Tina Düren

Research Group

• Home
• Research
• People
• Publications
• Teaching
• Contact

 

Department of Chemical Engineering, University of Bath

Surface area program

• Back to main page

Calculating the accessible surface area
For orthorhombic unit cells

This program can be used to calculate the accessible surface area of orthorhombic unit cells. It is the easiest version. So if you want to understand the underlying algorithm this is the best place to start. It is also quicker than the non-othorhombic version of the code but can only be used for orthorhombic unit cells.

Obtaining the code

The accessible surface area code is available under the General Public Licence. Read the conditions of the license before proceeding with the download .

Compiling the code

The program is written in Fortran 90 and is tested for the Intel compiler. It should compile and run with any other Fortran compiler. However, you might have to change the value for "realkind" the number that defines double precision numbers (it is 2 for the intel compilers, other compilers might use 8 or other values).
For the simplest way to compile the code with the intel compiler, type

ifort accessible_surface_area.f90 -o surface.exe

This will create an executable called "surface.exe"

Running the program

To run the program you need:

• A file containing the coordinates of the framework atoms
• A file containing the diameters of the framework atoms
• A file containing the simulation parameters

To start the program, type:

./surface.exe < input.dat

The "<" makes sure that the necessary data is read from the input file containing the simulation parameters.

Results

If you run the program with the sample file provided, your output should look something like this:

Calculating the accessible surface area for the following input parameters
-------------------------------------------------------------------------
File with framework coordinates: IRMOF1.coords
File with atom diameters: UFF.atoms
Probe diameter in A: 3.68100000000000

Accessible surface area in A^2: 3712.15
Accessible surface area per volume in m^2/cm^3: 2153.53
Accessible surface area per mass in m^2/g: 3650.06

Please note that the values can vary slightly depending on the computer and compiler used.

Acknowledgements

A big thank you to Lev Sarkisov for providing the first version of this code!

Thank you to Francois-Xavier Coudert for having a careful look at the program and pointing out a bug which was corrected on 08/08/08. The new version of the code is now online. Results with the previous version were only affected if you tried to change the code and run the program with different seeds for the random number generator which didn't lead to different results as it should have.