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Department of Chemical Engineering, University of Bath

Surface area program

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Calculating the accessible surface area
For non-orthorhombic unit cells

This program can be used to calculate the accessible surface area of both orthorhombic and non-orthorhombic unit cells. In contrast to the orthorhombic version of the code which uses a music molecule file as input, it uses an xyz as input which can be created from programs such as Diamond of Mercury..

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 .


Notes on extracting the archive and compiling the code are given here.

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:

./nonorthoSA.exe < input_x.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 files provided, your output should look something like this:

Calculating the accessible surface area for the following input parameters
-------------------------------------------------------------------------
File with framework coordinates: IRMOF1.xyz
File with atom diameters: UFF.atoms
Probe diameter in A: 3.681
Accessible surface area in A^2: 3715.51
Accessible surface area per volume in m^2/cm^3: 2155.48
Accessible surface area per mass in m^2/g: 3653.36


Calculating the accessible surface area for the following input parameters
-------------------------------------------------------------------------
File with framework coordinates: Cd121.xyz
File with atom diameters: UFF.atoms
Probe diameter in A: 3.681
Total surface area in Angstroms^2: 414.02
Total surface area per volume in m^2/cm^3: 1123.64
Total surface area per volume in m^2/g: 749.09

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 and to Houston Frost from Northwestern University who wrote the first version of the non-orthorhombic code!!