Package gov.nih.mipav.model.structures

Class Voro

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.structures.Voro

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

public class Voro
extends AlgorithmBase

Voro++ Copyright (c) 2008, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: (1) Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. (2) Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. (3) Neither the name of the University of California, Lawrence Berkeley National Laboratory, U.S. Dept. of Energy nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features, functionality or performance of the source code ("Enhancements") to anyone; however, if you choose to make your Enhancements available either publicly, or directly to Lawrence Berkeley National Laboratory, without imposing a separate written license agreement for such Enhancements, then you hereby grant the following license: a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, distribute, and sublicense such enhancements or derivative works thereof, in binary and source code form. Voro++, a 3D cell-based Voronoi library (http://math.lbl.gov/voro++/) By Chris H. Rycroft (Harvard University / Lawrence Berkeley Laboratory) ================================================================ Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually, rather than computing the Voronoi tessellation as a global network of vertices and edges. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (e.g. volume, centroid, number of faces) can be used to analyze a system of particles. Usage ===== Voro++ is released as free software through the Lawrence Berkeley National Laboratory - a detailed copyright notice is provided below, and the complete terms of the license can be found in the LICENSE file. I am very interested to hear from users of the software, so if you find this useful, please email me at chr@alum.mit.edu. Also, if you plan to publish an academic paper using this software, please consider citing one of the following publications: - Chris H. Rycroft, "Voro++: A three-dimensional Voronoi cell library in C++", Chaos 19, 041111 (2009). - Chris H. Rycroft, Gary S. Grest, James W. Landry, and Martin Z. Bazant, "Analysis of Granular Flow in a Pebble-Bed Nuclear Reactor", Phys. Rev. E 74, 021306 (2006). - Chris H. Rycroft, "Multiscale Modeling in Granular Flow", PhD thesis submitted to the Massachusetts Institute of Technology, September 2007. (http://seas.harvard.edu/~chr/publish/phd.html) The first reference contains a one-page overview of the library. The second reference contains some of the initial images that were made using a very early version of this code, to track small changes in packing fraction in a large particle simulation. The third reference discusses the use of 3D Voronoi cells, and describes the algorithms that were employed in the early version of this code. Since the publication of the above references, the algorithms in Voro++ have been significantly improved.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) static enum	Voro.blocks_mode
(package private) class	Voro.c_loop_all	\brief Class for looping over all of the particles in a container.
(package private) class	Voro.c_loop_all_periodic	\brief A class for looping over all particles in a container_periodic or container_periodic_poly class.
(package private) class	Voro.c_loop_base	\brief Base class for looping over particles in a container.
(package private) class	Voro.c_loop_order	\brief Class for looping over all of the particles specified in a pre-assembled particle_order class.
(package private) class	Voro.c_loop_order_periodic	\brief Class for looping over all of the particles specified in a pre-assembled particle_order class, for use with container_periodic classes.
(package private) class	Voro.c_loop_subset	\brief Class for looping over a subset of particles in a container.
(package private) static enum	Voro.c_loop_subset_mode	A type associated with a c_loop_subset class, determining what type of geometrical region to loop over.
(package private) class	Voro.container_base	\brief Class for representing a particle system in a three-dimensional rectangular box.
(package private) class	Voro.container_periodic_base	\brief Class for representing a particle system in a 3D periodic non-orthogonal periodic domain.
(package private) class	Voro.container_periodic_poly_radius_poly	\brief Extension of the container_periodic_base class for computing radical Voronoi tessellations.
(package private) class	Voro.container_periodic_radius_mono	\brief Extension of the container_periodic_base class for computing regular Voronoi tessellations.
(package private) class	Voro.container_poly_radius_poly	\brief Class containing all of the routines that are specific to computing the radical Voronoi tessellation.
(package private) class	Voro.container_radius_mono	\brief Extension of the container_base class for computing regular Voronoi tessellations.
(package private) class	Voro.dodecahedron_initial_shape
(package private) class	Voro.particle_order	\brief A class for storing ordering information when particles are added to a container.
(package private) class	Voro.particle_record	\brief Structure for holding information about a particle.
(package private) class	Voro.pre_container	\brief A class for storing an arbitrary number of particles without radius information, prior to setting up a container geometry.
(package private) class	Voro.pre_container_base	\brief A class for storing an arbitrary number of particles, prior to setting up a container geometry.
(package private) class	Voro.pre_container_poly	\brief A class for storing an arbitrary number of particles with radius information, prior to setting up a container geometry.
(package private) class	Voro.unitcell	\brief Class for computation of the unit Voronoi cell associated with a 3D non-rectangular periodic domain.
(package private) class	Voro.voro_base_unitcell
(package private) class	Voro.voro_base_wall_list	\brief A class for storing a list of pointers to walls.
(package private) class	Voro.voro_compute_container_periodic_poly_radius_poly	\brief Template for carrying out Voronoi cell computations.
(package private) class	Voro.voro_compute_container_periodic_radius_mono
(package private) class	Voro.voro_compute_container_poly_radius_poly	\brief Template for carrying out Voronoi cell computations.
(package private) class	Voro.voro_compute_container_radius_mono	\brief Template for carrying out Voronoi cell computations.
(package private) class	Voro.voronoicell	\brief Extension of the voronoicell_base class to represent a Voronoi cell without neighbor information.
(package private) class	Voro.voronoicell_base	\brief A class representing a single Voronoi cell.
(package private) class	Voro.voronoicell_neighbor	\brief Extension of the voronoicell_base class to represent a Voronoi cell with neighbor information.
(package private) class	Voro.wall	\brief Pure virtual class from which wall objects are derived.
(package private) class	Voro.wall_cone	\brief A class representing a conical wall object.
(package private) class	Voro.wall_cylinder	\brief A class representing a cylindrical wall object.
(package private) class	Voro.wall_cylinder_inv
(package private) class	Voro.wall_ellipsoid
(package private) class	Voro.wall_initial_shape
(package private) class	Voro.wall_l_shape
(package private) class	Voro.wall_plane	\brief A class representing a plane wall object.
(package private) class	Voro.wall_shell
(package private) class	Voro.wall_sphere	\brief A class representing a spherical wall object.
(package private) class	Voro.wall_torus

Nested classes/interfaces inherited from class java.lang.Thread

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
(package private) double	ax
(package private) double	ay
(package private) double	az
(package private) final double	big_tolerance_fac
(package private) Voro.blocks_mode	bm
(package private) double	bx
(package private) double	by
(package private) double	bz
(package private) double[]	cow0
(package private) double[]	cow1
(package private) double[]	cow2
(package private) double[]	cow3
(package private) double[]	cow4
(package private) double[]	cow5
(package private) double[]	cow6
(package private) char[]	custom_output
(package private) double[]	cyw0
(package private) double[]	cyw1
(package private) double[]	cyw2
(package private) double[]	cyw3
(package private) double[]	cyw4
(package private) double[]	cyw5
(package private) double[]	cyw6
(package private) final double	default_length
(package private) final double	default_radius	A radius to use as a placeholder when no other information is available.
(package private) final double	epsilon
(package private) String	fileNameBase
(package private) boolean	gnuplot_output
(package private) boolean	hc
(package private) boolean	help
(package private) final int	init_3_vertices	The initial memory allocation for the number of regular vertices of order 3.
(package private) final int	init_chunk_size	The initial size of the pre_container chunk index.
(package private) final int	init_delete_size	The initial size for the delete stack.
(package private) final int	init_delete2_size	The initial size for the auxiliary delete stack.
(package private) int	init_mem
(package private) final int	init_n_vertices	The initial memory allocation for the number of vertices of higher order.
(package private) final int	init_ordering_size	The default initial size for the ordering class.
(package private) final int	init_vertex_order	The initial memory allocation for the maximum vertex order.
(package private) final int	init_vertices	The initial memory allocation for the number of vertices.
(package private) final int	init_wall_size	The initial size for the wall pointer array.
(package private) final int	init_xsearch_size	The initial size for the extra search stack.
(package private) final double	large_number	A large number that is used in the computation.
(package private) double	ls
(package private) final int	max_chunk_size	The maximum size for the pre_container chunk index.
(package private) final int	max_delete_size	The maximum size for the delete stack.
(package private) final int	max_delete2_size	The maximum size for the auxiliary delete stack.
(package private) final int	max_n_vertices	The maximum memory allocation for the any particular order of vertex.
(package private) final int	max_ordering_size	The maximum size for the ordering class.
(package private) final int	max_particle_memory	The maximum amount of particle memory allocated for a single region.
(package private) final int	max_regions
(package private) final int	max_unit_voro_shells	The maximum number of shells of periodic images to test over.
(package private) final int	max_vertex_order	The maximum memory allocation for the maximum vertex order.
(package private) final int	max_vertices	The maximum memory allocation for the number of vertices.
(package private) final int	max_wall_size	The maximum size for the wall pointer array.
(package private) final int	max_xsearch_size	The maximum size for the extra search stack.
(package private) int	numberConeWall
(package private) int	numberCylinderWall
(package private) int	numberPlaneWall
(package private) int	numberRectangularBox
(package private) int	numberSphereWall
(package private) int[]	nx
(package private) int[]	ny
(package private) int[]	nz
(package private) final double	optimal_particles	A guess for the optimal number of particles per block, used to set up the container grid.
(package private) boolean	ordered
(package private) boolean	polydisperse
(package private) boolean	povp_output
(package private) boolean	povv_output
(package private) final int	pre_container_chunk_size	The chunk size in the pre_container classes.
(package private) double[]	pw0
(package private) double[]	pw1
(package private) double[]	pw2
(package private) double[]	pw3
(package private) double[]	rbw0
(package private) double[]	rbw1
(package private) double[]	rbw2
(package private) double[]	rbw3
(package private) double[]	rbw4
(package private) double[]	rbw5
(package private) double[]	sw0
(package private) double[]	sw1
(package private) double[]	sw2
(package private) double[]	sw3
(package private) final double	tolerance	If a point is within this distance of a cutting plane, then the code assumes that point exactly lies on the plane.
(package private) boolean	verbose
(package private) boolean	version
(package private) final int	VOROPP_CMD_LINE_ERROR	Voro++ returns this status code if it could not interpret the command line arguments passed to the command line utility.
(package private) final int	VOROPP_FILE_ERROR	Voro++ returns this status code if there is a file-related error, such as not being able to open file.
(package private) final int	VOROPP_INTERNAL_ERROR	Voro++ returns this status code if there is any type of internal error, if it detects that representation of the Voronoi cell is inconsistent.
(package private) final int	VOROPP_MEMORY_ERROR	Voro++ returns this status code if there is a memory allocation error, if one of the safe memory limits is exceeded.
(package private) final int	VOROPP_REPORT_OUT_OF_BOUNDS	If this is set to 1, then the code reports any instances of particles being put outside of the container geometry.
(package private) final int	VOROPP_VERBOSE	Voro++ can print a number of different status and debugging messages to notify the user of special behavior, and this macro sets the amount which are displayed.
(package private) final int[]	wl	\file v_base_wl.cc \brief The table of block worklists that are used during the cell computation, which is part of the voro_base class.
(package private) final int	wl_fgrid	The number of subregions that a block is subdivided into, which is twice the value of hgrid.
(package private) final int	wl_hgrid	Each region is divided into a grid of subregions, and a worklist is # finalructed for each.
(package private) final int	wl_hgridcu	The total number of worklists, set to the cube of hgrid.
(package private) final int	wl_seq_length	The number of elements in each worklist.
(package private) boolean	xperiodic
(package private) boolean	yperiodic
(package private) boolean	zperiodic

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

destFlag, destImage, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, srcImage, threadStopped

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
Voro()
Voro(boolean help, boolean hc, boolean version, char[] custom_output, boolean gnuplot_output, Voro.blocks_mode bm, double ls, int init_mem, int[] nx, int[] ny, int[] nz, boolean ordered, boolean xperiodic, boolean yperiodic, boolean zperiodic, boolean polydisperse, boolean verbose, int numberRectangularBox, double[] rbw0, double[] rbw1, double[] rbw2, double[] rbw3, double[] rbw4, double[] rbw5, int numberSphereWall, double[] sw0, double[] sw1, double[] sw2, double[] sw3, int numberPlaneWall, double[] pw0, double[] pw1, double[] pw2, double[] pw3, int numberCylinderWall, double[] cyw0, double[] cyw1, double[] cyw2, double[] cyw3, double[] cyw4, double[] cyw5, double[] cyw6, int numberConeWall, double[] cow0, double[] cow1, double[] cow2, double[] cow3, double[] cow4, double[] cow5, double[] cow6, boolean povp_output, boolean povv_output, double ax, double bx, double ay, double by, double az, double bz, String fileNameBase)

Method Summary

Modifier and Type	Method	Description
void	box_cut()
(package private) static double	calculate_solid_angle(double[] R1, int R1offset, double[] R2, int R2offset, double[] R3, int R3offset)
(package private) static double	calculate_solid_angle(Vector<Double> R1, int R1offset, Vector<Double> R2, int R2offset, Vector<Double> R3, int R3offset)
void	cell_statistics()
(package private) void	check_duplicate(int n, double x, double y, double z, int id, double[] qp)
(package private) void	cmd_line_output(Voro.c_loop_all vl, Voro.container_poly_radius_poly con, char[] format, RandomAccessFile outfile, RandomAccessFile gnu_file, RandomAccessFile povp_file, RandomAccessFile povv_file, boolean verbose, double[] vol, int[] vcc, int[] tp)
(package private) void	cmd_line_output(Voro.c_loop_all vl, Voro.container_radius_mono con, char[] format, RandomAccessFile outfile, RandomAccessFile gnu_file, RandomAccessFile povp_file, RandomAccessFile povv_file, boolean verbose, double[] vol, int[] vcc, int[] tp)
(package private) void	cmd_line_output(Voro.c_loop_order vl, Voro.container_poly_radius_poly con, char[] format, RandomAccessFile outfile, RandomAccessFile gnu_file, RandomAccessFile povp_file, RandomAccessFile povv_file, boolean verbose, double[] vol, int[] vcc, int[] tp)
(package private) void	cmd_line_output(Voro.c_loop_order vl, Voro.container_radius_mono con, char[] format, RandomAccessFile outfile, RandomAccessFile gnu_file, RandomAccessFile povp_file, RandomAccessFile povv_file, boolean verbose, double[] vol, int[] vcc, int[] tp)
void	convex_test()
(package private) static void	cross_product(double[] a, int aoffset, double[] b, int boffset, double[] c)
(package private) static void	cross_product(Vector<Double> a, int aoffset, Vector<Double> b, int boffset, Vector<Double> c)
void	custom_output()
(package private) void	custom_output_message()
void	cut_region()
void	cylinder()
void	cylinder_inv()
void	degenerate()
void	degenerate2()
(package private) static double	dot_product(double[] a, int aoffset, double[] b, int boffset)
(package private) static double	dot_product(Vector<Double> a, int aoffset, Vector<Double> b, int boffset)
(package private) void	draw_polygon(RandomAccessFile fp, Vector<Integer> f_vert, Vector<Double> v, int j)
void	ellipsoid()
(package private) void	error_message()
void	find_voro_cell()
void	finite_sys()
void	frustrum()
void	ghost_test()
boolean	has_dodec_sides(Vector<Integer> vi)
(package private) void	help_message()
void	I_shape()
void	import_nguyen()
void	import_rahman()
void	importList()
void	irregular()
void	lloyd_box()
void	loops()
void	minkowski()
void	neigh_test()
(package private) static void	normalize_vector(double[] x, int xoffset, double[] normalized, int normoffset)
(package private) static void	normalize_vector(double[] x, int xoffset, Vector normalized, int normoffset)
void	odd_even()
void	period()
void	platonic()
void	polycrystal_rahman()
void	polygons()
void	r_pts_interface()
void	rad_test()
void	radical()
void	random_points_10()
void	random_points_200()
void	runAlgorithm()	Actually runs the algorithm.
(package private) RandomAccessFile	safe_fopen(String filename, String mode)	\brief Opens a file and checks the operation was successful.
(package private) File	safe_fopen_file(String filename)
void	single_cell()
void	single_cell_2d()
void	sphere()
void	sphere_mesh()
void	split_cell()
void	superellipsoid()
void	tetrahedron()
void	timing_test()
void	torus()
void	tri_mesh()
(package private) static double	triple_product(double[] a, int aoffset, double[] b, int boffset, double[] c, int coffset)
(package private) static double	triple_product(Vector<Double> a, int aoffset, Vector<Double> b, int boffset, Vector<Double> c, int coffset)
(package private) void	version_message()
(package private) void	voro_fatal_error(String p, int status)	\brief Function for printing fatal error messages and exiting.
void	voro_lf()
(package private) void	voro_print_face_vertices(Vector<Integer> v, RandomAccessFile raFile)	\brief Prints a vector a face vertex information.
(package private) void	voro_print_face_vertices_stdout(Vector<Integer> v)
(package private) void	voro_print_positions(Vector<Double> v, RandomAccessFile raFile)	\brief Prints a vector of positions.
(package private) void	voro_print_positions_stdout(Vector<Double> v)
(package private) void	voro_print_vectorDouble(Vector<Double> v, RandomAccessFile raFile)	\brief Prints a vector of doubles.
(package private) void	voro_print_vectorDouble_stdout(Vector<Double> v)
(package private) void	voro_print_vectorInteger(Vector<Integer> v, RandomAccessFile raFile)	\brief Prints a vector of Integers.
(package private) void	voro_print_vectorInteger_stdout(Vector<Integer> v)

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

actionPerformed, addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, finalize, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

help

boolean help

hc

boolean hc

version

boolean version

custom_output

char[] custom_output

gnuplot_output

boolean gnuplot_output

bm

Voro.blocks_mode bm

ls

double ls

init_mem

int init_mem

nx

int[] nx

ny

int[] ny

nz

int[] nz

ordered

boolean ordered

xperiodic

boolean xperiodic

yperiodic

boolean yperiodic

zperiodic

boolean zperiodic

polydisperse

boolean polydisperse

verbose

boolean verbose

numberRectangularBox

int numberRectangularBox

rbw0

double[] rbw0

rbw1

double[] rbw1

rbw2

double[] rbw2

rbw3

double[] rbw3

rbw4

double[] rbw4

rbw5

double[] rbw5

numberSphereWall

int numberSphereWall

sw0

double[] sw0

sw1

double[] sw1

sw2

double[] sw2

sw3

double[] sw3

numberPlaneWall

int numberPlaneWall

pw0

double[] pw0

pw1

double[] pw1

pw2

double[] pw2

pw3

double[] pw3

numberCylinderWall

int numberCylinderWall

cyw0

double[] cyw0

cyw1

double[] cyw1

cyw2

double[] cyw2

cyw3

double[] cyw3

cyw4

double[] cyw4

cyw5

double[] cyw5

cyw6

double[] cyw6

numberConeWall

int numberConeWall

cow0

double[] cow0

cow1

double[] cow1

cow2

double[] cow2

cow3

double[] cow3

cow4

double[] cow4

cow5

double[] cow5

cow6

double[] cow6

povp_output

boolean povp_output

povv_output

boolean povv_output

ax

double ax

bx

double bx

ay

double ay

by

double by

az

double az

bz

double bz

fileNameBase

String fileNameBase

max_regions

final int max_regions

See Also:

• Constant Field Values

wl

final int[] wl

\file v_base_wl.cc \brief The table of block worklists that are used during the cell computation, which is part of the voro_base class. This file is automatically generated by worklist_gen.pl and it is not intended to be edited by hand.

wl_hgrid

final int wl_hgrid

Each region is divided into a grid of subregions, and a worklist is # finalructed for each. This parameter sets is set to half the number of # subregions that the block is divided into.

See Also:

• Constant Field Values

wl_fgrid

final int wl_fgrid

The number of subregions that a block is subdivided into, which is twice the value of hgrid.

See Also:

• Constant Field Values

wl_hgridcu

final int wl_hgridcu

The total number of worklists, set to the cube of hgrid.

See Also:

• Constant Field Values

wl_seq_length

final int wl_seq_length

The number of elements in each worklist.

See Also:

• Constant Field Values

init_vertices

final int init_vertices

The initial memory allocation for the number of vertices.

See Also:

• Constant Field Values

init_vertex_order

final int init_vertex_order

The initial memory allocation for the maximum vertex order.

See Also:

• Constant Field Values

init_3_vertices

final int init_3_vertices

The initial memory allocation for the number of regular vertices of order 3.

See Also:

• Constant Field Values

init_n_vertices

final int init_n_vertices

The initial memory allocation for the number of vertices of higher order.

See Also:

• Constant Field Values

init_delete_size

final int init_delete_size

The initial size for the delete stack.

See Also:

• Constant Field Values

init_delete2_size

final int init_delete2_size

The initial size for the auxiliary delete stack.

See Also:

• Constant Field Values

init_xsearch_size

final int init_xsearch_size

The initial size for the extra search stack.

See Also:

• Constant Field Values

init_wall_size

final int init_wall_size

The initial size for the wall pointer array.

See Also:

• Constant Field Values

init_ordering_size

final int init_ordering_size

The default initial size for the ordering class.

See Also:

• Constant Field Values

init_chunk_size

final int init_chunk_size

The initial size of the pre_container chunk index.

See Also:

• Constant Field Values

max_vertices

final int max_vertices

The maximum memory allocation for the number of vertices.

See Also:

• Constant Field Values

max_vertex_order

final int max_vertex_order

The maximum memory allocation for the maximum vertex order.

See Also:

• Constant Field Values

max_n_vertices

final int max_n_vertices

The maximum memory allocation for the any particular order of vertex.

See Also:

• Constant Field Values

max_delete_size

final int max_delete_size

The maximum size for the delete stack.

See Also:

• Constant Field Values

max_delete2_size

final int max_delete2_size

The maximum size for the auxiliary delete stack.

See Also:

• Constant Field Values

max_xsearch_size

final int max_xsearch_size

The maximum size for the extra search stack.

See Also:

• Constant Field Values

max_particle_memory

final int max_particle_memory

The maximum amount of particle memory allocated for a single region.

See Also:

• Constant Field Values

max_wall_size

final int max_wall_size

The maximum size for the wall pointer array.

See Also:

• Constant Field Values

max_ordering_size

final int max_ordering_size

The maximum size for the ordering class.

See Also:

• Constant Field Values

max_chunk_size

final int max_chunk_size

The maximum size for the pre_container chunk index.

See Also:

• Constant Field Values

pre_container_chunk_size

final int pre_container_chunk_size

The chunk size in the pre_container classes.

See Also:

• Constant Field Values

VOROPP_VERBOSE

final int VOROPP_VERBOSE

Voro++ can print a number of different status and debugging messages to notify the user of special behavior, and this macro sets the amount which are displayed. At level 0, no messages are printed. At level 1, messages about unusual cases during cell finalruction are printed, such as when the plane routine bails out due to floating point problems. At level 2, general messages about memory expansion are printed. At level 3, technical details about memory management are printed.

See Also:

• Constant Field Values

epsilon

final double epsilon

See Also:

• Constant Field Values

tolerance

final double tolerance

If a point is within this distance of a cutting plane, then the code assumes that point exactly lies on the plane.

See Also:

• Constant Field Values

big_tolerance_fac

final double big_tolerance_fac

See Also:

• Constant Field Values

default_length

final double default_length

See Also:

• Constant Field Values

large_number

final double large_number

A large number that is used in the computation.

See Also:

• Constant Field Values

default_radius

final double default_radius

A radius to use as a placeholder when no other information is available.

See Also:

• Constant Field Values

max_unit_voro_shells

final int max_unit_voro_shells

The maximum number of shells of periodic images to test over.

See Also:

• Constant Field Values

optimal_particles

final double optimal_particles

A guess for the optimal number of particles per block, used to set up the container grid.

See Also:

• Constant Field Values

VOROPP_REPORT_OUT_OF_BOUNDS

final int VOROPP_REPORT_OUT_OF_BOUNDS

If this is set to 1, then the code reports any instances of particles being put outside of the container geometry.

See Also:

• Constant Field Values

VOROPP_FILE_ERROR

final int VOROPP_FILE_ERROR

Voro++ returns this status code if there is a file-related error, such as not being able to open file.

See Also:

• Constant Field Values

VOROPP_MEMORY_ERROR

final int VOROPP_MEMORY_ERROR

Voro++ returns this status code if there is a memory allocation error, if one of the safe memory limits is exceeded.

See Also:

• Constant Field Values

VOROPP_INTERNAL_ERROR

final int VOROPP_INTERNAL_ERROR

Voro++ returns this status code if there is any type of internal error, if it detects that representation of the Voronoi cell is inconsistent. This status code will generally indicate a bug, and the developer should be contacted.

See Also:

• Constant Field Values

VOROPP_CMD_LINE_ERROR

final int VOROPP_CMD_LINE_ERROR

Voro++ returns this status code if it could not interpret the command line arguments passed to the command line utility.

See Also:

• Constant Field Values

Constructor Details

Voro

public Voro()

Voro

public Voro(boolean help,
 boolean hc,
 boolean version,
 char[] custom_output,
 boolean gnuplot_output,
 Voro.blocks_mode bm,
 double ls,
 int init_mem,
 int[] nx,
 int[] ny,
 int[] nz,
 boolean ordered,
 boolean xperiodic,
 boolean yperiodic,
 boolean zperiodic,
 boolean polydisperse,
 boolean verbose,
 int numberRectangularBox,
 double[] rbw0,
 double[] rbw1,
 double[] rbw2,
 double[] rbw3,
 double[] rbw4,
 double[] rbw5,
 int numberSphereWall,
 double[] sw0,
 double[] sw1,
 double[] sw2,
 double[] sw3,
 int numberPlaneWall,
 double[] pw0,
 double[] pw1,
 double[] pw2,
 double[] pw3,
 int numberCylinderWall,
 double[] cyw0,
 double[] cyw1,
 double[] cyw2,
 double[] cyw3,
 double[] cyw4,
 double[] cyw5,
 double[] cyw6,
 int numberConeWall,
 double[] cow0,
 double[] cow1,
 double[] cow2,
 double[] cow3,
 double[] cow4,
 double[] cow5,
 double[] cow6,
 boolean povp_output,
 boolean povv_output,
 double ax,
 double bx,
 double ay,
 double by,
 double az,
 double bz,
 String fileNameBase)

Method Details

runAlgorithm

public void runAlgorithm()

Description copied from class: AlgorithmBase

Actually runs the algorithm. Implemented by inheriting algorithms.

Specified by:

runAlgorithm in class AlgorithmBase

cmd_line_output

void cmd_line_output(Voro.c_loop_order vl,
 Voro.container_poly_radius_poly con,
 char[] format,
 RandomAccessFile outfile,
 RandomAccessFile gnu_file,
 RandomAccessFile povp_file,
 RandomAccessFile povv_file,
 boolean verbose,
 double[] vol,
 int[] vcc,
 int[] tp)

cmd_line_output

void cmd_line_output(Voro.c_loop_order vl,
 Voro.container_radius_mono con,
 char[] format,
 RandomAccessFile outfile,
 RandomAccessFile gnu_file,
 RandomAccessFile povp_file,
 RandomAccessFile povv_file,
 boolean verbose,
 double[] vol,
 int[] vcc,
 int[] tp)

cmd_line_output

void cmd_line_output(Voro.c_loop_all vl,
 Voro.container_poly_radius_poly con,
 char[] format,
 RandomAccessFile outfile,
 RandomAccessFile gnu_file,
 RandomAccessFile povp_file,
 RandomAccessFile povv_file,
 boolean verbose,
 double[] vol,
 int[] vcc,
 int[] tp)

cmd_line_output

void cmd_line_output(Voro.c_loop_all vl,
 Voro.container_radius_mono con,
 char[] format,
 RandomAccessFile outfile,
 RandomAccessFile gnu_file,
 RandomAccessFile povp_file,
 RandomAccessFile povv_file,
 boolean verbose,
 double[] vol,
 int[] vcc,
 int[] tp)

help_message

void help_message()

custom_output_message

void custom_output_message()

version_message

void version_message()

error_message

void error_message()

single_cell

public void single_cell()

convex_test

public void convex_test()

platonic

public void platonic()

importList

public void importList()

cylinder

public void cylinder()

frustrum

public void frustrum()

tetrahedron

public void tetrahedron()

torus

public void torus()

cell_statistics

public void cell_statistics()

custom_output

public void custom_output()

radical

public void radical()

box_cut

public void box_cut()

cut_region

public void cut_region()

irregular

public void irregular()

I_shape

public void I_shape()

superellipsoid

public void superellipsoid()

odd_even

public void odd_even()

loops

public void loops()

draw_polygon

void draw_polygon(RandomAccessFile fp,
 Vector<Integer> f_vert,
 Vector<Double> v,
 int j)

polygons

public void polygons()

find_voro_cell

public void find_voro_cell()

cylinder_inv

public void cylinder_inv()

ellipsoid

public void ellipsoid()

has_dodec_sides

public boolean has_dodec_sides(Vector<Integer> vi)

finite_sys

public void finite_sys()

ghost_test

public void ghost_test()

import_nguyen

public void import_nguyen()

import_rahman

public void import_rahman()

lloyd_box

public void lloyd_box()

minkowski

public void minkowski()

neigh_test

public void neigh_test()

period

public void period()

polycrystal_rahman

public void polycrystal_rahman()

r_pts_interface

public void r_pts_interface()

rad_test

public void rad_test()

random_points_10

public void random_points_10()

random_points_200

public void random_points_200()

single_cell_2d

public void single_cell_2d()

sphere

public void sphere()

sphere_mesh

public void sphere_mesh()

split_cell

public void split_cell()

tri_mesh

public void tri_mesh()

voro_lf

public void voro_lf()

timing_test

public void timing_test()

degenerate

public void degenerate()

degenerate2

public void degenerate2()

check_duplicate

void check_duplicate(int n,
 double x,
 double y,
 double z,
 int id,
 double[] qp)

voro_fatal_error

void voro_fatal_error(String p,
 int status)

\brief Function for printing fatal error messages and exiting. Function for printing fatal error messages and exiting. \param[in] p a pointer to the message to print. \param[in] status the status code to return with.

voro_print_positions

void voro_print_positions(Vector<Double> v,
 RandomAccessFile raFile)

\brief Prints a vector of positions. Prints a vector of positions as bracketed triplets. \param[in] v the vector to print. \param[in] fp the file stream to print to.

voro_print_positions_stdout

void voro_print_positions_stdout(Vector<Double> v)

safe_fopen

RandomAccessFile safe_fopen(String filename,
 String mode)

\brief Opens a file and checks the operation was successful. Opens a file, and checks the return value to ensure that the operation was successful. \param[in] filename the file to open. \param[in] mode the cstdio fopen mode to use. \return The file handle.

safe_fopen_file

File safe_fopen_file(String filename)

voro_print_vectorInteger

void voro_print_vectorInteger(Vector<Integer> v,
 RandomAccessFile raFile)

\brief Prints a vector of Integers. Prints a vector of Integers. \param[in] v the vector to print. \param[in] fp the file stream to print to.

voro_print_vectorInteger_stdout

void voro_print_vectorInteger_stdout(Vector<Integer> v)

voro_print_vectorDouble

void voro_print_vectorDouble(Vector<Double> v,
 RandomAccessFile raFile)

\brief Prints a vector of doubles. Prints a vector of doubles. \param[in] v the vector to print. \param[in] fp the file stream to print to.

voro_print_vectorDouble_stdout

void voro_print_vectorDouble_stdout(Vector<Double> v)

voro_print_face_vertices

void voro_print_face_vertices(Vector<Integer> v,
 RandomAccessFile raFile)

\brief Prints a vector a face vertex information. Prints a vector of face vertex information. A value is read, which corresponds to the number of vertices in the next face. The routine reads this number of values and prints them as a bracked list. This is repeated until the end of the vector is reached. \param[in] v the vector to interpret and print. \param[in] fp the file stream to print to.

voro_print_face_vertices_stdout

void voro_print_face_vertices_stdout(Vector<Integer> v)

dot_product

static double dot_product(double[] a,
 int aoffset,
 double[] b,
 int boffset)

dot_product

static double dot_product(Vector<Double> a,
 int aoffset,
 Vector<Double> b,
 int boffset)

cross_product

static void cross_product(double[] a,
 int aoffset,
 double[] b,
 int boffset,
 double[] c)

cross_product

static void cross_product(Vector<Double> a,
 int aoffset,
 Vector<Double> b,
 int boffset,
 Vector<Double> c)

triple_product

static double triple_product(double[] a,
 int aoffset,
 double[] b,
 int boffset,
 double[] c,
 int coffset)

triple_product

static double triple_product(Vector<Double> a,
 int aoffset,
 Vector<Double> b,
 int boffset,
 Vector<Double> c,
 int coffset)

normalize_vector

static void normalize_vector(double[] x,
 int xoffset,
 double[] normalized,
 int normoffset)

normalize_vector

static void normalize_vector(double[] x,
 int xoffset,
 Vector normalized,
 int normoffset)

calculate_solid_angle

static double calculate_solid_angle(double[] R1,
 int R1offset,
 double[] R2,
 int R2offset,
 double[] R3,
 int R3offset)

calculate_solid_angle

static double calculate_solid_angle(Vector<Double> R1,
 int R1offset,
 Vector<Double> R2,
 int R2offset,
 Vector<Double> R3,
 int R3offset)