libMesh::Copss Class Reference

#include <copss.h>

Inheritance diagram for libMesh::Copss:

Collaboration diagram for libMesh::Copss:

Public Member Functions
	Copss (CopssInit &init)
	~Copss ()
int	check_libmesh ()
void	start_time (struct tm *timeinfo)
void	end_time (struct tm *timeinfo)
EquationSystems	init_system (std::string input_file)
void	read_input ()
virtual void	create_object_mesh ()=0
EquationSystems	create_equation_systems ()
virtual void	run (EquationSystems &equation_systems)=0
void	destroy ()

Public Attributes
Parallel::Communicator *	comm_in
std::string	error_msg
std::string	output_msg
GetPot	input_file
std::string	control_fileName
std::string	test_name
bool	print_info
const Real	kB = 1.380662E-17
const Real	PI = libMesh::pi
Real	T
Real	kBT
Real	viscosity
Real	Rb
Real	drag_c
Real	Db
std::string	particle_type
Real	tc
Real	uc
Real	fc
Real	muc
unsigned int	dim
std::string	wall_type
std::vector< Real >	wall_params
std::vector< bool >	periodicity
std::vector< bool >	inlet
std::vector< Real >	inlet_pressure
std::vector< bool >	shear
std::vector< Real >	shear_rate
std::vector< unsigned int >	shear_direction
bool	generate_mesh
std::string	domain_mesh_file
std::vector< unsigned int >	n_mesh
std::vector< Fix * >	fixes
FixFactory *	fix_factory
unsigned int	numForceTypes
std::vector< std::string >	forceTypes
std::vector< Fix::type_force >	forces
Real	alpha
int	max_linear_iterations
Real	linear_solver_rtol
Real	linear_solver_atol
bool	user_defined_pc
bool	schur_user_ksp
Real	schur_user_ksp_rtol
Real	schur_user_ksp_atol
std::string	schur_pc_type
std::string	stokes_solver_type
StokesSolverType	solver_type
unsigned int	max_n_cheb
Real	tol_cheb
Real	eig_factor
Real	tol_eigen
bool	compute_eigen
bool	read_eigen
bool	with_hi
bool	with_brownian
std::size_t	random_seed
bool	adaptive_dt
std::vector< Real >	max_dr_coeff
Real	max_dr
bool	restart
std::size_t	restart_step
unsigned int	nstep
unsigned int	n_relax_step
bool	debug_info
unsigned int	write_interval
std::vector< std::string >	output_file
SerialMesh *	mesh
PointMesh< 3 > *	point_mesh
Real	min_mesh_size
Real	max_mesh_size
Real	search_radius_p
Real	search_radius_e
PMPeriodicBoundary *	pm_periodic_boundary
unsigned int	u_var
unsigned int	v_var
unsigned int	w_var
unsigned int	p_var
bool	reinit_stokes
unsigned int	NP
unsigned int	n_vec
Real	hminf
Real	hmaxf
Real	hmin
Real	hmax
bool	cheb_converge = false
unsigned int	n_chebyshev_failure = 0
Real	eig_min = 0
Real	eig_max = 0
const std::string	out_system_filename = "output_pm_system.e"
UniquePtr< NumericVector< Real > >	v0_ptr
ExodusII_IO *	exodus_ptr
Vec	U0
Vec	R0
Vec	R_mid
Vec	RIN
Vec	ROUT
Vec	dw
Vec	dw_mid
PetscViewer	viewer
Mat	M
PetscRandom	rand_ctx
PetscScalar	coef = 0.0
BrownianSystem *	brownian_sys
std::vector< Point >	center0
unsigned int	istart
unsigned int	o_step
Real	real_time
bool	update_neighbor_list_everyStep
unsigned int	neighbor_list_update_interval = 0
unsigned int	timestep_duration
bool	neighbor_list_update_flag
std::vector< Real >	vel0
std::vector< Real >	vel1

Protected Member Functions
void	read_system_info ()
void	read_physical_info ()
virtual void	read_particle_info ()=0
void	read_domain_info ()
void	read_force_info ()
virtual void	read_ggem_info ()=0
void	read_stokes_solver_info ()
void	read_chebyshev_info ()
void	read_run_info ()
void	read_restart_time ()
void	read_restart_eigenvalue ()
void	create_domain_mesh ()
void	create_periodic_boundary ()
virtual void	create_object ()=0
virtual void	attach_object_mesh (PMLinearImplicitSystem &system)=0
void	attach_period_boundary (PMLinearImplicitSystem &system)
virtual void	set_parameters (EquationSystems &equation_systems)=0
void	attach_fixes (PMLinearImplicitSystem &system)
void	solve_undisturbed_system (EquationSystems &equation_systems)
void	create_brownian_system (EquationSystems &equation_systems)
void	fixman_integrate (EquationSystems &equation_systems, unsigned int &i)
void	langevin_integrate (EquationSystems &equation_systems, unsigned int &i)
virtual void	update_object ()
virtual void	write_object (unsigned int step_id)=0

Protected Attributes
const int	o_precision = 6

Constructor & Destructor Documentation

libMesh::Copss::Copss

(

CopssInit &

init

)

class constructor

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libMesh::Copss::~Copss

(

)

class destructor

Member Function Documentation

void libMesh::Copss::attach_fixes ( PMLinearImplicitSystem &  system )

protected

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virtual void libMesh::Copss::attach_object_mesh ( PMLinearImplicitSystem &  system )

protectedpure virtual

Steps for create_equation_systems

Implemented in libMesh::CopssPointParticleSystem, and libMesh::CopssRigidParticleSystem.

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void libMesh::Copss::attach_period_boundary ( PMLinearImplicitSystem &  system )

protected

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int libMesh::Copss::check_libmesh

(

)

Check libmesh support

PETSC or laspack SLEPC AMR at least 2D

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void libMesh::Copss::create_brownian_system ( EquationSystems &  equation_systems )

protected

Create vectors and Shell Mat for use Create brownian system

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void libMesh::Copss::create_domain_mesh ( )

protected

Steps for create_object_mesh()

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EquationSystems libMesh::Copss::create_equation_systems

(

)

Create equation_system object step 1: initialize equation_systems using mesh; add a PMLinearImplicitSystem, system, to equation_systems; add variables step 3: attach_object_mesh() step 4: attach_period_boundary() step 5: initialize equation systems and preconditioning matrix step 5: set_parameters() for equation_systems step 6: Initialize the force field

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virtual void libMesh::Copss::create_object ( )

protectedpure virtual

Implemented in libMesh::CopssPointParticleSystem, and libMesh::CopssRigidParticleSystem.

virtual void libMesh::Copss::create_object_mesh ( )

pure virtual

Create object_mesh this object_mesh can be point_mesh or particle_mesh step 1: create_domain_mesh() step 2: create_periodid_boundary() step 3: create_object() step 4: create object_mesh by combining domain mesh, object and periodic boundary

Implemented in libMesh::CopssPointParticleSystem, and libMesh::CopssRigidParticleSystem.

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void libMesh::Copss::create_periodic_boundary ( )

protected

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void libMesh::Copss::destroy

(

)

destroy PETSC objects

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void libMesh::Copss::end_time

(

struct tm *

timeinfo

)

Print out end time

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void libMesh::Copss::fixman_integrate ( EquationSystems &  equation_systems, unsigned int &  i  )

protected

Integrate particle motions using Fixman's midpoint scheme

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EquationSystems libMesh::Copss::init_system

(

std::string

input_file

)

Build and initialized an Equation system step 1: read_input() step 2: create_object_mesh() step 3: create_equation_systems()

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void libMesh::Copss::langevin_integrate ( EquationSystems &  equation_systems, unsigned int &  i  )

protected

Integrate particle motions using overdamped Langevin(Brownian dynamics) scheme

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void libMesh::Copss::read_chebyshev_info ( )

protected

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void libMesh::Copss::read_domain_info ( )

protected

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void libMesh::Copss::read_force_info ( )

protected

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virtual void libMesh::Copss::read_ggem_info ( )

protectedpure virtual

Implemented in libMesh::CopssPointParticleSystem, and libMesh::CopssRigidParticleSystem.

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void libMesh::Copss::read_input

(

)

Read input and create necessary objects step 1: read_system_info() step 2: read_physical_info() step 3: read_particle_info() step 4: read_domain_info() step 5: read_force_info() step 6: read_ggem_info() step 7: read_stokes_solver_info() step 8: read_chebyshev_info() step 9: read_run_info()

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virtual void libMesh::Copss::read_particle_info ( )

protectedpure virtual

Implemented in libMesh::CopssPointParticleSystem, and libMesh::CopssRigidParticleSystem.

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void libMesh::Copss::read_physical_info ( )

protected

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void libMesh::Copss::read_restart_eigenvalue ( )

protected

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void libMesh::Copss::read_restart_time ( )

protected

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void libMesh::Copss::read_run_info ( )

protected

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void libMesh::Copss::read_stokes_solver_info ( )

protected

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void libMesh::Copss::read_system_info ( )

protected

Steps for read_input()

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virtual void libMesh::Copss::run ( EquationSystems &  equation_systems )

pure virtual

integrater step 1:

Implemented in libMesh::CopssRigidParticleSystem, and libMesh::CopssPointParticleSystem.

virtual void libMesh::Copss::set_parameters ( EquationSystems &  equation_systems )

protectedpure virtual

Implemented in libMesh::CopssPointParticleSystem, and libMesh::CopssRigidParticleSystem.

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void libMesh::Copss::solve_undisturbed_system ( EquationSystems &  equation_systems )

protected

Steps for integrate()

Compute undisturbed velocity field without particles. NOTE: We MUST re-init particle-mesh before solving Stokes

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void libMesh::Copss::start_time

(

struct tm *

timeinfo

)

Print out start time

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virtual void libMesh::Copss::update_object ( )

inlineprotectedvirtual

Reimplemented in libMesh::CopssPointParticleSystem, and libMesh::CopssRigidParticleSystem.

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virtual void libMesh::Copss::write_object ( unsigned int  step_id )

protectedpure virtual

Implemented in libMesh::CopssPointParticleSystem, and libMesh::CopssRigidParticleSystem.

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Member Data Documentation

bool libMesh::Copss::adaptive_dt

Real libMesh::Copss::alpha

BrownianSystem* libMesh::Copss::brownian_sys

std::vector<Point> libMesh::Copss::center0

bool libMesh::Copss::cheb_converge = false

PetscScalar libMesh::Copss::coef = 0.0

Parallel::Communicator* libMesh::Copss::comm_in

bool libMesh::Copss::compute_eigen

std::string libMesh::Copss::control_fileName

Real libMesh::Copss::Db

bool libMesh::Copss::debug_info

unsigned int libMesh::Copss::dim

std::string libMesh::Copss::domain_mesh_file

Real libMesh::Copss::drag_c

Vec libMesh::Copss::dw

Vec libMesh::Copss::dw_mid

Real libMesh::Copss::eig_factor

Real libMesh::Copss::eig_max = 0

Real libMesh::Copss::eig_min = 0

std::string libMesh::Copss::error_msg

ExodusII_IO* libMesh::Copss::exodus_ptr

Real libMesh::Copss::fc

FixFactory* libMesh::Copss::fix_factory

std::vector<Fix*> libMesh::Copss::fixes

std::vector<Fix::type_force> libMesh::Copss::forces

std::vector<std::string> libMesh::Copss::forceTypes

bool libMesh::Copss::generate_mesh

Real libMesh::Copss::hmax

Real libMesh::Copss::hmaxf

Real libMesh::Copss::hmin

Real libMesh::Copss::hminf

std::vector<bool> libMesh::Copss::inlet

std::vector<Real> libMesh::Copss::inlet_pressure

GetPot libMesh::Copss::input_file

unsigned int libMesh::Copss::istart

const Real libMesh::Copss::kB = 1.380662E-17

Real libMesh::Copss::kBT

Real libMesh::Copss::linear_solver_atol

Real libMesh::Copss::linear_solver_rtol

Mat libMesh::Copss::M

Real libMesh::Copss::max_dr

std::vector<Real> libMesh::Copss::max_dr_coeff

int libMesh::Copss::max_linear_iterations

Real libMesh::Copss::max_mesh_size

unsigned int libMesh::Copss::max_n_cheb

SerialMesh* libMesh::Copss::mesh

Real libMesh::Copss::min_mesh_size

Real libMesh::Copss::muc

unsigned int libMesh::Copss::n_chebyshev_failure = 0

std::vector<unsigned int> libMesh::Copss::n_mesh

unsigned int libMesh::Copss::n_relax_step

unsigned int libMesh::Copss::n_vec

bool libMesh::Copss::neighbor_list_update_flag

unsigned int libMesh::Copss::neighbor_list_update_interval = 0

unsigned int libMesh::Copss::NP

unsigned int libMesh::Copss::nstep

unsigned int libMesh::Copss::numForceTypes

const int libMesh::Copss::o_precision = 6

protected

unsigned int libMesh::Copss::o_step

const std::string libMesh::Copss::out_system_filename = "output_pm_system.e"

std::vector<std::string> libMesh::Copss::output_file

std::string libMesh::Copss::output_msg

unsigned int libMesh::Copss::p_var

std::string libMesh::Copss::particle_type

std::vector<bool> libMesh::Copss::periodicity

const Real libMesh::Copss::PI = libMesh::pi

PMPeriodicBoundary* libMesh::Copss::pm_periodic_boundary

PointMesh<3>* libMesh::Copss::point_mesh

bool libMesh::Copss::print_info

Vec libMesh::Copss::R0

Vec libMesh::Copss::R_mid

PetscRandom libMesh::Copss::rand_ctx

std::size_t libMesh::Copss::random_seed

Real libMesh::Copss::Rb

bool libMesh::Copss::read_eigen

Real libMesh::Copss::real_time

bool libMesh::Copss::reinit_stokes

bool libMesh::Copss::restart

std::size_t libMesh::Copss::restart_step

Vec libMesh::Copss::RIN

Vec libMesh::Copss::ROUT

std::string libMesh::Copss::schur_pc_type

bool libMesh::Copss::schur_user_ksp

Real libMesh::Copss::schur_user_ksp_atol

Real libMesh::Copss::schur_user_ksp_rtol

Real libMesh::Copss::search_radius_e

Real libMesh::Copss::search_radius_p

std::vector<bool> libMesh::Copss::shear

std::vector<unsigned int> libMesh::Copss::shear_direction

std::vector<Real> libMesh::Copss::shear_rate

StokesSolverType libMesh::Copss::solver_type

std::string libMesh::Copss::stokes_solver_type

Real libMesh::Copss::T

Real libMesh::Copss::tc

std::string libMesh::Copss::test_name

unsigned int libMesh::Copss::timestep_duration

Real libMesh::Copss::tol_cheb

Real libMesh::Copss::tol_eigen

Vec libMesh::Copss::U0

unsigned int libMesh::Copss::u_var

Real libMesh::Copss::uc

bool libMesh::Copss::update_neighbor_list_everyStep

bool libMesh::Copss::user_defined_pc

UniquePtr<NumericVector<Real> > libMesh::Copss::v0_ptr

unsigned int libMesh::Copss::v_var

std::vector<Real> libMesh::Copss::vel0

std::vector<Real> libMesh::Copss::vel1

PetscViewer libMesh::Copss::viewer

Real libMesh::Copss::viscosity

unsigned int libMesh::Copss::w_var

std::vector<Real> libMesh::Copss::wall_params

std::string libMesh::Copss::wall_type

bool libMesh::Copss::with_brownian

bool libMesh::Copss::with_hi

unsigned int libMesh::Copss::write_interval

---

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

• /home/cody/copss-hydrodynamics-public/src/copss.h
• /home/cody/copss-hydrodynamics-public/src/copss.C