#include <particle_mesh.h>

Inheritance diagram for libMesh::PointMesh< KDDim >:

Collaboration diagram for libMesh::PointMesh< KDDim >:

Public Member Functions
	PointMesh (libMesh::ParticleMesh< KDDim > &particle_mesh, const Real &search_radius_p, const Real &search_radius_e)

	PointMesh (MeshBase &mesh, std::vector< PolymerChain > &polymer_chains, const Real &search_radius_p, const Real &search_radius_e)

	PointMesh (MeshBase &mesh, PolymerChain &polymer_chain, const Real &search_radius_p, const Real &search_radius_e)

	~PointMesh ()

std::vector< PointParticle * >	particles () const

PolymerChain *	polymer_chain () const

std::size_t	num_particles () const

std::size_t	num_chains () const

std::size_t	num_bonds () const

bool	is_sorted () const

const std::map< const std::size_t, std::vector< std::size_t > > &	elem_neighbor_list () const

const std::vector< std::size_t >	elem_neighbor_list (const Elem *elem)

const std::vector< std::size_t >	local_elem_neighbor_list (const Elem *elem)

virtual void	clear_kd_tree ()

virtual void	build_particle_neighbor_list (const Point &query_pt, const bool is_sorted, std::vector< std::pair< std::size_t, Real > > &IndicesDists)

virtual void	build_particle_neighbor_list ()

virtual void	build_particle_neighbor_list_naively ()

virtual void	reinit_neighbor_vector ()

virtual void	build_elem_neighbor_list (const Elem *elem, const bool is_sorted, std::vector< std::size_t > &n_list)

virtual void	build_elem_neighbor_list ()

void	reinit (const bool &with_hi, bool &neighbor_list_update_flag)

void	update_particle_mesh (ParticleMesh< KDDim > *particle_mesh) const

void	print_point_info () const

void	print_elem_neighbor_list (std::ostream &out=libMesh::out) const

void	set_search_radius (const Real rp, const Real re)

Real	search_radius (const std::string &p_e) const

void	add_periodic_boundary (PMPeriodicBoundary &_periodic_bdry)

PMPeriodicBoundary *	pm_periodic_boundary ()

void	set_bead_velocity (const std::vector< Real > &vel)

const Real &	maximum_bead_velocity () const

const Real &	minimum_bead_velocity () const

const void	write_initial_surface_node_pos () const

Protected Member Functions
virtual void	construct_kd_tree ()

Constructor & Destructor Documentation

template<unsigned int KDDim>

libMesh::PointMesh< KDDim >::PointMesh	(	libMesh::ParticleMesh< KDDim > &	particle_mesh,
		const Real &	search_radius_p,
		const Real &	search_radius_e
	)

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template<unsigned int KDDim>

libMesh::PointMesh< KDDim >::PointMesh	(	MeshBase &	mesh,
		std::vector< PolymerChain > &	polymer_chains,
		const Real &	search_radius_p,
		const Real &	search_radius_e
	)

template<unsigned int KDDim>

libMesh::PointMesh< KDDim >::PointMesh	(	MeshBase &	mesh,
		PolymerChain &	polymer_chain,
		const Real &	search_radius_p,
		const Real &	search_radius_e
	)

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template<unsigned int KDDim>

libMesh::PointMesh< KDDim >::~PointMesh ( )

Member Function Documentation

template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::add_periodic_boundary ( PMPeriodicBoundary & _periodic_bdry )

inline

Add periodic boundary condition

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::build_elem_neighbor_list	(	const Elem *	elem,
		const bool	is_sorted,
		std::vector< std::size_t > &	n_list
	)

virtual

Build the neighbor list of partilces for a given elem Output the n_list, which gives the particle ids around elem's centroid within search_radius_e.

Note we don't need the distance between particles and elem centroid here, because this list is only used to evaluate element-wise load vector due to the neighboring particles.

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::build_elem_neighbor_list ( )

virtual

FIXME: Should we build this locally and globally(by allgather)???

Build the particle neighbor list for each element within the search radius this will generate the _elem_neighbor_list and _elem_neighbor_list_vector NOTE this takes advantage of KD Tree

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::build_particle_neighbor_list	(	const Point &	query_pt,
		const bool	is_sorted,
		std::vector< std::pair< std::size_t, Real > > &	IndicesDists
	)

virtual

Build the neighbor list of a particle within the search_radius_p using KD-tree. This includes the query particle itself, if the query_pt is also in the particle list. For example, the coords of the query_pt is the same as that of a particle in the list.

IndicesDists output pair<particle_id, distance> Note we need the particle distance to compute their interaction forces.

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::build_particle_neighbor_list ( )

virtual

Build the particle-particle neighbor list for all the particles with the search_radius_p using KD tree(logN complexity).

This directly call the function above! In fact, the particle neighbor list has been built in "reinit()", so this is NOT USED!

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::build_particle_neighbor_list_naively ( )

virtual

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::clear_kd_tree ( )

virtual

Clear the KD-Tree if need Note, different from the construct_kd_tree, this is a public function.

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::construct_kd_tree ( )

protectedvirtual

Build & initialize the KD tree through nanoFlann, if needed.

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template<unsigned int KDDim>

const std::map<const std::size_t, std::vector<std::size_t> >& libMesh::PointMesh< KDDim >::elem_neighbor_list ( ) const

inline

Return the information of element neighbor list around the search radius _search_radius_e Mapping between elem id and element neighbor list of particles

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template<unsigned int KDDim>

const std::vector<std::size_t> libMesh::PointMesh< KDDim >::elem_neighbor_list ( const Elem * elem )

inline

Return the particle neighbor list around a given element around the search radius _search_radius_e

template<unsigned int KDDim>

bool libMesh::PointMesh< KDDim >::is_sorted ( ) const

inline

Check if the neighbor list is constructed sortedly

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template<unsigned int KDDim>

const std::vector<std::size_t> libMesh::PointMesh< KDDim >::local_elem_neighbor_list ( const Elem * elem )

inline

Return the particle neighbor list around a given LOCAL element around the search radius _search_radius_e

template<unsigned int KDDim>

const Real& libMesh::PointMesh< KDDim >::maximum_bead_velocity ( ) const

inline

Set rigid particle velocity vel.size() = nui Calculate maximum point particle (or rigid particle surface nodes) velocity

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template<unsigned int KDDim>

const Real& libMesh::PointMesh< KDDim >::minimum_bead_velocity ( ) const

inline

Calculate minimum point particle (or rigid particle surface nodes) velocity

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template<unsigned int KDDim>

std::size_t libMesh::PointMesh< KDDim >::num_bonds ( ) const

inline

Return the total number of bonds

template<unsigned int KDDim>

std::size_t libMesh::PointMesh< KDDim >::num_chains ( ) const

inline

template<unsigned int KDDim>

std::size_t libMesh::PointMesh< KDDim >::num_particles ( ) const

inline

Return the total number of particles

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template<unsigned int KDDim>

std::vector<PointParticle*> libMesh::PointMesh< KDDim >::particles ( ) const

inline

Generate random point data within the bounding box and write the data to a local file "random_points_data.txt" Return the information of particles

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template<unsigned int KDDim>

PMPeriodicBoundary* libMesh::PointMesh< KDDim >::pm_periodic_boundary ( )

inline

Retrun the pointer to the periodic boundary for use

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template<unsigned int KDDim>

PolymerChain* libMesh::PointMesh< KDDim >::polymer_chain ( ) const

inline

Return the information of polymer chain

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::print_elem_neighbor_list ( std::ostream & out = libMesh::out ) const

print out the element neighbor list information

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::print_point_info ( ) const

print out the particle information

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::reinit	(	const bool &	with_hi,
		bool &	neighbor_list_update_flag
	)

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::reinit_neighbor_vector ( )

virtual

reinit neighbor distance for all particles

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template<unsigned int KDDim>

Real libMesh::PointMesh< KDDim >::search_radius ( const std::string & p_e ) const

Return the search radius

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::set_bead_velocity ( const std::vector< Real > & vel )

Set particle (bead or surface node) velocity vel.size() = nui

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template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::set_search_radius	(	const Real	rp,
		const Real	re
	)

inline

Set the values of search radii

template<unsigned int KDDim>

void libMesh::PointMesh< KDDim >::update_particle_mesh ( ParticleMesh< KDDim > * particle_mesh ) const

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template<unsigned int KDDim>

const void libMesh::PointMesh< KDDim >::write_initial_surface_node_pos ( ) const

Write bead positions to csv file

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

/home/cody/copss-hydrodynamics-public/src/particle_mesh.h
/home/cody/copss-hydrodynamics-public/src/point_mesh.h
/home/cody/copss-hydrodynamics-public/src/point_mesh.C

Public Member Functions

Protected Member Functions

Constructor & Destructor Documentation

Member Function Documentation