Interacting with Crystals: Adventures in Nanospace
David C Palmer
CrystalMaker Software Ltd, Begbroke Science Park, Oxfordshire, UK
Abstract
We have developed a suite of Mac programs designed to make
crystal structures and their diffraction properties accessible and fun!
Our core product, CrystalMaker®, provides real-time interactive
visualization of the atomic arrangements inside crystals and
molecules. A wide variety of data formats can be imported and
displayed using photo-realistic graphics. The non-modal program
design allows for active exploration of even the most complex
structures. CrystalMaker uses QuickTime™ to provide high-
resolution graphics output in a wide choice of file formats, plus
video recording and automatic QuickTime VR object generation.
CrystalMaker can be extended, via two helper applications,
CrystalDiffract® and SingleCrystal™, to provide simulation and
analysis of many common diffraction experiments.
Building Dynamical Models
Coping with Complexity
CrystalMaker was conceived some 12 years ago when one of us (David
Palmer) was working as a lecturer at the University of Cambridge. Faced with
teaching a traditional crystallography course to new geology students, we
turned to the graphics capabilities of the Mac to provide help.
The key challenges were to help students visualize three dimensional models
and to “see the wood for the trees” when presented with complex structures.
We overcame these challenges through the development of CrystalMaker: a
program to provide dynamical computer models that transcend the limitations
of traditional teaching methods. Using CrystalMaker, one can instantly simplify
a complex structure using stylized models, show or hide atoms, and zoom
interesting features whilst hiding background clutter. In so doing, one begins to
develop an intimate understanding of nano-scale, structural architecture.
Case Study: the Structure of Fluorite, CaF2
The CrystalMaker images above are different representations of one unit cell in
a fluorite (calcium fluoride) crystal. Moving from left-to-right, we pass from a
traditional “ball-and-stick” model to a stylized, “polyhedral” model.
The ball-and-stick model shows positions of different atom types (fluorine in
green, calcium in blue) and their chemical bonds (grey sticks). This is useful for
small structures or molecules, but can become too fussy for complex materials.
The polyhedral model on the right is much simpler. Groups of individually-
bonded atoms are replaced by polyhedra. For example, each fluorine atom with
its four nearest-neighbour calcium atoms is represented by a solid tetrahedron;
we can think of each fluorine atom as residing at the centre of a tetrahedron,
with calcium atoms at the vertices.
Polyhedral models are invaluable for understanding materials such as zeolites,
ceramics and many minerals. Whilst appearing complex, these structures
actually consist of the same basic sub-units (silicate groups) connected in
different ways—somewhat like “Lego” models made from the same bricks.
© 2007 CrystalMaker Software Limited
Crystal & Molecular Structures Visualization
CrystalMaker is an award-winning
program for visualizing the atomic
arrangements inside crystals and
molecules.
CrystalMaker imports diverse file
formats, providing high resolution
photo-realistic graphics, 3D stereo
® invaluable teaching and research aid.
CrystalMaker and QuickTime video/VR movies.
Elegant and Accessible Interface
The major controls are easily accessible via floating palettes. Data
can be edited using data browsers embedded within resizable
sheets. Multiple views and undo states are available at all times,
represented by thumbnail previews in the Overview Window.
Key Mac Technologies
CrystalMaker uses Quartz graphics for much of its visualization,
allowing us to control both 2D and 3D plotting, with high-quality
textboxes, arrows, scalebars and other annotation overlays.
A Video Recorder palette gives access to QuickTime movie
recording or automatic generation of QTVR objects. QuickTime is
also used to provide a wide range of graphics export formats.
Spotlight on Innovation Multiple Structures, Views and Histories
CrystalMaker is continually being developed. Forthcoming
CrystalMaker s Atom Info window (top right) lets users edit atom properties on the fly—and
versions will include Spotlight integration: browsing for chemical
control the site visibility and labelling. The Overview Window (bottom right) gives single-click
formulae, density, volume and other properties—from the Finder.
access to bookmarked structural Views, undo states (History) and recently-opened files.
X-ray Powder Diffraction
CrystalDiffract is a helper program, designed to
work with CrystalMaker to simulate x-ray and
neutron powder diffraction patterns from crystals.
Powder diffraction is one of the most important
ways of “fingerprinting” materials. CrystalDiffract
lets researchers compare their experimental data
directly with theoretical results, without having to
®
CrystalDiffract trawl through external (and expensive) databases.
CrystalMaker Integration, via Apple Events
A structure can be visualized in CrystalMaker, then, with a single menu
command, its diffraction pattern simulated in CrystalDiffract. Groups of files
can be dragged-and-dropped into CrystalDiffract, with the option of a
stacking display or mixture simulation, as demonstrated below.
Real-Time Parameter Control
CrystalDiffract goes beyond mere display and measurement, giving users full
control over the virtual diffraction experiment. Users can adjust parameters
such as wavelength, crystallite size and cell parameters, by clicking and
dragging a slider control as the diffraction pattern is recalculated in real time.
In the example shown on the left, the “b” cell parameter is being changed to
mimic the effects of a phase transition. Notice how the resulting diffraction
peaks (red) have become split, compared with the original (blue) pattern.
CrystalMaker®
SOFT WARE
Single-Crystal Diffraction
SingleCrystal works with CrystalMaker to
simulate diffraction patterns from crystals.
Diffraction from single crystals is the prime
technique in crystal structure determination.
Reversing this, by going from a known
structure to a simulated pattern, is an
SingleCrystal ™
Your Desktop Electron Microscope
SingleCrystal s simulation is highly-realistic and the mouse-driven real-time
control gives users a real sense of exploring “diffraction space”. Real diffraction
images can be dragged into a window, for easy comparison with the theoretical
pattern, which is then shown as an overlay.
As an education tool, SingleCrystal adds the ability to control experimental
parameters (such as crystal thickness, machine beam current, wavelength) to
aid the understanding of how these affect the formation of a diffraction pattern.
Stereographic Projections in the 21st Century
SingleCrystal features interactive “stereographic projections”, showing the
spatial arrangements of planes of atoms and vectors in a crystal lattice,
summarized in a handy two-dimensional plot.
About Us
CrystalMaker Software Ltd is an award-winning British company that develops,
sells and supports computer software for applications in chemistry, physics,
materials science and geology..
Founded by two former academics, our company is committed to the greater
understanding of science, through the use of innovative new technology. Our
focus is firmly on user interaction, with elegant interfaces and superb, photo-
realistic graphics.
Software Requirements
All of our Mac products are universal binaries
and require Mac OS X 10.3 or later. Free
demo versions (for Mac or Windows) can be
downloaded from our website:
http://www.crystalmaker.com
info@crystalmaker.com
We sell our software direct, thereby providing lower prices and higher-quality
service (including numerous free incremental updates via our website).
Education and multi-user discounts are available for all products.
www.crystalmaker.com