Package gov.nih.mipav.model.structures

Class Voro.voronoicell

java.lang.Object

gov.nih.mipav.model.structures.Voro.voronoicell_base

gov.nih.mipav.model.structures.Voro.voronoicell

Enclosing class:

Voro

class Voro.voronoicell
extends Voro.voronoicell_base

\brief Extension of the voronoicell_base class to represent a Voronoi cell without neighbor information. This class is an extension of the voronoicell_base class, in cases when is not necessary to track the IDs of neighboring particles associated with each face of the Voronoi cell.

Field Summary

Fields inherited from class gov.nih.mipav.model.structures.Voro.voronoicell_base

big_tol, current_delete_size, current_delete2_size, current_vertex_order, current_vertices, current_xsearch_size, ed, edmep, mask, mec, mem, mep, mne, ne, nemne, nu, p, pts, q, stacke_index, stacke2_index, stacke3_index, stackp_index, stackp2_index, stackp3_index, tol, tol_cu, up

Constructor Summary

Constructors

Constructor	Description
voronoicell()
voronoicell(double max_len_sq_)
voronoicell(Voro.container_periodic_poly_radius_poly con)
voronoicell(Voro.container_periodic_radius_mono con)
voronoicell(Voro.container_poly_radius_poly con)
voronoicell(Voro.container_radius_mono con)

Method Summary

Modifier and Type	Method	Description
void	init(double xmin, double xmax, double ymin, double ymax, double zmin, double zmax)	Initializes the Voronoi cell to be rectangular box with the given dimensions.
void	init_l_shape()	Initializes an L-shaped Voronoi cell of a fixed size for testing the convexity robustness.
void	init_octahedron(double l)	Initializes the cell to be an octahedron with vertices at (l,0,0), (-l,0,0), (0,l,0), (0,-l,0), (0,0,l), and (0,0,-l).
void	init_tetrahedron(double x0, double y0, double z0, double x1, double y1, double z1, double x2, double y2, double z2, double x3, double y3, double z3)	Initializes the cell to be a tetrahedron.
private void	n_add_memory_vertices(int i)
private void	n_add_memory_vorder(int i)
private void	n_allocate(int i, int m)
private void	n_allocate_aux1(int i)
private void	n_copy(int a, int b, int c, int d)
private void	n_copy_aux1(int a, int b)
private void	n_copy_aux1_shift(int a, int b)
private void	n_copy_pointer(int a, int b)
private void	n_copy_to_aux1(int i, int m)
private void	n_neighbors(Vector<Integer> v)
private void	n_set(int a, int b, int c)
private void	n_set_aux1(int k)
private void	n_set_aux2_copy(int a, int b)
private void	n_set_pointer(int p, int n)
private void	n_set_to_aux1(int j)
private void	n_set_to_aux1_offset(int k, int m)
private void	n_set_to_aux2(int j)
private void	n_switch_to_aux1(int i)
boolean	nplane(double x, double y, double z, double rsq, int p_id)	Cuts a Voronoi cell using by the plane corresponding to the perpendicular bisector of a particle.
boolean	nplane(double x, double y, double z, int p_id)	Cuts a Voronoi cell using by the plane corresponding to the perpendicular bisector of a particle.
void	operatorEquals(Voro.voronoicell c)	Copies the information from another voronoicell class into this class, extending memory allocation if necessary.
boolean	plane(double x, double y, double z)	Cuts a Voronoi cell using by the plane corresponding to the perpendicular bisector of a particle.
boolean	plane(double x, double y, double z, double rsq)	Cuts a Voronoi cell using by the plane corresponding to the perpendicular bisector of a particle.

Methods inherited from class gov.nih.mipav.model.structures.Voro.voronoicell_base

centroid, check_duplicates, check_memory_for_copy, check_memory_for_copy, check_relations, construct_relations, copy, cycle_down, cycle_up, delete, draw_gnuplot, draw_gnuplot, draw_pov, draw_pov, draw_pov_mesh, draw_pov_mesh, edc, face_areas, face_freq_table, face_orders, face_perimeters, face_vertices, init_base, init_octahedron_base, init_tetrahedron_base, max_radius_squared, minkowski, neighbors, normals, nplane, nplane, number_of_edges, number_of_faces, output_custom, output_custom, output_face_areas, output_face_areas, output_face_freq_table, output_face_freq_table, output_face_orders, output_face_orders, output_face_perimeters, output_face_perimeters, output_face_vertices, output_face_vertices, output_normals, output_normals, output_solid_angles, output_vertex_orders, output_vertex_orders, output_vertices, output_vertices, output_vertices, plane_intersects, plane_intersects_guess, print_edges, reset_edges, solid_angles, surface_area, total_edge_distance, translate, vertex_orders, vertices, vertices, volume

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

voronoicell

public voronoicell()

voronoicell

public voronoicell(double max_len_sq_)

voronoicell

public voronoicell(Voro.container_radius_mono con)

voronoicell

public voronoicell(Voro.container_periodic_radius_mono con)

voronoicell

public voronoicell(Voro.container_poly_radius_poly con)

voronoicell

public voronoicell(Voro.container_periodic_poly_radius_poly con)

Method Details

operatorEquals

public void operatorEquals(Voro.voronoicell c)

Copies the information from another voronoicell class into this class, extending memory allocation if necessary. \param[in] c the class to copy.

nplane

public boolean nplane(double x,
 double y,
 double z,
 double rsq,
 int p_id)

Cuts a Voronoi cell using by the plane corresponding to the perpendicular bisector of a particle. \param[in] (x,y,z) the position of the particle. \param[in] rsq the modulus squared of the vector. \param[in] p_id the plane ID, ignored for this case where no neighbor tracking is enabled. \return False if the plane cut deleted the cell entirely, true otherwise.

nplane

public boolean nplane(double x,
 double y,
 double z,
 int p_id)

Cuts a Voronoi cell using by the plane corresponding to the perpendicular bisector of a particle. \param[in] (x,y,z) the position of the particle. \param[in] p_id the plane ID, ignored for this case where no neighbor tracking is enabled. \return False if the plane cut deleted the cell entirely, true otherwise.

plane

public boolean plane(double x,
 double y,
 double z,
 double rsq)

Cuts a Voronoi cell using by the plane corresponding to the perpendicular bisector of a particle. \param[in] (x,y,z) the position of the particle. \param[in] rsq the modulus squared of the vector. \return False if the plane cut deleted the cell entirely, true otherwise.

plane

public boolean plane(double x,
 double y,
 double z)

Cuts a Voronoi cell using by the plane corresponding to the perpendicular bisector of a particle. \param[in] (x,y,z) the position of the particle. \return False if the plane cut deleted the cell entirely, true otherwise.

init

public void init(double xmin,
 double xmax,
 double ymin,
 double ymax,
 double zmin,
 double zmax)

Initializes the Voronoi cell to be rectangular box with the given dimensions. \param[in] (xmin,xmax) the minimum and maximum x coordinates. \param[in] (ymin,ymax) the minimum and maximum y coordinates. \param[in] (zmin,zmax) the minimum and maximum z coordinates.

init_octahedron

public void init_octahedron(double l)

Initializes the cell to be an octahedron with vertices at (l,0,0), (-l,0,0), (0,l,0), (0,-l,0), (0,0,l), and (0,0,-l). \param[in] l a parameter setting the size of the octahedron.

init_tetrahedron

public void init_tetrahedron(double x0,
 double y0,
 double z0,
 double x1,
 double y1,
 double z1,
 double x2,
 double y2,
 double z2,
 double x3,
 double y3,
 double z3)

Initializes the cell to be a tetrahedron. \param[in] (x0,y0,z0) the coordinates of the first vertex. \param[in] (x1,y1,z1) the coordinates of the second vertex. \param[in] (x2,y2,z2) the coordinates of the third vertex. \param[in] (x3,y3,z3) the coordinates of the fourth vertex.

init_l_shape

public void init_l_shape()

Initializes an L-shaped Voronoi cell of a fixed size for testing the convexity robustness.

n_allocate

private void n_allocate(int i,
 int m)

n_add_memory_vertices

private void n_add_memory_vertices(int i)

n_add_memory_vorder

private void n_add_memory_vorder(int i)

n_set_pointer

private void n_set_pointer(int p,
 int n)

n_copy

private void n_copy(int a,
 int b,
 int c,
 int d)

n_set

private void n_set(int a,
 int b,
 int c)

n_set_aux1

private void n_set_aux1(int k)

n_copy_aux1

private void n_copy_aux1(int a,
 int b)

n_copy_aux1_shift

private void n_copy_aux1_shift(int a,
 int b)

n_set_aux2_copy

private void n_set_aux2_copy(int a,
 int b)

n_copy_pointer

private void n_copy_pointer(int a,
 int b)

n_set_to_aux1

private void n_set_to_aux1(int j)

n_set_to_aux2

private void n_set_to_aux2(int j)

n_allocate_aux1

private void n_allocate_aux1(int i)

n_switch_to_aux1

private void n_switch_to_aux1(int i)

n_copy_to_aux1

private void n_copy_to_aux1(int i,
 int m)

n_set_to_aux1_offset

private void n_set_to_aux1_offset(int k,
 int m)

n_neighbors

private void n_neighbors(Vector<Integer> v)