#include <particle_mesh.h>

Inheritance diagram for libMesh::ParticleMesh< KDDim >:

Collaboration diagram for libMesh::ParticleMesh< KDDim >:

Public Member Functions
	ParticleMesh (MeshBase &mesh)

	ParticleMesh (MeshBase &mesh, const Real &search_radius_p, const Real &search_radius_e)

	ParticleMesh (MeshBase &mesh, PMPeriodicBoundary &pmpb, const Real &search_radius_p, const Real &search_radius_e)

	~ParticleMesh ()

void	read_particles_data (const std::string &filename, const std::string &particle_mesh_type)

void	read_particles_data_restart (const std::string &filename, const std::string &particle_mesh_type)

void	read_particles_data_restart (const std::string &filename, const unsigned int &o_step)

void	generate_random_particles (const std::size_t N, const Real bbox_XA, const Real bbox_XB, const Real bbox_YA, const Real bbox_YB, const Real bbox_ZA, const Real bbox_ZB)

void	generate_random_particles (const std::size_t N, const Point &bbox_min, const Point &bbox_max)

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

std::size_t	num_particles () const

bool	is_sorted () const

void	reinit ()

void	print_particle_info () 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 ()

MeshBase &	mesh ()

std::size_t	num_mesh_points () const

void	update_mesh (const std::vector< Point > &nodal_pos, const std::vector< Point > &nodal_vel)

void	zero_node_force ()

std::vector< Real >	mesh_size () const

void	volume_conservation ()

void	initial_particle_center_of_mass (std::vector< Point > &center0) const

void	write_particle (const unsigned int &step_id, const unsigned int &o_step, const Real &real_time, const std::vector< std::string > &output_file, unsigned int comm_in_rank) const

void	write_time (const unsigned int &step_id, const unsigned int &o_step, const Real &real_time, unsigned int comm_in_rank) const

void	write_particle_trajectory (const unsigned int &o_step, unsigned int comm_in_rank) const

void	write_surface_node (const unsigned int &o_step, unsigned int comm_in_rank) const

void	write_particle_mesh (const unsigned int &o_step) const

void	write_particle_mesh_restart () const

SerialMesh &	stitched_mesh ()

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

Protected Member Functions
virtual void	construct_kd_tree ()

Constructor & Destructor Documentation

template<unsigned int KDDim>

libMesh::ParticleMesh< KDDim >::ParticleMesh ( MeshBase & mesh )

template<unsigned int KDDim>

libMesh::ParticleMesh< KDDim >::ParticleMesh	(	MeshBase &	mesh,
		const Real &	search_radius_p,
		const Real &	search_radius_e
	)

template<unsigned int KDDim>

libMesh::ParticleMesh< KDDim >::ParticleMesh	(	MeshBase &	mesh,
		PMPeriodicBoundary &	pmpb,
		const Real &	search_radius_p,
		const Real &	search_radius_e
	)

template<unsigned int KDDim>

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

Member Function Documentation

template<unsigned int KDDim>

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

inline

Add periodic boundary condition

template<unsigned int KDDim>

void libMesh::ParticleMesh< 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::ParticleMesh< 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::ParticleMesh< 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 one of the particles 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::ParticleMesh< KDDim >::build_particle_neighbor_list ( )

virtual

Build the particle-particle neighbor list of particles within the search_radius_p using KD tree(logN complexity). This includes the original particle itself. 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::ParticleMesh< KDDim >::build_particle_neighbor_list_naively ( )

virtual

NOT ACTUALLY USED NOW, written only for the purpose of comparing with KD-Tree! Build the neighbor list of particles within the search radius directly! (N^2 complexity) This includes the original particle itself. NOTE that the particle list constructed from this function is not sorted!

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template<unsigned int KDDim>

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

protectedvirtual

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

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template<unsigned int KDDim>

std::map<const std::size_t, std::vector<std::size_t> > libMesh::ParticleMesh< 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

template<unsigned int KDDim>

const std::vector<std::size_t> libMesh::ParticleMesh< 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>

void libMesh::ParticleMesh< KDDim >::generate_random_particles	(	const std::size_t	N,
		const Real	bbox_XA,
		const Real	bbox_XB,
		const Real	bbox_YA,
		const Real	bbox_YB,
		const Real	bbox_ZA,
		const Real	bbox_ZB
	)

Read chromatin data (cylinder particle) from the local file. mesh_type = "surface_mesh" or "volume_mesh" Generate random particle coordinate data within the bounding box. with r = 1.0, den = 1.0;

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::generate_random_particles	(	const std::size_t	N,
		const Point &	bbox_min,
		const Point &	bbox_max
	)

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::initial_particle_center_of_mass ( std::vector< Point > & center0 ) const

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template<unsigned int KDDim>

bool libMesh::ParticleMesh< 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::ParticleMesh< 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>

MeshBase& libMesh::ParticleMesh< KDDim >::mesh ( )

inline

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template<unsigned int KDDim>

std::vector< Real > libMesh::ParticleMesh< KDDim >::mesh_size ( ) const

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template<unsigned int KDDim>

std::size_t libMesh::ParticleMesh< KDDim >::num_mesh_points ( ) const

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template<unsigned int KDDim>

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

inline

Return the total number of particles

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template<unsigned int KDDim>

std::vector<RigidParticle*> libMesh::ParticleMesh< KDDim >::particles ( ) const

inline

Return the information of particles

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template<unsigned int KDDim>

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

inline

Retrun the pointer to the periodic boundary for use

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template<unsigned int KDDim>

void libMesh::ParticleMesh< 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::ParticleMesh< KDDim >::print_particle_info ( ) const

print out the particle information

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::read_particles_data	(	const std::string &	filename,
		const std::string &	particle_mesh_type
	)

Read particle coordinate data from file mesh_type = "surface_mesh" or "volume_mesh" defaulty, we turn the "Electrostatics" off

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::read_particles_data_restart	(	const std::string &	filename,
		const std::string &	particle_mesh_type
	)

Read particle data from restart mesh files only surface mesh is allowed

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::read_particles_data_restart	(	const std::string &	filename,
		const unsigned int &	o_step
	)

Read particle data from output_surface_node_*.csv

template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::reinit ( )

Should we move this and above function to the ParticleMeshSystem??? Because we need dist-function to calculate the particle-wall force! Reinit the particle-mesh system. This includes: (1) build the particle-particle neighbor list according to search radius; (2) compute the force vectors on particles; (3) build the element-particle neighbor list according to search radius; (4) set the elem_id and proc_id for particles -— not incorporated: particle-wall repulsive force, which will be rebuilt in PMLinearSystem::reinit_particle_mesh()

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template<unsigned int KDDim>

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

Return the search radius

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template<unsigned int KDDim>

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

inline

Set the values of search radii

template<unsigned int KDDim>

SerialMesh & libMesh::ParticleMesh< KDDim >::stitched_mesh ( )

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::update_mesh	(	const std::vector< Point > &	nodal_pos,
		const std::vector< Point > &	nodal_vel
	)

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::volume_conservation ( )

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::write_particle	(	const unsigned int &	step_id,
		const unsigned int &	o_step,
		const Real &	real_time,
		const std::vector< std::string > &	output_file,
		unsigned int	comm_in_rank
	)		const

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::write_particle_mesh ( const unsigned int & o_step ) const

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::write_particle_mesh_restart ( ) const

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::write_particle_trajectory	(	const unsigned int &	o_step,
		unsigned int	comm_in_rank
	)		const

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::write_surface_node	(	const unsigned int &	o_step,
		unsigned int	comm_in_rank
	)		const

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::write_time	(	const unsigned int &	step_id,
		const unsigned int &	o_step,
		const Real &	real_time,
		unsigned int	comm_in_rank
	)		const

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template<unsigned int KDDim>

void libMesh::ParticleMesh< KDDim >::zero_node_force ( )

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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/particle_mesh.C

Public Member Functions

Protected Member Functions

Constructor & Destructor Documentation

Member Function Documentation