Time for a post on science: ZMC

Conventional crystal structure refinement and solution relies on an analysis of the Bragg peaks, the sharp, well-defined scattering in a diffraction pattern. In doing this, the structure can be considered as an array of identical unit cells, and this reduces the ‘solution’ of the crystal structure to the determination of the unit cell contents.

In a disordered material, while the average unit cell does indeed obey the space group symmetry of the crystal structure, such that solving the asymmetric unit within the cell ‘solves’ the structure, this is not the case for a disordered material — or even for what would generally be considered as an ordered material if considering instantaneous molecular and atomic motions.

Even an ordered crystal will show thermally induced vibrations of the atoms. If we could ‘freeze’ the crystal and look at the atoms, we would find that the space group symmetry is not obeyed. It is obeyed on average. In
a disordered material it could be that the average occupation of a given site is 50% one type of atom and 50% another, in which case no site obeys the average symmetry.

What does this mean for analysis of diffuse scattering? It means that you can no longer consider all unit cells as identical. It means that you have to now work with an ensemble of unit cells big enough that averaging across it
recovers the average and big enough that it can contain a statistically valid population of the local (short-range order) structures present in the crystal.

This means that analysis of diffuse scattering requires different tools from analysis of conventional Bragg scattering. ZMC is an attempt at a program to allow relatively ready implementation of a simulation of diffuse scattering from (particularly but not solely) molecular crystals.

ZMC is alpha software at best, and always will be; nothing about its performance is guaranteed nor promised. Despite my better judgement, I am putting it up for download. You can download the current ZMC at http://rsc.anu.edu.au/~goossens/ZMC.html for Windows, Linux (give it a try, I think I statically linked the binaries), Mac OS X and as source code.

You might find it useful to look at this first. Be aware that there are many versions of Linux (and OS X is not known for its long term user support or version to version compatibility), so your best bet might well be to contact me about the source code. If you can get g95 working (www.g95.org) then the compile is pretty trivial (he says hopefully…).

While ZMC is relatively straightforward to use, and a great deal of work has been undertaken to give it a usable (if text file-based) interface, it is not yet ‘production’ software (and never will be). It is written in Fortran90 and uses a module library developed by Dr Aidan Heerdegen, and some components of the system have not been tested on various combinations of hardware and operating system. Currently binaries exist for g95 on Intel Macintosh (Mac OS X 10.6), Intel Fortran Compiler on Debian stable on Intel i7 (ie, most Intel-compatible) and Windows xp, and that is about it. So far, once the modules are ported, the main program seems to compile without problems, but I am not in a position to make a general distribution.

Further, there is no comprehensive manual, though it comes with an in-progress version of what will one day, time permitting, be a manual. The program contains some basic help options, and the distribution packages contain a (simple) simulation that should work out of the box, and the adumbral manual contains some code that might be useful also.

Some things to note: ZMC is essentially a program for displacive relaxation/equilibration of the model crystal. Any occupancy ordering needs to be done externally. The software needs a suite of toolbox programs, which also need to be bundled with any distribution. These include programs for working with crystal geometry, calculating diffraction patterns (DIFFUSE, Butler, B. D. & Welberry, T. R. (1992). J. Appl. Cryst. 25, 391–399), performing any occupancy simulations and so on.

ZMC is used and the method described in the following publications, amongst others:

D.J.Goossens, A.P.Heerdegen, E.J.Chan and T.R.Welberry, ‘Monte Carlo Modelling of Diffuse Scattering from Single Crystals: The Program ZMC‘, Metallurgical and Materials Transactions A, 42A (2011) 23-31. DOI: 10.1007/s11661-010-0199-1.

D.J.Goossens and T.R.Welberry, ‘Diffuse Scattering from Molecular Crystals’, chapter in Diffuse Scattering and the Fundamental Properties of Materials, edited by Rozaliya I. Barabash, Gene E. Ice and Patrice E.A. Turchi. Momentum Press, 2009. Print ISBN: 978-1-60650-000-2. E-book ISBN: 978-1-60650-002-6

E.J.Chan, T.R.Welberry, D.J.Goossens, A.P.Heerdegen, A.G.Beasley and P.J.Chupas, ‘Single-crystal diffuse scattering studies on polymorphs of molecular crystals. I. The room-temperature polymorphs of the drug benzocaine’, Acta Cryst. B65 (2009) 382-392.

D.J.Goossens, A.G.Beasley, T.R.Welberry, M. J. Gutmann and R.O.Piltz, ‘Neutron diffuse scattering in deuterated para-terphenyl, C18D14‘, J. Phys.: Condens. Matt., 21 (2009) 124204.

D.J.Goossens and M.J.Gutmann,
‘Revealing how interactions lead to ordering in para-terphenyl’, Physical Review Letters, 102 (2009) 015505-1-4.

D.J.Goossens, A.P.Heerdegen, T.R.Welberry and A.G.Beasley,
‘The Molecular Conformation of Ibuprofen, C13H18O2, Through X-ray Diffuse
Scattering’, International Journal of Pharmaceutics 343 (2007) 59-68.

D.J.Goossens, T.R.Welberry, A.P. Heerdegen and M.J. Gutmann, ‘Simultaneous Fitting of X-ray and Neutron Diffuse Scattering Data’, Acta Crystallographica A A63 (2007) 30-35.


Tags: , , , , , , ,

About Darren

I'm a scientist by training, based in Australia.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: