This is the abstract base class to use for implementing new methods for analyzing the trajectory.
More...
#include <AnalysisBase.h>
Public Types | |
typedef std::vector< Action * > | Dependencies |
Public Member Functions | |
AnalysisBase (const ActionOptions &) | |
virtual void | activate () |
Set action to active. 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 | addForcesOnArguments (const std::vector< double > &forces) |
Add forces to arguments (used in apply) 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 () |
Apply an 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 () |
virtual void | beforeUpdate () |
Before Update. More... | |
double | bringBackInPbc (int i, double d1) const |
Takes one value and brings it back into the pbc of argument i. More... | |
StoreDataVessel * | buildDataStashes (ActionWithVessel *actionThatUses) |
Ensure that data required in other vessels is stored. More... | |
void | calculate () |
Calculate and apply do nothing all analysis is done during update step. 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) |
N.B. 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 |
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... | |
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... | |
double | difference (int, double, double) const |
Takes the difference taking into account pbc for arg i. More... | |
virtual bool | dissimilaritiesWereSet () const |
Ensures that dissimilarities were set somewhere. More... | |
virtual void | doJobsRequiredBeforeTaskList () |
Do any jobs that are required before the task list is undertaken. More... | |
virtual bool | doNotCalculateDerivatives () const |
Are we not calculating derivatives. 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... | |
unsigned | getActiveTask (const unsigned &ii) const |
Get the ith of the currently active tasks. More... | |
double | getArgument (const unsigned n) const |
Returns the value of an argument. More... | |
virtual std::vector< Value * > | getArgumentList () |
Overwrite getArguments so we get arguments from underlying class. More... | |
std::vector< std::string > | getArgumentNames () |
Get the list of argument names in the base. More... | |
virtual const std::vector< Value * > & | getArguments () const |
Returns an array of pointers to the arguments. More... | |
virtual const std::vector< AtomNumber > & | getAtomIndexes () const |
Get the indices of the atoms that have been stored. More... | |
const Tensor & | getBox () const |
Get box shape. 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... | |
virtual unsigned | getDataPointIndexInBase (const unsigned &idata) const |
Return the index of the data point in the base class. More... | |
const Dependencies & | getDependencies () const |
Return dependencies. More... | |
virtual double | getDissimilarity (const unsigned &i, const unsigned &j) |
Get the squared dissimilarity between two reference configurations. More... | |
virtual std::string | getDissimilarityInstruction () const |
Get the information on how dissimilarities were calculated for output PDB. 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... | |
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... | |
virtual std::string | getMetricName () const |
Get the name of the metric that is being used. More... | |
const std::string & | getName () const |
Returns the name. More... | |
virtual double | getNormalization () const |
Return the normalisation constant for the calculation. More... | |
virtual unsigned | getNumberOfArguments () const |
Returns the number of arguments. More... | |
unsigned | getNumberOfAtoms () const |
Get number of available atoms. More... | |
int | getNumberOfComponents () const |
Returns the number of values defined. More... | |
virtual unsigned | getNumberOfDataPoints () const |
Return the number of data points. More... | |
unsigned | getNumberOfDerivatives () |
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... | |
Value * | getPntrToArgument (const unsigned n) |
Return a pointer to specific argument. 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... | |
const std::vector< Vector > & | getPositions () const |
Get the array of all positions. More... | |
double | getProjection (unsigned i, unsigned j) const |
Get the scalar product between the gradients of two variables. More... | |
bool | getRestart () const |
Return true if we are doing a restart. More... | |
long int | getStep () const |
Return the present timestep. More... | |
virtual DataCollectionObject & | getStoredData (const unsigned &idata, const bool &calcdist) |
Get a reference configuration (in dimensionality reduction this returns the projection) More... | |
int | getStride () const |
Get the stride. 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 double | getWeight (const unsigned &idata) |
Return the weight of the ith point. More... | |
void | interpretArgumentList (const std::vector< std::string > &c, std::vector< Value *> &arg) |
Convert a list of argument names into a list of pointers to the values. 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... | |
bool | isOptionOn (const std::string &s) const |
Check if an option is on. More... | |
bool | isPeriodic () |
These overwrite things from inherited classes (this is a bit of a fudge) More... | |
void | lockContributors () |
void | lockRequests () |
These are required because we inherit from both ActionAtomistic and ActionWithArguments. More... | |
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 |
virtual bool | onStep () const |
Check if the action is active on this step. More... | |
template<class T > | |
void | parse (const std::string &key, T &t) |
Parse one keyword as generic type. More... | |
void | parseArgumentList (const std::string &key, std::vector< Value *> &args) |
Parse a list of arguments. More... | |
bool | parseArgumentList (const std::string &key, int i, std::vector< Value *> &args) |
Parse a numbered list of arguments. 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... | |
virtual void | performAnalysis ()=0 |
This actually performs the analysis. More... | |
virtual void | performTask (const unsigned &, const unsigned &, MultiValue &) const =0 |
Calculate one of the functions in the distribution. More... | |
virtual void | prepare () |
Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More... | |
void | readAtomsFromPDB (const PDB &pdb) |
Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More... | |
virtual void | readAtomsFromPDB (const PDB &) |
This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code. More... | |
void | requestArguments (const std::vector< Value *> &arg) |
Setup the dependencies. More... | |
void | requestAtoms (const std::vector< AtomNumber > &a, const bool clearDep=true) |
Request an array of atoms. More... | |
virtual void | retrieveAtoms () |
virtual void | retrieveDomain (std::string &min, std::string &max) |
What are the domains of the base quantities. More... | |
virtual void | runFinalJobs () |
This calls the analysis to be performed in the final step of the calculation i.e. 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 | setStride (const int &n) |
Set the value of the stride. More... | |
void | setValue (Value *, double) |
Set the value. More... | |
bool | taskIsCurrentlyActive (const unsigned &index) const |
Check whether or not a particular task is currently active. More... | |
virtual bool | threadSafe () const |
Is this action thread safe. More... | |
virtual void | transformBridgedDerivatives (const unsigned ¤t, MultiValue &invals, MultiValue &outvals) const |
Do the task if we have a bridge. More... | |
virtual void | turnOnDerivatives () |
Activate the calculation of derivatives. More... | |
void | unlockRequests () |
virtual void | update () |
This will call the analysis to be performed. More... | |
void | updateUniqueLocal () |
updates local unique atoms More... | |
void | useNumericalDerivatives () |
This forces the class to use numerical derivatives. More... | |
virtual bool | usingMemory () const |
Are we using memory in this calculation this affects the weights of points. 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 | |
BridgeVessel * | addBridgingVessel (ActionWithVessel *tome) |
Add a bridging vessel to the list of vessels. More... | |
void | addTaskToList (const unsigned &taskCode) |
Add a task to the full list. 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 | 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 | expandArgKeywordInPDB (PDB &pdb) |
This changes the arg keyword in the pdb file. More... | |
bool | getForcesFromVessels (std::vector< double > &forcesToApply) |
Retrieve the forces from all the vessels (used in apply) 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 | needsDerivatives () |
Turn on the derivatives in the vessel. More... | |
void | readVesselKeywords () |
Complete the setup of this object (this routine must be called after construction of ActionWithValue) 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 | setExtraCV (const std::string &name) |
void | setLowMemOption (const bool &) |
Set that we are using low memory. More... | |
void | setValue (const double &d) |
Set the default value (the one without name) More... | |
bool | usingLowMem () const |
Are we using low memory. More... | |
Protected Attributes | |
Atoms & | atoms |
unsigned | bridgeVariable |
This is used for numerical derivatives of bridge variables. More... | |
bool | contributorsAreUnlocked |
The terms in the series are locked. More... | |
bool | dertime |
This is also used to minimise computational expense in complex functions. More... | |
AnalysisBase * | my_input_data |
The Analysis action that we are reusing data from. More... | |
StoreDataVessel * | mydata |
A pointer to the object that stores data. More... | |
std::vector< unsigned > | taskFlags |
This list is used to update the neighbor list. More... | |
bool | weightHasDerivatives |
Does the weight have derivatives. More... | |
Friends | |
class | ReadDissimilarityMatrix |
class | ReselectLandmarks |
This is the abstract base class to use for implementing new methods for analyzing the trajectory.
You can find information on how to use it to implement new analysis methods here.
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inherited |
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explicit |
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virtualinherited |
Set action to active.
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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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inherited |
Add forces to arguments (used in apply)
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protectedinherited |
Add a task to the full list.
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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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inlinevirtual |
Apply an Action.
This method is called one time per step. The set of all Actions is applied in backward order.
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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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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inlineinherited |
Takes one value and brings it back into the pbc of argument i.
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inherited |
Ensure that data required in other vessels is stored.
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inlinevirtual |
Calculate and apply do nothing all analysis is done during update step.
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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inlinevirtual |
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::ActionAtomistic.
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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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inlinevirtualinherited |
Check if numerical derivatives should be used.
Reimplemented from PLMD::Action.
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inlinevirtualinherited |
Check if numerical derivatives should be performed.
Reimplemented in PLMD::ActionWithValue.
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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
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inherited |
Check if action should be updated.
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inherited |
Cite a paper see PlumedMain::cite.
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inherited |
Clear the dependence list for this Action.
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virtualinherited |
Clear the derivatives of values wrt parameters.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.
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inherited |
Clear the forces on the values.
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virtualinherited |
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inherited |
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inherited |
Set your value component to have no periodicity.
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inherited |
Set the value to be periodic with a particular domain.
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staticinherited |
Puts a message into the manual that the components always output.
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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.
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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.
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inlinevirtualinherited |
Set action to inactive.
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protectedinherited |
Deactivate all the tasks in the task list.
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inlineinherited |
Are derivatives required for this quantity.
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inlineinherited |
Takes the difference taking into account pbc for arg i.
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inlinevirtual |
Ensures that dissimilarities were set somewhere.
Reimplemented in PLMD::analysis::ReadAnalysisFrames, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::analysis::EuclideanDissimilarityMatrix.
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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.
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inlinevirtualinherited |
Are we not calculating derivatives.
Reimplemented in PLMD::multicolvar::MultiColvarBase.
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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.
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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.
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inherited |
Crash calculation and print documentation.
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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.
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inherited |
Exit with error code c.
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protectedinherited |
This changes the arg keyword in the pdb file.
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inherited |
Closes a file opened with Action::fclose().
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inherited |
Tell to the Action to flush open files.
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virtualinherited |
Finish running all the calculations.
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inherited |
Opens a file.
This is similar to plain fopen, but with some extra functionality.
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inlineinherited |
Get the absolute index of an atom.
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inlinevirtualinherited |
Get the vector of absolute indexes.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.
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inlineinherited |
Get the ith of the currently active tasks.
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inlineinherited |
Returns the value of an argument.
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inlinevirtual |
Overwrite getArguments so we get arguments from underlying class.
Reimplemented in PLMD::analysis::ReadAnalysisFrames, PLMD::dimred::ProjectNonLandmarkPoints, PLMD::dimred::SketchMapRead, and PLMD::dimred::DimensionalityReductionBase.
std::vector< std::string > PLMD::analysis::AnalysisBase::getArgumentNames | ( | ) |
Get the list of argument names in the base.
|
inlinevirtualinherited |
Returns an array of pointers to the arguments.
|
inlinevirtual |
Get the indices of the atoms that have been stored.
Reimplemented in PLMD::analysis::ReadAnalysisFrames.
|
inlineinherited |
Get box shape.
|
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.
|
inlinevirtual |
Return the index of the data point in the base class.
Reimplemented in PLMD::analysis::ReadAnalysisFrames, PLMD::dimred::SketchMapRead, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::analysis::LandmarkSelectionBase.
|
inlineinherited |
Return dependencies.
|
inlinevirtual |
Get the squared dissimilarity between two reference configurations.
Reimplemented in PLMD::analysis::ReadDissimilarityMatrix, PLMD::dimred::SketchMapRead, PLMD::analysis::LandmarkSelectionBase, and PLMD::analysis::EuclideanDissimilarityMatrix.
|
inlinevirtual |
Get the information on how dissimilarities were calculated for output PDB.
Reimplemented in PLMD::analysis::ReadAnalysisFrames, and PLMD::analysis::EuclideanDissimilarityMatrix.
|
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.
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inherited |
Just read one of the keywords and return the whole thing as a string.
|
inlineinherited |
Returns the label.
|
inlineinherited |
Get mass of i-th atom.
|
inlinevirtual |
Get the name of the metric that is being used.
|
inlineinherited |
Returns the name.
|
inlineprotectedinherited |
Return the value for the neighbor list tolerance.
|
inlinevirtual |
Return the normalisation constant for the calculation.
|
inlinevirtualinherited |
Returns the number of arguments.
Reimplemented in PLMD::vesselbase::ActionWithAveraging.
|
inlineinherited |
Get number of available atoms.
|
inlineinherited |
Returns the number of values defined.
|
inlinevirtual |
Return the number of data points.
Reimplemented in PLMD::analysis::ReadAnalysisFrames, PLMD::dimred::SketchMapRead, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::analysis::LandmarkSelectionBase.
|
inlinevirtual |
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)
|
inlineinherited |
Return a pointer to specific argument.
|
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.
|
inlineinherited |
Get the array of all positions.
|
inherited |
Get the scalar product between the gradients of two variables.
|
inlineinherited |
Return true if we are doing a restart.
|
protectedinherited |
Get the size of the buffer.
|
inherited |
Return the present timestep.
|
inlinevirtual |
Get a reference configuration (in dimensionality reduction this returns the projection)
Reimplemented in PLMD::analysis::ReadAnalysisFrames, PLMD::analysis::ReadDissimilarityMatrix, PLMD::dimred::ProjectNonLandmarkPoints, PLMD::dimred::SketchMapRead, and PLMD::analysis::LandmarkSelectionBase.
|
inherited |
Get the stride.
|
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
|
inlinevirtual |
Return the weight of the ith point.
Reimplemented in PLMD::analysis::ReadAnalysisFrames, PLMD::analysis::ReadDissimilarityMatrix, PLMD::dimred::SketchMapRead, and PLMD::analysis::LandmarkSelectionBase.
|
inherited |
Convert a list of argument names into a list of pointers to the values.
|
inherited |
Convert a set of read in strings into an atom list (this is used in parseAtomList)
|
inlineinherited |
Check if action is active.
|
inlineinherited |
Check if an option is on.
|
inlinevirtual |
These overwrite things from inherited classes (this is a bit of a fudge)
Implements PLMD::vesselbase::ActionWithVessel.
|
inherited |
|
inlinevirtual |
These are required because we inherit from both ActionAtomistic and ActionWithArguments.
Reimplemented from PLMD::Action.
|
inherited |
Make atoms whole, assuming they are in the proper order.
|
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 |
|
virtualinherited |
Check if the action is active on this step.
Reimplemented in PLMD::gridtools::ConvertToFES.
|
inherited |
Parse one keyword as generic type.
|
inherited |
Parse a list of arguments.
|
inherited |
Parse a numbered list of arguments.
|
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.
|
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.
|
pure virtual |
This actually performs the analysis.
Implemented in PLMD::analysis::ReadDissimilarityMatrix, PLMD::dimred::ProjectNonLandmarkPoints, PLMD::analysis::LandmarkSelectionBase, PLMD::analysis::OutputColvarFile, PLMD::analysis::ReadAnalysisFrames, PLMD::dimred::OutputPCAProjection, PLMD::analysis::OutputPDBFile, PLMD::dimred::DimensionalityReductionBase, PLMD::analysis::EuclideanDissimilarityMatrix, PLMD::dimred::PCA, and PLMD::analysis::PrintDissimilarityMatrix.
|
pure virtualinherited |
Calculate one of the functions in the distribution.
Implemented in PLMD::multicolvar::MultiColvarBase, PLMD::mapping::AdaptivePath, PLMD::analysis::Average, PLMD::vesselbase::ActionWithAveraging, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::adjmat::ClusterDistribution, PLMD::adjmat::ClusterDiameter, PLMD::adjmat::ClusterSize, PLMD::analysis::ReadDissimilarityMatrix, PLMD::adjmat::ClusterProperties, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::dimred::ProjectNonLandmarkPoints, PLMD::dimred::DimensionalityReductionBase, PLMD::analysis::LandmarkSelectionBase, PLMD::manyrestraints::ManyRestraintsBase, PLMD::analysis::ReadAnalysisFrames, PLMD::analysis::EuclideanDissimilarityMatrix, PLMD::analysis::OutputColvarFile, PLMD::dimred::OutputPCAProjection, PLMD::analysis::OutputPDBFile, PLMD::analysis::PrintDissimilarityMatrix, and PLMD::mapping::PathBase.
|
virtualinherited |
Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.
Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.
Reimplemented in PLMD::function::FuncPathMSD, PLMD::isdb::EMMI, PLMD::generic::Plumed, PLMD::multicolvar::MultiColvarBase, PLMD::generic::DumpMassCharge, PLMD::generic::Read, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::bias::ReweightTemperature, PLMD::colvar::Energy, PLMD::gridtools::ConvertToFES, PLMD::colvar::ExtraCV, and PLMD::colvar::CoordinationBase.
|
virtualinherited |
Read in an input file containing atom positions and calculate the action for the atomic configuration therin.
Reimplemented from PLMD::Action.
|
inlinevirtualinherited |
This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code.
Reimplemented in PLMD::ActionAtomistic.
|
protectedinherited |
Complete the setup of this object (this routine must be called after construction of ActionWithValue)
|
static |
|
inherited |
Setup the dependencies.
|
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 |
Resize all the functions when the number of derivatives change.
|
virtualinherited |
Reimplemented in PLMD::multicolvar::MultiColvarBase.
|
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.
|
virtual |
This calls the analysis to be performed in the final step of the calculation i.e.
when use_all_data is true
Reimplemented from PLMD::Action.
Reimplemented in PLMD::analysis::ReadDissimilarityMatrix.
|
inlineprotectedinherited |
Is the calculation being done in serial.
|
inlineprotectedinherited |
|
inherited |
Add the forces to the atoms.
|
inherited |
Calculate the gradients and store them for all the values (need for projections)
|
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.
|
inherited |
Set the value of the stride.
|
inlineprotectedinherited |
Set the default value (the one without name)
|
inherited |
Set the value.
|
inherited |
Check whether or not a particular task is currently active.
|
inlinevirtualinherited |
Is this action thread safe.
Reimplemented in PLMD::analysis::Histogram, and PLMD::multicolvar::MultiColvarBase.
|
virtualinherited |
Do the task if we have a bridge.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.
|
virtualinherited |
Activate the calculation of derivatives.
Reimplemented in PLMD::eds::EDS, PLMD::analysis::Histogram, PLMD::isdb::MetainferenceBase, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::adjmat::ClusterDiameter, PLMD::adjmat::ClusterSize, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ClusterAnalysisBase, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, and PLMD::gridtools::ActionWithIntegral.
|
inlinevirtual |
Reimplemented from PLMD::Action.
|
virtual |
This will call the analysis to be performed.
Reimplemented from PLMD::Action.
Reimplemented in PLMD::analysis::ReadDissimilarityMatrix, and PLMD::analysis::ReadAnalysisFrames.
|
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.
|
inlineprotectedinherited |
Are we using low memory.
|
inlinevirtual |
Are we using memory in this calculation this affects the weights of points.
|
inherited |
Issue a warning.
|
inlineinherited |
Does the weight have derivatives.
|
friend |
|
friend |
|
protectedinherited |
|
protectedinherited |
This is used for numerical derivatives of bridge variables.
|
inherited |
|
protectedinherited |
The terms in the series are locked.
|
protectedinherited |
This is also used to minimise computational expense in complex functions.
|
inherited |
|
inherited |
|
inherited |
Reference to the log stream.
|
inherited |
|
protected |
The Analysis action that we are reusing data from.
|
protectedinherited |
A pointer to the object that stores data.
|
inherited |
Reference to main plumed object.
|
protectedinherited |
This list is used to update the neighbor list.
|
protectedinherited |
Does the weight have derivatives.
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