Detailed Description

An Integrator numerically integrates the equations of motion.

Definition at line 29 of file Integrator.h.

#include <Integrator.h>

Inheritance diagram for DdMd::Integrator:

Public Member Functions
	Integrator (Simulation &simulation)
	Constructor. More...

	~Integrator ()
	Destructor. More...

void	readParameters (std::istream &in)
	Read saveInterval and saveFileName. More...

void	loadParameters (Serializable::IArchive &ar)
	Load saveInterval and saveFileName from restart archive. More...

void	save (Serializable::OArchive &ar)
	Save saveInterval and saveFileName from restart archive. More...

virtual void	run (int nStep)=0
	Run a simulation of iStep steps. More...

virtual void	clear ()
	Set integrator to initial state and clears all statistics. More...

virtual void	outputStatistics (std::ostream &out)
	Output timing statistics from a run. More...

double	time () const
	Get average time per processor of previous run. More...

int	iStep () const
	Get current time step index. 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	readParam (std::istream &in)
	Read the parameter file block. More...

virtual void	readParamOptional (std::istream &in)
	Read optional parameter file block. 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...

Public Member Functions inherited from DdMd::SimulationAccess
	SimulationAccess (Simulation &simulation)
	Constructor. More...

	~SimulationAccess ()
	Destructor. More...

Simulation &	simulation ()
	Get the parent simulation. More...

Boundary &	boundary ()
	Get the Boundary. More...

AtomStorage &	atomStorage ()
	Get the AtomStorage. More...

GroupStorage< 2 > &	bondStorage ()
	Get the BondStorage. More...

GroupStorage< 3 > &	angleStorage ()
	Get the AngleStorage. More...

GroupStorage< 4 > &	dihedralStorage ()
	Get the angleStorage. More...

PairPotential &	pairPotential ()
	Get the PairPotential. More...

BondPotential &	bondPotential ()
	Get the PairPotential. More...

AnglePotential &	anglePotential ()
	Get the AnglePotential. More...

DihedralPotential &	dihedralPotential ()
	Get the DihedralPotential. More...

ExternalPotential &	externalPotential ()
	Get the ExternalPotential. More...

EnergyEnsemble &	energyEnsemble ()
	Get the EnergyEnsemble. More...

BoundaryEnsemble &	boundaryEnsemble ()
	Get the BoundaryEnsemble. More...

Random &	random ()
	Get the Random number generator. More...

Domain &	domain ()
	Get the Domain. More...

Exchanger &	exchanger ()
	Get the Exchanger. More...

FileMaster &	fileMaster ()
	Get the FileMaster. More...

int	nAtomType ()
	Get maximum number of atom types. More...

int	nBondType ()
	Get maximum number of bond types. More...

int	nAngleType ()
	Get maximum number of angle types. More...

int	nDihedralType ()
	Get maximum number of dihedral types. More...

bool	hasExternal ()
	Does this simulation have an external potential? More...

AtomType &	atomType (int i)
	Get an AtomType descriptor for atomtype i. More...

MaskPolicy	maskedPairPolicy () const
	Return the value of the mask policy (MaskNone or MaskBonded). More...

bool	reverseUpdateFlag () const
	Are forces evaluated by reverse communication (true) or not (false)? More...

Protected Types

Protected Member Functions
virtual void	initDynamicalState ()
	Set any internal dynamical to default initial values. More...

virtual void	setup ()=0
	Setup integrator just before integration. More...

void	setIsSetup ()
	Mark the integrator as having been setup at least once. More...

bool	isSetup () const
	Has the setup() method been called at least once previously? More...

void	setupAtoms ()
	Setup state of atoms just before integration. More...

void	computeForces ()
	Compute forces for all local atoms, with timing. More...

void	computeForcesAndVirial ()
	Compute forces for all local atoms and virial, with timing. More...

bool	isExchangeNeeded (double skin)
	Determine whether an atom exchange and reneighboring is needed. More...

const std::string &	saveFileName () const
	Get restart file base name. More...

int	saveInterval () const
	Get interval for writing a restart file. 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 &param, bool next=true)
	Set this to the parent of a child component. More...

void	addComponent (ParamComponent &param, 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
int	iStep_
	Current step number. 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...

Member Enumeration Documentation

enum DdMd::Integrator::TimeId

protected

Timestamps for loop timing.

Definition at line 119 of file Integrator.h.

Constructor & Destructor Documentation

DdMd::Integrator::Integrator ( Simulation & simulation )

Constructor.

Definition at line 48 of file Integrator.cpp.

DdMd::Integrator::~Integrator ( )

Destructor.

Definition at line 59 of file Integrator.cpp.

Member Function Documentation

void DdMd::Integrator::readParameters ( std::istream & in )

virtual

Read saveInterval and saveFileName.

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Reimplemented in DdMd::NvtLangevinIntegrator, DdMd::NptIntegrator, DdMd::NphIntegrator, DdMd::NveIntegrator, and DdMd::NvtIntegrator.

Definition at line 65 of file Integrator.cpp.

References DdMd::Analyzer::baseInterval, and UTIL_THROW.

Referenced by DdMd::NvtIntegrator::readParameters(), DdMd::NveIntegrator::readParameters(), DdMd::NphIntegrator::readParameters(), DdMd::NptIntegrator::readParameters(), and DdMd::NvtLangevinIntegrator::readParameters().

void DdMd::Integrator::loadParameters ( Serializable::IArchive & ar )

virtual

Load saveInterval and saveFileName from restart archive.

Parameters

ar	input archive

Reimplemented from Util::ParamComposite.

Reimplemented in DdMd::NvtLangevinIntegrator, DdMd::NptIntegrator, DdMd::NveIntegrator, DdMd::NphIntegrator, and DdMd::NvtIntegrator.

Definition at line 83 of file Integrator.cpp.

References DdMd::Analyzer::baseInterval, iStep_, and UTIL_THROW.

Referenced by DdMd::NvtIntegrator::loadParameters(), DdMd::NphIntegrator::loadParameters(), DdMd::NveIntegrator::loadParameters(), DdMd::NptIntegrator::loadParameters(), and DdMd::NvtLangevinIntegrator::loadParameters().

void DdMd::Integrator::save ( Serializable::OArchive & ar )

virtual

Save saveInterval and saveFileName from restart archive.

Parameters

ar	input archive

Reimplemented from Util::ParamComposite.

Reimplemented in DdMd::NvtLangevinIntegrator, DdMd::NptIntegrator, DdMd::NveIntegrator, DdMd::NvtIntegrator, and DdMd::NphIntegrator.

Definition at line 105 of file Integrator.cpp.

References iStep_.

Referenced by DdMd::NphIntegrator::save(), DdMd::NvtIntegrator::save(), DdMd::NveIntegrator::save(), DdMd::NptIntegrator::save(), and DdMd::NvtLangevinIntegrator::save().

virtual void DdMd::Integrator::run ( int nStep )

pure virtual

Run a simulation of iStep steps.

Parameters

nStep number of steps to run.

Implemented in DdMd::TwoStepIntegrator.

void DdMd::Integrator::clear ( )

virtual

Set integrator to initial state and clears all statistics.

This method resset iStep = 0, calls initDynamicalState(), calls the AnalyzerManger::clear(), clears the internal Timer and all timing statistics, clear the additional timing statistics maintained by the Exchanger class, and clears the memory usage statistics for the Buffer, PairList, and storage classes.

Definition at line 539 of file Integrator.cpp.

References DdMd::Simulation::analyzerManager(), DdMd::SimulationAccess::angleStorage(), DdMd::SimulationAccess::atomStorage(), DdMd::SimulationAccess::bondStorage(), DdMd::Simulation::buffer(), DdMd::DdTimer::clear(), DdMd::AnalyzerManager::clear(), DdMd::PairList::clearStatistics(), DdMd::GroupStorage< N >::clearStatistics(), DdMd::Buffer::clearStatistics(), DdMd::AtomStorage::clearStatistics(), DdMd::SimulationAccess::dihedralStorage(), DdMd::Simulation::exchanger(), initDynamicalState(), iStep_, DdMd::PairPotential::pairList(), DdMd::SimulationAccess::pairPotential(), DdMd::SimulationAccess::simulation(), and DdMd::Exchanger::timer().

Referenced by DdMd::NvtIntegrator::setup(), DdMd::NphIntegrator::setup(), DdMd::NveIntegrator::setup(), DdMd::NptIntegrator::setup(), and DdMd::NvtLangevinIntegrator::setup().

void DdMd::Integrator::outputStatistics ( std::ostream & out )

virtual

Output timing statistics from a run.

This method may only be called on the domain master processor.

Parameters

out	output stream to which to write timing statistics.

Definition at line 329 of file Integrator.cpp.

References DdMd::SimulationAccess::atomStorage(), DdMd::PairList::buildCounter(), DdMd::Domain::communicator(), DdMd::SimulationAccess::domain(), DdMd::SimulationAccess::hasExternal(), iStep_, DdMd::SimulationAccess::nAngleType(), DdMd::AtomStorage::nAtomTotal(), DdMd::SimulationAccess::nBondType(), DdMd::SimulationAccess::nDihedralType(), DdMd::PairPotential::pairList(), DdMd::SimulationAccess::pairPotential(), DdMd::DdTimer::time(), time(), and UTIL_THROW.

double DdMd::Integrator::time ( ) const

Get average time per processor of previous run.

Definition at line 313 of file Integrator.cpp.

References DdMd::SimulationAccess::domain(), DdMd::DdTimer::reduce(), and DdMd::DdTimer::time().

Referenced by outputStatistics().

int DdMd::Integrator::iStep ( ) const

inline

Get current time step index.

Definition at line 228 of file Integrator.h.

void DdMd::Integrator::initDynamicalState ( )

inlineprotectedvirtual

Set any internal dynamical to default initial values.

This method should be called before the main loop the first time the integrator is used, within the setup() method, and should be called by the clear() method.

Reimplemented in DdMd::NvtIntegrator, DdMd::NptIntegrator, and DdMd::NphIntegrator.

Definition at line 248 of file Integrator.h.

Referenced by clear().

virtual void DdMd::Integrator::setup ( )

protectedpure virtual

Setup integrator just before integration.

This method is always called within the run method before the main loop. It should not set arbitrary default values for any independent internal state variables that cannot be calculated from the system configuration.

Implemented in DdMd::NvtLangevinIntegrator, DdMd::NptIntegrator, DdMd::NphIntegrator, DdMd::NveIntegrator, and DdMd::NvtIntegrator.

Referenced by DdMd::TwoStepIntegrator::run().

void DdMd::Integrator::setIsSetup ( )

inlineprotected

Mark the integrator as having been setup at least once.

Must be called from within the setup method.

Definition at line 240 of file Integrator.h.

Referenced by DdMd::NvtIntegrator::setup(), DdMd::NphIntegrator::setup(), DdMd::NveIntegrator::setup(), DdMd::NptIntegrator::setup(), and DdMd::NvtLangevinIntegrator::setup().

bool DdMd::Integrator::isSetup ( ) const

inlineprotected

Has the setup() method been called at least once previously?

Definition at line 234 of file Integrator.h.

Referenced by DdMd::NvtIntegrator::setup(), DdMd::NphIntegrator::setup(), DdMd::NveIntegrator::setup(), DdMd::NptIntegrator::setup(), and DdMd::NvtLangevinIntegrator::setup().

void DdMd::Integrator::setupAtoms ( )

protected

Setup state of atoms just before integration.

Exchange atoms, build PairList and compute Forces. Should be called in all subclass setup methods.

Definition at line 118 of file Integrator.cpp.

References DdMd::SimulationAccess::atomStorage(), DdMd::SimulationAccess::boundary(), DdMd::SimulationAccess::boundaryEnsemble(), DdMd::PairPotential::buildCellList(), DdMd::PairPotential::buildPairList(), DdMd::AtomStorage::clearSnapshot(), DdMd::Simulation::computeForces(), DdMd::Simulation::computeForcesAndVirial(), DdMd::Exchanger::exchange(), DdMd::SimulationAccess::exchanger(), DdMd::AtomStorage::makeSnapshot(), DdMd::SimulationAccess::pairPotential(), DdMd::SimulationAccess::simulation(), DdMd::AtomStorage::transformGenToCart(), and UTIL_THROW.

Referenced by DdMd::NvtIntegrator::setup(), DdMd::NphIntegrator::setup(), DdMd::NveIntegrator::setup(), DdMd::NptIntegrator::setup(), and DdMd::NvtLangevinIntegrator::setup().

void DdMd::Integrator::computeForces ( )

protected

Compute forces for all local atoms, with timing.

Identical to Simulation::forceCompute(), with added timing. Upon return, forces are correct for all local atoms. Values of the forces on ghost atoms are undefined. Executes reverse communication if needed, and emits Simulation::forceSignal().

Definition at line 146 of file Integrator.cpp.

Referenced by DdMd::TwoStepIntegrator::run().

void DdMd::Integrator::computeForcesAndVirial ( )

protected

Compute forces for all local atoms and virial, with timing.

Identical to Simulation::computeForcesAndVirial(), with timing. Upon return, forces are correct for all local atoms. Values of the forces on ghost atoms are undefined. Executes reverse communication if needed, and emits Simulation::forceSignal().

Definition at line 195 of file Integrator.cpp.