Running A + B ==> AB

In order to run the reaction you need to start the program and choose the reaction A + B==> AB


Hit return when you see this screen
 

Click on the A + B ==> AB button and hit return when you see this screen
Click here for detailed instructions for these startup screens


Go dialog

Next machine makes many plots. The plots will be described below. Eventually you are presented with a button labeled "click here to start the trajectories"


You must hit enter or push the button to go on!


Running The Program

Next you get a very complicated looking screen: There are three windows to display the trajectories and many buttons


Let us go through the parts of the screen. First let us consider the various windows. There are general controls accoss the top and three windows labeled "Plot on potential energy surface", "animation", "Positions vs time" which display the simulations. You can click on each window to bring it forward and watch the plots. We will discuss each part below.


General controls

The Image below shows the general controls


You do not need to use any of the controls to run the program. However, if you click on the buttons you can change how the program performs.


Next it is useful to discuss the plots

Plot on potential energy surface

The first plot is a plot a potential energy surface. Here is a picture of the potential energy surface.


The potential energy surface is a contour plot of the potential energy of the system as a function of r_AB the distance from A to B and the angle between A and B in radial coordinates. In this case the potential looks like a morse potential of r_AB; there is a minimum at a distance of 1.0 angstroms, a repulsive potential at short distances and an attractive potential at long distances. The potential actually looks like a bulls-eye because the potentail is symmetric in the angular direction.

Students sometimes have trouble seeing contour plots of potential energy surfaces. There is a tutorial on contour plots in section 7G and 8A of R. I. Masel, Kinetics and Catalysis, Wiley 2001. There is also an excel spreadsheet which displays contour plots and allows students to manipulate them. The spreadsheet is available from The Wiley website


Trajectories on potential energy surfaces

Here are two trajectories on the potential energy surface.


The trajectories are plots of the position of atom A relative to B as a function of time. Notice that in no case does a reaction occur.

Animation

We also include an animation of the reaction to help students see the motion. Once the program is running, you can click anywhere on the window to bring the animation forward. Then you can watch the positions of the atoms evolve. Look at the final state. A comes in. Does A scatter away.

Positions versus time

Finally we include a plot of the position versus time. Once the program is running, you can click anywhere on the window to bring the animation forward. I find that the position vs time plots are hard to understand as they are generated, but if you plot them, there is considerable information. A discussion of the information can be found in Chapter 8 of R. I. Masel, Kinetics and Catalysis, Wiley 2001


The ending dialog

After all of the trajectories run you will be presented with a dialog like:


Hit alt-f4 to exit after you are done printing.


There is more information on the ReactMD website.
Click here to visit the ReactMD website

Click here for updates to the documentation

For further information about applications of this program please look in Chapter 9 of R. I. Masel, Principles of Adsorption and Reaction on Solid Surfaces, Wiley 1996 or Chapter 8 of R. I. Masel, Kinetics and Catalysis, Wiley 2001