Neper Reference Manual

The documentation for Neper 2.0.5

A software package for polycrystal generation and meshing
9 February 2016

Romain Quey

c 20032015 Romain Quey

Copyright
Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies.

Table of Contents
Conditions of Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Copying Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
User Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1

The Neper Project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

1.1.1 Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.1.2 Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.2 Installing Neper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3 Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3.1 Calling a Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3.2 Initialization File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3.3 Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3.3.1 Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1.3.3.2 Argument Separators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

3
3
3
4
5
5
5
6
6
6

Tessellation Module (-T) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

2.1

Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.1.1 Input Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.1.2 Tessellation Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.1.3 Transformation Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1.4 Crystal Orientation Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1.5 Regularization Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1.6 Filtering Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.1.7 Output Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.1.8 Post-Processing Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.1.9 Debugging Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.2 Output Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.2.1 Tessellation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.2.2 Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.3 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Meshing Module (-M) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

3.1

Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.1.1 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.1.2 Input Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.1.3 Meshing Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.1.4 Raster Tessellation Meshing Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.1.5 Mesh Cleaning Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.1.6 Mesh Partitioning Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.1.7 Field Transport Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.1.8 Output Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.1.9 Post-Processing Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.1.10 Advanced Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.2 Output Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.2.1 Mesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.2.2 Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3.3 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

19
19
19
19
21
22
22
23
23
24
25
26
26
26
26

ii

Neper 2.0.5

Visualization Module (-V) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

4.1

Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.1 Input Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.2 Tessellation Data Loading and Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.3 Mesh Data Loading and Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.4 Point Data Loading and Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.5 Coordinate System Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.6 Slice Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.7 Show Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.8 Camera Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.9 Output Image Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.1.10 Scripting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Appendix A
A.1
A.2
A.3
A.4
A.5
A.6
A.7

B.1
B.2
B.3

Expressions and Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Mathematical and Logical Expressions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Tessellation Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Raster Tessellation Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Mesh Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Point Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Rotations and Orientations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Colours . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Appendix B

30
30
30
33
37
38
38
39
41
41
42

43
43
45
45
46
46
47

File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Tessellation File (.tess) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Raster Tessellation File (.tesr) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Position File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Appendix C

Developers Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

C.1 Code Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

C.1.1 Source Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.1.2 Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.2 Contributing to Neper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.2.1 Coding Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.2.2 Adding a New Option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.2.3 Compilation Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3 Testing Module (-D) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3.1 Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3.1.1 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3.1.2 Input Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3.1.3 Testing Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
C.3.2 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

55
55
56
57
57
57
57
58
59
59
59
59
59

Appendix D

Versions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Appendix E

GNU General Public License . . . . . . . . . . . . . . . . . . . 65

Option Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

Conditions of Use

Conditions of Use
Copying Conditions
Neper is free software; this means that everyone is free to use it and to redistribute it on a
free basis. Neper is not in the public domain; it is copyrighted and there are restrictions on its
distribution, but these restrictions are designed to permit everything that a good cooperating
citizen would want to do. What is not allowed is to try to prevent others from further sharing
any version of Neper that they might get from you.
Specifically, we want to make sure that you have the right to give away copies of Neper, that
you receive source code or else can get it if you want it, that you can change Neper or use pieces
of Neper in new free programs, and that you know you can do these things.
To make sure that everyone has such rights, we have to forbid you to deprive anyone else of
these rights. For example, if you distribute copies of Neper, you must give the recipients all the
rights that you have. You must make sure that they, too, receive or can get the source code.
And you must tell them their rights.
Also, for our own protection, we must make certain that everyone finds out that there is no
warranty for Neper. If Neper is modified by someone else and passed on, we want their recipients
to know that what they have is not what we distributed, so that any problems introduced by
others will not reflect on our reputation.
The precise conditions of the license for Neper are found in the General Public License that
accompanies the source code (see Appendix E [GNU General Public License], page 65). Further
information about this license is available from the GNU Project webpage http://www.gnu.
org/copyleft/gpl-faq.html.
The Neper software package can be downloaded from http://neper.sourceforge.net. It also
has two dedicated mailing lists,
neper-announce: the read-only list for important news: new releases, bug fixes, etc. (low
traffic, highly recommended!)
To subscribe, visit https://lists.sourceforge.net/lists/listinfo/neper-announce.
The list is archived at http: / / sourceforge . net / mailarchive / forum . php ?
forum_name=neper-announce.
neper-users: the read-write list for users. Please send all questions, bug reports, requests
or any errors or omissions in this manual to this list.
To subscribe, visit https://lists.sourceforge.net/lists/listinfo/neper-users;
to send a message, use [email protected]. The list is archived at
http://sourceforge.net/mailarchive/forum.php?forum_name=neper-users.
The best way to get help is by checking out the list archives or by sending a message to the
neper-users list. There is no need to subscribe to the list to send a message nor receive a reply.

User Guidelines
If you use Neper for your own work, please,
mention it explicitly in your reports (books, papers, talks, . . . ).
cite the following paper: R. Quey, P.R. Dawson, F. Barbe. Large-scale 3D random polycrystals for the finite element method: Generation, meshing and remeshing. Computer
Methods in Applied Mechanics and Engineering, vol. 200, pp. 17291745, 2011.

Chapter 1: Introduction

1 Introduction
1.1 The Neper Project
1.1.1 Description
Neper is a software package for polycrystal generation and meshing. The polycrystals can be
1D, 2D or 3D. Neper is built around three modules,
Module -T is the module for generating polycrystals, which is carried out by tessellation of a
bounded domain of space. Several types of tessellations are available: Voronoi tessellations,
hardcore Voronoi tessellations, centroidal Voronoi tessellations, Laguerre tessellations and
regular tessellations. The tessellated domain can be cubic, cylindrical or of any other convex
shape. The tessellations can then be deformed for generating elongated cells. Crystal orientations are provided for the grains. Module -T also enables to generate 2-scale polycrystals,
which are obtained by generating tessellations into the cells of a primary tessellation. Finally, module -T includes a regularization capability to remove the small features of the
tessellations, which then enables better-quality meshing. The output is a tessellation file at
scalar or raster format.
Module -M is the module for meshing polycrystals described as tessellation files. Two capabilities are available: meshing into tetrahedral elements that conform to the tessellation
morphology or meshing into regular hexahedral elements. Tetrahedron meshing includes
features that are necessary to get good-quality meshes: optimized meshing rules and multimeshing (the concurrent use of several meshing algorithms). Remeshing is also available to
generate a new, good-quality mesh from a deformed mesh. Tetrahedron meshing of raster
tessellations works for 1D and 2D tessellations only.
Module -V is the visualization module. It enables to generate publication-quality images of
the tessellations and meshes. It is also possible to visualize data on them using colours or
displacements of the nodes (for meshes) and to plot data on slices of the mesh. The output
is a PNG image file.
Neper aims to be an easy-to-use, efficient and robust tool. All the input data are prescribed
non-interactively, using command lines and/or ASCII files. This makes it possible to automate
all treatments.

1.1.2 Resources
Several, complementary resources describing the Neper capabilities are available,
The Neper reference manual, which is the present document. It describes all the Neper
capabilities. It is made of one chapter for each module, which describes the available
commands and result files and provides some examples. The manual comes both as a PDF
file and an info file. Provided that the info file is properly installed at your site, it can be
accessed by the command: info neper.
The Neper homepage, http://neper.sourceforge.net. It is where the Neper distribution
can be downloaded from. The page also provides an introduction to Neper.
The Neper reference paper, R. Quey, P.R. Dawson and F. Barbe, Large-scale 3D random
polycrystals for the finite element method: Generation, meshing and remeshing, Comput.
Methods Appl. Mech. Engrg., vol. 200, pp. 1729-1745, 2011.. It provides details on the
algorithms. It can be downloaded from the Neper homepage or by following this link:
http://neper.sourceforge.net/docs/neper-reference-paper.pdf.

Neper 2.0.5

1.2 Installing Neper

Neper is written in (mostly ANSI) C and a very little C++. It can run on any Unix-like system.
Neper can be compiled using CMake, a standard open-source build system. The main steps are
as follows,
Create a build directory, for example as a subdirectory of Nepers src directory,
$ mkdir build
Run CMake from within the build directory, pointing to Nepers src directory,
$ cd build
$ cmake ..
To build Neper, simply type,
$ make
or, for a fast, multithreaded built,
$ make -jN
where N is the number of cores on a processor of the machine + 1.
To install Neper, type,
$ make install (as root)
This will use the default configuration options and should work out of the box on condition
that the required libraries are available and installed in standard system locations. A finer
configuration can be achieved before building Neper, as described in the following.
Neper has mandatory as well as optional dependencies. Some dependencies are managed at
compilation time,
the GSL library (mandatory)
It is likely to be available on your system or from your system package manager (binary
and development packages). Alternatively, the source code version can be obtained from
the GSL homepage, http://www.gnu.org/software/gsl.
the libmatheval library (optional, included by default)
It is likely to be available on your system or from your system package manager (binary
and development packages). Alternatively, the source code version can be obtained from
the libmatheval homepage, http://www.gnu.org/software/libmatheval.
the libScotch library (optional, not included by default)
Module -M includes mesh partitioning, which requires the libScotch library (version 5.1.12
or later). It can be downloaded from the Scotch homepage, www . labri . fr / perso /
pelegrin/scotch.
the pthread library (needed only with Scotch version >= 6.0.0, not included by default)
libScotch version 6.0.0 or later requires the pthread library. It is likely to be available on
your system or from your system package manager.
Optional dependencies can be toggled on / off using CMakes GUI (cmake-gui) or ccmake, by
setting variables HAVE_LIBRARYNAME to ON or OFF, respectively. The commands would be,
$ cmake-gui ..
or,
$ ccmake ..
The additional variables HAVE_DEBUGGING, HAVE_PROFILING and HAVE_OPTIMIZATION are
for development and should not be changed from their default values for production use (OFF,
OFF and ON, respectively); warnings are printed at Neper execution otherwise.
The following dependencies are only needed at run time,

Chapter 1: Introduction

the Gmsh program (mandatory for module -M)

This version on Neper is intended to work with Gmsh (version 2.4.2 or later), which can
be downloaded from http://www.geuz.org/gmsh. A working Gmsh installation must be
available on your system. (Compiling Gmsh from the source code provides faster meshing.)
the POV-Ray program (mandatory for module -V)
Module -V uses POV-Ray to produce publication-quality images of the tessellations and
meshes. POV-Ray can be downloaded from http://www.povray.org. POV-Ray must be
available in the terminal through the command: povray.
Finally, the Neper installation can be tested out by running a series of tests, as follows,
$ neper --test
For a proper Neper installation, all tests should pass. (The command actually is an alias for
neper -D all -runmode fast, see Appendix C [Developers Guide], page 55 for details.)

1.3 Getting Started

Using Neper consists in running the command neper in a terminal, with a list of arguments,
$ neper list_of_arguments
The arguments define the problem for Neper to solve. Neper then returns output in ASCII
files, together with some messages in the terminal. Neper includes some general-purpose selfexplanatory commands,
$ neper --help
$ neper --version
$ neper --license

1.3.1 Calling a Module

A typical Neper invocation consists in calling a module and providing it with a number of
arguments,
$ neper module_name module_arguments
The module names are -T, -M and -V. The module arguments can include both required input
data and options. Input data (when not a file name) and options start by -. The options can
be given in arbitrary order and are to be specified as follows: option_name option_argument.
Any option takes one and only one argument. The options can be written both in British English and in American English, even if only the British English versions are provided in this
manual. String completion is available for all options, so they may be abbreviated as long
as the abbreviation is not ambiguous. For example, in module -T, option -regularization
can be abbreviated to -reg. Logical options can be selected or disabled by providing as argument the value 1 or 0, respectively. For option arguments that are integer or real numbers,
mathematical or logical expressions can be used if libmatheval is available (for the list and
format of mathematical and logical expressions, see Section A.1 [Mathematical and Logical
Expressions], page 43). For example, in module -T, option -rcl 0.5 can also be written as
-rcl 1/2 or -rcl "cos(pi/3)". Options are tagged by importance level in the reference manual: [Option] or [Secondary option]. Prerequisites are tagged [Prerequisite], input data are
tagged [Input Data] and post-processing options are tagged [Post-processing]. Module -V has
some exceptions with respect to the previous rules: the argument cannot be given in arbitrary
order, string completion is not available and option -loop takes several arguments.

1.3.2 Initialization File

When Neper is started, it reads commands from an initialization file, $HOME/.neperrc, if that
file exists. Another initialization file can be specified using option --rcfile, which must be
done before calling a module,

Neper 2.0.5

$ neper --rcfile my_file module_name module_arguments

To disable the reading of an initialization file, use option --rcfile with none as value of
my_file.
When a module of Neper is called, Neper looks for the occurrence of neper module_name in
the initialization file, then reads all arguments until the subsequent occurrence of neper (which
should denote the beginning of another module option field) or the end of the file. Moreover, any
comments can be written using neper comments. The arguments may be any legal arguments,
but are typically limited to frequently-used options.
An example of initialization file is provided below,
neper comments -----------------------------------------------------This is my initialization file (~/.neperrc).
neper -T -reg 1
neper -M -gmsh my_gmsh_path
neper comments -----------------------------------------------------If the initialization file is not found, or if neper module_name is not found in the file, Neper will
only consider the command line arguments. Also note that if an argument is initialized several
times (for example, both in the initialization file and at the command line), the last specified
value is retained.

1.3.3 Conventions
1.3.3.1 Manual
The Neper documentation is maintained as a Texinfo manual. Here are the writing conventions
used in the document,
1. A command that can be typed in a terminal is printed like this, or, in the case of a major
command, like
$ this
2. a program (or command) option is printed like this;
3. The name of a variable is printed like this;
4. A meta-syntactic variable (i.e. something that stands for another piece of text) is printed
like this;
5. Literal examples are printed like this;
6. File names are printed like this.

1.3.3.2 Argument Separators

Some options may take several values, which can be combined using separators, as specified in
the option descriptions (see Chapter 2 [Tessellation Module (-T)], page 7, Chapter 3 [Meshing
Module (-M)], page 17 and Chapter 4 [Visualization Module (-V)], page 29). There actually are
two separators,
1. The , separator is used to provide several arguments with no dependency between each
other, that is, whose corresponding actions can be processed independently. For instance,
in module -T, the -format option can take argument tess,ply to get the tessellation both
in Nepers tessellation format .tess and in Ply format .ply.
2. The : separator is used to combine several arguments that show dependency between
each other, that is, whose corresponding actions cannot be processed independently. For
instance, in module -M, the meshing option -mesh3dalgo takes as argument a combination
of a meshing algorithm, mesh, and a meshing optimization algorithm, opti, under the
form mesh:opti. Optimization is applied after meshing, hence the dependency.
In module -T, the :: super-separator is used for 2-scale tessellation generation.

Chapter 2: Tessellation Module (-T)

2 Tessellation Module (-T)

Module -T enables to generate tessellations of a bounded domain of space, in 1D, 2D or 3D.
It also enables to generate 2-scale tessellations, which are tessellations for which each cell is in
turn subdivided into a tessellation. Module -T also enables to regularize the tessellations for
better-quality meshing. The tessellations are provided in scalar (vector) or raster formats.
Tessellation is achieved by using various kinds of tessellation algorithms: Voronoi tessellation,
hardcore Voronoi tessellation, centroidal Voronoi tessellation or Laguerre tessellation. This
enables to generate a wide variety of morphologies. The seeds of the cells can be distributed
randomly in the domain, which leads to random equiaxed morphology, or else so as to get
columnar, bamboo, lamellar or regular morphologies (squares in 2D and cubes or truncated
octahedra in 3D). The last possibility is to load a custom distribution of seeds. For Laguerre
tessellations, the weight distribution can be specified (option -weight). Finally, the tessellations
can be scaled to get flat or elongated cells (option -scale).
2-scale tessellations can be obtained by providing 2 levels of tessellation information to the
options using the :: separator. Moreover, different option values can be assigned to the second
scale tessellations by collecting them, prefixed by the primary tessellation cell number, in a file
loaded using @file_name (an example is provided in the Examples section).
The domain of space in which the tessellation is created can be of any convex shape. In 3D,
cuboidal, cylindrical and ellipsoidal shapes are directly supported while other morphologies can
be defined from a set of planes (option -domain). Regarding the bounded nature of the domain,
three types of tessellation can be created: standard tessellations, for which all seeds are located
inside the domain, periodic tessellations, whose cells show periodicity conditions at the domain
boundary, and subdomain-type tessellations, for which seeds can be located inside or outside
the domain (option -ttype; periodic and subdomain tessellations are only available in raster
format).
Crystal orientations are also provided for the cells. The orientations are randomly distributed
according to a uniform distribution, either in the 3D space or along a specific orientation fibre
(option -ori, which can be used in conjunction with -morpho). They can be provided according
to different descriptors (option -oridescriptor).
Regularization can be applied to the tessellations, which consists in removing their small edges
and faces (option -regularization). This is a necessary step for getting good-quality meshes
using module -M (see Chapter 3 [Meshing Module (-M)], page 17).
Output files describe the tessellation either are the scalar format .tess or raster format .tesr
(see Appendix B [File Formats], page 49). Both are input files of module -M (see Chapter 3
[Meshing Module (-M)], page 17) and module -V (see Chapter 4 [Visualization Module (-V)],
page 29). Third-party software file formats are also available.
Here is what a typical run of module -T looks like,
$ neper -T -n 10 -id 1 -reg 1
========================
N
e
p
e
r
=======================
Info
: A software package for polycrystal generation and meshing.
Info
: Version 2.0.0
Info
: Built with: gsl libmatheval
Info
: Loading initialization file /foo/bar/.neperrc...
Info
: --------------------------------------------------------------Info
: MODULE -T loaded with arguments:
Info
: [ini file]
Info
: [com line] -n 10 -id 1 -reg 1

Neper 2.0.5

Info
: --------------------------------------------------------------Info
: Reading input data...
Info
: Creating domain...
Info
: Creating tessellation...
Info
:
- Distributing seeds...
Info
:
- Running tessellation...
Info
: Regularizing tessellation...
Info
:
- loop 2/2: 100% del=14
Info
: Writing tessellation...
Info
:
[o] Writing file n10-id1.tess...
Info
:
[o] Wrote file n10-id1.tess.
Info
: Elapsed time: 0.019 secs.
========================================================================

2.1 Arguments
2.1.1 Input Data
Options are detailed below for regular, 1-scale tessellations. For 2-scale tessellations, combine
the option argument values at the 2 successive scales with ::. An example is -n 10::10.
[Input data]
Number of cells of the tessellation. The argument can be a mathematical expression based
on the vol variable, which is the volume of the domain. For regular morphologies (truncated
octahedra, etc., see option -morpho), the argument must be the number of cells along a
dimension of the domain. For lamella morphology (see option -morpho), the value of n depends on the properties of the lamella structure and so the argument must be from_morpho.
Possible values: any. Default value: none.

-n integer or char_string

[Input data]
Identifier of the tessellation. It defines the seed used by the random number generator to
compute the positions (optionally weights) of the seeds.
Possible values: any. Default value: random.

-id integer

Is it also possible to load a tessellation or a raster tessellation from a file,

-loadtess file_name

[Input data]

Load a tessellation from a file. Provide as argument the file name.

Possible values: any. Default value: none.
[Input data]
Load a raster tessellation from a file.
Provide as argument the file
name.
To load only a subregion of a raster tessellation, use the syntax
file_name:crop(xmin|xmax|ymin|ymax|zmin|zmax), where xmin, xmax, ymin,
ymax, zmin and zmax are the minimum and maximum positions along x, y and z,
respectively. For 2D raster tessellations, the z boundaries can be omitted. For 1D raster
tessellations, the y and z boundaries can be omitted. To scale the number of points of
a raster tessellation, use the syntax file_name:scale(factor), where factor is the
scaling factor, or file_name:scale(factor_x|factor_y|factor_z), where factor_x,
factor_y and factor_z are the scaling factor along x, y and z, respectively. For 2D raster
tessellations, the z factor can be omitted. For 1D raster tessellations, the y and z factors
can be omitted.
Possible values: any. Default value: none.

-loadtesr file_name

Chapter 2: Tessellation Module (-T)

Finally, it is possible to load a set of points. Points are used for statistics only (option
-statpoint) and should not be seen as the seeds of the tessellation (to load particular seeds,
use option -morpho).
[Input data]
Load points from a file. See Section B.3 [Position File], page 53 for the file format. Provide
as argument the file name.
Possible values: any. Default value: none.

-loadpoint file_name

2.1.2 Tessellation Options

-dim integer

[Option]

Specify the dimension of the tessellation.

Possible values: 1, 2 or 3. Default value: 3.
[Option]
Specify the type and size of the domain.
In 3D, for a cuboidal shape,
provide
cube(size_x,size_y,size_z),
for
a
cylindrical
shape,
provide
cylinder(height,diameter) and for a spherical shape, provide sphere(diameter) In
2D, for a rectangular shape, provide square(size_x,size_y) and for a circular shape,
provide circle(radius). In 1D, provide segment(size_x). To specify the number of
facets, facet_nb, of a circle, cylinder or sphere domain, use circle(radius,facet_nb),
cylinder(height,diameter,facet_nb) or sphere(diameter,facet_nb).
For an
arbitrary 3D shape, provide planes(file_name), where file_name is the name of
a file containing the total number of planes then, for each plane, the 4 parameters
of its equation (d, a, b and c, for an equation of the form a x + b y + c z = d).
The plane normal, (a, b, c), must be an outgoing vector of the domain.
For an
arbitrary 2D shape, proceed in the same way.
For a tessellation cell, provide
cell(file_name,cell_id), where file_name is the name of the tessellation file and
cell_id is the cell identifier. To rotate, scale and/or translate the domain, append
rotate(axis_x,axis_y,axis_z,theta), scale(x_factor,y_factor,z_factor) and/or
translate(x_delta,y_delta,z_delta,theta), respectively, using the : separator. An
example is sphere(1,100):translate(-0.5,-0.5,-0.5):rotate(1,0,0,45) .
Possible values: see above list. Default value: cube(1,1,1) in 3D, square(1,1) in 2D
and segment(1) in 1D.

-domain char_string

[Option]
Type of morphology of the cells. For random tessellations, it can be either equiaxed
(equiaxed), columnar (columnar(dir), where dir is the columnar direction and can be
x, y or z) or bamboo-like (bamboo(dir), where dir is the bamboo direction and can
be x, y or z). To get a lamella morphology, provide lamella(w=w,v=v). Argument
w=w is mandatory and argument v=v is optional. Argument w=w enables to specify the
absolute lamella width w. In the case of multiscale tessellation, for specifying cell-by-cell
width values, use the syntax @file_name where file_name is the name of a file containing
the list of widths. Argument v=v enables to specify the lamella plane normals v. Use the
syntax @file_name where file_name is the name of a file containing the list of lamella
plane normals (one for each parent cell, as the 3 coordinates of the plane normals). Regular
morphologies also are available: squares (square) in 2D, cubes (cube) and truncated octahedra (tocta) in 3D. To load a particular set of seeds, use the syntax @file_name where
file_name is the name of the seed position file (see Section B.3 [Position File], page 53).
Possible values: see above list. Default value: equiaxed.

-morpho char_string

10

Neper 2.0.5

[Option]
Use this option to get a hardcore tessellation. Provide as argument the radius of the exclusion
sphere surrounding each of the seeds.
Possible values: any. Default value: 0.

-hardcore real

[Option]
Use this option to get a centroidal tessellation. Note that the generation of a centroidal
tessellation is based on Lloyds algorithm and can be two to three orders of magnitude as
long as for the equivalent tessellation. See options -centroidfact, -centroidconv and
-centroiditermax for convergence criteria.
Possible values: 0 or 1. Default value: 0.

-centroid logical

[Secondary option]
This option can be used with option -morpho centroid, to specify the factor by which the
seed positions are shifted between their current positions and the centroid positions, at each
iteration. (Lloyds algorithm is obtained for a value of 1, but a lower value can lead to faster
convergence.)
Possible values: 0 to 1. Default value: 0.5.

-centroidfact real

[Secondary option]
This option can be used with option -morpho centroid, to specify the maximum tolerance
on the distance between the seeds and the cell centroids. The tolerance is relative to the
average cell radius.
Possible values: any > 0. Default value: 0.02.

-centroidconv real

[Secondary option]
This option can be used with option -morpho centroid, to specify the maximum number of
iterations.
Possible values: any. Default value: 1000.

-centroiditermax integer

[Option]
Use this option to generate a Laguerre tessellation. To define the weights associated
to the seeds, the first way is to load values from a file using the syntax @file_name,
where file_name is the name of the file. The second way is to provide as argument an
expression for the distribution of the weight values. The current algorithm generates the
weights then distributes the seeds by decreasing weight values. As a weight also stands
for the radius of a sphere of exclusion, the algorithm may fail to distribute all seeds, in
which case an error is returned. The expression is a probability density function of the
form function(param1,param2,...). The available functions are: dirac(mean) for the
Dirac distribution, gaussian(mean,sig) for the Gaussian distribution of mean mean and
standard deviation sig, flat(mean,radius) for the flat distribution of mean mean and
radius radius, bernoulli(val1,val2,p) for a Bernoulli-type distribution of probability p,
where val1 is the value associated with probability 1 p and val2 is the value associated
with probability p. The distributions can be truncated by passing a minimum and a
maximum value as parameter to the function: function(param1,param2,...,min,max).
It is also possible to provide a weighted sum of probability density functions, which is
particularly appropriate to get multimodal distributions. The argument must be of the form:
function1_weight*function1(...)+function2_weight*function2(...)+...,
where
functionid_weight is a real number representing the additive weight of the distribution.
Possible values: any. Default value: none.

-weight char_string

[Option]
Specify the type of tessellation. standard means that all seeds are located inside the domain.
periodic means that cells show periodicity conditions at the domain boundary. For semperiodicity, provide periodic(dir), where dir stands for the periodicity direction(s),

-ttype char_string

Chapter 2: Tessellation Module (-T)

11

among x, y and z. For several directions, combine them with ,. subdomain means
that seeds can be located inside and outside the domain. periodic and subdomain are
only available for raster tessellations (-format tesr).
Possible values: standard, periodic or subdomain. Default value: standard.
[Secondary option]
This option can be used to randomize the positions of the seeds. Provide as argument the
radius of the sphere (circle in 2D, segment in 1D) in which each position is randomized, according to a uniform distribution, and an identifier for the randomization, combined with :.
Possible values: any:any. Default value: none.

-randomize real:integer

[Secondary option]
This option can be used to sort the tessellation cells (typically to facilitate data postprocessing). Provide as argument the mathematical expression used for sorting (see
Section A.1 [Mathematical and Logical Expressions], page 43).
Possible values: any. Default value: none.

-sort char_string

2.1.3 Transformation Options

[Option]
Specify the factors in the x, y and z directions by which the tessellation is to be scaled once
generated. In 2D, the z value can be omitted. In 1D, the y and z values can be omitted.
Possible values: any. Default value: none.

-scale real:real:real

[Option]
Clip a tessellation by one or several planes.
For a scalar tessellation, provide
planes(file_name), where file_name is the name of a file containing the total number of
planes then, for each plane, the 4 parameters of its equation (d, a, b and c, for an equation
of the form a x + b y + c z = d). The plane normal, (a, b, c), must be an outgoing vector of
the clipped domain.
Possible values: any. Default value: none.

-clip char_string(...)

2.1.4 Crystal Orientation Options

[Option]
Specify the type of crystal orientation distribution. It can be either 3D for orientations in the
3D space, or fibre(dir,coo_x,coo_y,coo_z) for orientations along a specific fibre (crystal
direction (coo_x, coo_y, coo_z) parallel to sample direction dir, where dir can be x, y,
or z). Crystal orientations are distributed randomly according to a uniform distribution in
the specified space.
Possible values: 3D or fibre(...). Default value: 3D.

-ori char_string

[Secondary option]
Specify the crystal symmetry. This is used to reduce the domain of definition of the orientation descriptors.
Possible values: triclinic or cubic. Default value: triclinic.

-oricrysym char_string

2.1.5 Regularization Options

[Option]
Enable tessellation regularization. Regularization removes the small edges and, indirectly,
the small faces. In return, faces can become non-planar (in 3D). This is controlled by options
-fmax, -sel and -mloop. Using regularization enables to get better-quality meshes using
module -M (see Chapter 3 [Meshing Module (-M)], page 17).
Possible values: 0 or 1. Default value: 0.

-regularization logical

12

Neper 2.0.5

[Option]
Maximum allowed face flatness fault (in degrees). The flatness fault is the maximum angle
between the normals at two locations on a face.
Possible values: 0 to 180. Default value: 20.

-fmax real

[Secondary option]
Absolute or relative small edge (maximum) length. rsel is defined relative to the average cell size (volume in 3D, area in 2D and length in 1D). The default -rsel 1 leads to
a length of 0.25 for a unit volume cell in 3D, 0.125 for a unit area cell in 2D and 0.2 for
a unit length cell in 1D. The value also enables to avoid mesh refinement with the default
meshing parameters (see Chapter 3 [Meshing Module (-M)], page 17). It is also possible
to specify values on a per-cell basis. The first way is to use the syntax default_sel,cell_
expr1:cell_sel1,cell_expr2:cell_sel2..., where default_sel is the default small edge
length, cell_expri is an expression defining the set of cells i and cell_seli is the corresponding small edge length. cell_expri can be any expression based on variables provided
in Section A.2 [Tessellation Keys], page 43. The expressions are processed one after the other.
When processing expression cell_expri, the matching cells are assigned cell_seli as small
edge length. Typically, option -rsel should be passed the same argument than option -rcl
of module -M, see Chapter 3 [Meshing Module (-M)], page 17. The second way is to load
values from an external file using the syntax @file_name, where file_name is the name of
the file containing the length values.
Possible values: any. Default value: -rsel 1.

-sel or -rsel real

[Secondary option]
Maximum number of regularization loops. During each loop, the small edges are considered
in turn from the shortest to the largest. Regularization stops when the maximum number of
loops is reached or no edges are deleted within a loop.
Possible values: any. Default value: 2.

-mloop integer

2.1.6 Filtering Options

The following option can be used to clean up a raster tessellation. For meshing of a 2D raster
tessellation, make sure to use -filter size.
[Option]
Filter a raster tessellation. The available filters can be combined with :. Filter size
removes, for each cell, the parts of a cell that are not properly connected to the rest of the
cell, namely, that do not share with it at least a raster point edge for a 2D tessellation and
a raster point face for a 3D tessellation. Use argument size(dim) to override the type of
neighbouring, where dim is equal to 1 for edge and 2 for face. Filter noise removes points
(or bunch of points) indexed 0 by progressively collapsing them.
Possible values: any. Default value: none.

-filter char_string

2.1.7 Output Options

-o file_name

[Option]

Specify the output file name.

Possible values: any. Default value: none.
[Option]
Specify the format of the output file(s). The available formats are the Neper tess and
tesr, the Gmsh geo, the Ply ply, the Wavefront obj and the 3DEC 3dec.
Orientations for the cells can be obtained using ori (see also options starting by -ori).
Combine the values with ,.
Possible values: tess, tesr, geo, ply, obj, 3dec, ori. Default value: tess.

-format char_string

Chapter 2: Tessellation Module (-T)

13

[Option]
Specify the format of the raster output file(s). The available formats are ASCII (ascii),
8-bit binary (binary8), 16-bit binary (binary16) and 32-bit binary (binary32).
Possible values: ascii, binary8, binary16, binary32. Default value: binary16.

-tesrformat char_string

[Option]
Specify the number of points of a raster tessellation along a direction of the domain. In case
of a domain of different lengths along the different directions, the argument stands for the
geometrical average of the number of points along the different directions, so that the raster
points are as cubic as possible. To specify different values along the x, y and z directions,
combine the values with :.
Possible values: any. Default value: 20.

-tesrsize integer

[Option]
Select the orientation descriptor used in the .tess, .tesr and .ori files. It can be Euler
angles in Bunge, Kocks or Roe convention (e, ek, er), rotation matrix (g), axis / angle or
rotation (rtheta), Rodrigues vector (R) or quaternion (q).
Possible values: above-mentioned values. Default value: e.

-oridescriptor char_string

[Option]
Specify the format of the .ori output file. The available formats are: the Neper-native plain
(i.e. only the descriptors on successive lines), the Zset/Zebulon geof and the FEpX fepx.
Possible values: above-mentioned values. Default value: plain.

-oriformat char_string

2.1.8 Post-Processing Options

The first options apply to the cells and seeds of a tessellation or a raster tessellation, independently of its dimension,
[Post-processing]
Provide statistics on the tessellation cells. Give as argument the keys as described in
Section A.2 [Tessellation Keys], page 43 for a tessellation and Section A.3 [Raster Tessellation Keys], page 45 for a raster tessellation (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stcell.

-statcell char_string

[Post-processing]
Provide statistics on the tessellation seeds. Give as argument the keys as described in
Section A.2 [Tessellation Keys], page 43 for a tessellation and Section A.3 [Raster Tessellation Keys], page 45 for a raster tessellation (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stseed.

-statseed char_string

For tessellations, it is also possible to get statistics on an entity-basis,

[Post-processing]
Provide statistics on the tessellation vertices. Give as argument the keys as described in
Section A.2 [Tessellation Keys], page 43 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stver.

-statver char_string

[Post-processing]
Provide statistics on the tessellation edges. Give as argument the keys as described in
Section A.2 [Tessellation Keys], page 43 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stedge.

-statedge char_string

14

Neper 2.0.5

[Post-processing]
Provide statistics on the tessellation faces. Give as argument the keys as described in
Section A.2 [Tessellation Keys], page 43 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stface.

-statface char_string

[Post-processing]
Provide statistics on the tessellation polyhedra. Give as argument the keys as described in
Section A.2 [Tessellation Keys], page 43 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stpoly.

-statpoly char_string

Finally, it is possible to get statistics for a particular set of points. The option applies to a
tessellation.
[Post-processing]
Provide statistics on points. The points must be loaded with option -loadpoint. Give as
argument the keys as described in Section A.5 [Point Keys], page 46 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stpoint.

-statpoint char_string

2.1.9 Debugging Options

[Input data]
Check a tessellation file. Provide as argument the file name. Use this option if the tessellation
file fails to load using option -loadtess or in other modules.
Possible values: any. Default value: none.

-checktess file_name

2.2 Output Files

2.2.1 Tessellation
Neper tessellation file: .tess
It contains a scalar description of the tessellation. See Appendix B [File Formats], page 49
for the file syntax.
Neper raster tessellation: .tesr
It contains a raster description of the tessellation. See Appendix B [File Formats], page 49
for the file syntax.
Gmsh geometry file: .geo
It contains a minimal description of the tessellation written under the Gmsh geometry file
format .geo. This file can be opened with Gmsh for visualization.
Ply file: .ply
It contains a description of the tessellation written under the standard Polygon File Format .ply.
Wavefront geometry file: .obj
It contains a description of the tessellation written under the Wavefront geometry format
.obj.
3DEC file: .3dec
It contains a description of the tessellation written under the 3DEC format .3dec.
Orientation file: .ori
It contains crystal orientations for the tessellation cells. The orientations are written on successive lines, using the descriptor specified by option -oridescriptor (see also Section A.6

Chapter 2: Tessellation Module (-T)

15

[Rotations and Orientations], page 46) and the writing convention specified by option
-oriformat.

2.2.2 Statistics
Statistics files are provided for cells, seeds, vertices, edges, faces, polyhedra and points. They are
formatted with one entity per line. Each line contains the data specified to the corresponding
-stat option and described in Section A.2 [Tessellation Keys], page 43 and Section A.3 [Raster
Tessellation Keys], page 45 (files .stcell and .stseed only).
Tessellation cell statistics file, .stcell.
Tessellation seed statistics file, .stseed.
Tessellation vertex statistics file, .stver.
Tessellation edge statistics file, .stedge.
Tessellation face statistics file, .stface.
Tessellation polyhedron statistics file, .stpoly.
Point statistics file, .stpoint.

2.3 Examples
Below are some examples of use of neper -T.
1. Generate a Voronoi tessellation containing 100 cells (with identifier = 1).
$ neper -T -n 100 -id 1
2. Use an elongated domain and generate a Voronoi tessellation containing 100 cells.
$ neper -T -n 100 -id 1 -domain "cube(3,1,0.33)"
3. Generate a Voronoi tessellation containing 100 cells and scale it to get elongated cells.
$ neper -T -n 100 -id 1 -scale 3:1:0.33
4. Generate a Voronoi tessellation containing 100 cells and apply regularization.
$ neper -T -n 100 -id 1 -reg 1
5. Generate a 2D Voronoi tessellation containing 100 cells.
$ neper -T -n 100 -id 1 -dim 2
6. Generate a 2D Voronoi tessellation containing 100 cells at raster format with 50 points
along each coordinate axis; apply filtering to prepare it for meshing.
$ neper -T -n 100 -id 1 -dim 2 -format tesr -tesrsize 50 -filter size
7. Generate a Voronoi tessellation containing 100 cells and get, for each cell, its volume and
its number of faces.
$ neper -T -n 100 -id 1 -statcell vol,facenb
8. Generate a 2-scale Voronoi tessellation containing 100 10 cells.
$ neper -T -n 100::10 -id 1::1
9. Generate a 2-scale Voronoi tessellation containing 3 primary cells divided into 1, 10 and
100 secondary cells, respectively.
$ neper -T -n 3::@myfile -id 1::1
myfile:
1 1
2 10
3 100
10. Generate a 2-scale Voronoi tessellation containing 2 3 cells with specific seed coordinates
at both scales (files coo1 and coo2).
$ neper -T -n 2::3 -id 1::1 -morpho @coo1::@coo2

16

Neper 2.0.5

coo1:
0.25 0.5 0.5
0.75 0.5 0.5

coo2:
1 0.25
1 0.25
2 0.75
2 0.75

0.25
0.75
0.25
0.75

0.5
0.5
0.5
0.5

Chapter 3: Meshing Module (-M)

17

3 Meshing Module (-M)

Module -M is the module for meshing scalar and raster tessellations. Two meshing strategies are
available. Free (or unstructured) meshing creates a conforming mesh into tetrahedral elements
(triangular in 2D, line in 1D). Mapped meshing generates a non-conforming mesh into regular
hexahedral elements (rectangular in 2D, line in 1D). Free meshing is carried out so that the
elements have sizes as close as possible to a desired target value, and show high quality, that
is, equilateral shapes. The input file is a tessellation file (.tess) or a raster tessellation file
(.tesr), as provided by module -T. Standard, 1-scale tessellations and 2-scale tessellations are
supported. Free meshing of raster tessellations works for 1D and 2D tessellations only. The
output mesh can be written in various formats.
The target element size of the mesh can be specified through the element characteristic
length (cl). It stands for the length of a 1D element, the length of the edge of a triangle
or quadrilateral element (2D) and the length of an edge of a tetrahedral or hexahedral element
(3D). For convenience, a relative characteristic length (rcl) is also defined, whose value is relative to the average cell size and provides a medium number of elements. It is also possible
to specify a cl (or rcl) value on a per-cell basis, or to specify different values along the three
coordinate axes.
For free meshing, mesh quality is ensured to the greatest extent possible using several advanced
capabilities,
Optimized meshing rules. The mesh properties are controlled by size parameters (options
-cl, -rcl, etc.) and a size gradient parameter used for 1D meshing (option -pl).
Multimeshing. Each tessellation face and volume is meshed separately of the others, with
several meshing algorithms, until a target mesh quality is reached. This is controlled by
options starting by -meshqual, and options -mesh2dalgo and -mesh3dalgo.
Note that, in general, tessellation regularization is also necessary to ensure good-quality meshing,
see Chapter 2 [Tessellation Module (-T)], page 7.
Remeshing can also be applied to generate a new, good-quality mesh from a mesh containing
poor-quality elements. The variables defined on the old mesh can be transported on the new
mesh (options starting by -transport).
For mapped meshing, mesh cleaning options enable to remove isolated elements or duplicate
nodes, or to duplicate nodes subjected to singularity behaviour (options -clean, -dupnodemerge
and -singnodedup).
Mesh partitioning enables to divide the mesh nodes and elements into several sets while minimizing the interfaces between them1 , for parallel finite element calculations. Partitioning can
return any number of partitions, or more efficiently, can be carried out according to a given
parallel computer architecture (option -part).
In the output mesh, the individual entities of the tessellations (the vertices, edges, faces and
polyhedra) can be described by element sets (option -dim). Node sets of the vertices, edges
and faces of the boundary of the tessellation are also provided for prescribing the boundary
conditions (option -nset). The surface element sets are also provided (option -faset). The
mesh order can be 1 or 2 (option -order). Statistical data can be obtained on the meshes
(options starting by -stat).

Each partition being assigned to a processor in the finite element calculation, the minimization of the interfaces
between the partitions is done in terms of the number of necessary communications between processors.

18

Neper 2.0.5

Here is what a typical run of module -M looks like,

$ neper -M n10-id1.tess
========================
N
e
p
e
r
=======================
Info
: A software package for polycrystal generation and meshing.
Info
: Version 2.0.0
Info
: Built with: gsl libmatheval
Info
: Loading initialization file /foo/bar/.neperrc...
Info
: --------------------------------------------------------------Info
: MODULE -M loaded with arguments:
Info
: [ini file] -gmsh /foo/bar/bin/gmsh
Info
: [com line] n10-id1.tess
Info
: --------------------------------------------------------------Info
: Reading input data...
Info
:
- Reading arguments...
Info
: Loading input data...
Info
:
- Loading tessellation...
Info
:
[i] Parsing file n10-id1.tess...
Info
:
[i] Parsed file n10-id1.tess.
Info
: Meshing...
Info
:
- Preparing... (cl = 0.2321) 100%
Info
:
- 0D meshing... 100%
Info
:
- 1D meshing... 100%
Info
:
- 2D meshing... 100% (0.69|0.86/96%| 4%| 0%)
Info
:
> Checking 2D mesh for pinching out...
Info
:
- 3D meshing... 100% (0.89|0.91/100%| 0%| 0%)
Info
:
- Searching nsets...
Info
: Writing mesh results...
Info
:
- Preparing mesh...
Info
:
- Mesh properties:
Info
:
> Node number:
289
Info
:
> Elt number:
996
Info
:
> Mesh volume:
1.000
Info
:
- Writing mesh...
Info
:
[o] Writing file n10-id1.msh...
Info
:
[o] Wrote file n10-id1.msh.
Info
: Elapsed time: 8.414 secs.
========================================================================

Chapter 3: Meshing Module (-M)

19

3.1 Arguments
3.1.1 Prerequisites
[Prerequisite]
Specify the path of the Gmsh binary (for meshing into triangle and tetrahedral elements).
Possible values: any. Default value: gmsh.

-gmsh path_name

3.1.2 Input Data

In normal use, the input data is a tessellation file, a raster tessellation file or a mesh file,
[Input data]
Name of the input file. It can be a tessellation file (.tess), a raster tessellation file (.tesr) or
a mesh file for remeshing (.msh). To load several of them (namely, both a tessellation file and
a mesh file for remeshing), combine them with ,. To overwrite the coordinates of the nodes
of a mesh, use the syntax file_name:nodecoo_file_name, where file_name is the name
of the mesh file and nodecoo_file_name is the name of the file containing the coordinates
of the nodes (see Section B.3 [Position File], page 53). To load only a subregion of a raster
tessellation, use the syntax file_name:crop(xmin|xmax|ymin|ymax|zmin|zmax), where
xmin, xmax, ymin, ymax, zmin and zmax are the minimum and maximum positions
along x, y and z, respectively. For 2D raster tessellations, the z boundaries can be omitted.
For 1D raster tessellations, the y and z boundaries can be omitted. To scale the number of
points of a raster tessellation, use the syntax file_name:scale(factor), where factor is
the scaling factor, or file_name:scale(factor_x|factor_y|factor_z), where factor_x,
factor_y and factor_z are the scaling factor along x, y and z, respectively. For 2D raster
tessellations, the z factor can be omitted. For 1D raster tessellations, the y and z factors can
be omitted.
Possible values: any. Default value: none.

file_name

It is also possible to load a result mesh from a file. (Using option -o along with this capability
avoids overwriting the input data.)

-loadmesh file_name

[Input data]

Load a mesh from a file (.msh format).

Possible values: any. Default value: none.
Finally, it is possible to load a set of points (useful for statistics, see option -statpoint),
[Input data]
Load points from a file. See Section B.3 [Position File], page 53 for the file format. Provide
as argument the file name.
Possible values: any. Default value: none.

-loadpoint file_name

3.1.3 Meshing Options

[Option]
Type of elements, among tetrahedral (tet) and hexahedral (hex). (The 2D counterparts,
tri and quad, can also be used and are equivalent.)
Possible values: tet, hex. Default value: tet.

-elttype char_string

[Option]
Absolute or relative characteristic length of the elements. rcl is defined relative to the average
cell size. The default -rcl 1 leads to a mesh with about 100 elements per cell in average
(64 in 2D, 5 in 1D). For free meshing, it is also possible to get non-uniform characteristic

-cl or -rcl real

20

Neper 2.0.5

length distributions, as detailed in the following. To define a characteristic length on a

per-cell basis, the first way is to use the syntax default_cl,cell_expr1:cell_cl1,cell_
expr2:cell_cl2..., where default_cl is the default characteristic length, cell_expri is an
expression defining the set of cells i and cell_cli is the corresponding characteristic length.
cell_expri can be any expression based on variables provided in Section A.2 [Tessellation
Keys], page 43 for tessellations, Section A.3 [Raster Tessellation Keys], page 45 for raster
tessellations and Section A.4 [Mesh Keys], page 45 for meshes. The expressions are processed
one after the other. When processing expression cell_expri, the matching cells are assigned
cell_cli as characteristic length. A typical use is -rcl val1,body==0:val2 to get interior
cells meshed with rcl=val1 and boundary cells meshed with rcl=val2. The second way is
to load values from an external file using the syntax @file_name, where file_name is the
name of the file containing the characteristic length values.
Possible values: any. Default value: -rcl 1.
[Option]
Specify the meshing dimension. By default, it is equal to the input data dimension
(inputdim). To get meshes of several dimensions in output, provide the values combined
with ,. Provide all for all and none for none. Note that the meshes of all dimensions
are systematically written into a .msh mesh file unless :msh is appended to the option argument. If a mesh dimension of 3 is required, but the input data is 2D, the 3D mesh is obtained
by extrusion of the 2D mesh.
Possible values: 0 to 3, all, none, inputdim. Default value: inputdim.

-dim char_string

[Option]
Specify the mesh order. 1 means 2-node line elements, 3-node triangle elements, 4-node
quadrangle elements, 4-node tetrahedral elements and 8-node hexahedral elements. 2 means
3-node line elements, 6-node triangle elements, 8-node quadrangle elements, 10-node tetrahedral elements and 20-node hexahedral elements.
Possible values: 1 or 2. Default value: 1.

-order integer

[Secondary option]
Progression factor for the element characteristic lengths. This value is the maximum ratio
between the lengths of two adjacent 1D elements.
Possible values: any >= 1. Default value: 2.

-pl real

[Secondary option]
Specify ratios between the cl-values along the different coordinate axes. Provide the values
combined with :. For example, 2:1:1 leads to elements twice as long in the x direction as
in the y and z directions.
Possible values: none. Default value: any.

-clratio char_string

[Secondary option]
Minimum characteristic length of the elements. Using this option is not recommended.
Possible values: any. Default value: none.

-clmin real

The following options define the multimeshing algorithm (for 2D and 3D free meshings). Multimeshing consists in using several meshing algorithms concurrently, for each face or polyhedron,
until a minimum, target mesh quality is reached. The mesh quality factor, O, accounts for both
the element sizes and aspect ratios. It is given by O = Odis Osize 1 , where Odis and Osize
range from 0 (poor quality) to 1 (high quality) and is a factor equal to 0.8. Therefore, O
also ranges from 0 (poor quality) to 1 (high quality). See the Neper reference paper for further
information. The minimum quality value can be modified using option -meshqualmin. The
values of O and Odis can be modified using options -meshqualexpr and -meshqualdisexpr.

Chapter 3: Meshing Module (-M)

21

The value of the target mesh quality significantly influences meshing speed and output mesh
quality. While a value of 0 provides fastest meshing, a value of 1 provides best-quality meshing.
The default value provides an effective balance. The meshing algorithms are taken from the
Gmsh1 and Netgen2 libraries (options -mesh2dalgo and -mesh3dalgo).
[Option]
Specify the minimum, target value of mesh quality, O, as defined by option -meshqualexpr.
Possible values: 0 to 1. Default value: 0.9.

-meshqualmin real

-meshqualexpr char_string

[Option]

Specify the expression of mesh quality, O, as a function of Odis and Osize.

Possible values: any. Default value: Odis^0.8*Osize^0.2.
[Secondary option]
Specify the expression of the mesh element distortion parameter, Odis, as a function of the
element distortion parameter dis (see the Neper reference paper).
Possible values: any. Default value: dis^(exp((dis^0.1)/(dis^0.1-1))).

-meshqualdisexpr char_string

[Secondary option]
Specify the 2D meshing algorithms (combine with ,). The available values are mead (MeshAdapt), dela (Delaunay) and fron (Frontal).
Possible values: mead, dela, fron. Default value: mead,dela,fron.

-mesh2dalgo char_string

[Secondary option]
Specify the 3D meshing algorithms (combine with ,). Each algorithm has format
mesh:opti, where mesh and opti stand for the meshing and mesh optimization algorithms.
The available values of mesh are currently limited to netg (Netgen). The available values of
opti are gmsh (Gmsh), netg (Netgen) and gmne (Gmsh + Netgen). Use none for none.
Possible values:
netg:none, netg:gmsh, netg:netg, netg:gmne.
Default value:
netg:gmsh,netg:netg,netg:gmne.

-mesh3dalgo char_string

3.1.4 Raster Tessellation Meshing Options

Raster tessellation meshing implies interface reconstruction, interface mesh smoothing then
remeshing. The following options enable to control interface smoothing.
[Secondary option]
Method for smoothing the interface meshes reconstructed from raster tessellations. Laplacian
smoothing (laplacian) is an iterative method that consists in modifying the coordinates
of a node using the coordinates of the neighbouring nodes. At iteration i, the position of a
node, Xi , is calculated from its previous position, Xi1 , and the position of the barycentre of
the neighbouring nodes (weighted barycentre, considering the inverse of the distance between
n
n
the node and the neighbour), Xi1
, as follows: Xi = (1 A) Xi1 + A Xi1
. A [0, 1]
an adjustable parameter (see option -tesrsmoothfact). The number of iterations is set by
option -tesrsmoothitermax. There is no stop criterion, so itermax will always be reached.
Possible values: laplacian or none. Default value: laplacian.

-tesrsmooth char_string

[Secondary option]
Factor used for the interface mesh smoothing (A in option -tesrsmooth).
Possible values: 0 to 1. Default value: 0.5.

-tesrsmoothfact real

1
2

Ch. Geuzaine and J.-F. Remacle, Gmsh: a three-dimensional finite element mesh generator with built-in pre- and
post-processing facilities, International Journal for Numerical Methods in Engineering, 79, 13091331, 2009.
J. Schoberl, Netgen, an advancing front 2d/3d-mesh generator based on abstract rules. Comput. Visual. Sci., 52,
141, 1997.

22

Neper 2.0.5

-tesrsmoothitermax integer

[Secondary option]

Number of iterations used for interface mesh smoothing.

Possible values: any >= 0. Default value: 5.

3.1.5 Mesh Cleaning Options

The following options are specific to mapped meshing of raster tessellations containing voids.
[Secondary option]
Clean the mesh so that it consists of a set of connected elements. Provide as argument the
level of cleaning. A value of 1 indicates that two elements should be considered connected
to each other if they share at least a vertex. A value of 2 indicates that two elements should
be considered connected to each other if they share at least a face. Using this option, the
elements (or bunches of elements) that are not connected to the main skeleton are removed.
Possible values: 0 to 2. Default value: 0.

-clean integer

[Secondary option]
Duplicate nodes which are the subject of singularity. Such a node belongs to several elements
which share only a node or an edge, which provides a singularity behaviour. In Mechanics,
it corresponds to imposing a common displacement, while the point can carry no stress. In
Thermics, it corresponds to imposing a given temperature at a particular location shared by
two bodies, but not enabling heat flux to operate at that location. When this option is enabled, such a node is duplicated, so that each body has its own node. Option -dupnodemerge
enables to merge back duplicate nodes.
Possible values: 0 or 1. Default value: 0.

-singnodedup logical

[Secondary option]
Merge duplicate nodes. Provide as argument the distance between nodes below which two
nodes are merged. Note that Neper does not generate meshes with duplicate nodes, except
using option -singnodedup.
Possible values: 0. Default value: any>0.

-dupnodemerge real

3.1.6 Mesh Partitioning Options

Mesh partitioning is achieved using the libScotch library3 . The principle of mesh partitioning
is to create partitions of same size while minimizing the interfaces between them. This affects
the same load to all computation units and minimizes communications between them, therefore
minimizes the total computation time. There are two available strategies for mesh partitioning.
The first one creates partitions and arranges them independently of each other. The other one
consists in optimizing the size and arrangment of the partitions based on a given computer cluster
architecture to minimize computation time further. For those clusters that contain processors
each with several cores, the communication time between cores of a processor is much lower
than the communication time between cores of different processors. To minimize the global
communication time, partitions which are processed by cores of the same processor can be
grouped together. Partitioning is applied to the higher-dimension mesh. On top of defining
the partitions, it renumbers the nodes and elements by increasing partition identifier and writes
partitions as element and node sets (vtk, inp and geof formats). This can be managed using
option -part.
[Option]
Specify the number of partitions or a computer cluster architecture. Using the first option,
the number of partition can be any. At the opposite, for a computer cluster architecture, the

-part integer or char_string

F. Pellegrini, Scotch and libScotch 5.1 Users Guide, INRIA Bordeaux Sud-Ouest, ENSEIRB & LaBRI, UMR
CNRS 5800, 2008.

Chapter 3: Meshing Module (-M)

23

total number of partitions must be a power of 2. An architecture can be specified in two ways.
First, for clusters that contain processors each with several cores, the number of processors
and the number of cores per processor can be combined using the : separator. A ratio of
10 is considered between the computation time between cores located on different processors
and the one between cores of the same processor. Second, the name of a file describing the
cluster architecture at the Scotch format can be provided.
Possible values: any. Default value: none.
[Secondary option]
Provide the rate of element partition balancing. The partitioning algorithm applies to the
nodes; the element partitions are determined afterwards and can be somewhat unbalanced.
This option enables to enforce balancing. It is highly CPU-sensitive.
Possible values: 0 to 1. Default value: 0.5.

-partbalancing real

[Secondary option]
Specify the partitioning method. Provide the partitioning expression in Scotchs jargon, or
none for none.
Possible values: any. Default value: see_the_source.

-partmethod char_string

3.1.7 Field Transport Options

[Option]
Use this option for transporting data from a parent mesh to a child mesh (both 3D).
The parent mesh is the input mesh and the child mesh is the result mesh (created
by remeshing or loaded with -loadmesh).
A transport entry must have format
entity_type:data_type:file_name, where entity_type must be elt, data_type
is the type of data, under format integerX or realX, where X is the dimension, and
file_name is the name of the file containing the parent data. For several data transports,
combine the transport entries with ,.
Possible values: any. Default value: none.

-transport char_string:char_string:file_name,...

3.1.8 Output Options

-o file_name

[Option]

Specify the output file name.

Possible values: any. Default value: none.
[Option]
Specify the format of the output file(s). Mesh formats are: the Gmsh msh, the VTK vtk,
the Abaqus inp, the Zset/Zebulon geof and the FEpX fepx (for the FEpX legacy format, provide fepx:legacy). The tessellation file format tess is also available. Combine
arguments with ,.
Possible values: anyone of the above list. Default value: msh.

-format char_string

[Option]
Specify the node sets to provide, among: faces, edges, vertices for all domain faces,
edges and vertices, and facebodies and edgebodies for all face and edge bodies. Provide
all for all and none for none. To get the node sets corresponding to individual entities,
provide their labels. For a cuboidal domain, they are [x-z][0,1] for the domain faces,
[x-z][0,1][x-z][0,1] for the edges, and [x-z][0,1][x-z][0,1][x-z][0,1] for the vertices. For a cylindrical domain, they are z[0,1] for the z faces, and f[1,2,...] for the faces
on the circular part of the domain. For other domains, they are f[1,2,...] for the faces.
For cylindrical and other types of domains, the edge and vertex labels are obtained from
the face labels as for cuboidal domains. For a 2D mesh (generated from a 2D tessellation),

-nset char_string

24

Neper 2.0.5

the labels are [x-y][0,1] for the edges and [x-y][0,1][x-y][0,1] for the vertices. For a
1D mesh (generated from a 1D tessellation), the labels are x[0,1] for the vertices. Append
body to a label to get only the body nodes of the set. Combine labels with ,.
Possible values: see above. Default value: faces in 3D, edges in 2D and vertices in 1D.
[Option]
Specify the domain surface meshes to provide. Use faces for all faces. To get the fasets
corresponding to individual faces, provide their labels (see option -nset). Combine them
with ,. Provide none for none.
Possible values: see above. Default value: none.

-faset char_string

3.1.9 Post-Processing Options

The following options provide statistics on the nodes (nodes), 0D elements (elt0d) and
element sets (elset0d), 1D elements (elt1d) and element sets (elset1d), 2D elements
(elt2d) and element sets (elset2d) and 3D elements (elt3d) and element sets (elset3d).
Also note that the elt and elset labels can be used in place of eltnd and elsetnd, where
n is the higher mesh dimension. This enables to use the same command whatever the higher
mesh dimension is.
[Post-processing]
Provide statistics on the nodes. Provide as argument the keys as described in Section A.4
[Mesh Keys], page 45 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stnode.

-statnode char_string

[Post-processing]
Provide statistics on the 0D elements. Provide as argument the keys as described in
Section A.4 [Mesh Keys], page 45 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stelt0d.

-statelt0d char_string

[Post-processing]
Provide statistics on the 1D elements. Provide as argument the keys as described in
Section A.4 [Mesh Keys], page 45 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stelt1d.

-statelt1d char_string

[Post-processing]
Provide statistics on the 2D elements. Provide as argument the keys as described in
Section A.4 [Mesh Keys], page 45 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stelt2d.

-statelt2d char_string

[Post-processing]
Provide statistics on the 3D elements. Provide as argument the keys as described in
Section A.4 [Mesh Keys], page 45 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stelt3d.

-statelt3d char_string

[Post-processing]
Provide statistics on the 0D element sets. Provide as argument the keys as described in
Section A.4 [Mesh Keys], page 45 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stelset0d.

-statelset0d char_string

Chapter 3: Meshing Module (-M)

25

[Post-processing]
Provide statistics on the 1D element sets. Provide as argument the keys as described in
Section A.4 [Mesh Keys], page 45 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stelset1d.

-statelset1d char_string

[Post-processing]
Provide statistics on the 2D element sets. Provide as argument the keys as described in
Section A.4 [Mesh Keys], page 45 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stelset2d.

-statelset2d char_string

[Post-processing]
Provide statistics on the 3D element sets. Provide as argument the keys as described in
Section A.4 [Mesh Keys], page 45 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stelset3d.

-statelset3d char_string

[Post-processing]
Provide statistics on points. The points must be loaded with option -loadpoint. Provide as
argument the keys as described in Section A.5 [Point Keys], page 46 (combine with ,).
Possible values: any. Default value: none.
Result file: extension .stpoint.

-statpoint char_string

3.1.10 Advanced Options

These advanced options set running conditions for the meshing libraries (triangle and tetrahedral
meshing),
[Secondary option]
Maximum difference between the characteristic length cl and the average element length (for
each polyhedron). Neper tries its best to get the average element size to match cl. Use this
option to change the tolerance on the relative difference between the two. This is a highly
CPU-sensitive capability (increasing this value can be efficient to speed up meshing).
Possible values: any. Default value: 0.02.

-mesh3dclconv real

[Secondary option]
Maximum processing time allowed to the meshing library for meshing a tessellation face (in
seconds).
Possible values: any. Default value: 1000.

-mesh2dmaxtime real

[Secondary option]
This option is similar to -mesh2dmaxtime, but the actual maximum time is the product of
the maximum processing time of the previous meshings by the value provided in argument.
Possible values: any. Default value: 100.

-mesh2drmaxtime real

-mesh2diter integer

[Secondary option]

Maximum 2D meshing attempts for a particular face (in case of failure).

Possible values: any. Default value: 3.
[Secondary option]
Maximum processing time allowed to the meshing library for meshing a tessellation volume
(in seconds).
Possible values: any. Default value: 1000.

-mesh3dmaxtime real

26

Neper 2.0.5

[Secondary option]
This option is similar to -mesh3dmaxtime, but the actual maximum time is the product of
the maximum processing time of the previous meshings by the value provided in argument.
Possible values: any. Default value: 100.

-mesh3drmaxtime real

[Secondary option]
Maximum 3D meshing attempts for a particular volume (in case of failure).
Possible values: any. Default value: 3.

-mesh3diter integer

3.2 Output Files

3.2.1 Mesh
The mesh can be written in the following formats,

Gmsh format: file .msh

VTK format: file .vtk
Abaqus format: file .inp
Zset/Zebulon format: file .geof
FEpX format: files .mesh, .grain and .bcs (.parms, .mesh, .surf, .opt and .bcs in
legacy mode)

3.2.2 Statistics
Statistics files are provided for nodes, elements, element sets and points. They are formatted
with one entity per line. Each line contains the data specified to the corresponding -stat option
and described in Section A.4 [Mesh Keys], page 45.

Node statistics file, .stnode.

(Higher-dimension) element statistics file, .stelt.
(Higher-dimension) element set statistics file, .stelset.
0D element statistics file, .stelt0d.
1D element statistics file, .stelt1d.
2D element statistics file, .stelt2d.
3D element statistics file, .stelt3d.
0D element set statistics file, .stelset0d.
1D element set statistics file, .stelset1d.
2D element set statistics file, .stelset2d.
3D element set statistics file, .stelset3d.
Point statistics file, .stpoint.

3.3 Examples
Below are some examples of use of neper -M,
1. Mesh tessellation n100-id1.tess.
$ neper -M n100-id1.tess
2. Mesh 2D raster tessellation n100-id1.tesr.
$ neper -M n100-id1.tesr
3. Mesh tessellation n100-id1.tess with a mesh size of rcl = 0.5 and in 2nd-order elements.
$ neper -M n100-id1.tess -rcl 0.5 -order 2

Chapter 3: Meshing Module (-M)

27

4. Mesh tessellation n100-id1.tess with small elements for the interior cells and bigger elements for the boundary cells.
$ neper -M n100-id1.tess -rcl "0.2,body==0:0.5"
5. Remesh mesh n150_def.msh (comprising poor-quality elements) into a clean, new mesh.
Transport the scalar data of file n150_def.data from the deformed mesh to the new mesh.
$ neper -M n150.tess,n150_def.msh -transport elt:real1:n150_def.data
-rcl 0.5 -o n150_new
6. Mesh tessellation n100-id1.tess and partition the mesh into 8 partitions.
$ neper -M n100-id1.tess -part 8
7. Mesh tessellation n100-id1.tess into regular hexahedral elements (non-conformal mesh).
$ neper -M n100-id1.tess -elt hex
8. Mesh tessellation n100-id1.tess and get, for each element, its radius ratio and its volume.
$ neper -M n100-id1.tess -statelt rr,vol

Chapter 4: Visualization Module (-V)

29

4 Visualization Module (-V)

Module -V is the Neper visualization module, with which the tessellations and meshes can be
printed as publication-quality images. It is also possible to visualize data on them using colours
and transparency, or displacements of the nodes and to plot data on slices of the mesh. Points
of specific size and colour can also be shown. The output is a PNG image file. The POV-Ray
ray-tracing library is used for generating the images.
Contrary to other modules, module -V processes the command arguments one after the other.
Typically, using module -V consists in loading a tessellation or a mesh, then data fields to render
them. The data can apply to the tessellation entities: polyhedra, faces, edges and vertices, to
the mesh entities: 3D, 2D, 1D and 0D elements and nodes, and to points (options starting by
-data). The entities that are to be visible, for example particular tessellation cells, element
sets or elements, can also be specified (options starting by -show). The way they are plotted:
camera position and angle, projection type, image size, etc., can be set up too (options starting
by -camera or -image). Finally, the coordinate system can be added.
Here is what a typical run of module -V looks like,
$ neper -V n10-id1.tess,n10-id1.msh -dataelsetcol id -print img
========================
N
e
p
e
r
=======================
Info
: A software package for polycrystal generation and meshing.
Info
: Version 2.0.0
Info
: Built with: gsl libmatheval
Info
: Loading initialization file /foo/bar/.neperrc...
Info
: --------------------------------------------------------------Info
: MODULE -V loaded with arguments:
Info
: [ini file]
Info
: [com line] n10-id1.tess,n10-id1.msh -dataelsetcol id -print img
Info
: --------------------------------------------------------------Info
: Loading tessellation...
Info
:
[i] Parsing file n10-id1.tess...
Info
:
[i] Parsed file n10-id1.tess.
Info
: Loading mesh...
Info
:
[i] Parsing file n10-id1.msh...
Info
:
[i] Parsed file n10-id1.msh.
Info
: Reconstructing mesh...
Info
: Reading data (elset3d, col)...
Info
: Printing image...
Info
:
[o] Writing file img.pov...
Info
:
- Printing mesh...
Info
:
> Reducing data...
Info
:
. Number of 3D elt faces reduced by 89% (to 422).
Info
:
. Number of 3D elt edges reduced by 50% (to 633).
Info
:
. Number of 0D elts
reduced by 100% (to 0).
Info
:
[o] Wrote file img.pov.
Info
:
- Generating png file (1200x900 pixels)...
Info
:
[o] Writing file img.png...
Info
:
[o] Wrote file img.png.
Info
: Printing scale...
Info
: Elapsed time: 0.759 secs.
========================================================================

30

Neper 2.0.5

4.1 Arguments
4.1.1 Input Data
[Input data]
Name of the input file. It can be a tessellation file (.tess), a raster tessellation file (.tesr),
a mesh file (.msh) or a point file (see Section B.3 [Position File], page 53). To load several of
them, combine them with ,.
Possible values: any. Default value: none.

file_name

4.1.2 Tessellation Data Loading and Rendering

The following options enable to define the properties (colour and size) of the tessellation cells
or entities (polyhedra, faces, edges and vertices). This can be done either directly, by specifying
the property values (e.g. the RGB channel values for colour) or indirectly, e.g. using scalar values
that are rendered in colour using a given colour scheme. In this case, a scale image is generated
in addition to the tessellation image. The scale properties can be set up (minimum, maximum
and tick values).
The following options apply to the cells of a tessellation or a raster tessellation, independently
of its dimension,
[Option]
Set the colours of the tessellation cells. The argument can be one of the following: (i) id for
colouring based on the identifier, using a colour palette (see Section A.7 [Colours], page 47),
(ii) ori for colouring based on the crystal orientations, (iii) the name of a colour that will
be used for all cells (see Section A.7 [Colours], page 47), (iv) the name of a file containing a
list of colours (provided as RGB channel values), or (v) a string indicating how the colours
can be obtained. The string has the format var:file_name, where var can be id for
identifiers, ori for crystal orientations or scal for scalar values, and file_name is the
name of the file containing the data. The colour schemes used to derive the colours from the
data can be specified with option -datacellcolscheme.
Possible values: any. Default value: white.

-datacellcol char_string

[Option]
Set the colour scheme used to get colours from the data of the tessellation cells loaded with
option -datacellcol. The type of colour scheme depends on the type of data. For crystal
orientations, the colour scheme can be: R for Rodrigues vector colouring; for scalar data,
the colour scheme can be any list of colours.
Possible values: "R" for crystal orientations and any list of colours for scalars.
Default
value:
"R" for crystal orientations and "blue,cyan,yellow,red" for
scalars.

-datacellcolscheme char_string

[Option]
Set the transparency of the tessellation cells. Provide as argument a value that applies to all
cells or @file_name to load values from a file.
Possible values: 0 to 1. Default value: 0.

-datacelltrs real

[Option]
Set the scale relative to the -datacellcol scal data. Provide as argument the start and
end values combined with :. To specify the tick values, provide as argument the start value,
the intermediate tick values then the end value, combined with :.
Possible values: any. Default value: data minimum:data maximum.

-datacellscale char_string

Chapter 4: Visualization Module (-V)

-datacellscaletitle char_string

31

[Option]

Set the title of the scale relative to the -datacellcol scal data.
Possible values: any. Default value: none.
For tessellations, it is also possible to set data on an entity-basis,
[Option]
Set the colours of the tessellation polyhedra. The argument can be one of the following:
(i) id for colouring based on the identifier, using a colour palette (see Section A.7 [Colours],
page 47), (ii) the name of a colour that will be used for all polyhedra (see Section A.7
[Colours], page 47), (iii) the name of a file containing a list of colours (provided as RGB
channel values), or (iv) a string indicating how the colours can be obtained. The string has the
format var:file_name, where var can be id for identifiers, ori for crystal orientations
or scal for scalar values, and file_name is the name of the file containing the data.
The colour schemes used to derive the colours from the data can be specified with option
-datapolycolscheme.
Possible values: any. Default value: white.

-datapolycol char_string

[Option]
Set the colour scheme used to get colours from the data of the tessellation polyhedra loaded
with option -datapolycol. The type of colour scheme depends on the type of data. For
crystal orientations, the colour scheme can be: R for Rodrigues vector colouring; for scalar
data, the colour scheme can be any list of colours.
Possible values: "R" for crystal orientations and any list of colours for scalars.
Default
value:
"R" for crystal orientations and "blue,cyan,yellow,red" for
scalars.

-datapolycolscheme char_string

[Option]
Set the transparency of the tessellation polyhedra. Provide as argument a value that applies
to all polyhedra or @file_name to load values from a file.
Possible values: 0 to 1. Default value: 0.

-datapolytrs real

[Option]
Set the scale relative to the -datapolycol scal data. Provide as argument the start and
end values combined with :. To specify the tick values, provide as argument the start value,
the intermediate tick values then the end value, combined with :.
Possible values: any. Default value: data minimum:data maximum.

-datapolyscale char_string

-datapolyscaletitle char_string

[Option]

Set the title of the scale relative to the -datapolycol scal data.
Possible values: any. Default value: none.
[Option]
Set the colours of the tessellation faces. See option -datapolycol for the argument format.
Possible values: any. Default value: white.

-datafacecol char_string

[Option]
Set the colour scheme used to get colours from the data of the tessellation faces loaded with
option -datafacecol. See option -datapolycolscheme for the argument format.
Possible values:
see option -datapolycolscheme.
Default value:
see option
-datapolycolscheme.

-datafacecolscheme char_string

[Option]
Set the transparency of the tessellation faces. Provide as argument a value that applies to
all faces or @file_name to load values from a file.
Possible values: 0 to 1. Default value: 0.

-datafacetrs real

32

Neper 2.0.5

[Option]
Set the scale relative to the -datafacecol scal data. Provide as argument the start and
end values combined with :. To specify the tick values, provide as argument the start value,
the intermediate tick values then the end value, combined with :.
Possible values: any. Default value: data minimum:data maximum.

-datafacescale char_string

-datafacescaletitle char_string

[Option]

Set the title of the scale relative to the -datafacecol scal data.
Possible values: any. Default value: none.
[Option]
Set the radii of the tessellation edges. The argument can be one of the following: a real value
that will be used for all entities or the name of a file containing a list of radii.
Possible values: any. Default value: tessellation dependent.

-dataedgerad char_string

[Option]
Set the colours of the tessellation edges. See option -datapolycol for the argument format.
Possible values: any. Default value: black.

-dataedgecol char_string

[Option]
Set the colour scheme used to get colours from the data of the tessellation edges loaded with
option -dataedgecol. See option -datapolycolscheme for the argument format.
Possible values:
see option -datapolycolscheme.
Default value:
see option
-datapolycolscheme.

-dataedgecolscheme char_string

[Option]
Set the transparency of the tessellation edges. Provide as argument a value that applies to
all edges or @file_name to load values from a file.
Possible values: 0 to 1. Default value: 0.

-dataedgetrs real

[Option]
Set the scale relative to the -dataedgecol scal data. Provide as argument the start and
end values combined with :. To specify the tick values, provide as argument the start value,
the intermediate tick values then the end value, combined with :.
Possible values: any. Default value: data minimum:data maximum.

-dataedgescale char_string

-dataedgescaletitle char_string

[Option]

Set the title of the scale relative to the -dataedgecol scal data.
Possible values: any. Default value: none.
[Option]
Set the radii of the tessellation vertices. See option -dataedgerad for the argument format.
Possible values: any. Default value: tessellation dependent.

-dataverrad char_string

[Option]
Set the colours of the tessellation vertices. See option -datapolycol for the argument format.
Possible values: any. Default value: black.

-datavercol char_string

[Option]
Set the colour scheme used to get colours from the data of the tessellation vertices loaded
with option -datavercol. See option -datapolycolscheme for the argument format.
Possible values:
see option -datapolycolscheme.
Default value:
see option
-datapolycolscheme.

-datavercolscheme char_string

Chapter 4: Visualization Module (-V)

33

[Option]
Set the transparency of the tessellation vertices. Provide as argument a value that applies to
all vertices or @file_name to load values from a file.
Possible values: 0 to 1. Default value: 0.

-datavertrs real

[Option]
Set the scale relative to the -datavercol scal data. Provide as argument the start and
end values combined with :. To specify the tick values, provide as argument the start value,
the intermediate tick values then the end value, combined with :.
Possible values: any. Default value: data minimum:data maximum.

-dataverscale char_string

-dataverscaletitle char_string

[Option]

Set the title of the scale relative to the -datavercol scal data.
Possible values: any. Default value: none.
[Option]
Set the radii of the tessellation seeds. See option -dataedgerad for the argument format.
Possible values: any. Default value: tessellation dependent.

-dataseedrad char_string

[Option]
Set the colours of the tessellation seeds. See option -datapolycol for the argument format.
Possible values: any. Default value: grey.

-dataseedcol char_string

[Option]
Set the colour scheme used to get colours from the data of the tessellation seeds loaded with
option -dataseedcol. See option -datapolycolscheme for the argument format.
Possible values:
see option -datapolycolscheme.
Default value:
see option
-datapolycolscheme.

-dataseedcolscheme char_string

[Option]
Set the scale relative to the -dataseedcol scal data. Provide as argument the start and
end values combined with :. To specify the tick values, provide as argument the start value,
the intermediate tick values then the end value, combined with :.
Possible values: any. Default value: data minimum:data maximum.

-dataseedscale char_string

-dataseedscaletitle char_string

[Option]

Set the title of the scale relative to the -dataseedcol scal data.
Possible values: any. Default value: none.
Below are options specific to raster tessellations,

-datarptedgerad real

[Option]

Set the radius of the edges of the raster points.

Possible values: any. Default value: proportional to the raster point size.
[Option]
Set the colour of the edges of the raster points. Provide as argument the name of a colour
that will be used for all points (see Section A.7 [Colours], page 47).
Possible values: any. Default value: black.

-datarptedgecol char_string

4.1.3 Mesh Data Loading and Rendering

The following options enable to define the properties (colour, size, etc.) of the mesh entities
(3D, 2D, 1D and 0D elements, and nodes). This can be done either directly, by specifying the
property values (e.g. the RGB channel values for colour) or indirectly, e.g. using scalar values
that are rendered in colour using a given colour scheme. In this case, a scale image is generated

34

Neper 2.0.5

in addition to the mesh image. The scale properties can be set up (start and end values, tick
values).
The options are listed below for 3D elements (elt3d) and element sets (elset3d), 2D elements
(elt2d) and element sets (elset2d), 1D elements (elt1d) and element sets (elset1d),
0D elements (elt0d) and element sets (elset0d) and nodes (nodes). Also note that the
elt and elset labels can be used in place of eltnd and elsetnd, where n is the highest
mesh dimension. This enables to use the same command whatever the highest mesh dimension
is.
The following options enable to load data relative to the 3D mesh elements. Note that the
options can be applied to element sets by changing elt to elset.
[Option]
Set the colours of the 3D elements. The argument can be one of the following: (i) id for
the default colour palette (see Section A.7 [Colours], page 47), (ii) the name of a colour
that will be used for all elements (see Section A.7 [Colours], page 47), (iii) the name of a
file containing a list of colours (provided as RGB channel values), (iv) a string indicating
how the colours can be obtained, or (v) from_nodes to derive the colours of the elements
from the colours of the nodes (the node colours must be loaded using option -datanodecol).
In case (iv), the string has the format var:file_name, where var can be ori for crystal
orientations or scal for scalar values, and file_name is the name of the file containing
the data. The colour schemes used to derive the colours from the data can be specified with
option -dataelt3dcolscheme.
Possible values: any. Default value: white.

-dataelt3dcol char_string

[Option]
Set the colour scheme used to get colours from the data of the 3D elements loaded with
option -dataelt3dcol. The type of colour scheme depends on the type of data. For crystal
orientations, the colour scheme can be: R for Rodrigues vector colouring; for scalar data,
the colour scheme can be any list of colours.
Possible values: "R" for crystal orientations and any list of colours for scalars.
Default
value:
"R" for crystal orientations and "blue,cyan,yellow,red" for
scalars.

-dataelt3dcolscheme char_string

[Option]
Set the scale relative to the -dataelt3dcol scal data. Provide as argument the minimum
and maximum values combined with :. To specify the tick values, provide as argument the
minimum, the intermediate tick values then the maximum, combined with :.
Possible values: any. Default value: data minimum:data maximum.

-dataelt3dscale char_string

-dataelt3dscaletitle char_string

[Option]

Set the title of the scale relative to the -dataelt3dcol scal data.
Possible values: any. Default value: none.

-dataelt3dedgerad real

[Option]

Set the radius of the edges of the 3D elements.

Possible values: any. Default value: mesh dependent.
[Option]
Set the colour of the edges of the 3D elements. Provide as argument the name of a colour
that will be used for all elements (see Section A.7 [Colours], page 47).
Possible values: any. Default value: black.

-dataelt3dedgecol char_string

The following options enable to load data relative to the 2D elements. Note that the options
can be applied to element sets by changing elt to elset.

Chapter 4: Visualization Module (-V)

35

[Option]
Set the colours of the 2D elements. See option -dataelt3dcol for the argument format.
Possible values: any. Default value: white.

-dataelt2dcol char_string

[Option]
Set the colour scheme used to get colours from the data of the 2D elements loaded with
option -dataelt2dcol. See option -dataelt3dcolscheme for the argument format.
Possible values:
see option -dataelt3dcolscheme.
Default value:
see option
-dataelt3dcolscheme.

-dataelt2dcolscheme char_string

[Option]
Set the scale relative to the -dataelt2dcol scal data. Provide as argument the minimum
and maximum values combined with :. To specify the tick values, provide as argument the
minimum, the intermediate tick values then the maximum, combined with :.
Possible values: any. Default value: data minimum:data maximum.

-dataelt2dscale char_string

-dataelt2dscaletitle char_string

[Option]

Set the title of the scale relative to the -dataelt2dcol scal data.
Possible values: any. Default value: none.

-dataelt2dedgerad real

[Option]

Set the radius of the edges of the 2D elements.

Possible values: any. Default value: mesh dependent.
[Option]
Set the colours of the edges of the 3D elements. See option -dataelt3dedgecol for the
argument format.
Possible values: any. Default value: black.

-dataelt2dedgecol char_string

The following options enable to load data relative to the 1D elements. Note that the options
can be applied to element sets by changing elt to elset.
[Option]
Set the colours of the 1D elements. See option -dataelt3dcol for the argument format.
Possible values: any. Default value: black.

-dataelt1dcol char_string

[Option]
Set the colour scheme used to get colours from the data of the 1D elements loaded with
option -dataelt1dcol. See option -dataelt3dcolscheme for the argument format.
Possible values:
see option -dataelt3dcolscheme.
Default value:
see option
-dataelt3dcolscheme.

-dataelt1dcolscheme char_string

[Option]
Set the scale relative to the -dataelt1dcol scal data. Provide as argument the minimum
and maximum values combined with :. To specify the tick values, provide as argument the
minimum, the intermediate tick values then the maximum, combined with :.
Possible values: any. Default value: data minimum:data maximum.

-dataelt1dscale char_string

-dataelt1dscaletitle char_string

[Option]

Set the title of the scale relative to the -dataelt1dcol scal data.
Possible values: any. Default value: none.

-dataelt1drad char_string
Set the radius of the 1D elements.
Possible values: any. Default value: mesh dependent.

[Option]

36

Neper 2.0.5

The following options enable to load data relative to the 0D mesh elements. Note that the
options can be applied to element sets by changing elt to elset.
[Option]
Set the colours of the 0D elements. See option -dataelt3dcol for the argument format.
Possible values: any. Default value: black.

-dataelt0dcol char_string

[Option]
Set the colour scheme used to get colours from the data of the 0D elements loaded with
option -dataelt0dcol. See option -dataelt3dcolscheme for the argument format.
Possible values:
see option -dataelt3dcolscheme.
Default value:
see option
-dataelt3dcolscheme.

-dataelt0dcolscheme char_string

[Option]
Set the scale relative to the -dataelt0dcol scal data. Provide as argument the minimum
and maximum values combined with :. To specify the tick values, provide as argument the
minimum, the intermediate tick values then the maximum, combined with :.
Possible values: any. Default value: data minimum:data maximum.

-dataelt0dscale char_string

-dataelt0dscaletitle char_string

[Option]

Set the title of the scale relative to the -dataelt0dcol scal data.
Possible values: any. Default value: none.

-dataelt0drad char_string

[Option]

Set the radius of the 0D elements.

Possible values: any. Default value: mesh dependent.
The following options enable to load data relative to the nodes.
[Option]
Set the coordinates of the nodes. The argument can be the name of a file containing a list of
coordinates, or a string indicating how the coordinates can be obtained. The string has the
format var:file_name, where var can be disp for displacements, and file_name is the
name of the file containing the data.
Possible values: any. Default value: none.

-datanodecoo char_string

-datanodecoofact real

[Option]

Set the value of the scaling factor to apply to the displacements of the nodes.
Possible values: any. Default value: 1.

-datanoderad file_name

[Option]

Set the radius of the nodes.

Possible values: any. Default value: mesh dependent.

-datanodecol file_name

[Option]

Set the colours of the nodes. See option -dataelt3dcol for the argument format.
Possible values: any. Default value: black.
[Option]
Set the colour scheme used to get colours from the data of the nodes loaded with option
-datanodecol. See option -dataelt3dcolscheme for the argument format.
Possible values:
see option -dataelt3dcolscheme.
Default value:
see option
-dataelt3dcolscheme.

-datanodecolscheme char_string

Chapter 4: Visualization Module (-V)

37

[Option]
Set the scale relative to the -datanodecol scal data. Provide as argument the minimum
and maximum values combined with :. To specify the tick values, provide as argument the
minimum, the intermediate tick values then the maximum, combined with :.
Possible values: any. Default value: data minimum:data maximum.

-datanodescale char_string

-datanodescaletitle char_string

[Option]

Set the title of the scale relative to the -datanodecol scal data.
Possible values: any. Default value: none.

4.1.4 Point Data Loading and Rendering

The following options enable to define the properties (colour, shape, size, etc.) of points loaded
as input. This can be done either directly, by specifying the property values (e.g. the RGB
channel values for colour) or indirectly, e.g. using scalar values that are rendered in colour using
a given colour scheme. In this case, a scale image is generated in addition to the image. The
scale properties can be set up (start and end values, tick values).
[Option]
Set the coordinates of the points. The argument can be the name of a file containing a list of
coordinates, or a string indicating how the coordinates can be obtained. The string has the
format var:file_name, where var can be disp for displacements, and file_name is the
name of the file containing the data.
Possible values: any. Default value: none.

-datapointcoo char_string

-datapointcoofact real

[Option]

Set the value of the scaling factor to apply to the displacements of the points.
Possible values: any. Default value: 1.
[Option]
Set the radius (and shape) of the points. The argument can be a value that applies to all
points, a file containing a list of radii, or a string indicating how the radii can be obtained.
The string has the format var:file_name, where var stands for the morphology of the
points and file_name is the name of the file containing the morphology parameters. For
cube shape, var must be cube and the file must contain, for each point, the radius (half of
the edge length) then the coordinates of the three axes (which also is the rotation matrix that
brings the reference axes into coincidence with the cube axes). For cylinder shape, var must
be cyl and the file must contain, for each point, the radius, the length, then the coordinates
of the axis. For ellipsoidal shape, var must be ell and the file must contain, for each point,
the three radii then the coordinates of the three axes. The last capability is very specific: if
the points are plotted in Rodrigues space, appending :rodrigues to the option argument
enables to account for space distortion.
Possible values: any. Default value: point set dependent.

-datapointrad char_string

[Option]
Set the colours of the points. The argument can be one of the following: (i) id for the
default colour palette (see Section A.7 [Colours], page 47), (ii) the name of a colour that will
be used for all points (see Section A.7 [Colours], page 47), (iii) the name of a file containing
a list of colours (provided as RGB channel values) or (iv) a string indicating how the colours
can be obtained,. In case (iv), the string has the format var:file_name, where var can be
ori for crystal orientations or scal for scalar values, and file_name is the name of the
file containing the data. The colour schemes used to derive the colours from the data can be
specified with option -datapointcolscheme.
Possible values: any. Default value: grey.

-datapointcol char_string

38

Neper 2.0.5

[Option]
Set the colour scheme used to get colours from the data of the points loaded with
option -datapoint. The type of colour scheme depends on the type of data. For crystal
orientations, the colour scheme can be: R for Rodrigues vector colouring; for scalar data,
the colour scheme can be any list of colours.
Possible values: "R" for crystal orientations and any list of colours for scalars.
Default
value:
"R" for crystal orientations and "blue,cyan,yellow,red" for
scalars.

-datapointcolscheme char_string

[Option]
Set the transparency of the points. Provide as argument a value that applies to all points or
@file_name to load values from a file.
Possible values: 0 to 1. Default value: 0.

-datapointtrs real

[Option]
Set the scale relative to the -datapointcol scal data. Provide as argument the minimum
and maximum values combined with :. To specify the tick values, provide as argument the
minimum, the intermediate tick values then the maximum, combined with :.
Possible values: any. Default value: data minimum:data maximum.

-datapointscale char_string

-datapointscaletitle char_string

[Option]

Set the title of the scale relative to the -datapointcol scal data.
Possible values: any. Default value: none.

4.1.5 Coordinate System Rendering

[Option]
Set the coordinates of the origin of the coordinate system. Combine the coordinates with :.
Possible values: any. Default value: 0:0:0.

-datacsyscoo char_string

-datacsyslength real

[Option]

Set the length of the coordinate system axes.

Possible values: any. Default value: 0.2.

-datacsysrad real

[Option]

Set the radius of the coordinate system axes.

Possible values: any. Default value: 0.01.

-datacsyslabel char_string

[Option]

Set the labels of the coordinate system axes. Combine the labels with :.
Possible values: any. Default value: X1:X2:X3.
[Option]
Set the colour of the coordinate system. Provide as argument any colour as detailed in
Section A.7 [Colours], page 47.
Possible values: any. Default value: 32|32|32.

-datacsyscol char_string

4.1.6 Slice Settings

[Option]
Use this option to plot one (or several) slice(s) of the mesh. Provide as argument the equation(s) of the plane(s), under the form a*x+b*y+c*z=d or any equivalent mathematical
expression. Combine with ,.
Possible values: any. Default value: none.

-slicemesh char_string

Chapter 4: Visualization Module (-V)

39

4.1.7 Show Settings

The following options apply to the full tessellations or mesh.

-showtess logical

[Option]

Use this option to show or hide the tessellation.

Possible values: 0 or 1. Default value: 1 if tess loaded and no mesh.

-showtesr logical

[Option]

Use this option to show or hide the raster tessellation.

Possible values: 0 or 1. Default value: 1 if tesr loaded and no mesh.

-showmesh logical

[Option]

Use this option to show or hide the mesh.

Possible values: 0 or 1. Default value: 1 if mesh loaded and no slice.

-showmeshslice logical

[Option]

Use this option to show or hide the mesh slice(s).

Possible values: 0 or 1. Default value: 1 if existing slice(s).
[Option]
Use this option to show or hide the points. To show only specific points, provide @file_name
to load point numbers from a file.
Possible values: any. Default value: none.

-showpoint logical or char_string

The following option applies to the cells of a tessellation or a raster tessellation, independently
of its dimension,
[Option]
Specify the cells to show. The argument can be: all for all, none for none, @file_name
to load polyhedron identifiers from a file, or any expression based on the keys listed in
Section A.2 [Tessellation Keys], page 43 or Section A.3 [Raster Tessellation Keys], page 45.
Possible values: any. Default value: all.

-showcell char_string

For tessellations, it is also possible to set visibility on an entity-basis,

[Option]
Specify the polyhedra to show. The argument can be: all for all, none for none,
@file_name to load polyhedron identifiers from a file, or any expression based on the keys
listed in Section A.2 [Tessellation Keys], page 43.
Possible values: any. Default value: all.

-showpoly char_string

[Option]
Specify the faces to show. The argument can be: all for all, none for none, @file_name
to load face identifiers from a file, or any expression based on the keys listed in Section A.2
[Tessellation Keys], page 43. The following specific keys are also available: cell_shown and
poly_shown.
Possible values: any. Default value: none.

-showface char_string

[Option]
Specify the edges to show. The argument can be: all for all, none for none, @file_name
to load edge numbers from a file, or any expression based on the keys listed in Section A.2
[Tessellation Keys], page 43. The following specific keys are also available: cell_shown,
poly_shown and face_shown.
Possible values: any. Default value: cell_shown.

-showedge char_string

40

Neper 2.0.5

[Option]
Specify the vertices to show. The argument can be: all for all, none for none, @file_name
to load vertex numbers from a file, or any expression based on the keys listed in Section A.2
[Tessellation Keys], page 43. The following specific keys are also available: cell_shown,
poly_shown, face_shown and edge_shown.
Possible values: any. Default value: none.

-showver char_string

[Option]
Specify the seeds to show. The argument can be: all for all, none for none, @file_name
to load seed numbers from a file, or any expression based on the keys listed in Section A.2
[Tessellation Keys], page 43. The following specific key is also available: cell_shown.
Possible values: any. Default value: none.

-showseed char_string

[Secondary option]
Show the interpolations of the tessellation faces (if any). The interpolation edges are printed
in grey with a radius equal to the radius of the face edges.
Possible values: 0 or 1. Default value: 0.

-showfaceinter logical

The following options apply to the entities of the mesh. The options apply to 3D elements
(elt3d) and element sets (elset3d), 2D elements (elt2d) and element sets (elset2d),
1D elements (elt1d) and element sets (elset1d), 0D elements (elt0d) and element sets
(elset0d), and nodes (nodes). Also note that the elt and elset labels can be used in
place of eltnd and elsetnd, where n is the highest mesh dimension. This enables to use the
same command whatever the highest mesh dimension is.
In the following option descriptions, note that any options can be applied to element sets by
changing elt to elset.
[Option]
Specify the 3D elements to show. The argument can be: all for all, none for none,
@file_name to load element identifiers from a file, or any expression based on the keys
listed in Section A.4 [Mesh Keys], page 45.
Possible values: any. Default value: all if highest mesh dim. is 3 and none otherwise.

-showelt3d char_string

[Option]
Specify the 2D elements to show. The argument can be: all for all, none for none,
@file_name to load element identifiers from a file, or any expression based on the keys
listed in Section A.4 [Mesh Keys], page 45. The following specific key is also available:
elt3d_shown.
Possible values: any. Default value: all if highest mesh dim. is 2 and none otherwise.

-showelt2d char_string

[Option]
Specify the 1D elements to show. The argument can be: all for all , none for none,
@file_name to load element numbers from a file, or any expression based on the keys
listed in Section A.4 [Mesh Keys], page 45. The following specific keys are also available:
elt2d_shown and elt3d_shown.
Possible values: any. Default value: all if highest mesh dim. is 1 and none otherwise.

-showelt1d char_string

[Option]
Specify the 0D elements to show. The argument can be: all for all none for none,
@file_name to load element numbers from a file, or any expression based on the keys
listed in Section A.4 [Mesh Keys], page 45. The following specific keys are also available:
elt1d_shown, elt2d_shown and elt3d_shown.
Possible values: any. Default value: all if highest mesh dim. is 0 and none otherwise.

-showelt0d char_string

Chapter 4: Visualization Module (-V)

41

[Option]
Specify the nodes to show. The argument can be: all for all , none for none, @file_name
to load node numbers from a file, or any expression based on the keys listed in Section A.4
[Mesh Keys], page 45. The following specific keys are also available: elt0d_shown,
elt1d_shown, elt2d_shown and elt3d_shown.
Possible values: any. Default value: none.

-shownode char_string

-showcsys logical

[Option]

Show the coordinate system.

Possible values: 0 or 1. Default value: 0.
[Option]
Show the shadows. If you want colours not affected by shadowing, switch this option off.
Possible values: 0 or 1. Default value: 1 in 3D and 0 in 2D and 1D.

-showshadow logical

4.1.8 Camera Settings

[Option]
Specify the camera coordinates. By default, the camera is shifted by a vector alpha*v from
the tessellation or mesh centre. The coordinates of vector v are denoted as vx, vy and vz
(= 3.462, -5.770 and 4.327, respectively, in 3D and 0, 0 and 8, respectively, in 2D and 1D).
The scalar alpha is equal to the length of the tessellation or mesh (taken as the maximum
of the lengths in the 3 directions). The coordinates of the tessellation or mesh centre are
denoted as x, y and z (if both a tessellation and a mesh have been loaded, the mesh is
considered). Provide as argument the expression for the 3 coordinates, combined with :.
Possible values: any. Default value: x+alpha*vx:y+alpha*vy:z+alpha*vz.

-cameracoo char_string:char_string:char_string

[Option]
Specify the location the camera looks at. By default, the camera looks at the tessellation or
mesh centre. The coordinates of the tessellation or mesh centre are denoted as x, y and z
(if both a tessellation and a mesh have been loaded, the mesh is considered). Provide as
argument the expression for the 3 coordinates, combined with :.
Possible values: any. Default value: x:y:z.

-cameralookat char_string:char_string:char_string

[Option]
Specify the opening angle of the camera along the horizontal direction (in degrees). The
opening angle along the vertical direction is determined from the opening along the horizontal
direction and the image size ratio.
Possible values: any. Default value: 25.

-cameraangle real

[Option]
Specify the sky vector of the camera (vertical direction). Provide as argument the coordinates
combined with :.
Possible values: any. Default value: 0:0:1.

-camerasky real:real:real

[Option]
Specify the type of projection of the camera.
Possible values: perspective or orthographic. Default value: perspective for 3D and
orthographic for 2D and 1D.

-cameraprojection char_string

4.1.9 Output Image Settings

[Option]
Specify the size of the image (in pixels). Provide as argument the width and height, combined
with :.
Possible values: any. Default value: 1200:900.

-imagesize int:int

42

Neper 2.0.5

-imagebackground char_string

[Option]
Provide as argument any colour as detailed in

Specify the colour of the background.

Section A.7 [Colours], page 47.
Possible values: any. Default value: white.

[Option]
Use antialiasing to produce a smoother image. Switch antialiasing off for faster image generation or smaller image file.
Possible values: 0 or 1. Default value: 1.

-imageantialias logical

-imageformat char_string

[Option]
It can be the PNG format (.png) or the POV-Ray

Specify the output image format.

format (.pov). Combine with ,.
Possible values: png or pov. Default value: png.

4.1.10 Scripting
[Option]
Use this option to make a loop. Provide as argument the name of the loop variable, its initial
value, the loop increment value, the final value then the commands to execute. An example
of use of the -loop / -endloop capability is provided in the Examples Section.
Possible values: any. Default value: none.

-loop char_string real real real ... -endloop .

Appendix A: Expressions and Keys

43

Appendix A Expressions and Keys

A.1 Mathematical and Logical Expressions
Neper can handle mathematical expressions. It makes use of the GNU libmatheval library. The
expression must contain no space, tabulation or new-line characters, and match the following
syntax1 :
Supported constants are (names that should be used are given in parenthesis): e (e), log2(e)
(log2e), log10(e) (log10e), ln(2) (ln2), ln(10) (ln10), pi (pi), pi / 2 (pi_2), pi / 4 (pi_4), 1 /
pi (1_pi), 2 / pi (2_pi), 2 / sqrt(pi) (2_sqrtpi), sqrt(2) (sqrt) and sqrt(1 / 2) (sqrt1_2).
Variable name is any combination of alphanumericals and _ characters beginning with a nondigit that is not elementary function name.
Supported elementary functions are (names that should be used are given in parenthesis): exponential (exp), logarithmic (log), square root (sqrt), sine (sin), cosine (cos), tangent (tan),
cotangent (cot), secant (sec), cosecant (csc), inverse sine (asin), inverse cosine (acos), inverse tangent (atan), inverse cotangent (acot), inverse secant (asec), inverse cosecant (acsc),
hyperbolic sine (sinh), cosine (cosh), hyperbolic tangent (tanh), hyperbolic cotangent (coth),
hyperbolic secant (sech), hyperbolic cosecant (csch), hyperbolic inverse sine (asinh), hyperbolic inverse cosine (acosh), hyperbolic inverse tangent (atanh), hyperbolic inverse cotangent
(acoth), hyperbolic inverse secant (asech), hyperbolic inverse cosecant (acsch), absolute value
(abs), Heaviside step function (step) with value 1 defined for x = 0, Dirac delta function with
infinity (delta) and not-a-number (nandelta) values defined for x = 0, and error function (erf).
Supported unary operation is unary minus (-).
Supported binary operations are addition (+), subtraction (+), multiplication (*), division
multiplication (/) and exponentiation (^).
Usual mathematical rules regarding operation precedence apply. Parenthesis (( and ))
could be used to change priority order.
Neper includes additional functions: the minimum and maximum functions (min(a,b) and
max(a,b), respectively). a and b can be any expression as described above. Moreover, square
brackets ([ and ]) and curly brackets ({ and }) can be used instead of the parentheses.
The logical operators supported are: = (==), 6= (!=), (>=), (<=), > (>), < (<), AND (&&)
and OR (||).

A.2 Tessellation Keys

Available keys for tessellation seeds, vertices, edges, faces and polyhedra are provided below.
Also note that the descriptors apply to cells if they are tagged to apply to polyhedra and the
tessellation is 3D, faces and the tessellation is 2D or edges and the tessellation is 1D.
To turn a key value into a value relative to the mean over all entities (e.g. the relative cell size),
append the key expression with the :rel modifier. To turn a key value into a value which holds
for a unit cell size, append the key expression with the :uc modifier. To use as a reference only
the body or true entities (see below), append b or t to the modifiers, respectively.
Key
id
x
y
z
1

Descriptor
Identifier
x coordinate
y coordinate
z coordinate

Taken from the libmatheval documentation.

Apply to
seed, ver,
seed, ver,
seed, ver,
seed, ver,

edge,
edge,
edge,
edge,

face,
face,
face,
face,

poly
poly
poly
poly

44

w
true
body
state
domtype

length
area
vol
size
diameq
circularity
sphericity
dihangleav,
dihanglemin,
dihanglemax
dihanglelist
ff
cyl
vernb
edgenb
facenb
polynb
neighnb
verlist
edgelist
facelist
npolylist
facearealist
faceeqlist
polyscale1
facescale1

Neper 2.0.5

Laguerre weight
true level
body level
state
type of domain (0 if on a domain vertex, 1
if on a domain edge and 2 if on a domain
face)
length
area
volume
size (length/area/volume in 1D/2D/3D)
diameter of the equivalent circle/sphere in
2D/3D, length in 1D
circularity (2D counterpart of sphericity)
sphericity2
average, minium and maximum dihedral
angle

seed
ver, edge,
ver, edge,
ver, edge,
ver, edge,

dihedral angle list

flatness fault (in degrees)
whether or not is used to describe the circular part of a cylinder domain
number of vertices
number of edges
number of faces
number of polyhedra
Number of neighbours of an edge, face or
polyhedron3
vertex list
edge list
face list
neighbouring polyhedron list4
face area list
face equation list5
scale-1 polyhedron (2-scale tessellation)
scale-1 face (2-scale tessellation)

face, poly
face
edge

face, poly
face, poly
face, poly
face

edge
face, poly
poly
cell
poly, face, edge
face
poly
face, poly

edge, face, poly

ver, face, poly
ver, edge, poly
ver, edge, face
edge, face, poly
poly
poly
poly
poly
poly
poly
poly
face

The list variables (verlist, etc.) are not available for sorting (option -sort).
For a cell, the body and true variables are defined as follows,
body is an integer equal to 0 if the cell is at the domain boundary, i.e. if it shares at least
one face with it (edge in 2D, vertex in 1D), and is equal to 1 or higher otherwise. This is
determined as follows: if a cell is surrounded by cells with body values equal to or higher
than n, its body value is equal to n + 1. Therefore, body tends to increase with the distance
to the domain boundary and can be used to define cells that may suffer from boundary
effects.
2
3
4
5

Sphericity of a polyhedron = ratio of the surface area of the sphere of equivalent volume to the surface area of
the polyhedron.
Neighbour of an edge, face or polyhedron = touching entity of the same type (edges for an edge, . . . )
If a polyhedron has no neighbour on a face, a negative value is returned instead of the neighbour id.
A face equation is specified by the parameters d, a, b and c, with the equation being: ax + by + cz = d. The
vector (a, b, c) is pointing outwards of the polyhedron.

Appendix A: Expressions and Keys

45

true is an integer equal to 0 it the cell shape is biased by the domain boundary, and is
equal to 1 or higher otherwise. A value higher than 0 is achieved if and only if any seed
that would have been located outside the domain (where it could not be) would not have
affected the shape of the cell. This condition is fulfilled if the distance between the seed of
the cell and any of its vertices is lower than the minimum distance between a vertex of the
cell and the domain boundary. true is extended to values higher than 1 in the same way
as body: if a cell is surrounded by cells with true values equal to or higher than n, its true
value is equal to n + 1. As body, true tends to increase with the distance to the domain
boundary, and true body. true is especially useful for statistics on the cells (morphology,
mesh, etc.), for which only cells with true 1 should be considered.
For entities of lower dimension than cells (vertices, edges and faces), body and true are equal
to the maximum body or true values of the cells they belong to.

A.3 Raster Tessellation Keys

Available keys for raster tessellation seeds and cells are provided below.
Key
id
x
y
z
w
size
diameq

Descriptor
Identifier
x coordinate
y coordinate
z coordinate
Laguerre weight
size (length/area/volume in 1D/2D/3D)
diameter of the equivalent circle/sphere in
2D/3D, length in 1D

Apply to
seed, cell
seed, cell
seed, cell
seed, cell
seed
cell
cell

A.4 Mesh Keys

Available keys for mesh node, elements and element sets (of all dimensions) and points are
provided below.
Key
id
x
y
z
dim
elset0d
elset1d
elset2d
elset3d
part
cyl
vol
area
length
rr
rrav,
rrmax
Osize

rrmin,

Descriptor
Identifier
x coordinate
y coordinate
z coordinate
dimension (= lowest parent elt dimension)
0D elset
1D elset
2D elset
3D elset
partition
whether or not is used to describe the circular part of a cylinder domain
volume
area
length
radius ratio
average, min and max radius ratios

Apply to
node, nD elt, nD
node, nD elt, nD
node, nD elt, nD
node, nD elt, nD
node
0D elt
1D elt
2D elt
3D elt
nD elt, node
1D elt, 1D elset

Osize

3D elset

3D
2D
1D
3D
3D

elset
elset
elset
elset

elt, 3D elset
elt
elt, 3D elt, 1D elset
elt
elset

46

eltnb
true
body
domtype

2dmeshp
2dmeshd
2dmeshv
2dmeshn

Neper 2.0.5

number of elements
true level
body level
type of domain (0 if on a domain vertex, 1
if on a domain edge and 2 if on a domain
face)
coordinates of the closest point of the 2D
mesh
distance to 2dmeshp
vector to 2dmeshp
outgoing normal vector of the 2D mesh at
2dmeshp

nD elset
nD elt, nD elset
nD elt, nD elset
2D elset, 1D elset, 0D elset,
2D elt, 1D elt, 0D elt
node, 3D elt
node, 3D elt
node, 3D elt
node, 3D elt,

nD stands for an arbitrary dimension (from 0D to 3D). Variables starting by 2dmesh are only
available for statistics (options starting by -stat of module -M); for elements, they apply to the
centroids.

A.5 Point Keys

Available keys for points are provided below.

Key
id
x
y
z
cell
elt3d
elset3d
2dmeshp
2dmeshd
2dmeshv
2dmeshn

Descriptor
Identifier
x coordinate
y coordinate
z coordinate
cell
3D element
3D elset
coordinates of the closest point of the 2D
mesh
distance to 2dmeshp
vector to 2dmeshp
outgoing normal vector of the 2D mesh at
2dmeshp

Apply to
point
point
point
point
point
point
point
point

Require

point
point
point

mesh
mesh
mesh

tessellation
mesh
mesh
mesh

A.6 Rotations and Orientations

Rotations and orientations can be described using the following descriptors (see Orilib, http://
orilib.sourceforge.net, for more information).

Key
g
rtheta
R
q
e
ek
er

Descriptor
Rotation matrix
Rotation axis / angle pair
Rodrigues vector
Quaternion
Euler angles (Bunge convention)
Euler angles (Kocks convention)
Euler angles (Roe convention)

Number of variables
9
4
3
4
3
3
3

Appendix A: Expressions and Keys

47

A.7 Colours
The available colours are provided below, with their corresponding RGB channel
values. Any other colour can be defined from the RGB channel values, under format
R_value|G_value|B_value.
( 0,
( 0,
(255,
( 0,
(128,
(127,
(128,
( 0,
( 0,
( 64,
(192,
(139,
(255,
(248,
( 0,
(245,
(240,
(255,
(255,
(255,
( 0,
(240,
(255,
( 0,
( 70,
(255,
( 72,
(255,
(135,
(240,
(255,
(255,
(255,
(255,
(255,
( 60,
(238,
(255,
(188,
(139,
( 30,
(222,
(250,
( 64,
( 72,
(255,
(250,

0,
255,
255,
255,
0,
255,
128,
128,
191,
64,
192,
0,
140,
248,
0,
255,
128,
127,
250,
250,
100,
248,
255,
139,
130,
245,
61,
160,
206,
255,
218,
99,
105,
235,
228,
179,
130,
239,
143,
69,
144,
184,
240,
224,
209,
228,
235,

0)
0)
0)
255)
0)
0)
0)
128)
255)
64)
192)
0)
0)
255)
205)
250)
128)
80)
240)
205)
0)
255)
224)
139)
180)
238)
139)
122)
250)
240)
185)
71)
180)
205)
181)
113)
238)
213)
143)
19)
255)
135)
230)
208)
204)
225)
215)

black
green
yellow
cyan
maroon
chartreuse
olive
teal
deepskyblue
darkgrey
silver
darkred
darkorange
ghostwhite
mediumblue
mintcream
lightcoral
coral
floralwhite
lemonchiffon
darkgreen
aliceblue
lightyellow
darkcyan
steelblue
seashell
darkslateblue
lightsalmon
lightskyblue
honeydew
peachpuff
tomato
hotpink
blanchedalmond
moccasin
mediumseagreen
violet
papayawhip
rosybrown
saddlebrown
dodgerblue
burlywood
linen
turquoise
mediumturquoise
mistyrose
antiquewhite

(255, 0, 0)
( 0, 0, 255)
(255, 0, 255)
(255, 255, 255)
( 0, 0, 128)
( 0, 255, 127)
(128, 0, 128)
(128, 128, 128)
(124, 252, 0)
(255, 69, 0)
(255, 250, 250)
( 0, 0, 139)
(240, 255, 255)
(255, 255, 240)
(255, 182, 193)
( 75, 0, 130)
(255, 192, 203)
(250, 128, 114)
(127, 255, 212)
(255, 215, 0)
(255, 165, 0)
(224, 255, 255)
(139, 0, 139)
(205, 133, 63)
(255, 240, 245)
( 0, 250, 154)
(184, 134, 11)
(255, 228, 196)
(250, 250, 210)
(255, 248, 220)
(245, 245, 245)
(112, 128, 144)
(253, 245, 230)
(189, 183, 107)
( 0, 206, 209)
(199, 21, 133)
(173, 255, 47)
(143, 188, 143)
(255, 20, 147)
(148, 0, 211)
(119, 136, 153)
(255, 222, 173)
(123, 104, 238)
(135, 206, 235)
(245, 245, 220)
(210, 180, 140)
(216, 191, 216)

red
blue
magenta
white
navy
springgreen
purple
grey
lawngreen
orangered
snow
darkblue
azure
ivory
lightpink
indigo
pink
salmon
aquamarine
gold
orange
lightcyan
darkmagenta
peru
lavenderblush
mediumspringgreen
darkgoldenrod
bisque
lightgoldenrodyellow
cornsilk
whitesmoke
slategrey
oldlace
darkkhaki
darkturquoise
mediumvioletred
greenyellow
darkseagreen
deeppink
darkviolet
lightslategrey
navajowhite
mediumslateblue
skyblue
beige
tan
thistle

48

Neper 2.0.5

( 50, 205, 50) limegreen

(233, 150, 122) darksalmon
(176, 196, 222) lightsteelblue
( 65, 105, 225) royalblue
(152, 251, 152) palegreen
(220, 20, 60) crimson
(245, 222, 179) wheat
(186, 85, 211) mediumorchid
(230, 230, 250) lavender
(240, 230, 140) khaki
(144, 238, 144) lightgreen
(175, 238, 238) paleturquoise
( 47, 79, 79) darkslategrey
(153, 50, 204) darkorchid
( 46, 139, 87) seagreen
(154, 205, 50) yellowgreen
(138, 43, 226) blueviolet
(219, 112, 147) palevioletred
(107, 142, 35) olivedrab
(147, 112, 219) mediumpurple
(244, 164, 96) sandybrown
( 85, 107, 47) darkolivegreen
(102, 205, 170) mediumaquamarine
(106, 90, 205) slateblue
(238, 232, 170) palegoldenrod
( 34, 139, 34) forestgreen
( 25, 25, 112) midnightblue
( 32, 178, 170) lightseagreen
(211, 211, 211) lightgrey
(218, 112, 214) orchid
(100, 149, 237) cornflowerblue
(160, 82, 45) sienna
(178, 34, 34) firebrick
(176, 224, 230) powderblue
(205, 92, 92) indianred
(105, 105, 105) dimgrey
(173, 216, 230) lightblue
(210, 105, 30) chocolate
(165, 42, 42) brown
(218, 165, 32) goldenrod
(220, 220, 220) gainsboro
(221, 160, 221) plum
( 95, 158, 160) cadetblue
The default colour palette (used for options -datacellcol, -dataelt3dcol, etc.)
is
defined from the above colour list, by excluding colours of brightness below 0.2 and
above 0.8. The brightness is defined as the average of the channel values divided by 255.
The resulting list of colours is: red, green, blue, yellow, magenta, cyan, chartreuse,
springgreen, olive, purple, teal, grey, deepskyblue, lawngreen, darkgrey, orangered,
silver, darkorange, mediumblue, indigo, lightcoral, coral, salmon, aquamarine, gold,
orange, darkmagenta, darkcyan, peru, steelblue, mediumspringgreen, darkslateblue,
darkgoldenrod, lightsalmon, lightskyblue, tomato, slategrey, hotpink, darkkhaki,
darkturquoise, mediumseagreen, mediumvioletred, violet, greenyellow, darkseagreen,
rosybrown, deeppink, saddlebrown, darkviolet, dodgerblue, lightslategrey, burlywood,
mediumslateblue, turquoise, skyblue, mediumturquoise, tan, limegreen, darksalmon,
lightsteelblue, royalblue, palegreen, crimson, mediumorchid, khaki, lightgreen,
darkslategrey, darkorchid, seagreen, yellowgreen, blueviolet, palevioletred,
olivedrab, mediumpurple, sandybrown, darkolivegreen, mediumaquamarine, slateblue,
forestgreen, midnightblue, lightseagreen, orchid, cornflowerblue, sienna, firebrick,
indianred, dimgrey, chocolate, brown, goldenrod, plum and cadetblue.

Appendix B: File Formats

49

Appendix B File Formats

B.1 Tessellation File (.tess)
Here are details on the .tess file format version 2.0. Developers should note that read and write
functions are available as neut_tess_fscanf and neut_tess_fprintf, defined in directories
neut/neut_tess/neut_tess_fscanf and neut/neut_tess/neut_tess_fprintf.
***tess
**format
format
**general
dim type
**cell
number_of_cells
[*id
cell1_id cell2_id ... ]
[*seed
seed_id seed_x seed_y seed_z seed_weight
... ]
[*ori
descriptor
cellid_param1 cellid_param2 ...
... ]
**vertex
total_number_of_vertices
ver_id ver_x ver_y ver_z ver_state
...
**edge
total_number_of_edges
edge_id ver_1 ver_2 edge_state
...
**face
total_number_of_faces
face_id number_of_vertices ver_1 ver_2 ...
number_of_edges
edge_1* edge_2* ...
face_eq_d face_eq_a face_eq_b face_eq_c
face_state face_point face_point_x face_point_y face_point_z
...
**polyhedron
total_number_of_polyhedra
poly_id number_of_faces face_1* face_2* ...
...
**domain
*general
dom_type
*vertex
total_number_of_dom_vertices
dom_ver_id dom_ver_x dom_ver_y dom_ver_z dom_ver_label
number_of_dom_tess_vertices ver_1
...

50

Neper 2.0.5

*edge
total_number_of_dom_edges
dom_edge_id dom_edge_label
number_of_dom_tess_edges edge_1 edge_2 ...
dom_ver_1 dom_ver_2
...
*face
total_number_of_dom_faces
dom_face_id number_of_dom_vertices dom_ver_1 dom_ver_2 ...
number_of_dom_edges
dom_edge_1 dom_edge_2 ...
dom_face_eq_d dom_face_eq_a dom_face_eq_b dom_face_eq_c
dom_face_label
number_of_dom_tess_faces dom_tess_face_1 dom_tess_face_2 ...
...
***end
where (with identifiers being integer numbers),
***tess denotes the beginning of a tessellation file.
**format denotes the beginning of the format field.
format is the file format, currently 2.0 (character string).
**general denotes the beginning of the general information field.
dim is the dimension of the tessellation (1, 2 or 3).
type is the type of tessellation (always standard).
**cell denotes the beginning of the cell field.
number_of_cells is the number of cells.
*id denotes the beginning of an optional identifier field. It the field is not present, the cells
are considered to be numbered contiguously from 1.
cell1_id, cell2_id, . . . are the actual identifiers of the cells.
*seed denotes the beginning of a seed field.
seed_id is the identifier of a seed and ranges from 1 to number_of_cells.
seed_x, seed_y and seed_z are the three coordinates of a seed (real numbers).
seed_weight is the weight of a seed (real number).
*ori denotes the beginning of an optional crystal orientation field.
descriptor is the descriptor used to parametrize the crystal orientations. See Section A.6
[Rotations and Orientations], page 46 for the list of available descriptors.
cellid_param1, cellid_param2, . . . are the values of the orientation descriptor of cell id.
**vertex denotes the beginning of the vertex field.
total_number_of_vertices is the total number of vertices.
ver_id is the identifier of a vertex and ranges from 1 to total_number_of_vertices.
ver_x, ver_y and ver_z are the three coordinates of a vertex (real numbers).
ver_state is an integer indicating the state of a vertex. For a standard tessellation (no
regularization), it equals 0. For a regularized tessellation, it equals 0 if the vertex has not
been modified by regularization and is higher than 0 otherwise.
**edge denotes the beginning of the edge field.
total_number_of_edges is the total number of edges.
edge_id is the identifier of an edge and ranges from 1 to total_number_of_edges.

Appendix B: File Formats

51

ver_1, ver_2, ... are identifiers of vertices.

edge_state is an integer indicating the state of an edge (always 0).
**face denotes the beginning of the face field. It is present for a tessellation of dimension
2 or 3.
total_number_of_faces is the total number of faces.
face_id is the identifier of a face and ranges from 1 to total_number_of_faces.
number_of_vertices is the number of vertices of a face.
number_of_edges is the number of edges of a face.
edge_1*, edge_2*, ... are identifiers of the edges of a face, signed according to their
orientation in the face.
face_eq_a, face_eq_b, face_eq_c and face_eq_d are the parameters of the equation of
a face: face eq a x + face eq b y + face eq c z = face eq d. The parameters are scaled so
that face eq a2 + face eq b2 + face eq c 2 = 1.
face_state is an integer indicating the state of a face. For a standard tessellation (no
regularization), it equals 0. For a regularized tessellation, it equals 0 if it has not been
modified by regularization and 1 otherwise.
face_point is an integer indicating the point used for the interpolation of a face. For a
standard tessellation (no regularization), it equals 0. For a regularized tessellation: if the
point is the face barycentre, it equals 0; if the point is one of the face vertices, it equals
to the position of the vertex in the list of vertices of the face. It equals -1 if the point is
undefined.
face_point_x, face_point_y and face_point_z are the coordinates of the point used for
the interpolation of a face (equal 0 if undefined).
**polyhedron denotes the beginning of the polyhedron field. It is present for a tessellation
of dimension 3.
total_number_of_polyhedra is the total number of polyhedra.
poly_id is the identifier of a polyhedron and ranges from 1 to total_number_of_
polyhedra.
number_of_faces is the number of faces of a polyhedron.
face_1*, face_2*, ... are identifiers of the faces of a polyhedron, signed according to their
orientations in the polyhedron (positive if the normal of the face is pointing outwards and
negative if it is pointing inwards).
**domain denotes the beginning of the domain field.
*general denotes the beginning of the domain general information field.
dom_type is the type of the domain (one of cube, cylinder, square, circle, poly and
planes).
*vertex denotes the beginning of the domain vertex field.
total_number_of_dom_vertices is the total number of domain vertices.
dom_ver_id is the identifier of a domain vertex and ranges between 1 to total_number_
of_dom_vertices.
dom_ver_x, dom_ver_y and dom_ver_z are the three coordinates of a domain vertex (real
numbers).
dom_ver_label is the label of a domain vertex.
number_of_dom_tess_vertices is the number of tessellation vertices of a domain vertex
(must be 1).
*edge denotes the beginning of the domain edge field (for a tessellation of dimension 2
or 3).

52

Neper 2.0.5

total_number_of_dom_edges is the total number of domain edges.

dom_edge_id is the identifier of a domain edge and ranges between 1 to total_number_
of_dom_edges.
dom_ver_1, dom_ver_2, ... are identifiers of the domain vertices of a domain edge or face.
dom_edge_label is the label of a domain edge.
number_of_dom_tess_edges is the number of tessellation edges of a domain edge.
*face denotes the beginning of the domain face field (for a tessellation of dimension 3).
total_number_of_dom_faces is the total number of domain faces.
dom_face_id is the identifier of a domain face and ranges from 1 to total_number_of_
dom_faces.
number_of_dom_vertices is the number of domain vertices of a domain face.
number_of_dom_edges is the number of domain edges of a domain face.
dom_edge_1, dom_edge_2, ... are identifiers of the domain edges of a domain face.
dom_face_eq_a, dom_face_eq_b, dom_face_eq_c and dom_face_eq_d are the parameters
of the equation of a domain face and are defined in the same way than face_eq_a, etc. (see
above).
dom_face_label is the label of a domain face. If dom_type is cube, it is one of x0, x1,
y0, y1, z0 or z1. If dom_type is cylinder, it is one of z0, z1, f1, f2, . . .
Otherwise, it is one of f1, f2, . . .
number_of_dom_tess_faces is the number of tessellation faces of a domain face.
dom_tess_face_1, dom_tess_face_2, ... are the identifiers of the tessellation faces of a
domain face.
***end denotes the end of a tessellation file.

B.2 Raster Tessellation File (.tesr)

Here are details on the .tesr file format version 2.0. The developers should note that read
and write functions are available as neut_tesr_fscanf and neut_tesr_fprintf, defined in
directories neut/neut_tesr/neut_tesr_fscanf and neut/neut_tesr/neut_tesr_fprintf.
***tesr
**format
format data_format
**general
dimension
size1 [size2 size3]
rpt_size1 [rpt_size2 rpt_size3]
[**cell
number_of_cells
[*id
cell1_id cell2_id ...]]
[*seed
seed_id seed_x seed_y seed_z seed_weight
... ]
[*ori
descriptor
cellid_param1 cellid_param2 ...]]
**data
rpt1_cell rpt2_cell ...

Appendix B: File Formats

53

or
*file data_file_name
***end
where,
***tesr denotes the beginning of a raster tessellation file.
**format denotes the beginning of the format field.
format is the file format, currently 2.0 (character string).
data_format is the format of the data in field **data. It can be either ascii, binary8
(8-bit binary), binary16 (16-bit binary) or binary32 (32-bit binary). The * suffix can be
added to binary16 and binary32 to switch byte ordering (from LittleEndian to BigEndian,
and vice versa).
**general denotes the beginning of the general information field.
dimension is the dimension of the raster tessellation.
size1, size2 and size3 are the raster sizes along the 3 coordinate axes. The number of
sizes must match dimension.
rpt_size1, rpt_size2 and rpt_size3 are the point sizes along the 3 coordinate axes. The
number of sizes must match dimension.
**cell denotes the beginning of an optional cell field.
number_of_cells is the number of cells.
*id denotes the beginning of an optional identifier field. If the field is present, the cell
identifiers listed under **data are supposed to be numbered contiguously from 1 (or 0 in
case of void), and their actual identifiers are considered to be the ones provided in the list.
The actual identifiers are used in output files.
cell1_id, cell2_id, . . . are the actual identifiers of the cells.
*seed denotes the beginning of a seed field.
seed_id is the identifier of a seed and ranges from 1 to number_of_cells.
seed_x, seed_y and seed_z are the three coordinates of a seed (real numbers).
seed_weight is the weight of a seed (real number).
*ori denotes the beginning of an optional crystal orientation field. It requires field *id.
descriptor is the descriptor used to parametrize the crystal orientations. See Section A.6
[Rotations and Orientations], page 46 for the list of available descriptors.
cellid_param1, cellid_param2, . . . are the values of the orientation descriptor of cell id.
**data denotes the beginning of the data field. Data can be provided in the .tesr file or
in a separate file, using *file, see below.
rptid_cell is the cell raster point id belongs to. The cell identifiers should start from 1.
Use 0 for voids.
*file denotes the beginning of a file field.
data_file_name is the name of a file that contains the data. Typically, it is a .raw file.

B.3 Position File

A position file lists the coordinates of a given number of points. The file must contain 1 coordinate per point in 1D, 2 coordinates per point in 2D and 3 coordinates per point in 3D.
A coordinate can be an integer or real number. A real number can have an arbitrary number
of digits, but the decimal mark must be .. The coordinates can be separated from each other
by spaces, tabulators or newlines (any number as well as arbitrary combinations of them are

54

Neper 2.0.5

supported). However, a good practice is to format the file with one line per point. An example
of a position file containing 5 points in 3D is as follows,
2.1235 9.4544 5.2145
5.9564 3.6884 9.2145
2.2547 3.2658 8.2514
8.2515 9.4157 2.9454
0.5874 4.2848 2.4874

Appendix C: Developers Guide

55

Appendix C Developers Guide

This chapter provides information useful to anyone who plans to contribute to Neper or wishes
to better understand how it works. The code structure is detailed and information are given on
how to efficiently contribute to it. If you are missing information, complain!

C.1 Code Structure

The Neper root directory content is as follows (the slash character / denotes directories),
COPYING: license terms
README: information about other files and directories in the directory
VERSIONS: information on the versions of Neper
src/: source code directory
doc/: documentation directory
Details on the src/ and doc/ directories are provided in the following.

C.1.1 Source Code

Nepers source code is located in directory src/ and consists of roughly 85,000 lines shared
between 200 directories and 800 text files. The src/ directory contains the following files and
directories,
neper_.h and neper.c
These are the main source code header file and source code file of Neper. neper.c contains
the program main function. It reads the arguments passed at the command line and runs
the corresponding functions, which can be one of the program module.
neper_t/, neper_m/, neper_v/ and neper_d/
These are directories that contain the source code of each of the program modules. The
modules aim to be independent from each other as much as possible, that is, a function of
a given module will never calls a function of another module (with a few exceptions).
neut/
neut stands for Neper utilities. The directory contains utility functions specific to Neper
and used by several modules.
contrib/
This directory contains utility functions not specific to Neper. The first one is ut, which is
a collection of general-purpose, low-level C functions (memory allocation, etc.). The second
one is orilib, which is a collection of routines for orientation manipulation (see http://
orilib.sourceforge.net). The last one is ANN, a library for nearest neighbour searching
(see www.cs.umd.edu/~mount/ANN). Although these libraries also are distributed alone
(and might be already installed on your system), they are included into Neper instead of
being considered as dependencies (contrary to the GSL, libmatheval, . . . ), to make Nepers
installation easier.
CMakeLists.txt, neper_config.h.in and cmake/
These files and directories are specific to the building system, CMake. CMakeLists.txt is
the CMake source file, which tells CMake where to find the program source files, how to
manage dependencies, where to install Neper, etc. neper_config.h.in is a small configuration file that is useful to CMake for managing dependencies and program version numbers.
cmake/ contains .cmake files which help CMake locating the dependencies on the system
(library and header files).

56

Neper 2.0.5

A module directory, neper_X/, where X stands for the module letter (one of t, m, v or d),
is structured as follows,
neper_X.h, neper_X_.h and neper_X.c
These are the source code header files and source code file of the module. neper_X.c
contains the module function, neper_X. neper_X_.h is the source code header file, which
is #included in neper_X.c and contains a bunch of #includes to all necessary library
header files. neper_X.h contains the prototype of the module function and is #included in
neper_.h. Hence, files _.h are local header files while files .h are header files #included into
a upper-level source code header file. This is true anywhere in the source code. Moreover,
any function specific to module X is prefixed neX_.
neX_input/ and structIn_X.h
The neX_input/ directory contains functions for reading the value of the arguments passed
to module X from the command line. The information are recorded into an IN C structure,
which is declared in file structIn_X.h.
neX_foo/, neX_bar/, etc.
Each of these directories is associated to a specific task of the module and contains a function
of the same name (neX_foo, etc.) which is called from function neper_X. Each directory
contains a directory tree structure.
CMakeLists.txt
This file tells CMake where to find the source files and how to manage dependencies in
the module. It is used by the upper-level CMakeLists.txt file (there is no lower-level
CMakeLists.txt file).
The neut directory is roughly structured as follows,
CMakeLists.txt
This file tells CMake where to find the source files and how to manage dependencies in
the module. It is used by the upper-level CMakeLists.txt file (there is no lower-level
CMakeLists.txt file).
neut.h, neut_t.h, neut_m.h and neut_v.h
These files are source code header files that #include header files of neut (which contain
function prototypes) and are #included in the modules. neut.h #includes all header files
while the three others #include header files only necessary to the corresponding module
(this speeds up compilation at development stage).
neut_structs/
This directory contains header files which defines all C structures used in the program.
neut_foo/, neut_bar/, etc.
Each of these directories contain functions specific to a particular C structure. For example,
neut_tess contains functions relative to the TESS structure, which describes a tessellation.

C.1.2 Documentation
Nepers documentation is located in directory doc/. It is written in Texinfo, the GNU software
documentation system. The documentation consists of a collection of .texi files (text files).
The documentation may be compiled in PDF, info or html format by running make pdf, make
info or make html, respectively. In official releases, both the PDF and info documentation files
are built and included in the archive.

Appendix C: Developers Guide

57

C.2 Contributing to Neper

C.2.1 Coding Conventions
Neper is written following the GNU Coding Standards (http: / / www . gnu . org / prep /
standards), with the exception that braces are not indented (because there is so often 3+
loop levels in Neper). Please follow this convention. Here are a few tips and other remarks,
For Vim, put the following commands in file $HOME/.vimrc:
:set sw=2
:set cindent
:syntax enable
:set textwidth=72
Your can run indent -bli0 source_files for automatic formatting.
Break up the code into meaningful chunks using blank lines. Never use more than one single
blank line to separate parts of the code.
Neper admits no compilation warnings. Please fix all of them up.
Please help us maintaining good documentation by documenting any capability you may
add.

C.2.2 Adding a New Option

In modules -T, -M and -D, adding a new option can be done by following the successive steps,
Add a variable to the IN structure to record the value of the option (file structIn_X.h).
If necessary, allocate / free the variable in the neX_in_set_zero and neX_in_free functions
(file neX_input1.c) Assign it a default value in net_input_options_default (file neX_
input3.c).
Add the option to the option list in net_input_options_set (file neX_input3.c), taking
as an example another option of the same type (integer, etc.).
Where appropriate in the source code, add a new function for the new option (if necessary
in a new file or directory). The function should be executed depending on the value of the
option.
If adding one or several files or directories, add the source file(s) to the source file list in
the CMakeLists.txt file of the corresponding module.
Make sure the whole thing compiles and runs properly for your purpose.
Make sure your own changes did not break anything in the rest of the code by running
full testing, using module -D as detailed in the following. You may also want to add a test
specific to the new option.
You may submit your code by email to [email protected] for inclusion into
Nepers official distribution.
In module -V, options are processed differently. Instead of being recorded in a C structure, they
are read one after the other and associated functions are executed along the way. To add a new
option, take an existing option as an example.

C.2.3 Compilation Options

For development, several compilation options can be changed from their default values. This
must be done at configuration stage, using commands ccmake .. or cmake-gui ... The
compilation options are,
HAVE_DEBUGGING
Setting the option to ON turns on the debugging compilation flag -g, which is required for
debugging with gdb and valgrind, turns on the compilation flag -Werror, which makes

58

Neper 2.0.5

all compilation warnings into errors, and also runs internal tests during Neper execution at
place where the code is otherwise considered as robust.
HAVE_OPTIMIZATION
Setting this option to OFF disables code optimization, which is useful for debugging with
gdb and valgrind.
HAVE_PROFILING
Setting this option to ON turns on the code profiling compilation flag -pg, which is required
for profiling with gprof. This is a highy CPU-sensitive option, which should be used only
when profiling is actually carried out.

C.3 Testing Module (-D)

Module -D is the module for testing Neper (which is helpful for development, hence the name).
Module -D makes Neper run predefined commands on itself, for module -T (Chapter 2 [Tessellation Module (-T)], page 7), module -M (Chapter 3 [Meshing Module (-M)], page 17) and
module -V (Chapter 4 [Visualization Module (-V)], page 29). The output of each command
is checked and a report of how many tests have failed (if any) is provided. For any properlyinstalled, official release of Neper, all tests should succeed. The module runs in a temporary
directory created into the working directory and named neper_testing. The directory is erased
once testing completes.
A typical use is to run neper -D all, which tests all modules. The tests can only be run
on specific modules or on specific commands of a module (option -test), which is handy for
debugging.
Here is what a typical run of module -D looks like,
$ neper -D all -run fast
========================
N
e
p
e
r
=======================
Info
: A software package for polycrystal generation and meshing.
Info
: Version 2.0.0
Info
: Built with: gsl libmatheval libscotch
Info
: Loading initialization file /foo/bar/.neperrc...
Info
: --------------------------------------------------------------Info
: MODULE -D loaded with arguments:
Info
: [ini file] (none)
Info
: [com line] all -run fast
Info
: --------------------------------------------------------------Info
: Reading input data...
Info
: Running in fast mode...
Info
: Testing module -T... (80 tests)
Info
:
- Preparing...
Info
:
[ 1] -n 2 ........................................... passed
Info
:
[ 2] -n 2 -id 1 ..................................... passed
[...]
Info
:
[80] -n 2 -id 1 -statpoint id,x,y,z,poly ............ passed
Info
:
- 80 tests, passed: 80, skipped: 0, failed: 0.
Info
: Testing module -M... (64 tests)
Info
:
- Preparing...
Info
:
[ 1] n2-id1.tess .................................... passed
Info
:
[ 2] n2-id1.tess -elt hex ........................... passed

Appendix C: Developers Guide

59

[...]
Info
:
[64] n2-id1-dim2.tesr -rcl 0.7 -for msh,geof,inp .... passed
Info
:
- 64 tests, passed: 64, skipped: 0, failed: 0.
Info
: Testing module -V... (137 tests)
Info
:
- Preparing...
Info
:
[ 1] n2-id1.tess -print foo ......................... passed
Info
:
[ 2] n2-id1.tess -showcell none -showcell all
[...] passed
[...]
Info
:
[137] n2-id1.msh -loop F 1 0.1 1.2 -datanodecoo [...] passed
Info
:
- 137 tests, passed: 137, skipped: 0, failed: 0.
Info
: Elapsed time: 209.715 secs.
========================================================================

C.3.1 Arguments
C.3.1.1 Prerequisites
[Prerequisite]
Specify the path of the current Neper binary (on which the tests are run). On most Unix
systems, Neper will be able to find it by itself; use this option otherwise.
Possible values: any. Default value: current_binary_path.

-binary path_name

C.3.1.2 Input Data

[Input data]
Modules on which the tests are run. Provide all for all, none for none or a list of modules
combined with ,, e.g. -T,-M.
Possible values: any. Default value: none.

char_string

C.3.1.3 Testing Options

[Option]
Specify the list of tests to run. Provide all for all, none for none, last for the last one
of the tests, or a list of test numbers combined with ,.
Possible values: any. Default value: all.

-test char_string

[Input data]
Specify the running mode. This changes the number of cells. Provide fast, normal,
extensive, paranoiac to use 2, 32, 512 and 8192-cell tessellations, respectively.
Possible values:
fast, normal, extensive or paranoiac.
Default value:
normal.

-runmode char_string

C.3.2 Examples
Below are some examples of use of neper -D.
1. Test all modules.
$ neper -D all
2. Test module -T only.
$ neper -D -T
3. Run specific tests of module -T.
$ neper -D -T -test 10,12,45,57

Appendix D: Versions

Appendix D Versions
New in 2.0.5 (9 Feb 2016):
- module -T: fixed up -domain planes in 3D, added -domain sphere, added
rotate, translate and scale arguments to -domain, added normal
specification in -morpho lamella, minor other improvements.
- module -M: fixed up vtk output.
- module -V: added -datacellcol id:filename, fixed up options -data*col id.
- module -D: minor improvements.
New in 2.0.4 (22 Jun 2015):
- module -T: fixed up regularization in 2D, extended -morpho planes to
2D, added semi-periodicity for raster tessellations, minor fixes.
- module -M: fixed up 2D mesh output in Abaqus format, minor fixes.
- module -V: fixed up -datacellcolscheme, improved -cameracoo to account
for the tessellation/mesh dimensions.
New in 2.0.3 (27 Nov 2014):
- module -M: fixed up bug on Mac OS X, fixed up Ctrl-C, fixed up and
speed up option -statpoint 2dmesh*.
- module -T: improved options for 2-scale tessellations, added option
-clip.
New in 2.0.2 (29 Sep 2014):
- module -T: fixed up regularization of cylinder tessellations, fixed up
option -domain planes, added tessellation cell domain, fixed up 3dec
and ply support, added Wavefront obj format, added / fixed up
tessellation keys.
- module -M: added vtk mesh format, fixed up fepx and geof mesh formats,
added extrusion of a 2D mesh to get a 3D mesh (option -dim), fixed up
topology reconstruction.
- module -V: added points plotting as cubes, spheres, cylinders or
ellipsoids (options -showpoint and -datapoint*).
New in 2.0.1 (12 Mar 2014):
- Fixed up compilation on some systems, added support for libscotch
version 6.0, small fixes and cleanups.
- module -T: enabled square and cube tessellations in .tess format,
fixed up cell sorting, made option -id mandatory, improved
regularization of 2D tessellations, added bunch of tessellation
keys, small fixes.
- module -M: added domtype mesh key.
- module -V: fixed up simultaneous tess and mesh printing, fixed up
colouring based on id, improved camera positioning for 2D and 1D
inputs, added coordinate system, improved option -slicemesh, added
options -data*scaletitle, improved -data*scale options.
New in 2.0.0 (10 Jan 2014):
- General: Full restructuring and added many new features.
Neper now
has 3 main modules: tessellation module (-T), meshing module (-M) and
visualization module (-V); details are provided below. Added
developers guide and module (-D). Documentation has been much

61

62

Neper 2.0.5

improved.
- module -T: added several tessellation algorithms (hardcore Voronoi
and Laguerre Voronoi); added orientation generation (was previously in
-O); significantly sped up tessellation; included and significantly
sped up regularization (was previously in -FM); added 2-scale
polycrystal generation; added 2D and 1D supports; improved statistics;
enabled both scalar (tess) and raster (tesr) outputs; cleaned up tess
file.
- module -M: module for free and mapped meshings (merging of -FM and
-MM). Removed regularization (now in -T); added per-cell mesh size
definition; sped up multimeshing; improved statistics.
- module -V: full restructuring; added support for 2D and 1D
tessellations and meshes; the way all entities are shown (cells,
polyhedra, faces, edges, vertices, germs, 3D/2D/1D/0D element sets and
elements, nodes) can be set in great detail; added transparency.
New in 1.10.3 (26 Nov 2012):
- module -T: added 3dec geometry format, added option -checktess, minor
improvements, added individual file extension support in -stattess,
changed option -neigh 1 to -statp i,f,npl,fal,feql.
- module -FM: added 3dec geometry format; changed "top" and "bot" nset
names for cylindrical domains to "z0" and "z1"; minor bug fixes;
improved fev format support; added individual file extension support in
options -stattess and -statmesh.
- module -O: minor bug fixes.
- module -MM: sped up meshing; fixed -domain, -scale and -nset options,
add .nper file for periodicity conditions; fixed msh output for meshes
with different element dimensions; minor other bug fixes.
- module -VS: sped up meshing reconstruction and PNG file generation,
added option -camerasky, added option -showeltedge, sped up mesh
reconstruction, minor fixes
- documentation: minor fixes.
- General: minor fixes.
New in 1.10.2 (O9 Aug 2012):
- module -T: fixed -centroid option.
- module -FM: fixed list of available meshing algorithms.
tests.
- module -MM: fixed nset syntax in inp (Abaqus) files.
- module -VS: added capability to plot mapped meshes.
- General: various minor improvements, code cleaning.

Added

New in 1.10.1 (08 June 2012):

- Bug fix to get Neper working after invoquing make install.
New in 1.10.0 (04 June 2012):
- General: New (hopefully simpler) installation procedure based on Cmake.
Added support for domains of any convex polyhedral shape.
- module -VS: major code rewriting and option changes. New capabilities
for defining the colours and sizes of the tessellation / mesh
(including gradients).
Added options to show only specific parts of the
tessellation / mesh and to view slices of a mesh. Other small

Appendix D: Versions

enhancements.
- module -T : added option -domain to specify the shape of the domain
(cuboidal, cylindrical or of any convex shape), small bug fixes, added
centroid Voronoi tessellation generation (option -centroid), merged
option -centrecoo into option -morpho, added polyhedron centroid
coordinates in file .stt3, changed option -load to -loadtess, added
output format .ply (thanks Ehsan!).
- module -FM: mesh partitionning needs libscotch version 5.1.12 or later,
small bug fixes, changed default value of -faset to "" (i.e. no faset
in output), fixed bug for Abaqus output, added polyhedron centroid
coordinates in file .stt3, added output format .ply (geometry only).
- module -MM: new options -dsize and -scale, new option -loadmesh, new
option -outdim, changed arguments of -ttype, changed default value of
-faset to "" (i.e. no faset in output), fixed bug for Abaqus output,
small bug fixes.
New in 1.9.2 (Sep 2011):
- module -T: added option -morpho for specifying the type of grain
structure (equiaxed, columnar or bamboo), merged option -regular
with -morpho, added post-processing -neighbour option for information
on the polyhedron neighbours, added geo (Gmsh geometry) output format
(mostly for visualization), fixed bugs.
- module -MM: proper processing of the input tess files, added msh
(Gmsh) and inp (Abaqus) output formats, added options -morpho and
-centrecoo (as in module -T), small bug fixes, code cleaning.
- module -FM: added geo (Gmsh geometry) output format (mostly for
visualization), small bug fixes.
- documentation: small corrections.
New in 1.9.1 (May 2011):
- module -FM: fixed bug occurring when -mesh3dalgo is not set by the
user.
Small other bug fixes.
- module -MM: small bug fixes.
New in 1.9.0 (Apr 2011):
This is a major release.
Neper now has its own paper:
"R.Quey, P.R. Dawson and F. Barbe.
Large-scale 3D random polycrystal
for the finite element method: Generation, meshing and remeshing.
Computer Methods in Applied Mechanics and Engineering,
Vol. 200, pp. 1729--1745, 2011."
Please cite it in your works if you use Neper.
- General: added option --rcfile to disregard / change the
initialization file; big distribution and source clean up; bug fixes.
- module -T: added capability to generate regular morphologies
(truncated octahedra), tess file format bumped to 1.9; big clean up.
- module -FM: included multimeshing, remeshing and mesh partitioning
capabilities; big clean up.
Neper now uses the *standard* Gmsh
distribution for 2D and 3D meshings (versions >=2.4.2).
Strongly
reduced memory usage.
- module -O: added capability to handle different orientation
descriptors.
- module -VS: new visualization module to generate publication-quality

63

64

Neper 2.0.5

images (PNG format) of the tessellations, meshes and more...

New in 1.8.1 (Aug 2009):
- upgraded website at http://neper.sourceforge.net
- module -T: new file format ***tess1.8, new option -restart to load an
existing tessellation (not through std input any more), new option
-printformat, bug fixes.
- module -MM: bug fixes.
- module -FM: new output format mae, new option -restart to restart from
an existing geometry or mesh (options -mesh and -conv removed); new
options -printformat and -maeextension; better mesh numbering (+ new
options -elementfirstid and -nodefirstid), new way to choose the node
sets to output (-nset 4), fixed option -estat, renamed -bwcy-clmin to
-clmin, cleaned bunch of options, bug fixes.
- module -O: added option -euleranglesconvention (Bunge, Roe & Kocks);
new output formats mae and geof (option -format).
- manual: some corrections.
New in 1.8.0 (Jul 2009):
- First GPL-distributed version of Neper.

Appendix E: GNU General Public License

65

Appendix E GNU General Public License

GNU General Public License
Version 3, 29 June 2007
c 2007 Free Software Foundation, Inc. http://fsf.org/
Copyright
Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.

Preamble
The GNU General Public License is a free, copyleft license for software and other kinds of works.
The licenses for most software and other practical works are designed to take away your freedom
to share and change the works. By contrast, the GNU General Public License is intended to
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free software for all its users. We, the Free Software Foundation, use the GNU General Public
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When we speak of free software, we are referring to freedom, not price. Our General Public
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To protect your rights, we need to prevent others from denying you these rights or asking you
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For example, if you distribute copies of such a program, whether gratis or for a fee, you must
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Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on
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For the developers and authors protection, the GPL clearly explains that there is no warranty
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be marked as changed, so that their problems will not be attributed erroneously to authors of
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Some devices are designed to deny users access to install or run modified versions of the software
inside them, although the manufacturer can do so. This is fundamentally incompatible with
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Finally, every program is threatened constantly by software patents. States should not allow
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the program non-free.

66

Neper 2.0.5

The precise terms and conditions for copying, distribution and modification follow.

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Appendix E: GNU General Public License

2.

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4.

5.

67

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Neper 2.0.5

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Appendix E: GNU General Public License

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available to the distrib in source code form), and must require no special password or key
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7. Additional Terms.
Additional permissions are terms that supplement the terms of this License by making
exceptions from one or more of its conditions. Additional permissions that are applicable
to the entire Program shall be treated as though they were included in this License, to the
extent that they are valid under applicable law. If additional permissions apply only to part
of the Program, that part may be used separately under those permissions, but the entire
Program remains governed by this License without regard to the additional permissions.
When you convey a copy of a covered work, you may at your option remove any additional
permissions from that copy, or from any part of it. (Additional permissions may be written
to require their own removal in certain cases when you modify the work.) You may place
additional permissions on material, added by you to a covered work, for which you have or
can give appropriate copyright permission.
Notwithstanding any other provision of this License, for material you add to a covered work,
you may (if authorized by the copyright holders of that material) supplement the terms of
this License with terms:
a. Disclaiming warranty or limiting liability differently from the terms of sections 15 and
16 of this License; or

70

Neper 2.0.5

b. Requiring preservation of specified reasonable legal notices or author attributions in

that material or in the Appropriate Legal Notices displayed by works containing it; or
c. Prohibiting misrepresentation of the origin of that material, or requiring that modified
versions of such material be marked in reasonable ways as different from the original
version; or
d. Limiting the use for distribity purposes of names of licensors or authors of the material;
or
e. Declining to grant rights under trademark law for use of some trade names, trademarks,
or service marks; or
f. Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability
to the recipient, for any liability that these contractual assumptions directly impose on
those licensors and authors.
All other non-permissive additional terms are considered further restrictions within the
meaning of section 10. If the Program as you received it, or any part of it, contains a notice
stating that it is governed by this License along with a term that is a further restriction,
you may remove that term. If a license document contains a further restriction but permits
relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not
survive such relicensing or conveying.
If you add terms to a covered work in accord with this section, you must place, in the
relevant source files, a statement of the additional terms that apply to those files, or a
notice indicating where to find the applicable terms.
Additional terms, permissive or non-permissive, may be stated in the form of a separately
written license, or stated as exceptions; the above requirements apply either way.
8. Termination.
You may not propagate or modify a covered work except as expressly provided under this
License. Any attempt otherwise to propagate or modify it is void, and will automatically
terminate your rights under this License (including any patent licenses granted under the
third paragraph of section 11).
However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly
and finally terminates your license, and (b) permanently, if the copyright holder fails to
notify you of the violation by some reasonable means prior to 60 days after the cessation.
Moreover, your license from a particular copyright holder is reinstated permanently if the
copyright holder notifies you of the violation by some reasonable means, this is the first
time you have received notice of violation of this License (for any work) from that copyright
holder, and you cure the violation prior to 30 days after your receipt of the notice.
Termination of your rights under this section does not terminate the licenses of parties
who have received copies or rights from you under this License. If your rights have been
terminated and not permanently reinstated, you do not qualify to receive new licenses for
the same material under section 10.
9. Acceptance Not Required for Having Copies.
You are not required to accept this License in order to receive or run a copy of the Program.
Ancillary propagation of a covered work occurring solely as a consequence of using peer-topeer transmission to receive a copy likewise does not require acceptance. However, nothing
other than this License grants you permission to propagate or modify any covered work.
These actions infringe copyright if you do not accept this License. Therefore, by modifying
or propagating a covered work, you indicate your acceptance of this License to do so.

Appendix E: GNU General Public License

71

10. Automatic Licensing of Downstream Recipients.

Each time you convey a covered work, the recipient automatically receives a license from
the original licensors, to run, modify and propagate that work, subject to this License. You
are not responsible for enforcing compliance by third parties with this License.
An entity transaction is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If
propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the
partys predecessor in interest had or could give under the previous paragraph, plus a right
to possession of the Corresponding Source of the work from the predecessor in interest, if
the predecessor has it or can get it with reasonable efforts.
You may not impose any further restrictions on the exercise of the rights granted or affirmed
under this License. For example, you may not impose a license fee, royalty, or other charge
for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed
by making, using, selling, offering for sale, or importing the Program or any portion of it.
11. Patents.
A contributor is a copyright holder who authorizes use under this License of the Program
or a work on which the Program is based. The work thus licensed is called the contributors
contributor version.
A contributors essential patent claims are all patent claims owned or controlled by the
contributor, whether already acquired or hereafter acquired, that would be infringed by some
manner, permitted by this License, of making, using, or selling its contributor version, but
do not include claims that would be infringed only as a consequence of further modification
of the contributor version. For purposes of this definition, control includes the right to
grant patent sublicenses in a manner consistent with the requirements of this License.
Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the
contributors essential patent claims, to make, use, sell, offer for sale, import and otherwise
run, modify and propagate the contents of its contributor version.
In the following three paragraphs, a patent license is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to
practice a patent or covenant not to sue for patent infringement). To grant such a patent
license to a party means to make such an agreement or commitment not to enforce a patent
against the party.
If you convey a covered work, knowingly relying on a patent license, and the Corresponding
Source of the work is not available for anyone to copy, free of charge and under the terms of
this License, through a distribly available network server or other readily accessible means,
then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to
deprive yourself of the benefit of the patent license for this particular work, or (3) arrange,
in a manner consistent with the requirements of this License, to extend the patent license
to downstream recipients. Knowingly relying means you have actual knowledge that, but
for the patent license, your conveying the covered work in a country, or your recipients use
of the covered work in a country, would infringe one or more identifiable patents in that
country that you have reason to believe are valid.
If, pursuant to or in connection with a single transaction or arrangement, you convey, or
propagate by procuring conveyance of, a covered work, and grant a patent license to some
of the parties receiving the covered work authorizing them to use, propagate, modify or
convey a specific copy of the covered work, then the patent license you grant is automatically
extended to all recipients of the covered work and works based on it.

72

Neper 2.0.5

A patent license is discriminatory if it does not include within the scope of its coverage,
prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights
that are specifically granted under this License. You may not convey a covered work if you
are a party to an arrangement with a third party that is in the business of distributing
software, under which you make payment to the third party based on the extent of your
activity of conveying the work, and under which the third party grants, to any of the
parties who would receive the covered work from you, a discriminatory patent license (a)
in connection with copies of the covered work conveyed by you (or copies made from those
copies), or (b) primarily for and in connection with specific products or compilations that
contain the covered work, unless you entered into that arrangement, or that patent license
was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting any implied license or
other defenses to infringement that may otherwise be available to you under applicable
patent law.
12. No Surrender of Others Freedom.
If conditions are imposed on you (whether by court order, agreement or otherwise) that
contradict the conditions of this License, they do not excuse you from the conditions of this
License. If you cannot convey a covered work so as to satisfy simultaneously your obligations
under this License and any other pertinent obligations, then as a consequence you may not
convey it at all. For example, if you agree to terms that obligate you to collect a royalty
for further conveying from those to whom you convey the Program, the only way you could
satisfy both those terms and this License would be to refrain entirely from conveying the
Program.
13. Use with the GNU Affero General Public License.
Notwithstanding any other provision of this License, you have permission to link or combine
any covered work with a work licensed under version 3 of the GNU Affero General Public
License into a single combined work, and to convey the resulting work. The terms of
this License will continue to apply to the part which is the covered work, but the special
requirements of the GNU Affero General Public License, section 13, concerning interaction
through a network will apply to the combination as such.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of the GNU General
Public License from time to time. Such new versions will be similar in spirit to the present
version, but may differ in detail to address new problems or concerns.
Each version is given a distinguishing version number. If the Program specifies that a
certain numbered version of the GNU General Public License or any later version applies
to it, you have the option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software Foundation. If the Program
does not specify a version number of the GNU General Public License, you may choose any
version ever published by the Free Software Foundation.
If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxys distrib statement of acceptance of a version
permanently authorizes you to choose that version for the Program.
Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing
to follow a later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRIT-

Appendix E: GNU General Public License

73

ING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM AS IS WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR
IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE
RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH
YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE
TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE
THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA
BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED
OF THE POSSIBILITY OF SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided above cannot be given local
legal effect according to their terms, reviewing courts shall apply local law that most closely
approximates an absolute waiver of all civil liability in connection with the Program, unless
a warranty or assumption of liability accompanies a copy of the Program in return for a fee.

END OF TERMS AND CONDITIONS

How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest possible use to the distrib,
the best way to achieve this is to make it free software which everyone can redistribute and
change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of
each source file to most effectively state the exclusion of warranty; and each file should have at
least the copyright line and a pointer to where the full notice is found.
one line to give the programs name and a brief idea of what it does.
Copyright (C) year name of author
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or (at
your option) any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see http://www.gnu.org/licenses/.

Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short notice like this when it starts
in an interactive mode:
program Copyright (C) year name of author

74

Neper 2.0.5

This program comes with ABSOLUTELY NO WARRANTY; for details type show w.
This is free software, and you are welcome to redistribute it
under certain conditions; type show c for details.

The hypothetical commands show w and show c should show the appropriate parts of the
General Public License. Of course, your programs commands might be different; for a GUI
interface, you would use an about box.
You should also get your employer (if you work as a programmer) or school, if any, to sign a
copyright disclaimer for the program, if necessary. For more information on this, and how to
apply and follow the GNU GPL, see http://www.gnu.org/licenses/.
The GNU General Public License does not permit incorporating your program into proprietary
programs. If your program is a subroutine library, you may consider it more useful to permit
linking proprietary applications with the library. If this is what you want to do, use the GNU
Lesser General Public License instead of this License. But first, please read http://www.gnu.
org/philosophy/why-not-lgpl.html.

Option Index

75

Option Index
-cameraangle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-cameracoo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-cameralookat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-cameraprojection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-camerasky . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-centroid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-centroidconv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-centroidfact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-centroiditermax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-checktess . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-cl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-clean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-clip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-clmin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-clratio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-datacellcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-datacellcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-datacellscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-datacellscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-datacelltrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-datacsyscol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-datacsyscoo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-datacsyslabel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-datacsyslength . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-datacsysrad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataedgecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataedgecolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataedgerad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataedgescale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataedgescaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataedgetrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset0dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset0dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset0drad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset0dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset0dscaletitle . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset1dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset1dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset1drad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset1dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset1dscaletitle . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset2dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset2dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset2dedgecol . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset2dedgerad . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset2dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset2dscaletitle . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset3dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset3dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset3dedgecol . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset3dedgerad . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset3dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelset3dscaletitle . . . . . . . . . . . . . . . . . . . . . . . .
-dataelt0dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelt0dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelt0drad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelt0dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelt0dscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelt1dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelt1dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-dataelt1drad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

41
41
41
41
41
10
10
10
10
14
19
22
11
20
20
30
30
30
31
30
38
38
38
38
38
32
32
32
32
32
32
36
36
36
36
36
35
35
35
35
35
34
35
35
35
35
35
34
34
34
34
34
34
36
36
36
36
36
35
35
35

-dataelt1dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
-dataelt1dscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
-dataelt2dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
-dataelt2dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
-dataelt2dedgecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
-dataelt2dedgerad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
-dataelt2dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
-dataelt2dscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
-dataelt3dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
-dataelt3dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
-dataelt3dedgecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
-dataelt3dedgerad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
-dataelt3dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
-dataelt3dscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
-datafacecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-datafacecolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-datafacescale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
-datafacescaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
-datafacetrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-datanodecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
-datanodecolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
-datanodecoo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
-datanodecoofact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
-datanoderad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
-datanodescale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
-datanodescaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
-datapointcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
-datapointcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
-datapointcoo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
-datapointcoofact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
-datapointrad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
-datapointscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
-datapointscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
-datapointtrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
-datapolycol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-datapolycolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-datapolyscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-datapolyscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-datapolytrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-datarptedgecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
-datarptedgerad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
-dataseedcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
-dataseedcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
-dataseedrad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
-dataseedscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
-dataseedscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
-datavercol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
-datavercolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
-dataverrad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
-dataverscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
-dataverscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
-datavertrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
-dim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
-dim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
-domain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
-dupnodemerge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
-elttype . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
-endloop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
-faset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
-filter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
-fmax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

76

-format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12, 23
-hardcore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
-id . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
-imageantialias . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
-imagebackground . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
-imageformat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
-imagesize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
-loadmesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
-loadpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9, 19
-loadtesr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
-loadtess . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
-loop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
-mesh2dalgo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
-mesh2diter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
-mesh2dmaxtime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
-mesh2drmaxtime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
-mesh3dalgo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
-mesh3dclconv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
-mesh3diter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
-mesh3dmaxtime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
-mesh3drmaxtime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
-meshqualdisexpr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
-meshqualexpr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
-meshqualmin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
-mloop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
-morpho . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
-n . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
-nset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
-o . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12, 23
-order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
-ori . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
-oricrysym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
-oridescriptor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
-oriformat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
-part . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
-partbalancing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
-partmethod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
-pl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
-randomize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
-rcl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
-regularization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
-rsel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
-runmode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
-scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
-sel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
-showcell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-showcsys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
-showedge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-showelset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
-showelset0d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
-showelset1d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Neper 2.0.5

-showelset2d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showelset3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showelt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showelt0d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showelt1d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showelt2d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showelt3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showfaceinter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showmesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showmeshslice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-shownode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showpoly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showseed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showshadow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showtesr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showtess . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-showver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-singnodedup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-slicemesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-sort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statcell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statedge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statelset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statelset0d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statelset1d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statelset2d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statelset3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statelt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statelt0d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statelt1d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statelt2d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statelt3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statnode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statpoly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statseed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-statver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-tesrformat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-tesrsize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-tesrsmooth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-tesrsmoothfact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-tesrsmoothitermax . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-ttype . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-weight. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

40
40
40
40
40
40
40
39
40
39
39
41
39
39
40
41
39
39
40
22
38
11
13
13
24
24
25
25
25
24
24
24
24
24
14
24
14
25
14
13
13
13
13
21
21
22
59
23
10
10