Verlet Class Reference

the md methods based on the velocity-Verlet equation More...

#include <verlet.h>

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Public Member Functions
	Verlet (const Parameter &param_in, UnitCell &unit_in)
	~Verlet ()
Public Member Functions inherited from MD_base
	MD_base (const Parameter &param_in, UnitCell &unit_in)
virtual	~MD_base ()

Private Member Functions
void	setup (ModuleESolver::ESolver *p_esolver, const std::string &global_readin_dir)
	init before running md, calculate energy, force, and stress of the initial configuration.
void	first_half (std::ofstream &ofs)
	the first half of equation of motion, update velocities and positions
void	second_half ()
	the second half of equation of motion, update velocities
void	restart (const std::string &global_readin_dir)
	restart MD when md_restart is true
void	print_md (std::ofstream &ofs, const bool &cal_stress)
	output MD information such as energy, temperature, and pressure
void	write_restart (const std::string &global_out_dir)
	write the information into files used for MD restarting
void	apply_thermostat ()
	apply specifical thermostats according to the input para
void	thermalize (const int &nraise, const double &current_temp, const double &target_temp)
	rescale atomic velocities

Additional Inherited Members
Public Attributes inherited from MD_base
bool	stop
	MD stop or not.
double	t_current
	current temperature
int	step_
	the MD step finished in current calculation
int	step_rst_
	the MD step finished in previous calculations
int	frozen_freedom_
	the fixed freedom of the system
double *	allmass
	atom mass
ModuleBase::Vector3< double > *	pos
	atom displacements liuyu modify 2023-03-22
ModuleBase::Vector3< double > *	vel
	atom velocity
ModuleBase::Vector3< int > *	ionmbl
	atom is frozen or not
ModuleBase::Vector3< double > *	force
	force of each atom
ModuleBase::matrix	virial
	virial for this lattice
ModuleBase::matrix	stress
	stress for this lattice
double	potential =0.0
	potential energy
double	kinetic
	kinetic energy
Protected Member Functions inherited from MD_base
virtual void	update_pos ()
	perform one step update of pos due to atomic velocity
virtual void	update_vel (const ModuleBase::Vector3< double > *force)
	perform half-step update of vel due to atomic force
Protected Attributes inherited from MD_base
const MD_para &	mdp
	input parameters used in md
UnitCell &	ucell
	unitcell information
double	energy_ =0.0
	total energy of the system
bool	cal_stress
	whether calculate stress
int	my_rank
	MPI rank of the processor.
double	md_dt
	Time increment (hbar/E_hartree)
double	md_tfirst
	Temperature (in Hartree, 1 Hartree ~ 3E5 K)
double	md_tlast
	Target temperature.

Detailed Description

the md methods based on the velocity-Verlet equation

Constructor & Destructor Documentation

Verlet()

Verlet::Verlet	(	const Parameter &	param_in,
		UnitCell &	unit_in
	)

~Verlet()

Verlet::~Verlet

(

)

Member Function Documentation

apply_thermostat()

void Verlet::apply_thermostat ( void  )

private

apply specifical thermostats according to the input para

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first_half()

void Verlet::first_half ( std::ofstream &  ofs )

privatevirtual

the first half of equation of motion, update velocities and positions

Parameters

ofs	determine the output files

Reimplemented from MD_base.

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print_md()

void Verlet::print_md ( std::ofstream &  ofs, const bool &  cal_stress  )

privatevirtual

output MD information such as energy, temperature, and pressure

Parameters

ofs	determine the output files
cal_stress	whether calculate and output stress

Reimplemented from MD_base.

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restart()

void Verlet::restart ( const std::string &  global_readin_dir )

privatevirtual

restart MD when md_restart is true

Parameters

global_readin_dir

directory of files for reading

Reimplemented from MD_base.

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second_half()

void Verlet::second_half ( void  )

privatevirtual

the second half of equation of motion, update velocities

Reimplemented from MD_base.

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setup()

void Verlet::setup ( ModuleESolver::ESolver *  p_esolver, const std::string &  global_readin_dir  )

privatevirtual

init before running md, calculate energy, force, and stress of the initial configuration.

Parameters

p_esolver	the energy solver used in md
global_readin_dir	directory of files for reading

Reimplemented from MD_base.

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thermalize()

void Verlet::thermalize ( const int &  nraise, const double &  current_temp, const double &  target_temp  )

private

rescale atomic velocities

Parameters

nraise	a parameter related to thermostats
current_temp	the current temperature
target_temp	the target temperature

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write_restart()

void Verlet::write_restart ( const std::string &  global_out_dir )

privatevirtual

write the information into files used for MD restarting

Parameters

global_out_dir

directory of output files

Reimplemented from MD_base.

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

• /home/runner/work/abacus-develop/abacus-develop/source/source_md/verlet.h
• /home/runner/work/abacus-develop/abacus-develop/source/source_md/verlet.cpp