A class for mesh data. More...

#include <mesh.h>

Collaboration diagram for fe::Mesh:

Public Member Functions
	Mesh ()
	Constructor.

	Mesh (inp::MeshDeck *deck)
	Constructor. More...

	Mesh (size_t dim=0)
	Constructor. More...

void	print (int nt=0, int lvl=0) const
	Prints the information about the instance of the object. More...

std::string	printStr (int nt=0, int lvl=0) const
	Returns the string containing information about the instance of the object. More...

Accessor methods
size_t	getDimension () const
	Get the dimension of the domain. More...

size_t	getNumNodes () const
	Get the number of nodes. More...

size_t	getNumElements () const
	Get the number of elements. More...

size_t	getNumDofs () const
	Get the number of dofs. More...

size_t	getElementType () const
	Get the type of element in mesh. More...

double	getMeshSize () const
	Get the mesh size. More...

util::Point3	getNode (const size_t &i) const
	Get coordinates of node i. More...

double	getNodalVolume (const size_t &i) const
	Get nodal volume of node i. More...

const std::vector< util::Point3 > &	getNodes () const
	Get the nodes data. More...

std::vector< util::Point3 > &	getNodes ()

const std::vector< util::Point3 > *	getNodesP () const
	Get the pointer to nodes data. More...

std::vector< util::Point3 > *	getNodesP ()

const std::vector< uint8_t > *	getFixityP () const
	Get the pointer to fixity data. More...

std::vector< uint8_t > *	getFixityP ()

const std::vector< uint8_t > &	getFixity () const
	Get the reference to fixity data. More...

std::vector< uint8_t > &	getFixity ()

const std::vector< double > &	getNodalVolumes () const
	Get the nodal volume data. More...

std::vector< double > &	getNodalVolumes ()

const std::vector< double > *	getNodalVolumesP () const
	Get the pointer to nodal volume data. More...

std::vector< double > *	getNodalVolumesP ()

const std::vector< size_t >	getPrescribedNodes () const
	Get the vector of indicies with prescribed values from the couplign method. More...

std::vector< size_t >	getPrescribedNodes ()

const std::vector< util::Point3 >	getPrescribedValues () const
	Get the vector of values of the prescribed nodes from the couplign method. More...

std::vector< util::Point3 >	getPrescribedValues ()

bool	isNodeFree (const size_t &i, const unsigned int &dof) const
	Return true if node is free. More...

std::vector< size_t >	getElementConnectivity (const size_t &i) const
	Get the connectivity of element. More...

std::vector< util::Point3 >	getElementConnectivityNodes (const size_t &i) const
	Get the vertices of element. More...

const std::vector< size_t > &	getElementConnectivities () const
	Get the reference to element-node connectivity data. More...

std::vector< size_t > &	getElementConnectivities ()

const std::vector< size_t > *	getElementConnectivitiesP () const
	Get the pointer to element-node connectivity data. More...

std::vector< size_t > *	getElementConnectivitiesP ()

const std::pair< std::vector< double >, std::vector< double > > &	getBoundingBox () const
	Get the bounding box of the mesh. More...

Setter methods
void	setMeshData (const size_t &dim, std::vector< util::Point3 > &nodes, std::vector< double > &volumes)
	Set the mesh data for finite difference simulations. More...

void	setNodes (std::vector< util::Point3 > &nodes)
	Set the nodal data of the mesh. More...

void	setNodalVolumes (std::vector< double > &volumes)
	Set the nodal volume data of the mesh. More...

void	setFixity (std::vector< uint8_t > &fixity)
	Set nodal fixity masks. More...

void	setFixity (const size_t &i, const unsigned int &dof, const bool &flag)
	Set the fixity to free (0) or fixed (1) More...

void	setMeshSize (const double &h)
	Set the mesh size. More...

void	readFromFile (inp::MeshDeck *deck, const std::string &filename)
	Reads mesh data from the file and populates other data. More...

void	clearElementData ()
	Clear element-node connectivity data.

Private Member Functions
Utility methods
void	createData (const std::string &filename, bool ref_config, bool is_centroid_based, bool has_coupling_data)
	Reads mesh data from the file and populates other data. More...

void	nodesAtCentroid ()
	Converts standard fem mesh to particle mesh with nodes at the center of element.

void	computeVol ()
	Compute the nodal volume. More...

void	computeBBox ()
	Compute the bounding box

void	computeMeshSize ()
	Compute the mesh size. More...

Private Attributes
std::pair< std::vector< double >, std::vector< double > >	d_bbox
	Bounding box. More...

size_t	d_dim
	Dimension of the mesh.

std::string	d_filename
	Filename to read mesh data.

std::vector< int >	d_gInvMap
	Map from global id to reduced global id. More...

std::vector< size_t >	d_gMap
	Map from global reduced id to default global id. More...

double	d_h
	Mesh size.

bool	d_keepElementConn
	Specify if we keep the element connectivity data.

size_t	d_numDofs
	Number of dofs = (dimension) times (number of nodes)

std::string	d_spatialDiscretization
	Tag for spatial discretization type. More...

Mesh data
size_t	d_numNodes
	Number of nodes.

size_t	d_numElems
	Number of elements.

size_t	d_eType
	Element type. More...

size_t	d_eNumVertex
	Number of vertex per element. More...

std::vector< util::Point3 >	d_nodes
	Vector of initial (reference) coordinates of nodes.

std::vector< size_t >	d_enc
	Element-node connectivity data. More...

std::vector< std::vector< size_t > >	d_nec
	Node-element connectivity data. More...

std::vector< uint8_t >	d_fix
	Vector of fixity mask of each node. More...

std::vector< double >	d_vol
	Vector of volume of each node. More...

std::vector< size_t >	d_prescribed_nodes
	Vector with the indicies of all nodes with prescribed boundary data. More...

std::vector< util::Point3 >	d_prescribed_values
	Vector with the values of all nodes with prescribed boundary data. More...

Detailed Description

A class for mesh data.

In this class the mesh data such as nodes, element-node connectivity, node-element connectivity are stored. The class also stores fixity mask of nodes which indicates if x-, y-, or z-dof of the node is fixed or free.

We currently only support mesh with only one type of elements, i.e. mesh can not have mix of two types of elements. For example, we can not have mesh with triangle and quadrangle elements together.

This class is used in both finite difference implementation and finite element implementation. For finite difference, we only require nodal volume. If the mesh file contains nodal volume, we skip reading element-node and node-element connectivity, however if mesh file does not have nodal volume data, we read connectivity data and compute the nodal volume.

Constructor & Destructor Documentation

◆ Mesh() [1/2]

fe::Mesh::Mesh ( size_t dim = 0 )

explicit

Constructor.

Parameters

dim	Dimension of the problem

◆ Mesh() [2/2]

fe::Mesh::Mesh ( inp::MeshDeck * deck )

explicit

Constructor.

The constructor initializes the data using input deck, performs checks on input data, and reads mesh file and populates the mesh related data. The mesh file of **.csv**, **.vtu (VTK)** and **.msh (Gmsh)** are supported.

Parameters

deck	Input deck which contains user-specified information

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Member Function Documentation

◆ computeMeshSize()

void fe::Mesh::computeMeshSize ( )

private

Compute the mesh size.

This method searches for minimum distance between any two mesh nodes and stores it as a mesh size.

Referenced by Mesh().

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◆ computeVol()

void fe::Mesh::computeVol ( )

private

Compute the nodal volume.

This method requires element-node connectivity data to compute the nodal volumes. Formula for volume of a node $ i$ is given by

$V_i = \sum_{e \in \mathbf{N}_i} \int_{T_e} N_i(x) dx,$

where $\mathbf{N}_i$ is a list of elements which have node $ i$ as its vertex, $ T_e$ is the element domain, $ N_i$ is the shape function of the node $ i$ in element e.

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◆ createData()

void fe::Mesh::createData	(	const std::string &	filename,
		bool	ref_config,
		bool	is_centroid_based,
		bool	has_coupling_data
	)

private

Reads mesh data from the file and populates other data.

This function calls reader methods in namespace rw::reader to read the mesh file. For finite difference implementation, we support **.csv** mesh file which has nodal coordinates and nodal volumes data.

However, for finite element implementation, we require either **.vtu** or **.msh** file with element-node connectivity data.

Parameters

filename	Name of the mesh file
ref_config	Base the mesh on reference configuration (obtain reference configuration using point data and displacement data)
is_centroid_based	Specify if we create node at the center of element
has_coupling_data	Specify if we read the additional data needed for coupling

Referenced by Mesh().

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◆ getBoundingBox()

const std::pair<std::vector<double>, std::vector<double> >& fe::Mesh::getBoundingBox ( ) const

inline

Get the bounding box of the mesh.

Returns: box Bounding box

Referenced by model::Output::Output().

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◆ getDimension()

size_t fe::Mesh::getDimension ( ) const

inline

Get the dimension of the domain.

Returns: N Dimension

Referenced by loading::InitialCondition::apply().

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◆ getElementConnectivities()

const std::vector<size_t>& fe::Mesh::getElementConnectivities ( ) const

inline

Get the reference to element-node connectivity data.

Returns: reference Reference

◆ getElementConnectivitiesP()

const std::vector<size_t>* fe::Mesh::getElementConnectivitiesP ( ) const

inline

Get the pointer to element-node connectivity data.

Returns: pointer Pointer

Referenced by model::Output::Output().

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◆ getElementConnectivity()

std::vector<size_t> fe::Mesh::getElementConnectivity ( const size_t & i ) const

inline

Get the connectivity of element.

Since we store connectivity in a single vector, we use fe::Mesh::d_eNumVertex to get the connectivity of element. Given element e, the connectivity of e begins from location $i_0 = e*d\_eNumVertex + 0$ upto $i_{n-1} = e*d\_eNumVertex + d\_eNumVertex - 1$ .

So the connectivity of e is d_enc[ $i_0$ ], d_enc[ $ i_1 $ ], ..., d_end[ $i_{n-1}$ ]

Parameters

i	Id of an element

Returns: vector Vector of nodal ids

◆ getElementConnectivityNodes()

std::vector<util::Point3> fe::Mesh::getElementConnectivityNodes ( const size_t & i ) const

inline

Get the vertices of element.

Parameters

i	Id of an element

Returns: vector Vector of vertices

◆ getElementType()

size_t fe::Mesh::getElementType ( ) const

inline

Get the type of element in mesh.

Returns: type Element type (using VTK convention)

Referenced by model::Output::Output().

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◆ getFixity()

const std::vector<uint8_t>& fe::Mesh::getFixity ( ) const

inline

Get the reference to fixity data.

Returns: reference Reference to fixity data

◆ getFixityP()

const std::vector<uint8_t>* fe::Mesh::getFixityP ( ) const

inline

Get the pointer to fixity data.

Returns: pointer Pointer to fixity data

Referenced by model::Output::Output().

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◆ getMeshSize()

double fe::Mesh::getMeshSize ( ) const

inline

Get the mesh size.

Returns: h Mesh size

Referenced by loading::FLoading::apply(), material::pd::RNPBond::RNPBond(), and geometry::VolumeCorrection::VolumeCorrection().

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◆ getNodalVolume()

double fe::Mesh::getNodalVolume ( const size_t & i ) const

inline

Get nodal volume of node i.

Parameters

i	Id of the node

Returns: vol Volume

Referenced by model::Output::Output().

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◆ getNodalVolumes()

const std::vector<double>& fe::Mesh::getNodalVolumes ( ) const

inline

Get the nodal volume data.

Returns: Vector Vector of nodal volume

◆ getNodalVolumesP()

const std::vector<double>* fe::Mesh::getNodalVolumesP ( ) const

inline

Get the pointer to nodal volume data.

Returns: Pointer to nodal volume data

Referenced by model::Output::Output().

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◆ getNode()

util::Point3 fe::Mesh::getNode ( const size_t & i ) const

inline

Get coordinates of node i.

Parameters

i	Id of the node

Returns: coords Coordinates

Referenced by loading::FLoading::apply(), loading::ULoading::apply(), loading::InitialCondition::apply(), geometry::DampingGeom::computeDampingCoefficient(), loading::FLoading::FLoading(), and loading::ULoading::ULoading().

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◆ getNodes()

const std::vector<util::Point3>& fe::Mesh::getNodes ( ) const

inline

Get the nodes data.

Returns: nodes Nodes data

◆ getNodesP()

const std::vector<util::Point3>* fe::Mesh::getNodesP ( ) const

inline

Get the pointer to nodes data.

Returns: pointer Pointer to nodes data

Referenced by tools::pp::Compute::Compute(), util::StateBasedHelperFunctions::dilatation(), model::Output::Output(), util::StateBasedHelperFunctions::StateBasedHelperFunctions(), and geometry::VolumeCorrection::VolumeCorrection().

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◆ getNumDofs()

size_t fe::Mesh::getNumDofs ( ) const

inline

Get the number of dofs.

Returns: N Number of dofs

◆ getNumElements()

size_t fe::Mesh::getNumElements ( ) const

inline

Get the number of elements.

Returns: N Number of elements

Referenced by model::Output::Output().

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◆ getNumNodes()

size_t fe::Mesh::getNumNodes ( ) const

inline

Get the number of nodes.

Returns: N number of nodes

Referenced by loading::InitialCondition::apply(), tools::pp::Compute::Compute(), geometry::DampingGeom::computeDampingCoefficient(), geometry::DampingGeom::DampingGeom(), loading::FLoading::FLoading(), model::Output::Output(), and loading::ULoading::ULoading().

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◆ getPrescribedNodes()

const std::vector<size_t> fe::Mesh::getPrescribedNodes ( ) const

inline

Get the vector of indicies with prescribed values from the couplign method.

Returns: Vector with the indicies

Referenced by loading::ULoading::ULoading().

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◆ getPrescribedValues()

const std::vector<util::Point3> fe::Mesh::getPrescribedValues ( ) const

inline

Get the vector of values of the prescribed nodes from the couplign method.

Returns: Vector with the prescribed values

Referenced by loading::ULoading::apply().

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◆ isNodeFree()

bool fe::Mesh::isNodeFree	(	const size_t &	i,
		const unsigned int &	dof
	)		const

inline

Return true if node is free.

Parameters

i	Id of node
dof	Dof to check for

Returns: bool True if dof is free else false

Referenced by loading::InitialCondition::apply().

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◆ print()

void fe::Mesh::print	(	int	nt = `0`,
		int	lvl = `0`
	)		const

inline

Prints the information about the instance of the object.

Parameters

nt	Number of tabs to append before each line of string
lvl	Level of information sought (higher level means more information)

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◆ printStr()

std::string fe::Mesh::printStr	(	int	nt = `0`,
		int	lvl = `0`
	)		const

Returns the string containing information about the instance of the object.

Parameters

nt	Number of tabs to append before each line of string
lvl	Level of information sought (higher level means more information)

Returns: string String containing information about this object

Referenced by print().

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◆ readFromFile()

void fe::Mesh::readFromFile	(	inp::MeshDeck *	deck,
		const std::string &	filename
	)

Reads mesh data from the file and populates other data.

Parameters

deck	Mesh deck
filename	Name of the mesh file

◆ setFixity() [1/2]

void fe::Mesh::setFixity	(	const size_t &	i,
		const unsigned int &	dof,
		const bool &	flag
	)

Set the fixity to free (0) or fixed (1)

Parameters

i	Id of node
dof	Dof which is affected
flag	Set fixity to fixed if true or free

◆ setFixity() [2/2]

void fe::Mesh::setFixity ( std::vector< uint8_t > & fixity )

Set nodal fixity masks.

Parameters

fixity Reference to fixity of all nodes

Referenced by loading::ULoading::ULoading().

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◆ setMeshData()

void fe::Mesh::setMeshData	(	const size_t &	dim,
		std::vector< util::Point3 > &	nodes,
		std::vector< double > &	volumes
	)

Set the mesh data for finite difference simulations.

Parameters

dim	Dimension
nodes	Reference to nodes reference configuration
volumes	Reference to nodal volumes

◆ setMeshSize()

void fe::Mesh::setMeshSize ( const double & h )

Set the mesh size.

Parameters

h Mesh size

◆ setNodalVolumes()

void fe::Mesh::setNodalVolumes ( std::vector< double > & volumes )

Set the nodal volume data of the mesh.

Parameters

volumes Reference to nodal volumes

◆ setNodes()

void fe::Mesh::setNodes ( std::vector< util::Point3 > & nodes )

Set the nodal data of the mesh.

Parameters

nodes Reference to nodes reference configuration

Field Documentation

◆ d_bbox

std::pair<std::vector<double>, std::vector<double> > fe::Mesh::d_bbox

private

Bounding box.

Returns: (xmin,ymin,zmin) and (xmax,ymax,zmax)

Referenced by getBoundingBox().

◆ d_enc

std::vector<size_t> fe::Mesh::d_enc

private

Element-node connectivity data.

Structure: First d_eNumVertex data gives the connectivity of first element, and next d_eNumVertex data gives the connectivity of second element and so on and so fourth.

Referenced by getElementConnectivities(), getElementConnectivitiesP(), getElementConnectivity(), getElementConnectivityNodes(), and getNumElements().

◆ d_eNumVertex

size_t fe::Mesh::d_eNumVertex

private

Number of vertex per element.

This information is useful in getting the connectivity for a given element. We assume that the mesh has only one type of elements and based on that assumption we store the element-node connectivity in a single vector.

The value for different elements are

Line element: 2,
Triangle element: 3,
Quadrilateral element: 4,
Tetrahedral element: 4

Referenced by getElementConnectivity(), getElementConnectivityNodes(), and getNumElements().

◆ d_eType

size_t fe::Mesh::d_eType

private

Element type.

We follow VTK convention to identify the elements:

Line element = 3,
Triangle element = 5,
Pixel element = 8,
Quadrilateral element = 9,
Tetrahedral element = 10

Referenced by getElementType().

◆ d_fix

std::vector<uint8_t> fe::Mesh::d_fix

private

Vector of fixity mask of each node.

First bit represents x-dof, second represents y-dof, and third represents z-dof. 0 represents free dof and 1 represents fixed dof.

We store data in uint8_t type which can hold 8 bit. At present we only use first 3 bits.

Referenced by getFixity(), getFixityP(), and isNodeFree().

◆ d_gInvMap

std::vector<int> fe::Mesh::d_gInvMap

private

Map from global id to reduced global id.

This is a inverse of d_gMap

◆ d_gMap

std::vector<size_t> fe::Mesh::d_gMap

private

Map from global reduced id to default global id.

We assign number to each free dof where number ranges from 0 to total number of free dofs. This is referred to set of global reduced id. This new set of ids are subset of set of global ids of all dofs, and therefore, "reduced" word is used.

d_gMap provides a map from global reduced id to global id.

Note: Needed only when the discretization is "weak_finite_element" for the assembly of the mass matrix.

◆ d_nec

std::vector<std::vector<size_t> > fe::Mesh::d_nec

private

Node-element connectivity data.

At present, this data is never populated.

◆ d_prescribed_nodes

std::vector<size_t> fe::Mesh::d_prescribed_nodes

private

Vector with the indicies of all nodes with prescribed boundary data.

For coupling with other codes, e.g. FEM or PUM, prescribed values for displacement or force are given by the local method and applied to these PD nodes.

Referenced by getPrescribedNodes().

◆ d_prescribed_values

std::vector<util::Point3> fe::Mesh::d_prescribed_values

private

Vector with the values of all nodes with prescribed boundary data.

For coupling with other codes, e.g. FEM or PUM, prescribed values for displacement or force are given by the local method and applied to these PD nodes.

Referenced by getPrescribedValues().

◆ d_spatialDiscretization

std::string fe::Mesh::d_spatialDiscretization

private

Tag for spatial discretization type.

List of valid values are:

finite_difference
weak_finite_element
nodal_finite_element
truss_finite_element

Referenced by Mesh().

◆ d_vol

std::vector<double> fe::Mesh::d_vol

private

Vector of volume of each node.

For uniform square mesh, the volume is simply $ h^2 $ in 2-d and $ h^3$ in 3-d, where $ h$ is the mesh size. For general mesh, the volume is computed using the element-node connectivity of the mesh.

Referenced by getNodalVolume(), getNodalVolumes(), getNodalVolumesP(), and Mesh().

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

/root/project/src/fe/mesh.h
/root/project/src/fe/mesh.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Mesh() [1/2]

◆ Mesh() [2/2]

Member Function Documentation

◆ computeMeshSize()

◆ computeVol()

◆ createData()

◆ getBoundingBox()

◆ getDimension()

◆ getElementConnectivities()

◆ getElementConnectivitiesP()

◆ getElementConnectivity()

◆ getElementConnectivityNodes()

◆ getElementType()

◆ getFixity()

◆ getFixityP()

◆ getMeshSize()

◆ getNodalVolume()

◆ getNodalVolumes()

◆ getNodalVolumesP()

◆ getNode()

◆ getNodes()

◆ getNodesP()

◆ getNumDofs()

◆ getNumElements()

◆ getNumNodes()

◆ getPrescribedNodes()

◆ getPrescribedValues()

◆ isNodeFree()

◆ print()

◆ printStr()

◆ readFromFile()

◆ setFixity() [1/2]

◆ setFixity() [2/2]

◆ setMeshData()

◆ setMeshSize()

◆ setNodalVolumes()

◆ setNodes()

Field Documentation

◆ d_bbox

◆ d_enc

◆ d_eNumVertex

◆ d_eType

◆ d_fix

◆ d_gInvMap

◆ d_gMap

◆ d_nec

◆ d_prescribed_nodes

◆ d_prescribed_values

◆ d_spatialDiscretization

◆ d_vol