Focused Ion Beam Molecular Dynamics

3-D Molecular Dynamics Simulation of a Gallium FIB on Silicon

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Version 0.1.0-beta - published on 24 Apr 2018

doi:10.4231/D3Z02ZB6J cite this

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See the  FIBMD GitHUB Homepage for a detailed description of tool output and a tutorial on using the provided Ovito template for visualization. 

This is a tool used for modeling the effects of a focused ion beam against a silicon film, including sputtering, crater formation, and nanopore formation. The user adjustable parameters are focused on what would be adjusted in an experimental setting, such as beam energy, angle of incidence, spot size (FWHM), current, and silicon temperature. Real-time output of the simulation is available through periodically reported simulated time and system temperature. The py3DMol jupyter package is used to provide a built in 3D viewer of the system.

Simulation Details

In this tool, the Stillinger-Weber atomic potential is used for silicon-silicon interactions, while a Molière atomic potential is used for silicon-gallium and gallium-gallium interactions. The silicon FIB target is presented as a film with the outermost layer of atoms in the x-y planes fixed in position and the top and bottom 'z' surfaces exposed to vacuum. FIB ions will be incident to the top 'z' surface, and as atoms are sputtered from either the top or bottom of the film, they are relocated into fixed planes above the target for convenient counting. 

Descriptions of each input parameter are provided in the 'Input Descriptions' tab on the left menu:

The simulation begins with an initialization of the silicon temperature through a Berendsen thermostat applied uniformly to the domain. Once system temperature has approached to within 30 K of the target, a gallium ion is randomly positioned above the surface according to the assigned FWHM. It is then assigned kinetic energy equivalent to the beam energy and a velocity vector according to the angle of incidence. As the ion deposits energy to the target, a Berendsen thermostat with a time constant of 0.1 ps is applied to silicon atoms within 1.5 nm of the clamped edges to model conduction out of the film. To aid in resolution of the fast moving ions, one of two timestep values is chosen according to the atom with the highest kinetic energy in the system: 0.02 fs for energies above 600 eV and 0.2 fs for energies below 600 eV.

Tool Output

There are 3 forms of output available in this tool. 

Log Files

After hitting the 'run' button, an output log documenting the progress of the simulation is provided under the 'output' tab. This includes the current time of the simulation, some initialization parameters, temperature of the system, and a notification for when the time step size changes. The contents within this output window are available for download by clicking the 'out.log' link under 'File Download Links' within the tool. See the GitHub page for a more detailed explanation of these contents.


Visualization is provided through two methods: in-tool through py3DMol and out of tool through an xyz file. In-tool visualization is accessed by clicking the 'Update Viewer' button, which will refresh the viewing window with the atomic positions of the most recent output step. The contents of this window may be rotated by click-dragging, zoomed with the scroll wheel or two-touch up/down with supported track pads, and translated with control + click-drag. 

A more comprehensive output file containing atomic positions and kinetic energies at multiple timesteps is provided through the 'data/' link under 'File Download Links'. This follows a typical .xyz file format, with a row for each atom and columns corresponding to the x, y, z atomic coordinates, atomic type, and kinetic energy in eV. This file may be used for much more detailed analysis using a program like Ovito. A suggested Ovito program state for viewing this file is provided by the 'data/OvitoTemplate.ovito' link under 'File Download Links'. See the GitHub FIBMD page for a tutorial on using this.

GitHub FIBMD Homepage

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Joshua M. Stout -- Mechanical Science and Engineering at the University of Illinois Urbana-Champaign

Jonathan B. Freund --Mechanical Science and Engineering & Aerospace Engineering at the University of Illinois Urbana-Champaign

Harley T. Johnson -- Mechanical Science and Engineering at the University of Illinois Urbana-Champaign


Frank H. Stillinger and Thomas A. Weber,  Computer simulation of local order in condensed phases of silicon, Phys. Rev. B 31, 5262 (1984).

Moliere G, Theory of scattering of fast charged particles. I, single scattering in a screened Coulomb field, Z. Naturf. A 2, 133 (1947).


K. Das, H. T. Johnson, and J. B. Freund, Atomic-scale thermocapillary flow in focused ion beam milling, Physics of Fluids 27, 052003 (2015).

K. Das, J. B. Freund, and H. T. Johnson, Mechanisms of material removal and mass transport in focused ion beam nanopore formation, Journal of Applied Physics 117, 085304 (2015).

K. Das, J. B. Freund, and H. T. Johnson, A fib induced boiling mechanism for rapid nanopore formation, Nanotechnology 25, 035303 (2014).

M. Z. Hossain, J. B. Freund, and H. T. Johnson, Ion impact energy distribution and sputtering of Si and Ge, Journal of Applied Physics 111, 103513 (2012).

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N. Kalyanasundaram, J. B. Freund, and H. T. Johnson, A multiscale crater function model for ion-induced pattern formation in silicon, Journal of Physics: Condensed Matter 21, 224018 (2009).

M. Ghazisaeidi, J. B. Freund, and H. T. Johnson, Statistical characterization of surface defects created by Ar ion bombardment of crystalline silicon, Journal of Applied Physics 104, 054304 (2008).

M. Z. Hossain, J. B. Freund, and H. T. Johnson, Differential sputter yields in Si1-xGex, Journal of Applied Physics 103, 073508 (2008).

N. Kalyanasundaram, M. Ghazisaeidi, J. B. Freund, and H. T. Johnson, Single impact crater functions for ion bombardment of silicon, Applied Physics Letters 92, 131909 (2008).

N. Kalyanasundaram, M. Wood, J. B. Freund, and H. Johnson, Stress evolution to steady state in ion bombardment of silicon, Mechanics Research Communications 35, Multiscale Modeling, 50-56 (2008).

N. Kalyanasundaram, M. Moore, J. B. Freund, and H. T. Johnson, Stress evolution due to medium-energy ion bombardment of silicon, Acta Materialia 54, 483-491 (2006).

N Kalyanasundaram, J. B. Freund, and H. T. Johnson, Atomistic Determination of Continuum Mechanical Properties of Ion-Bombarded Silicon, Journal of Engineering Materials and Technology 127, 457-461 (2005).

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Cite this work

Researchers should cite this work as follows:

  • Joshua Michael Stout (2018), "Focused Ion Beam Molecular Dynamics," (DOI: 10.4231/D3Z02ZB6J).

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