Visualization Software For Molecular Dynamics Simulation

Transcription

1 Visualization Software For Molecular Dynamics Simulation Foo Jong Chen Mechanical Engineering National University of Singapore

2 1. Introduction In the field of study of molecular structure of different materials, there is an increasing interest in the behavior of materials at the nanometer scale because at such small scales, materials exhibit unique properties scientists and engineers. They often need to have a good three-dimensional view of the structure in order to further their studies on those structures as well as make decisions on a higher level as to whether the materials are useful for a particular purpose. The 3-D view of the molecular structure has to be generated in a labor and cost efficiency manner so that more effort can be spent on researching new uses for the material after the study of the molecular structure. Hence, in this project, a type of software for the visualization of three-dimensional molecular arrangement is developed. The code calculates the positions of the molecules as the material deforms, hence the software developed in this project will be used to display the 3-D arrangement of molecules. This program will aid in the prediction of the response of nanometer scale materials to external loads based on how molecules interact with one another. Currently, there are a series of different programs available on the internet that will enable us to view these 3-D presentations of molecular structures. These softwares are namely Raswin [1] and VMD [2]. Unfortunately, most of the programs do not read in a simple DAT file and hence the programs cannot be used unless ENT or PDB (Protein Data Bank) files are created. 2. Materials and Methods 2.1 What is OpenGL? OpenGL is a software interface to graphics hardware. This interface consists of about 120 distinct commands, which you use to specify the objects and operations needed to produce interactive three-dimensional applications. OpenGL is designed to work efficiently even if the computer that displays the graphics created isn't the computer that develops that particular graphics program. OpenGL is also designed as a streamlined, hardware-independent interface to be implemented on many different hardware platforms. It provides a set of low-level functions for programming in 3D. The features incorporated in OpenGL are lighting, back face culling, z-buffering etc. However it does not provide any functions for interfacing to the mouse or keyboard or for creating a window for displaying on. OpenGL is NOT a language (despite many beliefs). It is a C library. Normally programs are written in C/C++ which will call the library functions to perform the 3D. It is also possible to use other languages but with lesser efficiency. OpenGL will work on Windows, Unix, Linux and many other platforms.

3 2.2 Use of C and OpenGL Programming First of all, a research on whether using C or C++ (Object-Oriented) programming would be more efficiency in coding the program is conducted. After reading up on different 3-D graphics reference books, it is found out that using C language is more suitable for the molecular program as most of the references based their coding on C. Next, an in-depth understanding of OpenGL is attained in order to start the coding process. There are several sources taken for the reading of OpenGL. OpenGL Superbible is a relatively useful reference book which gives the reader a good start to understanding 3-D graphics and OpenGL DLLs. Another useful source is the website as it gives a basic walk-through of the functionalities of OpenGL and the C coding process although the website is mostly devoted to game programming enthusiasts. The following step is to synthesize the C language coding using the dynamic functions that are available in the GLUT/GLU DLL (Dynamic Link Library). Once the program has undergone repetitive and different cases testing, it is ready to be used for any molecular data given in a normal DAT or Notepad file. The program will readily read the data present in the file and subsequently generate a window displaying the molecular structure with the molecules located at their respective 3-D positions.

4 3. Results As mentioned in the previous chapter, after the coding of the Molecular Visualization Program is being done, test running of the program is conducted in order to delete all the compiling and runtime bugs that lie in the code. The figure below displays a sample visualization model of the material Oxygen (sample molecular structure data is not accurate) after the test running process.

5 Figure 1 Molecular Structure of Oxygen Items Description of Items Title Atomic Analysis Black Lines at position Z=0 Green spheres Red spheres Cyan spheres Title of the program Gridlines to show Z=0 plane Type 1 molecule Type 2 molecule Type 3 molecule 4. Discussion 4.1 Research Process The process of understanding and learning the functionalities of OpenGL takes a large amount of research time. And as in all programming process, a combination of coding, test-running and fine-tuning must be done to ensure the program runs properly to the specified criteria and is free of bugs It also has to withstand repetitive usage without crashing. Furthermore, it has to run under extreme circumstances for example: having a huge number of molecules to calculate and then to display them on the screen.

6 4.2 Objectives Primary objectives such as being able to learn OpenGL and apply it to create a 3-D molecular structure in Windows have been met. However, additional functions such as real-time interactive identification of each molecule and real-time re-arrangement of the molecules have not been incorporated to the program due to the lack of time and programming knowledge. A further course on 3-D graphics programming would aid the programmer in implementing the above-mentioned functions. A greater improvement in the interactive toolbar available on the displaying window is also possible with the use of Windows programming. 5. Conclusions and Recommendations Through the development of the OpenGL molecular visualization program, the wonders of 3-D graphics programming have been uncovered. However, a greater depth of study on programming and OpenGL library is needed to fully utilize the power of 3-D graphics programming. The project is only considered a partial success as although the primary objective of creating a 3-D presentation of the molecular structure of a material is achieved, efforts on incorporating additional functions such as displaying the information of every molecule interactively on screen have not been successful. More hours of programming study, research and program testing is needed to fine-tune the program to meet the secondary objectives. In summary, with the aid of advanced computer technology, scientist and engineer s studies on materials on the nano basis will be greatly enhanced. The usage of OpenGL in programming 3-D visualization graphics for the research of structures of materials in the nanometer scale can be further explored. The present program developed has a lot of room for improvement and more research time is recommended for the development of this program or a new program based on OpenGL to aid the studies of both students and professors in the university. [1] [2]