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Documentation for the Neper Voronoi Tesselation software
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  Neper Reference Manual The documentation for Neper 2.0.0A software package for polycrystal generation and meshing10 January 2014 Romain Quey  Copyright c   2003–2013 Romain QueyPermission 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 .....................................................................  1User Guidelines .........................................................................  1 1 Introduction  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  3 1.1 The Neper Project  ................................................................  31.1.1 Description ...................................................................  31.1.2 Resources  ....................................................................  31.2 Installing Neper  ...................................................................  41.3 Getting Started  ...................................................................  51.3.1 Calling a Module  .............................................................  51.3.2 Initialization File  .............................................................  51.3.3 Conventions  ..................................................................  61.3.3.1 Manual ..................................................................  61.3.3.2 Argument Separators  ....................................................  6 2 Tessellation Module (-T) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  7 2.1 Arguments  ........................................................................  82.1.1 Input Data  ...................................................................  82.1.2 Tessellation Options  ..........................................................  92.1.3 Crystal Orientation Options  .................................................  112.1.4 Regularization Options  ......................................................  112.1.5 Filtering Options ............................................................  122.1.6 Output Options  .............................................................  122.1.7 Post-Processing Options .....................................................  122.1.8 Debugging Options ..........................................................  132.2 Output Files  .....................................................................  142.2.1 Tessellation ..................................................................  142.2.2 Statistics ....................................................................  142.3 Examples  ........................................................................  14 3 Meshing Module (-M)  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  17 3.1 Arguments .......................................................................  193.1.1 Prerequisites  ................................................................  193.1.2 Input Data ..................................................................  193.1.3 Meshing Options  ............................................................  193.1.4 Raster Tessellation Meshing Options .........................................  213.1.5 Mesh Cleaning Options ......................................................  223.1.6 Mesh Partitioning Options ...................................................  223.1.7 Field Transport Options .....................................................  233.1.8 Output Options  .............................................................  233.1.9 Post-Processing Options .....................................................  243.1.10 Advanced Options ..........................................................  253.2 Output Files  .....................................................................  263.2.1 Mesh ........................................................................  263.2.2 Statistics ....................................................................  263.3 Examples  ........................................................................  26  ii Neper 2.0.0 4 Visualization Module (-V) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  29 4.1 Arguments .......................................................................  304.1.1 Input Data ..................................................................  304.1.2 Tessellation Data Loading and Rendering  ....................................  304.1.3 Mesh Data Loading and Rendering  ..........................................  334.1.4 Slice Settings ................................................................  364.1.5 Show Settings  ...............................................................  364.1.6 Camera Settings .............................................................  384.1.7 Output Image Settings  ......................................................  394.1.8 Scripting  ....................................................................  394.1.9 Advanced Options ...........................................................  394.2 Output Files  .....................................................................  394.3 Examples  ........................................................................  40 Appendix A Expressions and Keys . . . . . . . . . . . . . . . . . . . . . . . . . . .  41 A.1 Mathematical and Logical Expressions  ...........................................  41A.2 Tessellation Keys  ................................................................  41A.3 Raster Tessellation Keys .........................................................  43A.4 Mesh Keys  ......................................................................  43A.5 Rotations and Orientations  ......................................................  44A.6 Colours ..........................................................................  44 Appendix B File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  47 B.1 Tessellation File (‘ .tess ’) ........................................................  47B.2 Raster Tessellation File (‘ .tesr ’) .................................................  50B.3 Position File .....................................................................  51 Appendix C Developer’s Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  53 C.1 Code Structure  ..................................................................  53C.1.1 Source Code  ................................................................  53C.1.2 Documentation  .............................................................  54C.2 Contributing to Neper  ...........................................................  55C.2.1 Coding Conventions .........................................................  55C.2.2 Adding a New Option .......................................................  55C.2.3 Compilation Options ........................................................  55C.3 Testing Module (-D) .............................................................  56C.3.1 Arguments ..................................................................  57C.3.1.1 Prerequisites ...........................................................  57C.3.1.2 Input Data .............................................................  57C.3.1.3 Testing Options ........................................................  57C.3.2 Examples ...................................................................  57 Appendix D Versions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  59Appendix E GNU General Public License . . . . . . . . . . . . . . . . . . .  63Option Index  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  73
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