This is used to create PLMD::Action objects that are computed by calculating the same function multiple times.
More...
#include <ActionWithVessel.h>
Public Types | |
typedef std::vector< Action * > | Dependencies |
Public Member Functions | |
ActionWithVessel (const ActionOptions &ao) | |
~ActionWithVessel () | |
void | lockContributors () |
unsigned | getCurrentNumberOfActiveTasks () const |
Get the number of tasks that are currently active. More... | |
bool | taskIsCurrentlyActive (const unsigned &index) const |
Check whether or not a particular task is currently active. More... | |
bool | derivativesAreRequired () const |
Are derivatives required for this quantity. More... | |
virtual bool | threadSafe () const |
Is this action thread safe. More... | |
virtual void | finishComputations (const std::vector< double > &buffer) |
Finish running all the calculations. More... | |
virtual bool | isPeriodic ()=0 |
Are the base quantities periodic. More... | |
virtual void | retrieveDomain (std::string &min, std::string &max) |
What are the domains of the base quantities. More... | |
virtual unsigned | getNumberOfDerivatives ()=0 |
Get the number of derivatives for final calculated quantity. 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... | |
Vessel * | getPntrToVessel (const unsigned &i) |
Get a pointer to the ith vessel. More... | |
virtual void | doJobsRequiredBeforeTaskList () |
Do any jobs that are required before the task list is undertaken. More... | |
unsigned | getFullNumberOfTasks () const |
Get the full size of the taskList dynamic list. More... | |
unsigned | getPositionInFullTaskList (const unsigned &ii) const |
Get the position of the ith active task in the full list. More... | |
unsigned | getTaskCode (const unsigned &ii) const |
Get the code for the ii th task in the list. More... | |
unsigned | getActiveTask (const unsigned &ii) const |
Get the ith of the currently active tasks. More... | |
virtual void | performTask (const unsigned &, const unsigned &, MultiValue &) const =0 |
Calculate one of the functions in the distribution. More... | |
virtual void | transformBridgedDerivatives (const unsigned ¤t, MultiValue &invals, MultiValue &outvals) const |
Do the task if we have a bridge. More... | |
StoreDataVessel * | buildDataStashes (ActionWithVessel *actionThatUses) |
Ensure that data required in other vessels is stored. More... | |
virtual void | applyBridgeForces (const std::vector< double > &bb) |
Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume. More... | |
Vessel * | getVesselWithName (const std::string &mynam) |
These are overwritten in MultiColvarFunction. More... | |
bool | weightWithDerivatives () const |
Does the weight have derivatives. More... | |
unsigned | getPositionInCurrentTaskList (const unsigned &myind) const |
Return the position in the current task list. More... | |
virtual void | normalizeVector (std::vector< double > &vals) const |
These normalizes vectors and is used in StoreDataVessel. More... | |
virtual void | normalizeVectorDerivatives (MultiValue &myvals) const |
bool | checkUpdate () const |
Check if action should be updated. More... | |
void | addDependency (Action *) |
Specify that this Action depends on another one. More... | |
void | clearDependencies () |
Clear the dependence list for this Action. More... | |
long int | getStep () const |
Return the present timestep. More... | |
double | getTime () const |
Return the present time. More... | |
double | getTimeStep () const |
Return the timestep. More... | |
bool | getRestart () const |
Return true if we are doing a restart. More... | |
bool | getCPT () const |
Return true if we are doing at a checkpoint step. More... | |
std::string | getKeyword (const std::string &key) |
Just read one of the keywords and return the whole thing as a string. More... | |
template<class T > | |
void | parse (const std::string &key, T &t) |
Parse one keyword as generic type. More... | |
template<class T > | |
bool | parseNumbered (const std::string &key, const int no, T &t) |
Parse one numbered keyword as generic type. More... | |
template<class T > | |
void | parseVector (const std::string &key, std::vector< T > &t) |
Parse one keyword as std::vector. More... | |
template<class T > | |
bool | parseNumberedVector (const std::string &key, const int no, std::vector< T > &t) |
Parse a vector with a number. More... | |
void | parseFlag (const std::string &key, bool &t) |
Parse one keyword as boolean flag. More... | |
void | error (const std::string &msg) const |
Crash calculation and print documentation. More... | |
void | warning (const std::string &msg) |
Issue a warning. More... | |
void | exit (int c=0) |
Exit with error code c. More... | |
void | checkRead () |
Check if Action was properly read. More... | |
virtual void | prepare () |
Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More... | |
virtual void | lockRequests () |
virtual void | unlockRequests () |
virtual void | calculate ()=0 |
Calculate an Action. More... | |
virtual void | apply ()=0 |
Apply an Action. More... | |
virtual void | beforeUpdate () |
Before Update. More... | |
virtual void | update () |
Update. More... | |
virtual void | runFinalJobs () |
RunFinalJobs This method is called once at the very end of the calculation. More... | |
void | fflush () |
Tell to the Action to flush open files. More... | |
virtual std::string | getDocumentation () const |
const std::string & | getLabel () const |
Returns the label. More... | |
const std::string & | getName () const |
Returns the name. More... | |
virtual void | activate () |
Set action to active. More... | |
virtual void | setOption (const std::string &s) |
virtual void | clearOptions () |
virtual void | deactivate () |
Set action to inactive. More... | |
bool | isActive () const |
Check if action is active. More... | |
bool | isOptionOn (const std::string &s) const |
Check if an option is on. More... | |
const Dependencies & | getDependencies () const |
Return dependencies. More... | |
virtual bool | checkNumericalDerivatives () const |
Check if numerical derivatives should be performed. More... | |
virtual bool | checkNeedsGradients () const |
Check if the action needs gradient. More... | |
virtual void | calculateNumericalDerivatives (ActionWithValue *a=NULL) |
Perform calculation using numerical derivatives N.B. More... | |
FILE * | fopen (const char *path, const char *mode) |
Opens a file. More... | |
int | fclose (FILE *fp) |
Closes a file opened with Action::fclose(). More... | |
void | calculateFromPDB (const PDB &) |
Calculate the action given a pdb file as input. More... | |
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... | |
bool | getExchangeStep () const |
Check if we are on an exchange step. More... | |
std::string | cite (const std::string &s) |
Cite a paper see PlumedMain::cite. More... | |
Static Public Member Functions | |
static void | registerKeywords (Keywords &keys) |
Public Attributes | |
PlumedMain & | plumed |
Reference to main plumed object. More... | |
Log & | log |
Reference to the log stream. More... | |
std::set< FILE * > | files |
Communicator & | comm |
Communicator & | multi_sim_comm |
const Keywords & | keywords |
Protected Member Functions | |
void | addVessel (const std::string &name, const std::string &input, const int numlab=0) |
Add a vessel to the list of vessels. More... | |
void | addVessel (Vessel *vv) |
BridgeVessel * | addBridgingVessel (ActionWithVessel *tome) |
Add a bridging vessel to the list of vessels. More... | |
void | readVesselKeywords () |
Complete the setup of this object (this routine must be called after construction of ActionWithValue) More... | |
void | needsDerivatives () |
Turn on the derivatives in the vessel. More... | |
double | getTolerance () const |
Return the value of the tolerance. More... | |
double | getNLTolerance () const |
Return the value for the neighbor list tolerance. More... | |
void | runAllTasks () |
Calculate the values of all the vessels. More... | |
void | resizeFunctions () |
Resize all the functions when the number of derivatives change. 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... | |
bool | getForcesFromVessels (std::vector< double > &forcesToApply) |
Retrieve the forces from all the vessels (used in apply) More... | |
bool | serialCalculation () const |
Is the calculation being done in serial. More... | |
bool | usingLowMem () const |
Are we using low memory. More... | |
void | setLowMemOption (const bool &) |
Set that we are using low memory. More... | |
void | deactivateAllTasks () |
Deactivate all the tasks in the task list. More... | |
unsigned | getSizeOfBuffer (unsigned &bufsize) |
Get the size of the buffer. More... | |
void | addTaskToList (const unsigned &taskCode) |
Add a task to the full list. More... | |
Protected Attributes | |
bool | dertime |
This is also used to minimise computational expense in complex functions. More... | |
bool | contributorsAreUnlocked |
The terms in the series are locked. More... | |
bool | weightHasDerivatives |
Does the weight have derivatives. More... | |
unsigned | bridgeVariable |
This is used for numerical derivatives of bridge variables. More... | |
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... | |
Private Attributes | |
bool | serial |
Do all calculations in serial. More... | |
bool | lowmem |
Lower memory requirements. More... | |
bool | noderiv |
Are we skipping the calculation of the derivatives. More... | |
bool | actionIsBridged |
This tells plumed that this is used in a bridge. More... | |
unsigned | maxderivatives |
The maximum number of derivatives we can use before we need to invoke lowmem. More... | |
double | tolerance |
The tolerance on the accumulators. More... | |
double | nl_tolerance |
Tolerance for quantities being put in neighbor lists. More... | |
std::vector< Vessel * > | functions |
Pointers to the functions we are using on each value. More... | |
std::vector< double > | tmpforces |
Tempory storage for forces. More... | |
std::vector< unsigned > | fullTaskList |
Ths full list of tasks we have to perform. More... | |
unsigned | nactive_tasks |
The current number of active tasks. More... | |
std::vector< unsigned > | indexOfTaskInFullList |
The indices of the tasks in the full list of tasks. More... | |
std::vector< unsigned > | partialTaskList |
The list of currently active tasks. More... | |
std::vector< unsigned > | der_list |
The list of atoms involved in derivatives (we keep a copy here to avoid resizing) More... | |
std::vector< double > | buffer |
The buffer that we use (we keep a copy here to avoid resizing) More... | |
bool | timers |
Do we want to output information on the timings of different parts of the calculation. More... | |
Stopwatch & | stopwatch |
The stopwatch that times the different parts of the calculation. More... | |
bool | dertime_can_be_off |
These are used to minmise computational expense in complex functions. More... | |
Friends | |
class | Vessel |
class | ShortcutVessel |
class | FunctionVessel |
class | StoreDataVessel |
class | BridgeVessel |
class | ActionWithInputVessel |
class | OrderingVessel |
This is used to create PLMD::Action objects that are computed by calculating the same function multiple times.
This is used in PLMD::MultiColvar.
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inherited |
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explicit |
PLMD::vesselbase::ActionWithVessel::~ActionWithVessel | ( | ) |
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virtualinherited |
Set action to active.
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protected |
Add a bridging vessel to the list of vessels.
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inherited |
Specify that this Action depends on another one.
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protected |
Add a task to the full list.
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protected |
Add a vessel to the list of vessels.
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protected |
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pure virtualinherited |
Apply an Action.
This method is called one time per step. The set of all Actions is applied in backward order.
Implemented in PLMD::analysis::Histogram, PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::multicolvar::MultiColvarBase, PLMD::ves::BasisFunctions, PLMD::generic::FitToTemplate, PLMD::ves::TargetDistribution, PLMD::generic::WrapAround, PLMD::ves::VesBias, PLMD::generic::Include, PLMD::generic::DumpAtoms, PLMD::generic::Group, PLMD::generic::EffectiveEnergyDrift, PLMD::analysis::Analysis, PLMD::generic::WholeMolecules, PLMD::multicolvar::MultiColvarDensity, PLMD::adjmat::Sprint, PLMD::generic::DumpMassCharge, PLMD::analysis::Average, PLMD::mapping::Mapping, PLMD::generic::ResetCell, PLMD::multicolvar::DistanceFromContour, PLMD::generic::UpdateIf, PLMD::ves::OutputFesBias, PLMD::generic::Print, PLMD::ves::OutputBasisFunctions, PLMD::ves::OutputTargetDistribution, PLMD::adjmat::OutputCluster, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::manyrestraints::ManyRestraintsBase, PLMD::generic::DumpProjections, PLMD::generic::Debug, PLMD::adjmat::DumpGraph, PLMD::Colvar, PLMD::adjmat::ClusteringBase, PLMD::bias::Bias, PLMD::generic::Time, PLMD::function::Function, PLMD::ActionWithVirtualAtom, PLMD::gridtools::ActionWithInputGrid, PLMD::bias::ReweightBase, PLMD::gridtools::ActionWithIntegral, PLMD::ActionSetup, and PLMD::gridtools::GridPrintingBase.
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inlinevirtual |
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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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.
StoreDataVessel * PLMD::vesselbase::ActionWithVessel::buildDataStashes | ( | ActionWithVessel * | actionThatUses | ) |
Ensure that data required in other vessels is stored.
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pure virtualinherited |
Calculate an Action.
This method is called one or more times per step. The set of all Actions is calculated in forward order.
Implemented in PLMD::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::ves::VesLinearExpansion, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::function::Matheval, PLMD::function::FuncSumHills, PLMD::isdb::EMMI, PLMD::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::isdb::RDC, PLMD::eds::EDS, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::generic::FitToTemplate, PLMD::bias::MaxEnt, PLMD::multicolvar::MultiColvarBase, PLMD::generic::WrapAround, PLMD::isdb::Rescale, PLMD::generic::Include, PLMD::function::FuncPathMSD, PLMD::generic::DumpAtoms, PLMD::colvar::Dimer, PLMD::bias::ExtendedLagrangian, PLMD::generic::Group, PLMD::colvar::ContactMap, PLMD::colvar::Distance, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::MovingRestraint, PLMD::colvar::ERMSD, PLMD::analysis::Analysis, PLMD::isdb::SAXS, PLMD::generic::WholeMolecules, PLMD::colvar::DRMSD, PLMD::function::Target, PLMD::isdb::JCoupling, PLMD::generic::DumpMassCharge, PLMD::adjmat::Sprint, PLMD::bias::External, PLMD::colvar::Torsion, PLMD::analysis::Average, PLMD::colvar::EEFSolv, PLMD::generic::ResetCell, PLMD::mapping::AdaptivePath, PLMD::colvar::Gyration, PLMD::multicolvar::CenterOfMultiColvar, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::isdb::FretEfficiency, PLMD::multicolvar::DistanceFromContour, PLMD::ves::OutputFesBias, PLMD::colvar::PathMSDBase, PLMD::generic::UpdateIf, PLMD::function::Combine, PLMD::isdb::PRE, PLMD::ves::OutputBasisFunctions, PLMD::generic::Print, PLMD::function::LocalEnsemble, PLMD::ves::OutputTargetDistribution, PLMD::adjmat::OutputCluster, PLMD::vatom::Center, PLMD::vatom::FixedAtom, PLMD::bias::BiasValue, PLMD::generic::Read, PLMD::isdb::NOE, PLMD::generic::RandomExchanges, PLMD::colvar::Puckering, PLMD::function::Piecewise, PLMD::multicolvar::DumpMultiColvar, PLMD::adjmat::ClusterDistribution, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::bias::LWalls, PLMD::isdb::Select, PLMD::vatom::COM, PLMD::bias::UWalls, PLMD::colvar::Position, PLMD::adjmat::ClusterDiameter, PLMD::analysis::Committor, PLMD::adjmat::ClusterSize, PLMD::colvar::Constant, PLMD::bias::Restraint, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::adjmat::ClusterProperties, PLMD::function::Ensemble, PLMD::colvar::Energy, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::function::Stats, PLMD::colvar::Dipole, PLMD::function::Sort, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::generic::Debug, PLMD::colvar::Template, PLMD::generic::DumpProjections, PLMD::manyrestraints::ManyRestraintsBase, PLMD::vatom::Ghost, PLMD::colvar::Cell, PLMD::adjmat::DumpGraph, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::generic::Time, PLMD::adjmat::ClusteringBase, PLMD::gridtools::ActionWithGrid, PLMD::colvar::MultiRMSD, PLMD::colvar::RMSD, PLMD::colvar::PCARMSD, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::ActionSetup, PLMD::gridtools::GridPrintingBase, and PLMD::mapping::PathBase.
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This loops over all the vessels calculating them and also sets all the element derivatives equal to zero.
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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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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::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::multicolvar::MultiColvarBase, PLMD::ActionAtomistic, PLMD::multicolvar::DumpMultiColvar, PLMD::ActionWithArguments, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithInputVessel.
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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 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 |
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inlinevirtualinherited |
Set action to inactive.
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protected |
Deactivate all the tasks in the task list.
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inline |
Are derivatives required for this quantity.
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virtual |
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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inherited |
Crash calculation and print documentation.
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inherited |
Exit with error code c.
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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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virtual |
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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inline |
Get the ith of the currently active tasks.
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inherited |
Return true if we are doing at a checkpoint step.
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inline |
Get the number of tasks that are currently active.
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inlineinherited |
Return dependencies.
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virtualinherited |
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inherited |
Check if we are on an exchange step.
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protected |
Retrieve the forces from all the vessels (used in apply)
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inline |
Get the full size of the taskList dynamic list.
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inherited |
Just read one of the keywords and return the whole thing as a string.
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inlineinherited |
Returns the label.
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inlineinherited |
Returns the name.
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inlineprotected |
Return the value for the neighbor list tolerance.
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pure virtual |
Get the number of derivatives for final calculated quantity.
Implemented in PLMD::analysis::Histogram, PLMD::multicolvar::MultiColvarBase, PLMD::mapping::Mapping, PLMD::adjmat::ClusterWithSurface, PLMD::vesselbase::ActionWithAveraging, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ActionWithInputMatrix, PLMD::manyrestraints::ManyRestraintsBase, PLMD::gridtools::ContourFindingBase, and PLMD::gridtools::ActionWithIntegral.
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inlinevirtual |
Get the number of quantities that are calculated during each task.
Reimplemented in PLMD::analysis::Histogram, PLMD::gridtools::FindSphericalContour, PLMD::gridtools::FindContour, PLMD::multicolvar::MultiColvarDensity, PLMD::gridtools::FindContourSurface, PLMD::multicolvar::LocalAverage, PLMD::multicolvar::DistanceFromContour, PLMD::adjmat::ClusterWithSurface, 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.
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inline |
Get the number of vessels.
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inline |
Get a pointer to the ith vessel.
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inline |
Return the position in the current task list.
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inline |
Get the position of the ith active task in the full list.
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inlineinherited |
Return true if we are doing a restart.
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protected |
Get the size of the buffer.
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inherited |
Return the present timestep.
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inline |
Get the code for the ii th task in the list.
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inherited |
Return the present time.
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inherited |
Return the timestep.
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inlineprotected |
Return the value of the tolerance.
Vessel * PLMD::vesselbase::ActionWithVessel::getVesselWithName | ( | const std::string & | mynam | ) |
These are overwritten in MultiColvarFunction.
Return a particular named vessel
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inlineinherited |
Check if action is active.
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inlineinherited |
Check if an option is on.
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pure virtual |
Are the base quantities periodic.
Implemented in PLMD::analysis::Histogram, PLMD::multicolvar::XDistances, PLMD::multicolvar::XYTorsion, PLMD::multicolvar::Distances, PLMD::analysis::Analysis, PLMD::gridtools::FindContour, PLMD::multicolvar::XYDistances, PLMD::multicolvar::AlphaBeta, PLMD::multicolvar::MultiColvarDensity, PLMD::analysis::Average, PLMD::multicolvar::Angles, PLMD::multicolvar::LocalAverage, PLMD::multicolvar::XAngles, PLMD::multicolvar::CoordinationNumbers, PLMD::multicolvar::DistanceFromContour, PLMD::crystallization::InterMolecularTorsions, PLMD::multicolvar::DihedralCorrelation, PLMD::gridtools::FourierTransform, PLMD::multicolvar::NumberOfLinks, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::multicolvar::Torsions, PLMD::mapping::Mapping, PLMD::adjmat::AdjacencyMatrixBase, PLMD::gridtools::ConvertToFES, PLMD::multicolvar::Bridge, PLMD::multicolvar::InPlaneDistances, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ActionWithInputMatrix, PLMD::gridtools::InterpolateGrid, PLMD::multicolvar::Density, PLMD::crystallization::VectorMultiColvar, PLMD::multicolvar::MultiColvarCombine, PLMD::adjmat::ClusterAnalysisBase, PLMD::multicolvar::MultiColvarProduct, PLMD::gridtools::ContourFindingBase, PLMD::crystallization::CubicHarmonicBase, PLMD::manyrestraints::ManyRestraintsBase, PLMD::crystallization::OrientationSphere, and PLMD::gridtools::ActionWithIntegral.
void PLMD::vesselbase::ActionWithVessel::lockContributors | ( | ) |
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inlinevirtualinherited |
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protected |
Turn on the derivatives in the vessel.
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inlinevirtual |
These normalizes vectors and is used in StoreDataVessel.
Reimplemented in PLMD::multicolvar::LocalAverage, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::crystallization::VectorMultiColvar, and PLMD::crystallization::MoleculeOrientation.
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inlinevirtual |
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inherited |
Parse one keyword as generic type.
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inherited |
Parse one keyword as boolean flag.
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inherited |
Parse one numbered keyword as generic type.
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inherited |
Parse a vector with a number.
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inherited |
Parse one keyword as std::vector.
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pure virtual |
Calculate one of the functions in the distribution.
Implemented in PLMD::multicolvar::MultiColvarBase, PLMD::analysis::PCA, PLMD::analysis::Average, PLMD::mapping::AdaptivePath, PLMD::adjmat::ClusterDistribution, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::adjmat::ClusterDiameter, PLMD::adjmat::ClusterSize, PLMD::adjmat::ClusterProperties, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::manyrestraints::ManyRestraintsBase, PLMD::analysis::AnalysisWithLandmarks, PLMD::gridtools::ActionWithGrid, and PLMD::mapping::PathBase.
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virtualinherited |
Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.
Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.
Reimplemented in PLMD::isdb::EMMI, PLMD::multicolvar::MultiColvarBase, PLMD::function::FuncPathMSD, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::generic::Read, PLMD::bias::ReweightTemperature, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.
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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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protected |
Complete the setup of this object (this routine must be called after construction of ActionWithValue)
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static |
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protected |
Resize all the functions when the number of derivatives change.
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virtual |
What are the domains of the base quantities.
Reimplemented in PLMD::multicolvar::XYTorsion, PLMD::crystallization::InterMolecularTorsions, and PLMD::multicolvar::Torsions.
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protected |
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::analysis::Analysis, PLMD::gridtools::ConvertToFES, and PLMD::gridtools::GridPrintingBase.
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inlineprotected |
Is the calculation being done in serial.
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inlineprotected |
Set that we are using low memory.
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virtualinherited |
bool PLMD::vesselbase::ActionWithVessel::taskIsCurrentlyActive | ( | const unsigned & | index | ) | const |
Check whether or not a particular task is currently active.
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inlinevirtual |
Is this action thread safe.
Reimplemented in PLMD::analysis::Histogram, and PLMD::multicolvar::MultiColvarBase.
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virtual |
Do the task if we have a bridge.
Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.
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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::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::ves::Optimizer, PLMD::isdb::RDC, PLMD::eds::EDS, PLMD::ves::TargetDistribution, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::multicolvar::VolumeTetrapore, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::isdb::SAXS, PLMD::generic::DumpMassCharge, PLMD::isdb::JCoupling, PLMD::mapping::AdaptivePath, PLMD::generic::Print, PLMD::ves::OutputFesBias, PLMD::isdb::PRE, PLMD::adjmat::OutputCluster, PLMD::generic::Read, PLMD::isdb::NOE, PLMD::multicolvar::DumpMultiColvar, PLMD::vesselbase::ActionWithAveraging, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, and PLMD::gridtools::GridPrintingBase.
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inlineprotected |
Are we using low memory.
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inherited |
Issue a warning.
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inline |
Does the weight have derivatives.
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friend |
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friend |
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friend |
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friend |
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friend |
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friend |
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friend |
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private |
This tells plumed that this is used in a bridge.
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protected |
This is used for numerical derivatives of bridge variables.
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private |
The buffer that we use (we keep a copy here to avoid resizing)
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inherited |
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protected |
The terms in the series are locked.
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private |
The list of atoms involved in derivatives (we keep a copy here to avoid resizing)
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protected |
This is also used to minimise computational expense in complex functions.
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private |
These are used to minmise computational expense in complex functions.
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inherited |
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private |
Ths full list of tasks we have to perform.
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private |
Pointers to the functions we are using on each value.
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private |
The indices of the tasks in the full list of tasks.
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inherited |
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inherited |
Reference to the log stream.
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private |
Lower memory requirements.
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private |
The maximum number of derivatives we can use before we need to invoke lowmem.
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inherited |
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protected |
A pointer to the object that stores data.
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private |
The current number of active tasks.
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private |
Tolerance for quantities being put in neighbor lists.
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private |
Are we skipping the calculation of the derivatives.
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private |
The list of currently active tasks.
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inherited |
Reference to main plumed object.
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private |
Do all calculations in serial.
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private |
The stopwatch that times the different parts of the calculation.
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protected |
This list is used to update the neighbor list.
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private |
Do we want to output information on the timings of different parts of the calculation.
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private |
Tempory storage for forces.
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private |
The tolerance on the accumulators.
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protected |
Does the weight have derivatives.
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