Detailed Description

Abstract reader/writer for configuration files.

Each concrete subclass of ConfigIo implements a specific file format by implementing the pure virtual readConfig and writeConfig methods.

Definition at line 49 of file ddMd/configIos/ConfigIo.h.

#include <ConfigIo.h>

Inheritance diagram for DdMd::ConfigIo:

Public Member Functions
	ConfigIo ()
	Default constructor. More...

	ConfigIo (Simulation &simulation)
	Constructor. More...

virtual	~ConfigIo ()
	Destructor. More...

void	associate (Domain &domain, Boundary &boundary, AtomStorage &atomStorage, BondStorage &bondStorage, AngleStorage &angleStorage, DihedralStorage &dihedralStorage, Buffer &buffer)
	Associate with related objects. More...

virtual void	readConfig (std::ifstream &file, MaskPolicy maskPolicy)=0
	Read a configuration file. More...

virtual void	writeConfig (std::ofstream &file)=0
	Write configuration file. 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...

Protected Member Functions
void	setAtomMasks ()
	Set Mask data on all atoms. More...

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

Boundary &	boundary ()
	Get Boundary by reference. More...

AtomStorage &	atomStorage ()
	Get AtomStorage by reference. More...

AtomDistributor &	atomDistributor ()
	Get the AtomDistributor by reference. More...

AtomCollector &	atomCollector ()
	Get the AtomCollector by reference. More...

BondStorage &	bondStorage ()
	Get BondStorage by reference. More...

GroupDistributor< 2 > &	bondDistributor ()
	Get the bondDistributor by reference. More...

GroupCollector< 2 > &	bondCollector ()
	Get the bond collector by reference. More...

AngleStorage &	angleStorage ()
	Get AngleStorage by reference. More...

GroupDistributor< 3 > &	angleDistributor ()
	Get the angle distributor by reference. More...

GroupCollector< 3 > &	angleCollector ()
	Get the angle collector by reference. More...

DihedralStorage &	dihedralStorage ()
	Get DihedralStorage by reference. More...

GroupDistributor< 4 > &	dihedralDistributor ()
	Get the dihedral distributor by reference. More...

GroupCollector< 4 > &	dihedralCollector ()
	Get the dihedral collector by reference. 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...

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...

Constructor & Destructor Documentation

DdMd::ConfigIo::ConfigIo ( )

Default constructor.

Definition at line 46 of file ddMd/configIos/ConfigIo.cpp.

References Util::ParamComposite::setClassName().

DdMd::ConfigIo::ConfigIo ( Simulation & simulation )

Constructor.

Parameters

simulation parent Simulation object.

Definition at line 64 of file ddMd/configIos/ConfigIo.cpp.

References DdMd::Simulation::angleStorage(), associate(), DdMd::Simulation::atomStorage(), DdMd::Simulation::bondStorage(), DdMd::Simulation::boundary(), DdMd::Simulation::buffer(), DdMd::Simulation::dihedralStorage(), DdMd::Simulation::domain(), and Util::ParamComposite::setClassName().

DdMd::ConfigIo::~ConfigIo ( )

virtual

Destructor.

Definition at line 98 of file ddMd/configIos/ConfigIo.cpp.

Member Function Documentation

void DdMd::ConfigIo::associate	(	Domain &	domain,
		Boundary &	boundary,
		AtomStorage &	atomStorage,
		BondStorage &	bondStorage,
		AngleStorage &	angleStorage,
		DihedralStorage &	dihedralStorage,
		Buffer &	buffer
	)

Associate with related objects.

Required iff instantiated with default constructor.

Definition at line 104 of file ddMd/configIos/ConfigIo.cpp.

References DdMd::GroupDistributor< N >::add(), angleStorage(), DdMd::Group< N >::atomId(), atomStorage(), bondStorage(), boundary(), DdMd::GroupStorage< N >::computeNTotal(), dihedralStorage(), domain(), DdMd::GroupDistributor< N >::newPtr(), DdMd::GroupCollector< N >::nextPtr(), DdMd::GroupStorage< N >::nTotal(), DdMd::GroupDistributor< N >::receive(), DdMd::GroupCollector< N >::send(), DdMd::GroupDistributor< N >::send(), DdMd::GroupCollector< N >::setup(), and DdMd::GroupDistributor< N >::setup().

Referenced by ConfigIo().

virtual void DdMd::ConfigIo::readConfig	(	std::ifstream &	file,
		MaskPolicy	maskPolicy
	)

pure virtual

Read a configuration file.

This method reads a configuration file from the master processor, and distributes atoms and groups among the processors. It should be implemented using an AtomDistributor object. When Atoms are added to the AtomDistributor on the master processor, the atomic coordinates should be in generalized / scaled coordinates, such that 0 <= position[i] < 1.0 for i =0,..,2. Atomic positions that lie slightly outside the domain [0.0 ,1.0] will automatically be shifted into this domain by the AtomDistributor::addAtom() method before being assigned to processors or distributed.

Upon entry (preconditions):

The configuration file must be open for reading.
The AtomStorage must be set for generalized / scaled coordinates.

Upon return (postconditions):

Each processor owns all atoms in its domain, and no others. Each atom is owned by one and only one processor.
Each atom position is in the primary simulation cell.
Atom coordinates are in scaled form, between 0.0 and 1.0.
Each processor owns every group that contains one or more of the atoms that it owns, and no empty groups. A group may be ``owned" by more than one processor.
All Atom Mask data is set correctly for specified maskPolicy.
There are no ghost atoms on any processor.

Parameters

file	input file stream (must be open on master).
maskPolicy	MaskPolicy to be used in setting atom masks

Implemented in DdMd::DdMdOrderedConfigIo, DdMd::LammpsConfigIo, DdMd::DdMdConfigIo, and DdMd::SerializeConfigIo.

virtual void DdMd::ConfigIo::writeConfig ( std::ofstream & file )

pure virtual

Write configuration file.

This function writes a file on the master processor by collecting atom and group data from all processors. Implementations must work correctly when atom positions stored in either Cartesian or scaled / generalized coordinates on entry and exit, by testing AtomStorage::isCartesian(), and converting coordinate systems as needed before writing each position file. Atomic positions may be written in Cartesian or generalized coordinates, depending on the file format, but the same convention should be used in writeConfig() and readConfig() in each class. Some file formats may allow atom and groups to be written in arbitrary order. Atomic positions may be written "as is", and may lie slightly outside the primary cell, because they will be shifted back by the AtomDistributor used to implement readConfig(). This function may not modify actual Atom positions or change the AtomStorage isCartesian() flag.

Usage:

When used within Simulation::readCommands() to implement the WRITE_CONFIG command, atomic coordinates will be scaled / generalized on both entry and exit.
When used within an Analyzer, to dump configuration files, atomic coordinates will be Cartesian on entry and exit.

Parameters