MSE2094
Analytic Methods in Material Science

Assignment #9: Molecular Dynamics Model

Ronald D. Kriz
College of Engineering
Virginia Tech

Part I:
Molecular Dynamics Model: Fortran Program and Visualization of Results

Objective: This assignment is designed to introduce you to using the UNIX workstation.

In this assignment you will learn how to:

• Execute a simple molecular dynamic Fortran program
• Visualize the results in AVS

Your grade will be based on creating the following files in your own personal directory so that I can reproduce your results by going into your directory and accessing your files. You can work together as a team on this project but I expect everyone to generate your own files. I may randomly ask students to reproduce these results. The files I expect to see in your directory are:

• Makefile
• anim_balls_color.c
• anim_balls_color.exe
• box.fld
• md.out
• md3.in
• molec_dyn.f
• molec_dyn.x

INSTRUCTIONS:

A molecular dynamic procedure that is already outlined in some detail in the topics section of the MSE2094 Class Notebook assumes a working knowledge of UNIX, therefore for this assignment a more extensive procedure is listed below that will supplement the procedure already listed. On We have already introduced you to some basic UNIX skills, like how to logon, move around in directories and how to use the "vi" editor.

1. Logon to your account on planet-name.smvc.vt.edu

Either go into the sciviz lab (Hancock 202A) or login remotely to planet-name.smvc.vt.edu

logon: your username

password: your password

List files by using the UNIX command "ls -lag" and you will see a directory named assign#8 Go into the assign#8 directory by using the UNIX command "cd assign#8" which gets you into the assign#8 directory. List the contents of this directory by using the UNIX command "ls -lag" and you will see that this directory is empty. To check your position in the diretory tree structure use the UNIX command pwd (p-rint w-orking d-irectory) and the path to your directory will be listed, e.g. /home/username/assign#8. Your assignment is to create the files already mentioned above and transfer these three files into the assign#8 directory.

2. Open a Netscape window

Either use the handout of the molecular dynamics exercise or open a netscape window by opening another UNIX c-shell window and typing in the command "netscape" which will bring up netscape. Click on the home button and the sciviz home page (http://www.sv.vt.edu) will appear. Select (click on hypertext with left mouse button) Courseware Development, MSE2094, additonal information, Molecular Dynamics and the web page on Understanding Molecualr Dynamics will appear. Scroll down to the flashing Molecular Dynamics Exercise section and you should see five hypertext files:

• molec-dyn.f
• Sample Inputs
• anim-balls-color.c
• Makefile
• box.fld

3. Download files from Netscape

Down load copies of each of these files, for example select molec-dyn.f and you will see a copy of the Fortran program. With the left mouse button under "File" choose "save as" and a new window should appear. In this window with the left mouse button select the appropriate directory name which is your lastname to store these files. You will have to play with this window a bit until you get the hang of it. Once you are in your directory (your-lastname) type the name of the Fortran program, molec_dyn.f in the lowest space of the window. After submitting this selection the new file should now be stored in your directory. You can confirm this by going back to the shell window which is already located in your directory and use the UNIX command "ls -lag" and you should see the new file named molec_dyn.f in your directory. Similarly download anim-balls-color.c, Makefile, and box.fld. You will notice the other files are easier to download because the location has already been established. Notice that the file Makefile is named Makefile.color which needs to be renamed to Makefile. This change in a filename is done by using the UNIX command "mv Makefile.color Makefile". Notice when you select Sample Inputs you have a choice, select the file named "md3.in" the same as you did with the "molec-dyn.f file". Before we can use these files a few modifications must be made.

• Modify the molec_dyn.f program

  Using the "vi" editor remove the first five lines of the molec_dyn.f program which are html hypertext lines. Use the UNIX command "vi molec_dyn.f" and the shell window lists the contents of the file. With the arrow keys on the right of the keyboard you can move the cursor to the lines to be deleted and then type the vi delete line comand "dd" and you will see the line removed. After the five lines have been removed go down about 20 lines to the statement OPEN(UNIT=2, FILE='md.in') and change md.in to md3.in by using the correct vi commands. I'll pass out a list of vi commands in class that should work. When finished with the editing changes save your modified file by pressing the esc key on the keyboard to remove your from the input mode and type the following sequence :wq to save the changes to the file.

• Modify the Makefile program

  Again using the vi editor replace the spaces with tabs in the last two line of this file. Makefiles are very special UNIX files that require the use of tabs. Unfortunately Web browsers replace tabs with spaces so that you can't tell the difference. Unfortunately UNIX Makefiles grew up with the vi editor and hence Makefiles depend on special features unique to the vi editor. Hence it is definitely necessary to learn how to use the vi editor if you are to work with UNIX systems.

SUGGESTION

I suggest that your work in groups and (unique to each class I make specific recommendations on how to orgainze groups to complete this project)