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 |
typedef std::set< FILE * > ::iterator | files_iterator |
Public Member Functions | |
ActionWithVessel (const ActionOptions &ao) | |
~ActionWithVessel () | |
void | unlockContributors () |
void | lockContributors () |
virtual void | finishTaskListUpdate () |
virtual void | deactivate_task () |
Activate the jth colvar Deactivate the current task in future loops. More... | |
void | chainRuleForElementDerivatives (const unsigned &, const unsigned &, const double &, Vessel *) |
Merge the derivatives. More... | |
void | chainRuleForElementDerivatives (const unsigned &, const unsigned &, const unsigned &, const unsigned &, const double &, Vessel *) |
virtual void | mergeDerivatives (const unsigned &ider, const double &df) |
virtual void | clearDerivativesAfterTask (const unsigned &) |
bool | derivativesAreRequired () const |
Are derivatives required for this quantity. More... | |
virtual void | finishComputations () |
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 () |
Get the number of quantities that are calculated during each task. More... | |
virtual void | getIndexList (const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices) |
Get the list of indices that have derivatives. More... | |
void | activateTheseTasks (std::vector< bool > &addtionalTasks) |
Switch on additional tasks. More... | |
virtual void | doJobsRequiredBeforeTaskList () |
Do any jobs that are required before the task list is undertaken. More... | |
unsigned | getFullNumberOfTasks () const |
Get the full size of the taskList dynamic list. More... | |
virtual void | performTask ()=0 |
Get the index for a particular numbered task. More... | |
void | setElementDerivative (const unsigned &, const double &) |
Set the derivative of the jth element wrt to a numbered element. More... | |
void | addElementDerivative (const unsigned &, const double &) |
Add some derivative of the quantity in the sum wrt to a numbered element. More... | |
void | setElementValue (const unsigned &, const double &) |
Set the value of the element. More... | |
void | addElementValue (const unsigned &, const double &) |
Add to an element value. More... | |
double | getElementValue (const unsigned &ival) const |
Get the value of this element. More... | |
double | getElementDerivative (const unsigned &) const |
Retrieve the derivative of the quantity in the sum wrt to a numbered element. More... | |
virtual StoreDataVessel * | buildDataStashes () |
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... | |
virtual void | activateIndexes (const unsigned &, const unsigned &, const std::vector< unsigned > &) |
These are overwritten in MultiColvarFunction. More... | |
Vessel * | getVesselWithName (const std::string &mynam) |
Return a particular named vessel. More... | |
void | addDependency (Action *) |
Specify that this Action depends on another one. More... | |
void | clearDependencies () |
Clear the dependence list for this Action. More... | |
long int | getStep () const |
Return the present timestep. More... | |
double | getTime () const |
Return the present time. More... | |
double | getTimeStep () const |
Return the timestep. More... | |
template<class T > | |
void | parse (const std::string &key, T &t) |
Parse one keyword as generic type. More... | |
template<class T > | |
bool | parseNumbered (const std::string &key, const int no, T &t) |
Parse one numbered keyword as generic type. More... | |
template<class T > | |
void | parseVector (const std::string &key, std::vector< T > &t) |
Parse one keyword as std::vector. More... | |
template<class T > | |
bool | parseNumberedVector (const std::string &key, const int no, std::vector< T > &t) |
Parse a vector with a number. More... | |
void | parseFlag (const std::string &key, bool &t) |
Parse one keyword as boolean flag. More... | |
void | error (const std::string &msg) const |
Crash calculation and print documentation. More... | |
void | warning (const std::string &msg) |
Issue a warning. More... | |
void | exit (int c=0) |
Exit with error code c. More... | |
void | checkRead () |
Check if Action was properly read. More... | |
virtual void | 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 | 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 | setMaximumNumberOfDerivatives (const unsigned &) |
Set the maximum number of derivatives. More... | |
void | addVessel (const std::string &name, const std::string &input, const int numlab=0) |
Add a vessel to the list of vessels. More... | |
void | addVessel (Vessel *vv) |
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... | |
unsigned | getNumberOfVessels () const |
Get the number of vessels. More... | |
Vessel * | getPntrToVessel (const unsigned &i) |
Get a pointer to the ith vessel. More... | |
void | runAllTasks () |
Calculate the values of all the vessels. More... | |
void | resizeFunctions () |
Resize all the functions when the number of derivatives change. More... | |
bool | calculateAllVessels () |
This loops over all the vessels calculating them and also sets all the element derivatives equal to zero. More... | |
bool | getForcesFromVessels (std::vector< double > &forcesToApply) |
Retrieve the forces from all the vessels (used in apply) More... | |
void | accumulateDerivative (const unsigned &ider, const double &df) |
This is used to accumulate the derivatives when we merge using chainRuleForElementDerivatives. More... | |
void | clearAfterTask () |
Clear tempory data that is calculated for each task. More... | |
bool | serialCalculation () const |
Is the calculation being done in serial. More... | |
bool | usingLowMem () const |
Are we using low memory. More... | |
void | setLowMemOption (const bool &) |
Set that we are using low memory. More... | |
unsigned | getCurrentNumberOfActiveTasks () const |
Get the number of tasks that are currently active. More... | |
unsigned | getActiveTask (const unsigned &ii) const |
Get the ith of the currently active tasks. More... | |
unsigned | getPositionInFullTaskList (const unsigned &ii) const |
Get the position of the ith active task in the full list. More... | |
unsigned | getCurrentPositionInTaskList () const |
Get the current task's position in the task list. More... | |
unsigned | getCurrentTask () const |
Return the number that provides instructions for the current task. More... | |
void | deactivateAllTasks () |
Deactivate all the tasks in the task list. More... | |
void | deactivateTasksInRange (const unsigned &lower, const unsigned &upper) |
Deactivate all tasks with i in lower \(\le\) i < upper. More... | |
void | addTaskToList (const unsigned &taskCode) |
Add a task to the full list. More... | |
Protected Attributes | |
std::vector< bool > | thisval_wasset |
A boolean that makes sure we don't accumulate very wrong derivatives. More... | |
bool | contributorsAreUnlocked |
The terms in the series are locked. More... | |
bool | weightHasDerivatives |
Does the weight have derivatives. More... | |
unsigned | bridgeVariable |
This is used for numerical derivatives of bridge variables. More... | |
Private Attributes | |
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... | |
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< double > | thisval |
The value of the current element in the sum. More... | |
std::vector< double > | derivatives |
Vector of derivatives for the object. More... | |
unsigned | current_buffer_start |
The buffers we use for mpi summing DistributionFunction objects. More... | |
unsigned | current_buffer_stride |
std::vector< double > | buffer |
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... | |
unsigned | task_index |
unsigned | current |
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 > | taskFlags |
This list is used to update the neighbor list. More... | |
Friends | |
class | Vessel |
class | ShortcutVessel |
class | FunctionVessel |
class | StoreDataVessel |
class | BridgeVessel |
class | ActionWithInputVessel |
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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inherited |
PLMD::vesselbase::ActionWithVessel::ActionWithVessel | ( | const ActionOptions & | ao | ) |
PLMD::vesselbase::ActionWithVessel::~ActionWithVessel | ( | ) |
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inlineprotected |
This is used to accumulate the derivatives when we merge using chainRuleForElementDerivatives.
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virtualinherited |
Set action to active.
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inlinevirtual |
These are overwritten in MultiColvarFunction.
Reimplemented in PLMD::multicolvar::MultiColvarBase.
void PLMD::vesselbase::ActionWithVessel::activateTheseTasks | ( | std::vector< bool > & | addtionalTasks | ) |
Switch on additional tasks.
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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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inline |
Add some derivative of the quantity in the sum wrt to a numbered element.
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inline |
Add to an element value.
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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::Analysis, PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, PLMD::generic::WholeMolecules, PLMD::generic::Group, PLMD::generic::DumpAtoms, PLMD::generic::FitToTemplate, PLMD::multicolvar::Sprint, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::IMD, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::generic::Print, PLMD::generic::Include, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::manyrestraints::ManyRestraintsBase, PLMD::generic::Debug, PLMD::Colvar, PLMD::generic::Time, PLMD::bias::Bias, PLMD::generic::DumpProjections, PLMD::function::Function, PLMD::ActionWithVirtualAtom, and PLMD::ActionSetup.
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inlinevirtual |
Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume.
Reimplemented in PLMD::multicolvar::ActionVolume, and PLMD::manyrestraints::ManyRestraintsBase.
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virtual |
Ensure that data required in other vessels is stored.
Reimplemented in PLMD::multicolvar::MultiColvarBase, and PLMD::crystallization::VectorMultiColvar.
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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::bias::MetaD, PLMD::function::FuncSumHills, PLMD::function::Matheval, PLMD::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::RDC, PLMD::colvar::Distance, PLMD::bias::MovingRestraint, PLMD::generic::WholeMolecules, PLMD::multicolvar::ActionVolume, PLMD::generic::Group, PLMD::bias::External, PLMD::generic::DumpAtoms, PLMD::generic::FitToTemplate, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::multicolvar::MultiColvarFunction, PLMD::colvar::ContactMap, PLMD::function::Combine, PLMD::bias::BiasValue, PLMD::colvar::DRMSD, PLMD::colvar::Gyration, PLMD::colvar::NOE, PLMD::IMD, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::colvar::PathMSDBase, PLMD::function::Piecewise, PLMD::colvar::Position, PLMD::vatom::Center, PLMD::colvar::Torsion, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::MultiColvar, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::generic::Include, PLMD::generic::Print, PLMD::bias::Restraint, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::vatom::COM, PLMD::colvar::Energy, PLMD::function::Sort, PLMD::generic::DumpDerivatives, PLMD::colvar::Constant, PLMD::generic::DumpForces, PLMD::manyrestraints::ManyRestraintsBase, PLMD::function::Ensemble, PLMD::generic::Debug, PLMD::vatom::Ghost, PLMD::colvar::Dipole, PLMD::colvar::Cell, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::colvar::Template, PLMD::function::Target, PLMD::generic::Time, PLMD::generic::DumpProjections, PLMD::colvar::MultiRMSD, PLMD::colvar::RMSD, PLMD::colvar::CoordinationBase, PLMD::ActionSetup, and PLMD::mapping::PathBase.
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protected |
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::analysis::Analysis, PLMD::ActionAtomistic, PLMD::multicolvar::ActionVolume, PLMD::multicolvar::MultiColvarFunction, PLMD::ActionWithArguments, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithInputVessel.
void PLMD::vesselbase::ActionWithVessel::chainRuleForElementDerivatives | ( | const unsigned & | iout, |
const unsigned & | ider, | ||
const double & | df, | ||
Vessel * | valout | ||
) |
Merge the derivatives.
void PLMD::vesselbase::ActionWithVessel::chainRuleForElementDerivatives | ( | const unsigned & | iout, |
const unsigned & | ider, | ||
const unsigned & | stride, | ||
const unsigned & | off, | ||
const double & | df, | ||
Vessel * | valout | ||
) |
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inlinevirtualinherited |
Check if the action needs gradient.
Reimplemented in PLMD::bias::MetaD, 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 |
Cite a paper see PlumedMain::cite.
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protected |
Clear tempory data that is calculated for each task.
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inherited |
Clear the dependence list for this Action.
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virtual |
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virtualinherited |
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inlinevirtualinherited |
Set action to inactive.
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virtual |
Activate the jth colvar Deactivate the current task in future loops.
Reimplemented in PLMD::multicolvar::ActionVolume, and PLMD::manyrestraints::ManyRestraintsBase.
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protected |
Deactivate all the tasks in the task list.
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protected |
Deactivate all tasks with i in lower \(\le\) i < upper.
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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::multicolvar::ActionVolume, PLMD::multicolvar::Angles, PLMD::multicolvar::Bridge, PLMD::multicolvar::AdjacencyMatrixAction, and PLMD::manyrestraints::ManyRestraintsBase.
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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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inlinevirtual |
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inherited |
Opens a file.
This is similar to plain fopen, but with some extra functionality.
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inlineprotected |
Get the ith of the currently active tasks.
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inlineprotected |
Get the number of tasks that are currently active.
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inlineprotected |
Get the current task's position in the task list.
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inlineprotected |
Return the number that provides instructions for the current task.
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inlineinherited |
Return dependencies.
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virtualinherited |
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inline |
Retrieve the derivative of the quantity in the sum wrt to a numbered element.
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inline |
Get the value of this element.
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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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virtual |
Get the list of indices that have derivatives.
Reimplemented in PLMD::multicolvar::MultiColvarBase, and PLMD::multicolvar::Density.
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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::Analysis, PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::mapping::Mapping, and PLMD::manyrestraints::ManyRestraintsBase.
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inlinevirtual |
Get the number of quantities that are calculated during each task.
Reimplemented in PLMD::multicolvar::MultiColvarBase, PLMD::crystallization::VectorMultiColvar, PLMD::multicolvar::ActionVolume, PLMD::multicolvar::LocalAverage, and PLMD::multicolvar::Density.
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inlineprotected |
Get the number of vessels.
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inlineprotected |
Get a pointer to the ith vessel.
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inlineprotected |
Get the position of the ith active task in the full list.
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inherited |
Return the present timestep.
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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 | ) |
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::Analysis, PLMD::multicolvar::Distances, PLMD::multicolvar::XDistances, PLMD::multicolvar::ActionVolume, PLMD::multicolvar::AlphaBeta, PLMD::multicolvar::LocalAverage, PLMD::multicolvar::Angles, PLMD::crystallization::VectorMultiColvar, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::multicolvar::DihedralCorrelation, PLMD::multicolvar::NumberOfLinks, PLMD::multicolvar::Torsions, PLMD::multicolvar::CoordinationNumbers, PLMD::multicolvar::Bridge, PLMD::mapping::Mapping, PLMD::crystallization::SimpleCubic, PLMD::multicolvar::AdjacencyMatrixAction, PLMD::multicolvar::Density, PLMD::crystallization::Tetrahedral, PLMD::manyrestraints::ManyRestraintsBase, PLMD::crystallization::Fccubic, and PLMD::crystallization::OrientationSphere.
void PLMD::vesselbase::ActionWithVessel::lockContributors | ( | ) |
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inlinevirtualinherited |
Reimplemented in PLMD::ActionAtomistic, PLMD::analysis::Analysis, PLMD::ActionWithArguments, and PLMD::mapping::Mapping.
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virtual |
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protected |
Turn on the derivatives in the vessel.
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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 |
Get the index for a particular numbered task.
Calculate one of the functions in the distribution
Implemented in PLMD::multicolvar::MultiColvarBase, PLMD::analysis::Histogram, PLMD::multicolvar::ActionVolume, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::manyrestraints::UWalls, PLMD::analysis::AnalysisWithLandmarks, 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::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Read, PLMD::generic::Print, 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::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.
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inlineprotected |
Is the calculation being done in serial.
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inline |
Set the derivative of the jth element wrt to a numbered element.
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inline |
Set the value of the element.
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inlineprotected |
Set that we are using low memory.
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protected |
Set the maximum number of derivatives.
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virtualinherited |
void PLMD::vesselbase::ActionWithVessel::unlockContributors | ( | ) |
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inlinevirtualinherited |
Reimplemented in PLMD::ActionAtomistic, PLMD::analysis::Analysis, PLMD::ActionWithArguments, and PLMD::mapping::Mapping.
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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::analysis::Analysis, PLMD::generic::DumpAtoms, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::generic::Print, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, and PLMD::generic::DumpProjections.
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inlineprotected |
Are we using low memory.
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inherited |
Issue a warning.
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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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protected |
This is used for numerical derivatives of bridge variables.
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private |
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inherited |
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protected |
The terms in the series are locked.
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private |
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private |
The buffers we use for mpi summing DistributionFunction objects.
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private |
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private |
Vector of derivatives for the object.
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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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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 |
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private |
This list is used to update the neighbor list.
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private |
The value of the current element in the sum.
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protected |
A boolean that makes sure we don't accumulate very wrong derivatives.
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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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