Computation of Electron Diffraction
Patterns from Molecular Dynamics
|This program, MolecDynamED.exe, will
perform some simple molecular dynamics and simultaneously compute the time-averaged
electron diffraction pattern. The diffraction pattern computed is that of a randomly
oriented molecule, identical to a powder pattern rather than the pattern produced by a
single crystal. These diffraction patterns have complete radial symmetry.
This program was specifically designed to model results from electron diffraction on
charged molecules or clusters levitated in a radio frequency trap.
MolecDynamED.exe is a Windows executable. The executable and a few support files are
located in a zipped file here and are freely available
for both scientific users and the merely curious.
A brief introduction to using the program: This
program is a fairly complex application and what is presented here will only be cursory.
But even without a complete explanation one can still use it as a small window into the
graceful undulations of the microscopic. Viewing in 3-dimensions can be near awe
- On initial execution the program will begin to simulate the motion of a small collection
of atoms. It will be much smoother than the cute little graphic to the right. It is also
interactive, in that the molecule can be rotated and zoomed in real-time. The Run-Stop button can be double clicked as desired.
- The center top panel (or page) represents the molecular dynamics. The lower right page
contains the time-averaged atomic radial distribution function (averaged over all atom
types for viewing), while the lower left page has the final electron diffraction pattern.
- In the Molecular Dynamics Page, there are
views for simulation step counts, and molecular energies. Controls there can be used to
change the simulation step size and the number of steps between user interface redraws.
The number of steps between accumulations of the radial atomic distribution can also be
- During simulation the molecule can effectively be made to have contact with a heat bath.
This occurs periodically for an initial number of steps (shown in the controls). It also
occurs whenever ReinforceT is
clicked. The temperature of the heat bath can be varied. As you will notice, many of these
fragile molecules easily evaporate at low temperatures.
- Pages and controls are interactive and zoomable. Plots are also highly
for using this specialized graphical user interface can be found here. All of the
molecular viewing controls can be found in the interface under: Controls and Energy Graphs::View Controls. It
also supports red/green glasses (with red on right). There are a large number of
interactive settings here. A few most commonly used:
Potentials: This simulation is
simplest to use when set on Lennard-Jones particle-particle interactions. To the
uninitiated these are approximations to rare gas, Argon-Argon or Xenon-Xenon,
interactions. This interaction can be tuned by changing sigma
and epsilon. We recommend sticking to the
Lennard-Jones potential. If you would like to explore other potentials please see the technical notes or contact me.
FCC reset: This will generate a
new molecule from a near-spherical piece of a face-centered-cubic lattice. Anywhere from 2
to hundreds of atoms. Choose the desired size and atom type. With a few hundred atoms the
simulation begins to slow and requires more patience (or larger step sizes and a little
inaccuracy). Hundreds or thousands of atoms can be used to demonstrate melting or
New/Save: New molecular geometries can be
input and output at any stage. These use our standard ASCII
- View Controls::Drawing::max bond
length - helpful to change the maximum length considered to be a
bond and drawn with a line.
- View Controls::Atom Hiding -
It can be particularly helpful to hide atoms with many neighbors (high coordination
number) to see the outer atoms in a cluster. Or hide the atoms behind the pane of the
- Molecular Motion Controls -
To avoid an initial explosion or implosion it can be helpful to expand or shrink the
molecule before starting the simulation. This is most needed when an initial geometry is
far from the lowest energy configuration.
- Energy Graphs - Allows
viewing the exchange of kinetic and potential energy. Total energy will be conserved as
long as the stepsize is not so too large that numeric accuracy is lost.
(The second line in the file is the maximum distance to be considered a bond.)
To calculate the diffraction pattern, all atom types in the molecule require an atomic
scattering factor file (
*.scf). A handful of these are provided. They bear
names of the atomic name and atomic charge. Usually these are accessed automatically if
they are within the ScatteringFactors subdirectory.
Again, some additional information on using the AlphaSquared
graphical user interface can be found here. The molecule
viewing panel is interactive, for starters: zoom-in is '+', zoom-out is '-'. Arrow keys
Note that this
program is intended for experimental simulation not mass distribution. No harm can be done
in running the program incorrectly, but it would not be surprising to find a bug or two in
the program. (More effort was intentionally dedicated to exploration than robustness.) Due
to its highly technical and exploratory nature, many features are indicated only in the
source code. If you have interest in those features, please contact me.
Revision notes and technical info are here.
Source code is available from the author on special request. It uses the AlphaSquared graphical user interface.
Development of this program was funded primarily by The Rowland Institute for Science, under the direction
of Joel Parks. The program was written exclusively by Douglas Cameron.