Neper

Neper Reference Manual
The documentation for Neper 3.0.2

A software package for polycrystal generation and meshing
16 February 2017
Romain Quey
Copyright
c 2003–2016 Romain Quey
Permission is granted to make and distribute verbatim copies of this manual provided the copy-
right notice and this permission notice are preserved on all copies.
i
Table of Contents
Conditions of Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Copying Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
User Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1 The Neper Project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1.1 Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1.2 Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 Installing Neper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.3.1 Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.3.2 Argument Separators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.3.3 Initialization File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.4 Reading this Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2 Tessellation Module (-T) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

2.1 Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.1.1 Input Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.1.2 Morphology Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.1.3 Transformation Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.1.4 Crystal Orientation Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.1.5 Regularization Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.1.6 Output Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.1.7 Post-Processing Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.1.8 Debugging Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.2 Output Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.2.1 Tessellation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.2.2 Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.2.3 Tessellation Optimization Log Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
3 Meshing Module (-M) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

3.1 Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.1.1 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.1.2 Input Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.1.3 Meshing Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.1.4 Raster Tessellation Meshing Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.1.5 Mesh Cleaning Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.1.6 Transformation Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.1.7 Mesh Partitioning Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.1.8 Field Transport Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
3.1.9 Output Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
3.1.10 Post-Processing Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
3.1.11 Advanced Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3.2 Output Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3.2.1 Mesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3.2.2 Periodicity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
ii Neper 3.0.2
3.2.3 Interfaces. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3.2.4 Statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3.3 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
4 Visualization Module (-V) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

4.1 Arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
4.1.1 Prerequisites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
4.1.2 Input Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
4.1.3 Tessellation Data Loading and Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
4.1.4 Mesh Data Loading and Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
4.1.5 Point Data Loading and Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
4.1.6 Coordinate System Rendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
4.1.7 Slice Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
4.1.8 Show Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
4.1.9 Camera Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
4.1.10 Output Image Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
4.1.11 Scripting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
4.1.12 Advanced Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
4.2 Output Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
4.3 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Appendix A Expressions and Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

A.1 Mathematical and Logical Expressions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
A.1.1 Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
A.1.2 Binary Operators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
A.2 Tessellation Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
A.3 Raster Tessellation Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
A.4 Tessellation Update Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
A.4.1 Time Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
A.4.2 Variable Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
A.4.3 Objective Function Value Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
A.4.4 Statistical Distribution Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
A.5 Mesh Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
A.6 Point Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
A.7 Rotations and Orientations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
A.8 Colours . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Appendix B File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

B.1 Tessellation File (.tess) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
B.2 Raster Tessellation File (.tesr) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
B.3 Multiscale Cell File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
B.4 Position File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Appendix C Developer’s Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

C.1 Code Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
C.1.1 Source Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
C.1.2 Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
C.2 Contributing to Neper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
C.2.1 Coding Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
C.2.2 Adding a New Option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
C.2.3 Compilation Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
C.2.4 Testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
iii
Appendix D Versions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Appendix E GNU General Public License . . . . . . . . . . . . . . . . . . . 79
Option Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Conditions of Use 1
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 79). 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 neper-users@lists.sourceforge.net. 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 poly-
crystals for the finite element method: Generation, meshing and remeshing. Computer
Methods in Applied Mechanics and Engineering, vol. 200, pp. 1729–1745, 2011.
Chapter 1: Introduction 3
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
2D or 3D. Neper is built around three modules:
• Module -T generates polycrystals as tessellations. The two main capabilities are: (i) the
generation of tessellations from cell properties (e.g. a size distribution) and (ii) the genera-
tion of multiscale tessellations (i.e. including cell subdivisions). These capabilities can also
be used together. Tessellations are Laguerre (or Voronoi) tessellations and are therefore
composed of convex cells. Finally, the tessellations can be “regularized” by removing their
smallest features (edges and faces), which enables good-quality meshing with module -M.
Periodicity conditions can be prescribed. Crystal orientations are provided for the grains.
The output is a tessellation file written at a scalar (vectorial) or raster format.
• Module -M meshes polycrystals described as tessellation files. Two meshing techniques are
available: free (or unstructured) meshing, which generates triangular/tetrahedral elements
that follow the grain shapes, and mapped meshing, which generates regular brick elements
that do not necessarily follow the grain shapes. Free meshing into good-quality elements
is ensured by optimized meshing rules, and multimeshing—the concurrent use of several
meshing algorithms. Remeshing is also available and is similar to meshing except that it
takes a mesh as input. Cohesive elements can be inserted at interfaces. The output is a
mesh file that can be written under several formats.
• Module -V generates publication-quality images of tessellations and meshes. Colouring and
transparency of the different entities can be set up in detail and mesh nodes can be displaced.
Mesh slicing is also available. 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, so that all treatments can be automated.
1.1.2 Resources
Several, complementary resources describing Neper are available:
• The Neper reference manual, which is this document, describes all of Neper’s capabilities.
Each module is the subject of a specific chapter, which describes the available commands
and result files, and provides examples. The manual is available at the PDF and info
formats.1
• The Neper website, http://neper.sourceforge.net, is where Neper’s official distribution
can be downloaded from. It also provides an illustrative introduction to Neper.
• The Neper GitHub repository, http://github.com/rquey/neper, is the page for develop-
ment. It is also where the latest version of Neper can be downloaded from.
• 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.”, describes the regularization /
meshing methodologies. It can be downloaded from the Neper homepage or directly from
this link: http://neper.sourceforge.net/docs/neper-reference-paper.pdf.
1
Provided that the info file is properly installed at your site, it can be accessed by the command: info neper.
4 Neper 3.0.2
1.2 Installing Neper

Neper is written in (mostly ANSI) C and a little C++, and it can run on any Unix-like system.
Neper must be compiled using CMake, by following these steps:
• Create a build directory, for instance as a subdirectory of Neper’s src directory,
$ mkdir build
• Run CMake from within the build directory, pointing to Neper’s src directory,
$ cd build
$ cmake ..
• Build Neper,
$ make
Use option ‘-jN’ to turn multithreading on, where N is 1 + the number of cores of a processor.
• Install Neper on your system (as root),
$ make install
This procedure uses the default configuration options and should work out of the box on con-
dition that the required dependencies are available in standard system locations. If needed, a
finer configuration can be achieved, before building Neper, by running
$ ccmake ..
or
$ cmake-gui ..
Several of Neper’s dependencies can be managed at this stage. Some of them are optional and
can be enabled or disabled through variables HAVE_LIBRARY. The dependencies are:
• the GNU Scientific Library (GSL, mandatory, enabled 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 downloaded from http: / /www .gnu .org /
software/gsl.
• the NLopt library (optional, enabled by default). It is needed by module -T for tessellation
generation from cell properties. 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 downloaded from http://ab-initio.mit.edu/wiki/index.php/NLopt.
• the libScotch library (version 5.1.12 or higher, optional, disabled by default). It is needed
by module -M for mesh partitioning. The source code can be downloaded from www.labri.
fr/perso/pelegrin/scotch.
• the pthread library (optional, disabled by default). It is needed if libScotch version 6.0.0
or higher is enabled. It is likely to be available on your system or from your system package
manager.
The other dependencies are needed at run time only (they are not linked against Neper’s binary):
• the Gmsh program (version 2.4.2 or higher, excluding version 2.5.1, mandatory for
module -M). A binary, or the source code, can be downloaded from http://www.geuz.
org/gmsh (compiling from the source code speeds up meshing significantly). Gmsh must be
available at the terminal as the command gmsh, or the path to its binary must be specified
with option -gmsh (in module -M).
• the POV-Ray program (mandatory for module -V). It is likely to be available on your
system or from your system package manager (binary package); alternatively, a binary, or
the source code, can be downloaded from http://www.povray.org. POV-Ray must be
available at the terminal as the command povray, or the path to its binary must be specified
with option -povray (in module -V).
Finally, the Neper installation can be tested out by running

$ make test
1.3 Getting Started

The ‘neper’ binary must be run in a terminal, followed by a list of arguments,
$ neper list_of_arguments
In return, Neper writes messages in the terminal and results in ASCII files.
The list of arguments describes the problem to solve. There are several general-purpose, self-
explanatory arguments:
$ neper --help
$ neper --version
$ neper --license
This section provides information on how to call Neper’s modules, properly format option ar-
guments and set up an initialization file.
1.3.1 Modules
To call a module, run:
$ neper module_name module_arguments
where the module name can be -T, -M or -V, and 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 provided in arbitrary order and each of them is followed by a single argument
(no space). American-english variants of options can be used. String completion is available
for all options, so they may be abbreviated as long as the abbreviation is not ambiguous. For
instance, in module -T, option -regularization can be abbreviated to -reg. Logical options
can be enabled or disabled by providing argument values of ‘1’ or ‘0’, respectively. Integer
or real argument values can be written as mathematical or logical expressions (for details on
expressions, see Section A.1 [Mathematical and Logical Expressions], page 51). For instance, in
module -T, option -rcl 0.5 can also be written as -rcl 1/2 or -rcl "cos(pi/3)". Module -V
shows some exceptions with respect to these rules: the argument cannot be listed in arbitrary
order, string completion is not available and option -loop takes several arguments.
1.3.2 Argument Separators

Some options may take several argument values. These values can be combined using separators
(see Chapter 2 [Tessellation Module (-T)], page 9, Chapter 3 [Meshing Module (-M)], page 23
and Chapter 4 [Visualization Module (-V)], page 35 for details on each option). There are three
possible separators:
• The ‘,’ separator combines uncorrelated arguments, i.e. arguments of the same type, which
can be processed independently from each others. Such arguments can be output file for-
mats, for instance.
• The ‘:’ separator is used to combine correlated arguments, i.e. arguments of different types,
which cannot be processed independently from each others. Such arguments can be values
of a variable in different directions, for instance.
• The ‘::’ separator is used in module -T for assigning argument values at the different scales
of a multiscale tessellation. It is a “super-separator” that takes precedence over the ‘,’ and
‘:’ separators.
6 Neper 3.0.2
1.3.3 Initialization File

When Neper is run, it starts by reading commands from an initialization file, $HOME/.neperrc,
if that file exists. Another initialization file can be specified with option --rcfile, before calling
a module,
$ neper --rcfile my_file module_name module_arguments
To disable the reading of an initialization file, use option --rcfile none.
When a module of Neper is called, Neper looks for the occurrence of ‘neper module_name’ in the
initialization file and then reads all arguments until the next occurrence of ‘neper’ (which should
denote the beginning of another module option field) or the end of the file. The arguments may
be any legal arguments but are typically limited to frequently-used options. Moreover, any field
of comments can be preceded by ‘neper comments’.
Here is an example of initialization file:
neper comments ------------------------------------------------------
This is my initialization file.
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 inside it, Neper will
consider only the command line arguments. Also, if an argument is initialized several times (for
instance, both in the initialization file and at the command line), only the last specified value is
used.
1.4 Reading this Manual

This manual is maintained as a Texinfo manual. Here are the writing conventions used in the
document:
• A command that can be typed in a terminal is printed like this, or, in the case of a major
command, like
$ this
• A program (or command) option is printed like this.
• The name of a variable is printed like this.
• A meta-syntactic variable (i.e. something that stands for another piece of text) is printed
like this.
• Literal examples are printed like ‘this’.
• File names are printed like this.
Module arguments are tagged by type and importance level:
• Prerequisites are tagged ‘[Prerequisite]’. They should be placed in the initialization file.
• Input data are tagged ‘[Input Data]’.
• Standard options are tagged ‘[Option]’.
• Secondary options, which should be used only for fine-tuning and if you really know what
you are doing, are tagged ‘[Secondary option]’.
• Post-processing options are tagged ‘[Post-processing]’.
Some abbreviations are used consistently for options and contribute to Neper’s jargon:
algo algorithm
arch architecture
cl characteristic length
col colour
conv convergence
coo coordinate
crysym crystal symmetry
csys coordinate system
dim dimension
dis distribution or distortion
dof degree of freedom
dup duplicate(d)
elset element set
elt element
expr expression
fact factor
faset element face set
geo geometry
id identifier
ini initial
inter interpolation
iter iteration
max maximum
min minimum
morpho morphology
neigh neighbour
nset node set
opti optimization
ori orientation
part partition
poly polyhedron
pov POV-Ray file
qual quality
rad radius
rcl relative characteristic length
rmax relative maximum
sing singular
stat statistics
surf surface
tesr raster tessellation
tess scalar tessellation
tmp temporary
trs transparency
val value
var variable
ver vertex
Chapter 2: Tessellation Module (-T) 9
2 Tessellation Module (-T)

Module -T generates tessellations and multiscale tessellations of a bounded domain of space,
in 2D or 3D. Periodicity and semi-periodicity conditions can be prescribed. Module -T also
enables to regularize the tessellations for better-quality meshing. The tessellations are provided
in scalar (vectorial) or raster formats.
Tessellations can be generated from various types of morphological cell properties (option
-morpho). Several predefined properties are available, such as those obtained by grain growth
in metals (which are described by cell size and sphericity distributions). Custom properties can
be specified using various metrics, including the size, the sphericity, the centroid or even the
actual shape (using a raster tessellation), either in terms of distributions (when applicable) or
on a per-cell basis. The generated tessellations are Laguerre (or Voronoi) tessellations whose
seed attributes are set by optimization to obtain the desired cell properties. Of course, il is also
possible to generate standard tessellations (e.g. Poisson-Voronoi tessellations).
Multiscale tessellations are characterized by the subdivision of the cells of a primary tessellation
into secondary tessellations (and so on) and are obtained by combining into one, using the
‘::’ separator, the option arguments that apply at the successive scales. The same value can
be used for defining the tessellations at a given scale, or different values can be loaded from a
multiscale cell file (see Section B.3 [Multiscale Cell File], page 67). So, all capabilities available
for generating a standard (single-scale) tessellations are available for generating the tessellations
at the different scales of a multiscale tessellation. Examples are provided in the following.
The domain of space in which the tessellation is created can be of any convex shape. In 3D,
cuboidal, cylindrical and spherical shapes are directly supported while other morphologies can
be defined from a set of planes (option -domain). Periodicity or semi-periodicity conditions can
be applied to the tessellation (option -periodicity).
Crystal orientations are also provided for the cells. The orientations are randomly distributed ac-
cording to a uniform distribution, either in the 3D space or along a specific orientation fibre (op-
tion -ori). They can be provided according to different descriptors (option -oridescriptor).
Regularization can be applied to the tessellations and consists in removing their small edges
and faces (option -regularization) which otherwise are highly detrimental to good-quality
meshing with module -M (see Chapter 3 [Meshing Module (-M)], page 23). It it not available
for periodic tessellations yet.
Output files describe the tessellation either at the scalar format .tess or at the raster format
.tesr (see Appendix B [File Formats], page 61). Both are input files of module -M (see Chapter 3
[Meshing Module (-M)], page 23) and module -V (see Chapter 4 [Visualization Module (-V)],
page 35). 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 3.0.0
Info : Built with: gsl nlopt muparser
Info : <http://neper.sourceforge.net>
Info : Copyright (C) 2003-2016, and GNU GPL’d, by Romain Quey.
Info : Comments and bug reports: <neper-users@lists.sourceforge.net>.
Info : Loading initialization file ‘/home/rquey/.neperrc’...
Info : ---------------------------------------------------------------
Info : MODULE -T loaded with arguments:
10 Neper 3.0.2
Info : [ini file]

Info : [com line] -n 10 -id 1 -morpho gg -reg 1
Info : ---------------------------------------------------------------
Info : Reading input data...
Info : Creating domain...
Info : Creating tessellation...
Info : - Running tessellation...
Info : > Entering optimization...
Info : > Setting seeds... 100%
Info : > Initial solution: f =3.623581896
Info : > Iteration 2864: fmin=0.077875850 f=0.077875946
Info : > Reached ‘dvalditer’ criterion.
Info : Regularizing tessellation...
Info : - loop 1/2: 100% del=2
Info : Writing tessellation...
Info : [o] Writing file ‘n10-id1.tess’...
Info : [o] Wrote file ‘n10-id1.tess’.
Info : Elapsed time: 3.333 secs.
========================================================================
2.1 Arguments
2.1.1 Input Data
-n integer or char_string [Input data]
Specify the number of cells of the tessellation. The argument can be a mathematical expres-
sion based on the size variable, which is the size of the domain (volume in 3D, area in 2D).
For regular morphologies (cubes, lamellae, etc., see option -morpho), the number of cells is
defined from option -morpho and so the argument must be ‘from_morpho’.
Possible values: any. Default value: none.
-id integer [Input data]

Specify the identifier of the tessellation. It defines the seed used by the random number
generator to compute the (initial) seed positions.
Possible values: any. Default value: 1.
-dim integer [Option]

Specify the dimension of the tessellation.
Possible values: 2 or 3. Default value: 3.
-domain char_string [Option]

Specify the domain morphology. In 3D, for a cuboidal shape, pro-
vide ‘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(diameter)’. To specify the number of facets,
facet_nb, of a circle, cylinder or sphere domain, use ‘circle(diameter,facet_nb)’,
‘cylinder(height,diameter,facet_nb)’ or ‘sphere(diameter,facet_nb)’. For
an arbitrary convex 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 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
transform the domain, append a transformation to the domain name using the ‘:’
separator. Available transformations are: ‘rotate(axis_x,axis_y,axis_z,angle)’ for a
rotation about an axis/angle pair, ‘scale(x_factor,y_factor,z_factor)’ for scaling,
‘translate(x_delta,y_delta,z_delta)’ for a translation and ‘split(dir)’ for splitting
the domain in half along direction ‘dir’ (‘x’, ‘y’ or ‘z’), which can be used to apply symme-
tries. An example is ‘sphere(1,100):translate(-0.5,-0.5,-0.5):scale(0.5,1,2)’.
Possible values: see above list. Default value: cube(1,1,1) in 3D and square(1,1) in
2D.
-periodicity char_string [Option]

Specify the periodicity conditions that apply to the domain (and therefore to the tessellation).
Provide as argument ‘0’ (or ‘none’) for no periodicity, ‘1’ (or ‘all’) for full periodicity, or a
list of periodicity directions (among ‘x’, ‘y’ and ‘z’) combined with ‘,’ for semi-periodicity.
Possible values: see above list. Default value: 0.
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.
-loadtesr file_name [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 values 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 value can be omitted.
Finally, it is possible to load a set of points. These points are used only for statistics, in option
-statpoint; they are not seed points of the tessellation (see option -morphooptiini instead).
-loadpoint file_name [Input data]

Load points from a file. See Section B.4 [Position File], page 68 for the file format. Provide
as argument the file name.
2.1.2 Morphology Options

These options can be used to set the cell morphology. If you want to set seeds attributes instead,
use ‘-morphooptiini ... -morpho voronoi’.
-morpho char_string [Option]

Specify morphological properties of the cells. It can be done either by using a special morphol-
ogy string (as defined below), or by specifying custom cell properties such as sizes, sphericities,
centroids, or even exact shapes (using a raster tessellation).
(i) The special morphology strings are:
• ‘voronoi’ for a standard Poisson-Voronoi tessellation;
• ‘graingrowth’ or ‘gg’ for grain-growth statistical properties, which mean a wider grain size
distribution and higher grain sphericities than in a Voronoi tessellation (it actually is an alias
12 Neper 3.0.2
for ‘diameq:lognormal(1,0.35),sphericity:lognormal(0.145,0.03,1-x)’, see below);

• ‘centroidal’ for a centroidal tessellation1 (it actually is an alias for ‘centroid:seed’,
see below);
• ‘cube(N)’ / ‘square(N)’ for a regular tessellation into cubic / square cells, where ‘N’ is
the number of cells along a direction, or ‘cube(N1,N2,N3)’ / ‘square(N1,N2)’ for a regular
tessellation into cubic / square cells, where ‘N1’, ‘N2’ and ‘N3’ are the number of cells along
the different directions.
• ‘lamellar(w=w,v=v)’ for a lamellar morphology. Argument ‘w=w’ is mandatory and argu-
ment ‘v=v’ is optional. Argument ‘w=w’ enables to specify the absolute lamella width w. For
specifying several widths, combine them with ‘:’. In the case of a multiscale tessellation, for
specifying cell-by-cell width values, use the syntax ‘file(file_name)’ where file_name is
the name of a multiscale cell file containing the list of widths (see Section B.3 [Multiscale
Cell File], page 67). Argument ‘v=v’ enables to specify the lamella plane normals v. For
randomly-distributed normals taken from a uniform distribution, use ‘random’. For a direc-
tion of the parent crystal, use ‘crysdir(dir_x,dir_y,dir_z)’, where (dir x, dir y, dir z) is
the crystal direction. For specifying cell-by-cell normals, use the syntax ‘file(file_name)’
where file_name is the name of a multiscale cell file containing the list of lamella plane
normals (see Section B.3 [Multiscale Cell File], page 67).
(ii) Custom morphological properties can be defined by providing as argument the cell prop-
erty and its value, combined with the ‘:’ separator. The available properties are:
• ‘size’ for the size (volume in 3D and area in 2D) and ‘diameq’ for the equivalent diameter;
• ‘sphericity’ for the sphericity and • ‘centroid’ for the centroid;
• ‘centroidsize’ for combined centroid and size, and ‘centroiddiameq’ for combined cen-
troid and equivalent diameter;
• ‘tesr’ for cells of a raster tessellation.
Sizes, sphericities can be defined by statistical distributions or on a per-cell basis, while cen-
troids can be defined only on a per-cell basis. The statistical distributions can be: a Dirac
distribution, ‘dirac(mean)’, a normal distribution, ‘normal(mean,sig)’, lognormal distri-
butions, ‘lognormal(mean,sig)’ or ‘lognormal(mean,sig,1-x)’ (which means the variable
is (1 − the cell property)), or a sum of distributions of increasing averages, for example,
‘0.3*normal(mean1,sig1)+0.7*normal(mean2,sig2)’. An interval of possible values can
also be provided using ‘interval(min,max)’. Cell-by-cell values can be provided using
‘file(file_name)’, where ‘file_name’ is the name of the file containing the cell values.
For ‘centroid’, provide ‘seed’ to get a centroidal tessellation. For ‘tesr’, ‘file_name’ is the
name of the raster tessellation file.
To specify several properties, combine them with ‘,’.
Possible values: any. Default value: voronoi.
-morphooptiini coo:coo_char_string,weight:weight_char_string [Option]
Specify the initial positions and weights of the seeds. Different arguments are available,
depending on the value of option -morpho.
‘weight_char_string’ can be a real value, any mathematical expression based on variables
‘radeq’ and ‘diameq’ (see Section A.2 [Tessellation Keys], page 52) and their average values,
‘avradeq’ and ‘avdiameq’, respectively, or ‘file(file_name)’ to load values from a file.
The default depends on the value of option ‘-morpho’: for ‘voronoi’, it is ‘0’, for a cell-
size statistical distribution, it is ‘avradeq’, and for cell-based size values (including -morpho
tesr) , it is ‘radeq’.
‘coo_char_string’ can be ‘random’ for random positions, ‘packing’ for positions set by
(rough) dense sphere packing using the weights as sphere radii, ‘centroid’ for cell centroids,
or ‘file(file_name)’ to load values from a file. The default depends on the value of option
1
centroidal is not recommended as it does not correspond to a morphological property per se; size and/or
sphericity properties should be used instead.
‘-morpho’: for ‘voronoi’, it is ‘random’, for a cell-size statistical distribution, it is ‘none’, and
for cell-based coordinate values (including -morpho tesr), it is ‘centroid’.
Possible values: see above list. Default value: default.
-morphooptiobjective char_string [Secondary option]
Specify the objective function. For statistical distributions, the available values of the
goodness-of-fit test are ‘chi2’ (Chi-square test), ‘ks’ (Kolmogorov-Smirnov test), ‘kuiper’
(Kuiper’s test), ‘cmv’ (Cramér-Von Mises test), ‘ad’ (Anderson-Darling test), ‘FL2’ (L2 -norm
on F ), ‘FL2w’ (weighted L2 -norm on F )2 , and the default value is ‘FL2w’. For ‘centroid’, a
Minkowski distance between the seeds and centroids is used, and can be ‘L1’, ‘L2’ or ‘Linf’.
For a raster tessellation, the distance function is used, which can be computed on different re-
gions. The available values are ‘vol’ for the full volume and ‘surf’ for only the surface voxels
of the cells. The surface voxels can be computed using different connexity rules: connexities
of 0, 1 and 2 indicate that two voxels form a connex set if they share at least a vertex, edge
of face, respectively (they lead to decreasing numbers of surface voxels). ‘surf’ assumes a
connexity level of 1; to set the connexity level, use ‘surflevel’, where level is the connexity
level. The default value is ‘surf’.
Possible values: any. Default value: default.
-morphooptidof char_string [Secondary option]
Specify the degrees of freedom. The available values are ‘x’, ‘y’ and ‘z’ for the 3 coordinates,
and ‘w’ for the weights. Combine with ‘,’.
Possible values: see above list. Default value: x,y,z,w.
-morphooptistop char_string [Secondary option]
Specify the stopping criteria of the optimization process. Note that you do not have to define
all criteria; in most cases, only one or two are needed. A stopping expression must be of
the form ‘var=val’, where ‘var’ is a variable and ‘val’ is its value. The available variables
are: an absolute or relative error on the value of the objective function, ‘eps’ or ‘reps’, an
absolute or relative error on the components of the solution vector, ‘xeps’ or ‘xreps’, a value
of the objective function, ‘val’, a value of the derivative of the (minimum of the) objective
function with respect to the iteration number, ‘dvalditer’, a maximum number of iterations,
‘itermax’, or a maximum computation time, ‘time’, Combine them with ‘,’. Optimization
stops as soon as one stopping criterion is matched. Optimization can also be stopped anytime
by invoquing the Ctrl+C command.
Possible values: any. Default value: dvalditer=1e-5 (val=1e-4,iter=1e4 for -morpho
centroidal).
-morphooptialgo char_string [Secondary option]
Specify the optimization algorithm. The available values are ‘subplex’ (Subplex), ‘praxis’
(Praxis), ‘neldermead’ (Nelder-Mead), ‘cobyla’ (Cobyla), ‘bobyqa’ (Bobyqa) and ‘newuoa’
(Newuoa) — only ‘subplex’ and ‘praxis’ are recommended. In the case of -morpho
centroidal, another available value is ‘lloyd’ (Lloyd’s algorithm); to specify the seed dis-
placement factor (from the seed to the centroid), use ‘lloyd(factor)’ (the default value is
2). Another available value is ‘random’, for which seeds are moved randomly by the distance
specified using -morphooptiinistep (use only if you really know what you are doing).
Possible values: any. Default value: subplex (lloyd for -morpho centroidal).
-morphooptialgoneigh char_string [Secondary option]
Specify the neighbour search algorithm. The available values are ‘ann’ (ANN) and ‘qsort’
(direct computation with qsort). ‘ann’ is much faster.
Possible values: any. Default value: ann.
2 QN
Weighting by 1/ i=0 |F − pi | where p0 = 0 and pi are the cumulative proportions of the distribution modes.
For a unimodal distribution, the expression simplifies to 1/(F (1 − F )).
14 Neper 3.0.2
-morphooptigrid char_string [Secondary option]

Specify the grid used to discretize the distributions. Provide ‘regular(min,max,bin_nb)’,
where min and max are the minimum and maximum values of the grid interval, respectively,
and bin_nb is the number of bins.
Possible values: any. Default value: regular(-1,10,1100).
-morphooptismooth real [Secondary option]

Specify the width of the Gaussian distribution which is assigned to each cell data to compute
the distributions.
Possible values: any. Default value: 0.05.
-morphooptideltamax real [Secondary option]

Specify the maximal value by which each variable is allowed to change during optimization.
direction (relative to the average cell size) and each seed is allowed to grow (weight value).
Possible values: any>=0. Default value: HUGE_VAL.
-morphooptiinistep real [Secondary option]

Specify the step used to perturb the seed positions and weights when optimization begins.
The argument can be a function of diameq, the average equivalent cell diameter.
Possible values: any>0. Default value: diameq/10.
-morphooptilogtime char_string [Secondary option]

Log the time taken during the optimization process. The keys are provided in Section A.4
[Tessellation Update Keys], page 54.
-morphooptilogvar char_string [Secondary option]

Log the variables, i.e. the seed attributes, during the optimization process. The keys are
provided in Section A.4 [Tessellation Update Keys], page 54.
-morphooptilogval char_string [Secondary option]

Log the value of the objective function during the optimization process. The keys are provided
in Section A.4 [Tessellation Update Keys], page 54.
-morphooptilogdis char_string [Secondary option]

Log the distributions during the optimization process. The keys are provided in Section A.4
[Tessellation Update Keys], page 54.
2.1.3 Transformation Options

-sort char_string [Secondary option]
Sort the tessellation cells (typically to facilitate data post-processing). Provide as argument
the mathematical expression used for sorting (see Section A.1 [Mathematical and Logical
Expressions], page 51).
-scale real:real:real [Option]

Scale the tessellation by given factors in the x, y and z directions once it is generated. In 2D,
the z value can be omitted.
-transform char_string(...) [Option]

Apply transformations to a tessellation.
The following transformation apply to a scalar tessellation:
• ‘scale(x_fact,y_fact,z_fact)’ scales a tessellation by x_fact, y_fact and z_fact along
directions x, y and z, respectively. For a 2D tessellation, z_fact can be omitted.
• ‘rotate(axis_x,axis_y,axis_z,angle)’ for a rotation about an axis/angle pair.
The following transformation apply to a raster tessellation:
• ‘autocrop’ reduces the raster to its minimal size.
• ‘rasterscale(x_fact,y_fact,z_fact)’ scales the number of points of the raster by factors
x_fact, y_fact and z_fact along directions x, y and z, respectively. For a 2D tessellation,
z_fact can be omitted.
• ‘rmsat’ removes the cell “satellites”, i.e. parts disconnected from the cell bulk.
• ‘grow’ grows the cells to fill the domain.
• ‘tessinter(tess_file)’ computes the intersection with tessellation tess_file.
Several transformations can be applied successively by combining them with ‘,’.
2.1.4 Crystal Orientation Options

-ori char_string [Option]
Specify the type of crystal orientation distribution. It can be:
• ‘3D’ for orientations in the 3D space;
• ‘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’);
• an ideal orientation, see Section A.7 [Rotations and Orientations], page 57;
• a discrete orientation defined using an orientation descriptor:
‘g(g11,g12,g13,g21,g22,g23,g31,g32,g33,)’ for a rotation matrix, ‘e(e1,e2,e3)’ for Eu-
ler angles in Bunge convention, ‘ek(ek1,ek2,ek3)’ for Euler angles in Kocks convention,
‘er(er1,er2,er3)’ for Euler angles in Roe convention, ‘rtheta(r1,r2,r3,theta)’ for an
axis / angle (in degrees) pair, ‘q(q1,q2,q3,q4)’ for a quaternion, ‘R(R1,R2,R3)’ for a Ro-
drigues vector and ‘m(h,k,l,u,v,w)’ for Miller indices;
• ‘equal’ for orientations equal to the one of the parent cell;
• ‘file(filename):des’ for reading orientations from file filename and written using the
descriptor des (see Section A.7 [Rotations and Orientations], page 57); if Euler angles (e),
the descriptor can be omitted.
For ‘3D’ and ‘fibre’, crystal orientations are distributed randomly according to a uniform
distribution in the specified space.
Possible values: see above list. Default value: 3D.
-oricrysym char_string [Secondary option]

Specify the crystal symmetry. This is used to reduce the domain of definition of the orienta-
tion descriptors.
Possible values: triclinic, cubic or hexagonal. Default value: triclinic.
2.1.5 Regularization Options

-regularization logical [Option]
Regularize a tessellation, that is, 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 23).
16 Neper 3.0.2
-fmax real [Option]

Specify the maximum allowed face flatness fault (in degrees). The flatness fault is the maxi-
mum angle between the normals at two locations on a face.
Possible values: 0 to 180. Default value: 20.
-sel or -rsel real [Secondary option]

Specify the absolute or relative small edge (maximum) length. rsel is defined relative to the
average cell size (volume in 3D and area in 2D). The default -rsel 1 leads to a length of 0.25
for a unit volume cell in 3D and 0.125 for a unit area cell in 2D. The value also enables to avoid
mesh refinement with the default meshing parameters (see Chapter 3 [Meshing Module (-M)],
page 23). 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 52. 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 23. 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.
-mloop integer [Secondary option]

Specify the 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 during a loop.
2.1.6 Output Options

-o file_name [Option]
Specify the output file name.
-format char_string [Option]

Specify the format of the output file(s). For scalar tessellations, the available formats are
the Neper ‘tess’, the Gmsh ‘geo’, the Ply ‘ply’, the Wavefront ‘obj’, the 3dec ‘3dec’
and the Surface Evolver ‘fe’. For raster tessellations, the available formats are the Neper
‘tesr’ and the Kitware ‘vtk’. Orientations for the cells can be obtained using ‘ori’ (see
also options starting by ‘-ori’). Combine the values with ‘,’.
Possible values: tess, geo, ply, obj, 3dec, fe, tesr, vtk, ori. Default value: tess.
-tesrformat char_string [Option]

Specify the format of the raster output file(s). The available formats are ASCII (‘ascii’),
8-bit binary / unsigned char-type (‘binary8’), 16-bit binary / short-type (‘binary16’ and
‘binary16_big’) and 32-bit binary / int-type (‘binary32’ and ‘binary32_big’). Formats
‘binary16’ and ‘binary32’ mean little endianness while formats ‘binary16_big’ and
‘binary32_big’ mean big endianness.3
Possible values: ascii, binary8, binary16, binary16_big, binary32, binary32_big.
Default value: binary16 or binary_big (depending on the system).
3
Endianness is both written in the tesr file and tested on the system when reading the tesr file, so that the user
normally does not have to care about it (even when transferring files across systems).
-tesrsize integer [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 ‘:’.
-oridescriptor char_string [Option]
Specify 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 of
rotation (rtheta), angle of rotation (theta), Rodrigues vector (R) or quaternion (q).
Possible values: above-mentioned values. Default value: e.
-oriformat 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/Zébulon geof and the FEpX fepx.
Possible values: above-mentioned values. Default value: plain.
2.1.7 Post-Processing Options

The first options apply to the cells and seeds of a tessellation or a raster tessellation, indepen-
dently of its dimension,
-statcell char_string [Post-processing]
Provide statistics on the tessellation cells. Give as argument the keys as described in
Section A.2 [Tessellation Keys], page 52 for a tessellation and Section A.3 [Raster Tessel-
lation Keys], page 54 for a raster tessellation (combine with ‘,’).
Result file: extension .stcell.
-statseed char_string [Post-processing]
Provide statistics on the tessellation seeds. Give as argument the keys as described in
Section A.2 [Tessellation Keys], page 52 for a tessellation and Section A.3 [Raster Tessel-
lation Keys], page 54 for a raster tessellation (combine with ‘,’).
Result file: extension .stseed.
For a tessellation, it is also possible to get statistics on an entity-basis,
-statver char_string [Post-processing]
Provide statistics on the tessellation vertices. Give as argument the keys as described in
Section A.2 [Tessellation Keys], page 52 (combine with ‘,’).
Result file: extension .stver.
-statedge char_string [Post-processing]
Provide statistics on the tessellation edges. Give as argument the keys as described in
Result file: extension .stedge.
-statface char_string [Post-processing]
Provide statistics on the tessellation faces. Give as argument the keys as described in
Result file: extension .stface.
18 Neper 3.0.2
-statpoly char_string [Post-processing]

Provide statistics on the tessellation polyhedra. Give as argument the keys as described in
Result file: extension .stpoly.
Finally, it is possible to get statistics for a particular set of points. The option applies to a
tessellation.
-statpoint char_string [Post-processing]
Provide statistics on points. The points must be loaded with option -loadpoint. Give as
argument the keys as described in Section A.6 [Point Keys], page 56 (combine with ‘,’).
Result file: extension .stpoint.
2.1.8 Debugging Options

-checktess file_name [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.
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 61
for the file syntax.
• Neper raster tessellation file: .tesr
It contains a raster description of the tessellation. See Appendix B [File Formats], page 61
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 For-
mat” .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.
• VTK file: .vtk
It contains a description of the raster tessellation written under the VTK format .vtk as
supported by Amitex ffpt. Binary data are always written using BigEndians.
• Orientation file: .ori
It contains crystal orientations for the tessellation cells. The orientations are written on suc-
cessive lines, using the descriptor specified by option -oridescriptor (see also Section A.7
[Rotations and Orientations], page 57) 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 52 and Section A.3 [Raster
Tessellation Keys], page 54 (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.
2.2.3 Tessellation Optimization Log Files

Log files are provided for the time, variables, statistical distributions and objective function
value. The files contain the data specified to the corresponding -morphooptilog option and
described on Section A.4 [Tessellation Update Keys], page 54.
• Time file, .logtime.
• Variables, i.e. seed attributes, file, .logvar.
• Statistical distribution files, .logdisid, where id is the identifier of the distribution.
• Objective function value file, .logval.
• Target raster tessellation file, -obj.tesr.
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 apply regularization.
$ neper -T -n 100 -id 1 -reg 1
4. Generate a 2D Voronoi tessellation containing 100 cells.
$ neper -T -n 100 -id 1 -dim 2
5. Generate a tessellation containing 100 cells with experimental grain-growth morphological
properties.
$ neper -T -n 100 -id 1 -morpho gg
6. Generate a tessellation containing 100 cells with experimental grain-growth morphological
properties, and get the equivalent diameters and sphericities of the cells.
$ neper -T -n 100 -id 1 -morpho gg -statcell diameq:rel,sphericity
7. Generate a 2-scale Voronoi tessellation containing 100 × 10 cells.
$ neper -T -n 100::10 -id 1::1
8. Generate a 2-scale tessellation containing 10 primary cells with grain-growth morphological
properties, each one divided into lamellae of width 0.1.
$ neper -T -n 10::from_morpho -id 1::1 -morpho "gg::lamellar(w=0.1)"
20 Neper 3.0.2
9. Generate a 2-scale Voronoi tessellation containing 10 primary cells with grain-growth mor-
phological properties, each one divided into lamellae of widths loaded from file lam_width
and plane normals loaded from file lam_normal.
$ neper -T -n 10::from_morpho -id 1::1 -morpho "gg::lamellar(w=file(lam_
width),v=file(lam_normal))"
lam_width:
1 0.05
2 0.10
3 0.05
4 0.10
5 0.05
6 0.10
7 0.05
8 0.10
9 0.05
10 0.10
lam_normal:
1 1.000000 0.000000 0.000000
2 0.000000 1.000000 0.000000
3 1.000000 0.000000 0.000000
4 0.000000 1.000000 0.000000
5 1.000000 0.000000 0.000000
6 0.000000 1.000000 0.000000
7 1.000000 0.000000 0.000000
8 0.000000 1.000000 0.000000
9 1.000000 0.000000 0.000000
10 0.000000 1.000000 0.000000
10. Generate a 2-scale Voronoi tessellation containing 3 primary cells divided into 1, 10 and
100 secondary cells, respectively.
$ neper -T -n "3::file(myfile)" -id 1::1
myfile:
1 1
2 10
3 100
11. 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 \
-morphooptiini "coo:file(coo1),weight:0::coo:file(coo2),weight:0" \
-morpho voronoi
coo1:
0.25 0.50 0.50
0.75 0.50 0.50
coo2:
1 0.25 0.10 0.50
1 0.25 0.50 0.50
1 0.25 0.90 0.50
2 0.75 0.50 0.10
2 0.75 0.50 0.50
2 0.75 0.50 0.90
Note that coo1 is a simple position file (see Section B.4 [Position File], page 68) while coo2
is a multiscale cell file (see Section B.3 [Multiscale Cell File], page 67).
Chapter 3: Meshing Module (-M) 23
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). Mapped (or structured) meshing generates a non-conforming mesh into
regular hexahedral elements (quadrangular in 2D). Free meshing is carried out so that the
elements have sizes as close as possible to the 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 tessellations, multiscale tessellations and periodic (or
semi-periodic) tessellations are supported. Free meshing of raster tessellations works for 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 triangu-
lar or quadrangular 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 cl (or rcl) values 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 9.
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 min-
imizing 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).
1
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.
24 Neper 3.0.2
Here is what a typical run of module -M looks like,
$ neper -M n10-id1.tess
======================== N e p e r =======================
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% (0.72|0.87/83%|11%| 6%)
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: 287
Info : > Elt number: 1006
Info : > Mesh volume: 1.000
Info : - Writing mesh...
Info : [o] Writing file ‘n10-id1.msh’...
Info : [o] Wrote file ‘n10-id1.msh’.
========================================================================
3.1 Arguments
3.1.1 Prerequisites
-gmsh path_name [Prerequisite]
Specify the path of the Gmsh binary (for meshing into triangle and tetrahedral elements).
Possible values: any. Default value: gmsh.
-tmp path_name [Prerequisite]

Specify the path of the temporary directory (used by Gmsh).
Possible values: any. Default value: ".".
3.1.2 Input Data

In normal use, the input data is a tessellation file, a raster tessellation file or a mesh file,
file_name [Input data]

Specify the 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.4 [Position
File], page 68). 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. 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.
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).
Finally, it is possible to load a set of points. These points are used only for statistics, in option
-statpoint,
-loadpoint file_name [Input data]

Load points from a file. See Section B.4 [Position File], page 68 for the file format. Provide
as argument the file name.
3.1.3 Meshing Options

-elttype char_string [Option]
Specify the 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.
26 Neper 3.0.2
-cl or -rcl real [Option]

Specify the 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). For free meshing, it is also possible to get non-uniform characteristic
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 52 for tessellations, Section A.3 [Raster Tessellation Keys], page 54 for raster
tessellations and Section A.5 [Mesh Keys], page 55 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.
-dim char_string [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 always 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.
-order integer [Option]

Specify the mesh order. 1 means 2-node linear elements, 3-node triangular elements, 4-
node quadrangular elements, 4-node tetrahedral elements and 8-node hexahedral elements.
2 means 3-node linear elements, 6-node triangular elements, 8-node quadrangular elements,
10-node tetrahedral elements and 20-node hexahedral elements.
-pl real [Secondary option]

Specify the progression factor for the element characteristic lengths. This value is the maxi-
mum ratio between the lengths of two adjacent 1D elements.
Possible values: any >= 1. Default value: 2.
-clratio char_string [Secondary option]

Specify the 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.
-clmin real [Not recommended option]

Specify the minimum characteristic length of the elements.
The following options define the multimeshing algorithm (for 2D and 3D free meshings). Multi-
meshing 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 α × Osize 1−α , where Odis and Osize
range from 0 (poor quality) to 1 (high quality) and α 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 more
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.
The value of the target mesh quality significantly influences meshing speed and output mesh
quality. A value of 0 provides the fastest meshing while a value of 1 provides the 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).
-meshqualmin real [Option]
Specify the minimum, target value of mesh quality, O, as defined by option -meshqualexpr.
Possible values: 0 to 1. Default value: 0.9.
-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.
-meshqualdisexpr char_string [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))).
-mesh2dalgo char_string [Secondary option]
Specify the 2D meshing algorithms (combine with ‘,’). The available values are mead (Me-
shAdapt), dela (Delaunay) and fron (Frontal).
Possible values: mead, dela, fron. Default value: mead,dela,fron.
-mesh3dalgo 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.
-interface char_string [Secondary option]
Specify the type of interface meshing. Provide ‘continuous’ for a continuous mesh at in-
terfaces, with shared nodes between neighbour element sets (which are associated to the
tessellation cells). Provide ‘discontinuous’ for a discontinuous mesh at interfaces, with
distinct nodes for the neighbour element sets. Provide ‘cohesive’ for cohesive elements at
interfaces, joining the neigbour element sets. See option -faset for the output format.
Possible values: see above. Default value: continuous.
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.
-tesrsmooth char_string [Secondary option]
Method for smoothing the interface meshes reconstructed from raster tessellations. Laplacian
smoothing (‘laplacian’) is an iterative method that modifies the coordinates of a node
1
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, 1309–1331, 2009.
2
J. Schoberl, Netgen, an advancing front 2d/3d-mesh generator based on abstract rules. Comput. Visual. Sci., 52,
1–41, 1997.
28 Neper 3.0.2
using the coordinates of the neighbouring nodes. At iteration i, the position of a node,
Xi , is calculated from its previous position, Xi−1 , 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), Xi−1 , as follows: Xi = (1 − A) Xi−1 + A Xi−1 . A ∈ [0, 1] is
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.
-tesrsmoothfact real [Secondary option]
Specify the factor used for the interface mesh smoothing (A in option -tesrsmooth).
-tesrsmoothitermax integer [Secondary option]
Specify the 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.
-clean integer [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.
-singnodedup logical [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 en-
abled, such a node is duplicated, so that each body has its own node. Option -dupnodemerge
enables to merge back duplicate nodes.
-dupnodemerge real [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 options -singnodedup or -interface.
Possible values: 0. Default value: any>0.
3.1.6 Transformation Options

-scale real:real:real [Option]
Scale the mesh by given factors in the x, y and z directions once it is generated. In 2D, the
z value can be omitted.
3.1.7 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
3
F. Pellegrini, Scotch and libScotch 5.1 User’s Guide, INRIA Bordeaux Sud-Ouest, ENSEIRB & LaBRI, UMR
CNRS 5800, 2008.
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, while the second
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 made of 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.
-part integer or char_string [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
total number of partitions must be a power of 2. An architecture can be specified in two ways.
First, for clusters that contain processors made of 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.
-partbalancing real [Secondary option]
Specify the rate of element partition balancing. The partitioning algorithm applies to
the nodes; the element partitions are determined afterwards and can be somewhat unbal-
anced. This option enables to enforce balancing, but getting a full balancing is highly CPU-
demanding.
-partmethod char_string [Secondary option]
Specify the partitioning method. Provide the partitioning expression in Scotch’s jargon, or
‘none’ for none.
Possible values: any. Default value: see_the_source.
3.1.8 Field Transport Options

-transport char_string:char_string:file_name,... [Option]
Transport data from a parent mesh to a child mesh. The parent mesh is the input mesh and
the child mesh is the result mesh (created by remeshing or loaded with -loadmesh). A trans-
port entry must have format ‘entity_type:data_type:file_name’, where ‘entity_type’
must be ‘node’ or ‘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 ‘,’. Nodal data are trans-
ported by interpolation using the shape functions (2D only). Element data are transported
by considering the parent element which the centroid of the new element belongs to.
3.1.9 Output Options

-o file_name [Option]
Specify the output file name.
30 Neper 3.0.2
-format char_string [Option]

Specify the format of the output file(s). Mesh formats are: the Gmsh ‘msh’, the VTK ‘vtk’,
the Abaqus ‘inp’, the Zset/Zébulon ‘geof’ and the FEpX ‘fepx’ (for the FEpX legacy format,
provide ‘fepx:legacy’). For ‘msh’, append ‘:format’ to specify the format, which can be
‘ascii’ or ‘binary’ (default ‘ascii’). The tessellation file format ‘tess’ is also available.
Combine arguments with ‘,’.
Possible values: see above. Default value: msh.
-nset 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 ver-
tices. 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), the
labels are [x-y][0,1] for the edges and [x-y][0,1][x-y][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 and edges in 2D.
-faset char_string [Option]
Specify the element surface meshes (edge meshes in 2D) to provide. Use ‘faces’ for all
domain faces. To get the meshes of individual faces, provide their labels (see option -nset).
For internal mesh faces (edges in 2D) as created by ‘-interface discontinuous’, provide
‘internal’. Combine them with ‘,’. Provide none for none.
Possible values: see above. Default value: none.
3.1.10 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.
-statnode char_string [Post-processing]
Provide statistics on the nodes. Provide as argument the keys as described in Section A.5
[Mesh Keys], page 55 (combine with ‘,’).
Result file: extension .stnode.
-statelt0d char_string [Post-processing]
Provide statistics on the 0D elements. Provide as argument the keys as described in
Section A.5 [Mesh Keys], page 55 (combine with ‘,’).
Result file: extension .stelt0d.


-statelset0d char_string [Post-processing]

Provide statistics on the 0D element sets. Provide as argument the keys as described in
Result file: extension .stelset0d.



-statpoint 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.6 [Point Keys], page 56 (combine with ‘,’).
Result file: extension .stpoint.
3.1.11 Advanced Options

These advanced options set running conditions for the meshing libraries (triangle and tetrahedral
meshing),
-mesh3dclconv real [Secondary option]

Specify the 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).
32 Neper 3.0.2
-mesh2dmaxtime real [Secondary option]

Specify the maximum processing time allowed to the meshing library for meshing a tessellation
face (in seconds).
-mesh2drmaxtime real [Secondary option]

Specify a factor used to determine the maximum processing time allowed to the meshing
library for meshing a tessellation face. This option is similar to -mesh2dmaxtime, but the
actual maximum time is the product of the maximum processing time of the previous mesh-
ings by the value provided in argument.
-mesh2diter integer [Secondary option]

Specify the maximum number of 2D meshing attempts for a particular face (in case of failure).
-mesh3dmaxtime real [Secondary option]

Specify the maximum processing time allowed to the meshing library for meshing a tessellation
polyhedron (in seconds).
-mesh3drmaxtime real [Secondary option]

Specify a factor used to determine the maximum processing time allowed to the meshing
library for meshing a tessellation polyhedron. 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.
-mesh3diter integer [Secondary option]

Specify the maximum number of 3D meshing attempts for a particular polyhedron (in case
of failure).
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/Zébulon format: file .geof
• FEpX format: files .mesh, .grain and .bcs (.parms, .mesh, .surf, .opt and .bcs in
legacy mode)
3.2.2 Periodicity
• File .per. For each slave node, the file provides (one slave node per line): the node id, the
master node id and the shift vector of the slave.
3.2.3 Interfaces
• File .intl. For each 2D interface, the file provide (one 2D interface per line): the labels of
the two element sets of the interface.
3.2.4 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.5 [Mesh Keys], page 55.
• Node statistics file, .stnode.
• (Higher-dimension) element statistics file, .stelt.
• (Higher-dimension) element set statistics file, .stelset.
• 0D element statistics file, .stelt0d.
• 0D element set statistics file, .stelset0d.
• 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
4. Mesh tessellation n100-id1.tess with small elements for the interior cells and bigger ele-
ments 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 divide 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) 35
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 : ---------------------------------------------------------------
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 90% (to 410).
Info : . Number of 3D elt edges reduced by 50% (to 615).
Info : . Number of 0D elts reduced by 100% (to 0).
Info : [o] Wrote file ‘img.pov’.
Info : - Generating png file (1080x1080 pixels)...
Info : [o] Writing file ‘img.png’...
Info : [o] Wrote file ‘img.png’.
36 Neper 3.0.2
Info : Printing scale...

========================================================================
4.1 Arguments
4.1.1 Prerequisites
-povray path_name [Prerequisite]

Specify the path of the POV-Ray binary (for generating PNG images).
Possible values: any. Default value: povray.
4.1.2 Input Data
file_name [Input data]

Specify the 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.4 [Position File], page 68). To
load several of them, combine them with ‘,’.
4.1.3 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 converted 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,
-datacellcol char_string [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.8 [Colours], page 57),
(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.8 [Colours], page 57), (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,
‘scal’ for scalar ‘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.
-datacellcolscheme 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.
-datacelltrs real [Option]

Set the transparency of the tessellation cells. Provide as argument a value that applies to all
cells or ‘file(file_name)’ to load values from a file.
-datacellscale char_string [Option]
Set the scale relative to the ‘-datacellcol scal’ data. Provide as argument the start and
end values, combined with ‘:’. To specify the intermediate values, provide as argument the
start value, the intermediate values and then the end value, combined with ‘:’. The labels of
the scale follow the format used for the start value.
Possible values: any. Default value: data minimum:data maximum.
-datacellscaletitle char_string [Option]
Set the title of the scale relative to the ‘-datacellcol scal’ data.
For tessellations, it is also possible to set data on a per-entity basis,
-datapolycol char_string [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.8 [Colours],
page 57), (ii) ‘scaleid(scale)’ for colouring based on the identifier of the scale tessella-
tion the polyhedron belongs to, using a colour palette (see Section A.8 [Colours], page 57),
(iii) the name of a colour that will be used for all polyhedra (see Section A.8 [Colours],
page 57), (iv) the name of a file containing a list of colours (provided as RGB channel val-
ues), or (v) a string indicating how the colours can be obtained. 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 -datapolycolscheme.
-datapolycolscheme 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.
scalars.
-datapolytrs real [Option]
Set the transparency of the tessellation polyhedra. Provide as argument a value that applies
to all polyhedra or ‘file(file_name)’ to load values from a file.
-datapolyscale char_string [Option]
Set the scale relative to the ‘-datapolycol scal’ data. Provide as argument the start and
-datapolyscaletitle char_string [Option]
Set the title of the scale relative to the ‘-datapolycol scal’ data.
38 Neper 3.0.2
-datafacecol char_string [Option]

Set the colours of the tessellation faces. See option -datapolycol for the argument format.
-datafacecolscheme 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.
-datafacetrs real [Option]
Set the transparency of the tessellation faces. Provide as argument a value that applies to
all faces or ‘file(file_name)’ to load values from a file.
-datafacescale char_string [Option]
Set the scale relative to the ‘-datafacecol scal’ data. Provide as argument the start and
-datafacescaletitle char_string [Option]
Set the title of the scale relative to the ‘-datafacecol scal’ data.
-dataedgerad char_string [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.
-dataedgecol char_string [Option]
Set the colours of the tessellation edges. See option -datapolycol for the argument format.
Possible values: any. Default value: black.
-dataedgecolscheme 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.
-datapolycolscheme.
-dataedgetrs real [Option]
Set the transparency of the tessellation edges. Provide as argument a value that applies to
all edges or ‘file(file_name)’ to load values from a file.
-dataedgescale char_string [Option]
Set the scale relative to the ‘-dataedgecol scal’ data. Provide as argument the start and
-dataedgescaletitle char_string [Option]
Set the title of the scale relative to the ‘-dataedgecol scal’ data.
-dataverrad char_string [Option]

Set the radii of the tessellation vertices. See option -dataedgerad for the argument format.
-datavercol char_string [Option]
Set the colours of the tessellation vertices. See option -datapolycol for the argument format.
-datavercolscheme 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.
-datapolycolscheme.
-datavertrs real [Option]
Set the transparency of the tessellation vertices. Provide as argument a value that applies to
all vertices or ‘file(file_name)’ to load values from a file.
-dataverscale char_string [Option]
Set the scale relative to the ‘-datavercol scal’ data. Provide as argument the start and
-dataverscaletitle char_string [Option]
Set the title of the scale relative to the ‘-datavercol scal’ data.
-dataseedrad char_string [Option]
Set the radii of the tessellation seeds. See option -dataedgerad for the argument format.
-dataseedcol char_string [Option]
Set the colours of the tessellation seeds. See option -datapolycol for the argument format.
Possible values: any. Default value: grey.
-dataseedcolscheme 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.
-datapolycolscheme.
-dataseedscale char_string [Option]
Set the scale relative to the ‘-dataseedcol scal’ data. Provide as argument the start and
-dataseedscaletitle char_string [Option]
Set the title of the scale relative to the ‘-dataseedcol scal’ data.
Below are options specific to raster tessellations,
40 Neper 3.0.2
-datarptedgerad real [Option]

Set the radius of the edges of the raster points.
Possible values: any. Default value: proportional to the raster point size.
-datarptedgecol char_string [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.8 [Colours], page 57).
4.1.4 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
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’.
-dataelt3dcol char_string [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.8 [Colours], page 57), (ii) the name of a colour
that will be used for all elements (see Section A.8 [Colours], page 57), (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.
-dataelt3dcolscheme 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
scalars.
-dataelt3dscale char_string [Option]
Set the scale relative to the ‘-dataelt3dcol scal’ data. Provide as argument the start and
-dataelt3dscaletitle char_string [Option]

Set the title of the scale relative to the ‘-dataelt3dcol scal’ data.
-dataelt3dedgerad real [Option]

Set the radius of the edges of the 3D elements.
Possible values: any. Default value: mesh dependent.
-dataelt3dedgecol char_string [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.8 [Colours], page 57).
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’.

Set the colours of the 2D elements. See option -dataelt3dcol for the argument format.

option -dataelt2dcol. See option -dataelt3dcolscheme for the argument format.
Possible values: see option -dataelt3dcolscheme. Default value: see option
-dataelt3dcolscheme.


-dataelt2dedgerad real [Option]

Set the radius of the edges of the 2D elements.
-dataelt2dedgecol char_string [Option]

Set the colours of the edges of the 3D elements. See option -dataelt3dedgecol for the
argument format.
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’.

42 Neper 3.0.2

-dataelt1drad char_string [Option]
Set the radius of the 1D elements.
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’.
-dataelt0drad char_string [Option]
Set the radius of the 0D elements.
The following options enable to load data relative to the nodes.

-datanodecoo char_string [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.
-datanodecoofact real [Option]
Set the value of the scaling factor to apply to the displacements of the nodes.
-datanoderad file_name [Option]
Set the radius of the nodes.
-datanodecol file_name [Option]
Set the colours of the nodes. See option -dataelt3dcol for the argument format.
-datanodecolscheme char_string [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.
-datanodescale char_string [Option]
Set the scale relative to the ‘-datanodecol scal’ data. Provide as argument the start and
-datanodescaletitle char_string [Option]
Set the title of the scale relative to the ‘-datanodecol scal’ data.
4.1.5 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).
-datapointcoo char_string [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.
-datapointcoofact real [Option]
Set the value of the scaling factor to apply to the displacements of the points.
-datapointrad char_string [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
44 Neper 3.0.2
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.
-datapointcol 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.8 [Colours], page 57), (ii) the name of a colour that will
be used for all points (see Section A.8 [Colours], page 57), (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
‘id’ for identifiers, ‘scal’ for scalar ‘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.
-datapointcolscheme char_string [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
scalars.
-datapointtrs real [Option]

Set the transparency of the points. Provide as argument a value that applies to all points or
‘file(file_name)’ to load values from a file.
-datapointscale char_string [Option]

Set the scale relative to the ‘-datapointcol scal’ data. Provide as argument the start and
-datapointscaletitle char_string [Option]

Set the title of the scale relative to the ‘-datapointcol scal’ data.
4.1.6 Coordinate System Rendering

-datacsyscoo char_string [Option]
Set the coordinates of the origin of the coordinate system. Combine the coordinates with ‘:’.
Possible values: any. Default value: 0:0:0.
-datacsyslength real [Option]

Set the length of the coordinate system axes.
-datacsysrad real [Option]
Set the radius of the coordinate system axes.
-datacsyslabel char_string [Option]
Set the labels of the coordinate system axes. Combine the labels with ‘:’.
Possible values: any. Default value: X1:X2:X3.
-datacsyscol char_string [Option]
Set the colour of the coordinate system. Provide as argument any colour as detailed in
Section A.8 [Colours], page 57.
Possible values: any. Default value: 32|32|32.
4.1.7 Slice Settings

-slicemesh char_string [Option]
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
‘,’.
4.1.8 Show Settings

The following options apply to the full tessellations or mesh.
-showtess logical [Option]
Show or hide the tessellation.
Possible values: 0 or 1. Default value: 1 if tess loaded and no mesh.
-showtesr logical [Option]
Show or hide the raster tessellation.
Possible values: 0 or 1. Default value: 1 if tesr loaded and no mesh.
-showmesh logical [Option]
Show or hide the mesh.
Possible values: 0 or 1. Default value: 1 if mesh loaded and no slice.
-showmeshslice logical [Option]
Show or hide the mesh slice(s).
Possible values: 0 or 1. Default value: 1 if existing slice(s).
-showpoint logical or char_string [Option]
Show or hide the points. To show only specific points, provide ‘file(file_name)’ to load
point numbers from a file.
The following option applies to the cells of a tessellation or a raster tessellation, independently
of its dimension,
-showcell char_string [Option]
Specify the cells to show. The argument can be: ‘all’ for all, ‘none’ for none,
‘file(file_name)’ to load polyhedron identifiers from a file, or any expression based on the
keys listed in Section A.2 [Tessellation Keys], page 52 or Section A.3 [Raster Tessellation
Keys], page 54.
Possible values: any. Default value: all.
46 Neper 3.0.2
For tessellations, it is also possible to set visibility on a per-entity basis,

-showpoly char_string [Option]
Specify the polyhedra to show. The argument can be: ‘all’ for all, ‘none’ for none,
‘file(file_name)’ to load polyhedron identifiers from a file, or any expression based on
the keys listed in Section A.2 [Tessellation Keys], page 52.
Possible values: any. Default value: all.
-showface char_string [Option]
Specify the faces to show. The argument can be: ‘all’ for all, ‘none’ for none,
‘file(file_name)’ to load face identifiers from a file, or any expression based on the keys
listed in Section A.2 [Tessellation Keys], page 52. The following specific keys are also
available: ‘cell_shown’ and ‘poly_shown’.
-showedge char_string [Option]
Specify the edges to show. The argument can be: ‘all’ for all, ‘none’ for none,
‘file(file_name)’ to load edge numbers from a file, or any expression based on the keys
listed in Section A.2 [Tessellation Keys], page 52. The following specific keys are also
available: ‘cell_shown’, ‘poly_shown’ and ‘face_shown’.
Possible values: any. Default value: cell_shown.
-showver char_string [Option]
Specify the vertices to show. The argument can be: ‘all’ for all, ‘none’ for none,
‘file(file_name)’ to load vertex numbers from a file, or any expression based on the keys
listed in Section A.2 [Tessellation Keys], page 52. The following specific keys are also avail-
able: ‘cell_shown’, ‘poly_shown’, ‘face_shown’ and ‘edge_shown’.
-showseed char_string [Option]
Specify the seeds to show. The argument can be: ‘all’ for all, ‘none’ for none,
‘file(file_name)’ to load seed numbers from a file, or any expression based on the keys
listed in Section A.2 [Tessellation Keys], page 52. The following specific key is also available:
‘cell_shown’.
-showfaceinter logical [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.
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’.
-showelt3d char_string [Option]
Specify the 3D elements to show. The argument can be: ‘all’ for all, ‘none’ for none,
‘file(file_name)’ to load element identifiers from a file, or any expression based on the
keys listed in Section A.5 [Mesh Keys], page 55.
Possible values: any. Default value: all if highest mesh dim. is 3 and none otherwise.

Specify the 2D elements to show. The argument can be: ‘all’ for all, ‘none’ for none,
‘file(file_name)’ to load element identifiers from a file, or any expression based on the
keys listed in Section A.5 [Mesh Keys], page 55. The following specific key is also available:
‘elt3d_shown’.

Specify the 1D elements to show. The argument can be: ‘all’ for all , ‘none’ for none,
‘file(file_name)’ to load element numbers from a file, or any expression based on the keys
listed in Section A.5 [Mesh Keys], page 55. The following specific keys are also available:
‘elt2d_shown’ and ‘elt3d_shown’.

Specify the 0D elements to show. The argument can be: ‘all’ for all ‘none’ for none,
‘file(file_name)’ to load element numbers from a file, or any expression based on the keys
‘elt1d_shown’, ‘elt2d_shown’ and ‘elt3d_shown’.
-shownode char_string [Option]

Specify the nodes to show. The argument can be: ‘all’ for all , ‘none’ for none,
‘file(file_name)’ to load node numbers from a file, or any expression based on the keys
‘elt0d_shown’, ‘elt1d_shown’, ‘elt2d_shown’ and ‘elt3d_shown’.
-showcsys logical [Option]

Show the coordinate system.
-showshadow logical [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.
4.1.9 Camera Settings

-cameracoo char_string:char_string:char_string [Option]
Specify the camera coordinates. By default, the camera is shifted by a vector 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 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+vx:y+vy:z+vz.
-cameralookat 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.
48 Neper 3.0.2
-cameraangle real [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.
-camerasky real:real: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.
-cameraprojection char_string [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.
4.1.10 Output Image Settings

-imagesize int:int [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.
-imagebackground char_string [Option]

Specify the colour of the background. Provide as argument any colour as detailed in
Section A.8 [Colours], page 57.
-imageantialias logical [Option]

Use antialiasing to produce a smoother image. Switch antialiasing off for faster image gener-
ation or smaller image file.
-imageformat char_string [Option]

Specify the output image format. It can be the PNG format (.png) or the POV-Ray
format (.pov). Combine with ‘,’.
Possible values: png or pov. Default value: png.
4.1.11 Scripting
-loop char_string real real real ... -endloop [Option]
Create a loop of commands. 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.
4.1.12 Advanced Options

-includepov char_string [Option]
Use this option to include additional objects to the image, under the form of a POV-Ray file.
Provide as argument the name of the POV-Ray file.
4.2 Output Files

The output files are,
• PNG file, .png: a bitmapped image (the alpha channel is off).
• POV-Ray file, .pov: a POV-Ray script file.
A PNG image can be obtained from a POV-Ray file by invoquing POV-Ray as follows (see the
POV-Ray documentation for details and further commands), povray file.pov +Wimage_width
+Himage_height -D +A0.2.
4.3 Examples
Below are some examples of use of neper -V.
1. Print out tessellation n10-id1.tess with cells coloured from their identifiers and an image
size of 900 × 450 pixels.
$ neper -V n10-id1.tess -datacellcol id -imagesize 900:450 -print img
2. Print out tessellation n10-id1.tess with cells coloured from crystal orientations and semi-
transparency.
$ neper -V n10-id1.tess -datacellcol ori -datacelltrs 0.5 -print img
3. Print out mesh n10-id1.msh with elements coloured from scalar values written in file v and
a scale ranging from 0 to 100.
$ neper -V n10-id1.msh -dataeltcol scal:v -dataeltscale 0:100
-print img
4. Print out mesh n10-id1.msh with elements coloured from nodal scalar values written in
file v and a scale ranging from 0 to 100.
$ neper -V n10-id1.msh -datanodecol scal:v -dataeltcol from_nodes
-dataeltscale 0:100 -print img
5. Print out the 10 first cells of a 100-cell tessellation, coloured from their identifiers and semi-
transparency, and with edges shown in red and vertices shown as green spheres of radius
0.01.
$ neper -V n100-id1.tess -showcell "id<=10"
-datacellcol id -datacelltrs 0.5
-showedge cell_shown -showver cell_shown
-dataverrad 0.01 -dataedgecol red -datavercol green
-print img
6. Print out the interior element sets of mesh n100-id1.msh and show the 1D elements.
$ neper -V n100-id1.tess,n100-id1.msh -dataelsetcol id
-showelset ’body>0’ -showelt1d elt3d_shown -print img
7. Print out 3 slices of mesh n100-id1.msh.
$ neper -V n100-id1.msh -dataelsetcol id
-slicemesh "x=0.5,y=0.5,z=0.5" -print img
8. Print out slices of mesh n100-id1.msh, at z coordinates ranging from 0.1 to 0.9 by step
of 0.1, each slice being printed in a separate file.
$ neper -V n100-id1.msh -dataelsetcol id
-loop Z 0.1 0.1 0.9
-slicemesh "z=Z" -print imgZ
-endloop
Appendix A: Expressions and Keys 51
Appendix A Expressions and Keys
A.1 Mathematical and Logical Expressions

Neper can handle mathematical expressions. It makes use of the muparser library. The expres-
sion must contain no space, tabulation or new-line characters, and match the following syntax1 .
A.1.1 Functions
The following table gives an overview of the functions supported by the default implementation.
It lists the function names, the number of arguments and a brief description.
Name Description
sin sine function
cos cosine function
tan tangens function
asin arcus sine function
acos arcus cosine function
atan arcus tangens function
sinh hyperbolic sine function
cosh hyperbolic cosine
tanh hyperbolic tangens function
asinh hyperbolic arcus sine function
acosh hyperbolic arcus tangens function
atanh hyperbolic arcur tangens function
log2 logarithm to the base 2
log10 logarithm to the base 10
log logarithm to the base 10
ln logarithm to base e (2.71828. . . )
exp e raised to the power of x
sqrt square root of a value
sign sign function: -1 if x < 0; 1 if x > 0
rint round to nearest integer
abs absolute value
min min of all arguments
max max of all arguments
sum sum of all arguments
avg mean value of all arguments
A.1.2 Binary Operators

The following table lists the default binary operators supported by the parser.
Operator Description Priority

&& logical and 1
|| logical or 2
<= less or equal 4
>= greater or equal 4
!= not equal 4
== equal 4
1
Taken from the muparser documentation, see http: / /beltoforion .de /article .php ?a=muparser for more
information.
52 Neper 3.0.2
> greater than 4

< less than 4
+ addition 5
- subtraction 5
* multiplication 6
/ division 6
^ raise x to the power of y 7
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 and faces and the tessellation is 2D.
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 Descriptor Apply to

id Identifier seed, ver, edge, face, poly
x x coordinate seed, ver, edge, face, poly
y y coordinate seed, ver, edge, face, poly
z z coordinate seed, ver, edge, face, poly
w weight (width for a lamella tessellation) seed
true true level ver, edge, face, poly
body body level ver, edge, face, poly
state state ver, edge, face, poly
domtype type of domain (0 if on a domain vertex, 1 ver, edge, face
if on a domain edge and 2 if on a domain
face)
length length edge
area area face, poly
vol volume poly
size size (area/volume in 2D/3D) cell
diameq diameter of the equivalent circle/sphere in face, poly
2D/3D
radeq radius of the equivalent circle/sphere in face, poly
2D/3D
circularity circularity (2D counterpart of sphericity) face
sphericity sphericity2 poly
convexity convexity3 face4 , poly
dihangleav, average, minium and maximum dihedral face, poly
dihanglemin, angle
dihanglemax
dihanglelist dihedral angle list face, poly
ff flatness fault (in degrees) face
2
Sphericity of a polyhedron = ratio of the surface area of the sphere of equivalent volume to the surface area of
the polyhedron.
3
Convexity of a polyhedron (face) = ratio of the volume (area) of the polyhedron (face) to the volume (area) of
the convex hull of the polyhedron (face).
4
Applies only to a 2D tessellation.
theta disorientation angle (in degrees) edge (in 2D), face (in 3D)
cyl whether or not is used to describe the cir- edge
cular part of a cylinder domain
vernb number of vertices edge, face, poly
edgenb number of edges ver, face, poly
facenb number of faces ver, edge, poly
polynb number of polyhedra ver, edge, face
neighnb Number of neighbours of a face or polyhe- face, poly
dron5
verlist vertex list face, poly
edgelist edge list face, poly
facelist face list edge, poly
nfacelist neighbouring face list face
npolylist neighbouring polyhedron list6 poly
facearealist face area list poly
faceeqlist face equation list7 poly
vercoolist list of vertex coordinates face, poly
scaleid(scale) Identifier of the corresponding cell at scale cell
scale
lamid lamella width id8 face, poly
modeid mode id9 face, poly
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), 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.
• 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.
5
Neighbour of a face or polyhedron = touching entity of the same type (faces for a face, . . . ).
6
If a polyhedron has no neighbour on a face, a negative value is returned instead of the neighbour id.
7
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.
8
In the case of a lamellar tessellation with several lamella widths, lamid stands for the actual lamellar width of
the cell (starting from 1).
9
In the case of a multimodal tessellation (e.g. in terms of cell size), modeid stands for the actual mode (starting
from 1).
54 Neper 3.0.2
A.3 Raster Tessellation Keys

Available keys for raster tessellation seeds and cells are provided below. Mathematical and
logical expressions based on these keys can also be used. 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.

id identifier seed, cell
x x coordinate seed, cell
y y coordinate seed, cell
z z coordinate seed, cell
w Laguerre weight seed
size size (area/volume in 2D/3D) cell
diameq diameter of the equivalent circle/sphere in cell
2D/3D
radeq radius of the equivalent circle/sphere in cell
2D/3D
convexity convexity10 cell
A.4 Tessellation Update Keys

A.4.1 Time Keys
The available keys for option -morphooptilogtime are provided below. Use ‘iter(factor)’,
where ‘factor’ is an integer reduction factor, to log values only at specific iteration numbers.

iter iteration number n/a
varupdateqty number of updated variables n/a
seedupdateqty number of updated seeds n/a
seedupdatelist list of updated seeds n/a
cellupdateqty number of updated cells n/a
cellupdatelist list of updated cells n/a
var time for variable update n/a
seed time for seed update n/a
cell_init time for cell update initialization n/a
cell_kdtree time for cell update kdtree computation n/a
cell_shift time for cell update shift computation n/a
cell_neigh time for cell update neigh. computation n/a
cell_cell time for cell update cell computation n/a
cell_other time for cell update others n/a
cell_total total time for cell update n/a
val time for (objective function) value update n/a
total total time n/a
cumtotal cumulative total time n/a
10
Convexity of a cell = ratio of the volume of the cell to the volume of the convex hull of the cell.
A.4.2 Variable Keys

The available keys for option -morphooptilogvar are provided below. Use ‘iter(factor)’,

id identifier seed
x x coordinate seed
y y coordinate seed
z z coordinate seed
w weight seed
A.4.3 Objective Function Value Keys

The available keys for option -morphooptilogval are provided below. Use ‘iter(factor)’,

val value n/a
valmin minimal value n/a
val(i) ith subvalue n/a
val0(i) ith subvalue, without smoothing n/a
A.4.4 Statistical Distribution Keys

The available keys for option -morphooptilogdis are provided below. PDF stands for prob-
ability density function and CDF stands for cumulative probability density function. Use
‘iter(factor)’, where ‘factor’ is a reduction factor, to log values only at specific iteration
numbers.

x x coordinate n/a
tarpdf target PDF n/a
tarcdf target CDF n/a
curpdf current PDF n/a
curcdf current CDF n/a
tarpdf0 target PDF, not smoothed n/a
tarcdf0 target CDF, not smoothed n/a
curcdf0 current CDF, not smoothed n/a
A.5 Mesh Keys

Available keys for mesh node, elements and element sets (of all dimensions) and points are
provided below.

id identifier node, nD elt, nD elset
x x coordinate node, nD elt, nD elset
y y coordinate node, nD elt, nD elset
z z coordinate node, nD elt, nD elset
56 Neper 3.0.2
dim dimension (= lowest parent elt dimension) node

elset0d 0D elset 0D elt
part partition nD elt, node
cyl whether or not is used to describe the cir- 1D elt, 1D elset
cular part of a cylinder domain
vol volume 3D elt, 3D elset
area area 2D elt
length length 1D elt, 3D elt, 1D elset
rr radius ratio 3D elt
rrav, rrmin, average, min and max radius ratios 3D elset
rrmax
Osize Osize 3D elset
eltnb number of elements nD elset
true true level nD elt, nD elset
body body level nD elt, nD elset
domtype type of domain (0 if on a domain vertex, 1 2D elset, 1D elset, 0D elset,
if on a domain edge and 2 if on a domain 2D elt, 1D elt, 0D elt
face)
2dmeshp coordinates of the closest point of the 2D node, 3D elt
mesh
2dmeshd distance to ‘2dmeshp’ node, 3D elt
2dmeshv vector to ‘2dmeshp’ node, 3D elt
2dmeshn outgoing normal vector of the 2D mesh at node, 3D elt
‘2dmeshp’
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.6 Point Keys

Available keys for points are provided below.
Key Descriptor Apply to Require

id Identifier point
x x coordinate point
y y coordinate point
z z coordinate point
cell cell point tessellation
elt containing element point mesh
elset containing elset point mesh
2dmeshp coordinates of the closest point of the 2D point 3D mesh
mesh
2dmeshd distance to ‘2dmeshp’ point 3D mesh
2dmeshv vector to ‘2dmeshp’ point 3D mesh
2dmeshn outgoing normal vector of the 2D mesh at point 3D mesh
‘2dmeshp’
A.7 Rotations and Orientations

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

g Rotation matrix 9
rtheta Rotation axis / angle pair 4
R Rodrigues vector 3
q Quaternion 4
e Euler angles (Bunge convention) 3
ek Euler angles (Kocks convention) 3
er Euler angles (Roe convention) 3
Keys are available for ideal orientations:
Cube (0 0 1) [1 0 0]
Goss (0 1 1) [1 0 0]
U (1 0 1) [1̄ 0 1]
45NDCube (0 0 1) [1 1̄ 0]
S1 (1 2 3) [6 3 4̄]
S2 (1̄ 2 3) [6 3̄ 4]
S3 (1 2̄ 3) [6 3̄ 4̄]
S4 (1̄ 2̄ 3) [6 3 4]
Brass1 (1 1 0) [1 1̄ 2]
Brass2 (1̄ 1 0) [1 1 2̄]
Copper1 (1 1 2) [1 1 1̄]
Copper2 (1̄ 1 2) [1 1̄ 1]
A.8 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, 0) black (255, 0, 0) red
( 0, 255, 0) green ( 0, 0, 255) blue
(255, 255, 0) yellow (255, 0, 255) magenta
( 0, 255, 255) cyan (255, 255, 255) white
(128, 0, 0) maroon ( 0, 0, 128) navy
(127, 255, 0) chartreuse ( 0, 255, 127) springgreen
(128, 128, 0) olive (128, 0, 128) purple
( 0, 128, 128) teal (128, 128, 128) grey
( 0, 191, 255) deepskyblue (124, 252, 0) lawngreen
( 64, 64, 64) darkgrey (255, 69, 0) orangered
(192, 192, 192) silver (255, 250, 250) snow
(139, 0, 0) darkred ( 0, 0, 139) darkblue
(255, 140, 0) darkorange (240, 255, 255) azure
(248, 248, 255) ghostwhite (255, 255, 240) ivory
( 0, 0, 205) mediumblue (255, 182, 193) lightpink
(245, 255, 250) mintcream ( 75, 0, 130) indigo
(240, 128, 128) lightcoral (255, 192, 203) pink
(255, 127, 80) coral (250, 128, 114) salmon
58 Neper 3.0.2
(255, 250, 240) floralwhite (127, 255, 212) aquamarine

(255, 250, 205) lemonchiffon (255, 215, 0) gold
( 0, 100, 0) darkgreen (255, 165, 0) orange
(240, 248, 255) aliceblue (224, 255, 255) lightcyan
(255, 255, 224) lightyellow (139, 0, 139) darkmagenta
( 0, 139, 139) darkcyan (205, 133, 63) peru
( 70, 130, 180) steelblue (255, 240, 245) lavenderblush
(255, 245, 238) seashell ( 0, 250, 154) mediumspringgreen
( 72, 61, 139) darkslateblue (184, 134, 11) darkgoldenrod
(255, 160, 122) lightsalmon (255, 228, 196) bisque
(135, 206, 250) lightskyblue (250, 250, 210) lightgoldenrodyellow
(240, 255, 240) honeydew (255, 248, 220) cornsilk
(255, 218, 185) peachpuff (245, 245, 245) whitesmoke
(255, 99, 71) tomato (112, 128, 144) slategrey
(255, 105, 180) hotpink (253, 245, 230) oldlace
(255, 235, 205) blanchedalmond (189, 183, 107) darkkhaki
(255, 228, 181) moccasin ( 0, 206, 209) darkturquoise
( 60, 179, 113) mediumseagreen (199, 21, 133) mediumvioletred
(238, 130, 238) violet (173, 255, 47) greenyellow
(255, 239, 213) papayawhip (143, 188, 143) darkseagreen
(188, 143, 143) rosybrown (255, 20, 147) deeppink
(139, 69, 19) saddlebrown (148, 0, 211) darkviolet
( 30, 144, 255) dodgerblue (119, 136, 153) lightslategrey
(222, 184, 135) burlywood (255, 222, 173) navajowhite
(250, 240, 230) linen (123, 104, 238) mediumslateblue
( 64, 224, 208) turquoise (135, 206, 235) skyblue
( 72, 209, 204) mediumturquoise (245, 245, 220) beige
(255, 228, 225) mistyrose (210, 180, 140) tan
(250, 235, 215) antiquewhite (216, 191, 216) thistle
( 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 61
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 ...
... ]
[*lamid
cell1_lamid cell2_lamid ... ]
[*modeid
cell1_modeid cell2_modeid ... ]
[*crysym
crysym]
**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
62 Neper 3.0.2
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
...
*edge
total_number_of_dom_edges
dom_edge_id dom_ver_1 dom_ver_2 dom_edge_label
number_of_dom_tess_edges edge_1 edge_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 ...
...
**periodic
*general
per_x per_y per_z
per_dist_x per_dist_y per_dist_z
*seed
slave_seed_qty
slave_seed_id master_seed_id per_shift_x per_shift_y per_shift_z
...
*vertex
slave_ver_qty
slave_ver_id master_ver_id per_shift_x per_shift_y per_shift_z
...
*edge
slave_edge_qty
slave_edge_id master_edge_id per_shift_x per_shift_y per_shift_z slave_edge_
ori
...
*face
slave_face_qty
slave_face_id master_face_id per_shift_x per_shift_y per_shift_z slave_face_
ori
...
**scale
*general
number_of_scales
*cellid
cell1_id cell1_scale1 cell1_scale2 ... cell1_scalenumber_of_scales
...
***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.
• *lamid denotes the beginning of an optional lamella identifier field.
• cell1_lamid, cell2_lamid, . . . are the lamella identifiers of the cells.
• *modeid denotes the beginning of an optional mode identifier field.
• cell1_modeid, cell2_modeid, . . . are the mode identifiers of the cells.
• crysym is the crystal symmetry (triclinic, cubic or hexagonal).
• *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.7
[Rotations and Orientations], page 57 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.
• 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.
64 Neper 3.0.2
• 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).
• 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.
• **periodicity denotes the beginning of the periodicity field.
• *general denotes the beginning of the periodicity general information field.
• per_x, per_y and per_z are booleans indicating x, y, and z periodicity.
• per_dist_x, per_dist_y and per_dist_z are the periodicity distances along x, y, and z.
• *seed denotes the beginning of the periodicity seed field.
• slave_seed_qty is the number of slave seeds.
• slave_seed_id is the identifier of a slave seed.
• master_seed_id is the identifier of the master of a slave seed.
• per_shift_x, per_shift_y and per_shift_z are the shifts of a slave seed (or vertex, etc.)
relative to its master, along x, y and z. The values can be -1, 0 or 1.
• *vertex denotes the beginning of the periodicity vertex field.
• slave_vertex_qty is the number of slave vertices.
• slave_vertex_id is the identifier of a slave vertex.
• master_vertex_id is the identifier of the master of a slave vertex.
• *edge denotes the beginning of the periodicity edge field.
• slave_edge_qty is the number of slave edges.
• slave_edge_id is the identifier of a slave edge.
• master_edge_id is the identifier of the master of a slave edge.
• slave_edge_ori is the orientation of the slave edge with respect to the master edge: 1 if
identical, -1 if opposite.
• *face denotes the beginning of the periodicity face field (for a tessellation of dimension 3).
• slave_face_qty is the number of slave faces.
• slave_face_id is the identifier of a slave face.
• master_face_id is the identifier of the master of a slave face.
• slave_face_ori is the orientation of the slave face with respect to the master face: 1 if
identical, -1 if opposite.
• number_of_scales is the number of scales.
• cell1_scale1, cell1_scale2, . . . are the identifiers of the cells of the scale-1, scale-2, . . .
tessellations which the cell belongs to.
66 Neper 3.0.2
B.2 Raster Tessellation File (.tesr)

Here are details on the .tesr file format version 2.0. 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. Compared to
a tessellation file (.tess), a raster tessellation file can include cell morphological properties such
as their centroids or volumes. This is due to the fact that, for a raster tessellation, these
properties are both in small number and relatively expensive to compute.
***tesr
**format
format data_format
**general
dimension
size_x size_y [size_z]
rptsize_x rptsize_y [rptsize_z]
[**cell
number_of_cells
[*id
cell1_id cell2_id ...]
[*seed
seed_id seed_x seed_y [seed_z] seed_weight
... ]
[*ori
descriptor
cell1_param1 cell1_param2 ...
cell2_param1 cell2_param2 ...
...]
[*coo
cell1_x cell1_y [cell1_z]
cell2_x cell2_y [cell2_z]
... ]
[*vol
cell1_vol
cell2_vol
... ]
[*convexity
cell1_convexity
cell2_convexity
... ]
]
**data
rpt1_cell rpt2_cell ...
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, LittleEndian), binary16_big (16-bit binary, BigEndian),
binary32 (32-bit binary, LittleEndian) or binary32_big (32-bit binary, BigEndian).
• **general denotes the beginning of the general information field.
• dimension is the dimension of the raster tessellation.
• size_x, size_y and size_z are the raster sizes along the 3 coordinate axes. The number
of sizes must match dimension.
• rptsize_x, rptsize_y and rptsize_z 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.
• descriptor is the descriptor used to parametrize the crystal orientations. See Section A.7
[Rotations and Orientations], page 57 for the list of available descriptors.
• cellid_param1, cellid_param2, . . . are the values of the orientation descriptor of cell id.
• *coo denotes the beginning of an optional centroid field.
• cellid_x, cellid_y and cellid_z are the coordinates of the centroids of cell id.
• *vol denotes the beginning of an optional volume field.
• cellid_vol is the volume of cell id.
• *convexity denotes the beginning of an optional convexity field.
• cellid_convexity is the convexity 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 Multiscale Cell File

A multiscale cell file provides cell-by-cell values for a multiscale tessellation. It contains, for
each cell, its multiscale identifier, mid, and the value(s). A cell multiscale identifier (mid) is
a character string identifying a cell at a specific scale. For a given cell, C, mid combines the
identifiers of the cells that C belongs to, at successive scales, to its own id, separated by ‘::’.
For a 1-scale tessellation, mid equals id. For a 2-scale tessellation composed of 2 × 3 cells, the
mids are equal to 1::1, 1::2, 1::3, 2::1, 2::2 and 2::3. An example of a multiscale cell file
providing integer values for these cells is:
68 Neper 3.0.2
1::1 3
1::2 4
1::3 5
2::1 4
2::2 2
2::3 1
B.4 Position File

A position file lists the coordinates of a given number of points. The file must contain 1 coor-
dinate per point in 1D, 2 coordinates per point in 2D and 3 coordinates per point in 3D. While
the dimension can be known from the context in which the file is read, it can also be specified
by appending ‘:dim’ to the name of the position file, where dim is the dimension. 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 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:
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: Developer’s Guide 69
Appendix C Developer’s 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

Neper’s 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/ and neper_v/
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, . . . ), to make Neper easier to
install.
• 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 configura-
tion 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).
70 Neper 3.0.2
A module directory, neper_X/, where ‘X’ stands for the module letter (one of ‘t’, ‘m’ or ‘v’), 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 con-
tains the module function, ‘neper_X’. neper_X_.h is the source code header file, which
is #include’ed 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 #include’ed
in neper_.h. Hence, files _.h are local header files while files .h are header files #include’ed
into a upper-level source code header file. This is true anywhere in the source code. More-
over, 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
Neper’s 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: Developer’s Guide 71
C.2 Contributing to Neper

The Neper development repository is hosted on GitHub: https://github.com/rquey/neper.
Code contributions to be included in Neper’s official (public) version should be submitted as
pull requests on this respository.
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. Always use a 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 and -M, 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 make test (or ctest). You may also want to add a test specific to the new
option.
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,
72 Neper 3.0.2
• DEVEL_DEBUGGING_FLAG
Setting the option to ON turns on the debugging compilation flag ‘-g’, which is required
for debugging with gdb and valgrind, and turns on the compilation flag ‘-Werror’, which
makes all compilation warnings into errors.
• DEVEL_DEBUGGING_TEST
Setting the option to ON runs internal tests during Neper execution at places where the code
is otherwise considered robust.
• DEVEL_OPTIMIZATION
Setting this option to OFF disables code optimization, which is useful for debugging with
gdb and valgrind.
• DEVEL_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.2.4 Testing
The code can be tested using CTest. The usual way is as follows:
$ ctest
It is also possible to run only some of the tests.
• Option -R selects the tests whose name contains a character string:
$ ctest -R string
As test names start by the letter of the module they refer to, followed by character ‘_’, it
becomes handy to run tests on a specific module, for example:
$ ctest -R T_
• Option -E selects the tests that do not contain a character string:
$ ctest -E string
• Option -I selects the tests from their numbers, for example:
$ ctest -I 3,5
Appendix D: Versions 73
Appendix D Versions
New in 3.0.2 (16 Feb 2017):
- module -T: added -transform scale and transform rotate for scalar
tessellations (.tess), fixed -morpho with -periodic, fixed -morpho
with non-unitary domains, fixed -statedge/-statface theta with
-oricrysym hexagonal, improved -ori, added -morpho
lamellar(v=crysdir), added ***tess/**cell/*crysym section to .tess
file, fixed -morphooptialgo random, small fixes.
- module -M: fixed -interface cohesive in 2D and 3D (for Abaqus), enable
-interface discontinuous and cohesive for periodic tessellations,
added -format msh:binary, fixed faset internal for 3D, added
-transport node:..., changed point keys "elt3d" and "elset3d" into "elt"
and "elset" (now apply to 3D or 2D), small fixes.
- documentation: minor fixes.
New in 3.0.1 (01 Dec 2016):

- module -T: fixed up options -periodic and -morphooptialgoneigh qsort,
added tessellation key ‘modeid’ (for cells), added -morpho
cube(N1,N2,N3) and -morpho square(N1,N2), enabled -loadtess -scale,
added -oricrysym hexagonal, added tessellation keys ’nfacelist’ and
’theta’, cleaned code, fixed documentation of .tess file, added tests
on conflicing options.
- module -M: added option -scale, fixed hexahedral meshing of periodic
tessellations, added physical groups to .msh, fixed 2D meshes in
Abaqus (.inp) file, fixed up option -faset internal.
- module -V: fixed options -dataseed*.
- general: removed libmatheval dependency, fixed testing.
New in 3.0.0 (12 Sep 2016):

- module -T: added 3 major capabilities: (i) tessellation generation
from morphological cell properties (options starting by -morpho),
(ii) multiscale tessellation generation (using the :: separator), and
(iii) periodic and semi-periodic tessellation generation (option
-periodic); made some other improvements and some clean up all over
the place.
- module -M: added ability to mesh the new tessellations, including
periodic tessellations; added interface meshing using cohesive
elements (option -interface); made small other improvements.
- module -V: made small improvements.
- module -D: replaced by "make test" using CTest.
- new development website: https://github.com/rquey/neper.
New in 2.0.5 (06 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.
74 Neper 3.0.2
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
developer’s guide and module (-D). Documentation has been much
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. Added
tests.
- module -MM: fixed nset syntax in inp (Abaqus) files.
- module -VS: added capability to plot mapped meshes.
- General: various minor improvements, code cleaning.
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
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
76 Neper 3.0.2
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
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 79
Appendix E GNU General Public License

GNU General Public License
Version 3, 29 June 2007

Copyright
c 2007 Free Software Foundation, Inc. http://fsf.org/
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
guarantee your freedom to share and change all versions of a program—to make sure it remains
free software for all its users. We, the Free Software Foundation, use the GNU General Public
License for most of our software; it applies also to any other work released this way by its
authors. You can apply it to your programs, too.
When we speak of free software, we are referring to freedom, not price. Our General Public
Licenses are designed to make sure that you have the freedom to distribute copies of free software
(and charge for them if you wish), that you receive source code or can get it if you want it, that
you can change the software or use pieces of it in new free programs, and that you know you
can do these things.
To protect your rights, we need to prevent others from denying you these rights or asking you
to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of
the software, or if you modify it: responsibilities to respect the freedom of others.
For example, if you distribute copies of such a program, whether gratis or for a fee, you must
pass on to the recipients the same freedoms that you received. You must make sure that they,
too, receive or can get the source code. And you must show them these terms so they know
their rights.
Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on
the software, and (2) offer you this License giving you legal permission to copy, distribute and/or
modify it.
For the developers’ and authors’ protection, the GPL clearly explains that there is no warranty
for this free software. For both users’ and authors’ sake, the GPL requires that modified versions
be marked as changed, so that their problems will not be attributed erroneously to authors of
previous versions.
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
the aim of protecting users’ freedom to change the software. The systematic pattern of such
abuse occurs in the area of products for individuals to use, which is precisely where it is most
unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for
those products. If such problems arise substantially in other domains, we stand ready to extend
this provision to those domains in future versions of the GPL, as needed to protect the freedom
of users.
Finally, every program is threatened constantly by software patents. States should not allow
patents to restrict development and use of software on general-purpose computers, but in those
that do, we wish to avoid the special danger that patents applied to a free program could make it
effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render
the program non-free.
80 Neper 3.0.2
The precise terms and conditions for copying, distribution and modification follow.
TERMS AND CONDITIONS

0. Definitions.
“This License” refers to version 3 of the GNU General Public License.
“Copyright” also means copyright-like laws that apply to other kinds of works, such as
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“The Program” refers to any copyrightable work licensed under this License. Each licensee
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A “covered work” means either the unmodified Program or a work based on the Program.
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The “source code” for a work means the preferred form of the work for making modifications
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A “Standard Interface” means an interface that either is an official standard defined by a
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The “System Libraries” of an executable work include anything, other than the work as a
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that the work is specifically designed to require, such as by intimate data communication
or control flow between those subprograms and other parts of the work.
The Corresponding Source need not include anything that users can regenerate automati-
cally from other parts of the Corresponding Source.
The Corresponding Source for a work in source code form is that same work.
2. Basic Permissions.
All rights granted under this License are granted for the term of copyright on the Program,
and are irrevocable provided the stated conditions are met. This License explicitly affirms
your unlimited permission to run the unmodified Program. The output from running a
covered work is covered by this License only if the output, given its content, constitutes
a covered work. This License acknowledges your rights of fair use or other equivalent, as
provided by copyright law.
You may make, run and propagate covered works that you do not convey, without conditions
so long as your license otherwise remains in force. You may convey covered works to others
for the sole purpose of having them make modifications exclusively for you, or provide
you with facilities for running those works, provided that you comply with the terms of
this License in conveying all material for which you do not control copyright. Those thus
making or running the covered works for you must do so exclusively on your behalf, under
your direction and control, on terms that prohibit them from making any copies of your
copyrighted material outside their relationship with you.
Conveying under any other circumstances is permitted solely under the conditions stated
below. Sublicensing is not allowed; section 10 makes it unnecessary.
3. Protecting Users’ Legal Rights From Anti-Circumvention Law.
No covered work shall be deemed part of an effective technological measure under any
applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on
20 December 1996, or similar laws prohibiting or restricting circumvention of such measures.
When you convey a covered work, you waive any legal power to forbid circumvention of
technological measures to the extent such circumvention is effected by exercising rights
under this License with respect to the covered work, and you disclaim any intention to limit
operation or modification of the work as a means of enforcing, against the work’s users,
your or third parties’ legal rights to forbid circumvention of technological measures.
4. Conveying Verbatim Copies.
You may convey verbatim copies of the Program’s source code as you receive it, in any
medium, provided that you conspicuously and appropriately publish on each copy an ap-
propriate copyright notice; keep intact all notices stating that this License and any non-
permissive terms added in accord with section 7 apply to the code; keep intact all notices
of the absence of any warranty; and give all recipients a copy of this License along with the
Program.
You may charge any price or no price for each copy that you convey, and you may offer
support or warranty protection for a fee.
5. Conveying Modified Source Versions.
You may convey a work based on the Program, or the modifications to produce it from the
Program, in the form of source code under the terms of section 4, provided that you also
meet all of these conditions:
a. The work must carry prominent notices stating that you modified it, and giving a
relevant date.
b. The work must carry prominent notices stating that it is released under this License
and any conditions added under section 7. This requirement modifies the requirement
in section 4 to “keep intact all notices”.
82 Neper 3.0.2
c. You must license the entire work, as a whole, under this License to anyone who comes
into possession of a copy. This License will therefore apply, along with any applicable
section 7 additional terms, to the whole of the work, and all its parts, regardless of how
they are packaged. This License gives no permission to license the work in any other
way, but it does not invalidate such permission if you have separately received it.
d. If the work has interactive user interfaces, each must display Appropriate Legal Notices;
however, if the Program has interactive interfaces that do not display Appropriate Legal
Notices, your work need not make them do so.
A compilation of a covered work with other separate and independent works, which are not
by their nature extensions of the covered work, and which are not combined with it such as
to form a larger program, in or on a volume of a storage or distribution medium, is called an
“aggregate” if the compilation and its resulting copyright are not used to limit the access or
legal rights of the compilation’s users beyond what the individual works permit. Inclusion
of a covered work in an aggregate does not cause this License to apply to the other parts
of the aggregate.
6. Conveying Non-Source Forms.
You may convey a covered work in object code form under the terms of sections 4 and 5,
provided that you also convey the machine-readable Corresponding Source under the terms
of this License, in one of these ways:
a. Convey the object code in, or embodied in, a physical product (including a physical
distribution medium), accompanied by the Corresponding Source fixed on a durable
physical medium customarily used for software interchange.
b. Convey the object code in, or embodied in, a physical product (including a physical
distribution medium), accompanied by a written offer, valid for at least three years and
valid for as long as you offer spare parts or customer support for that product model,
to give anyone who possesses the object code either (1) a copy of the Corresponding
Source for all the software in the product that is covered by this License, on a durable
physical medium customarily used for software interchange, for a price no more than
your reasonable cost of physically performing this conveying of source, or (2) access to
copy the Corresponding Source from a network server at no charge.
c. Convey individual copies of the object code with a copy of the written offer to provide
the Corresponding Source. This alternative is allowed only occasionally and noncom-
mercially, and only if you received the object code with such an offer, in accord with
subsection 6b.
d. Convey the object code by offering access from a designated place (gratis or for a
charge), and offer equivalent access to the Corresponding Source in the same way
through the same place at no further charge. You need not require recipients to copy the
Corresponding Source along with the object code. If the place to copy the object code
is a network server, the Corresponding Source may be on a different server (operated by
you or a third party) that supports equivalent copying facilities, provided you maintain
clear directions next to the object code saying where to find the Corresponding Source.
Regardless of what server hosts the Corresponding Source, you remain obligated to
ensure that it is available for as long as needed to satisfy these requirements.
e. Convey the object code using peer-to-peer transmission, provided you inform other
peers where the object code and Corresponding Source of the work are being offered
to the general distrib at no charge under subsection 6d.
A separable portion of the object code, whose source code is excluded from the Corre-
sponding Source as a System Library, need not be included in conveying the object code
work.
A “User Product” is either (1) a “consumer product”, which means any tangible personal
property which is normally used for personal, family, or household purposes, or (2) anything
designed or sold for incorporation into a dwelling. In determining whether a product is a
consumer product, doubtful cases shall be resolved in favor of coverage. For a particular
product received by a particular user, “normally used” refers to a typical or common use of
that class of product, regardless of the status of the particular user or of the way in which the
particular user actually uses, or expects or is expected to use, the product. A product is a
consumer product regardless of whether the product has substantial commercial, industrial
or non-consumer uses, unless such uses represent the only significant mode of use of the
product.
“Installation Information” for a User Product means any methods, procedures, authoriza-
tion keys, or other information required to install and execute modified versions of a covered
work in that User Product from a modified version of its Corresponding Source. The infor-
mation must suffice to ensure that the continued functioning of the modified object code is
in no case prevented or interfered with solely because modification has been made.
If you convey an object code work under this section in, or with, or specifically for use in,
a User Product, and the conveying occurs as part of a transaction in which the right of
possession and use of the User Product is transferred to the recipient in perpetuity or for
a fixed term (regardless of how the transaction is characterized), the Corresponding Source
conveyed under this section must be accompanied by the Installation Information. But this
requirement does not apply if neither you nor any third party retains the ability to install
modified object code on the User Product (for example, the work has been installed in
ROM).
The requirement to provide Installation Information does not include a requirement to con-
tinue to provide support service, warranty, or updates for a work that has been modified or
installed by the recipient, or for the User Product in which it has been modified or installed.
Access to a network may be denied when the modification itself materially and adversely
affects the operation of the network or violates the rules and protocols for communication
across the network.
Corresponding Source conveyed, and Installation Information provided, in accord with this
section must be in a format that is distribly documented (and with an implementation
available to the distrib in source code form), and must require no special password or key
for unpacking, reading or copying.
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
84 Neper 3.0.2
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 con-
veys 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 gov-
erned 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 copy-
right 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-to-
peer 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.
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 sub-
stantially 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 trans-
action who receives a copy of the work also receives whatever licenses to the work the
party’s 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 (includ-
ing 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 contributor’s
“contributor version”.
A contributor’s “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
contributor’s 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 commit-
ment, 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 recipient’s 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.
86 Neper 3.0.2
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 Gen-
eral Public License can be used, that proxy’s 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 addi-
tional 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 PERMIT-
TED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRIT-
ING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PRO-
GRAM “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 MOD-
IFIES 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 program’s 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
88 Neper 3.0.2
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 program’s 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 89
Option Index
--help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 -dataelt2dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
--license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 -dataelt2dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
--version . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 -dataelt2dedgecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
-cameraangle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 -dataelt2dedgerad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
-cameracoo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 -dataelt2dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
-cameralookat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 -dataelt2dscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
-cameraprojection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 -dataelt3dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
-camerasky . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 -dataelt3dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
-checktess . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 -dataelt3dedgecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
-cl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 -dataelt3dedgerad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
-clean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 -dataelt3dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
-clmin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 -dataelt3dscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
-clratio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 -datafacecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
-datacellcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 -datafacecolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
-datacellcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 -datafacescale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
-datacellscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 -datafacescaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
-datacellscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 -datafacetrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
-datacelltrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 -datanodecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
-datacsyscol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 -datanodecolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
-datacsyscoo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 -datanodecoo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
-datacsyslabel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 -datanodecoofact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
-datacsyslength . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 -datanoderad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
-datacsysrad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 -datanodescale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
-dataedgecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 -datanodescaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
-dataedgecolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 -datapointcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
-dataedgerad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 -datapointcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
-dataedgescale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 -datapointcoo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
-dataedgescaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 -datapointcoofact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
-dataedgetrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 -datapointrad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
-dataelset0dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -datapointscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
-dataelset0dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . 42 -datapointscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
-dataelset0drad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -datapointtrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
-dataelset0dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -datapolycol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
-dataelset0dscaletitle . . . . . . . . . . . . . . . . . . . . . . . . 42 -datapolycolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
-dataelset1dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 -datapolyscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
-dataelset1dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . 42 -datapolyscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
-dataelset1drad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -datapolytrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
-dataelset1dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -datarptedgecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
-dataelset1dscaletitle . . . . . . . . . . . . . . . . . . . . . . . . 42 -datarptedgerad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-dataelset2dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 -dataseedcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-dataelset2dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . 41 -dataseedcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-dataelset2dedgecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 -dataseedrad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-dataelset2dedgerad . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 -dataseedscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-dataelset2dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 -dataseedscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-dataelset2dscaletitle . . . . . . . . . . . . . . . . . . . . . . . . 41 -datavercol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-dataelset3dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 -datavercolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-dataelset3dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . 40 -dataverrad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-dataelset3dedgecol . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 -dataverscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-dataelset3dedgerad . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 -dataverscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-dataelset3dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 -datavertrs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
-dataelset3dscaletitle . . . . . . . . . . . . . . . . . . . . . . . . 41 -dim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
-dataelt0dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -dim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
-dataelt0dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -domain. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
-dataelt0drad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -dupnodemerge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
-dataelt0dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -elttype . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
-dataelt0dscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -endloop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
-dataelt1dcol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 -faset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
-dataelt1dcolscheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -fmax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
-dataelt1drad . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16, 30
-dataelt1dscale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -id . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
-dataelt1dscaletitle . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 -imageantialias . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
90 Neper 3.0.2
-imagebackground . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 -sel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
-imageformat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 -showcell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
-imagesize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 -showcsys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
-includepov . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 -showedge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
-interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 -showelset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
-loadmesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 -showelset0d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
-loadpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11, 25 -showelset1d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
-loadtesr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 -showelset2d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
-loadtess . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 -showelset3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
-loop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 -showelt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
-mesh2dalgo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 -showelt0d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
-mesh2diter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 -showelt1d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
-mesh2dmaxtime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 -showelt2d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
-mesh2drmaxtime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 -showelt3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
-mesh3dalgo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 -showface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
-mesh3dclconv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 -showfaceinter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
-mesh3diter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 -showmesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
-mesh3dmaxtime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 -showmeshslice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
-mesh3drmaxtime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 -shownode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
-meshqualdisexpr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 -showpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
-meshqualexpr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 -showpoly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
-meshqualmin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 -showseed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
-mloop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 -showshadow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
-morpho. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 -showtesr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
-morphooptialgo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
-showtess . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
-morphooptialgoneigh . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
-showver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
-morphooptideltamax . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
-singnodedup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
-morphooptidof . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
-slicemesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
-morphooptigrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
-sort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
-morphooptiini . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
-statcell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
-morphooptiinistep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
-statedge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
-morphooptilogdis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
-morphooptilogtime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 -statelset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
-morphooptilogval . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 -statelset0d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-morphooptilogvar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 -statelset1d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-morphooptiobjective . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 -statelset2d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-morphooptismooth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 -statelset3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-morphooptistop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 -statelt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
-n . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 -statelt0d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
-nset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 -statelt1d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
-o . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16, 29 -statelt2d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 -statelt3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-ori . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 -statface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
-oricrysym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 -statnode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
-oridescriptor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 -statpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
-oriformat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 -statpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
-part . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 -statpoly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
-partbalancing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 -statseed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
-partmethod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 -statver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
-periodicity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 -tesrformat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
-pl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 -tesrsize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
-rcl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 -tesrsmooth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
-regularization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 -tesrsmoothfact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
-rsel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 -tesrsmoothitermax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
-scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 -transform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
-scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 -transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

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Neper Reference Manual

The documentation for Neper 3.0.2

2 Tessellation Module (-T) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

3 Meshing Module (-M) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

4 Visualization Module (-V) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Appendix A Expressions and Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

Appendix B File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Appendix C Developer’s Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Appendix E GNU General Public License . . . . . . . . . . . . . . . . . . . 79

The Neper software package can be downloaded from http://neper.sourceforge.net. It also

1.1 The Neper Project

1.2 Installing Neper

Finally, the Neper installation can be tested out by running

1.3 Getting Started

1.3.2 Argument Separators

1.3.3 Initialization File

1.4 Reading this Manual

2 Tessellation Module (-T)

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

$ neper -T -n 10 -id 1 -reg 1

Info : [ini file]

-id integer [Input data]

-dim integer [Option]

-domain char_string [Option]

-periodicity char_string [Option]

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

-loadtess file_name [Input data]

-loadtesr file_name [Input data]

-loadpoint file_name [Input data]

2.1.2 Morphology Options

-morpho char_string [Option]

for ‘diameq:lognormal(1,0.35),sphericity:lognormal(0.145,0.03,1-x)’, see below);

-morphooptigrid char_string [Secondary option]

-morphooptismooth real [Secondary option]

-morphooptideltamax real [Secondary option]

-morphooptiinistep real [Secondary option]

-morphooptilogtime char_string [Secondary option]

-morphooptilogvar char_string [Secondary option]

-morphooptilogval char_string [Secondary option]

-morphooptilogdis char_string [Secondary option]

2.1.3 Transformation Options

-scale real:real:real [Option]

-transform char_string(...) [Option]

2.1.4 Crystal Orientation Options

-oricrysym char_string [Secondary option]

2.1.5 Regularization Options

-fmax real [Option]

-sel or -rsel real [Secondary option]

-mloop integer [Secondary option]

2.1.6 Output Options

-format char_string [Option]

-tesrformat char_string [Option]

-tesrsize integer [Option]

2.1.7 Post-Processing Options

-statpoly char_string [Post-processing]

2.1.8 Debugging Options

2.2 Output Files

2.2.3 Tessellation Optimization Log Files

3 Meshing Module (-M)