Brownian dynamics simulator. More...

#include <BdSimulator.h>

Inheritance diagram for Pscf::Rpg::BdSimulator< D >:

Public Member Functions
	BdSimulator (System< D > &system)
	Constructor.
	~BdSimulator ()
	Destructor.
virtual void	readParameters (std::istream &in)
	Read parameters for a MC simulation.
Primary Actions: Simulation and Analysis
void	simulate (int nStep)
	Perform a field theoretic Monte-Carlo simulation.
virtual void	analyze (int min, int max, std::string classname, std::string filename)
	Read and analyze a trajectory file.
virtual void	outputTimers (std::ostream &out) const
	Output timing results.
Miscellaneous
bool	hasBdStep () const
	Does this BdSimulator have an associated BdStep?
BdStep< D > &	stepper ()
	Get BdStep.
AnalyzerManager< D > &	analyzerManager ()
	Get AnalyzerManger.
Factory< TrajectoryReader< D > > &	trajectoryReaderFactory ()
	Get the trajectory reader factory by reference.
Public Member Functions inherited from Pscf::Rpg::Simulator< D >
	Simulator (System< D > &system)
	Constructor.
	~Simulator ()
	Destructor.
void	allocate ()
	Allocate required memory.
void	clearData ()
	Clear field eigen-components and hamiltonian components.
virtual void	outputMdeCounter (std::ostream &out) const
	Output MDE counter.
virtual void	clearTimers ()
	Clear timers.
long	iStep ()
	Return the current converged simulation step index.
long	iTotalStep ()
	Return the current simulation step index.
void	analyzeChi ()
	Perform eigenvalue analysis of projected chi matrix.
DArray< double > const &	chiEvals () const
	Get an array of the eigenvalues of the projected chi matrix.
double	chiEval (int a) const
	Get a single eigenvalue of the projected chi matrix.
DMatrix< double > const &	chiEvecs () const
	Get the matrix of all eigenvectors of the projected chi matrix.
double	chiEvecs (int a, int i) const
	Get one element of an eigenvector of the projected chi matrix.
DArray< double > const &	sc () const
	Get all components of the vector S.
double	sc (int a) const
	Get a single component of the S vector.
void	computeHamiltonian ()
	Compute the Hamiltonian used in field theoretic simulations.
double	hamiltonian () const
	Get the Hamiltonian used in field theoretic simulations.
double	idealHamiltonian () const
	Get ideal gas contribution (-lnQ) to MC Hamiltonian.
double	fieldHamiltonian () const
	Get the quadratic field contribution (HW) to MC Hamiltonian.
double	perturbationHamiltonian () const
	Get the perturbation to the standard Hamiltonian (if any).
bool	hasHamiltonian () const
	Has the MC Hamiltonian been computed for current w and c fields?
void	computeWc ()
	Compute eigenvector components of the current w fields.
DArray< RField< D > > const &	wc () const
	Get all eigenvector components of the current w fields.
RField< D > const &	wc (int a) const
	Get one eigenvector component of the current w fields.
bool	hasWc () const
	Are eigen-components of current w fields valid ?
void	computeCc ()
	Compute eigenvector components of the current c fields.
DArray< RField< D > > const &	cc () const
	Get all eigenvector components of the current c fields.
RField< D > const &	cc (int a) const
	Get one eigenvector component of the current c fields.
bool	hasCc () const
	Are eigen-components of current c fields valid ?
void	computeDc ()
	Compute functional derivatives of the Hamiltonian.
DArray< RField< D > > const &	dc () const
	Get all of the current d fields.
RField< D > const &	dc (int i) const
	Get one eigenvector component of the current d fields.
bool	hasDc () const
	Are the current d fields valid ?
void	saveState ()
	Save a copy of the fts move state.
void	restoreState ()
	Restore the saved copy of the fts move state.
void	clearState ()
	Clear the saved copy of the fts state.
System< D > &	system ()
	Get parent system by reference.
Compressor< D > &	compressor ()
	Get the compressor by non-const reference.
Compressor< D > const &	compressor () const
	Get the compressor by const reference.
bool	hasCompressor () const
	Does this Simulator have a Compressor object?
Random &	random ()
	Get random number generator by reference.
CudaRandom &	cudaRandom ()
	Get cuda random number generator by reference.
bool	hasPerturbation () const
	Does this Simulator have a Perturbation?
Perturbation< D > const &	perturbation () const
	Get the associated Perturbation by const reference.
Perturbation< D > &	perturbation ()
	Get the perturbation factory by non-const reference.
bool	hasRamp () const
	Does this Simulator have a Ramp?
Ramp< D > const &	ramp () const
	Get the associated Ramp by const reference.
Ramp< D > &	ramp ()
	Get the ramp by non-const reference.
Public Member Functions inherited from Util::ParamComposite
	ParamComposite ()
	Constructor.
	ParamComposite (const ParamComposite &other)
	Copy constructor.
	ParamComposite (int capacity)
	Constructor.
virtual	~ParamComposite ()
	Virtual destructor.
void	resetParam ()
	Resets ParamComposite to its empty state.
virtual void	readParam (std::istream &in)
	Read the parameter file block.
virtual void	readParamOptional (std::istream &in)
	Read optional parameter file block.
virtual void	writeParam (std::ostream &out) const
	Write all parameters to an output stream.
virtual void	load (Serializable::IArchive &ar)
	Load all parameters from an input archive.
virtual void	loadOptional (Serializable::IArchive &ar)
	Load an optional ParamComposite.
virtual void	loadParameters (Serializable::IArchive &ar)
	Load state from archive, without adding Begin and End lines.
virtual void	save (Serializable::OArchive &ar)
	Saves all parameters to an archive.
void	saveOptional (Serializable::OArchive &ar)
	Saves isActive flag, and then calls save() iff isActive is true.
void	readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
	Add and read a required child ParamComposite.
void	readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
	Add and attempt to read an optional child ParamComposite.
template<typename Type>
ScalarParam< Type > &	read (std::istream &in, const char *label, Type &value)
	Add and read a new required ScalarParam < Type > object.
template<typename Type>
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object.
template<typename Type>
CArrayParam< Type > &	readCArray (std::istream &in, const char label, Type value, int n)
	Add and read a required C array parameter.
template<typename Type>
CArrayParam< Type > &	readOptionalCArray (std::istream &in, const char label, Type value, int n)
	Add and read an optional C array parameter.
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.
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.
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.
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.
template<typename Type, int N>
FSArrayParam< Type, N > &	readFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size)
	Add and read a required FSArray < Type, N > array parameter.
template<typename Type, int N>
FSArrayParam< Type, N > &	readOptionalFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size)
	Add and read an optional FSArray < Type, N > array parameter.
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.
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.
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.
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.
template<typename Type>
DSymmMatrixParam< Type > &	readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read a required symmetrix DMatrix.
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.
Begin &	readBegin (std::istream &in, const char *label, bool isRequired=true)
	Add and read a class label and opening bracket.
End &	readEnd (std::istream &in)
	Add and read the closing bracket.
Blank &	readBlank (std::istream &in)
	Add and read a new Blank object, representing a blank line.
void	loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load a required child ParamComposite.
void	loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load an optional child ParamComposite if isActive.
template<typename Type>
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
	Add and load a new ScalarParam < Type > object.
template<typename Type>
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
	Add and load new required ScalarParam < Type > object.
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.
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.
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.
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.
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.
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.
template<typename Type, int N>
FSArrayParam< Type, N > &	loadFSArray (Serializable::IArchive &ar, const char *label, FSArray< Type, N > &array, int size, bool isRequired)
	Add and load an FSArray < Type, N > array parameter.
template<typename Type, int N>
FSArrayParam< Type, N > &	loadFSArray (Serializable::IArchive &ar, const char *label, FSArray< Type, N > &array, int size)
	Add and load a required FSArray < Type > array parameter.
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.
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.
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.
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.
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.
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.
void	addParamComposite (ParamComposite &child, bool next=true)
	Add a child ParamComposite object to the format array.
Begin &	addBegin (const char *label)
	Add a Begin object representing a class name and bracket.
End &	addEnd ()
	Add a closing bracket.
Blank &	addBlank ()
	Create and add a new Blank object, representing a blank line.
std::string	className () const
	Get class name string.
bool	isRequired () const
	Is this ParamComposite required in the input file?
bool	isActive () const
	Is this parameter active?
Public Member Functions inherited from Util::ParamComponent
virtual	~ParamComponent ()
	Destructor.
void	setIndent (const ParamComponent &parent, bool next=true)
	Set indent level.
std::string	indent () const
	Return indent string for this object (string of spaces).
template<class Archive>
void	serialize (Archive &ar, const unsigned int version)
	Serialize this ParamComponent as a string.
Public Member Functions inherited from Util::Serializable
virtual	~Serializable ()
	Destructor.
Public Member Functions inherited from Util::MpiFileIo
	MpiFileIo ()
	Constructor.
	MpiFileIo (const MpiFileIo &other)
	Copy constructor.
bool	isIoProcessor () const
	Can this processor do file I/O ?

Protected Member Functions
void	setClassName (const char *className)
	Set class name string.
void	readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
	Add and read a required child ParamComposite.
void	readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
	Add and attempt to read an optional child ParamComposite.
template<typename Type>
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object.
Protected Member Functions inherited from Pscf::Rpg::Simulator< D >
void	readRandomSeed (std::istream &in)
	Read random seed and initialize random number generators.
CompressorFactory< D > &	compressorFactory ()
	Get the compressor factory by reference.
void	readCompressor (std::istream &in, bool &isEnd)
	Optionally read a Compressor parameter file block.
PerturbationFactory< D > &	perturbationFactory ()
	Get the perturbation factory by reference.
void	readPerturbation (std::istream &in, bool &isEnd)
	Optionally read a Perturbation parameter file block.
void	setPerturbation (Perturbation< D > *ptr)
	Set the associated perturbation.
RampFactory< D > &	rampFactory ()
	Get the ramp factory by reference.
void	readRamp (std::istream &in, bool &isEnd)
	Optionally read a Ramp parameter file block.
void	setRamp (Ramp< D > *ptr)
	Set the associated ramp.
void	setClassName (const char *className)
	Set class name string.
void	setClassName (const char *className)
	Set class name string.
void	setIsRequired (bool isRequired)
	Set or unset the isActive flag.
void	setIsActive (bool isActive)
	Set or unset the isActive flag.
void	setParent (ParamComponent &param, bool next=true)
	Set this to the parent of a child component.
void	addComponent (ParamComponent &param, bool isLeaf=true)
	Add a new ParamComponent object to the format array.
template<typename Type>
ScalarParam< Type > &	add (std::istream &in, const char *label, Type &value, bool isRequired=true)
	Add a new required ScalarParam < Type > object.
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.
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.
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.
template<typename Type, int N>
FSArrayParam< Type, N > &	addFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size, bool isRequired=true)
	Add (but do not read) a FSArray < Type, N > array parameter.
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.
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.
Protected Member Functions inherited from Util::ParamComponent
	ParamComponent ()
	Constructor.
	ParamComponent (const ParamComponent &other)
	Copy constructor.

Additional Inherited Members
Public Types inherited from Util::Serializable
typedef BinaryFileOArchive	OArchive
	Type of output archive used by save method.
typedef BinaryFileIArchive	IArchive
	Type of input archive used by load method.
Static Public Member Functions inherited from Util::ParamComponent
static void	initStatic ()
	Initialize static echo member to false.
static void	setEcho (bool echo=true)
	Enable or disable echoing for all subclasses of ParamComponent.
static bool	echo ()
	Get echo parameter.
Protected Attributes inherited from Pscf::Rpg::Simulator< D >
Random	random_
	Random number generator.
CudaRandom	cudaRandom_
	Random number generator.
DArray< RField< D > >	wc_
	Eigenvector components of w fields on a real space grid.
DArray< RField< D > >	cc_
	Eigenvector components of c fields on a real space grid.
DArray< RField< D > >	dc_
	Components of d fields on a real space grid.
SimState< D >	state_
	State saved during fts simulation.
double	hamiltonian_
	Field theoretic Hamiltonian H[W] (extensive value).
double	idealHamiltonian_
	Ideal gas contribution (lnQ) to Hamiltonian H[W].
double	fieldHamiltonian_
	Field contribution (H_W) to Hamiltonian.
double	perturbationHamiltonian_
	Perturbation to the standard Hamiltonian (if any).
long	iStep_
	Simulation step counter.
long	iTotalStep_
	Simulation step counter.
long	seed_
	Random number generator seed.
bool	hasHamiltonian_
	Has the Hamiltonian been computed for the current w and c fields?
bool	hasWc_
	Have eigen-components of the current w fields been computed ?
bool	hasCc_
	Have eigen-components of the current c fields been computed ?
bool	hasDc_
	Have functional derivatives of H[W] been computed ?