Neper Reference Manual The documentation for Neper 4.2.0 A software package for polycrystal generation and meshing 11 June 2021 Romain Quey Copyright c 2003{2021 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 Description :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 3 1.2 Resources and Support::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 3 1.3 Installing Neper:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 4 1.4 Getting Started :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 6 1.4.1 Modules :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 6 1.4.2 Argument Separators:::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 6 1.4.3 Initialization File:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 7 1.5 Reading this Manual ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 7 2 Tessellation Module (-T) ::::::::::::::::::::::::::::::::::::: 11 2.1 Arguments ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 12 2.1.1 Input Data :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 12 2.1.2 Morphology and Group Options :::::::::::::::::::::::::::::::::::::::::::::: 14 2.1.3 Crystal Orientation Options:::::::::::::::::::::::::::::::::::::::::::::::::: 19 2.1.4 Transformation Options :::::::::::::::::::::::::::::::::::::::::::::::::::::: 20 2.1.5 Regularization Options::::::::::::::::::::::::::::::::::::::::::::::::::::::: 21 2.1.6 Output Options:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 22 2.1.7 Post-Processing Options ::::::::::::::::::::::::::::::::::::::::::::::::::::: 23 2.1.8 Debugging Options :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 25 2.2 Output Files:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 25 2.2.1 Tessellation :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 25 2.2.2 Statistics :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 25 2.2.3 Tessellation Optimization Log Files :::::::::::::::::::::::::::::::::::::::::: 26 2.2.4 Orientation Optimization Log Files::::::::::::::::::::::::::::::::::::::::::: 26 2.3 Examples ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 26 3 Meshing Module (-M) :::::::::::::::::::::::::::::::::::::::: 29 3.1 Arguments ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 31 3.1.1 Prerequisites ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 31 3.1.2 Input Data :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 31 3.1.3 Meshing Options::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 31 3.1.4 Raster Tessellation Meshing Options ::::::::::::::::::::::::::::::::::::::::: 34 3.1.5 Mesh Cleaning Options :::::::::::::::::::::::::::::::::::::::::::::::::::::: 34 3.1.6 Transformation Options :::::::::::::::::::::::::::::::::::::::::::::::::::::: 35 3.1.7 Mesh Partitioning Options ::::::::::::::::::::::::::::::::::::::::::::::::::: 36 3.1.8 Field Transport Options ::::::::::::::::::::::::::::::::::::::::::::::::::::: 36 3.1.9 Output Options:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 37 3.1.10 Post-Processing Options :::::::::::::::::::::::::::::::::::::::::::::::::::: 38 3.1.11 Advanced Options :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 40 3.2 Output Files:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 41 3.2.1 Mesh :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 41 3.2.2 Interfaces :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 41 ii Neper 4.2.0 3.2.3 Statistics :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 41 3.3 Examples ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 42 4 Simulation Module (-S) :::::::::::::::::::::::::::::::::::::: 43 4.1 Arguments ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 44 4.1.1 Input Data :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 44 4.1.2 Results Options :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 44 4.1.3 Output Options:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 45 4.2 Output Directory ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 45 4.3 Examples ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 45 5 Visualization Module (-V) ::::::::::::::::::::::::::::::::::: 47 5.1 Arguments ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 48 5.1.1 Prerequisites ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 48 5.1.2 Input Data :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 48 5.1.3 Space Options ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 48 5.1.4 Tessellation Data Loading and Rendering::::::::::::::::::::::::::::::::::::: 49 5.1.5 Mesh Data Loading and Rendering ::::::::::::::::::::::::::::::::::::::::::: 54 5.1.6 Point Data Loading and Rendering ::::::::::::::::::::::::::::::::::::::::::: 58 5.1.7 Coordinate System Rendering :::::::::::::::::::::::::::::::::::::::::::::::: 59 5.1.8 Slice Settings :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 60 5.1.9 Show Settings:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 60 5.1.10 Camera Settings :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 63 5.1.11 Output Image Settings :::::::::::::::::::::::::::::::::::::::::::::::::::::: 63 5.1.12 Scripting ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 64 5.1.13 Output Options::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 64 5.1.14 Print Options::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 64 5.1.15 Advanced Options :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 64 5.2 Output Files:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 64 5.3 Examples ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 65 Appendix A Expressions and Keys :::::::::::::::::::::::::::: 67 A.1 Mathematical and Logical Expressions:::::::::::::::::::::::::::::::::::::::::::: 67 A.1.1 Functions ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 67 A.1.2 Binary Operators:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 67 A.1.3 Ternary Operators::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 68 A.1.4 Statistical Distributions ::::::::::::::::::::::::::::::::::::::::::::::::::::: 68 A.2 Tessellation Keys::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 69 A.3 Raster Tessellation Keys ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 72 A.4 Tessellation Optimization Keys ::::::::::::::::::::::::::::::::::::::::::::::::::: 73 A.4.1 Time Keys :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 73 A.4.2 Variable Keys ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 74 A.4.3 Objective Function Value Keys :::::::::::::::::::::::::::::::::::::::::::::: 74 A.4.4 Statistical Distribution Keys::::::::::::::::::::::::::::::::::::::::::::::::: 75 A.4.5 Raster Tessellation Voxel Keys::::::::::::::::::::::::::::::::::::::::::::::: 75 A.5 Orientation Optimization Keys ::::::::::::::::::::::::::::::::::::::::::::::::::: 75 A.5.1 Variable Keys ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 75 A.6 Mesh Keys ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 76 A.7 Point Keys ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 77 A.8 Simulation Results ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 78 A.9 Rotations and Orientations ::::::::::::::::::::::::::::::::::::::::::::::::::::::: 78 A.10 Crystal Symmetries ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 79 A.11 Colors and Color Maps :::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 79 iii A.12 Colors :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 79 A.13 Color Maps ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 81 A.13.1 Color Map for Integer Values ::::::::::::::::::::::::::::::::::::::::::::::: 81 A.13.2 Color Maps for Real Values::::::::::::::::::::::::::::::::::::::::::::::::: 81 Appendix B File and Directory Formats :::::::::::::::::::::: 83 B.1 Tessellation File (.tess) ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 83 B.2 Raster Tessellation File (.tesr) :::::::::::::::::::::::::::::::::::::::::::::::::: 88 B.3 Multiscale Cell File::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 91 B.4 Position File ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 91 B.5 Mesh File (.msh) ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 91 B.6 Simulation Directory (.sim) :::::::::::::::::::::::::::::::::::::::::::::::::::::: 95 Appendix C Developer's Guide :::::::::::::::::::::::::::::::: 97 C.1 Code Structure:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::