Detailed Description

A post-processor for analyzing outputs of MD simulations.

Definition at line 30 of file Processor.h.

#include <Processor.h>

Inheritance diagram for Tools::Processor:

Public Member Functions
	Processor ()
	Constructor. More...

	~Processor ()
	Destructor. More...

Initialization
void	setOptions (int argc, char const argv)
	Process command line options. More...

void	readParam ()
	Read parameter file specified in command line. More...

void	readParam (const char *filename)
	Open, read, and close parameter file. More...

void	readParameters (std::istream &in)
	Read parameters. More...

void	readCommands ()
	Read command file specified in command line. More...

void	readCommands (std::istream &in)
	Read and execute commands from a command file. More...

ConfigReader Interface
void	setConfigReader (const std::string &configReaderName)
	Set ConfigReader style (creates a ConfigReader). More...

ConfigReader &	configReader ()
	Return the current ConfigReader (create default if necessary). More...

void	readConfig (std::ifstream &in)
	Read a single configuration file. More...

void	readConfig (const std::string &filename)
	Open, read and close a configuration file. More...

void	analyzeConfigs (const std::string &baseFileName, int min, int max, int interval=1)
	Read and analyze a sequence of numbered configuration files. More...

ConfigWriter Interface
void	setConfigWriter (const std::string &configWriterName)
	Set ConfigWriter style (creates a ConfigWriter). More...

ConfigWriter &	configWriter ()
	Return the current ConfigWriter (create default if necessary). More...

void	writeConfig (std::ofstream &in)
	Write a single configuration file. More...

void	writeConfig (const std::string &filename)
	Open, write and close a configuration file. More...

Trajectory File Interface
void	setTrajectoryReader (const std::string &trajectoryStyle)
	Set TrajectoryReader style (creates a TrajectoryReader). More...

TrajectoryReader &	trajectoryReader ()
	Return the current TrajectoryReader (create default if necessary). More...

void	analyzeTrajectory (const std::string &filename)
	Open, read, analyze and close a single trajectory file. More...

Miscellaneous functions
FileMaster &	fileMaster ()
	Return FileMaster if active, or throw Exception. More...

Public Member Functions inherited from Tools::Configuration
	Configuration ()
	Constructor. More...

	~Configuration ()
	Destructor. More...

void	readParam (const char *filename)
	Open, read, and close parameter file. More...

void	readParameters (std::istream &in)
	Read parameters. More...

void	clear ()
	Clear all atoms and groups. More...

Boundary &	boundary ()
	Get the Boundary by non-const reference. More...

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

GroupStorage< 2 > &	bonds ()
	Get the Bond storage. More...

GroupStorage< 3 > &	angles ()
	Get the Angle storage. More...

GroupStorage< 4 > &	dihedrals ()
	Get the Dihedral storage. More...

GroupStorage< 4 > &	impropers ()
	Get the Improper dihedral storage. More...

int	nSpecies () const
	Number of species. More...

Species &	species (int i)
	Get a particular species identified by 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...

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...

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 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...

Constructor & Destructor Documentation

Tools::Processor::Processor ( )

Constructor.

Definition at line 25 of file Processor.cpp.

References Util::ParamComposite::setClassName().

Tools::Processor::~Processor ( )

Destructor.

Definition at line 37 of file Processor.cpp.

Member Function Documentation

void Tools::Processor::setOptions	(	int	argc,
		char const	argv
	)

Process command line options.

Parameters

argc	number of arguments
argv	array of argument C-strings

Definition at line 50 of file Processor.cpp.

References Util::Log::file(), Util::FileMaster::setCommandFileName(), Util::ParamComponent::setEcho(), and Util::FileMaster::setParamFileName().

void Tools::Processor::readParam ( )

Read parameter file specified in command line.

Definition at line 76 of file Processor.cpp.

References Util::FileMaster::paramFile(), Util::FileMaster::paramFileName(), and UTIL_THROW.

Referenced by readParam().

void Tools::Processor::readParam ( const char * filename )

Open, read, and close parameter file.

Parameters

filename input parameter file name

Definition at line 87 of file Processor.cpp.

References readParam().

void Tools::Processor::readParameters ( std::istream & in )

virtual

Read parameters.

Parameters

in	input command file stream

Reimplemented from Util::ParamComposite.

Definition at line 98 of file Processor.cpp.

References Util::ParamComposite::readParamComposite(), Util::ParamComposite::readParamCompositeOptional(), and Tools::Configuration::readParameters().

void Tools::Processor::readCommands ( )

Read command file specified in command line.

Definition at line 108 of file Processor.cpp.

References Util::FileMaster::commandFile(), and Util::FileMaster::commandFileName().

void Tools::Processor::readCommands ( std::istream & in )

Read and execute commands from a command file.

Parameters

in	input command file stream

Definition at line 121 of file Processor.cpp.

References analyzeTrajectory(), configReader(), configWriter(), Util::Log::file(), Util::FileMaster::openInputFile(), Util::FileMaster::openOutputFile(), Tools::ConfigWriter::readAuxiliaryFile(), Tools::ConfigReader::readAuxiliaryFile(), Tools::ConfigReader::readConfig(), setConfigReader(), setConfigWriter(), setTrajectoryReader(), and Tools::ConfigWriter::writeConfig().

void Tools::Processor::setConfigReader ( const std::string & configReaderName )

Set ConfigReader style (creates a ConfigReader).

Parameters

configReaderName identifier for ConfigReader subclass

Definition at line 211 of file Processor.cpp.

References Tools::ConfigReaderFactory::factory(), and UTIL_THROW.

Referenced by readCommands().

ConfigReader & Tools::Processor::configReader ( )

Return the current ConfigReader (create default if necessary).

Definition at line 227 of file Processor.cpp.

Referenced by readCommands(), and readConfig().

void Tools::Processor::readConfig ( std::ifstream & in )

Read a single configuration file.

Definition at line 239 of file Processor.cpp.

References Tools::Configuration::clear(), configReader(), and Tools::ConfigReader::readConfig().

Referenced by analyzeConfigs(), and readConfig().

void Tools::Processor::readConfig ( const std::string & filename )

Open, read and close a configuration file.

Definition at line 248 of file Processor.cpp.

References readConfig().

void Tools::Processor::analyzeConfigs	(	const std::string &	baseFileName,
		int	min,
		int	max,
		int	interval = `1`
	)

Read and analyze a sequence of numbered configuration files.

This function reads and analyzes a sequence of configuration files that were generated by running a previous simulation. The function reads files with names of the form inputPrefix() + n for integer suffixes min <= n <= max with subsequent values differing by the specified interval.

Parameters

baseFileName	root name for dump files (without int suffix)
min	integer suffix of first configuration file name
max	integer suffix of last configuration file name
interval	interval between subsequent timestep values

Definition at line 259 of file Processor.cpp.

References Tools::Configuration::clear(), Util::Log::file(), Tools::AnalyzerManager::output(), readConfig(), Tools::AnalyzerManager::sample(), Tools::AnalyzerManager::setup(), and UTIL_THROW.

void Tools::Processor::setConfigWriter ( const std::string & configWriterName )

Set ConfigWriter style (creates a ConfigWriter).

Parameters

configWriterName identifier for ConfigWriter subclass

Definition at line 327 of file Processor.cpp.

References Tools::ConfigWriterFactory::factory(), and UTIL_THROW.

Referenced by readCommands().

ConfigWriter & Tools::Processor::configWriter ( )

Return the current ConfigWriter (create default if necessary).

Definition at line 341 of file Processor.cpp.