View 3D Structures Manual

This software may be used for simple "ad-hoc" data analysis and visualization of 3D particle data. However, I do not intent to replace any other software – this is just a small tool for basic usage. Everything is provided as-is, so you should feel free to modify it for your own purpose. Nevertheless, this software may contain bugs and issues. — Philip.

Setup

This software requires Windows Vista or any higher Version of Windows (for example Windows 7, 2008 R2) and the DirectX 11 runtime. Of course, you should install all published service packs, patches and runtime updates (.net 4.0).

Furthermore, a graphics processing unit with DirectX 10 feature level is required. If you are not sure about your hardware capabilities then have a look which shader model is supported; shader model SM 4.0 is needed. This level of hardware features has been introduced by nVidia GeForce 8 Series, AMD/ATI Radeon HD 2000 Series and Intel GMA X3100.

There are no other prerequisites to this software. Just copy all files in the folder of your choice. I compiled one version for x86 and one for x64 systems.

Basics

The most fundamental task in the data analysis is, of course, any import of 3D data. The application will start with an empty window (except toolbars etc.). Click the Import-Button [1] to load your 3D data. First you select the file which contains the data and then you select the corresponding import filter (for example MPE F-Praktikum).

If your data import was completed with success, the application will offer several options for data analysis. The next section describes this in further detail. For the moment just use the default settings, so you will get a first impression of your 3d data.

Startup Window

Mouse, keybpard or UI buttons can modify the camera position. While the right mouse button is pressed, the camera will follow your movements. Furthermore, you can zoom in or out of the scene using the wheel of your mouse. All functions are also available via keyboard, e.g. :

W
turn camera upward
S
turn camera down
A (or D)
turn camera left (or right)
Q (or E)
zoom in (or zoom out)
Z
reset camera (polar angle only)
H
reset camera (azimutal angle only)
N
reset zoom
Q
shows buttons (for easier usage with pointing devices)

The current position of the camera is shown in the status bar [5]. In some situations, it might be helpful to freeze the camera in a specific direction. This can be done using the buttons [6,7] which lock either the azimuthal or the polar angle of the camera. It is also possible to set the camera position using a form [4].

Data Analysis

Data analysis performed by this tool is rather simple and it is performed in four stages. This feature is slected by the input gesture Ctrl+A or by pressing the button Analyze data.

Files

Processed particle data may be stored and loaded to files. Both, opening and saving files, are just as usual.

Configuration

Options on the 3D rendering are found in "View" - "Configure...". Shaders for different quality levels are provided.

Data File Specifications

Binary Simulation Data (SimERMR):
Each file starts with a magic number, followed by the description of the particle set and the data of each particle:
Description Size/Type Comment
Magic Number 1 byte 0x79
Version 1 byte 0x02
Number of particles 4 bytes, int N
Number of dimensions 4 bytes, int dim
Size of each block 4 bytes, int
Boundary box dim x 8 bytes, double
Particle positions N x dim * 8 bytes, double for each particle the coordinates are stored in ascending order, i.g. Particle1.x, Particle1.y, Particle1.z, Particle2.x, ...
Particle data N * 9 bytes, (byte, double) for each particle a structure consisting of information about its species (byte) and description (double) is stored
CSV (F-Praktikum):
Each line of this textfile contains the position of a particle (x,y,z). For a line the RegEx is given by
([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\s){3,}
and all other lines which are not matching this RegEx will be ignored.

References

  1. Structural properties of dense hard sphere packings, B.A. Klumov, S.A. Khrapak, G. E. Morfill, arXiv:1101.5545v1 [cond-mat.soft] (2011)
  2. Accurate determination of crystal structures based on averaged local bond oder parameters, W. Lechner and C. Dellago, JCP 129, 114 707 (2008)
  3. Structural properties of complex plasmas in a homogeneous dc discharge, S. Mitic et al., PRL 101, 123002 (2008)