3 * Fixed an error in the check_facets diagnostic routine. Thanks to Tristan
4 Carrier-Baudouin (Université catholique de Louvain) for pointing this out.
5 * More changes for older MS Visual C++ compatability
7 Version 0.4.4 (January 17th 2012)
8 =================================
9 * Fixed an error in pointer arithmetic that was introduced in version 0.4,
10 which would occur in cases where the delete stack was extended when a large
11 number of vertices were being removed. Thanks to Jeff Johnson (Lawrence
12 Berkeley Laboratory) and Matt Freeman (Texas A&M University) for pointing
15 Version 0.4.3 (November 12th 2011)
16 ==================================
17 * Removed spurious Gnuplot output line from torus.cc example
18 * More changes for better Visual C++ compatibility
19 * Fixed indexing error in worklist generation routine. This had no effect
20 on the generated worklists, but would become apparent in other situations.
21 * Added rad_option.hh to the list of files included by voro++.hh for
23 * Fix errors in Gnuplot commands in the basic examples README file. Thanks to
24 William-Fernando Oquendo (National University of Colombia) for pointing this
26 * Fixed memory allocation issue in face_freq_table routine - thanks to Lingti
27 Kong for pointing this out
28 * Minor cleanups and optimizations to wall classes
30 Version 0.4.2 (September 23rd 2011)
31 ===================================
32 * Fixed a bug in the put_remap routine where a z periodic boolean was
33 switched to an x periodic boolean. This would only be noticed when using
34 mixed periodic boundary conditions and importing particles that need to be
36 * The pid function in the c_loop_base class was mistakenly labeled as double
37 instead of int - this is now fixed. Thanks to William-Fernando Oquendo
38 (National University of Colombia) for pointing this out.
39 * Fixed an extremely subtle bounds checking issue that would only materialize
40 for the radical Voronoi tessellation with large particle radii. Thanks to
41 Richard Martin and Maciej Haranczyk (Lawrence Berkeley Laboratory) for
42 pointing out the original problem.
43 * Fixed other problems with the radical tessellation. Originally, the
44 algorithms were concieved for with hard spheres in mind, where the particles
45 would not overlap, and an assumption was used in the cutoff procedure that
46 made use of this, but would not be true in general.
47 * Removed more bracket initializations like "double a(3);" for better
48 consistency, and more compatibility with older versions of MS Visual C++.
49 Thanks to Martin Brehm for help with this.
50 * Factored out the regular/radical inline routines into separate classes, so
51 that they don't have to be duplicated in the container_periodic classes
52 * Fixed problems with the container_periodic classes referencing the wrong
53 loop classes. Thanks to Wang Chuncheng (Nanyang Technological University) for
55 * Added c_loop_order_periodic class for doing ordered loops with the periodic
57 * Updated the README file in the src directory. The detailed description of
58 each file has been removed since this is difficult to maintain and this
59 information is already present in the class reference manual.
60 * Fixed an error in the pre_container selection of the optimal computational
62 * Code comment cleanups, particularly in wall.hh
63 * Minor man page reformatting
64 * Updated Doxyfile to version 1.7.5.1
66 Version 0.4.1 (September 7th 2011)
67 ==================================
68 * Fixed bug in command-line utility that would give incorrect results when
69 using the "-c" option for custom output. Thanks to Prof. Aldo Romero
70 (CINVESTAV-Unidad Queretaro) for pointing this out.
71 * Added some additional documentation about neighbor information
73 Version 0.4 (August 30th 2011)
74 ==============================
75 * New classes called container_periodic and container_periodic_poly that carry
76 out Voronoi computations in 3D periodic parallelepiped unit cells have been
77 added. This adds significant complexity to the computation, and the memory
78 organization of these classes is different, requiring allocation for ghost
79 regions. Currently these classes cannot be accessed by the command-line
80 utility, but will be integrated further in future releases. These classes are
81 currently mainly exploited by a sister software project Zeo++ for chemical
82 informatics (Maciej Haranczyk, Chris Rycroft, Thomas Willems, Richard Martin)
83 to be released in late 2011.
84 * As part of the new container_periodic classes, a new class called unitcell
85 has been added, which will compute the Voronoi cell for a single particle in
86 a 3D periodic parallelepiped class. The Voronoi cell is formed by the
87 influences of the periodic images of itself only. This turns out to be an
88 important component of the calculations done by the container_periodic
89 classes but can also be used independently.
90 * The container classes now have a routine called find_voronoi_cell that will
91 take a given position vector and return the Voronoi cell which is contained
92 within. For the regular Voronoi tessellation, this is just the Voronoi cell
93 corresponding to the closest particle (by definition). For the radical
94 Voronoi tessellation, this is weighted by the particle radii.
95 * The library is now enclosed within the "voro" namespace. This requires
96 specifying "using namespace voro;" in the preamble of codes or prepending
97 "voro::" to access functions. This greatly minimizes the possiblity of naming
98 conflicts when using multiple libraries, particularly since many of the
99 classes iin the library have fairly generic names (eg. "container"). Thanks to
100 Allan Johns (Dr. D Studios) for suggesting this.
101 * Voro++ can now be built as a static library that can be installed and linked
102 to. As part of this, the .cc and .hh files have been significantly revised
103 with some small inline functions and template code being written into the
105 * Previously, all of the voronoicell output routines sent data to an output
106 stream. However, input and output are now carried out using the STL vector
107 class, allowing for programs to directly link to and use Voro++ output. The
108 STL vector class has been chosen since it the simplest and most standard
109 mechanism for returning a variable amount of data. Several new examples are
110 provided to demonstrate this functionality, for both the voronoicell class
111 and the container class.
112 * A common issue has been that the order of particles in the output file does
113 not match the input file, since Voro++ internally sorts particles according
114 to their position. A new class called voro_order has been provided, which can
115 link to particles as they are stored, allowing for the Voronoi computation to
116 be carried out in the same order as the input file. The core computation
117 routines can be run with a variety of different loops, and a new example
118 "loops.cc" is provided to demonstrate this.
119 * The order of parameters to certain functions have been changed to take
120 advantage of the C++ default parameter mechanism wherever possible
121 * The container and container_poly classes are now derived from a base class,
122 rather than being different instances of a template. This simplifies the code
123 and stops common routines from being duplicated. The core Voronoi computation
124 routine is now held within a voro_compute class, which can be instantiated on
125 any container with the correct access functions.
126 * The voronoicell and voronoicell_neighbor classes are now derived from a
127 common base class, rather than being different instances of a template. This
128 simplifies the code and stops common routines from being duplicated. The core
129 nplane routine is now a function template that can be instantiated on the
131 * All output routines have been switched from using C++ iostreams to using the C
132 cstdio library. This has been done for increased performance. In general the
133 cstdio routines run significantly faster than the comparable iostream
134 routines: for one file import test, using fscanf from cstdio was five times
135 as fast as the comparable << operator from iostream. As another example,
136 the program "cylinder.cc", which uses both file import and export, runs
137 approximately twice as fast before. Since many people use Voro++ to batch
138 process large numbers of input files, this increase in input/output speed
140 * The Gnuplot output routines now merge individual lines into contiguous paths
141 wherever possible, resulting in a ~15% reduction in their file size and a
142 noticeable improvement in rendering speed
143 * Previously, the POV-Ray output routines could create cylinders where the start
144 and end points matched. This was a benign problem, due to the fact the vertex
145 positions within Voro++ were held to higher precision than the POV-Ray output
146 file, meaning that distinct vertices could appear to be at the same position;
147 a perl script was provided to post-process and remove these. However, Voro++
148 now scans each cylinder before saving to file to automatically remove these
149 cases from consideration.
150 * Pointer arithmetic is now used within a number of critical cell computation
151 routines, and gives a speedup of 10%-20% in many cases. On some typical
152 problems on typical machines, Voro++ currently computes around 50,000
153 cells/second. New machines can achieve upwards of 70,000 cells/second.
154 * A new pre-container mechanism is provided, which can read in a file of
155 unknown length, and then make a guess at the correct computational grid size
156 to use. This removes the need for specifying a length scale with the
157 command-line utility. However, a length scale or grid decomposition can still
158 be manually specified.
159 * Removed the option to compile in single-precision. This was a highly
160 specialized feature, and it appears better to allow users who wish to do this
161 to make their own modifications. This option also conflicted with building
162 Voro++ as a standard static library.
163 * Fixed a benign bug in the block computation list that would cause it to get
165 * Numerous small improvements to memory allocation routines
166 * Added routines to copy a Voronoi cell
167 * Created a new wall_list class to handle a list of walls. This simplifies the
168 command-line utility code.
169 * Labels in the worklist that are used in the transition from the radius search
170 to the block search have been optimized
171 * The command-line utility can now produce POV-Ray output. Also, the main loop
172 in the utility has been combined so that the Voronoi tessellation is only
173 carried out once, even if POV-Ray and Gnuplot output is also required.
174 * The command-line utility does range checking on the filename to prevent
176 * The routines that put particles into a container now do so more reliably for
177 periodic cases, remapping them into the primary domain if necessary
178 * A number of the POV-Ray header files have been altered to directly make use
179 of a right-handed coordinate system in which the z axis points upwards. This
180 matches the Gnuplot style, and the style used in many scientific simulations.
181 It avoids the need for a rotation or matrix transformation when rendering
182 many of the particle packings. Some of the test particle packings have been
183 transformed to ensure consistency with previous renderings.
184 * Some POV-Ray files have been cleaned up and there are additional comments
185 * Fixed a bug in the print_all_custom() routine, affecting "%P" output. Thanks
186 to David Waroquiers (Université Catholique de Louvain, Belgium) for pointing
188 * Fixed a bug that caused the neighbor list not to be outputted in the same
189 order as the other plane diagnostic routines. Thanks to Olufemi Olorode
190 (Texas A&M University) for pointing this out.
191 * Removed the add_vertex() and init_test() routines, which were mainly used for
193 * Updated Doxyfile to version 1.7.4
195 Version 0.3.1 (September 29, 2009)
196 ==================================
197 * Carried out a major overhaul of the source code comments that are used by
198 Doxygen. Several errors in the documentation were fixed.
199 * Additional comments in the Makefiles, and added the "phony target" keyword
200 * Many code cleanups and standardizations. Some double and triple loops
201 were concatenated into one to reduce the amount of indentation.
202 * Fixed the import.cc example program
203 * Updated Doxyfile to version 1.6.1
205 Version 0.3 (August 17, 2009)
206 =============================
207 * In response to feedback from several people, the routines for computing
208 statistics about computed Voronoi cells have been significantly revised,
209 extended, and put within a common framework. The voronoicell class now has a
210 large number of routines of the form output_...() that will print cell
211 information to an output stream. There are also a number of new, simple
212 routines for computing basic statistics such as the number of edges and faces
213 of each cell. All of these routines can now be used during the container
214 analysis, by making use of the new print_custom() routine, which can output
215 according to a given format string, that uses control sequences similar to
216 the standard C printf() routine.
217 * Renamed the "radical" example directory to "custom", and added two
218 new programs called "cell_statistics.cc" and "custom_output.cc" for
219 demonstrating the new output routines for the voronoicell and container
221 * Added a routine for computing the centroid of a Voronoi cell
222 * Added new routines for computing neighbor normals, in response to a
223 request from Dave Greenwood
224 * Removed unnecessary trailing tabs and spaces in the source code
225 * Fixed a few text justification problems, and altered some of the comments
226 in the example programs
227 * Improved the command-line utility, allowing it to specify custom information
228 in the output. Implemented better error checking on command-line arguments.
229 * Removed the facets() routine, since this has been superseded by the new
230 output_...() routines. This also rendered some functions in the neighbor_none
231 and neighbor_track classes obsolete, and they have also been removed.
232 * Some reorganization of the cell.hh and container.hh header files to group
233 similar functions together
234 * Added torus.cc example that shows how to write custom walls as derived
236 * Updated Doxyfile to version 1.5.9
238 Version 0.2.7 (March 25, 2009)
239 ==============================
240 * Added some missing cstdlib and cstring header files that cause compilation
241 errors on some systems
242 * Some text cleanups in the main README file and cmd_line.cc
243 * The worklist_gen.pl script was in DOS format. It has been switched to Unix
244 format to match the rest of the code.
245 * Fixed some incorrect inequalities in degenerate2.cc
246 * Improved some error messages in container.cc
248 Version 0.2.6 (March 23, 2009)
249 ==============================
250 * Significantly improved the error messages generated by the code. It now
251 makes use of the exit() routine rather than throwing errors, and it returns
252 various status codes (defined in config.hh) for different types of abnormal
254 * Changed two occurences of "cin" to "cout" in the draw_particles routines
255 * Corrected error in comment in the tetrahedron example
256 * Minor comment cleanups of the worklist_gen.pl script
257 * Updated Doxyfile to version 1.5.8
258 * Added a routine print_facet_information() in response to a problem
260 * Many of the cell based statistics routines (like number_of_faces() and
261 facets()) internally track their progress by temporarily flipping the edge
262 table entries to negative values, so that they know where they have already
263 been. The common code that was used at the end of each of these functions for
264 resetting the edges back to positive has now been made into a private inline
265 function called reset_edges().
266 * Fixed a missing initialization of max_radius to zero in the radius_poly
267 class. This should not have ever caused any errors, as max_radius would
268 always have been big enough. However if max_radius was initially set to a
269 large value, it could have potentially made the code run slower.
270 * Fixed the code layout in the suretest class header
271 * Added some additional checks in the command-line utility to screen out
272 invalid command-line arguments. Switched the test on the number of
273 computational blocks to use floating point arithmetic, because integers
274 could potentially overflow and become negative.
275 * Included several more of the POV-Ray header files that were used to create
276 the example images on the website
277 * Removed a "cout" statement in the wall_cone class
278 * Cleanup of the README files for the basic examples and the wall examples
280 Version 0.2.5 (January 1, 2009)
281 ===============================
282 * Added the DOE acknowledgements to the code overview document
284 Version 0.2.4 (December 14, 2008)
285 =================================
286 * Added the code overview PDF document to the package, in the docs directory
287 * Fixed some spelling errors in the comments
288 * Many more documentation updates
290 Version 0.2.3 (December 9, 2008)
291 ================================
292 * Removed an unused variable that was reported by the Portland C compiler
293 * Documentation updates
294 * Added the import.pov script
295 * Added some simple functions to solve the problem from Stefan Eibl of counting
297 * Renamed the facets_loop to voropp_loop
299 Version 0.2.2 (November 19, 2008)
300 =================================
301 * Main README file updated
303 Version 0.2.1 (November 3, 2008)
304 ================================
305 * Much more documentation
306 * Brief Doxygen class comments
307 * Updated Doxyfile to version 1.5.7
309 Version 0.2 (October 31, 2008)
310 ==============================
311 * Updated some occurrences of char* with const char* for compatability with
312 version 4.2 of the GNU C++ compiler
313 * Making use of default parameters in the wall classes
314 * The command-line utility can now add walls
316 Version 0.1 (August 22, 2008)
317 =============================
318 * Initial version uploaded to the web