Provides the keyword XANGLES More...
Public Types | |
typedef std::vector< Action * > | Dependencies |
Public Member Functions | |
XAngles (const ActionOptions &) | |
virtual void | activate () |
Set action to active. More... | |
void | addAtomDerivatives (const int &, const unsigned &, const Vector &, multicolvar::AtomValuePack &) const |
Add some derivatives to a particular component of a particular atom. 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 | addDependency (Action *) |
Specify that this Action depends on another one. 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 | allowToAccessGlobalForces () |
Allow calls to modifyGlobalForce() More... | |
void | apply () override |
Apply the forces from this action. More... | |
virtual void | applyBridgeForces (const std::vector< double > &bb) |
Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume. More... | |
void | applyForces () |
void | applyPbc (std::vector< Vector > &dlist, unsigned max_index=0) const |
Apply PBCs over a set of distance vectors. More... | |
virtual void | beforeUpdate () |
Before Update. More... | |
StoreDataVessel * | buildDataStashes (ActionWithVessel *actionThatUses) |
Ensure that data required in other vessels is stored. More... | |
void | calculate () override |
Do the calculation. More... | |
void | calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum) |
Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More... | |
void | calculateFromPDB (const PDB &) |
Calculate the action given a pdb file as input. More... | |
void | calculateNumericalDerivatives (ActionWithValue *a=NULL) override |
Calculate numerical derivatives. More... | |
double | calculateWeight (const unsigned &taskCode, const double &weight, AtomValuePack &) const override |
You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations. More... | |
void | changeBox (const Tensor &newbox) |
Change the box shape. More... | |
virtual void | checkFieldsAllowed () |
virtual bool | checkNeedsGradients () const |
Check if the action needs gradient. More... | |
bool | checkNumericalDerivatives () const override |
Check if numerical derivatives should be used. More... | |
virtual bool | checkNumericalDerivatives () const |
Check if numerical derivatives should be performed. More... | |
void | checkRead () |
Check if Action was properly read. More... | |
bool | checkUpdate () const |
Check if action should be updated. More... | |
std::string | cite (const std::string &s) |
Cite a paper see PlumedMain::cite. More... | |
void | clearDependencies () |
Clear the dependence list for this Action. More... | |
virtual void | clearDerivatives () |
Clear the derivatives of values wrt parameters. More... | |
void | clearInputForces () |
Clear the forces on the values. More... | |
virtual void | clearOptions () |
void | clearOutputForces () |
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... | |
double | compute (const unsigned &tindex, AtomValuePack &myatoms) const override |
This is replaced once we have a function to calculate the cv. More... | |
Value * | copyOutput (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... | |
Value * | copyOutput (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... | |
virtual void | deactivate () |
Set action to inactive. More... | |
bool | derivativesAreRequired () const |
Are derivatives required for this quantity. More... | |
virtual void | doJobsRequiredBeforeTaskList () |
Do any jobs that are required before the task list is undertaken. More... | |
bool | doNotCalculateDerivatives () const override |
Ensure that derivatives are only calculated when needed. More... | |
virtual void | doNotCalculateDirector () |
This makes sure we are not calculating the director when we do LocalAverage. More... | |
void | doNotForce () |
Skip atom forces - use with care. More... | |
void | doNotRetrieve () |
Skip atom retrieval - use with care. More... | |
void | error (const std::string &msg) const |
Crash calculation and print documentation. More... | |
bool | exists (const std::string &name) const |
Check if a value with a particular name is present. More... | |
void | exit (int c=0) |
Exit with error code c. More... | |
int | fclose (FILE *fp) |
Closes a file opened with Action::fclose(). More... | |
void | fflush () |
Tell to the Action to flush open files. More... | |
virtual void | finishComputations (const std::vector< double > &buffer) |
Finish running all the calculations. More... | |
FILE * | fopen (const char *path, const char *mode) |
Opens a file. More... | |
AtomNumber | getAbsoluteIndex (int i) const |
Get the absolute index of an atom. More... | |
virtual const std::vector< AtomNumber > & | getAbsoluteIndexes () const |
Get the vector of absolute indexes. More... | |
virtual AtomNumber | getAbsoluteIndexOfCentralAtom (const unsigned &i) const |
Get the absolute index of the central atom. More... | |
unsigned | getActiveTask (const unsigned &ii) const |
Get the ith of the currently active tasks. More... | |
MultiColvarBase * | getBaseMultiColvar (const unsigned &icolv) const |
Get the icolv th base multicolvar. More... | |
const Tensor & | getBox () const |
Get box shape. More... | |
virtual void | getCentralAtomPack (const unsigned &basn, const unsigned &curr, CatomPack &mypack) |
virtual Vector | getCentralAtomPos (const unsigned &curr) |
Get the index where the central atom is stored. More... | |
double | getCharge (int i) const |
Get charge of i-th atom. 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... | |
bool | getCPT () const |
Return true if we are doing at a checkpoint step. More... | |
unsigned | getCurrentNumberOfActiveTasks () const |
Get the number of tasks that are currently active. More... | |
const Dependencies & | getDependencies () const |
Return dependencies. More... | |
virtual std::string | getDocumentation () const |
const double & | getEnergy () const |
Get energy. More... | |
bool | getExchangeStep () const |
Check if we are on an exchange step. More... | |
unsigned | getFullNumberOfTasks () const |
Get the full size of the taskList dynamic list. More... | |
const Vector & | getGlobalPosition (AtomNumber) const |
Get position of i-th atom (access by absolute AtomNumber). More... | |
virtual void | getInputData (const unsigned &ind, const bool &normed, const multicolvar::AtomValuePack &myatoms, std::vector< double > &orient) const |
Get an input data. More... | |
virtual MultiValue & | getInputDerivatives (const unsigned &iatom, const bool &normed, const multicolvar::AtomValuePack &myatoms) const |
Retrieve the input derivatives. More... | |
std::string | getKeyword (const std::string &key) |
Just read one of the keywords and return the whole thing as a string. More... | |
const std::string & | getLabel () const |
Returns the label. More... | |
double | getMass (int i) const |
Get mass of i-th atom. More... | |
const std::string & | getName () const |
Returns the name. More... | |
unsigned | getNumberOfAtoms () const |
Get number of available atoms. More... | |
unsigned | getNumberOfBaseMultiColvars () const |
Get the number of base multicolvars. More... | |
int | getNumberOfComponents () const |
Returns the number of values defined. More... | |
unsigned | getNumberOfDerivatives () override |
Get the number of derivatives for this action. More... | |
virtual unsigned | getNumberOfQuantities () const |
Get the number of quantities that are calculated during each task. More... | |
unsigned | getNumberOfVessels () const |
Get the number of vessels. 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... | |
const Pbc & | getPbc () const |
Get reference to Pbc. More... | |
Vessel * | getPntrToVessel (const unsigned &i) |
Get a pointer to the ith vessel. More... | |
const Vector & | getPosition (int) const |
Get position of i-th atom (access by relative index) More... | |
unsigned | getPositionInCurrentTaskList (const unsigned &myind) const |
Return the position in the current task list. More... | |
unsigned | getPositionInFullTaskList (const unsigned &ii) const |
Get the position of the ith active task in the full list. More... | |
virtual Vector | getPositionOfAtomForLinkCells (const unsigned &iatom) const |
This gets the position of an atom for the link cell setup. More... | |
const std::vector< Vector > & | getPositions () const |
Get the array of all positions. More... | |
bool | getRestart () const |
Return true if we are doing a restart. More... | |
Vector | getSeparation (const Vector &vec1, const Vector &vec2) const |
Get the separation between a pair of vectors. More... | |
long int | getStep () const |
Return the present timestep. More... | |
unsigned | getTaskCode (const unsigned &ii) const |
Get the code for the ii th task in the list. More... | |
double | getTime () const |
Return the present time. More... | |
double | getTimeStep () const |
Return the timestep. More... | |
unsigned | getTotAtoms () const |
Get total number of atoms, including virtual ones. More... | |
const std::set< AtomNumber > & | getUnique () const |
const std::set< AtomNumber > & | getUniqueLocal () const |
Vessel * | getVesselWithName (const std::string &mynam) |
These are overwritten in MultiColvarFunction. More... | |
virtual bool | hasDifferentiableOrientation () const |
This is true if multicolvar is calculating a vector or if the multicolvar is the density. 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... | |
bool | isActive () const |
Check if action is active. More... | |
virtual bool | isCurrentlyActive (const unsigned &code) |
Checks if an task is being performed at the present time. More... | |
virtual bool | isDensity () const |
Is this a density? More... | |
bool | isOptionOn (const std::string &s) const |
Check if an option is on. More... | |
bool | isPeriodic () override |
Returns the number of coordinates of the field. More... | |
void | lockContributors () |
void | lockRequests () override |
void | makeWhole () |
Make atoms whole, assuming they are in the proper order. More... | |
double & | modifyForceOnEnergy () |
Get a reference to force on energy. More... | |
double & | modifyForceOnExtraCV () |
Get a reference to force on extraCV. More... | |
std::vector< Vector > & | modifyForces () |
Get a reference to forces array. More... | |
Vector & | modifyGlobalForce (AtomNumber) |
Get modifiable force of i-th atom (access by absolute AtomNumber). More... | |
Pbc & | modifyGlobalPbc () |
Get modifiable PBC Should be used by action that need to modify the stored box. More... | |
Vector & | modifyGlobalPosition (AtomNumber) |
Get modifiable position of i-th atom (access by absolute AtomNumber). More... | |
Tensor & | modifyGlobalVirial () |
Get modifiable virial Should be used by action that need to modify the stored virial. More... | |
Tensor & | modifyVirial () |
Get a reference to virial array. More... | |
virtual void | normalizeVector (std::vector< double > &vals) const |
These normalizes vectors and is used in StoreDataVessel. More... | |
virtual void | normalizeVectorDerivatives (MultiValue &myvals) const |
template<class T > | |
void | parse (const std::string &key, T &t) |
Parse one keyword as generic type. 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 | parseFlag (const std::string &key, bool &t) |
Parse one keyword as boolean flag. More... | |
template<class T > | |
bool | parseNumbered (const std::string &key, const int no, T &t) |
Parse one numbered keyword as generic type. More... | |
template<class T > | |
bool | parseNumberedVector (const std::string &key, const int no, std::vector< T > &t) |
Parse a vector with a number. More... | |
template<class T > | |
void | parseVector (const std::string &key, std::vector< T > &t) |
Parse one keyword as std::vector. More... | |
void | pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const |
Applies PBCs to a seriens of positions or distances. More... | |
Vector | pbcDistance (const Vector &, const Vector &) const |
Compute the pbc distance between two positions. More... | |
void | performTask (const unsigned &, const unsigned &, MultiValue &) const override |
Perform one of the tasks. More... | |
void | prepare () override |
Do some setup before the calculation. More... | |
void | readAtomsFromPDB (const PDB &pdb) override |
Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More... | |
void | requestAtoms (const std::vector< AtomNumber > &a, const bool clearDep=true) |
Request an array of atoms. More... | |
void | retrieveAtoms () override |
This is overwritten here in order to make sure that we do not retrieve atoms multiple times. More... | |
virtual void | retrieveDomain (std::string &min, std::string &max) |
What are the domains of the base quantities. More... | |
virtual void | runFinalJobs () |
RunFinalJobs This method is called once at the very end of the calculation. More... | |
void | setForcesOnAtoms (const std::vector< double > &forcesToApply, unsigned ind=0) |
Add the forces to the atoms. More... | |
void | setGradientsIfNeeded () |
Calculate the gradients and store them for all the values (need for projections) More... | |
void | setNotPeriodic () |
Set your default value to have no periodicity. More... | |
virtual void | setOption (const std::string &s) |
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... | |
bool | storedValueIsActive (const unsigned &iatom) |
Is the iatom'th stored value currently active. More... | |
bool | taskIsCurrentlyActive (const unsigned &index) const |
Check whether or not a particular task is currently active. More... | |
bool | threadSafe () const override |
Is it safe to use multithreading. More... | |
virtual void | transformBridgedDerivatives (const unsigned ¤t, MultiValue &invals, MultiValue &outvals) const |
Do the task if we have a bridge. More... | |
void | turnOnDerivatives () override |
Turn on the derivatives. More... | |
void | unlockRequests () override |
virtual void | update () |
Update. More... | |
virtual void | updateActiveAtoms (AtomValuePack &myatoms) const |
Update the active atoms. More... | |
void | updateUniqueLocal () |
updates local unique atoms More... | |
void | useNumericalDerivatives () |
This forces the class to use numerical derivatives. More... | |
bool | usesPbc () const |
Do we use pbc to calculate this quantity. More... | |
void | warning (const std::string &msg) |
Issue a warning. More... | |
bool | weightWithDerivatives () const |
Does the weight have derivatives. More... | |
Static Public Member Functions | |
static void | componentsAreNotOptional (Keywords &keys) |
Puts a message into the manual that the components always output. More... | |
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 | registerKeywords (Keywords &keys) |
static void | useCustomisableComponents (Keywords &keys) |
The components in the action will depend on the user. More... | |
Public Attributes | |
Communicator & | comm |
std::set< FILE * > | files |
const Keywords & | keywords |
Log & | log |
Reference to the log stream. More... | |
Communicator & | multi_sim_comm |
PlumedMain & | plumed |
Reference to main plumed object. More... | |
Protected Member Functions | |
void | accumulateSymmetryFunction (const int &ival, const unsigned &iatom, const double &val, const Vector &der, const Tensor &vir, multicolvar::AtomValuePack &myatoms) const |
This is used to accumulate functions of the coordination sphere. Ensures weights are taken into account. More... | |
BridgeVessel * | addBridgingVessel (ActionWithVessel *tome) |
Add a bridging vessel to the list of vessels. More... | |
void | addTaskToList (const unsigned &taskCode) |
Add a task to the list of tasks. 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 (std::unique_ptr< Vessel > vv) |
void | buildSets () |
Build sets by taking one multicolvar from each base. More... | |
void | calculateAllVessels (const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list) |
This loops over all the vessels calculating them and also sets all the element derivatives equal to zero. More... | |
void | deactivateAllTasks () |
Deactivate all the tasks in the task list. More... | |
void | decodeIndexToAtoms (const unsigned &taskCode, std::vector< unsigned > &atoms) const |
Decode indices if there are 2 or 3 atoms involved. More... | |
bool | filtersUsedAsInput () |
Function that recursively checks if filters have been used in the input to a multicolvar we need this to ensure that setupLinkCells is run in calculate with some actions. More... | |
bool | getForcesFromVessels (std::vector< double > &forcesToApply) |
Retrieve the forces from all the vessels (used in apply) More... | |
double | getLinkCellCutoff () const |
Get the cutoff for the link cells. More... | |
double | getNLTolerance () const |
Return the value for the neighbor list tolerance. More... | |
Value * | getPntrToComponent (int i) |
Return a pointer to the component by index. More... | |
Value * | getPntrToComponent (const std::string &name) |
Return a pointer to the value by name. More... | |
Value * | getPntrToValue () |
Get a pointer to the default value. More... | |
unsigned | getSizeOfBuffer (unsigned &bufsize) |
Get the size of the buffer. More... | |
double | getTolerance () const |
Return the value of the tolerance. More... | |
void | mergeInputDerivatives (const unsigned &ival, const unsigned &start, const unsigned &end, const unsigned &jatom, const std::vector< double > &der, MultiValue &myder, AtomValuePack &myatoms) const |
This routine take the vector of input derivatives and adds all the vectors to ivalth output derivatives In other words end-start sets of derivatives come in and one set of derivatives come out. More... | |
void | needsDerivatives () |
Turn on the derivatives in the vessel. More... | |
bool | parseMultiColvarAtomList (const std::string &key, const int &num, std::vector< AtomNumber > &t) |
Read in some atoms. More... | |
void | readAtomsLikeKeyword (const std::string &key, const int &natoms, std::vector< AtomNumber > &all_atoms) |
Read in ATOMS keyword. More... | |
void | readGroupKeywords (const std::string &key0, const std::string &key1, const std::string &key2, const std::string &key3, const bool &no_third_dim_accum, const bool &symmetric, std::vector< AtomNumber > &all_atoms) |
Read in three groups of atoms. More... | |
void | readThreeGroups (const std::string &key1, const std::string &key2, const std::string &key3, const bool &allow2, const bool &no_third_dim_accum, std::vector< AtomNumber > &all_atoms) |
Read in three groups of atoms and construct CVs involving at least one. More... | |
void | readTwoGroups (const std::string &key0, const std::string &key1, const std::string &key2, std::vector< AtomNumber > &all_atoms) |
Read in two groups of atoms and setup multicolvars to calculate. More... | |
void | readVesselKeywords () |
Complete the setup of this object (this routine must be called after construction of ActionWithValue) More... | |
void | resizeBookeepingArray (const unsigned &num1, const unsigned &num2) |
This resizes the arrays that are used for link cell update. More... | |
void | resizeFunctions () |
Resize all the functions when the number of derivatives change. More... | |
void | runAllTasks () |
Calculate the values of all the vessels. More... | |
bool | serialCalculation () const |
Is the calculation being done in serial. More... | |
void | setAtomsForCentralAtom (const std::vector< bool > &catom_ind) |
Set which atoms are to be used to calculate the central atom position. More... | |
void | setExtraCV (const std::string &name) |
void | setLinkCellCutoff (const double &lcut, double tcut=-1.0) |
Set the value of the cutoff for the link cells. More... | |
void | setLowMemOption (const bool &) |
Set that we are using low memory. More... | |
void | setupActiveTaskSet (std::vector< unsigned > &active_tasks, const std::string &input_label) |
Setup the link cells and neighbour list stuff. More... | |
bool | setupCurrentAtomList (const unsigned &taskCode, AtomValuePack &myatoms) const |
This sets up the list of atoms that are involved in this colvar. More... | |
void | setupLinkCells () |
Setup link cells in order to make this calculation faster. More... | |
void | setupMultiColvarBase (const std::vector< AtomNumber > &atoms) |
Finish setting up the multicolvar base. More... | |
void | setupNonUseSpeciesLinkCells (const unsigned &) |
This does setup of link cell stuff that is specific to the non-use of the usespecies keyword. More... | |
void | setValue (const double &d) |
Set the default value (the one without name) More... | |
void | splitInputDerivatives (const unsigned &ival, const unsigned &start, const unsigned &end, const unsigned &jatom, const std::vector< double > &der, MultiValue &myder, AtomValuePack &myatoms) const |
This routine take the ith set of input derivatives and adds it to each of the (end-start) output derivatives In other words one set of derivatives comes in and end-start sets of derivatives come out. More... | |
bool | usingLowMem () const |
Are we using low memory. More... | |
Protected Attributes | |
std::vector< std::vector< unsigned > > | ablocks |
Blocks of atom numbers. More... | |
std::vector< std::pair< unsigned, unsigned > > | atom_lab |
This is used to keep track of what is calculated where. More... | |
Atoms & | atoms |
Matrix< std::pair< unsigned, unsigned > > | bookeeping |
This remembers where the boundaries are for the tasks. It makes link cells work fast. More... | |
unsigned | bridgeVariable |
This is used for numerical derivatives of bridge variables. More... | |
bool | contributorsAreUnlocked |
The terms in the series are locked. More... | |
std::vector< unsigned > | decoder |
This is used when turning cvcodes into atom numbers. More... | |
bool | dertime |
This is also used to minimise computational expense in complex functions. More... | |
bool | matsums |
Are we doing sums of matrix rows. More... | |
std::vector< vesselbase::StoreDataVessel * > | mybasedata |
The vessels in these multicolvars in which the data is stored. More... | |
std::vector< MultiColvarBase * > | mybasemulticolvars |
The multicolvars from which we construct these quantities. More... | |
StoreDataVessel * | mydata |
A pointer to the object that stores data. More... | |
unsigned | nblock |
Number of atoms in each block. More... | |
std::vector< unsigned > | taskFlags |
This list is used to update the neighbor list. More... | |
bool | usespecies |
Using the species keyword to read in atoms. More... | |
bool | weightHasDerivatives |
Does the weight have derivatives. More... | |
Private Attributes | |
unsigned | myc |
SwitchingFunction | sf1 |
bool | use_sf |
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inherited |
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explicit |
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protectedinherited |
This is used to accumulate functions of the coordination sphere. Ensures weights are taken into account.
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virtualinherited |
Set action to active.
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inherited |
Add some derivatives to a particular component of a particular atom.
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protectedinherited |
Add a bridging vessel to the list of vessels.
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inherited |
Add a value with a name like label.name.
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inherited |
Add a value with a name like label.name that has derivatives.
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inherited |
Specify that this Action depends on another one.
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protectedinherited |
Add a task to the list of tasks.
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inherited |
Add a value with the name label.
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inherited |
Add a value with the name label that has derivatives.
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protectedinherited |
Add a vessel to the list of vessels.
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protectedinherited |
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inlineinherited |
Allow calls to modifyGlobalForce()
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overridevirtualinherited |
Apply the forces from this action.
Implements PLMD::Action.
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inlinevirtualinherited |
Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.
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inherited |
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inherited |
Apply PBCs over a set of distance vectors.
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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.
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inherited |
Ensure that data required in other vessels is stored.
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protectedinherited |
Build sets by taking one multicolvar from each base.
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overridevirtualinherited |
Do the calculation.
Implements PLMD::Action.
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protectedinherited |
This loops over all the vessels calculating them and also sets all the element derivatives equal to zero.
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inherited |
Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic.
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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
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overridevirtualinherited |
Calculate numerical derivatives.
Reimplemented from PLMD::ActionAtomistic.
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overridevirtual |
You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations.
Reimplemented from PLMD::multicolvar::MultiColvarBase.
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inherited |
Change the box shape.
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inlinevirtualinherited |
Reimplemented in PLMD::piv::PIV, and PLMD::colvar::ContactMap.
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inlinevirtualinherited |
Check if the action needs gradient.
Reimplemented in PLMD::bias::MetaD, PLMD::bias::PBMetaD, and PLMD::generic::DumpProjections.
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inlineoverridevirtualinherited |
Check if numerical derivatives should be used.
Reimplemented from PLMD::Action.
|
inlinevirtualinherited |
Check if numerical derivatives should be performed.
Reimplemented in PLMD::ActionWithValue.
|
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
|
inherited |
Check if action should be updated.
|
inherited |
Cite a paper see PlumedMain::cite.
|
inherited |
Clear the dependence list for this Action.
|
virtualinherited |
Clear the derivatives of values wrt parameters.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.
|
inherited |
Clear the forces on the values.
|
virtualinherited |
|
inherited |
|
inherited |
Set your value component to have no periodicity.
|
inherited |
Set the value to be periodic with a particular domain.
|
staticinherited |
Puts a message into the manual that the components always output.
|
overridevirtual |
This is replaced once we have a function to calculate the cv.
Implements PLMD::multicolvar::MultiColvarBase.
|
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.
|
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.
|
inlinevirtualinherited |
Set action to inactive.
|
protectedinherited |
Deactivate all the tasks in the task list.
|
protectedinherited |
Decode indices if there are 2 or 3 atoms involved.
|
inlineinherited |
Are derivatives required for this quantity.
|
virtualinherited |
Do any jobs that are required before the task list is undertaken.
Reimplemented in PLMD::manyrestraints::ManyRestraintsBase, PLMD::multicolvar::VolumeGradientBase, and PLMD::multicolvar::MultiColvarFilter.
|
inlineoverridevirtualinherited |
Ensure that derivatives are only calculated when needed.
Reimplemented from PLMD::ActionWithValue.
|
inlinevirtualinherited |
This makes sure we are not calculating the director when we do LocalAverage.
Reimplemented in PLMD::crystallization::VectorMultiColvar.
|
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.
|
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.
|
inherited |
Crash calculation and print documentation.
|
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.
|
inherited |
Exit with error code c.
|
inherited |
Closes a file opened with Action::fclose().
|
inherited |
Tell to the Action to flush open files.
|
protectedinherited |
Function that recursively checks if filters have been used in the input to a multicolvar we need this to ensure that setupLinkCells is run in calculate with some actions.
|
virtualinherited |
Finish running all the calculations.
|
inherited |
Opens a file.
This is similar to plain fopen, but with some extra functionality.
|
inlineinherited |
Get the absolute index of an atom.
|
inlinevirtualinherited |
Get the vector of absolute indexes.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.
|
inlinevirtualinherited |
Get the absolute index of the central atom.
Reimplemented in PLMD::adjmat::ClusterWithSurface, PLMD::adjmat::AdjacencyMatrixBase, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ActionWithInputMatrix, PLMD::crystallization::MoleculeOrientation, and PLMD::crystallization::MoleculePlane.
|
inlineinherited |
Get the ith of the currently active tasks.
|
inlineinherited |
Get the icolv th base multicolvar.
|
inlineinherited |
Get box shape.
|
virtualinherited |
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.
|
virtualinherited |
Get the index where the central atom is stored.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.
|
inlineinherited |
Get charge of i-th atom.
|
inherited |
get a string that contains all the available components
|
inherited |
get a vector that contains the label for all the components
|
inherited |
Return true if we are doing at a checkpoint step.
|
inlineinherited |
Get the number of tasks that are currently active.
|
inlineinherited |
Return dependencies.
|
virtualinherited |
|
inlineinherited |
Get energy.
|
inherited |
Check if we are on an exchange step.
|
protectedinherited |
Retrieve the forces from all the vessels (used in apply)
|
inlineinherited |
Get the full size of the taskList dynamic list.
|
inlineinherited |
Get position of i-th atom (access by absolute AtomNumber).
With direct access to the global atom array.
|
virtualinherited |
Get an input data.
Reimplemented in PLMD::adjmat::ClusterWithSurface, and PLMD::adjmat::ActionWithInputMatrix.
|
virtualinherited |
Retrieve the input derivatives.
Reimplemented in PLMD::adjmat::ClusterWithSurface, and PLMD::adjmat::ActionWithInputMatrix.
|
inherited |
Just read one of the keywords and return the whole thing as a string.
|
inlineinherited |
Returns the label.
|
protectedinherited |
Get the cutoff for the link cells.
|
inlineinherited |
Get mass of i-th atom.
|
inlineinherited |
Returns the name.
|
inlineprotectedinherited |
Return the value for the neighbor list tolerance.
|
inlineinherited |
Get number of available atoms.
|
inlineinherited |
Get the number of base multicolvars.
|
inlineinherited |
Returns the number of values defined.
|
inlineoverridevirtualinherited |
Get the number of derivatives for this action.
Implements PLMD::ActionWithValue.
|
inlinevirtualinherited |
Get the number of quantities that are calculated during each task.
Reimplemented in PLMD::analysis::Histogram, PLMD::pamm::PAMM, PLMD::gridtools::FindSphericalContour, PLMD::gridtools::FindContour, PLMD::multicolvar::MultiColvarDensity, PLMD::gridtools::FindContourSurface, PLMD::multicolvar::LocalAverage, PLMD::multicolvar::DistanceFromContour, PLMD::adjmat::ClusterWithSurface, PLMD::vesselbase::ActionWithAveraging, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::gridtools::ConvertToFES, PLMD::adjmat::TopologyMatrix, PLMD::crystallization::VectorMultiColvar, PLMD::adjmat::ActionWithInputMatrix, PLMD::gridtools::InterpolateGrid, PLMD::multicolvar::ActionVolume, PLMD::adjmat::ClusterAnalysisBase, PLMD::multicolvar::MultiColvarFilter, and PLMD::crystallization::Gradient.
|
inlineinherited |
Get the number of vessels.
|
inlineinherited |
Get the value of one of the components of the PLMD::Action.
|
inlineinherited |
Get the value with a specific name (N.B. if there is no such value this returns zero)
|
protectedinherited |
Return a pointer to the component by index.
|
protectedinherited |
Return a pointer to the value by name.
|
protectedinherited |
Get a pointer to the default value.
|
inlineinherited |
Get a pointer to the ith vessel.
|
inlineinherited |
Get position of i-th atom (access by relative index)
|
inlineinherited |
Return the position in the current task list.
|
inlineinherited |
Get the position of the ith active task in the full list.
|
inlinevirtualinherited |
This gets the position of an atom for the link cell setup.
Reimplemented in PLMD::adjmat::ClusterWithSurface, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ActionWithInputMatrix, and PLMD::adjmat::ClusterAnalysisBase.
|
inlineinherited |
Get the array of all positions.
|
inlineinherited |
Return true if we are doing a restart.
|
inherited |
Get the separation between a pair of vectors.
|
protectedinherited |
Get the size of the buffer.
|
inherited |
Return the present timestep.
|
inlineinherited |
Get the code for the ii th task in the list.
|
inherited |
Return the present time.
|
inherited |
Return the timestep.
|
inlineprotectedinherited |
Return the value of the tolerance.
|
inlineinherited |
Get total number of atoms, including virtual ones.
Can be used to make a loop on modifyGlobalPosition or getGlobalPosition.
|
inlineinherited |
|
inlineinherited |
|
inherited |
These are overwritten in MultiColvarFunction.
Return a particular named vessel
|
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.
|
inherited |
Convert a set of read in strings into an atom list (this is used in parseAtomList)
|
inlineinherited |
Check if action is active.
|
inlinevirtualinherited |
Checks if an task is being performed at the present time.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.
|
inlinevirtualinherited |
Is this a density?
Reimplemented in PLMD::multicolvar::DistanceFromContour, and PLMD::multicolvar::Density.
|
inlineinherited |
Check if an option is on.
|
inlineoverridevirtual |
Returns the number of coordinates of the field.
Implements PLMD::vesselbase::ActionWithVessel.
|
inherited |
|
inlineoverridevirtualinherited |
Reimplemented from PLMD::Action.
Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.
|
inherited |
Make atoms whole, assuming they are in the proper order.
|
protectedinherited |
This routine take the vector of input derivatives and adds all the vectors to ivalth output derivatives In other words end-start sets of derivatives come in and one set of derivatives come out.
|
inlineinherited |
Get a reference to force on energy.
|
inlineinherited |
Get a reference to force on extraCV.
|
inlineinherited |
Get a reference to forces array.
|
inlineinherited |
Get modifiable force of i-th atom (access by absolute AtomNumber).
|
inlineinherited |
Get modifiable PBC Should be used by action that need to modify the stored box.
|
inlineinherited |
Get modifiable position of i-th atom (access by absolute AtomNumber).
|
inlineinherited |
Get modifiable virial Should be used by action that need to modify the stored virial.
|
inlineinherited |
Get a reference to virial array.
|
protectedinherited |
Turn on the derivatives in the vessel.
|
staticinherited |
Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.
|
inlinevirtualinherited |
These normalizes vectors and is used in StoreDataVessel.
Reimplemented in PLMD::multicolvar::LocalAverage, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::crystallization::VectorMultiColvar, and PLMD::crystallization::MoleculeOrientation.
|
inlinevirtualinherited |
|
inherited |
Parse one keyword as generic type.
|
inherited |
Parse a list of atoms without a numbered keyword.
|
inherited |
Parse an list of atom with a numbred keyword.
|
inherited |
Parse one keyword as boolean flag.
|
protectedinherited |
Read in some atoms.
|
inherited |
Parse one numbered keyword as generic type.
|
inherited |
Parse a vector with a number.
|
inherited |
Parse one keyword as std::vector.
|
inherited |
Applies PBCs to a seriens of positions or distances.
Compute the pbc distance between two positions.
|
overridevirtualinherited |
Perform one of the tasks.
Implements PLMD::vesselbase::ActionWithVessel.
|
overridevirtualinherited |
Do some setup before the calculation.
Reimplemented from PLMD::Action.
|
overridevirtualinherited |
Read in an input file containing atom positions and calculate the action for the atomic configuration therin.
Reimplemented from PLMD::Action.
|
protectedinherited |
Read in ATOMS keyword.
|
protectedinherited |
Read in three groups of atoms.
|
protectedinherited |
Read in three groups of atoms and construct CVs involving at least one.
|
protectedinherited |
Read in two groups of atoms and setup multicolvars to calculate.
|
protectedinherited |
Complete the setup of this object (this routine must be called after construction of ActionWithValue)
|
static |
|
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
|
protectedinherited |
This resizes the arrays that are used for link cell update.
|
protectedinherited |
Resize all the functions when the number of derivatives change.
|
overridevirtualinherited |
This is overwritten here in order to make sure that we do not retrieve atoms multiple times.
Reimplemented from PLMD::ActionAtomistic.
|
virtualinherited |
What are the domains of the base quantities.
Reimplemented in PLMD::multicolvar::XYTorsion, PLMD::crystallization::InterMolecularTorsions, and PLMD::multicolvar::Torsions.
|
protectedinherited |
Calculate the values of all the vessels.
|
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::vesselbase::ActionWithAveraging, PLMD::analysis::AnalysisBase, PLMD::gridtools::ConvertToFES, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::gridtools::GridPrintingBase.
|
inlineprotectedinherited |
Is the calculation being done in serial.
|
protectedinherited |
Set which atoms are to be used to calculate the central atom position.
|
inlineprotectedinherited |
|
inherited |
Add the forces to the atoms.
|
inherited |
Calculate the gradients and store them for all the values (need for projections)
|
protectedinherited |
Set the value of the cutoff for the link cells.
|
inlineprotectedinherited |
Set that we are using low memory.
|
inherited |
Set your default value to have no periodicity.
|
virtualinherited |
|
inherited |
Set the value to be periodic with a particular domain.
|
protectedinherited |
Setup the link cells and neighbour list stuff.
|
protectedinherited |
This sets up the list of atoms that are involved in this colvar.
|
protectedinherited |
Setup link cells in order to make this calculation faster.
|
protectedinherited |
Finish setting up the multicolvar base.
|
protectedinherited |
This does setup of link cell stuff that is specific to the non-use of the usespecies keyword.
|
inlineprotectedinherited |
Set the default value (the one without name)
|
inherited |
Set the value.
|
protectedinherited |
This routine take the ith set of input derivatives and adds it to each of the (end-start) output derivatives In other words one set of derivatives comes in and end-start sets of derivatives come out.
|
inherited |
Is the iatom'th stored value currently active.
|
inherited |
Check whether or not a particular task is currently active.
|
inlineoverridevirtualinherited |
Is it safe to use multithreading.
Reimplemented from PLMD::vesselbase::ActionWithVessel.
|
virtualinherited |
Do the task if we have a bridge.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.
|
overridevirtualinherited |
Turn on the derivatives.
Reimplemented from PLMD::ActionWithValue.
|
inlineoverridevirtualinherited |
Reimplemented from PLMD::Action.
Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.
|
inlinevirtualinherited |
Update.
This method is called one time per step. The set of all Actions is updated in forward order.
Reimplemented in PLMD::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::logmfd::LogMFD, PLMD::ves::VesLinearExpansion, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::eds::EDS, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::ves::TargetDistribution, PLMD::ves::VesDeltaF, PLMD::bias::MaxEnt, PLMD::generic::Plumed, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeTetrapore, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::mapping::AdaptivePath, PLMD::generic::DumpMassCharge, PLMD::isdb::JCoupling, PLMD::ves::OutputFesBias, PLMD::generic::Read, PLMD::analysis::AnalysisBase, PLMD::generic::Print, PLMD::isdb::PRE, PLMD::vesselbase::ActionWithAveraging, PLMD::adjmat::OutputCluster, PLMD::isdb::NOE, PLMD::multicolvar::DumpMultiColvar, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::analysis::ReadDissimilarityMatrix, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, PLMD::analysis::ReadAnalysisFrames, and PLMD::gridtools::GridPrintingBase.
|
virtualinherited |
Update the active atoms.
|
inherited |
updates local unique atoms
|
staticinherited |
The components in the action will depend on the user.
|
inlineinherited |
This forces the class to use numerical derivatives.
|
inlineinherited |
Do we use pbc to calculate this quantity.
|
inlineprotectedinherited |
Are we using low memory.
|
inherited |
Issue a warning.
|
inlineinherited |
Does the weight have derivatives.
|
protectedinherited |
Blocks of atom numbers.
|
protectedinherited |
This is used to keep track of what is calculated where.
|
protectedinherited |
|
protectedinherited |
This remembers where the boundaries are for the tasks. It makes link cells work fast.
|
protectedinherited |
This is used for numerical derivatives of bridge variables.
|
inherited |
|
protectedinherited |
The terms in the series are locked.
|
protectedinherited |
This is used when turning cvcodes into atom numbers.
|
protectedinherited |
This is also used to minimise computational expense in complex functions.
|
inherited |
|
inherited |
|
inherited |
Reference to the log stream.
|
protectedinherited |
Are we doing sums of matrix rows.
|
inherited |
|
protectedinherited |
The vessels in these multicolvars in which the data is stored.
|
protectedinherited |
The multicolvars from which we construct these quantities.
|
private |
|
protectedinherited |
A pointer to the object that stores data.
|
protectedinherited |
Number of atoms in each block.
|
inherited |
Reference to main plumed object.
|
private |
|
protectedinherited |
This list is used to update the neighbor list.
|
private |
|
protectedinherited |
Using the species keyword to read in atoms.
|
protectedinherited |
Does the weight have derivatives.
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