mrmd::io Namespace Reference

Namespaces
namespace	impl

Classes
class	DumpH5MD
class	DumpProfile
class	RestoreH5MD

Typedefs
using	hid_t = int

Functions
void	dumpCSV (const std::string &filename, data::Atoms &atoms, bool dumpGhosts)
void	dumpGRO (const std::string &filename, data::Atoms &atoms, const data::Subdomain &subdomain, const real_t &timestamp, const std::string &title, const std::string &resName, const std::vector< std::string > &typeNames, bool dumpGhosts, bool dumpVelocities)
	format specification https://manual.gromacs.org/current/reference-manual/file-formats.html?highlight=gro#gro
void	dumpSingleProfile (const std::string &filename, const ScalarView::HostMirror &grid, const ScalarView::HostMirror &dataProfile, const real_t &normalizationFactor)
void	dumpThermoForce (const std::string &filename, const action::ThermodynamicForce &thermodynamicForce, const idx_t &typeId)
void	dumpThermoForce (const std::string &filename, const action::ThermodynamicForce &thermodynamicForce)
void	restoreGRO (const std::string &filename, data::Subdomain &subdomain, data::Atoms &atoms, bool containsGhostAtoms)
void	restoreLAMMPS (const std::string &filename, data::Atoms &atoms)
action::ThermodynamicForce	restoreThermoForce (const std::string &filename, const data::Subdomain &subdomain, const std::vector< real_t > &targetDensities, const std::vector< real_t > &thermodynamicForceModulations, const bool enforceSymmetry, const bool usePeriodicity, const idx_t maxNumForces)
data::Atoms	restoreAtoms (const std::string &filename)

Typedef Documentation

hid_t

using mrmd::io::hid_t = typedef int

Function Documentation

dumpCSV()

void mrmd::io::dumpCSV	(	const std::string &	filename,
		data::Atoms &	atoms,
		bool	dumpGhosts
	)

dumpGRO()

void mrmd::io::dumpGRO	(	const std::string &	filename,
		data::Atoms &	atoms,
		const data::Subdomain &	subdomain,
		const real_t &	timestamp,
		const std::string &	title,
		const std::string &	resName,
		const std::vector< std::string > &	typeNames,
		bool	dumpGhosts,
		bool	dumpVelocities
	)

format specification https://manual.gromacs.org/current/reference-manual/file-formats.html?highlight=gro#gro

dumpSingleProfile()

void mrmd::io::dumpSingleProfile	(	const std::string &	filename,
		const ScalarView::HostMirror &	grid,
		const ScalarView::HostMirror &	dataProfile,
		const real_t &	normalizationFactor
	)

dumpThermoForce() [1/2]

void mrmd::io::dumpThermoForce	(	const std::string &	filename,
		const action::ThermodynamicForce &	thermodynamicForce
	)

dumpThermoForce() [2/2]

void mrmd::io::dumpThermoForce	(	const std::string &	filename,
		const action::ThermodynamicForce &	thermodynamicForce,
		const idx_t &	typeId
	)

restoreAtoms()

data::Atoms mrmd::io::restoreAtoms

(

const std::string &

filename

)

restoreGRO()

void mrmd::io::restoreGRO	(	const std::string &	filename,
		data::Subdomain &	subdomain,
		data::Atoms &	atoms,
		bool	containsGhostAtoms
	)

restoreLAMMPS()

void mrmd::io::restoreLAMMPS	(	const std::string &	filename,
		data::Atoms &	atoms
	)

restoreThermoForce()

action::ThermodynamicForce mrmd::io::restoreThermoForce	(	const std::string &	filename,
		const data::Subdomain &	subdomain,
		const std::vector< real_t > &	targetDensities,
		const std::vector< real_t > &	thermodynamicForceModulations,
		const bool	enforceSymmetry,
		const bool	usePeriodicity,
		const idx_t	maxNumForces
	)