Detailed Description

A Modifier can modify the time evolution of the simulation.

Modifier is an abstract base class for classes that can modify the system during an MD simulation, and thus modify the time evolution defined by the integrator. The class declares a variety of virtual functions that, when re-implemented and activated by subclasses, will be invoked at specific points during the main integration loop, thus allowing the designer of a subclass to add almost arbitrary actions to the underlying integration algorithm.

The Modifier class declares interfaces for several virtual functions that that the integrator can be instructed to invoke at specific points within the body of the main integration loop. We refer to theses as integrator action functions. The name of each such function describes when it will be invoked. For example, the postForce() function is invoked (if at all) immediately after evaluation of all forces within the main integration loop. Modifier also declares several virtual functions with names that contain the words "pack" and "unpack", which we will call communication functions, that may be defined by subclasses to pack additional information into the messages that are communicated between processors during exchange and update steps.

Each subclass of Modifier will normally implement only a few of these possible action and communication functions. To record which virtual functions it defines, each subclass must also "activate" each such function by invoking the set() function within its constructor passing this function a named constant that activates a particular virtual function. Thus, for example, a subclass that implements the virtual postForce() function must also call the function set(Flags::PostForce) in its constructor. The constant Flags::PostForce and other named constants are defined as static constant members of the Modifier::Flags nested class. The name of each such constant is given by a capitalized version of the name of the corresponding virtual function. When the set() function is invoked to activate an integrator or communication function, it adds that function to list of functions that will be invoked at the appropriate point in the integration algorithm. The constants associated with communcation functions each activate a pair of associated "pack" and "unpack" function that must work together pack additional information into an MPI message on one processor and unpack it at the receiving processor.

Each Modifier also has an integer member named interval that determines the interval, in time steps, with which integrator actions should be taken. An activated integrator action function will be executed only during time steps that are multiples of this interval. Each Modifier object has a single interval value, which applies to all action function that it implements and activates. The value of the interval is initialized to 1 (i.e., every time step) in the base Modifier class constructor, but may be reset in the subclass readParameters function by invoking the readInterval() function to read a value from file.

The design of the Modifier class was inspired by the Lammps "Fix" base class, which provides a very flexible framework for designing algorithms that can modify the state of a system.

Definition at line 82 of file Modifier.h.

#include <Modifier.h>

Inheritance diagram for DdMd::Modifier:

Classes
class	Flags
	Bit flag constants associated with particular actions. More...

Public Member Functions
	Modifier ()
	Default constructor (for unit testing) More...

	Modifier (Simulation &simulation)
	Constructor (for use in simulation). More...

virtual	~Modifier ()
	Destructor. More...

Integration action functions
virtual void	setup ()
	Setup before entering the main loop. More...

virtual void	preIntegrate1 (long iStep)
	Call just before the first step of velocity-Verlet algorithm. More...

virtual void	postIntegrate1 (long iStep)
	Call just after the first step of velocity-Verlet algorithm. More...

virtual void	preTransform (long iStep)
	Call on exchange steps before transforming to scaled atomic coordinates. More...

virtual void	preExchange (long iStep)
	Call on exchange steps after transforming but before exchanging atoms. More...

virtual void	postExchange (long iStep)
	Call on exchange steps after atom exchange, before reneighboring. More...

virtual void	postNeighbor (long iStep)
	Call on exchange steps after re-building neighbor list (reneighboring). More...

virtual void	preUpdate (long iStep)
	Call on update steps before updating ghost positions. More...

virtual void	postUpdate (long iStep)
	Call on update steps after updating ghost positions. More...

virtual void	preForce (long iStep)
	Call after updating but before calculating forces. More...

virtual void	postForce (long iStep)
	Call after calculating forces. More...

virtual void	endOfStep (long iStep)
	Call at the end of the time step. More...

Interprocessor communication action functions
virtual void	packExchange ()
	Pack data into buffer used to exchange atoms. More...

virtual void	unpackExchange ()
	Unpack data from buffer used to exchange atoms. More...

virtual void	packUpdate ()
	Pack data into buffer used to update ghost positions. More...

virtual void	unpackUpdate ()
	Unpack data from buffer used to update ghost positions. More...

virtual void	packReverseUpdate ()
	Pack data into buffer used to reverse update forces. More...

virtual void	unpackReverseUpdate ()
	Unpack data from the buffer used to reverse update forces. More...

Bit Flags
bool	isSet (Bit flag) const
	Return true if a flag is set, false otherwise. More...

unsigned int	flags () const
	Return the unsigned int representation of all bit flags. More...

Interval functions
int	interval () const
	Get interval value. More...

bool	isAtInterval (long iStep) const
	Return true iff iStep is a multiple of the interval. 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	readParameters (std::istream &in)
	Read the body of parameter block, without begin and end lines. 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...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load state from archive, without adding Begin and End lines. More...

virtual void	save (Serializable::OArchive &ar)
	Saves all parameters to an archive. 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...

Static Public Member Functions
static void	initStatic ()
	Call this to guarantee initialization of static variables. 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
Simulation &	simulation ()
	Get the parent Simulation by reference. More...

void	set (Bit flag)
	Set the flag associated with a particular action. More...

void	readInterval (std::istream &in)
	Read parameter interval from file. More...

void	loadInterval (Serializable::IArchive &ar)
	Load parameter interval from input archive. More...

void	saveInterval (Serializable::OArchive &ar)
	Save interval parameter to an archive. 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...

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...

Constructor & Destructor Documentation

DdMd::Modifier::Modifier ( )

Default constructor (for unit testing)

Definition at line 49 of file Modifier.cpp.

DdMd::Modifier::Modifier ( Simulation & simulation )

Constructor (for use in simulation).

Definition at line 59 of file Modifier.cpp.

DdMd::Modifier::~Modifier ( )

virtual

Destructor.

Definition at line 69 of file Modifier.cpp.

Member Function Documentation

virtual void DdMd::Modifier::setup ( )

inlinevirtual

Setup before entering the main loop.

Definition at line 108 of file Modifier.h.

virtual void DdMd::Modifier::preIntegrate1 ( long iStep )

inlinevirtual

Call just before the first step of velocity-Verlet algorithm.

Atom positions are Cartesian on entry and return.

Definition at line 115 of file Modifier.h.

Referenced by DdMd::ModifierManager::preIntegrate1().

virtual void DdMd::Modifier::postIntegrate1 ( long iStep )

inlinevirtual

Call just after the first step of velocity-Verlet algorithm.

Atom positions are Cartesian on entry and return.

Definition at line 122 of file Modifier.h.

Referenced by DdMd::ModifierManager::postIntegrate1().

virtual void DdMd::Modifier::preTransform ( long iStep )

inlinevirtual

Call on exchange steps before transforming to scaled atomic coordinates.

Atom positions are Cartesian on entry and return.

Definition at line 129 of file Modifier.h.

Referenced by DdMd::ModifierManager::preTransform().

virtual void DdMd::Modifier::preExchange ( long iStep )

inlinevirtual

Call on exchange steps after transforming but before exchanging atoms.

Atom positions are scaled [0,1] on entry and return.

Definition at line 136 of file Modifier.h.

Referenced by DdMd::ModifierManager::preExchange().

virtual void DdMd::Modifier::postExchange ( long iStep )

inlinevirtual

Call on exchange steps after atom exchange, before reneighboring.

Atom positions are scaled [0,1] on entry and return.

Definition at line 143 of file Modifier.h.

Referenced by DdMd::ModifierManager::postExchange().

virtual void DdMd::Modifier::postNeighbor ( long iStep )

inlinevirtual

Call on exchange steps after re-building neighbor list (reneighboring).

Atom positions are scaled [0,1] on entry and return.

Definition at line 150 of file Modifier.h.

Referenced by DdMd::ModifierManager::postNeighbor().

virtual void DdMd::Modifier::preUpdate ( long iStep )

inlinevirtual

Call on update steps before updating ghost positions.

Atom positions are Cartesian on entry and return.

Definition at line 157 of file Modifier.h.

Referenced by DdMd::ModifierManager::preUpdate().

virtual void DdMd::Modifier::postUpdate ( long iStep )

inlinevirtual

Call on update steps after updating ghost positions.

Atom positions are Cartesian on entry and return.

Definition at line 164 of file Modifier.h.

Referenced by DdMd::ModifierManager::postUpdate().

virtual void DdMd::Modifier::preForce ( long iStep )

inlinevirtual

Call after updating but before calculating forces.

Atom positions are Cartesian on entry and return.

Definition at line 171 of file Modifier.h.

Referenced by DdMd::ModifierManager::preForce().

virtual void DdMd::Modifier::postForce ( long iStep )

inlinevirtual

Call after calculating forces.

Atom positions are Cartesian on entry and return.

Definition at line 178 of file Modifier.h.

Referenced by DdMd::ModifierManager::postForce().

virtual void DdMd::Modifier::endOfStep ( long iStep )

inlinevirtual

Call at the end of the time step.

Atom positions are Cartesian on entry and return.

Definition at line 185 of file Modifier.h.

Referenced by DdMd::ModifierManager::endOfStep().

virtual void DdMd::Modifier::packExchange ( )

inlinevirtual

Pack data into buffer used to exchange atoms.

Definition at line 194 of file Modifier.h.

Referenced by DdMd::ModifierManager::packExchange().

virtual void DdMd::Modifier::unpackExchange ( )

inlinevirtual

Unpack data from buffer used to exchange atoms.

Definition at line 199 of file Modifier.h.

Referenced by DdMd::ModifierManager::unpackExchange().

virtual void DdMd::Modifier::packUpdate ( )

inlinevirtual

Pack data into buffer used to update ghost positions.

Definition at line 204 of file Modifier.h.

Referenced by DdMd::ModifierManager::packUpdate().

virtual void DdMd::Modifier::unpackUpdate ( )

inlinevirtual

Unpack data from buffer used to update ghost positions.

Definition at line 209 of file Modifier.h.

Referenced by DdMd::ModifierManager::unpackUpdate().

virtual void DdMd::Modifier::packReverseUpdate ( )

inlinevirtual

Pack data into buffer used to reverse update forces.

Will only be used if reverse communication is enabled.

Definition at line 216 of file Modifier.h.

Referenced by DdMd::ModifierManager::packReverseUpdate().

virtual void DdMd::Modifier::unpackReverseUpdate ( )

inlinevirtual

Unpack data from the buffer used to reverse update forces.

Will only be used if reverse communication is enabled.

Definition at line 223 of file Modifier.h.

Referenced by DdMd::ModifierManager::unpackReverseUpdate().

bool DdMd::Modifier::isSet ( Bit flag ) const

Return true if a flag is set, false otherwise.

Definition at line 75 of file Modifier.cpp.

References Util::Bit::isSet().

Referenced by DdMd::ModifierManager::readParameters().

unsigned int DdMd::Modifier::flags ( ) const

Return the unsigned int representation of all bit flags.

Definition at line 81 of file Modifier.cpp.

int DdMd::Modifier::interval ( ) const

inline

Get interval value.

Definition at line 379 of file Modifier.h.

bool DdMd::Modifier::isAtInterval ( long iStep ) const

inline

Return true iff iStep is a multiple of the interval.

Parameters

iStep simulation step iStep

Definition at line 385 of file Modifier.h.

Referenced by DdMd::ModifierManager::endOfStep(), DdMd::ModifierManager::postExchange(), DdMd::ModifierManager::postForce(), DdMd::ModifierManager::postIntegrate1(), DdMd::ModifierManager::postNeighbor(), DdMd::ModifierManager::postUpdate(), DdMd::ModifierManager::preExchange(), DdMd::ModifierManager::preForce(), DdMd::ModifierManager::preIntegrate1(), DdMd::ModifierManager::preTransform(), and DdMd::ModifierManager::preUpdate().

void DdMd::Modifier::initStatic ( )

static

Call this to guarantee initialization of static variables.

Definition at line 37 of file Modifier.cpp.

Referenced by DdMd::initStatic().

Simulation & DdMd::Modifier::simulation ( )

inlineprotected

Get the parent Simulation by reference.

Definition at line 391 of file Modifier.h.

void DdMd::Modifier::set ( Bit flag )

protected

Set the flag associated with a particular action.

Definition at line 89 of file Modifier.cpp.

References Util::Bit::set().

void DdMd::Modifier::readInterval ( std::istream & in )

protected

Read parameter interval from file.

Parameters

in	input parameter file stream.

Definition at line 95 of file Modifier.cpp.

References UTIL_THROW.

void DdMd::Modifier::loadInterval ( Serializable::IArchive & ar )

protected

Load parameter interval from input archive.

Parameters

ar	input archive

Definition at line 114 of file Modifier.cpp.

References UTIL_THROW.

void DdMd::Modifier::saveInterval ( Serializable::OArchive & ar )

protected

Save interval parameter to an archive.

Parameters

ar	output archive

Definition at line 130 of file Modifier.cpp.

The documentation for this class was generated from the following files:

Detailed Description

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation