Software | Crystal Chemistry

File Download	Description
	CellVol code and documentation can be found at: https://github.com/CwilsonEd/CellVol A description of the method and a sample of it's applications is published in: Behavior of Occupied and Void Space in Molecular Crystal Structures at High Pressure. Cryst. Growth Des. 2022, 22, 2328−2341
MrPIXEL	MrPIXEL is a program that enables the energetics of crystal packing to be analysed quickly and easy through a user interface, using PIXEL, Python scripts and the widely known visualiser, Mercury.
	A Computer Program Package for Modelling Intermolecular Interactions This site makes available the CLP-PIXEL Package written by Angelo Gavezzotti for modelling intermolecular interactions in molecular crystal structures. We are very grateful to Professor Gavezzotti for making the code available to the community in this way. CLP-PIXEL is a theoretical approach to the evaluation of intermolecular potential energies, assuming that they can be subdivided into a Coulomb-polarization term, a dispersion term and a Pauli repulsion term. The CLP approach is implemented in two forms: the atom-atom form, AA-CLP: potentials depend on distances between atomic nuclei and are totally empirical. The evaluation of the lattice energy of a crystal structure requires only cell dimensions and atomic nuclear coordinates. the PIXEL form: intermolecular energies are calculated as numerical integrals over a large number of electron-density units, or 'pixels'. The method requires one ab initio molecular orbital calculation to prepare the molecular electron density in the form of discrete points on a grid. The download contains the programs both as source code (Fortran, in the directory \source) and in compiled form (\exe) suitable for use with Windows. A manual is provided (\doc) which contains a series of worked examples (\examples). The CLP-PIXEL programs are called using the batch files (or scripts held in \batch). Download the CLP-PIXEL software To install the program simply unzip the download into wherever location you wish to store it, though we recommend that spaces in folder names. The batch files in \batch will need to be edited to reflect the chosen location unless it is C:\CLP. The program should be cited as follows: AA-CLP applied to liquids as well as a description of the method: Gavezzotti, A. (2011) Efficient computer modeling of organic materials. The atom–atom, Coulomb–London–Pauli (AA-CLP) model for intermolecular electrostatic-polarization, dispersion and repulsion energies. New J. Chem. 35, 1360-1368. (https://doi.org/10.1039/C0NJ00982B) Application to crystal structures: Gavezzotti, A. (2013) Equilibrium structure and dynamics of organic crystals by Monte Carlo simulation: critical assessment of force fields and comparison with static packing analysis. New J. Chem, 37, 2110-2119. (https://doi.org/10.1039/C3NJ00181D) PIXEL: Gavezzotti A. (2005) Calculation of lattice energies of organic crystals: the PIXEL integration method in comparison with more traditional methods. Z. Krist. 220, 499-510. (https://doi.org/10.1524/zkri.220.5.499.65063) A comparison of PIXEL results with a large database of sublimation enthalpies is avilable in: Chickos, J.S. & Gavezzotti, A. (2019). Sublimation Enthalpies of Organic Compounds: A Very Large Database with a Match to Crystal Structure Determinations and a Comparison with Lattice Energies. Cryst. Growth Des. 19, 6566-6576. (https://doi.org/10.1021/acs.cgd.9b01006 ) An excellent introduction and discussion of the applications of both methods is available in: Gavezzotti, A. Molecular aggregation, Structure analysis and molecular simulation of crystals and liquids. Oxford University Press, Oxford 2007; 2nd Edition paperback, 2013. Further references are provided in the manual. The use of the CLP computer programs is unrestricted for all users and institutions. Questions about this download should be addressed in the first instance to Simon Parsons (S.Parsons@ed.ac.uk). Please note that the program is provided without warranty on an ‘as is’ basis, and it is the user’s responsibility to ensure that it is applied appropriately. Users should also ensure that they scan for viruses and other malware before installation.
	MRMOX For Python 3.7 - Updated version for use with the new CSD 2020 release. MERCURY based CSD Python API scripts that determine oxidation states for transition metals in crystal structures. The process is as described in "Automated oxidation-state assignment for metal sites in coordination complexes in the Cambridge Structural Database". For details, contact: Matt Reeves m.g.reeves@outlook.com Download: MRMOX_3.zip
	Further scripts and software are available on GitHub: https://github.com/MReevesoftware
MrMOX_2019	This version relates to the Python 2.7 CSD version that is no longer used. MrMOX- MERCURY based CSD Python API scripts that determine oxidation states for transition metals in crystal structures. The process is as described in "Automated oxidation-state assignment for metal sites in coordination complexes in the Cambridge Structural Database". For details, contact: Matt Reeves m.g.reeves@outlook.com
XNPP	A program to calculate the Flack parameter given cif and fcf files. For more information see: Use of intensity quotients and differences in absolute structure refinement (S. Parsons, H. D. Flack and T. Wagner)
ROTAX	The program ROTAX derives non-merohedral twin laws by identifying poorly fitting data during refinement and by transforming their indices by rotations or roto-inversions about possible direct- and reciprocal-lattice directions. Operations that transform these indices to integers are identified as possible twin laws. For more information see: The derivation of non-merohedral twin laws during refinement by analysis of poorly fitting intensity data and the refinement of non-merohedrally twinned crystal structures in the program CRYSTALS (R. I. Cooper, R. O. Gould, S. Parsons and D. J. Watkin)
HATTIE	Program for leverage analysis of crystallographic data. For more infromation see: Applications of Leverage Analysis in Structure Refinement (S. Parsons, T. Wagner, O. Presly, P. A. Wood and R. I. Cooper)