Procedure for importing and plotting you data using EXCEL

Color coding for this tutorial

Teal refers to the menu bar selection in EXCEL

Dark blue refers to the menu option choice

Violet refers to the button selection within the menu

 

Go to

File/Open

Menu:

Files of type: All files (*.*)

Select one of the rdf files

Select Open

In the Text Import Wizard menu select the option Fixed Width (radio button) This is step 1 of 3.

Select Next (to proceed from step 1 of 3 to step 2 of 3)

In step 2 of 3 scroll down until you see the numbers. Make sure that all columns of numbers are delimited. You can simply click between any two columns to create a black arrow that indicates that they are delimited. Once all columns of numbers are delimited

Select Finish.

You may have some header text that you can delete. Just select the cells that you wish to eliminate and push the delete button on your keyboard.

Select A , B, C etc. to include all of the data of interest. The entire columns of interest should turn black to indicate that it has been selected.

 

Go to

Format/Cells

In the Format Cells menu change category from general to number

Change decimal places to 5.

Select OK

 

Go to

Insert/Chart

Chart type is XY scatter and you can select lines by choosing the upper left option in the menu (this has no words but just looks like some squiggly lines).

 

Select Finish.

 

For the radial distribution function you are interested primarily in looking at the solvation shells around each atom in the simulation. This corresponds to columns A and B. Your plot should look something like this, but the details will depend upon the density and temperature of your simulation.

You can cut and paste this chart into a word document using

Crtl c while in EXCEL and Ctrl v while in WORD. This will allow you to make a document that contains a plot of

  1. The mean square displacement (msd)
  2. The radial distribution function (rdf)
  3. The velocity autocorrelation function (vacf)
  4. The spectral density of the vacf (vsd)

 

Please create one plot of each of these.

In the case of the data file rdf you also will find some data in column C. This is the total number of particles within the radius R given on the x-axis of the plot. Thus, the columns are

  1. The radial distance from each argon atom (defined to be zero)
  2. The radial distribution function g(r)
  3. The total number of particles with radius r, n(r)

The data in column C need not be plotted.

 

In the msd file the columns are

  1. The distance
  2. The mean square displacement
  3. The distance traveled

You do not need to plot the distance traveled except for your own edification.