magchain_visualization_software

Visualization Software developed to use with MagChain simulation software

1. MagChainGLViewer developed in C++

2. MagChainPyViewer developed in VPython

3. MagChainFileConverter developed in Python 3

Table of contents

• Description
• Table of contents
• Requirements
• Installation
• Usage
  • MagChainGlViewer
  • MagChainPyViewer
  • MagChainFileConverter
• Authors
• License

Description

1. MagChainGLViewer: 3D visualization application for the MagChain program.

2. MagChainPyViewer: 3D Visualization of trajectoryCG.xyz generated by MagChain

3. MagChainFileConverter: Graphical interface to convert the non-standard trajectoryGC.xyz to a standard .xyz file format. Moreover, an option for .pdb conversion is also available. This way the trajectory can be visualised with standard visualisation softwares as VMD or Pymol.

Requirements

1. MagChainGLViewer: C++ compiler together with the openGL development libraries. (As example, the freeGLUT distribution in openSUSE linux).

2. MagChainPyViewer: VPython script to be executed by VIDLE for VPython (with VPython libraries). Documentation on VPython can be found at: http://vpython.org/contents/doc.html and it can be downloaded:

• Linux: http://vpython.org/contents/download_linux.html
• Windows: http://vpython.org/contents/download_windows.html
• Mac: http://vpython.org/contents/download_mac.html

3. MagChainFileConverter: Python 3 installed with the following libraries

• PyQt5
• MdAnalysis

Installation

1. MagChainGLViewer: type "make" into the source folder and select the achitecture.

2. MagChainPyViewer: Non-required.

3. MagChainFileConverter: Non-required.

Usage

MagChainGLViewer

To use MagChainGLViewer, after compiling the C++ source file by make and having obtained the executable, just follow the next instructions:

• Open a console and type ./executable_name trajectoryCG_filename.xyz.

• For simplicity is better to have the trajectory file in the same directory where the MagChainGLViewer executable is.

• List of available commands (this list can be visualized by pressing the right-mousse button over the application window.)

   - 'P': Set perspective.
   - 'O': Set orthographic.
   - 'T': Activate Translations.
   - 'R': Activate Rotations.
   - 'a': Place axis reference at the center of the box.
   - 'A': Place axis reference at origin.
   - 'x': Rotate/Translate clockwise respect to the axis.
   - 'X': Rotate/Translate anti-clockwise respect to the axis.
   - 'y': Rotate/Translate clockwise respect to the axis.
   - 'Y': Rotate/Translate anti-clockwise respect to the axis.
   - 'z': Rotate/Translate clockwise respect to the axis.
   - 'Z': Rotate/Translate anti-clockwise respect to the axis.
   - '+': Zoom IN.
   - '-': Zoom OUT.
   - 'p': Toggle Play/Pause.   
   - 'r': Resart movie.                        
   - 'q': Restart view. 
   - 'Q': Quit the application.
  

MagChainPyViewer

• Run "Representation.py" using IDLE in the same folder where the trajectory generated by "MagChain" ("trajectoryCG.xyz") is.

• To help the visualization of the trajectory: · The perspective can be changed by moving the mouse while pressing the right button. · The image can be zoomed in/out by moving the mouse forward/backward while pressing the left and right buttons simultaneously.

MagChainFileConverter

• Run MagChainFileConverter.pyw (no console application) by double clicking or typing in the console python3 MagChainFileConverter.pyw

• Import the trajectoryCG.xyz file provided by MagChain using the Input files section

• Choose a folder to save the output converted file in the choose output folder section. In no folder is choosen the file will be saved in the current folder.

• Give a name for the output file and press the convert button.

Authors

1. J.S. Andreu

2. C. Calero

3. A. Giménez-Romero

License

This project is licensed under the GNU General Public License - see the LICENSE.md file for details