a set of read in strings into an atom list (this is used in parseAtomList) 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 makeWhole ()
 Make atoms whole, assuming they are in the proper order. More...
 
void allowToAccessGlobalForces ()
 Allow calls to modifyGlobalForce() More...
 
void updateUniqueLocal ()
 updates local unique atoms 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...
 
virtual void retrieveAtoms ()
 
void applyForces ()
 
void lockRequests ()
 
void unlockRequests ()
 
const std::set< AtomNumber > & getUnique () const
 
const std::set< AtomNumber > & getUniqueLocal () const
 
void readAtomsFromPDB (const PDB &pdb)
 Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...
 
bool checkUpdate () const
 Check if action should be updated. 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...
 
bool getRestart () const
 Return true if we are doing a restart. More...
 
bool getCPT () const
 Return true if we are doing at a checkpoint step. More...
 
std::string getKeyword (const std::string &key)
 Just read one of the keywords and return the whole thing as a string. 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 beforeUpdate ()
 Before Update. 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...
 
bool checkNumericalDerivatives () const
 Check if numerical derivatives should be used. 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...
 
void addValue ()
 Add a value with the name label. More...
 
void addValueWithDerivatives ()
 Add a value with the name label that has derivatives. More...
 
void setNotPeriodic ()
 Set your default value to have no periodicity. More...
 
void setPeriodic (const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
void setValue (Value *, double)
 Set the value. More...
 
void addComponent (const std::string &name)
 Add a value with a name like label.name. More...
 
void addComponentWithDerivatives (const std::string &name)
 Add a value with a name like label.name that has derivatives. More...
 
void componentIsNotPeriodic (const std::string &name)
 Set your value component to have no periodicity. More...
 
void componentIsPeriodic (const std::string &name, const std::string &min, const std::string &max)
 Set the value to be periodic with a particular domain. More...
 
virtual bool doNotCalculateDerivatives () const
 Are we not calculating derivatives. More...
 
double getOutputQuantity (const unsigned j) const
 Get the value of one of the components of the PLMD::Action. More...
 
double getOutputQuantity (const std::string &name) const
 Get the value with a specific name (N.B. if there is no such value this returns zero) More...
 
bool exists (const std::string &name) const
 Check if a value with a particular name is present. More...
 
ValuecopyOutput (const std::string &name) const
 Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
 
ValuecopyOutput (const unsigned &n) const
 Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
 
std::string getComponentsList () const
 get a string that contains all the available components More...
 
std::vector< std::string > getComponentsVector () const
 get a vector that contains the label for all the components More...
 
int getNumberOfComponents () const
 Returns the number of values defined. More...
 
void clearInputForces ()
 Clear the forces on the values. More...
 
virtual void clearDerivatives ()
 Clear the derivatives of values wrt parameters. More...
 
void setGradientsIfNeeded ()
 Calculate the gradients and store them for all the values (need for projections) More...
 
void useNumericalDerivatives ()
 This forces the class to use numerical derivatives. More...
 
virtual void checkFieldsAllowed ()
 
virtual void turnOnDerivatives ()
 Activate the calculation of derivatives. More...
 

Static Public Member Functions

static void registerKeywords (Keywords &keys)
 
static void noAnalyticalDerivatives (Keywords &keys)
 Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...
 
static void componentsAreNotOptional (Keywords &keys)
 Puts a message into the manual that the components always output. More...
 
static void useCustomisableComponents (Keywords &keys)
 The components in the action will depend on the user. More...
 

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 requestAtoms (const std::vector< AtomNumber > &a)
 
void setAtomsDerivatives (int, const Vector &)
 
void setAtomsDerivatives (Value *, int, const Vector &)
 
void setBoxDerivatives (const Tensor &)
 
void setBoxDerivatives (Value *, const Tensor &)
 
const TensorgetBoxDerivatives () const
 
const double & getForce () const
 
void apply ()
 Apply an Action. More...
 
void setBoxDerivativesNoPbc ()
 Set box derivatives automatically. More...
 
void setBoxDerivativesNoPbc (Value *)
 
ValuegetPntrToValue ()
 Get a pointer to the default value. More...
 
void setValue (const double &d)
 Set the default value (the one without name) More...
 
ValuegetPntrToComponent (int i)
 Return a pointer to the component by index. More...
 
ValuegetPntrToComponent (const std::string &name)
 Return a pointer to the value by name. More...
 

Protected Attributes

bool isEnergy
 
Atomsatoms
 

Private Attributes

bool components
 
bool scaled_components
 
bool pbc
 

Detailed Description

Provides the keyword DISTANCE

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ Distance()

PLMD::colvar::Distance::Distance ( const ActionOptions ao)
explicit

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

◆ addComponent()

void PLMD::ActionWithValue::addComponent ( const std::string &  name)
inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

void PLMD::ActionWithValue::addComponentWithDerivatives ( const std::string &  name)
inherited

Add a value with a name like label.name that has derivatives.

◆ addDependency()

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

Specify that this Action depends on another one.

◆ addValue()

void PLMD::ActionWithValue::addValue ( )
inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( )
inherited

Add a value with the name label that has derivatives.

◆ allowToAccessGlobalForces()

void PLMD::ActionAtomistic::allowToAccessGlobalForces ( )
inlineinherited

Allow calls to modifyGlobalForce()

◆ apply()

void PLMD::Colvar::apply ( )
protectedvirtualinherited

Apply an Action.

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

Implements PLMD::Action.

◆ applyForces()

void PLMD::ActionAtomistic::applyForces ( )
inherited

◆ 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::colvar::Distance::calculate ( )
virtual

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.

◆ calculateAtomicNumericalDerivatives()

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

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)
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::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::vesselbase::ActionWithAveraging, and PLMD::mapping::Mapping.

◆ changeBox()

void PLMD::ActionAtomistic::changeBox ( const Tensor newbox)
inherited

Change the box shape.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )
inlinevirtualinherited

Reimplemented in PLMD::colvar::ContactMap.

◆ checkIsEnergy()

bool PLMD::Colvar::checkIsEnergy ( )
inlineinherited

◆ 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() [1/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const
inlinevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [2/2]

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.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( )
virtualinherited

Clear the derivatives of values wrt parameters.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )
inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )
virtualinherited

◆ clearOutputForces()

void PLMD::ActionAtomistic::clearOutputForces ( )
inherited

◆ componentIsNotPeriodic()

void PLMD::ActionWithValue::componentIsNotPeriodic ( const std::string &  name)
inherited

Set your value component to have no periodicity.

◆ componentIsPeriodic()

void PLMD::ActionWithValue::componentIsPeriodic ( const std::string &  name,
const std::string &  min,
const std::string &  max 
)
inherited

Set the value to be periodic with a particular domain.

◆ componentsAreNotOptional()

void PLMD::ActionWithValue::componentsAreNotOptional ( Keywords keys)
staticinherited

Puts a message into the manual that the components always output.

◆ copyOutput() [1/2]

Value * PLMD::ActionWithValue::copyOutput ( const std::string &  name) const
inherited

Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

Value * PLMD::ActionWithValue::copyOutput ( const unsigned &  n) const
inherited

Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ deactivate()

void PLMD::Action::deactivate ( )
inlinevirtualinherited

Set action to inactive.

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const
inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ doNotForce()

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.

◆ doNotRetrieve()

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.

◆ error()

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

Crash calculation and print documentation.

◆ exists()

bool PLMD::ActionWithValue::exists ( const std::string &  name) const
inherited

Check if a value with a particular name is present.

This is only used in PLMD::ActionWithArguments. You should not use it when manipulating components.

◆ exit()

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

Exit with error code c.

◆ 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)

◆ getAbsoluteIndex()

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

Get the absolute index of an atom.

◆ getAbsoluteIndexes()

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

Get the vector of absolute indexes.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

◆ getBox()

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

Get box shape.

◆ getBoxDerivatives()

const Tensor& PLMD::Colvar::getBoxDerivatives ( ) const
protectedinherited

◆ getCharge()

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

Get charge of i-th atom.

◆ getComponentsList()

std::string PLMD::ActionWithValue::getComponentsList ( ) const
inherited

get a string that contains all the available components

◆ getComponentsVector()

std::vector< std::string > PLMD::ActionWithValue::getComponentsVector ( ) const
inherited

get a vector that contains the label for all the components

◆ 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

◆ getEnergy()

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

Get energy.

◆ getExchangeStep()

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

Check if we are on an exchange step.

◆ getForce()

const double& PLMD::Colvar::getForce ( ) const
protectedinherited

◆ 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.

◆ getMass()

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

Get mass of i-th atom.

◆ getName()

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

Returns the name.

◆ getNumberOfAtoms()

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

Get number of available atoms.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const
inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::Colvar::getNumberOfDerivatives ( )
inlinevirtualinherited

Implements PLMD::ActionWithValue.

Reimplemented in PLMD::colvar::Energy.

◆ getOutputQuantity() [1/2]

double PLMD::ActionWithValue::getOutputQuantity ( const unsigned  j) const
inlineinherited

Get the value of one of the components of the PLMD::Action.

◆ getOutputQuantity() [2/2]

double PLMD::ActionWithValue::getOutputQuantity ( const std::string &  name) const
inlineinherited

Get the value with a specific name (N.B. if there is no such value this returns zero)

◆ getPbc()

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

Get reference to Pbc.

◆ getPntrToComponent() [1/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( int  i)
protectedinherited

Return a pointer to the component by index.

◆ getPntrToComponent() [2/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( const std::string &  name)
protectedinherited

Return a pointer to the value by name.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )
protectedinherited

Get a pointer to the default value.

◆ getPosition() [1/2]

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

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

◆ getPosition() [2/2]

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

◆ getPositions()

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

Get the array of all positions.

◆ 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.

◆ getTime()

double PLMD::Action::getTime ( ) const
inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const
inherited

Return the timestep.

◆ getTotAtoms()

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)

◆ getUnique()

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

◆ getUniqueLocal()

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

◆ interpretAtomList()

void PLMD::ActionAtomistic::interpretAtomList ( std::vector< std::string > &  strings,
std::vector< AtomNumber > &  t 
)
inherited

Convert a set of read in strings into an atom list (this is used in parseAtomList)

◆ 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()

void PLMD::ActionAtomistic::lockRequests ( )
inlinevirtualinherited

◆ makeWhole()

void PLMD::ActionAtomistic::makeWhole ( )
inherited

Make atoms whole, assuming they are in the proper order.

◆ modifyForceOnEnergy()

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

Get a reference to force on energy.

◆ modifyForces()

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

Get a reference to forces array.

◆ modifyGlobalForce()

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

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

Warning
Should be used by action that need to modify the stored atomic forces. This should be used with great care since the plumed core does not usually keep all these forces up to date. In particular, if an action require this, one should during constructor call allowToAccessGlobalForces(). Notice that for efficiency reason plumed does not check if this is done!

◆ modifyGlobalPbc()

Pbc & PLMD::ActionAtomistic::modifyGlobalPbc ( )
inlineinherited

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

◆ modifyGlobalVirial()

Tensor & PLMD::ActionAtomistic::modifyGlobalVirial ( )
inlineinherited

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

◆ modifyPosition()

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

◆ modifyVirial()

Tensor & PLMD::ActionAtomistic::modifyVirial ( )
inlineinherited

Get a reference to virial array.

◆ noAnalyticalDerivatives()

void PLMD::ActionWithValue::noAnalyticalDerivatives ( Keywords keys)
staticinherited

Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.

◆ parse()

template<class T >
void PLMD::Action::parse ( const std::string &  key,
T &  t 
)
inherited

Parse one keyword as generic type.

◆ parseAtomList() [1/2]

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

Parse a list of atoms without a numbered keyword.

◆ parseAtomList() [2/2]

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

Parse an list of atom with a numbred keyword.

◆ 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.

◆ pbcApply()

void PLMD::ActionAtomistic::pbcApply ( std::vector< Vector > &  dlist,
unsigned  max_index = 0 
) const
inherited

Applies PBCs to a seriens of positions or distances.

◆ pbcDistance()

Vector PLMD::ActionAtomistic::pbcDistance ( const Vector v1,
const Vector v2 
) const
inherited

Compute the pbc distance between two positions.

◆ 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::multicolvar::MultiColvarBase, PLMD::function::FuncPathMSD, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::generic::Read, PLMD::bias::ReweightTemperature, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.

◆ readAtomsFromPDB()

void PLMD::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.

◆ registerKeywords()

void PLMD::colvar::Distance::registerKeywords ( Keywords keys)
static

◆ requestAtoms()

void PLMD::Colvar::requestAtoms ( const std::vector< AtomNumber > &  a)
protectedinherited

◆ retrieveAtoms()

void PLMD::ActionAtomistic::retrieveAtoms ( )
virtualinherited

◆ 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::analysis::Analysis, PLMD::gridtools::ConvertToFES, and PLMD::gridtools::GridPrintingBase.

◆ setAtomsDerivatives() [1/2]

void PLMD::Colvar::setAtomsDerivatives ( int  i,
const Vector d 
)
inlineprotectedinherited

◆ setAtomsDerivatives() [2/2]

void PLMD::Colvar::setAtomsDerivatives ( Value v,
int  i,
const Vector d 
)
inlineprotectedinherited

◆ setBoxDerivatives() [1/2]

void PLMD::Colvar::setBoxDerivatives ( const Tensor d)
inlineprotectedinherited

◆ setBoxDerivatives() [2/2]

void PLMD::Colvar::setBoxDerivatives ( Value v,
const Tensor d 
)
inlineprotectedinherited

◆ setBoxDerivativesNoPbc() [1/2]

void PLMD::Colvar::setBoxDerivativesNoPbc ( )
inlineprotectedinherited

Set box derivatives automatically.

It should be called after the setAtomsDerivatives has been used for all single atoms.

Warning
It only works for collective variable NOT using PBCs!

◆ setBoxDerivativesNoPbc() [2/2]

void PLMD::Colvar::setBoxDerivativesNoPbc ( Value v)
protectedinherited

◆ setForcesOnAtoms()

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

Add the forces to the atoms.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )
inherited

Calculate the gradients and store them for all the values (need for projections)

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )
inherited

Set your default value to have no periodicity.

◆ setOption()

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

◆ setPeriodic()

void PLMD::ActionWithValue::setPeriodic ( const std::string &  min,
const std::string &  max 
)
inherited

Set the value to be periodic with a particular domain.

◆ setValue() [1/2]

void PLMD::ActionWithValue::setValue ( const double &  d)
inlineprotectedinherited

Set the default value (the one without name)

◆ setValue() [2/2]

void PLMD::ActionWithValue::setValue ( Value ,
double   
)
inherited

Set the value.

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )
virtualinherited

◆ unlockRequests()

void PLMD::ActionAtomistic::unlockRequests ( )
inlinevirtualinherited

◆ update()

virtual void PLMD::Action::update ( )
inlinevirtualinherited

◆ updateUniqueLocal()

void PLMD::ActionAtomistic::updateUniqueLocal ( )
inherited

updates local unique atoms

◆ useCustomisableComponents()

void PLMD::ActionWithValue::useCustomisableComponents ( Keywords keys)
staticinherited

The components in the action will depend on the user.

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )
inlineinherited

This forces the class to use numerical derivatives.

◆ warning()

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

Issue a warning.

Member Data Documentation

◆ atoms

Atoms& PLMD::ActionAtomistic::atoms
protectedinherited

◆ comm

Communicator& PLMD::Action::comm
inherited

◆ components

bool PLMD::colvar::Distance::components
private

◆ files

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

◆ isEnergy

bool PLMD::Colvar::isEnergy
protectedinherited

◆ keywords

const Keywords& PLMD::Action::keywords
inherited

◆ log

Log& PLMD::Action::log
inherited

Reference to the log stream.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm
inherited

◆ pbc

bool PLMD::colvar::Distance::pbc
private

◆ plumed

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

◆ scaled_components

bool PLMD::colvar::Distance::scaled_components
private

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