Detailed Description
Command interpreter and Command Manager for an MdSimulation.
The implementation of the readStandardCommand() function defines the standard, built-in commands for an MdSimulation. Additional commands may be added in the optional CommandManager section of the parameter file and then invoked in the command file.
The default Factory<Command> object for an MdCommandManager is an MdCommandFactory.
Definition at line 38 of file MdCommandManager.h.
#include <MdCommandManager.h>
Inheritance diagram for McMd::MdCommandManager:
Public Member Functions | |
| MdCommandManager (MdSimulation &simulation) | |
| Constructor. More... | |
| MdCommandManager (MdSimulation &simulation, MdSystem &system) | |
| Constructor. More... | |
| virtual | ~MdCommandManager () |
| Destructor. More... | |
 Public Member Functions inherited from McMd::CommandManager | |
| CommandManager () | |
| Constructor. More... | |
| virtual | ~CommandManager () |
| Destructor. More... | |
| bool | readCommand (std::string name, std::istream &in) |
| Attempt to read a command line, execute if recognized. More... | |
| Public Member Functions inherited from Util::Manager< Command > | |
| Manager (bool uniqueNames=false) | |
| Constructor. More... | |
| virtual | ~Manager () |
| Destructor. More... | |
| void | addSubfactory (Factory< Command > &subfactory) |
| Set a SubFactory for this Manager. More... | |
| void | setFactory (Factory< Command > &factory) |
| Associate a Factory with this Manager. More... | |
| void | setFactory (Factory< Command > *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 | readParameters (std::istream &in) |
| Read child blocks, return when closing bracket encountered. 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 (Command &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< Command > & | factory () |
| Return a reference to the factory. More... | |
| bool | hasFactory () const |
| Return true if this Manager has a Factory, false otherwise. More... | |
| Command & | operator[] (int i) const |
| Mimic C array subscripting. More... | |
| Command * | 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... | |
Protected Member Functions | |
| virtual Util::Factory< Command > * | newDefaultFactory () const |
| Create and return pointer to a new MdCommandFactory object. More... | |
| MdSimulation & | simulation () const |
| Get parent MdSimulation by reference. More... | |
| MdSystem & | system () const |
| Get associated MdSystem by reference. More... | |
| virtual bool | readStandardCommand (std::string command, std::istream &in) |
| Attempt to read one of the standard built-in commands. More... | |
| Protected Member Functions inherited from Util::Manager< Command > | |
| 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... | |
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 Attributes inherited from Util::Manager< Command > | |
| Factory< Command > * | factoryPtr_ |
| Pointer to an associated Factory<Data> object. More... | |
Constructor & Destructor Documentation
| McMd::MdCommandManager::MdCommandManager | ( | MdSimulation & | simulation | ) |
Constructor.
- Parameters
-
simulation parent MdSimulation
Definition at line 22 of file MdCommandManager.cpp.
| McMd::MdCommandManager::MdCommandManager | ( | MdSimulation & | simulation, |
| MdSystem & | system | ||
| ) |
Constructor.
- Parameters
-
simulation parent Simulation system associated MdSystem
Definition at line 32 of file MdCommandManager.cpp.
|
virtual |
Destructor.
Definition at line 40 of file MdCommandManager.cpp.
Member Function Documentation
Create and return pointer to a new MdCommandFactory object.
Reimplemented from Util::Manager< Command >.
Definition at line 44 of file MdCommandManager.cpp.
References simulation(), and system().
|
inlineprotected |
Get parent MdSimulation by reference.
Definition at line 109 of file MdCommandManager.h.
Referenced by newDefaultFactory(), and readStandardCommand().
|
inlineprotected |
Get associated MdSystem by reference.
Definition at line 116 of file MdCommandManager.h.
Referenced by newDefaultFactory(), and readStandardCommand().
|
protectedvirtual |
Attempt to read one of the standard built-in commands.
Precondition: The command identifier should have been read from stream in, and should be passed as string parameter command. If the command name is matched, any further parameters required by the command are read from stream in, the command is executed, the function returns a true value. If the command name is not recognized, this function immediately returns false.
- Parameters
-
command command name (capitalized identifer) in input stream from which command was read
Reimplemented from McMd::CommandManager.
Definition at line 49 of file MdCommandManager.cpp.
References Util::DArray< Data >::allocate(), McMd::MdSimulation::analyzeConfigs(), McMd::MdSimulation::analyzeTrajectory(), McMd::MdSystem::anglePotential(), McMd::MdSystem::bondPotential(), McMd::System::boundary(), McMd::MdSystem::dihedralPotential(), Util::Log::file(), McMd::MdSystem::generateMolecules(), McMd::Simulation::nAtomType(), McMd::Simulation::nSpecies(), McMd::MdSystem::pairPotential(), McMd::MdSystem::readConfig(), McMd::MdSystem::removeDriftVelocity(), McMd::PairPotential::set(), McMd::DihedralPotential::set(), McMd::BondPotential::set(), McMd::AnglePotential::set(), McMd::MdSystem::setBoltzmannVelocities(), McMd::System::setConfigIo(), McMd::MdSimulation::simulate(), simulation(), system(), UTIL_THROW, McMd::System::writeConfig(), and McMd::Simulation::writeParam().
The documentation for this class was generated from the following files:
