Molecular Dynamic Electron Diffraction

Molecular Dynamic ED

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 inspiring.

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 changed.

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 interactive. Techniques 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:
- 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 monitor.
- 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.

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 evaporation.

New/Save: New molecular geometries can be input and output at any stage. These use our standard ASCII *.geo format. (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 rotate.

signal 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.