Detailed Description

A molecular dynamics simulation of a single MdSystem.

Definition at line 26 of file MdSimulation.h.

#include <MdSimulation.h>

Inheritance diagram for McMd::MdSimulation:

Public Member Functions
	MdSimulation (MPI::Intracomm &communicator)
	Constructor. More...

	MdSimulation ()
	Constructor. More...

virtual	~MdSimulation ()
	Destructor. More...

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

void	readParam ()
	Read parameters from the default parameter istream. More...

void	readParam (std::istream &in)
	Read parameter file. More...

virtual void	readParameters (std::istream &in)
	Read parameters from stream, without begin and end lines. More...

Serialization and Restart Files
void	load (const std::string &filename)
	Read a restart file. More...

virtual void	loadParameters (Serializable::IArchive &ar)
	Load parameter file section of archive. More...

void	save (const std::string &filename)
	Write a restart file. More...

virtual void	save (Serializable::OArchive &ar)
	Save internal state to an archive. More...

Command Script
void	readCommands ()
	Read and execute commands from a default command file. More...

void	readCommands (std::istream &in)
	Read and execute commands from a specific input stream. More...

bool	readCommand (std::string command, std::istream &in)
	Read and execute a single command from an input stream. More...

Simulation and Analysis Operations
void	simulate (int endStep, bool isContinuation=false)
	Run an MD simulation of specified length. More...

void	analyzeConfigs (int min, int max, std::string basename)
	Read and analyze a sequence of configuration files. More...

void	analyzeTrajectory (int min, int max, std::string classname, std::string filename)
	Read and analyze a trajectory file. More...

Miscellaneous
const MdSystem &	system () const
	Get the MdSystem being simulated by const reference. More...

MdSystem &	system ()
	Get the MdSystem being simulated by reference. More...

virtual bool	isValid () const
	Return true if this MdSimulation valid, or throw an Exception. More...

Public Member Functions inherited from McMd::Simulation
	Simulation (MPI::Intracomm &communicator)
	Constructor. More...

	Simulation ()
	Constructor. More...

virtual	~Simulation ()
	Destructor. More...

void	outputOptions (std::ostream &out) const
	Output a list of options enabled and disabled during compilation. More...

virtual void	setIoCommunicator (MPI::Intracomm &communicator)
	Set MPI job to read one parameter file and one command file. More...

void	setIoCommunicator ()
	Set MPI job to read one parameter file and one command file. More...

void	writeParam (std::string filename)
	Open output, write and close an output parameter file. More...

void	allocateMoleculeSet (Util::ArraySet< Molecule > &set, int speciesId) const
	Allocate and initialize a molecule set for one Species. More...

Molecule &	getMolecule (int speciesId)
	Get a new molecule from a reservoir of unused Molecule objects. More...

void	returnMolecule (Molecule &molecule)
	Return a molecule to a reservoir of unused molecules. More...

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

Species &	species (int i)
	Get a specific Species by reference. More...

Factory< Analyzer > &	analyzerFactory ()
	Return the Analyzer factory by reference. More...

Factory< Species > &	speciesFactory ()
	Return the Species Factory by reference. More...

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

MPI::Intracomm &	communicator ()
	Get the MPI communicator by reference. More...

int	iStep () const
	Get value of step index for main MC or MD loop. More...

int	nAtomType () const
	Get the number of atom types. More...

const AtomType &	atomType (int i) const
	Get a single AtomType object by const reference. More...

const Array< AtomType > &	atomTypes () const
	Get a const Array of all AtomType objects. More...

int	nSpecies () const
	Get the number of Species in this Simulation. More...

const Species &	species (int i) const
	Get a specific Species by const reference. More...

int	moleculeCapacity () const
	Get the total number of Molecules allocated. More...

int	atomCapacity () const
	Get the total number of Atoms allocated. More...

int	nSystem () const
	Get the number of Systems in this Simulation. More...

bool	hasSpecies () const
	Has data for all species structures and capacities. More...

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

int	nBondType () const
	Get the number of bond types. More...

int	bondCapacity () const
	Get the total number of Bonds allocated. More...

int	nAngleType () const
	Get the number of angle types. More...

int	angleCapacity () const
	Get the total number of Angles allocated. More...

int	nDihedralType () const
	Get the number of dihedral types. More...

int	dihedralCapacity () const
	Get the total number of Dihedrals allocated. More...

int	hasCoulomb () const
	Does a Coulomb potential exist? More...

int	hasExternal () const
	Does an external potential exist? More...

int	nLinkType () const
	Get the number of link types. More...

bool	hasCommunicator () const
	Does the simulation have an associated MPI communicator? 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	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...

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 McMd::Simulation
void	setAnalyzerManager (AnalyzerManager *ptr)
	Set the associated AnalyzerManager. More...

AnalyzerManager &	analyzerManager ()
	Get the associated AnalyzerManager by reference. More...

void	setCommandManager (CommandManager *ptr)
	Set the associated CommandManager. More...

CommandManager &	commandManager ()
	Get the associated CommandManager 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...

Protected Attributes inherited from McMd::Simulation
int	iStep_
	Step index for main MC or MD loop. More...

int	nSystem_
	Number of Systems of interacting molecules (> 1 in Gibbs ensemble). More...

Constructor & Destructor Documentation

McMd::MdSimulation::MdSimulation ( MPI::Intracomm & communicator )

Constructor.

Definition at line 47 of file MdSimulation.cpp.

References McMd::Simulation::fileMaster(), McMd::Simulation::setAnalyzerManager(), Util::ParamComposite::setClassName(), McMd::Simulation::setCommandManager(), McMd::System::setFileMaster(), McMd::System::setId(), McMd::System::setSimulation(), and UTIL_CHECK.

McMd::MdSimulation::MdSimulation ( )

Constructor.

Definition at line 79 of file MdSimulation.cpp.

References McMd::Simulation::fileMaster(), McMd::Simulation::setAnalyzerManager(), Util::ParamComposite::setClassName(), McMd::Simulation::setCommandManager(), McMd::System::setFileMaster(), McMd::System::setId(), McMd::System::setSimulation(), and UTIL_CHECK.

McMd::MdSimulation::~MdSimulation ( )

virtual

Destructor.

Definition at line 110 of file MdSimulation.cpp.

Member Function Documentation

void McMd::MdSimulation::setOptions	(	int	argc,
		char **	argv
	)

Process command line options.

Main options:

-q Query: Print list of enabled/disabled features

-e Echo: Enable echoing of parameter file on read

-r filename. Restart: restart from specified file

-p filename. Parameter: Specify a parameter file

-c filename. Command: Specify a command file

-i filename. Input: Specify path prefix for input files

-o filename. Input: Specify path prefix for output files

The -p and -r options are mutually exclusive: When a simulation is restarted, all information required from a parameter file is in the restart file.

Parameters

argc	number of arguments
argv	vector of pointers to char* string arguments

Definition at line 125 of file MdSimulation.cpp.

References Util::Log::file(), McMd::Simulation::fileMaster(), load(), McMd::Simulation::outputOptions(), Util::FileMaster::setCommandFileName(), Util::ParamComponent::setEcho(), McMd::System::setExpectPerturbation(), Util::FileMaster::setInputPrefix(), McMd::Simulation::setIoCommunicator(), Util::FileMaster::setOutputPrefix(), Util::FileMaster::setParamFileName(), system(), and UTIL_THROW.

void McMd::MdSimulation::readParam ( )

Read parameters from the default parameter istream.

Calls readParam(std::istream&) internally, with a default parameter file istream given by the return value of FileMaster::paramFile().

Single parameter file: If compiled as a serial program (ifndef UTIL_MPI) or as a parallel program in mode that uses a single parameter file (i.e., with option -f), the parameter file name is the argument passed to the -p command line option, if the main program is invoked with the -p option, or the parameter file is read from standard input, std::cin, if not invoked with a -p option.

Multiple parameter files: If compiled as a parallel program (ifdef UITL_MPI) and used in a mode with separate parameter files for independent simulations (i.e., without the -f option), then the parameter file for the simulation performed by processor number n is file named n/filename, where "filename" is either the argument of the -p command line option, if invoked with that option, or the default string filename = "param".

Precondition: : Call after setOptions().

Definition at line 289 of file MdSimulation.cpp.

References McMd::Simulation::fileMaster().

void McMd::MdSimulation::readParam ( std::istream & in )

virtual

Read parameter file.

Returns and does nothing if in process of restarting (i.e., if the main program was invoked with -r option).

Precondition: : Call after setOptions().

Parameters

in	parameter file stream

Reimplemented from Util::ParamComposite.

Definition at line 297 of file MdSimulation.cpp.

References Util::ParamComposite::className(), Util::ParamComposite::readBegin(), Util::ParamComposite::readEnd(), and readParameters().

void McMd::MdSimulation::readParameters ( std::istream & in )

virtual

Read parameters from stream, without begin and end lines.

Parameters

in	input stream

Reimplemented from McMd::Simulation.

Definition at line 262 of file MdSimulation.cpp.

References McMd::Simulation::analyzerManager(), McMd::Analyzer::baseInterval, McMd::Simulation::commandManager(), isValid(), Util::ParamComposite::readParamComposite(), Util::ParamComposite::readParamCompositeOptional(), McMd::Simulation::readParameters(), and UTIL_THROW.

Referenced by readParam().

void McMd::MdSimulation::load ( const std::string & filename )

Read a restart file.

Open, load, and close binary restart file.

Parameters

filename base file name for all restart files.

Definition at line 687 of file MdSimulation.cpp.

References Util::BinaryFileIArchive::file(), McMd::Simulation::fileMaster(), Util::FileMaster::openRestartIFile(), and UTIL_THROW.

Referenced by setOptions().

void McMd::MdSimulation::loadParameters ( Serializable::IArchive & ar )

virtual

Load parameter file section of archive.

Parameters

ar	input/loading archive

Reimplemented from McMd::Simulation.

Definition at line 312 of file MdSimulation.cpp.

References McMd::Simulation::analyzerManager(), McMd::Simulation::commandManager(), McMd::Simulation::iStep_, isValid(), McMd::MdSystem::loadConfig(), Util::ParamComposite::loadParamComposite(), McMd::Simulation::loadParameters(), and UTIL_THROW.

void McMd::MdSimulation::save ( const std::string & filename )

Write a restart file.

Calls save(Serializable::OArchive) internally.

Parameters

filename restart file name

Definition at line 708 of file MdSimulation.cpp.

References Util::BinaryFileOArchive::file(), McMd::Simulation::fileMaster(), and Util::FileMaster::openRestartOFile().

Referenced by simulate().

void McMd::MdSimulation::save ( Serializable::OArchive & ar )

virtual

Save internal state to an archive.

Parameters

ar	output/saving archive

Reimplemented from McMd::Simulation.

Definition at line 337 of file MdSimulation.cpp.

References McMd::Simulation::analyzerManager(), McMd::Simulation::commandManager(), McMd::Simulation::iStep_, McMd::AnalyzerManager::save(), Util::Manager< Data >::save(), McMd::Simulation::save(), McMd::System::saveConfig(), and McMd::MdSystem::saveParameters().

void McMd::MdSimulation::readCommands ( )

Read and execute commands from a default command file.

This function calls readCommands(fileMaster().commandFile()).

Definition at line 419 of file MdSimulation.cpp.

References McMd::Simulation::fileMaster(), and UTIL_THROW.

void McMd::MdSimulation::readCommands ( std::istream & in )

Read and execute commands from a specific input stream.

Parameters

in	command script input stream.

Definition at line 354 of file MdSimulation.cpp.

References McMd::Simulation::commandManager(), McMd::Simulation::communicator(), Util::Log::file(), Util::getNextLine(), Util::MpiFileIo::hasIoCommunicator(), Util::MpiFileIo::isIoProcessor(), McMd::Simulation::iStep_, McMd::CommandManager::readCommand(), simulate(), and UTIL_THROW.

bool McMd::MdSimulation::readCommand	(	std::string	command,
		std::istream &	in
	)

Read and execute a single command from an input stream.

Usage: The capitalized command name must have been read from istream "in" and passed as the "command" argument. If the command name is recognized, any additional arguments are read from stream "in", the command is executed, and a value of true is returned. A value of false is returned iff the command name string is not recognized.

Calls commandManager().readCommand(command, in) internally.

Parameters

command	command name string
in	command input stream

Definition at line 431 of file MdSimulation.cpp.

References McMd::Simulation::commandManager(), and McMd::CommandManager::readCommand().

void McMd::MdSimulation::simulate	(	int	endStep,
		bool	isContinuation = `false`
	)

Run an MD simulation of specified length.

This method implements the main MD loop. The step counter iStep_ is incremented until it reaches endStep. Upon exit, iStep_ = endStep.

If isContinuation is false, the step counter iStep_ is initialized to zero, and analyzers and MdIntegrator are set to default initial states before entering the main loop. If isContinuation is true, no initialization is done before entering the main loop.

Preconditions: Atomic positions, velocities, and forces must all be initialized before this function is entered. If isContinuation is false, positions and forces must have been initialized by calling the readConfig() or load() method. The readconfig() method initializes velocities only for file formats that contain velocities. Otherwise, velocities can be initialized by the system().setBoltzmannVelocities() function, which can be invoked by a THERMALIZE command in the command script.

Parameters

endStep	Final value of MD step counter iStep_.
isContinuation	Is this a continuation of previous run?

Definition at line 437 of file MdSimulation.cpp.

References McMd::Simulation::analyzerManager(), McMd::Analyzer::baseInterval, McMd::PairList::buildCounter(), McMd::MdSystem::calculateForces(), McMd::MdSystem::coulombPotential(), Util::Log::file(), McMd::Simulation::iStep_, McMd::MdCoulombPotential::makeWaves(), McMd::PairList::maxNAtom(), McMd::PairList::maxNPair(), McMd::MdSystem::mdIntegrator(), McMd::AnalyzerManager::output(), McMd::MdPairPotential::pairList(), McMd::MdSystem::pairPotential(), McMd::AnalyzerManager::sample(), save(), McMd::MdIntegrator::setup(), McMd::AnalyzerManager::setup(), McMd::MdSystem::shiftAtoms(), Util::Timer::start(), McMd::MdIntegrator::step(), Util::Timer::stop(), system(), Util::Timer::time(), and UTIL_CHECK.

Referenced by readCommands(), and McMd::MdCommandManager::readStandardCommand().

void McMd::MdSimulation::analyzeConfigs	(	int	min,
		int	max,
		std::string	basename
	)

Read and analyze a sequence of configuration files.

This function reads and analyzes a sequence of configuration files that were normally generated by running a previous simulation using the ConfigWriter analyzer to periodically dump configurations. This function applies the sample() method of every Analyzer to each such stored configuration.

The function reads a sequence of configuration files with names of the form inputPrefix + basename + n , for integer suffixes in the range min <= n <= max. This is consistent with the output format format used by the WriteConfig class. The inputPrefix used in an analysis simulation is often a directory name, with a trailing directory separator "/", that is the same as the outputPrefix used in the earlier simulation run.

In parallel mode, for processor with MPI rank m, the path "m/" is prepended to the fileMaster input prefix, so that paths to all files associated with processor m begin with the string "m/inputPrefix" + basename.

Parameters