How to make a color Laplacian plot

This guide leads you through some of the tools for generating a two-dimensional continuous-color Laplacian plot in a way that is streamlined to deliver the final plot as high-quality PDF for inclusion in a LaTeX pdf document. Of course, the tools used can allow for easy redirection to other formats.
  1. When setting up the calculation, decide which three atoms will define the plot plane. Use the MOLDEN Z-matrix editor to renumber the structure with these atoms as the first three in the list. Then, the first atom will reside at the origin, the second atom will be on the z axis, and the third atom will be in the xz plane.
  2. Assuming you have used ADF for the calculation, then the next step is to convert the TAPE21 file to ascii format with the command "$ADFBIN/dmpkf TAPE21 > t21.ascii".
  3. Next, the program dgrid is used to convert the t21.ascii file into a t21.adf file as follows: "dgrid t21.ascii".
  4. Now the program dgrid is used to produce a file containing the Laplacian data at points on a 2D grid. The command used is "dgrid dgrid.inp" where a sample dgrid.inp file of this type can be seen by clicking here. In this case, the use of 319 x intervals and 319 y intervals together with the values=320 instruction ensures that the resulting grid data file will have 320 data lines each with 320 data points. This corresponds to the rows and columns of a square matrix, and is nearly ready for plotting.
  5. Take the matrix data file and rename it "matrix.dat". Use a text editor such as gvim to delete the header and footer lines that do not contain the data. Now matrix.dat should be a text file with 320 lines of data.
  6. Now you can execute a script to cause plotting of the data with gnuplot. An example of such a script can be seen by clicking here
  7. You will need to modify the xrange and yrange in the gnuplot script in order to plot the desired portion of your data set. To plot the whole range of data just use 0:319 in this case for both the x and y range.
  8. Now when you execute the script a matrix.eps file is produced. This matrix.eps file can be converted directly to pdf by typing "eps2pdf matrix" assuming you have the eps2pdf utility, available here. This utility is powerful and supports scaling and rotation. For example, use the "-r angle" option to rotate counterclockwise by the specified angle, in degrees.
  9. Finally, all the unwanted white space around the image can be automatically stripped away using the pdftrimwhite utility. Just use the command "pdftrimwhite filename.pdf" and this will return a new file called "pdftrimwhite.pdf" that contains only the image of interest.

Caption to the above Figure

Above is a plot of ∇2ρ for the model system (η2-AsPNMes)Nb(N[Me]Ph)3. Small arrows point to valence-shell charge concentrations (VSCCs) in the P-Nb and in the As-P bonding regions. Note the absence of any VSCC in the region near As where an electron lone pair might be expected.