Detailed Description
Manager for a set of Modifier objects.
An ModifierManager maintains a list of Modifier objects and provides methods to execute specified actions at various points before and during the main integration loop.
Definition at line 32 of file ModifierManager.h.
#include <ModifierManager.h>
Public Member Functions | |
| ModifierManager () | |
| Default constructor (for unit testing). More... | |
| ModifierManager (Simulation &simulation) | |
| Constructor (for use in Simulation). More... | |
| ~ModifierManager () | |
| Destructor. More... | |
| void | readParameters (std::istream &in) |
| Read main block of parameter file. More... | |
| Factory< Modifier > * | newDefaultFactory () const |
| Return pointer to a new default factory. More... | |
Integrator actions | |
| void | setup () |
| Setup before entering the main loop. More... | |
| void | preIntegrate1 (long iStep) |
| Call just before the first step of velocity-Verlet algorithm. More... | |
| void | postIntegrate1 (long iStep) |
| Call just after the first step of velocity-Verlet algorithm. More... | |
| void | preTransform (long iStep) |
| Call on exchange steps before transforming to scaled coordinates. More... | |
| void | preExchange (long iStep) |
| Call on exchange steps after transforming, before exchanging. More... | |
| void | postExchange (long iStep) |
| Call on exchange steps after atom exchange, before reneighboring. More... | |
| void | postNeighbor (long iStep) |
| Call on exchange steps after re-building the neighbor list. More... | |
| void | preUpdate (long iStep) |
| Call on update steps before updating ghost positions. More... | |
| void | postUpdate (long iStep) |
| Call on update steps after updating ghost positions. More... | |
| void | preForce (long iStep) |
| Call after updating but before calculating forces. More... | |
| void | postForce (long iStep) |
| Call after calculating forces. More... | |
| void | endOfStep (long iStep) |
| Call after 2nd integration step, at end of the time step. More... | |
Communication functions | |
| void | packExchange (long iStep) |
| Pack data into buffer used to exchange atoms. More... | |
| void | unpackExchange (long iStep) |
| Unpack data from buffer used to exchange atoms. More... | |
| void | packUpdate (long iStep) |
| Pack data into buffer used to update ghost positions. More... | |
| void | unpackUpdate (long iStep) |
| Unpack data from buffer used to update ghost positions. More... | |
| void | packReverseUpdate (long iStep) |
| Pack data into buffer used to reverse update forces. More... | |
| void | unpackReverseUpdate (long iStep) |
| Unpack data from the buffer used to reverse update forces. More... | |
 Public Member Functions inherited from Util::Manager< Modifier > | |
| Manager (bool uniqueNames=false) | |
| Constructor. More... | |
| virtual | ~Manager () |
| Destructor. More... | |
| void | addSubfactory (Factory< Modifier > &subfactory) |
| Set a SubFactory for this Manager. More... | |
| void | setFactory (Factory< Modifier > &factory) |
| Associate a Factory with this Manager. More... | |
| void | setFactory (Factory< Modifier > *factoryPtr) |
| Associated a Factory with this Manager (pass by pointer). More... | |
| virtual void | readParam (std::istream &in) |
| Read and create a set of objects. More... | |
| virtual void | readParamOptional (std::istream &in) |
| Optionally read and create a set of objects. More... | |
| virtual void | loadParameters (Serializable::IArchive &ar) |
| Load a set of objects to an output archive. More... | |
| virtual void | save (Serializable::OArchive &ar) |
| Save a set of objects to an output archive. More... | |
| void | append (Modifier &data, const std::string &name) |
| Append a Data object to the end of the sequence. More... | |
| int | size () const |
| Get logical size. More... | |
| std::string | className (int i) const |
| Get the subclass name for object number i. More... | |
| Factory< Modifier > & | factory () |
| Return a reference to the factory. More... | |
| bool | hasFactory () const |
| Return true if this Manager has a Factory, false otherwise. More... | |
| Modifier & | operator[] (int i) const |
| Mimic C array subscripting. More... | |
| Modifier * | findFirst (std::string const &className) |
| Return pointer to first object with specified class name. More... | |
| Public Member Functions inherited from Util::ParamComposite | |
| ParamComposite () | |
| Constructor. More... | |
| ParamComposite (const ParamComposite &other) | |
| Copy constructor. More... | |
| ParamComposite (int capacity) | |
| Constructor. More... | |
| virtual | ~ParamComposite () |
| Virtual destructor. More... | |
| void | resetParam () |
| Resets ParamComposite to its empty state. More... | |
| virtual void | writeParam (std::ostream &out) |
| Write all parameters to an output stream. More... | |
| virtual void | load (Serializable::IArchive &ar) |
| Load all parameters from an input archive. More... | |
| virtual void | loadOptional (Serializable::IArchive &ar) |
| Load an optional ParamComposite. More... | |
| void | saveOptional (Serializable::OArchive &ar) |
| Saves isActive flag, and then calls save() iff isActive is true. More... | |
| void | readParamComposite (std::istream &in, ParamComposite &child, bool next=true) |
| Add and read a required child ParamComposite. More... | |
| void | readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true) |
| Add and attempt to read an optional child ParamComposite. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | read (std::istream &in, const char *label, Type &value) |
| Add and read a new required ScalarParam < Type > object. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | readOptional (std::istream &in, const char *label, Type &value) |
| Add and read a new optional ScalarParam < Type > object. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | readCArray (std::istream &in, const char *label, Type *value, int n) |
| Add and read a required C array parameter. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | readOptionalCArray (std::istream &in, const char *label, Type *value, int n) |
| Add and read an optional C array parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | readDArray (std::istream &in, const char *label, DArray< Type > &array, int n) |
| Add and read a required DArray < Type > parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n) |
| Add and read an optional DArray < Type > parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | readFArray (std::istream &in, const char *label, FArray< Type, N > &array) |
| Add and read a required FArray < Type, N > array parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array) |
| Add and read an optional FArray < Type, N > array parameter. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | readCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np) |
| Add and read a required CArray2DParam < Type > 2D C-array. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | readOptionalCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np) |
| Add and read an optional CArray2DParam < Type > 2D C-array parameter. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | readDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n) |
| Add and read a required DMatrix < Type > matrix parameter. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n) |
| Add and read an optional DMatrix < Type > matrix parameter. More... | |
| template<typename Type > | |
| DSymmMatrixParam< Type > & | readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n) |
| Add and read a required symmetrix DMatrix. More... | |
| template<typename Type > | |
| DSymmMatrixParam< Type > & | readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n) |
| Add and read an optional DMatrix matrix parameter. More... | |
| Begin & | readBegin (std::istream &in, const char *label, bool isRequired=true) |
| Add and read a class label and opening bracket. More... | |
| End & | readEnd (std::istream &in) |
| Add and read the closing bracket. More... | |
| Blank & | readBlank (std::istream &in) |
| Add and read a new Blank object, representing a blank line. More... | |
| void | loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true) |
| Add and load a required child ParamComposite. More... | |
| void | loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true) |
| Add and load an optional child ParamComposite if isActive. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired) |
| Add and load a new ScalarParam < Type > object. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | loadParameter (Serializable::IArchive &ar, const char *label, Type &value) |
| Add and load new required ScalarParam < Type > object. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | loadCArray (Serializable::IArchive &ar, const char *label, Type *value, int n, bool isRequired) |
| Add a C array parameter and load its elements. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | loadCArray (Serializable::IArchive &ar, const char *label, Type *value, int n) |
| Add and load a required CArrayParam< Type > array parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired) |
| Add an load a DArray < Type > array parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n) |
| Add and load a required DArray< Type > array parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired) |
| Add and load an FArray < Type, N > fixed-size array parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array) |
| Add and load a required FArray < Type > array parameter. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | loadCArray2D (Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np, bool isRequired) |
| Add and load a CArray2DParam < Type > C 2D array parameter. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | loadCArray2D (Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np) |
| Add and load a required < Type > matrix parameter. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired) |
| Add and load a DMatrixParam < Type > matrix parameter. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n) |
| Add and load a required DMatrixParam < Type > matrix parameter. More... | |
| template<typename Type > | |
| DSymmMatrixParam< Type > & | loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired) |
| Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More... | |
| template<typename Type > | |
| DSymmMatrixParam< Type > & | loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n) |
| Add and load a required DSymmMatrixParam < Type > matrix parameter. More... | |
| void | addParamComposite (ParamComposite &child, bool next=true) |
| Add a child ParamComposite object to the format array. More... | |
| Begin & | addBegin (const char *label) |
| Add a Begin object representing a class name and bracket. More... | |
| End & | addEnd () |
| Add a closing bracket. More... | |
| Blank & | addBlank () |
| Create and add a new Blank object, representing a blank line. More... | |
| std::string | className () const |
| Get class name string. More... | |
| bool | isRequired () const |
| Is this ParamComposite required in the input file? More... | |
| bool | isActive () const |
| Is this parameter active? More... | |
| Public Member Functions inherited from Util::ParamComponent | |
| virtual | ~ParamComponent () |
| Destructor. More... | |
| void | setIndent (const ParamComponent &parent, bool next=true) |
| Set indent level. More... | |
| std::string | indent () const |
| Return indent string for this object (string of spaces). More... | |
| template<class Archive > | |
| void | serialize (Archive &ar, const unsigned int version) |
| Serialize this ParamComponent as a string. More... | |
| Public Member Functions inherited from Util::Serializable | |
| virtual | ~Serializable () |
| Destructor. More... | |
| Public Member Functions inherited from Util::MpiFileIo | |
| MpiFileIo () | |
| Constructor. More... | |
| MpiFileIo (const MpiFileIo &other) | |
| Copy constructor. More... | |
| bool | isIoProcessor () const |
| Can this processor do file I/O ? More... | |
| void | setIoCommunicator (MPI::Intracomm &communicator) |
| Set the communicator. More... | |
| void | clearCommunicator () |
| Clear (nullify) the communicator. More... | |
| bool | hasIoCommunicator () const |
| Does this object have an associated MPI communicator? More... | |
| MPI::Intracomm & | ioCommunicator () const |
| Get the MPI communicator by reference. More... | |
Additional Inherited Members | |
| Public Types inherited from Util::Serializable | |
| typedef BinaryFileOArchive | OArchive |
| Type of output archive used by save method. More... | |
| typedef BinaryFileIArchive | IArchive |
| Type of input archive used by load method. More... | |
| Static Public Member Functions inherited from Util::ParamComponent | |
| static void | initStatic () |
| Initialize static echo member to false. More... | |
| static void | setEcho (bool echo=true) |
| Enable or disable echoing for all subclasses of ParamComponent. More... | |
| static bool | echo () |
| Get echo parameter. More... | |
| Protected Member Functions inherited from Util::Manager< Modifier > | |
| void | beginReadManager (std::istream &in) |
| Read (or attempt to read) opening line: "ManagerName{". More... | |
| void | endReadManager () |
| Add closing bracket to output format. More... | |
| virtual void | initFactory () |
| Create factory if necessary. More... | |
| Protected Member Functions inherited from Util::ParamComposite | |
| void | setClassName (const char *className) |
| Set class name string. More... | |
| void | setIsRequired (bool isRequired) |
| Set or unset the isActive flag. More... | |
| void | setIsActive (bool isActive) |
| Set or unset the isActive flag. More... | |
| void | setParent (ParamComponent ¶m, bool next=true) |
| Set this to the parent of a child component. More... | |
| void | addComponent (ParamComponent ¶m, bool isLeaf=true) |
| Add a new ParamComponent object to the format array. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | add (std::istream &in, const char *label, Type &value, bool isRequired=true) |
| Add a new required ScalarParam < Type > object. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | addCArray (std::istream &in, const char *label, Type *value, int n, bool isRequired=true) |
| Add (but do not read) a required C array parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | addDArray (std::istream &in, const char *label, DArray< Type > &array, int n, bool isRequired=true) |
| Add (but do not read) a DArray < Type > parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | addFArray (std::istream &in, const char *label, FArray< Type, N > &array, bool isRequired=true) |
| Add (but do not read) a FArray < Type, N > array parameter. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | addCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np, bool isRequired=true) |
| Add (but do not read) a CArray2DParam < Type > 2D C-array. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | addDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired=true) |
| Add and read a required DMatrix < Type > matrix parameter. More... | |
| Protected Member Functions inherited from Util::ParamComponent | |
| ParamComponent () | |
| Constructor. More... | |
| ParamComponent (const ParamComponent &other) | |
| Copy constructor. More... | |
| Protected Attributes inherited from Util::Manager< Modifier > | |
| Factory< Modifier > * | factoryPtr_ |
| Pointer to an associated Factory<Data> object. More... | |
Constructor & Destructor Documentation
| DdMd::ModifierManager::ModifierManager | ( | ) |
Default constructor (for unit testing).
Definition at line 19 of file ModifierManager.cpp.
References Util::ParamComposite::setClassName().
| DdMd::ModifierManager::ModifierManager | ( | Simulation & | simulation | ) |
Constructor (for use in Simulation).
Definition at line 42 of file ModifierManager.cpp.
References Util::ParamComposite::setClassName().
| DdMd::ModifierManager::~ModifierManager | ( | ) |
Destructor.
Definition at line 65 of file ModifierManager.cpp.
Member Function Documentation
|
virtual |
Read main block of parameter file.
- Parameters
-
in input parameter file stream.
Reimplemented from Util::Manager< Modifier >.
Definition at line 73 of file ModifierManager.cpp.
References DdMd::Modifier::Flags::EndOfStep, DdMd::Modifier::Flags::Exchange, DdMd::Modifier::isSet(), DdMd::Modifier::Flags::PostExchange, DdMd::Modifier::Flags::PostForce, DdMd::Modifier::Flags::PostIntegrate1, DdMd::Modifier::Flags::PostNeighbor, DdMd::Modifier::Flags::PostUpdate, DdMd::Modifier::Flags::PreExchange, DdMd::Modifier::Flags::PreForce, DdMd::Modifier::Flags::PreIntegrate1, DdMd::Modifier::Flags::PreTransform, DdMd::Modifier::Flags::PreUpdate, Util::Manager< Data >::readParameters(), DdMd::Modifier::Flags::ReverseUpdate, DdMd::Modifier::Flags::Setup, Util::Manager< Modifier >::size(), and DdMd::Modifier::Flags::Update.
Return pointer to a new default factory.
Virtual, inherited from Manager<Modifier>.
Reimplemented from Util::Manager< Modifier >.
Definition at line 337 of file ModifierManager.cpp.
| void DdMd::ModifierManager::setup | ( | ) |
Setup before entering the main loop.
Definition at line 130 of file ModifierManager.cpp.
Referenced by DdMd::TwoStepIntegrator::run().
| void DdMd::ModifierManager::preIntegrate1 | ( | long | iStep | ) |
Call just before the first step of velocity-Verlet algorithm.
Definition at line 140 of file ModifierManager.cpp.
References DdMd::Modifier::isAtInterval(), and DdMd::Modifier::preIntegrate1().
Referenced by DdMd::TwoStepIntegrator::run().
| void DdMd::ModifierManager::postIntegrate1 | ( | long | iStep | ) |
Call just after the first step of velocity-Verlet algorithm.
Definition at line 152 of file ModifierManager.cpp.
References DdMd::Modifier::isAtInterval(), and DdMd::Modifier::postIntegrate1().
Referenced by DdMd::TwoStepIntegrator::run().
| void DdMd::ModifierManager::preTransform | ( | long | iStep | ) |
Call on exchange steps before transforming to scaled coordinates.
Definition at line 164 of file ModifierManager.cpp.
References DdMd::Modifier::isAtInterval(), and DdMd::Modifier::preTransform().
Referenced by DdMd::TwoStepIntegrator::run().
| void DdMd::ModifierManager::preExchange | ( | long | iStep | ) |
Call on exchange steps after transforming, before exchanging.
Definition at line 176 of file ModifierManager.cpp.
References DdMd::Modifier::isAtInterval(), and DdMd::Modifier::preExchange().
Referenced by DdMd::TwoStepIntegrator::run().
| void DdMd::ModifierManager::postExchange | ( | long | iStep | ) |
Call on exchange steps after atom exchange, before reneighboring.
Definition at line 188 of file ModifierManager.cpp.
References DdMd::Modifier::isAtInterval(), and DdMd::Modifier::postExchange().
Referenced by DdMd::TwoStepIntegrator::run().
| void DdMd::ModifierManager::postNeighbor | ( | long | iStep | ) |
Call on exchange steps after re-building the neighbor list.
Definition at line 200 of file ModifierManager.cpp.
References DdMd::Modifier::isAtInterval(), and DdMd::Modifier::postNeighbor().
Referenced by DdMd::TwoStepIntegrator::run().
| void DdMd::ModifierManager::preUpdate | ( | long | iStep | ) |
Call on update steps before updating ghost positions.
Definition at line 212 of file ModifierManager.cpp.
References DdMd::Modifier::isAtInterval(), and DdMd::Modifier::preUpdate().
Referenced by DdMd::TwoStepIntegrator::run().
| void DdMd::ModifierManager::postUpdate | ( | long | iStep | ) |
Call on update steps after updating ghost positions.
Definition at line 224 of file ModifierManager.cpp.
References DdMd::Modifier::isAtInterval(), and DdMd::Modifier::postUpdate().
Referenced by DdMd::TwoStepIntegrator::run().
| void DdMd::ModifierManager::preForce | ( | long | iStep | ) |
Call after updating but before calculating forces.
Definition at line 236 of file ModifierManager.cpp.
References DdMd::Modifier::isAtInterval(), and DdMd::Modifier::preForce().
Referenced by DdMd::TwoStepIntegrator::run().
| void DdMd::ModifierManager::postForce | ( | long | iStep | ) |
Call after calculating forces.
Definition at line 248 of file ModifierManager.cpp.
References DdMd::Modifier::isAtInterval(), and DdMd::Modifier::postForce().
Referenced by DdMd::TwoStepIntegrator::run().
| void DdMd::ModifierManager::endOfStep | ( | long | iStep | ) |
Call after 2nd integration step, at end of the time step.
Definition at line 260 of file ModifierManager.cpp.
References DdMd::Modifier::endOfStep(), and DdMd::Modifier::isAtInterval().
Referenced by DdMd::TwoStepIntegrator::run().
| void DdMd::ModifierManager::packExchange | ( | long | iStep | ) |
Pack data into buffer used to exchange atoms.
Definition at line 274 of file ModifierManager.cpp.
References DdMd::Modifier::packExchange().
| void DdMd::ModifierManager::unpackExchange | ( | long | iStep | ) |
Unpack data from buffer used to exchange atoms.
Definition at line 284 of file ModifierManager.cpp.
References DdMd::Modifier::unpackExchange().
| void DdMd::ModifierManager::packUpdate | ( | long | iStep | ) |
Pack data into buffer used to update ghost positions.
Definition at line 294 of file ModifierManager.cpp.
References DdMd::Modifier::packUpdate().
| void DdMd::ModifierManager::unpackUpdate | ( | long | iStep | ) |
Unpack data from buffer used to update ghost positions.
Definition at line 304 of file ModifierManager.cpp.
References DdMd::Modifier::unpackUpdate().
| void DdMd::ModifierManager::packReverseUpdate | ( | long | iStep | ) |
Pack data into buffer used to reverse update forces.
Used only if reverse communication is enabled.
Definition at line 314 of file ModifierManager.cpp.
References DdMd::Modifier::packReverseUpdate().
| void DdMd::ModifierManager::unpackReverseUpdate | ( | long | iStep | ) |
Unpack data from the buffer used to reverse update forces.
Used only if reverse communication is enabled.
Definition at line 324 of file ModifierManager.cpp.
References DdMd::Modifier::unpackReverseUpdate().
The documentation for this class was generated from the following files:
