Nose Hoover Chain. More...

#include <nhchain.h>

Inheritance diagram for Nose_Hoover:

Collaboration diagram for Nose_Hoover:

Public Member Functions
	Nose_Hoover (const Parameter &param_in, UnitCell &unit_in)

	~Nose_Hoover ()

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	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	restart (const std::string &global_readin_dir)
	restart MD when md_restart is true

void	particle_thermo ()
	perform half-step update of thermostats coupled with particles

void	baro_thermo ()
	perform half-step update of thermostats coupled with barostat

void	update_baro ()
	perform half-step update of barostat velocity

void	vel_baro ()
	perform half-step update of velocity due to barostat

void	target_stress ()
	determine target stress

void	couple_stress ()
	couple stress component due to md_pcouple

void	update_volume (std::ofstream &ofs)
	perform half-step update of volume

Private Attributes
const int	nc_tchain = 1
	the number of nc for nvt

const int	nc_pchain = 1
	the number of nc for npt

double	w [nys]
	scale evolution operator

int	tdof
	particle degree of freedom

double	t_target =0.0
	target temperature

double *	mass_eta
	mass of thermostats coupled with particles

double *	eta
	position of thermostats coupled with particles

double *	v_eta
	velocity of thermostats coupled with particles

double *	g_eta
	acceleration of thermostats coupled with particles

int	npt_flag
	whether NPT ensemble

double	mass_omega [6]
	mass of lattice component

double	v_omega [6]
	velocity of lattice component

double	pstart [6]
	initial stress components

double	pstop [6]
	final stress components

double	pfreq [6]
	Oscillation frequency, used to determine qmass of thermostats coupled with barostat.

int	pflag [6]
	control stress components

int	pdim
	pdim = pflag[0] + pflag[1] + pflag[2], number of barostatted dims

double	p_target [6]
	target stress components

double	p_hydro = 0.0
	target hydrostatic target pressure

double	p_current [6] = {0.0}
	current stress after coupled

double *	mass_peta
	mass of thermostats coupled with barostat

double *	peta
	position of thermostats coupled with barostat

double *	v_peta
	velocity of thermostats coupled with barostat

double *	g_peta
	acceleration of thermostats coupled with barostat

double	mtk_term =0
	mtk correction

double	md_tfreq
	Oscillation frequency, used to determine qmass of thermostats coupled with particles.

double	md_pfirst
	Initial pressure.

double	md_plast
	Final pressure.

double	md_pfreq
	Oscillation frequency, used to determine qmass of thermostats coupled with barostat.

Static Private Attributes
static const int	nys = 7
	the number of scale evolution operator

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

Nose Hoover Chain.

Nose-Hoover style non-Hamiltonian equations of motion. [Phys. Rev. A 31, 1695 (1985)] Designed to generate positions and velocities sampled from NVT and NPT ensemble.

Constructor & Destructor Documentation

◆ Nose_Hoover()

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

init NPT related variables

determine the NPT methods

The lattice must be lower-triangular under tri mode. e11 0 0 e21 e22 0 e31 e32 e33 Under Voigt notation, xx, yy, zz, yz, xz, xy.

determine whether NPT ensemble

allocate thermostats coupled with particles

allocate barostat and thermostats coupled with barostat

w[0] = 1;

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◆ ~Nose_Hoover()

Nose_Hoover::~Nose_Hoover ( )

Member Function Documentation

◆ baro_thermo()

void Nose_Hoover::baro_thermo ( )

private

perform half-step update of thermostats coupled with barostat

the freedom of lattice

update kenetic energy of lattice

update force

integrate loop

propogate v_peta

propogate peta

update rescale factor of lattice velocity

propogate g_peta

propogate v_peta

rescale lattice due to thermostats

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◆ couple_stress()

void Nose_Hoover::couple_stress ( )

private

couple stress component due to md_pcouple

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◆ first_half()

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

privatevirtual

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

Parameters

ofs	determine the output files

update thermostats coupled with barostat if NPT ensemble

update target T

update thermostats coupled with particles

update temperature and stress due to velocity rescaling

couple stress component due to md_pcouple

determine target stress

update v_omega

update vel due to barostat

perform half-step update of vel due to atomic force

perform half-step update of volume

perform one step update of pos due to atomic velocity

perform half-step update of volume

Reimplemented from MD_base.

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◆ particle_thermo()

void Nose_Hoover::particle_thermo ( )

private

perform half-step update of thermostats coupled with particles

update mass_eta

propogate g_eta

integrate loop

propogate v_eta

propogate eta

update rescale factor of particle velocity

propogate g_eta

propogate v_eta

rescale velocity due to thermostats

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◆ print_md()

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

privatevirtual

restart MD when md_restart is true

Parameters

global_readin_dir directory of files for reading

npt

Reimplemented from MD_base.

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◆ second_half()

void Nose_Hoover::second_half ( void )

privatevirtual

the second half of equation of motion, update velocities

perform half-step update of vel due to atomic force

update vel due to barostat

update temperature and kinetic energy due to velocity rescaling

update stress due to velocity rescaling

couple stress component due to md_pcouple

update v_omega

update thermostats coupled with particles

update thermostats coupled with barostat if NPT ensemble

Reimplemented from MD_base.

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◆ setup()

void Nose_Hoover::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

determine target temperature

init thermostats coupled with particles

NPT ensemble

determine target stress

couple stress component due to md_pcouple

init barostat

init thermostats coupled with barostat

Reimplemented from MD_base.

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◆ target_stress()

void Nose_Hoover::target_stress ( )

private

determine target stress

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◆ update_baro()

void Nose_Hoover::update_baro ( )

private

perform half-step update of barostat velocity

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◆ update_volume()

void Nose_Hoover::update_volume ( std::ofstream & ofs )

private

perform half-step update of volume

Parameters

ofs	determine the output files

tri mode, off-diagonal components, first half

Diagonal components

tri mode, off-diagonal components, second half

reset ucell and pos due to change of lattice

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◆ vel_baro()

void Nose_Hoover::vel_baro ( )

private

perform half-step update of velocity due to barostat

Note: I am not sure whether fixed atoms should update here

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◆ write_restart()

void Nose_Hoover::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

npt

Reimplemented from MD_base.

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Member Data Documentation

◆ eta

double* Nose_Hoover::eta

private

position of thermostats coupled with particles

◆ g_eta

double* Nose_Hoover::g_eta

private

acceleration of thermostats coupled with particles

◆ g_peta

double* Nose_Hoover::g_peta

private

acceleration of thermostats coupled with barostat

◆ mass_eta

double* Nose_Hoover::mass_eta

private

mass of thermostats coupled with particles

◆ mass_omega

double Nose_Hoover::mass_omega[6]

private

mass of lattice component

◆ mass_peta

double* Nose_Hoover::mass_peta

private

mass of thermostats coupled with barostat

◆ md_pfirst

double Nose_Hoover::md_pfirst

private

Initial pressure.

◆ md_pfreq

double Nose_Hoover::md_pfreq

private

Oscillation frequency, used to determine qmass of thermostats coupled with barostat.

◆ md_plast

double Nose_Hoover::md_plast

private

Final pressure.

◆ md_tfreq

double Nose_Hoover::md_tfreq

private

Oscillation frequency, used to determine qmass of thermostats coupled with particles.

◆ mtk_term

double Nose_Hoover::mtk_term =0

private

mtk correction

◆ nc_pchain

const int Nose_Hoover::nc_pchain = 1

private

the number of nc for npt

◆ nc_tchain

const int Nose_Hoover::nc_tchain = 1

private

the number of nc for nvt

◆ npt_flag

int Nose_Hoover::npt_flag

private

whether NPT ensemble

◆ nys

const int Nose_Hoover::nys = 7

staticprivate

the number of scale evolution operator

◆ p_current

double Nose_Hoover::p_current[6] = {0.0}

private

current stress after coupled

◆ p_hydro

double Nose_Hoover::p_hydro = 0.0

private

target hydrostatic target pressure

◆ p_target

double Nose_Hoover::p_target[6]

private

target stress components

◆ pdim

int Nose_Hoover::pdim

private

pdim = pflag[0] + pflag[1] + pflag[2], number of barostatted dims

◆ peta

double* Nose_Hoover::peta

private

position of thermostats coupled with barostat

◆ pflag

int Nose_Hoover::pflag[6]

private

control stress components

◆ pfreq

double Nose_Hoover::pfreq[6]

private

Oscillation frequency, used to determine qmass of thermostats coupled with barostat.

◆ pstart

double Nose_Hoover::pstart[6]

private

initial stress components

◆ pstop

double Nose_Hoover::pstop[6]

private

final stress components

◆ t_target

double Nose_Hoover::t_target =0.0

private

target temperature

◆ tdof

int Nose_Hoover::tdof

private

particle degree of freedom

◆ v_eta

double* Nose_Hoover::v_eta

private

velocity of thermostats coupled with particles

◆ v_omega

double Nose_Hoover::v_omega[6]

private

velocity of lattice component

◆ v_peta

double* Nose_Hoover::v_peta

private

velocity of thermostats coupled with barostat

◆ w

double Nose_Hoover::w[nys]

private

scale evolution operator

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

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

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Nose_Hoover()

◆ ~Nose_Hoover()

Member Function Documentation

◆ baro_thermo()

◆ couple_stress()

◆ first_half()

◆ particle_thermo()

◆ print_md()

◆ restart()

◆ second_half()

◆ setup()

◆ target_stress()

◆ update_baro()

◆ update_volume()

◆ vel_baro()

◆ write_restart()

Member Data Documentation

◆ eta

◆ g_eta

◆ g_peta

◆ mass_eta

◆ mass_omega

◆ mass_peta

◆ md_pfirst

◆ md_pfreq

◆ md_plast

◆ md_tfreq

◆ mtk_term

◆ nc_pchain

◆ nc_tchain

◆ npt_flag

◆ nys

◆ p_current

◆ p_hydro

◆ p_target

◆ pdim

◆ peta

◆ pflag

◆ pfreq

◆ pstart

◆ pstop

◆ t_target

◆ tdof

◆ v_eta

◆ v_omega

◆ v_peta

◆ w