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List of Figures

  1. Screenshot of the eFFview visualizer, playing back a dynamics simulation of a diamondoid nanoparticle being etched by a dense hydrogen plasma.
  2. Hydrogen atom, showing the optimized electron on top of the proton.
  3. Optimized hydrogen molecule, showing bond-centered electrons.
  4. Breaking the $ \mathrm {H_{2}}$ bond causes the electron pair to separate.
  5. Ground state potential energy surface of $ \mathrm {H_{2}}$ dissociation.
  6. Methane has electron pairs in tetrahedral positions.
  7. Dissociation of methane following removal of a CH valence electron.
  8. Starting from an .xyz file containing nuclear coordinates, we use xyz2cfg to guess the initial electron positions and sizes, then run eFF to get the final optimized .eff geometry.
  9. eFF predicted Auger fragmentation of core-ionized adamantane at 0 K, showing snapshots at 0, 5, and 35 fs.
  10. Electron dynamics during the Auger process at 300 K. The red valence electron fills the core hole after 7 fs, the the green electron is ejected after 12 fs, and the blue and purple electrons remain excited but bound over 50 fs.
  11. Building a minimized hydrogen box: (a) h2bulk_min, minimized from starting lattice; (b) h2bulk_anneal, after simulated annealing NVT dynamics from 3000 K to 0 K; (c) h2bulk_min2, reminimized from the last point of the simulated annealing run.
  12. Snapshot from the 15,300 K dynamics run after 2 picoseconds, showing electrons at full size and scaled by a factor of 0.1. The electrons are larger than at 0 K, and are shifted away from the bond midpoint, increasing the Pauli repulsion between the molecules and increasing the overall pressure.
  13. Equation of state for liquid deuterium at $ r_{s}$ = 2 bohr with varying temperature. eFF is applicable and consistent with the best theory over the entire temperature range shown.
  14. Bonding in periodic lithium solid.
  15. Nonperiodic lithium, representative local minima with energies per atom given relative to periodic structure.
  16. Expanding the lithium bulk structure twice in every dimension and reoptimizing causes a dendritic lithium structure to form, shown here as a stereo view.
  17. Electrons in dendritic lithium, showing interstitial electrons occupying spaces in between linear chains, two-dimensional meshes, and three-dimensional bulk-like structures. Electrons are scaled to 0.2 times their actual size.
  18. By default, eFF overlays nuclei and electrons together, but pressing n or e causes the nuclei or electrons to be displayed alone.
  19. Electrons above a threshold size are displayed separately as ionized electrons.
  20. Periodic boundary display. The left side shows how 1D, 2D, and 3D periodic boundary planes are depicted in eFF. The right side shows an example of a 3D periodic system, etching of a diamond film by a dense hydrogen plasma.
  21. Mouse controls in eFFview: dragging with the left button rotates, dragging with the right button translates, and rolling the scroll wheel up and down zooms in and out.
  22. The timer bar appears when the mouse is in the upper part of the screen, and controls the animation of multi-frame .eff files.
  23. Example eFFview keystrokes applied to a frame from a core-ionized diamondoid trajectory. By changing electron sizes, separating spin pairs, and adding velocity vectors, more subtle details are the Auger process are made visible.
  24. Different levels of detail are selected using the keys F1 (lowest) through F5 (highest); or Shift-1 through Shift-5, if the function keys are disabled. Lower levels of detail are faster to render.
  25. Hydrogen box generated with $ n_{x} = n_{y} = n_{z} = 2$, $ r_{s}$ = 2 bohr.
  26. Uniform electron gas generated with $ n_{x} = n_{y} = n_{z} = 2$, $ r_{s}$ = 1 bohr, electrons scaled by 0.2.
  27. Lithium solid generated with $ n_{x} = n_{y} = n_{z} = 2$, electrons scaled by 0.2.
  28. Lithium hydride solid generated with $ n_{x} = n_{y} = n_{z} = 2$, electrons scaled by 0.2.
  29. Beryllium solid generated with $ n_{x} = n_{y} = n_{z} = 2$, electrons scaled by 0.2.
  30. Diamond generated with $ n_{x} = n_{y} = n_{z} = 2$, electrons scaled by 0.2.

Julius 2008-04-29