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)

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...

void	setInputData (const std::map< std::string, std::string > &inputData)
	Set the input data: 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
void	error (const std::string &msg)
	Crash the command line tool with an error. More...

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...

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

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

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

void	compute_forces (const int natoms, double epsilon, double sigma, const std::vector< Vector > &positions, const double cell[3], double forcecutoff, const std::vector< std::vector< int > > &list, std::vector< Vector > &forces, double &engconf)

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

std::string	description () const override
	virtual function returning a one-line descriptor for the tool More...

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

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

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

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

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

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

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

bool	readInputFile (int argc, char *argv, FILE in, FILE *out)
	Read the arguments from an input file specified on the command line. More...

void	setRemainingToDefault (FILE *out)
	Set arguments from the default options provided to Keywords. More...

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

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

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

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

Private Attributes
std::map< std::string, std::string >	inputData
	The data read in from the command line stored in a map with the keywords. More...

const Keywords &	keywords
	The list of keywords for this CLTool. More...

const std::string	name
	The name of this command line tool. More...

bool	write_positions_first

bool	write_statistics_first

FILE *	write_statistics_fp

std::unique_ptr< FILE, decltype(deleter)>	write_statistics_fp_deleter {nullptr,deleter}

int	write_statistics_last_time_reopened

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

inherited

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

Enumerator
unset
commandline
ifile

Constructor & Destructor Documentation

◆ SimpleMD()

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

inlineexplicit

Member Function Documentation

◆ check_list()

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

inlineprivate

◆ compute_engkin()

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

inlineprivate

◆ compute_forces()

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

inlineprivate

◆ compute_list()

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

inlineprivate

◆ description()

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

inlineoverrideprivatevirtual

virtual function returning a one-line descriptor for the tool

Reimplemented from PLMD::CLTool.

◆ error()

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

protectedinherited

Crash the command line tool with an error.

◆ getInputData()

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

inlineinherited

◆ main()

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

inlineoverrideprivatevirtual

virtual function mapping to the specific main for each tool

Implements PLMD::CLTool.

◆ parse()

template<class T >

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

protectedinherited

Get the value of one of the command line arguments.

◆ parseFlag()

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

protectedinherited

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

◆ parseVector()

template<class T >

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

protectedinherited

◆ pbc()

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

inlineprivate

◆ randomize_velocities()

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

inlineprivate

◆ read_input()

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

inlineprivate

◆ read_natoms()

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

inlineprivate

◆ read_positions()

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

inlineprivate

◆ readCommandLineArgs()

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

privateinherited

Read the arguments from the command line.

◆ readInput()

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

inherited

Read the arguments from the command line.

◆ readInputFile()

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

privateinherited

Read the arguments from an input file specified on the command line.

◆ registerKeywords()

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

inlinestatic

◆ setInputData()

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

inlineinherited

Set the input data:

◆ setRemainingToDefault()

void PLMD::CLTool::setRemainingToDefault ( FILE * out )

privateinherited

Set arguments from the default options provided to Keywords.

◆ thermostat()

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

inlineprivate

◆ write_final_positions()

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

inlineprivate

◆ write_positions()

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

inlineprivate

◆ write_statistics()

void PLMD::cltools::SimpleMD::write_statistics	(	const std::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

◆ inputData

std::map<std::string,std::string> PLMD::CLTool::inputData

privateinherited

The data read in from the command line stored in a map with the keywords.

◆ inputdata

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

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

◆ keywords

const Keywords& PLMD::CLTool::keywords

privateinherited

The list of keywords for this CLTool.

◆ name

const std::string PLMD::CLTool::name

privateinherited

The name of this command line tool.

◆ write_positions_first

bool PLMD::cltools::SimpleMD::write_positions_first

private

◆ write_statistics_first

bool PLMD::cltools::SimpleMD::write_statistics_first

private

◆ write_statistics_fp

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

private

◆ write_statistics_fp_deleter

std::unique_ptr<FILE,decltype(deleter)> PLMD::cltools::SimpleMD::write_statistics_fp_deleter {nullptr,deleter}

private

◆ write_statistics_last_time_reopened

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

◆ anonymous enum

Constructor & Destructor Documentation

◆ SimpleMD()

Member Function Documentation

◆ check_list()

◆ compute_engkin()

◆ compute_forces()

◆ compute_list()

◆ description()

◆ error()

◆ getInputData()

◆ main()

◆ parse()

◆ parseFlag()

◆ parseVector()

◆ pbc()

◆ randomize_velocities()

◆ read_input()

◆ read_natoms()

◆ read_positions()

◆ readCommandLineArgs()

◆ readInput()

◆ readInputFile()

◆ registerKeywords()

◆ setInputData()

◆ setRemainingToDefault()

◆ thermostat()

◆ write_final_positions()

◆ write_positions()

◆ write_statistics()

Member Data Documentation

◆ inputData

◆ inputdata

◆ keywords

◆ name

◆ write_positions_first

◆ write_statistics_first

◆ write_statistics_fp

◆ write_statistics_fp_deleter

◆ write_statistics_last_time_reopened