#include <copss_point_particle_system.h>

Inheritance diagram for libMesh::CopssPointParticleSystem:

Collaboration diagram for libMesh::CopssPointParticleSystem:

[legend]

Public Member Functions
	CopssPointParticleSystem (CopssInit &init)

	~CopssPointParticleSystem ()

void	run (EquationSystems &equation_systems) override

Public Member Functions inherited from libMesh::Copss
	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 ()

EquationSystems	create_equation_systems ()

void	destroy ()

Protected Member Functions
void	read_particle_info () override

void	read_ggem_info () override

void	create_object () override

void	create_object_mesh () override

void	attach_object_mesh (PMLinearImplicitSystem &system) override

void	set_parameters (EquationSystems &equation_systems) override

void	update_object ()

void	write_object (unsigned int step_id) override

Protected Member Functions inherited from libMesh::Copss
void	read_system_info ()

void	read_physical_info ()

void	read_domain_info ()

void	read_force_info ()

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 ()

void	attach_period_boundary (PMLinearImplicitSystem &system)

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)

Protected Attributes
std::string	point_particle_model

unsigned int	Nb

unsigned int	Ns

unsigned int	nBonds

unsigned int	nChains

Real	bk

Real	Nks

Real	Ss2

Real	q0

Real	chain_length

Real	Dc

Real	max_spring_len

bool	chain_broken

Protected Attributes inherited from libMesh::Copss
const int	o_precision = 6

Additional Inherited Members
Public Attributes inherited from libMesh::Copss
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

Constructor & Destructor Documentation

libMesh::CopssPointParticleSystem::CopssPointParticleSystem ( CopssInit & init )

libMesh::CopssPointParticleSystem::~CopssPointParticleSystem ( )

Member Function Documentation

void libMesh::CopssPointParticleSystem::attach_object_mesh ( PMLinearImplicitSystem & system )

overrideprotectedvirtual

Steps for create_equation_systems

Implements libMesh::Copss.

Here is the call graph for this function:

void libMesh::CopssPointParticleSystem::create_object ( )

overrideprotectedvirtual

Implements libMesh::Copss.

Here is the call graph for this function:

Here is the caller graph for this function:

void libMesh::CopssPointParticleSystem::create_object_mesh ( )

overrideprotectedvirtual

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

Implements libMesh::Copss.

Here is the call graph for this function:

void libMesh::CopssPointParticleSystem::read_ggem_info ( )

overrideprotectedvirtual

Implements libMesh::Copss.

void libMesh::CopssPointParticleSystem::read_particle_info ( )

overrideprotectedvirtual

Implements libMesh::Copss.

Here is the call graph for this function:

void libMesh::CopssPointParticleSystem::run ( EquationSystems & equation_systems )

overridevirtual

integrater step 1:

Implements libMesh::Copss.

Here is the call graph for this function:

Here is the caller graph for this function:

void libMesh::CopssPointParticleSystem::set_parameters ( EquationSystems & equation_systems )

overrideprotectedvirtual

Implements libMesh::Copss.

void libMesh::CopssPointParticleSystem::update_object ( )

protectedvirtual

Reimplemented from libMesh::Copss.

Here is the call graph for this function:

Here is the caller graph for this function:

void libMesh::CopssPointParticleSystem::write_object ( unsigned int step_id )

overrideprotectedvirtual

Implements libMesh::Copss.

Here is the call graph for this function:

Member Data Documentation

Real libMesh::CopssPointParticleSystem::bk

protected

bool libMesh::CopssPointParticleSystem::chain_broken

protected

Real libMesh::CopssPointParticleSystem::chain_length

protected

Real libMesh::CopssPointParticleSystem::Dc

protected

Real libMesh::CopssPointParticleSystem::max_spring_len

protected

unsigned int libMesh::CopssPointParticleSystem::Nb

protected

unsigned int libMesh::CopssPointParticleSystem::nBonds

protected

unsigned int libMesh::CopssPointParticleSystem::nChains

protected

Real libMesh::CopssPointParticleSystem::Nks

protected

unsigned int libMesh::CopssPointParticleSystem::Ns

protected

std::string libMesh::CopssPointParticleSystem::point_particle_model

protected

Real libMesh::CopssPointParticleSystem::q0

protected

Real libMesh::CopssPointParticleSystem::Ss2

protected

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

/home/cody/copss-hydrodynamics-public/src/POINTPARTICLE/copss_point_particle_system.h
/home/cody/copss-hydrodynamics-public/src/POINTPARTICLE/copss_point_particle_system.C

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation