Provides the keyword UWALLS More...
Public Types | |
typedef std::vector< Action * > | Dependencies |
Public Member Functions | |
UWalls (const ActionOptions &) | |
virtual void | activate () |
Set action to active. More... | |
virtual void | addBridgeForces (const std::vector< double > &bb) |
Apply forces from the bridge. 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 | apply () override |
Deactivate task now does nothing. More... | |
void | applyBridgeForces (const std::vector< double > &bb) override |
Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume. More... | |
virtual void | beforeUpdate () |
Before Update. More... | |
StoreDataVessel * | buildDataStashes (ActionWithVessel *actionThatUses) |
Ensure that data required in other vessels is stored. More... | |
double | calcPotential (const double &val, double &df) const override |
Calculate the potential. More... | |
void | calculate () override |
Calculate an Action. More... | |
void | calculateFromPDB (const PDB &) |
Calculate the action given a pdb file as input. More... | |
virtual void | calculateNumericalDerivatives (ActionWithValue *a=NULL) |
Calculate the numerical derivatives N.B. More... | |
virtual void | calculateNumericalDerivatives (ActionWithValue *a=NULL) |
Perform calculation using numerical derivatives N.B. 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... | |
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... | |
void | clearDerivatives () override |
Don't actually clear the derivatives when this is called from plumed main. More... | |
void | clearInputForces () |
Clear the forces on the values. More... | |
virtual void | clearOptions () |
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... | |
void | deactivate_task (const unsigned &task_index) |
Routines that have to be defined so as not to have problems with virtual methods. More... | |
bool | derivativesAreRequired () const |
Are derivatives required for this quantity. More... | |
void | doJobsRequiredBeforeTaskList () override |
Do jobs required before tasks are undertaken. More... | |
virtual bool | doNotCalculateDerivatives () const |
Are we not calculating derivatives. 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... | |
unsigned | getActiveTask (const unsigned &ii) const |
Get the ith of the currently active tasks. 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 |
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... | |
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... | |
const std::string & | getName () const |
Returns the name. More... | |
int | getNumberOfComponents () const |
Returns the number of values defined. More... | |
unsigned | getNumberOfDerivatives () override |
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 std::string &name) const |
Get the value with a specific name (N.B. if there is no such value this returns zero) More... | |
double | getOutputQuantity (const unsigned j) const |
Get the value of one of the components of the PLMD::Action. More... | |
Vessel * | getPntrToVessel (const unsigned &i) |
Get a pointer to the ith vessel. 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... | |
bool | getRestart () const |
Return true if we are doing a restart. More... | |
long int | getStep () const |
Return the present timestep. 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... | |
Vessel * | getVesselWithName (const std::string &mynam) |
These are overwritten in MultiColvarFunction. 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 () override |
Are the base quantities periodic. More... | |
void | lockContributors () |
virtual void | lockRequests () |
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 | 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 | performTask (const unsigned &, const unsigned &, MultiValue &) const override |
This should never be called. More... | |
virtual void | prepare () |
Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More... | |
virtual void | 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... | |
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 | 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... | |
void | transformBridgedDerivatives (const unsigned ¤t, MultiValue &invals, MultiValue &outvals) const override |
This actually does the calculation. More... | |
virtual void | turnOnDerivatives () |
Activate the calculation of derivatives. More... | |
virtual void | unlockRequests () |
virtual void | update () |
Update. More... | |
void | useNumericalDerivatives () |
This forces the class to use numerical derivatives. 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 | addForcesOnArguments (const std::vector< double > &forces) |
Add forces to arguments (used in apply) 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... | |
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... | |
Vessel * | getPntrToArgument () |
Return a pointer to specific argument. More... | |
Value * | getPntrToComponent (const std::string &name) |
Return a pointer to the value by name. More... | |
Value * | getPntrToComponent (int i) |
Return a pointer to the component by index. 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 | readArgument (const std::string &type) |
What type of arguments are we reading in. 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 | 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 | |
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... | |
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... | |
Private Member Functions | |
int | getComponent (const std::string &name) const |
Return the index for the component named name. More... | |
Private Attributes | |
bool | actionIsBridged |
This tells plumed that this is used in a bridge. More... | |
bool | active |
Switch to activate Action on this step. More... | |
Dependencies | after |
Actions on which this Action depends. More... | |
Vessel * | arguments |
double | at |
vesselbase::ActionWithVessel * | aves |
Pointer to underlying action with vessel. More... | |
std::vector< double > | buffer |
The buffer that we use (we keep a copy here to avoid resizing) More... | |
std::vector< unsigned > | der_list |
The list of atoms involved in derivatives (we keep a copy here to avoid resizing) More... | |
bool | dertime_can_be_off |
These are used to minmise computational expense in complex functions. More... | |
bool | doCheckPoint |
double | eps |
double | exp |
std::vector< unsigned > | fullTaskList |
Ths full list of tasks we have to perform. More... | |
std::vector< std::unique_ptr< Vessel > > | functions |
Pointers to the functions we are using on each value. More... | |
std::vector< unsigned > | indexOfTaskInFullList |
The indices of the tasks in the full list of tasks. More... | |
double | kappa |
std::string | label |
Label of the Action, as set with LABEL= in the plumed.dat file. More... | |
std::vector< std::string > | line |
Directive line. More... | |
bool | lowmem |
Lower memory requirements. More... | |
unsigned | maxderivatives |
The maximum number of derivatives we can use before we need to invoke lowmem. More... | |
BridgeVessel * | myBridgeVessel |
unsigned | nactive_tasks |
The current number of active tasks. More... | |
const std::string | name |
Name of the directive in the plumed.dat file. More... | |
double | nl_tolerance |
Tolerance for quantities being put in neighbor lists. More... | |
bool | noderiv |
Are we skipping the calculation of the derivatives. More... | |
bool | numericalDerivatives |
Are we using numerical derivatives to differentiate. More... | |
double | offset |
std::set< std::string > | options |
Option that you might have enabled. More... | |
std::vector< unsigned > | partialTaskList |
The list of currently active tasks. More... | |
int | replica_index |
bool | restart |
bool | serial |
Do all calculations in serial. More... | |
Stopwatch & | stopwatch =*stopwatch_fwd |
The stopwatch that times the different parts of the calculation. More... | |
ForwardDecl< Stopwatch > | stopwatch_fwd |
int | stride |
bool | timers |
Do we want to output information on the timings of different parts of the calculation. More... | |
std::vector< double > | tmpforces |
Tempory storage for forces. More... | |
double | tolerance |
The tolerance on the accumulators. More... | |
double | update_from |
Update only after this time. More... | |
double | update_until |
Update only until this time. More... | |
std::vector< std::unique_ptr< Value > > | values |
An array containing the values for this action. More... | |
Provides the keyword UWALLS
|
inherited |
|
explicit |
|
virtualinherited |
Set action to active.
|
inlinevirtualinherited |
Apply forces from the bridge.
|
protectedinherited |
Add a bridging vessel to the list of vessels.
|
inherited |
Add a value with a name like label.name.
|
inherited |
Add a value with a name like label.name that has derivatives.
|
inherited |
Specify that this Action depends on another one.
|
protectedinherited |
Add forces to arguments (used in apply)
|
protectedinherited |
Add a task to the full list.
|
inherited |
Add a value with the name label.
|
inherited |
Add a value with the name label that has derivatives.
|
protectedinherited |
Add a vessel to the list of vessels.
|
protectedinherited |
|
overridevirtualinherited |
Deactivate task now does nothing.
Implements PLMD::Action.
|
inlineoverridevirtualinherited |
Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume.
Reimplemented from PLMD::vesselbase::ActionWithVessel.
|
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.
|
inherited |
Ensure that data required in other vessels is stored.
|
overridevirtual |
Calculate the potential.
Implements PLMD::manyrestraints::ManyRestraintsBase.
|
inlineoverridevirtualinherited |
Calculate an Action.
This method is called one or more times per step. The set of all Actions is calculated in forward order.
Implements PLMD::Action.
|
protectedinherited |
This loops over all the vessels calculating them and also sets all the element derivatives equal to zero.
|
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
|
virtualinherited |
Calculate the numerical derivatives N.B.
only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases
Reimplemented from PLMD::Action.
Reimplemented in PLMD::multicolvar::DumpMultiColvar.
|
virtualinherited |
Perform calculation using numerical derivatives N.B.
only pass an ActionWithValue to this routine if you know exactly what you are doing.
Reimplemented in PLMD::vesselbase::ActionWithAveraging, PLMD::multicolvar::DumpMultiColvar, PLMD::ActionAtomistic, PLMD::multicolvar::MultiColvarBase, PLMD::analysis::AnalysisBase, PLMD::ActionWithArguments, PLMD::mapping::Mapping, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::vesselbase::ActionWithInputVessel, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::mapping::PCAVars.
|
inlinevirtualinherited |
Reimplemented in PLMD::colvar::ContactMap, and PLMD::piv::PIV.
|
inlinevirtualinherited |
Check if the action needs gradient.
Reimplemented in PLMD::bias::MetaD, PLMD::bias::PBMetaD, and PLMD::generic::DumpProjections.
|
inlineoverridevirtualinherited |
Check if numerical derivatives should be used.
Reimplemented from PLMD::Action.
|
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.
|
inlineoverridevirtualinherited |
Don't actually clear the derivatives when this is called from plumed main.
They are calculated inside another action and clearing them would be bad
Reimplemented from PLMD::ActionWithValue.
|
inherited |
Clear the forces on the values.
|
virtualinherited |
|
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.
|
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.
|
inlineinherited |
Routines that have to be defined so as not to have problems with virtual methods.
|
protectedinherited |
Deactivate all the tasks in the task list.
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inlineinherited |
Are derivatives required for this quantity.
|
overridevirtualinherited |
Do jobs required before tasks are undertaken.
Reimplemented from PLMD::vesselbase::ActionWithVessel.
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inlinevirtualinherited |
Are we not calculating derivatives.
Reimplemented in PLMD::multicolvar::MultiColvarBase.
|
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.
|
virtualinherited |
Finish running all the calculations.
Reimplemented in PLMD::gridtools::ConvertToFES.
|
inherited |
Opens a file.
This is similar to plain fopen, but with some extra functionality.
|
inlineinherited |
Get the ith of the currently active tasks.
|
privateinherited |
Return the index for the component named name.
|
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 |
|
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.
|
inherited |
Just read one of the keywords and return the whole thing as a string.
|
inlineinherited |
Returns the label.
|
inlineinherited |
Returns the name.
|
inlineprotectedinherited |
Return the value for the neighbor list tolerance.
|
inlineinherited |
Returns the number of values defined.
|
inlineoverridevirtualinherited |
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::adjmat::ActionWithInputMatrix, PLMD::gridtools::InterpolateGrid, PLMD::multicolvar::ActionVolume, PLMD::adjmat::ClusterAnalysisBase, PLMD::multicolvar::MultiColvarFilter, PLMD::crystallization::VectorMultiColvar, and PLMD::crystallization::Gradient.
|
inlineinherited |
Get the number of vessels.
|
inlineinherited |
Get the value with a specific name (N.B. if there is no such value this returns zero)
|
inlineinherited |
Get the value of one of the components of the PLMD::Action.
|
inlineprotectedinherited |
Return a pointer to specific argument.
|
protectedinherited |
Return a pointer to the value by name.
|
protectedinherited |
Return a pointer to the component by index.
|
protectedinherited |
Get a pointer to the default value.
|
inlineinherited |
Get a pointer to the ith vessel.
|
inlineinherited |
Return the position in the current task list.
|
inlineinherited |
Get the position of the ith active task in the full list.
|
inlineinherited |
Return true if we are doing a restart.
|
protectedinherited |
Get the size of the buffer.
|
inherited |
Return the present timestep.
|
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.
|
inherited |
These are overwritten in MultiColvarFunction.
Return a particular named vessel
|
inlineinherited |
Check if action is active.
|
inlineinherited |
Check if an option is on.
|
inlineoverridevirtualinherited |
Are the base quantities periodic.
Implements PLMD::vesselbase::ActionWithVessel.
|
inherited |
|
inlinevirtualinherited |
|
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::MoleculeOrientation, and PLMD::crystallization::VectorMultiColvar.
|
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 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.
|
inlineoverridevirtualinherited |
This should never be called.
Implements PLMD::vesselbase::ActionWithVessel.
|
virtualinherited |
Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.
Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.
Reimplemented in PLMD::isdb::EMMI, PLMD::function::FuncPathMSD, PLMD::generic::Plumed, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, PLMD::colvar::ExtraCV, PLMD::colvar::CoordinationBase, PLMD::function::FuncPathGeneral, PLMD::maze::Optimizer, and PLMD::s2cm::S2ContactModel.
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protectedinherited |
What type of arguments are we reading in.
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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.
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protectedinherited |
Complete the setup of this object (this routine must be called after construction of ActionWithValue)
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static |
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protectedinherited |
Resize all the functions when the number of derivatives change.
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virtualinherited |
What are the domains of the base quantities.
Reimplemented in PLMD::multicolvar::XYTorsion, PLMD::multicolvar::Torsions, and PLMD::crystallization::InterMolecularTorsions.
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protectedinherited |
Calculate the values of all the vessels.
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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.
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inlineprotectedinherited |
Is the calculation being done in serial.
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inherited |
Calculate the gradients and store them for all the values (need for projections)
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inlineprotectedinherited |
Set that we are using low memory.
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inherited |
Set your default value to have no periodicity.
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virtualinherited |
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inherited |
Set the value to be periodic with a particular domain.
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inherited |
Set the value of the stride.
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inlineprotectedinherited |
Set the default value (the one without name)
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inherited |
Set the value.
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inherited |
Check whether or not a particular task is currently active.
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inlinevirtualinherited |
Is this action thread safe.
Reimplemented in PLMD::analysis::Histogram, and PLMD::multicolvar::MultiColvarBase.
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overridevirtualinherited |
This actually does the calculation.
Reimplemented from PLMD::vesselbase::ActionWithVessel.
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virtualinherited |
Activate the calculation of derivatives.
Reimplemented in PLMD::isdb::EMMI, 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, PLMD::gridtools::ActionWithIntegral, PLMD::eds::EDS, and PLMD::fisst::FISST.
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inlinevirtualinherited |
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inlinevirtualinherited |
Update.
This method is called one time per step. The set of all Actions is updated in forward order.
Reimplemented in PLMD::bias::MetaD, PLMD::isdb::CS2Backbone, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::ves::TargetDistribution, PLMD::ves::VesDeltaF, PLMD::opes::OPESexpanded, PLMD::generic::Plumed, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::multicolvar::VolumeTetrapore, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::mapping::AdaptivePath, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::analysis::AnalysisBase, PLMD::generic::DumpMassCharge, PLMD::generic::Print, PLMD::vesselbase::ActionWithAveraging, PLMD::adjmat::OutputCluster, PLMD::isdb::PRE, PLMD::multicolvar::DumpMultiColvar, PLMD::isdb::NOE, PLMD::generic::Flush, PLMD::analysis::ReadDissimilarityMatrix, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, PLMD::analysis::ReadAnalysisFrames, PLMD::gridtools::GridPrintingBase, PLMD::logmfd::LogMFD, PLMD::eds::EDS, and PLMD::fisst::FISST.
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staticinherited |
The components in the action will depend on the user.
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inlineinherited |
This forces the class to use numerical derivatives.
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inlineprotectedinherited |
Are we using low memory.
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inherited |
Issue a warning.
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inlineinherited |
Does the weight have derivatives.
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privateinherited |
This tells plumed that this is used in a bridge.
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privateinherited |
Switch to activate Action on this step.
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privateinherited |
Actions on which this Action depends.
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privateinherited |
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private |
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privateinherited |
Pointer to underlying action with vessel.
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protectedinherited |
This is used for numerical derivatives of bridge variables.
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privateinherited |
The buffer that we use (we keep a copy here to avoid resizing)
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inherited |
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protectedinherited |
The terms in the series are locked.
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privateinherited |
The list of atoms involved in derivatives (we keep a copy here to avoid resizing)
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protectedinherited |
This is also used to minimise computational expense in complex functions.
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privateinherited |
These are used to minmise computational expense in complex functions.
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privateinherited |
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private |
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private |
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inherited |
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privateinherited |
Ths full list of tasks we have to perform.
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privateinherited |
Pointers to the functions we are using on each value.
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privateinherited |
The indices of the tasks in the full list of tasks.
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private |
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inherited |
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privateinherited |
Label of the Action, as set with LABEL= in the plumed.dat file.
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privateinherited |
Directive line.
This line is progressively erased during Action construction so as to check if all the present keywords are correct.
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inherited |
Reference to the log stream.
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privateinherited |
Lower memory requirements.
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privateinherited |
The maximum number of derivatives we can use before we need to invoke lowmem.
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inherited |
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privateinherited |
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protectedinherited |
A pointer to the object that stores data.
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privateinherited |
The current number of active tasks.
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privateinherited |
Name of the directive in the plumed.dat file.
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privateinherited |
Tolerance for quantities being put in neighbor lists.
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privateinherited |
Are we skipping the calculation of the derivatives.
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privateinherited |
Are we using numerical derivatives to differentiate.
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private |
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privateinherited |
Option that you might have enabled.
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privateinherited |
The list of currently active tasks.
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inherited |
Reference to main plumed object.
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privateinherited |
|
privateinherited |
|
privateinherited |
Do all calculations in serial.
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privateinherited |
The stopwatch that times the different parts of the calculation.
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privateinherited |
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privateinherited |
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protectedinherited |
This list is used to update the neighbor list.
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privateinherited |
Do we want to output information on the timings of different parts of the calculation.
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privateinherited |
Tempory storage for forces.
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privateinherited |
The tolerance on the accumulators.
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privateinherited |
Update only after this time.
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privateinherited |
Update only until this time.
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privateinherited |
An array containing the values for this action.
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protectedinherited |
Does the weight have derivatives.
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