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. This version of the program deals only with with orthorhombic unit cells where the positions of all coordinates are given explicitly (i.e. no symmetry operations) in cartesian coordinates. Format of the coordinate file: The program reads a file that contains the coordinates in the same format as a music molecule file. 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 a sample file that contains the coordinates for IRMOF-1 / MOF-5 (H.Li, M. Eddaoudi, M. O'Keeffe, O.M. Yaghi, Nature 1999, 402, 276).
The general format of the coordinate file is as follows:
424
1 -16.98042 -17.94911 -16.79313 Oxygen 0.00 0 0
2 -14.21200 -17.92302 -16.81922 Carbon 0.00 0 0
3 -5.93930 -19.89297 -17.09045 Zinc 0.00 0 0
...
The first line contains the number of framework atoms in the unit cell, the following lines the coordinates. The first number has to be an integer number (here: a counter for the framework atoms, but this number does not play a role in calculating the accessible surface area). The following three numbers are the x, y an z coordinates in Angstrom, respectively. The fourth column contains the atom type. You must make sure that the atom names in your coordinate file are the same as in your atom diameter file or the program will stop! The last three numbers do not play any role in calculating the accessible surface area either. Please note that if you use a (slightly modified) music molecule file as input you can leave the Fund_Cell information at the bottom.