MD_func Namespace Reference

base functions in md More...

Functions
void	current_md_info (const int &my_rank, const std::string &file_dir, int &md_step, double &temperature)
	determine thr current md step and temperature
double	gaussrand ()
	generate a Gaussian random number
double	kinetic_energy (const int &natom, const ModuleBase::Vector3< double > *vel, const double *allmass)
	calculate the ionic kinetic energy
void	compute_stress (const UnitCell &unit_in, const ModuleBase::Vector3< double > *vel, const double *allmass, const bool &cal_stress, const ModuleBase::matrix &virial, ModuleBase::matrix &stress)
	calculate the total stress tensor
void	read_vel (const UnitCell &unit_in, ModuleBase::Vector3< double > *vel)
	read in atomic velocities from STRU
void	rescale_vel (const int &natom, const double &temperature, const double *allmass, const int &frozen_freedom, ModuleBase::Vector3< double > *vel)
	rescale the velocity to the target temperature
void	rand_vel (const int &natom, const double &temperature, const double *allmass, const int &frozen_freedom, const ModuleBase::Vector3< int > frozen, const ModuleBase::Vector3< int > *ionmbl, const int &my_rank, ModuleBase::Vector3< double > *vel)
	generate atomic velocities that satisfy the Boltzmann distribution
void	init_vel (const UnitCell &unit_in, const int &my_rank, const bool &restart, double &temperature, double *allmass, int &frozen_freedom, ModuleBase::Vector3< int > *ionmbl, ModuleBase::Vector3< double > *vel)
	initialize the atomic velocities
void	force_virial (ModuleESolver::ESolver *p_esolver, const int &istep, UnitCell &unit_in, double &potential, ModuleBase::Vector3< double > *force, const bool &cal_stress, ModuleBase::matrix &virial)
	calculate energy, forces and virial tensor
void	print_stress (std::ofstream &ofs, const ModuleBase::matrix &virial, const ModuleBase::matrix &stress)
	output the stress information
void	dump_info (const int &step, const std::string &global_out_dir, const UnitCell &unit_in, const Parameter &param_in, const ModuleBase::matrix &virial, const ModuleBase::Vector3< double > *force, const ModuleBase::Vector3< double > *vel)
	dump the md information
void	get_mass_mbl (const UnitCell &unit_in, double *allmass, ModuleBase::Vector3< int > &frozen, ModuleBase::Vector3< int > *ionmbl)
	obtain the atomic mass and whether the freedom is fixed
double	target_temp (const int &istep, const int &nstep, const double &tfirst, const double &tlast)
	get the target temperature of the current md step
double	current_temp (double &kinetic, const int &natom, const int &frozen_freedom, const double *allmass, const ModuleBase::Vector3< double > *vel)
	get the current temperature
void	temp_vector (const int &natom, const ModuleBase::Vector3< double > *vel, const double *allmass, ModuleBase::matrix &t_vector)
	get the temperature vectors

Detailed Description

base functions in md

Namespace MD_func contains several functions used in md.

Function Documentation

compute_stress()

void MD_func::compute_stress	(	const UnitCell &	unit_in,
		const ModuleBase::Vector3< double > *	vel,
		const double *	allmass,
		const bool &	cal_stress,
		const ModuleBase::matrix &	virial,
		ModuleBase::matrix &	stress
	)

calculate the total stress tensor

Parameters

unit_in	unitcell information
vel	the atomic velocities
allmass	atomic mass
cal_stress	whether calculate stress
virial	lattice virial tensor
stress	total stress tensor

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current_md_info()

void MD_func::current_md_info	(	const int &	my_rank,
		const std::string &	file_dir,
		int &	md_step,
		double &	temperature
	)

determine thr current md step and temperature

determine the current md step and temperature according to Restart_md.txt if md_restart is true

Parameters

my_rank	MPI rank of the processor
file_dir	the directory of read-in files
md_step	current md step
temperature	current temperature

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current_temp()

double MD_func::current_temp	(	double &	kinetic,
		const int &	natom,
		const int &	frozen_freedom,
		const double *	allmass,
		const ModuleBase::Vector3< double > *	vel
	)

get the current temperature

Parameters

kinetic	kinetic energy
natom	the number of atoms
frozen_freedom	the fixed freedom
allmass	atomic mass
vel	atomic velocities

Returns

the current temperature

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dump_info()

void MD_func::dump_info	(	const int &	step,
		const std::string &	global_out_dir,
		const UnitCell &	unit_in,
		const Parameter &	param_in,
		const ModuleBase::matrix &	virial,
		const ModuleBase::Vector3< double > *	force,
		const ModuleBase::Vector3< double > *	vel
	)

dump the md information

including md step, lattice constant, lattice vectors, lattice virial tensor, ion index, ion positions, ion velocities, ion forces

Parameters

step	current md step
global_out_dir	directory of output files
unit_in	unitcell information
param_in	input parameters used in md
virial	lattice virial tensor
force	atomic forces
vel	atomic velocities

< Angstrom

< Angstrom/fs

< kBar

< eV/Angstrom

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force_virial()

void MD_func::force_virial	(	ModuleESolver::ESolver *	p_esolver,
		const int &	istep,
		UnitCell &	unit_in,
		double &	potential,
		ModuleBase::Vector3< double > *	force,
		const bool &	cal_stress,
		ModuleBase::matrix &	virial
	)

calculate energy, forces and virial tensor

Parameters

p_esolver	enrergy solver
istep	current md step
unit_in	unitcell information
potential	potential energy
force	atomic forces
cal_stress	whether calculate stress
virial	lattice virial tensor

convert Rydberg to Hartree

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gaussrand()

double MD_func::gaussrand

(

)

generate a Gaussian random number

Returns

a Gaussian random number

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get_mass_mbl()

void MD_func::get_mass_mbl	(	const UnitCell &	unit_in,
		double *	allmass,
		ModuleBase::Vector3< int > &	frozen,
		ModuleBase::Vector3< int > *	ionmbl
	)

obtain the atomic mass and whether the freedom is fixed

Parameters

unit_in	unitcell information
allmass	atomic mass
frozen	the fixed freedom along three directions
ionmbl	determine whether the atomic freedom is fixed

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init_vel()

void MD_func::init_vel	(	const UnitCell &	unit_in,
		const int &	my_rank,
		const bool &	restart,
		double &	temperature,
		double *	allmass,
		int &	frozen_freedom,
		ModuleBase::Vector3< int > *	ionmbl,
		ModuleBase::Vector3< double > *	vel
	)

initialize the atomic velocities

Parameters

unit_in	unitcell information
my_rank	MPI rank of the processor
restart	whether restart the md
temperature	ion temperature
allmass	atomic mass
frozen_freedom	the fixed freedom
ionmbl	determine whether the atomic freedom is fixed
vel	the genarated atomic velocities

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kinetic_energy()

double MD_func::kinetic_energy	(	const int &	natom,
		const ModuleBase::Vector3< double > *	vel,
		const double *	allmass
	)

calculate the ionic kinetic energy

Parameters

natom	the number of atoms
vel	the atomic velocities
allmass	atomic mass

Returns

the ionic kinetic energy

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print_stress()

void MD_func::print_stress	(	std::ofstream &	ofs,
		const ModuleBase::matrix &	virial,
		const ModuleBase::matrix &	stress
	)

output the stress information

Parameters

ofs	determine the output files
virial	lattice virial tensor
stress	total stress tensor

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rand_vel()

void MD_func::rand_vel	(	const int &	natom,
		const double &	temperature,
		const double *	allmass,
		const int &	frozen_freedom,
		const ModuleBase::Vector3< int >	frozen,
		const ModuleBase::Vector3< int > *	ionmbl,
		const int &	my_rank,
		ModuleBase::Vector3< double > *	vel
	)

generate atomic velocities that satisfy the Boltzmann distribution

Parameters

natom	the number of atoms
temperature	ion temperature
allmass	atomic mass
frozen_freedom	the fixed freedom
frozen	the fixed freedom along three directions
ionmbl	determine whether the atomic freedom is fixed
my_rank	MPI rank of the processor
vel	the genarated atomic velocities

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read_vel()

void MD_func::read_vel	(	const UnitCell &	unit_in,
		ModuleBase::Vector3< double > *	vel
	)

read in atomic velocities from STRU

Parameters

unit_in	unitcell information
vel	the read-in atomic velocities

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rescale_vel()

void MD_func::rescale_vel	(	const int &	natom,
		const double &	temperature,
		const double *	allmass,
		const int &	frozen_freedom,
		ModuleBase::Vector3< double > *	vel
	)

rescale the velocity to the target temperature

Parameters

natom	the number of atoms
temperature	ion temperature
allmass	atomic mass
frozen_freedom	the fixed freedom
vel	the genarated atomic velocities

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target_temp()

double MD_func::target_temp	(	const int &	istep,
		const int &	nstep,
		const double &	tfirst,
		const double &	tlast
	)

get the target temperature of the current md step

Parameters

istep	the current md step
nstep	the total md step
tfirst	the initial temperature
tlast	the final temperature

Returns

the target temperature

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temp_vector()

void MD_func::temp_vector	(	const int &	natom,
		const ModuleBase::Vector3< double > *	vel,
		const double *	allmass,
		ModuleBase::matrix &	t_vector
	)

get the temperature vectors

Parameters

natom	the number of atoms
vel	atomic velocities
allmass	atomic mass
t_vector	the temperature vectors

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