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PLMD::multicolvar::XDistances Class Reference

Provides the keyword XDISTANCES More...

Inheritance diagram for PLMD::multicolvar::XDistances:
Inheritance graph
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Public Types

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

Public Member Functions

 XDistances (const ActionOptions &)
 
virtual double compute ()
 This is replaced once we have a function to calculate the cv. More...
 
bool isPeriodic ()
 Returns the number of coordinates of the field. More...
 
Vector getCentralAtom ()
 Get the position of the central atom. More...
 
const VectorgetPosition (unsigned) const
 Get the position of atom iatom. 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...
 
void finishTaskListUpdate ()
 Finish the update of the task list. More...
 
virtual void calculate ()
 Calculate the multicolvar. More...
 
void updateActiveAtoms ()
 Update the atoms that have derivatives. More...
 
Vector calculateCentralAtomPosition ()
 Calculate the position of the central atom. More...
 
double getMass (unsigned) const
 Get the mass of atom iatom. More...
 
double getMass (int i) const
 Get mass of i-th atom. More...
 
double getCharge (unsigned) const
 Get the charge of atom iatom. More...
 
double getCharge (int i) const
 Get charge of i-th atom. More...
 
AtomNumber getAbsoluteIndex (unsigned) const
 Get the absolute index of atom iatom. More...
 
AtomNumber getAbsoluteIndex (int i) const
 Get the absolute index of an atom. More...
 
unsigned getBaseQuantityIndex (const unsigned &code)
 Get base quantity index. More...
 
bool isCurrentlyActive (const unsigned &)
 Is this atom currently being copied. More...
 
Vector getPositionOfAtomForLinkCells (const unsigned &iatom)
 This is used in MultiColvarBase only - it is used to setup the link cells. More...
 
void turnOnDerivatives ()
 Turn on the derivatives. More...
 
void prepare ()
 Prepare for the calculation. More...
 
void performTask ()
 Perform one of the tasks. More...
 
virtual double doCalculation ()
 And a virtual function which actually computes the colvar. More...
 
void mergeDerivatives (const unsigned &ider, const double &df)
 These replace the functions in ActionWithVessel to make the code faster. More...
 
void clearDerivativesAfterTask (const unsigned &ider)
 
virtual void apply ()
 Apply the forces from this action. More...
 
unsigned getNumberOfDerivatives ()
 Get the number of derivatives for this action. More...
 
virtual unsigned getNumberOfQuantities ()
 Get the number of quantities that are calculated each time. More...
 
Vector retrieveCentralAtomPos ()
 Retrieve the position of the central atom. More...
 
virtual void calculateWeight ()
 You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations. More...
 
void getIndexList (const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices)
 Get the list of indices that have derivatives. More...
 
virtual bool isDensity ()
 Is this a density? More...
 
virtual
vesselbase::StoreDataVessel
buildDataStashes ()
 Store central atoms so that this can be used in a function. More...
 
void copyAtomListToFunction (MultiColvarBase *myfunction)
 Copy the list of atoms involved to a second MultiColvarBase (used by functions) More...
 
void quotientRule (const unsigned &uder, const unsigned &vder, const unsigned &iout)
 Calculate and store getElementValue(uder)/getElementValue(vder) and its derivatives in getElementValue(iout) More...
 
unsigned getInternalIndex (const AtomNumber &iatom) const
 Return the number of the colvar in which iatom is the first atom. More...
 
void copyActiveAtomsToFunction (MultiColvarBase *myfunction, const unsigned &start)
 Make sure the same list of atoms is active in a function. More...
 
void activateIndexes (const unsigned &istart, const unsigned &number, const std::vector< unsigned > &indexes)
 Activate the atoms that have derivatives from a storeDataVessel. More...
 
Vector getCentralAtomPosition (const unsigned &iatom) const
 Get the position of the iatom th central atom (used in multicolvarfunction) More...
 
void addCentralAtomDerivativeToFunction (const unsigned &iatom, const unsigned &jout, const unsigned &base_cv_no, const Vector &der, MultiColvarFunction *func)
 Add central atom derivatives to a multicolvar function. More...
 
virtual void getValueForTask (const unsigned &iatom, std::vector< double > &vals)
 Get the value for this task. More...
 
virtual void copyElementsToBridgedColvar (const double &weight, ActionVolume *)
 
virtual void addWeightedValueDerivatives (const unsigned &iatom, const unsigned &base_cv_no, const double &weight, MultiColvarFunction *func)
 Used to accumulate values. More...
 
virtual void finishWeightedAverageCalculation (MultiColvarFunction *func)
 Used for calculating weighted averages. More...
 
virtual void addOrientationDerivativesToBase (const unsigned &iatom, const unsigned &jstore, const unsigned &base_cv_no, const std::vector< double > &weight, MultiColvarFunction *func)
 Add derivatives to the orientations. More...
 
virtual bool hasDifferentiableOrientation () const
 This is true if multicolvar is calculating a vector or if the multicolvar is the density. More...
 
virtual void doNotCalculateDirector ()
 This makes sure we are not calculating the director when we do LocalAverage. More...
 
void requestAtoms (const std::vector< AtomNumber > &a)
 Request an array of atoms. 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...
 
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...
 
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 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...
 
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 ()
 
void unlockContributors ()
 
void lockContributors ()
 
virtual void deactivate_task ()
 Activate the jth colvar Deactivate the current task in future loops. More...
 
void chainRuleForElementDerivatives (const unsigned &, const unsigned &, const double &, Vessel *)
 Merge the derivatives. More...
 
void chainRuleForElementDerivatives (const unsigned &, const unsigned &, const unsigned &, const unsigned &, const double &, Vessel *)
 
bool derivativesAreRequired () const
 Are derivatives required for this quantity. More...
 
virtual void finishComputations ()
 Finish running all the calculations. More...
 
virtual void retrieveDomain (std::string &min, std::string &max)
 What are the domains of the base quantities. More...
 
void activateTheseTasks (std::vector< bool > &addtionalTasks)
 Switch on additional tasks. More...
 
virtual void doJobsRequiredBeforeTaskList ()
 Do any jobs that are required before the task list is undertaken. More...
 
unsigned getFullNumberOfTasks () const
 Get the full size of the taskList dynamic list. More...
 
void setElementDerivative (const unsigned &, const double &)
 Set the derivative of the jth element wrt to a numbered element. More...
 
void addElementDerivative (const unsigned &, const double &)
 Add some derivative of the quantity in the sum wrt to a numbered element. More...
 
void setElementValue (const unsigned &, const double &)
 Set the value of the element. More...
 
void addElementValue (const unsigned &, const double &)
 Add to an element value. More...
 
double getElementValue (const unsigned &ival) const
 Get the value of this element. More...
 
double getElementDerivative (const unsigned &) const
 Retrieve the derivative of the quantity in the sum wrt to a numbered element. More...
 
virtual void applyBridgeForces (const std::vector< double > &bb)
 Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume. More...
 
VesselgetVesselWithName (const std::string &mynam)
 Return a particular named vessel. 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 readAtoms (int &natoms)
 Read in all the keywords that can be used to define atoms. More...
 
void readAtomsLikeKeyword (const std::string &key, int &natoms)
 Read in ATOMS keyword. More...
 
void readTwoGroups (const std::string &key1, const std::string &key2)
 Read two group keywords. More...
 
void readThreeGroups (const std::string &key1, const std::string &key2, const std::string &key3, const bool &allow2)
 Read three groups. More...
 
void threeBodyNeighborList (const SwitchingFunction &sf)
 This is used to make neighbor list update fast when three atoms are involved in the colvar (e.g. ANGLES, WATERBRIDGE) More...
 
void addColvar (const std::vector< unsigned > &newatoms)
 Add a collective variable. More...
 
void addAtomsDerivatives (const int &, const Vector &)
 Add some derivatives for an atom. More...
 
void addAtomsDerivatives (const unsigned &, const unsigned &, const Vector &)
 Add some derivatives for an atom. More...
 
void addAtomsDerivativeOfWeight (const unsigned &i, const Vector &wder)
 Set the derivative of the weight (used in MEAN and HISTOGRAM) More...
 
void addCentralAtomDerivatives (const unsigned &iatom, const Tensor &der)
 Add derivatives to the central atom position. More...
 
void addTaskToList (const unsigned &taskCode)
 Add a task to the list of tasks. More...
 
void setupMultiColvarBase ()
 Finish setting up the multicolvar base. More...
 
void setLinkCellCutoff (const double &lcut)
 Set the value of the cutoff for the link cells. More...
 
void setupLinkCells ()
 Setup link cells in order to make this calculation faster. More...
 
Vector getSeparation (const Vector &vec1, const Vector &vec2) const
 Get the separation between a pair of vectors. More...
 
bool usesPbc () const
 Do we use pbc to calculate this quantity. More...
 
void addBoxDerivatives (const unsigned &, const Tensor &)
 Add some derivatives for a box. More...
 
void addBoxDerivatives (const Tensor &)
 Add some derivatives of the value to the virial. More...
 
double getCentralAtomDerivative (const unsigned &iatom, const unsigned &jcomp, const Vector &df)
 Retrieve derivative of central atom position wrt jcomp'th component of position of iatom'th atom. More...
 
void setWeight (const double &weight)
 Set a weight for this colvar (used in MEAN and HISTOGRAM) More...
 
void addBoxDerivativesOfWeight (const Tensor &vir)
 Set the derivative of the weight (used in MEAN and HISTOGRAM) More...
 
unsigned getNAtoms () const
 Get the number of atoms in this particular colvar. More...
 
void getCentralAtomIndexList (const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices) const
 Get the indices for the central atom. More...
 
bool setupCurrentAtomList (const unsigned &taskCode)
 This sets up the list of atoms that are involved in this colvar. More...
 
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...
 
void setMaximumNumberOfDerivatives (const unsigned &)
 Set the maximum number of derivatives. More...
 
void addVessel (const std::string &name, const std::string &input, const int numlab=0)
 Add a vessel to the list of vessels. More...
 
void addVessel (Vessel *vv)
 
BridgeVesseladdBridgingVessel (ActionWithVessel *tome)
 Add a bridging vessel to the list of vessels. More...
 
void readVesselKeywords ()
 Complete the setup of this object (this routine must be called after construction of ActionWithValue) More...
 
void needsDerivatives ()
 Turn on the derivatives in the vessel. More...
 
double getTolerance () const
 Return the value of the tolerance. More...
 
double getNLTolerance () const
 Return the value for the neighbor list tolerance. More...
 
unsigned getNumberOfVessels () const
 Get the number of vessels. More...
 
VesselgetPntrToVessel (const unsigned &i)
 Get a pointer to the ith vessel. More...
 
void runAllTasks ()
 Calculate the values of all the vessels. More...
 
void resizeFunctions ()
 Resize all the functions when the number of derivatives change. More...
 
bool calculateAllVessels ()
 This loops over all the vessels calculating them and also sets all the element derivatives equal to zero. More...
 
bool getForcesFromVessels (std::vector< double > &forcesToApply)
 Retrieve the forces from all the vessels (used in apply) More...
 
void accumulateDerivative (const unsigned &ider, const double &df)
 This is used to accumulate the derivatives when we merge using chainRuleForElementDerivatives. More...
 
void clearAfterTask ()
 Clear tempory data that is calculated for each task. More...
 
bool serialCalculation () const
 Is the calculation being done in serial. More...
 
bool usingLowMem () const
 Are we using low memory. More...
 
void setLowMemOption (const bool &)
 Set that we are using low memory. More...
 
unsigned getCurrentNumberOfActiveTasks () const
 Get the number of tasks that are currently active. More...
 
unsigned getActiveTask (const unsigned &ii) const
 Get the ith of the currently active tasks. More...
 
unsigned getPositionInFullTaskList (const unsigned &ii) const
 Get the position of the ith active task in the full list. More...
 
unsigned getCurrentPositionInTaskList () const
 Get the current task's position in the task list. More...
 
unsigned getCurrentTask () const
 Return the number that provides instructions for the current task. More...
 
void deactivateAllTasks ()
 Deactivate all the tasks in the task list. More...
 
void deactivateTasksInRange (const unsigned &lower, const unsigned &upper)
 Deactivate all tasks with i in lower \(\le\) i < upper. More...
 

Protected Attributes

DynamicList< unsigned > atoms_with_derivatives
 A dynamic list containing those atoms with derivatives. More...
 
bool usespecies
 Using the species keyword to read in atoms. More...
 
unsigned nblock
 Number of atoms in each block. More...
 
std::vector< unsigned > decoder
 This is used when turning cvcodes into atom numbers. More...
 
std::vector< std::vector
< unsigned > > 
ablocks
 Blocks of atom numbers. More...
 
unsigned natomsper
 Number of atoms in the cv - set at start of calculation. More...
 
std::vector< unsigned > current_atoms
 Vector containing the indices of the current atoms. More...
 
Atomsatoms
 
std::vector< bool > thisval_wasset
 A boolean that makes sure we don't accumulate very wrong derivatives. More...
 
bool contributorsAreUnlocked
 The terms in the series are locked. More...
 
bool weightHasDerivatives
 Does the weight have derivatives. More...
 
unsigned bridgeVariable
 This is used for numerical derivatives of bridge variables. More...
 

Private Attributes

unsigned myc
 

Detailed Description

Provides the keyword XDISTANCES

Provides the keyword ZDISTANCES

Provides the keyword YDISTANCES

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::multicolvar::XDistances::XDistances ( const ActionOptions ao)

Member Function Documentation

void PLMD::vesselbase::ActionWithVessel::accumulateDerivative ( const unsigned &  ider,
const double &  df 
)
inlineprotectedinherited

This is used to accumulate the derivatives when we merge using chainRuleForElementDerivatives.

void PLMD::Action::activate ( )
virtualinherited

Set action to active.

void PLMD::multicolvar::MultiColvarBase::activateIndexes ( const unsigned &  istart,
const unsigned &  number,
const std::vector< unsigned > &  indexes 
)
virtualinherited

Activate the atoms that have derivatives from a storeDataVessel.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

void PLMD::vesselbase::ActionWithVessel::activateTheseTasks ( std::vector< bool > &  addtionalTasks)
inherited

Switch on additional tasks.

void PLMD::multicolvar::MultiColvar::addAtomsDerivativeOfWeight ( const unsigned &  i,
const Vector wder 
)
inlineprotectedinherited

Set the derivative of the weight (used in MEAN and HISTOGRAM)

void PLMD::multicolvar::MultiColvar::addAtomsDerivatives ( const int &  iatom,
const Vector der 
)
inlineprotectedinherited

Add some derivatives for an atom.

void PLMD::multicolvar::MultiColvarBase::addAtomsDerivatives ( const unsigned &  ielem,
const unsigned &  iatom,
const Vector der 
)
inlineprotectedinherited

Add some derivatives for an atom.

void PLMD::multicolvar::MultiColvarBase::addBoxDerivatives ( const unsigned &  ielem,
const Tensor vir 
)
inlineprotectedinherited

Add some derivatives for a box.

void PLMD::multicolvar::MultiColvarBase::addBoxDerivatives ( const Tensor vir)
inlineprotectedinherited

Add some derivatives of the value to the virial.

void PLMD::multicolvar::MultiColvarBase::addBoxDerivativesOfWeight ( const Tensor vir)
inlineprotectedinherited

Set the derivative of the weight (used in MEAN and HISTOGRAM)

BridgeVessel * PLMD::vesselbase::ActionWithVessel::addBridgingVessel ( ActionWithVessel tome)
protectedinherited

Add a bridging vessel to the list of vessels.

void PLMD::multicolvar::MultiColvar::addCentralAtomDerivatives ( const unsigned &  iatom,
const Tensor der 
)
inlineprotectedinherited

Add derivatives to the central atom position.

void PLMD::multicolvar::MultiColvarBase::addCentralAtomDerivativeToFunction ( const unsigned &  iatom,
const unsigned &  jout,
const unsigned &  base_cv_no,
const Vector der,
MultiColvarFunction func 
)
inherited

Add central atom derivatives to a multicolvar function.

void PLMD::multicolvar::MultiColvar::addColvar ( const std::vector< unsigned > &  newatoms)
protectedinherited

Add a collective variable.

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

Add a value with a name like label.name.

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

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

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

Specify that this Action depends on another one.

void PLMD::vesselbase::ActionWithVessel::addElementDerivative ( const unsigned &  ider,
const double &  der 
)
inlineinherited

Add some derivative of the quantity in the sum wrt to a numbered element.

void PLMD::vesselbase::ActionWithVessel::addElementValue ( const unsigned &  ival,
const double &  val 
)
inlineinherited

Add to an element value.

void PLMD::multicolvar::MultiColvarBase::addOrientationDerivativesToBase ( const unsigned &  iatom,
const unsigned &  jstore,
const unsigned &  base_cv_no,
const std::vector< double > &  weight,
MultiColvarFunction func 
)
virtualinherited

Add derivatives to the orientations.

Reimplemented in PLMD::crystallization::VectorMultiColvar, and PLMD::multicolvar::Density.

void PLMD::multicolvar::MultiColvarBase::addTaskToList ( const unsigned &  taskCode)
protectedinherited

Add a task to the list of tasks.

void PLMD::ActionWithValue::addValue ( )
inherited

Add a value with the name label.

void PLMD::ActionWithValue::addValueWithDerivatives ( )
inherited

Add a value with the name label that has derivatives.

void PLMD::vesselbase::ActionWithVessel::addVessel ( const std::string &  name,
const std::string &  input,
const int  numlab = 0 
)
protectedinherited

Add a vessel to the list of vessels.

void PLMD::vesselbase::ActionWithVessel::addVessel ( Vessel vv)
protectedinherited
void PLMD::multicolvar::MultiColvarBase::addWeightedValueDerivatives ( const unsigned &  iatom,
const unsigned &  base_cv_no,
const double &  weight,
MultiColvarFunction func 
)
virtualinherited

Used to accumulate values.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

void PLMD::multicolvar::MultiColvarBase::apply ( )
virtualinherited

Apply the forces from this action.

Implements PLMD::Action.

Reimplemented in PLMD::multicolvar::Sprint.

virtual void PLMD::vesselbase::ActionWithVessel::applyBridgeForces ( const std::vector< double > &  bb)
inlinevirtualinherited

Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume.

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

void ActionAtomistic::applyForces ( )
inherited
vesselbase::StoreDataVessel * PLMD::multicolvar::MultiColvarBase::buildDataStashes ( )
virtualinherited

Store central atoms so that this can be used in a function.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

void PLMD::multicolvar::MultiColvar::calculate ( )
virtualinherited

Calculate the multicolvar.

Implements PLMD::Action.

bool PLMD::vesselbase::ActionWithVessel::calculateAllVessels ( )
protectedinherited

This loops over all the vessels calculating them and also sets all the element derivatives equal to zero.

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

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

Vector PLMD::multicolvar::MultiColvar::calculateCentralAtomPosition ( )
virtualinherited

Calculate the position of the central atom.

Implements PLMD::multicolvar::MultiColvarBase.

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 PLMD::multicolvar::MultiColvarBase::calculateWeight ( )
inlinevirtualinherited

You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations.

Reimplemented in PLMD::multicolvar::Angles, PLMD::multicolvar::NumberOfLinks, PLMD::multicolvar::Bridge, PLMD::multicolvar::AdjacencyMatrixAction, and PLMD::crystallization::OrientationSphere.

void PLMD::vesselbase::ActionWithVessel::chainRuleForElementDerivatives ( const unsigned &  iout,
const unsigned &  ider,
const double &  df,
Vessel valout 
)
inherited

Merge the derivatives.

void PLMD::vesselbase::ActionWithVessel::chainRuleForElementDerivatives ( const unsigned &  iout,
const unsigned &  ider,
const unsigned &  stride,
const unsigned &  off,
const double &  df,
Vessel valout 
)
inherited
void ActionAtomistic::changeBox ( const Tensor newbox)
inherited

Change the box shape.

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

Reimplemented in PLMD::colvar::ContactMap.

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

Check if the action needs gradient.

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

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

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

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::vesselbase::ActionWithVessel::clearAfterTask ( )
protectedinherited

Clear tempory data that is calculated for each task.

void PLMD::Action::clearDependencies ( )
inherited

Clear the dependence list for this Action.

void PLMD::ActionWithValue::clearDerivatives ( )
virtualinherited

Clear the derivatives of values wrt parameters.

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

void PLMD::multicolvar::MultiColvarBase::clearDerivativesAfterTask ( const unsigned &  ider)
virtualinherited
void PLMD::ActionWithValue::clearInputForces ( )
inherited

Clear the forces on the values.

void PLMD::Action::clearOptions ( )
virtualinherited
void ActionAtomistic::clearOutputForces ( )
inherited
void PLMD::ActionWithValue::componentIsNotPeriodic ( const std::string &  name)
inherited

Set your value component to have no periodicity.

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.

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

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

double PLMD::multicolvar::XDistances::compute ( )
virtual

This is replaced once we have a function to calculate the cv.

Implements PLMD::multicolvar::MultiColvarBase.

void PLMD::multicolvar::MultiColvarBase::copyActiveAtomsToFunction ( MultiColvarBase myfunction,
const unsigned &  start 
)
inherited

Make sure the same list of atoms is active in a function.

void PLMD::multicolvar::MultiColvarBase::copyAtomListToFunction ( MultiColvarBase myfunction)
inherited

Copy the list of atoms involved to a second MultiColvarBase (used by functions)

void PLMD::multicolvar::MultiColvarBase::copyElementsToBridgedColvar ( const double &  weight,
ActionVolume func 
)
virtualinherited
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.

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.

void PLMD::Action::deactivate ( )
inlinevirtualinherited

Set action to inactive.

void PLMD::vesselbase::ActionWithVessel::deactivate_task ( )
virtualinherited

Activate the jth colvar Deactivate the current task in future loops.

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

void PLMD::vesselbase::ActionWithVessel::deactivateAllTasks ( )
protectedinherited

Deactivate all the tasks in the task list.

void PLMD::vesselbase::ActionWithVessel::deactivateTasksInRange ( const unsigned &  lower,
const unsigned &  upper 
)
protectedinherited

Deactivate all tasks with i in lower \(\le\) i < upper.

bool PLMD::vesselbase::ActionWithVessel::derivativesAreRequired ( ) const
inlineinherited

Are derivatives required for this quantity.

double PLMD::multicolvar::MultiColvarBase::doCalculation ( )
virtualinherited

And a virtual function which actually computes the colvar.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

void PLMD::vesselbase::ActionWithVessel::doJobsRequiredBeforeTaskList ( )
virtualinherited
bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const
inlineinherited

Are we not calculating derivatives.

virtual void PLMD::multicolvar::MultiColvarBase::doNotCalculateDirector ( )
inlinevirtualinherited

This makes sure we are not calculating the director when we do LocalAverage.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

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.

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.

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.

void PLMD::vesselbase::ActionWithVessel::finishComputations ( )
virtualinherited

Finish running all the calculations.

void PLMD::multicolvar::MultiColvar::finishTaskListUpdate ( )
virtualinherited

Finish the update of the task list.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

void PLMD::multicolvar::MultiColvarBase::finishWeightedAverageCalculation ( MultiColvarFunction func)
virtualinherited

Used for calculating weighted averages.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

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::multicolvar::MultiColvar::getAbsoluteIndex ( unsigned  iatom) const
inlineinherited

Get the absolute index of atom iatom.

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.

unsigned PLMD::vesselbase::ActionWithVessel::getActiveTask ( const unsigned &  ii) const
inlineprotectedinherited

Get the ith of the currently active tasks.

unsigned PLMD::multicolvar::MultiColvar::getBaseQuantityIndex ( const unsigned &  code)
inlinevirtualinherited

Get base quantity index.

Implements PLMD::multicolvar::MultiColvarBase.

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

Get box shape.

Vector PLMD::multicolvar::XDistances::getCentralAtom ( )
virtual

Get the position of the central atom.

Implements PLMD::multicolvar::MultiColvar.

double PLMD::multicolvar::MultiColvarBase::getCentralAtomDerivative ( const unsigned &  iatom,
const unsigned &  jcomp,
const Vector df 
)
protectedinherited

Retrieve derivative of central atom position wrt jcomp'th component of position of iatom'th atom.

void PLMD::multicolvar::MultiColvarBase::getCentralAtomIndexList ( const unsigned &  ntotal,
const unsigned &  jstore,
const unsigned &  maxder,
std::vector< unsigned > &  indices 
) const
protectedinherited

Get the indices for the central atom.

Vector PLMD::multicolvar::MultiColvarBase::getCentralAtomPosition ( const unsigned &  iatom) const
inherited

Get the position of the iatom th central atom (used in multicolvarfunction)

double PLMD::multicolvar::MultiColvar::getCharge ( unsigned  iatom) const
inlineinherited

Get the charge of atom iatom.

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

Get charge of i-th atom.

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

get a string that contains all the available components

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

get a vector that contains the label for all the components

unsigned PLMD::vesselbase::ActionWithVessel::getCurrentNumberOfActiveTasks ( ) const
inlineprotectedinherited

Get the number of tasks that are currently active.

unsigned PLMD::vesselbase::ActionWithVessel::getCurrentPositionInTaskList ( ) const
inlineprotectedinherited

Get the current task's position in the task list.

unsigned PLMD::vesselbase::ActionWithVessel::getCurrentTask ( ) const
inlineprotectedinherited

Return the number that provides instructions for the current task.

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

Return dependencies.

std::string PLMD::Action::getDocumentation ( ) const
virtualinherited
double PLMD::vesselbase::ActionWithVessel::getElementDerivative ( const unsigned &  ider) const
inlineinherited

Retrieve the derivative of the quantity in the sum wrt to a numbered element.

double PLMD::vesselbase::ActionWithVessel::getElementValue ( const unsigned &  ival) const
inlineinherited

Get the value of this element.

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

Get energy.

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

Check if we are on an exchange step.

bool PLMD::vesselbase::ActionWithVessel::getForcesFromVessels ( std::vector< double > &  forcesToApply)
protectedinherited

Retrieve the forces from all the vessels (used in apply)

unsigned PLMD::vesselbase::ActionWithVessel::getFullNumberOfTasks ( ) const
inlineinherited

Get the full size of the taskList dynamic list.

void PLMD::multicolvar::MultiColvarBase::getIndexList ( const unsigned &  ntotal,
const unsigned &  jstore,
const unsigned &  maxder,
std::vector< unsigned > &  indices 
)
virtualinherited

Get the list of indices that have derivatives.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

unsigned PLMD::multicolvar::MultiColvarBase::getInternalIndex ( const AtomNumber iatom) const
inherited

Return the number of the colvar in which iatom is the first atom.

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

Returns the label.

double PLMD::multicolvar::MultiColvar::getMass ( unsigned  iatom) const
inlineinherited

Get the mass of atom iatom.

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::multicolvar::MultiColvarBase::getNAtoms ( ) const
inlineprotectedinherited

Get the number of atoms in this particular colvar.

double PLMD::vesselbase::ActionWithVessel::getNLTolerance ( ) const
inlineprotectedinherited

Return the value for the neighbor list tolerance.

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

Get number of available atoms.

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

Returns the number of values defined.

unsigned PLMD::multicolvar::MultiColvarBase::getNumberOfDerivatives ( )
inlinevirtualinherited

Get the number of derivatives for this action.

Implements PLMD::ActionWithValue.

unsigned PLMD::multicolvar::MultiColvarBase::getNumberOfQuantities ( )
inlinevirtualinherited

Get the number of quantities that are calculated each time.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

Reimplemented in PLMD::crystallization::VectorMultiColvar, PLMD::multicolvar::LocalAverage, and PLMD::multicolvar::Density.

unsigned PLMD::vesselbase::ActionWithVessel::getNumberOfVessels ( ) const
inlineprotectedinherited

Get the number of vessels.

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

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

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)

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

Get reference to Pbc.

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

Return a pointer to the component by index.

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

Return a pointer to the value by name.

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

Get a pointer to the default value.

Vessel * PLMD::vesselbase::ActionWithVessel::getPntrToVessel ( const unsigned &  i)
inlineprotectedinherited

Get a pointer to the ith vessel.

const Vector & PLMD::multicolvar::MultiColvar::getPosition ( unsigned  iatom) const
inlineinherited

Get the position of atom iatom.

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

unsigned PLMD::vesselbase::ActionWithVessel::getPositionInFullTaskList ( const unsigned &  ii) const
inlineprotectedinherited

Get the position of the ith active task in the full list.

Vector PLMD::multicolvar::MultiColvar::getPositionOfAtomForLinkCells ( const unsigned &  iatom)
inlinevirtualinherited

This is used in MultiColvarBase only - it is used to setup the link cells.

Implements PLMD::multicolvar::MultiColvarBase.

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

Get the array of all positions.

Vector PLMD::multicolvar::MultiColvarBase::getSeparation ( const Vector vec1,
const Vector vec2 
) const
protectedinherited

Get the separation between a pair of vectors.

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.

double PLMD::vesselbase::ActionWithVessel::getTolerance ( ) const
inlineprotectedinherited

Return the value of the tolerance.

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
void PLMD::multicolvar::MultiColvarBase::getValueForTask ( const unsigned &  iatom,
std::vector< double > &  vals 
)
virtualinherited

Get the value for this task.

Reimplemented in PLMD::crystallization::VectorMultiColvar, and PLMD::multicolvar::Density.

Vessel * PLMD::vesselbase::ActionWithVessel::getVesselWithName ( const std::string &  mynam)
inherited

Return a particular named vessel.

virtual bool PLMD::multicolvar::MultiColvarBase::hasDifferentiableOrientation ( ) const
inlinevirtualinherited

This is true if multicolvar is calculating a vector or if the multicolvar is the density.

Reimplemented in PLMD::crystallization::VectorMultiColvar, and PLMD::multicolvar::Density.

bool PLMD::Action::isActive ( ) const
inlineinherited

Check if action is active.

bool PLMD::multicolvar::MultiColvar::isCurrentlyActive ( const unsigned &  code)
inlinevirtualinherited

Is this atom currently being copied.

Implements PLMD::multicolvar::MultiColvarBase.

virtual bool PLMD::multicolvar::MultiColvarBase::isDensity ( )
inlinevirtualinherited

Is this a density?

Reimplemented in PLMD::multicolvar::Density.

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

Check if an option is on.

bool PLMD::multicolvar::XDistances::isPeriodic ( )
inlinevirtual

Returns the number of coordinates of the field.

Implements PLMD::vesselbase::ActionWithVessel.

void PLMD::vesselbase::ActionWithVessel::lockContributors ( )
inherited
void PLMD::ActionAtomistic::lockRequests ( )
inlinevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::Mapping.

void PLMD::multicolvar::MultiColvarBase::mergeDerivatives ( const unsigned &  ider,
const double &  df 
)
virtualinherited

These replace the functions in ActionWithVessel to make the code faster.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

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.

void PLMD::vesselbase::ActionWithVessel::needsDerivatives ( )
protectedinherited

Turn on the derivatives in the vessel.

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.

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::multicolvar::MultiColvarBase::performTask ( )
virtualinherited

Perform one of the tasks.

Implements PLMD::vesselbase::ActionWithVessel.

void PLMD::multicolvar::MultiColvarBase::prepare ( )
virtualinherited

Prepare for the calculation.

Reimplemented from PLMD::Action.

void PLMD::multicolvar::MultiColvarBase::quotientRule ( const unsigned &  uder,
const unsigned &  vder,
const unsigned &  iout 
)
inherited

Calculate and store getElementValue(uder)/getElementValue(vder) and its derivatives in getElementValue(iout)

void PLMD::multicolvar::MultiColvar::readAtoms ( int &  natoms)
protectedinherited

Read in all the keywords that can be used to define atoms.

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::multicolvar::MultiColvar::readAtomsLikeKeyword ( const std::string &  key,
int &  natoms 
)
protectedinherited

Read in ATOMS keyword.

void PLMD::multicolvar::MultiColvar::readThreeGroups ( const std::string &  key1,
const std::string &  key2,
const std::string &  key3,
const bool &  allow2 
)
protectedinherited

Read three groups.

void PLMD::multicolvar::MultiColvar::readTwoGroups ( const std::string &  key1,
const std::string &  key2 
)
protectedinherited

Read two group keywords.

void PLMD::vesselbase::ActionWithVessel::readVesselKeywords ( )
protectedinherited

Complete the setup of this object (this routine must be called after construction of ActionWithValue)

void PLMD::multicolvar::XDistances::registerKeywords ( Keywords keys)
static
void ActionAtomistic::requestAtoms ( const std::vector< AtomNumber > &  a)
inherited

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 PLMD::vesselbase::ActionWithVessel::resizeFunctions ( )
protectedinherited

Resize all the functions when the number of derivatives change.

void ActionAtomistic::retrieveAtoms ( )
inherited
Vector PLMD::multicolvar::MultiColvarBase::retrieveCentralAtomPos ( )
inherited

Retrieve the position of the central atom.

void PLMD::vesselbase::ActionWithVessel::retrieveDomain ( std::string &  min,
std::string &  max 
)
virtualinherited

What are the domains of the base quantities.

Reimplemented in PLMD::multicolvar::Torsions.

void PLMD::vesselbase::ActionWithVessel::runAllTasks ( )
protectedinherited

Calculate the values of all the vessels.

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.

bool PLMD::vesselbase::ActionWithVessel::serialCalculation ( ) const
inlineprotectedinherited

Is the calculation being done in serial.

void PLMD::vesselbase::ActionWithVessel::setElementDerivative ( const unsigned &  ider,
const double &  der 
)
inlineinherited

Set the derivative of the jth element wrt to a numbered element.

void PLMD::vesselbase::ActionWithVessel::setElementValue ( const unsigned &  ival,
const double &  val 
)
inlineinherited

Set the value of the element.

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

Add the forces to the atoms.

void PLMD::ActionWithValue::setGradientsIfNeeded ( )
inherited

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

void PLMD::multicolvar::MultiColvarBase::setLinkCellCutoff ( const double &  lcut)
protectedinherited

Set the value of the cutoff for the link cells.

void PLMD::vesselbase::ActionWithVessel::setLowMemOption ( const bool &  l)
inlineprotectedinherited

Set that we are using low memory.

void PLMD::vesselbase::ActionWithVessel::setMaximumNumberOfDerivatives ( const unsigned &  )
protectedinherited

Set the maximum number of derivatives.

void PLMD::ActionWithValue::setNotPeriodic ( )
inherited

Set your default value to have no periodicity.

void PLMD::Action::setOption ( const std::string &  s)
virtualinherited
void PLMD::ActionWithValue::setPeriodic ( const std::string &  min,
const std::string &  max 
)
inherited

Set the value to be periodic with a particular domain.

bool PLMD::multicolvar::MultiColvarBase::setupCurrentAtomList ( const unsigned &  taskCode)
protectedinherited

This sets up the list of atoms that are involved in this colvar.

void PLMD::multicolvar::MultiColvarBase::setupLinkCells ( )
protectedinherited

Setup link cells in order to make this calculation faster.

void PLMD::multicolvar::MultiColvarBase::setupMultiColvarBase ( )
protectedinherited

Finish setting up the multicolvar base.

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

Set the default value (the one without name)

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

Set the value.

void PLMD::multicolvar::MultiColvarBase::setWeight ( const double &  weight)
inlineprotectedinherited

Set a weight for this colvar (used in MEAN and HISTOGRAM)

void PLMD::multicolvar::MultiColvar::threeBodyNeighborList ( const SwitchingFunction sf)
protectedinherited

This is used to make neighbor list update fast when three atoms are involved in the colvar (e.g. ANGLES, WATERBRIDGE)

void PLMD::multicolvar::MultiColvarBase::turnOnDerivatives ( )
virtualinherited

Turn on the derivatives.

Reimplemented from PLMD::ActionWithValue.

void PLMD::vesselbase::ActionWithVessel::unlockContributors ( )
inherited
void PLMD::ActionAtomistic::unlockRequests ( )
inlinevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::Mapping.

virtual void PLMD::Action::update ( )
inlinevirtualinherited
void PLMD::multicolvar::MultiColvar::updateActiveAtoms ( )
virtualinherited

Update the atoms that have derivatives.

Implements PLMD::multicolvar::MultiColvarBase.

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

The components in the action will depend on the user.

void PLMD::ActionWithValue::useNumericalDerivatives ( )
inlineinherited

This forces the class to use numerical derivatives.

bool PLMD::multicolvar::MultiColvarBase::usesPbc ( ) const
inlineprotectedinherited

Do we use pbc to calculate this quantity.

bool PLMD::vesselbase::ActionWithVessel::usingLowMem ( ) const
inlineprotectedinherited

Are we using low memory.

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

Issue a warning.

Member Data Documentation

std::vector< std::vector<unsigned> > PLMD::multicolvar::MultiColvarBase::ablocks
protectedinherited

Blocks of atom numbers.

Atoms& PLMD::ActionAtomistic::atoms
protectedinherited
DynamicList<unsigned> PLMD::multicolvar::MultiColvarBase::atoms_with_derivatives
protectedinherited

A dynamic list containing those atoms with derivatives.

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable
protectedinherited

This is used for numerical derivatives of bridge variables.

Communicator& PLMD::Action::comm
inherited
bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked
protectedinherited

The terms in the series are locked.

std::vector<unsigned> PLMD::multicolvar::MultiColvarBase::current_atoms
protectedinherited

Vector containing the indices of the current atoms.

std::vector<unsigned> PLMD::multicolvar::MultiColvarBase::decoder
protectedinherited

This is used when turning cvcodes into atom numbers.

std::set<FILE*> PLMD::Action::files
inherited
const Keywords& PLMD::Action::keywords
inherited
Log& PLMD::Action::log
inherited

Reference to the log stream.

Communicator& PLMD::Action::multi_sim_comm
inherited
unsigned PLMD::multicolvar::XDistances::myc
private
unsigned PLMD::multicolvar::MultiColvarBase::natomsper
protectedinherited

Number of atoms in the cv - set at start of calculation.

unsigned PLMD::multicolvar::MultiColvarBase::nblock
protectedinherited

Number of atoms in each block.

PlumedMain& PLMD::Action::plumed
inherited

Reference to main plumed object.

std::vector<bool> PLMD::vesselbase::ActionWithVessel::thisval_wasset
protectedinherited

A boolean that makes sure we don't accumulate very wrong derivatives.

bool PLMD::multicolvar::MultiColvarBase::usespecies
protectedinherited

Using the species keyword to read in atoms.

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives
protectedinherited

Does the weight have derivatives.


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