Immersed-boundary method proposed by Taira and Colonius (2007). More...

#include <ibpm.h>

Inheritance diagram for IBPMSolver:

Public Member Functions
	IBPMSolver ()=default
	Default constructor. More...

	IBPMSolver (const MPI_Comm &world, const YAML::Node &node)
	Constructor. Initialize the IBPM solver. More...

	~IBPMSolver ()
	Default destructor. More...

PetscErrorCode	destroy ()
	Manually destroy data. More...

PetscErrorCode	init (const MPI_Comm &world, const YAML::Node &node)
	Initialize the IBPM solver. More...

PetscErrorCode	write ()
	Write solution, forces, and solvers info to files. More...

PetscErrorCode	ioInitialData ()
	Read or write initial data. More...

PetscErrorCode	advance ()
	Advance the solution by one time step. More...

bool	finished ()
	Evaluate if the simulation is finished. More...

Protected Member Functions
virtual PetscErrorCode	assembleRHSPoisson ()
	Assemble the RHS vector of the Poisson system. More...

virtual PetscErrorCode	createOperators ()
	Create operators. More...

virtual PetscErrorCode	createVectors ()
	Create vectors. More...

virtual PetscErrorCode	setNullSpace ()
	Set Poisson nullspace or pin pressure at a reference point. More...

virtual PetscErrorCode	writeSolutionHDF5 (const std::string &filePath)
	Write the solution fields into a HDF5 file. More...

virtual PetscErrorCode	writeRestartDataHDF5 (const std::string &filePath)
	Write data required to restart a simulation into a HDF5 file. More...

virtual PetscErrorCode	readRestartDataHDF5 (const std::string &filePath)
	Read data required to restart a simulation from a HDF5 file. More...

virtual PetscErrorCode	writeForcesASCII ()
	Write the forces acting on the bodies into an ASCII file. More...

virtual PetscErrorCode	assembleRHSVelocity ()
	Assemble the RHS vector of the velocity system. More...

virtual PetscErrorCode	solveVelocity ()
	Solve the velocity system. More...

virtual PetscErrorCode	solvePoisson ()
	Solve the Poisson system. More...

virtual PetscErrorCode	applyDivergenceFreeVelocity ()

virtual PetscErrorCode	updatePressure ()

virtual PetscErrorCode	createPetscViewerASCII (const std::string &filePath, const PetscFileMode &mode, PetscViewer &viewer)
	Create an ASCII PetscViewer. More...

virtual PetscErrorCode	writeLinSolversInfo ()
	Write numbers of iterations and residuals of solvers to file. More...

virtual PetscErrorCode	writeTimeHDF5 (const PetscReal &t, const std::string &filePath)
	Write the time value into a HDF5 file. More...

virtual PetscErrorCode	readTimeHDF5 (const std::string &filePath, PetscReal &t)
	Read the time value from a HDF5 file. More...

virtual PetscErrorCode	monitorProbes ()
	Monitor the solution at probes. More...

Protected Attributes
petibm::type::BodyPack	bodies
	Pack of immersed bodies. More...

Vec	P
	PETSc Vec object with pressure field and Lagrangian forces. More...

IS	isDE [2]
	Global index sets for pressure field and Lagrangian forces. More...

PetscLogStage	stageIntegrateForces
	Log stage for integrating the Lagrangian forces. More...

PetscViewer	forcesViewer
	ASCII PetscViewer object to output the forces. More...

MPI_Comm	comm
	MPI communicator. More...

PetscMPIInt	commSize
	Size of the MPI communicator. More...

PetscMPIInt	commRank
	Rank of the process in the MPI communicator. More...

YAML::Node	config
	YAML configuration settings. More...

petibm::type::Mesh	mesh
	Structured Cartesian mesh object. More...

petibm::type::Boundary	bc
	Information about the domain boundaries. More...

petibm::type::Solution	solution
	Data object holding the velocity and pressure fields. More...

petibm::type::TimeIntegration	convCoeffs
	Time scheme for the convective terms. More...

petibm::type::TimeIntegration	diffCoeffs
	Time scheme for the diffusion terms. More...

petibm::type::LinSolver	vSolver
	Velocity linear solver. More...

petibm::type::LinSolver	pSolver
	Poisson linear solver. More...

std::vector< petibm::type::Probe >	probes
	Probes to monitor the solution. More...

PetscReal	dt
	Time-step size. More...

PetscInt	ite
	Time-step index. More...

PetscReal	t
	Time value. More...

PetscInt	nstart
	Starting time-step index. More...

PetscInt	nt
	Number of time steps to compute. More...

PetscInt	nsave
	Frequency at which the solution fields are written to files. More...

PetscInt	nrestart
	Frequency at which data to restart are written to files. More...

PetscReal	nu
	Viscous diffusion coefficient. More...

Mat	L
	Laplacian operator. More...

Mat	LCorrection
	Laplacian correction operator for boundary conditions. More...

Mat	G
	Gradient operator. More...

Mat	D
	Divergence operator. More...

Mat	DCorrection
	Divergence correction for boundary conditions. More...

Mat	N
	Convective operator (matrix-free). More...

Mat	A
	Implicit operator for the velocity solver. More...

Mat	BNG
	Projection operator. More...

Mat	DBNG
	Poisson operator. More...

Vec	dP
	Pressure-correction vector. More...

Vec	bc1
	Inhomogeneous boundary terms for the velocity system. More...

Vec	rhs1
	Right-hand side vector of the velocity system. More...

Vec	rhs2
	Right-hand side vector of the Poisson system. More...

std::vector< Vec >	conv
	Explicit convective terms. More...

std::vector< Vec >	diff
	Explicit diffusion terms. More...

PetscBool	isRefP
	True if we pin the pressure at a reference point. More...

PetscLogStage	stageInitialize
	Log stage for the initialization phase. More...

PetscLogStage	stageRHSVelocity
	Log stage for assembling the RHS of the velocity system. More...

PetscLogStage	stageSolveVelocity
	Log stage for solving the velocity system. More...

PetscLogStage	stageRHSPoisson
	Log stage for assembling the RHS of the Poisson system. More...

PetscLogStage	stageSolvePoisson
	Log stage for solving the Poisson system. More...

PetscLogStage	stageUpdate
	Log stage for updating field variables. More...

PetscLogStage	stageWrite
	Log stage when write the solution fields. More...

PetscLogStage	stageMonitor
	Log stage for monitoring user-defined regions of the domain. More...

PetscViewer	solversViewer
	ASCII PetscViewer object to output solvers info. More...

Detailed Description

Immersed-boundary method proposed by Taira and Colonius (2007).

See also: IBPM solver (Taira & Colonius 2007), NavierStokesSolver

Definition at line 22 of file ibpm.h.

Constructor & Destructor Documentation

◆ IBPMSolver() [1/2]

IBPMSolver::IBPMSolver ( )

default

Default constructor.

◆ IBPMSolver() [2/2]

IBPMSolver::IBPMSolver	(	const MPI_Comm &	world,
		const YAML::Node &	node
	)

Constructor. Initialize the IBPM solver.

Parameters

world	[in] MPI communicator
node	[in] YAML configuration settings

Definition at line 17 of file ibpm.cpp.

◆ ~IBPMSolver()

IBPMSolver::~IBPMSolver ( )

Default destructor.

Definition at line 23 of file ibpm.cpp.

Member Function Documentation

◆ advance()

PetscErrorCode NavierStokesSolver::advance ( )

Advance the solution by one time step.

Definition at line 67 of file navierstokes.cpp.

◆ applyDivergenceFreeVelocity()

PetscErrorCode NavierStokesSolver::applyDivergenceFreeVelocity ( )

protectedvirtualinherited

Definition at line 583 of file navierstokes.cpp.

◆ assembleRHSPoisson()

PetscErrorCode IBPMSolver::assembleRHSPoisson ( )

protectedvirtual

Assemble the RHS vector of the Poisson system.

Reimplemented from NavierStokesSolver.

Definition at line 286 of file ibpm.cpp.

◆ assembleRHSVelocity()

PetscErrorCode NavierStokesSolver::assembleRHSVelocity ( )

protectedvirtualinherited

Assemble the RHS vector of the velocity system.

Reimplemented in DecoupledIBPMSolver.

Definition at line 432 of file navierstokes.cpp.

◆ createOperators()

PetscErrorCode IBPMSolver::createOperators ( )

protectedvirtual

Create operators.

Reimplemented from NavierStokesSolver.

Definition at line 100 of file ibpm.cpp.

◆ createPetscViewerASCII()

PetscErrorCode NavierStokesSolver::createPetscViewerASCII	(	const std::string &	filePath,
		const PetscFileMode &	mode,
		PetscViewer &	viewer
	)

protectedvirtualinherited

Create an ASCII PetscViewer.

Parameters

filePath	[in] Path of the file to write in
mode	[in] File mode
viewer	[out] PetscViewer object

Returns: PetscErrorCode

Definition at line 749 of file navierstokes.cpp.

◆ createVectors()

PetscErrorCode IBPMSolver::createVectors ( )

protectedvirtual

Create vectors.

Reimplemented from NavierStokesSolver.

Definition at line 206 of file ibpm.cpp.

◆ destroy()

PetscErrorCode IBPMSolver::destroy ( )

Manually destroy data.

Definition at line 37 of file ibpm.cpp.

◆ finished()

bool NavierStokesSolver::finished ( )

Evaluate if the simulation is finished.

Definition at line 73 of file navierstokes.cpp.

◆ init()

PetscErrorCode IBPMSolver::init	(	const MPI_Comm &	world,
		const YAML::Node &	node
	)

Initialize the IBPM solver.

Parameters

world	[in] MPI communicator
node	[in] YAML configuration settings

Returns: PetscErrorCode

Definition at line 54 of file ibpm.cpp.

◆ ioInitialData()

PetscErrorCode NavierStokesSolver::ioInitialData ( )

Read or write initial data.

Definition at line 64 of file navierstokes.cpp.

◆ monitorProbes()

PetscErrorCode NavierStokesSolver::monitorProbes ( )

protectedvirtualinherited

Monitor the solution at probes.

Definition at line 840 of file navierstokes.cpp.

◆ readRestartDataHDF5()

PetscErrorCode IBPMSolver::readRestartDataHDF5 ( const std::string & filePath )

protectedvirtual

Read data required to restart a simulation from a HDF5 file.

Parameters

filePath [in] Path of the file to read from

Returns: PetscErrorCode

Reimplemented from NavierStokesSolver.

Definition at line 357 of file ibpm.cpp.

◆ readTimeHDF5()

PetscErrorCode NavierStokesSolver::readTimeHDF5	(	const std::string &	filePath,
		PetscReal &	t
	)

protectedvirtualinherited

Read the time value from a HDF5 file.

Parameters

filePath	[in] Path of the file to read from
t	[out] Time

Returns: PetscErrorCode

Definition at line 818 of file navierstokes.cpp.

◆ setNullSpace()

PetscErrorCode IBPMSolver::setNullSpace ( )

protectedvirtual

Set Poisson nullspace or pin pressure at a reference point.

Reimplemented from NavierStokesSolver.

Definition at line 242 of file ibpm.cpp.

◆ solvePoisson()

PetscErrorCode NavierStokesSolver::solvePoisson ( )

protectedvirtualinherited

Solve the Poisson system.

Definition at line 566 of file navierstokes.cpp.

◆ solveVelocity()

PetscErrorCode NavierStokesSolver::solveVelocity ( )

protectedvirtualinherited

Solve the velocity system.

Definition at line 524 of file navierstokes.cpp.

◆ updatePressure()

PetscErrorCode NavierStokesSolver::updatePressure ( )

protectedvirtualinherited

Definition at line 601 of file navierstokes.cpp.

◆ write()

PetscErrorCode IBPMSolver::write ( )

Write solution, forces, and solvers info to files.

Definition at line 85 of file ibpm.cpp.

◆ writeForcesASCII()

PetscErrorCode IBPMSolver::writeForcesASCII ( )

protectedvirtual

Write the forces acting on the bodies into an ASCII file.

Definition at line 387 of file ibpm.cpp.

◆ writeLinSolversInfo()

PetscErrorCode NavierStokesSolver::writeLinSolversInfo ( )

protectedvirtualinherited

Write numbers of iterations and residuals of solvers to file.

Reimplemented in DecoupledIBPMSolver.

Definition at line 766 of file navierstokes.cpp.

◆ writeRestartDataHDF5()

PetscErrorCode IBPMSolver::writeRestartDataHDF5 ( const std::string & filePath )

protectedvirtual

Write data required to restart a simulation into a HDF5 file.

Parameters

filePath [in] Path of the file to write in

Returns: PetscErrorCode

Reimplemented from NavierStokesSolver.

Definition at line 338 of file ibpm.cpp.

◆ writeSolutionHDF5()

PetscErrorCode IBPMSolver::writeSolutionHDF5 ( const std::string & filePath )

protectedvirtual

Write the solution fields into a HDF5 file.

Parameters

filePath [in] Path of the file to write in

Returns: PetscErrorCode

Reimplemented from NavierStokesSolver.

Definition at line 316 of file ibpm.cpp.

◆ writeTimeHDF5()

PetscErrorCode NavierStokesSolver::writeTimeHDF5	(	const PetscReal &	t,
		const std::string &	filePath
	)

protectedvirtualinherited

Write the time value into a HDF5 file.

Parameters

t	[in] Time
filePath	[in] Path of the file to write in

Returns: PetscErrorCode

Definition at line 797 of file navierstokes.cpp.

Member Data Documentation

◆ A

Mat NavierStokesSolver::A

protectedinherited

Implicit operator for the velocity solver.

Definition at line 155 of file navierstokes.h.

◆ bc

petibm::type::Boundary NavierStokesSolver::bc

protectedinherited

Information about the domain boundaries.

Definition at line 92 of file navierstokes.h.

◆ bc1

Vec NavierStokesSolver::bc1

protectedinherited

Inhomogeneous boundary terms for the velocity system.

Definition at line 167 of file navierstokes.h.

◆ BNG

Mat NavierStokesSolver::BNG

protectedinherited

Projection operator.

Definition at line 158 of file navierstokes.h.

◆ bodies

petibm::type::BodyPack IBPMSolver::bodies

protected

Pack of immersed bodies.

Definition at line 61 of file ibpm.h.

◆ comm

MPI_Comm NavierStokesSolver::comm

protectedinherited

MPI communicator.

Definition at line 77 of file navierstokes.h.

◆ commRank

PetscMPIInt NavierStokesSolver::commRank

protectedinherited

Rank of the process in the MPI communicator.

Definition at line 83 of file navierstokes.h.

◆ commSize

PetscMPIInt NavierStokesSolver::commSize

protectedinherited

Size of the MPI communicator.

Definition at line 80 of file navierstokes.h.

◆ config

YAML::Node NavierStokesSolver::config

protectedinherited

YAML configuration settings.

Definition at line 86 of file navierstokes.h.

◆ conv

std::vector<Vec> NavierStokesSolver::conv

protectedinherited

Explicit convective terms.

Definition at line 176 of file navierstokes.h.

◆ convCoeffs

petibm::type::TimeIntegration NavierStokesSolver::convCoeffs

protectedinherited

Time scheme for the convective terms.

Definition at line 98 of file navierstokes.h.

◆ D

Mat NavierStokesSolver::D

protectedinherited

Divergence operator.

Definition at line 146 of file navierstokes.h.

◆ DBNG

Mat NavierStokesSolver::DBNG

protectedinherited

Poisson operator.

Definition at line 161 of file navierstokes.h.

◆ DCorrection

Mat NavierStokesSolver::DCorrection

protectedinherited

Divergence correction for boundary conditions.

Definition at line 149 of file navierstokes.h.

◆ diff

std::vector<Vec> NavierStokesSolver::diff

protectedinherited

Explicit diffusion terms.

Definition at line 179 of file navierstokes.h.

◆ diffCoeffs

petibm::type::TimeIntegration NavierStokesSolver::diffCoeffs

protectedinherited

Time scheme for the diffusion terms.

Definition at line 101 of file navierstokes.h.

◆ dP

Vec NavierStokesSolver::dP

protectedinherited

Pressure-correction vector.

Definition at line 164 of file navierstokes.h.

◆ dt

PetscReal NavierStokesSolver::dt

protectedinherited

Time-step size.

Definition at line 113 of file navierstokes.h.

◆ forcesViewer

PetscViewer IBPMSolver::forcesViewer

protected

ASCII PetscViewer object to output the forces.

Definition at line 73 of file ibpm.h.

◆ G

Mat NavierStokesSolver::G

protectedinherited

Gradient operator.

Definition at line 143 of file navierstokes.h.

◆ isDE

IS IBPMSolver::isDE[2]

protected

Global index sets for pressure field and Lagrangian forces.

Definition at line 67 of file ibpm.h.

◆ isRefP

PetscBool NavierStokesSolver::isRefP

protectedinherited

True if we pin the pressure at a reference point.

Definition at line 182 of file navierstokes.h.

◆ ite

PetscInt NavierStokesSolver::ite

protectedinherited

Time-step index.

Definition at line 116 of file navierstokes.h.

◆ L

Mat NavierStokesSolver::L

protectedinherited

Laplacian operator.

Definition at line 137 of file navierstokes.h.

◆ LCorrection

Mat NavierStokesSolver::LCorrection

protectedinherited

Laplacian correction operator for boundary conditions.

Definition at line 140 of file navierstokes.h.

◆ mesh

petibm::type::Mesh NavierStokesSolver::mesh

protectedinherited

Structured Cartesian mesh object.

Definition at line 89 of file navierstokes.h.

◆ N

Mat NavierStokesSolver::N

protectedinherited

Convective operator (matrix-free).

Definition at line 152 of file navierstokes.h.

◆ nrestart

PetscInt NavierStokesSolver::nrestart

protectedinherited

Frequency at which data to restart are written to files.

Definition at line 131 of file navierstokes.h.

◆ nsave

PetscInt NavierStokesSolver::nsave

protectedinherited

Frequency at which the solution fields are written to files.

Definition at line 128 of file navierstokes.h.

◆ nstart

PetscInt NavierStokesSolver::nstart

protectedinherited

Starting time-step index.

Definition at line 122 of file navierstokes.h.

◆ nt

PetscInt NavierStokesSolver::nt

protectedinherited

Number of time steps to compute.

Definition at line 125 of file navierstokes.h.

◆ nu

PetscReal NavierStokesSolver::nu

protectedinherited

Viscous diffusion coefficient.

Definition at line 134 of file navierstokes.h.

◆ P

Vec IBPMSolver::P

protected

PETSc Vec object with pressure field and Lagrangian forces.

Definition at line 64 of file ibpm.h.

◆ probes

std::vector<petibm::type::Probe> NavierStokesSolver::probes

protectedinherited

Probes to monitor the solution.

Definition at line 110 of file navierstokes.h.

◆ pSolver

petibm::type::LinSolver NavierStokesSolver::pSolver

protectedinherited

Poisson linear solver.

Definition at line 107 of file navierstokes.h.

◆ rhs1

Vec NavierStokesSolver::rhs1

protectedinherited

Right-hand side vector of the velocity system.

Definition at line 170 of file navierstokes.h.

◆ rhs2

Vec NavierStokesSolver::rhs2

protectedinherited

Right-hand side vector of the Poisson system.

Definition at line 173 of file navierstokes.h.

◆ solution

petibm::type::Solution NavierStokesSolver::solution

protectedinherited

Data object holding the velocity and pressure fields.

Definition at line 95 of file navierstokes.h.

◆ solversViewer

PetscViewer NavierStokesSolver::solversViewer

protectedinherited

ASCII PetscViewer object to output solvers info.

Definition at line 209 of file navierstokes.h.

◆ stageInitialize

PetscLogStage NavierStokesSolver::stageInitialize

protectedinherited

Log stage for the initialization phase.

Definition at line 185 of file navierstokes.h.

◆ stageIntegrateForces

PetscLogStage IBPMSolver::stageIntegrateForces

protected

Log stage for integrating the Lagrangian forces.

Definition at line 70 of file ibpm.h.

◆ stageMonitor

PetscLogStage NavierStokesSolver::stageMonitor

protectedinherited

Log stage for monitoring user-defined regions of the domain.

Definition at line 206 of file navierstokes.h.

◆ stageRHSPoisson

PetscLogStage NavierStokesSolver::stageRHSPoisson

protectedinherited

Log stage for assembling the RHS of the Poisson system.

Definition at line 194 of file navierstokes.h.

◆ stageRHSVelocity

PetscLogStage NavierStokesSolver::stageRHSVelocity

protectedinherited

Log stage for assembling the RHS of the velocity system.

Definition at line 188 of file navierstokes.h.

◆ stageSolvePoisson

PetscLogStage NavierStokesSolver::stageSolvePoisson

protectedinherited

Log stage for solving the Poisson system.

Definition at line 197 of file navierstokes.h.

◆ stageSolveVelocity

PetscLogStage NavierStokesSolver::stageSolveVelocity

protectedinherited

Log stage for solving the velocity system.

Definition at line 191 of file navierstokes.h.

◆ stageUpdate

PetscLogStage NavierStokesSolver::stageUpdate

protectedinherited

Log stage for updating field variables.

Definition at line 200 of file navierstokes.h.

◆ stageWrite

PetscLogStage NavierStokesSolver::stageWrite

protectedinherited

Log stage when write the solution fields.

Definition at line 203 of file navierstokes.h.

◆ t

PetscReal NavierStokesSolver::t

protectedinherited

Time value.

Definition at line 119 of file navierstokes.h.

◆ vSolver

petibm::type::LinSolver NavierStokesSolver::vSolver

protectedinherited

Velocity linear solver.

Definition at line 104 of file navierstokes.h.

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

applications/ibpm/ibpm.h
applications/ibpm/ibpm.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ IBPMSolver() [1/2]

◆ IBPMSolver() [2/2]

◆ ~IBPMSolver()

Member Function Documentation

◆ advance()

◆ applyDivergenceFreeVelocity()

◆ assembleRHSPoisson()

◆ assembleRHSVelocity()

◆ createOperators()

◆ createPetscViewerASCII()

◆ createVectors()

◆ destroy()

◆ finished()

◆ init()

◆ ioInitialData()

◆ monitorProbes()

◆ readRestartDataHDF5()

◆ readTimeHDF5()

◆ setNullSpace()

◆ solvePoisson()

◆ solveVelocity()

◆ updatePressure()

◆ write()

◆ writeForcesASCII()

◆ writeLinSolversInfo()

◆ writeRestartDataHDF5()

◆ writeSolutionHDF5()

◆ writeTimeHDF5()

Member Data Documentation

◆ A

◆ bc

◆ bc1

◆ BNG

◆ bodies

◆ comm

◆ commRank

◆ commSize

◆ config

◆ conv

◆ convCoeffs

◆ D

◆ DBNG

◆ DCorrection

◆ diff

◆ diffCoeffs

◆ dP

◆ dt

◆ forcesViewer

◆ G

◆ isDE

◆ isRefP

◆ ite

◆ L

◆ LCorrection

◆ mesh

◆ N

◆ nrestart

◆ nsave

◆ nstart

◆ nt

◆ nu

◆ P

◆ probes

◆ pSolver

◆ rhs1

◆ rhs2

◆ solution

◆ solversViewer

◆ stageInitialize

◆ stageIntegrateForces

◆ stageMonitor

◆ stageRHSPoisson

◆ stageRHSVelocity

◆ stageSolvePoisson

◆ stageSolveVelocity