MD_base Class Reference

base class of md More...

#include <md_base.h>

Inheritance diagram for MD_base:

Collaboration diagram for MD_base:

Public Member Functions
	MD_base (const Parameter &param_in, UnitCell &unit_in)
virtual	~MD_base ()
virtual 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.
virtual void	first_half (std::ofstream &ofs)
	the first half of equation of motion, update velocities and positions
virtual void	second_half ()
	the second half of equation of motion, update velocities
virtual void	print_md (std::ofstream &ofs, const bool &cal_stress)
	output MD information such as energy, temperature, and pressure
virtual void	write_restart (const std::string &global_out_dir)
	write the information into files used for MD restarting

Public Attributes
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
virtual void	restart (const std::string &global_readin_dir)
	restart MD when md_restart is true
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
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

base class of md

This class implements the velocity-Verlet method. The system is assumed to be isolated in the sense that it cannot exchange energy or particles with its environment, so that the energy of the system does not change with time.

Constructor & Destructor Documentation

MD_base()

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

convert to a.u. unit

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~MD_base()

MD_base::~MD_base ( )

virtual

Member Function Documentation

first_half()

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

virtual

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

Parameters

ofs	determine the output files

Reimplemented in FIRE, Langevin, MSST, Nose_Hoover, and Verlet.

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print_md()

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

virtual

output MD information such as energy, temperature, and pressure

Parameters

ofs	determine the output files
cal_stress	whether calculate and output stress

Reimplemented in FIRE, Langevin, MSST, Nose_Hoover, and Verlet.

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restart()

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

protectedvirtual

restart MD when md_restart is true

Parameters

global_readin_dir

directory of files for reading

Reimplemented in FIRE, Langevin, MSST, Nose_Hoover, and Verlet.

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second_half()

void MD_base::second_half ( void  )

virtual

the second half of equation of motion, update velocities

Reimplemented in FIRE, Langevin, MSST, Nose_Hoover, and Verlet.

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setup()

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

virtual

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 in FIRE, Langevin, MSST, Nose_Hoover, and Verlet.

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update_pos()

void MD_base::update_pos ( )

protectedvirtual

perform one step update of pos due to atomic velocity

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update_vel()

void MD_base::update_vel ( const ModuleBase::Vector3< double > *  force )

protectedvirtual

perform half-step update of vel due to atomic force

Parameters

force

atomic forces

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write_restart()

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

virtual

write the information into files used for MD restarting

Parameters

global_out_dir

directory of output files

Reimplemented in FIRE, Langevin, MSST, Nose_Hoover, and Verlet.

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Member Data Documentation

allmass

double* MD_base::allmass

atom mass

cal_stress

bool MD_base::cal_stress

protected

whether calculate stress

energy_

double MD_base::energy_ =0.0

protected

total energy of the system

force

ModuleBase::Vector3<double>* MD_base::force

force of each atom

frozen_freedom_

int MD_base::frozen_freedom_

the fixed freedom of the system

ionmbl

ModuleBase::Vector3<int>* MD_base::ionmbl

atom is frozen or not

kinetic

double MD_base::kinetic

kinetic energy

md_dt

double MD_base::md_dt

protected

Time increment (hbar/E_hartree)

md_tfirst

double MD_base::md_tfirst

protected

Temperature (in Hartree, 1 Hartree ~ 3E5 K)

md_tlast

double MD_base::md_tlast

protected

Target temperature.

mdp

const MD_para& MD_base::mdp

protected

input parameters used in md

my_rank

int MD_base::my_rank

protected

MPI rank of the processor.

pos

ModuleBase::Vector3<double>* MD_base::pos

atom displacements liuyu modify 2023-03-22

potential

double MD_base::potential =0.0

potential energy

step_

int MD_base::step_

the MD step finished in current calculation

step_rst_

int MD_base::step_rst_

the MD step finished in previous calculations

stop

bool MD_base::stop

MD stop or not.

stress

ModuleBase::matrix MD_base::stress

stress for this lattice

t_current

double MD_base::t_current

current temperature

ucell

UnitCell& MD_base::ucell

protected

unitcell information

vel

ModuleBase::Vector3<double>* MD_base::vel

atom velocity

virial

ModuleBase::matrix MD_base::virial

virial for this lattice

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