Inheritance diagram for PLMD::cltools::SimpleMD:

Public Types
enum	{ unset, commandline, ifile }
	How is the input specified on the command line or in an input file. More...

Public Member Functions
	SimpleMD (const CLToolOptions &co)

void	setInputData (const std::map< std::string, std::string > &inputData)
	Set the input data: More...

const std::map< std::string, std::string > &	getInputData ()

bool	readInput (int argc, char *argv, FILE in, FILE *out)
	Read the arguments from the command line. More...

Static Public Member Functions
static void	registerKeywords (Keywords &keys)

Public Attributes
enum PLMD::CLTool:: { ... }	inputdata
	How is the input specified on the command line or in an input file. More...

Protected Member Functions
template<class T >
bool	parse (const std::string &key, T &t)
	Get the value of one of the command line arguments. More...

void	parseFlag (const std::string &key, bool &t)
	Find out whether one of the command line flags is present or not. More...

void	error (const std::string &msg)
	Crash the command line tool with an error. More...

template<class T >
bool	parseVector (const std::string &key, std::vector< T > &t)

Private Member Functions
string	description () const
	virtual function returning a one-line descriptor for the tool More...

void	read_input (double &temperature, double &tstep, double &friction, double &forcecutoff, double &listcutoff, int &nstep, int &nconfig, int &nstat, bool &wrapatoms, string &inputfile, string &outputfile, string &trajfile, string &statfile, int &maxneighbours, int &ndim, int &idum)

void	read_natoms (const string &inputfile, int &natoms)

void	read_positions (const string &inputfile, int natoms, vector< Vector > &positions, double cell[3])

void	randomize_velocities (const int natoms, const int ndim, const double temperature, const vector< double > &masses, vector< Vector > &velocities, Random &random)

void	pbc (const double cell[3], const Vector &vin, Vector &vout)

void	check_list (const int natoms, const vector< Vector > &positions, const vector< Vector > &positions0, const double listcutoff, const double forcecutoff, bool &recompute)

void	compute_list (const int natoms, const int listsize, const vector< Vector > &positions, const double cell[3], const double listcutoff, vector< int > &point, vector< int > &list)

void	compute_forces (const int natoms, const int listsize, const vector< Vector > &positions, const double cell[3], double forcecutoff, const vector< int > &point, const vector< int > &list, vector< Vector > &forces, double &engconf)

void	compute_engkin (const int natoms, const vector< double > &masses, const vector< Vector > &velocities, double &engkin)

void	thermostat (const int natoms, const int ndim, const vector< double > &masses, const double dt, const double friction, const double temperature, vector< Vector > &velocities, double &engint, Random &random)

void	write_positions (const string &trajfile, int natoms, const vector< Vector > &positions, const double cell[3], const bool wrapatoms)

void	write_final_positions (const string &outputfile, int natoms, const vector< Vector > &positions, const double cell[3], const bool wrapatoms)

void	write_statistics (const string &statfile, const int istep, const double tstep, const int natoms, const int ndim, const double engkin, const double engconf, const double engint)

virtual int	main (FILE in, FILE out, PLMD::Communicator &pc)
	virtual function mapping to the specific main for each tool More...

Private Attributes
bool	write_positions_first

bool	write_statistics_first

int	write_statistics_last_time_reopened

FILE *	write_statistics_fp

Member Enumeration Documentation

anonymous enum

inherited

How is the input specified on the command line or in an input file.

Enumerator
unset
commandline
ifile

Constructor & Destructor Documentation

PLMD::cltools::SimpleMD::SimpleMD ( const CLToolOptions & co )

inlineexplicit

Member Function Documentation

void PLMD::cltools::SimpleMD::check_list	(	const int	natoms,
		const vector< Vector > &	positions,
		const vector< Vector > &	positions0,
		const double	listcutoff,
		const double	forcecutoff,
		bool &	recompute
	)

inlineprivate

void PLMD::cltools::SimpleMD::compute_engkin	(	const int	natoms,
		const vector< double > &	masses,
		const vector< Vector > &	velocities,
		double &	engkin
	)

inlineprivate

void PLMD::cltools::SimpleMD::compute_forces	(	const int	natoms,
		const int	listsize,
		const vector< Vector > &	positions,
		const double	cell[3],
		double	forcecutoff,
		const vector< int > &	point,
		const vector< int > &	list,
		vector< Vector > &	forces,
		double &	engconf
	)

inlineprivate

void PLMD::cltools::SimpleMD::compute_list	(	const int	natoms,
		const int	listsize,
		const vector< Vector > &	positions,
		const double	cell[3],
		const double	listcutoff,
		vector< int > &	point,
		vector< int > &	list
	)

inlineprivate

string PLMD::cltools::SimpleMD::description ( ) const

inlineprivatevirtual

virtual function returning a one-line descriptor for the tool

Reimplemented from PLMD::CLTool.

void PLMD::CLTool::error ( const std::string & msg )

protectedinherited

Crash the command line tool with an error.

const std::map<std::string,std::string>& PLMD::CLTool::getInputData ( )

inlineinherited

virtual int PLMD::cltools::SimpleMD::main	(	FILE *	in,
		FILE *	out,
		PLMD::Communicator &	pc
	)

inlineprivatevirtual

virtual function mapping to the specific main for each tool

Implements PLMD::CLTool.

template<class T >

bool PLMD::CLTool::parse	(	const std::string &	key,
		T &	t
	)

protectedinherited

Get the value of one of the command line arguments.

void PLMD::CLTool::parseFlag	(	const std::string &	key,
		bool &	t
	)

protectedinherited

Find out whether one of the command line flags is present or not.

template<class T >

bool PLMD::CLTool::parseVector	(	const std::string &	key,
		std::vector< T > &	t
	)

protectedinherited

void PLMD::cltools::SimpleMD::pbc	(	const double	cell[3],
		const Vector &	vin,
		Vector &	vout
	)

inlineprivate

void PLMD::cltools::SimpleMD::randomize_velocities	(	const int	natoms,
		const int	ndim,
		const double	temperature,
		const vector< double > &	masses,
		vector< Vector > &	velocities,
		Random &	random
	)

inlineprivate

void PLMD::cltools::SimpleMD::read_input	(	double &	temperature,
		double &	tstep,
		double &	friction,
		double &	forcecutoff,
		double &	listcutoff,
		int &	nstep,
		int &	nconfig,
		int &	nstat,
		bool &	wrapatoms,
		string &	inputfile,
		string &	outputfile,
		string &	trajfile,
		string &	statfile,
		int &	maxneighbours,
		int &	ndim,
		int &	idum
	)

inlineprivate

void PLMD::cltools::SimpleMD::read_natoms	(	const string &	inputfile,
		int &	natoms
	)

inlineprivate

void PLMD::cltools::SimpleMD::read_positions	(	const string &	inputfile,
		int	natoms,
		vector< Vector > &	positions,
		double	cell[3]
	)

inlineprivate

bool PLMD::CLTool::readInput	(	int	argc,
		char **	argv,
		FILE *	in,
		FILE *	out
	)

inherited

Read the arguments from the command line.

static void PLMD::cltools::SimpleMD::registerKeywords ( Keywords & keys )

inlinestatic

void PLMD::CLTool::setInputData ( const std::map< std::string, std::string > & inputData )

inlineinherited

Set the input data:

void PLMD::cltools::SimpleMD::thermostat	(	const int	natoms,
		const int	ndim,
		const vector< double > &	masses,
		const double	dt,
		const double	friction,
		const double	temperature,
		vector< Vector > &	velocities,
		double &	engint,
		Random &	random
	)

inlineprivate

void PLMD::cltools::SimpleMD::write_final_positions	(	const string &	outputfile,
		int	natoms,
		const vector< Vector > &	positions,
		const double	cell[3],
		const bool	wrapatoms
	)

inlineprivate

void PLMD::cltools::SimpleMD::write_positions	(	const string &	trajfile,
		int	natoms,
		const vector< Vector > &	positions,
		const double	cell[3],
		const bool	wrapatoms
	)

inlineprivate

void PLMD::cltools::SimpleMD::write_statistics	(	const string &	statfile,
		const int	istep,
		const double	tstep,
		const int	natoms,
		const int	ndim,
		const double	engkin,
		const double	engconf,
		const double	engint
	)

inlineprivate

Member Data Documentation

enum { ... } PLMD::CLTool::inputdata

How is the input specified on the command line or in an input file.

bool PLMD::cltools::SimpleMD::write_positions_first

private

bool PLMD::cltools::SimpleMD::write_statistics_first

private

FILE* PLMD::cltools::SimpleMD::write_statistics_fp

private

int PLMD::cltools::SimpleMD::write_statistics_last_time_reopened

private

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

cltools/SimpleMD.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation