Surface area program
Calculating the accessible surface area
The file containing the coordinates of the framework atoms
To calculate the accessible surface area, a file containing the positions of all the framework atoms is needed. Please note that the program does not handle symmetry operations and therefore the coordinates of all atoms in the unit cells need to be given explicitly in Cartesian (not reduced!) coordinates. Make sure that you add hydrogen atoms where necessary.Format of the coordinate file: The program reads the coordinates from an xyz-file that can be easily created from programs such as Diamond or Mercury. Ideally, your xyz file should have every framework atom only once (some programs give periodic images as well especially if framework atoms are sitting exactly on a cell vector e.g. in the origin itself). Don't worry if you can't find a method to eliminate these "double" atoms. The only thing that happens is that the program will create double the amount of trial insertions around that particular framework atom which shouldn't influence the final result.
Please note, that the accessible surface area program can be easily changed to read in the coordinates in any other format. The location where this has to be done is clearly marked in the program itself.
You can download two sample files:
- A file for a Zn-MOF having an orthorhombic unit cell: IRMOF1 / MOF5
Reference:
(H.Li, M. Eddaoudi, M. O'Keeffe, O.M. Yaghi, Nature 1999, 402, 276)
- A file for a Cd-MOF with a non-orthorhombic unitcell: Cd121
Reference:(A.D. Burrows et al.Dalton Trans., 2008, 2465)
The general format of the coordinate file is as follows:
424
Zn 7.57859 5.33741 5.33741
O 6.45800 6.45800 6.45800
O 7.28127 5.63473 3.46226
...
The first line contains the number of framework atoms in the unit cell, the following line is either empty or contains some comments. The Cartesian coordinates of the framework atoms follow. In the first column, the chemical symbol of the framework atom is given. The following three numbers are the x, y an z coordinates in Angstrom, respectively. You must make sure that for all types of framework atoms diameters are specified in your atom diameter file or the program will stop!