Table of Contents

1. Background
2. Use

Background

Based on .cif files, CLUSTERGEN¹ provides facilitates to identify and write .xyz files about dimers and clusters suitable for further analysis and quantum chemical computation. It equally offers the direct output in formats suitable for ADF and Gaussian.

To automate the identification of "interesting dimers", .cif model data may be converted batch-wise into intermediate .inp input files suitable for a sequential processing with CLUSTERGEN's .f90 source code. Similarly, it is possible to systematically build clusters. Three complementary definitions regarding the distance threshold of inner (reference) molecule and most outer neighbor are available.

Use

Put the .cif of interest, the .f90 source code of CLUSTERGEN (available from the author) and the two scripts into the same folder. A call of

python cif2clustergen.py

creates the intermediate .inp files. A subsequent

python serial_clustergen.py

then both compiles the source-code with gfortran, as well provides the results accessed by CLUSTERGEN.

Footnotes

¹ "CLUSTERGEN: a program for molecular cluster generation from crystallographic data", R. Kaminski, K. N. Jarzembska and S. Domagala in J. Appl. Cryst. (2013) 46, 540-543, doi:10.1107/S0021889813002173; Windows compiled executable on http://www.photocrystallography.eu/software.html.