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Note 53: SIMION 3D v6.0 Ion Optics Simulation Software

By Steven M. Colby and John J. Manura

(This poster was presented at the New Product Section at AVS'96)


What is SIMION?

The SIMION software is the industry standard for the modeling of electron and ion optics. The new release, SIMION 3D v6.0, represents a breakthrough in the capabilities of computer simulation. It's expanded versatility and power allow the simulation of highly complex systems, interactive parameter manipulation with immediate feedback, and multi-ion trajectory visualization (Manual Cover figure, file: avs96f0). The original SIMION was an electrostatic lens analysis and design program developed by D. C. McGilvery at Latrobe University, Bundoora Victoria, Australia, 1977. SIMION v6.0 for the PC, developed at the Idaho National Engineering Laboratory, shares little more than its name with the original McGilvery version. INEL's fifth major SIMION release, version 6.0, represents a quantum improvement over previous versions. This C based program can model complex problems using an ion optics workbench that can hold up to 20 2D and/or 3D electrostatic/magnetic potential arrays. Arrays can have up to 10,000,000 points. SIMION 3D's 32 bit virtual Graphics User Interface provides a highly interactive advanced user environment. All potential arrays are visualized as 3D objects that the user can cut away to inspect ion trajectories and potential energy surfaces. User programs have been greatly extended in versatility and power. A new geometry file option supports the definition of highly complex array geometry. Extensive algorithm modifications have dramatically improved this version's computational speed and accuracy.

New Features

Figure 1

Figure 1. Simulation of a Reflectron TOFMS

The Ion Optics Bench:

The new version includes many new features. Simulation takes place on an "Ion Optics Bench" (IOB) that can hold up to 200 individual 3D electrostatic or magnetic arrays. This allows sections of an instrument to be modeled and then positioned and sized individually. Each array can have a different symmetry or point resolution. In this way, complex systems or even entire instruments can be modeled. 3D views (with 32 bit graphics) can be cut open and rotated to observe interior structures and the paths of ions trajectories within objects, Figure 1. The source, reflector and detector are each individual elements that can be positioned within the IOB. The Source and Reflector are simulated with a higher resolution than the detector. The Red and Blue lines represent the trajectories ions of with different masses. For each mass two different initial kinetic energies are simulated.

Figure 2. Cutaway of a complicated TOF-SIMS source designed by David Dahl

The reflector has been cut open in order to show the paths of ions ionside. Defining Geometrys: Each array is defined using powerful geometry files or with SIMION's Modify function. The Modify function uses a new 32 bit graphical user interface. The ability to generate complex three dimensional shapes surpasses that found in some 3D CAD programs. Features include the ability to perform logical operations on shapes (subtract a triangle from a cylinder), the definition of hyperbolas and parabolas, and the ability to define elements whose magnetic strength or electrical potential vary with position, Figure 2. This geometry was defined using a "geometry file" that contained as series of instructions (similar in structure to C language functions) that defined the shape and properties of elements in the potential array.

Figure 3. Simulation of a FTMS Ion Trap

Time Dependent Fields:

Array potentials can now be changed so rapidly that it is possible to simulate time dependent electrodes, as those found in an ion trap or quadrupole mass spectrometer. Fluctuating potential energy surfaces can even be observed. It is highly illustrative to observe ions "rolling down the hill" during simulations. Rapid changes in electrode potentials allow for the quick optimization of instrument conditions. For example, the user can change the voltage on a lens element and immediately see how ion trajectories are affected. In Figure, 3 the circular motion of ions in an FTS ion trap is shown. At each phase of the simulation (ion introduction, stimulation, and detection), ions are made to change color so that the effects can be clearly observed. This example is particularly useful for demonstrating the effects of space charge.

Ion Simulation:

Ions can be flown singly or in groups, displayed as lines or flying dots, and automatically be re-flown to provide movie effects when needed. New data recording features allow the user to select the parameters to be recorded and to set a variety of conditions to trigger the recording function.

Figure 4

Figure 4. Screen Capture of the Ion Definition Menu

These conditions include time, position, and the crossing of boundaries. A new Data Recording menu allows the user to specify specific parameters to record and the format in which the information is saved. The Ion Deflection Menu shown in Figure 4 is a good example of the large range options available to the user in many parts of the program. In this case, we are shown the definition of the 4th of 10 groups of ions. This group has 20 members who differ by their initial kinetic energy. The record button on the lower left opens an equally diverse set of options.

Space Charge:

Charge repulsion can be simulated in three different ways. Coulombic repulsion can be simulated by either dividing the total charge among the ions defined or by indicating that each simulated ion should represent a specific number of actual ions. The repulsion of a beam of ions can be simulated by defining a "beam current" from which ions will be repelled, Figure 5. The view is of the potential energy (z-axis) along a cross-section (z & y-axis) of a 3D geometry. The simulation includes the effects of space charge repulsion and also of collisional dampening. The dampening has the effect of slowing the ions down. As a result, they tend to follow the electrostatic field lines and collide with one of the electrodes.

Figure 5. Simulation of Ions Passing Through a Simple Lens System

User Programs

A new user program interface and debugger simplifies the process of defining user programs. These programs may be used to control time dependent potentials. They can also be employed to simulate a variety of effects including the random generation or metastable fragmentation of ions. User programs can also be used to optimize conditions in an instrument. This is done through the recording of ion trajectories and the feedback of the results into an optimization routine. More advanced problems, like a Monte Carlo simulation of the scattering of ions at grids (2,3), are only possible with the new user programming features now available, Figure 6 shows the use of. random numbers to determine the starting conditions and "ionization" position in the simulation of a quadrupole. In this example, electrons (black) are generated at a filament (green) with a variety of initial conditions. Each group of electrons is then "converted" into ions (red) at a random time. For conversion, a user program gives the electrons a new charge and mass corresponding to a positive ion. The ions are given a random energy and direction from the appropriate distributions. By flying many groups of ions it was possible to map out the volume in which detected ions could be generated and study the efficiency of the ionization process.

Figure 6

Figure 6. Monte Carlo Simulation of Electron Impact Ionization In the Source of a Quadrupole Mass Spectrometer

Teaching Ion Optics Using SIMION:

A new "Student Lab Guide", written by Kennith Busch will be released this Fall. This Guide will include hands-on exercises directed toward the teaching of ion optics with SIMION 3D. Examples will be of interest to both chemists and physicists. These tools will be designed to teach both the basic principles of ion optics engineering as well as the function of specific instruments such as mass spectrometers and ion traps.


SIMION 3D 6.0 is intended to provide direct and highly interactive methods for simulating a wide variety of general ion optics problems. The program balances ease-of-use, speed, and accuracy to enable it to support many real-world applications. The result is a program that can model a wide range of problems including: Ion source and detector optics, time-of-flight instruments, and ion traps. For example, it has successfully simulated the Phi-Evans TOF instrument using voltages that are within a few percent of the as-built instrument. Even if you just use it as a scoping tool (saving the hard-to-use heavy artillery for later), it can provide useful insights into your problems and perhaps help speed you toward to your final goal. This version of SIMION requires at a minimum: A 386 class PC with numerical coprocessor (or above - e.g. Pentium or P6 recommended), 8 megabytes of RAM (16 or more recommended for large projects), and at least 50 megabytes of free hard disk drive (or more). The program makes use of a 32 bit DOS virtual memory GUI (Graphics User Interface - developed by the author) that runs in, DOS, Windows (3.xx, 95, NT - Intel machines) and OS/2 (inc. Warp). The GUI video drivers support: VGA and SVGA (VESA BIOS - up to 1280x1024). GUI printer/plotter drivers support: PostScript (B/W and color), PCL5 (B/W and color), HPGL2, and HPGL.

Classes: Scientific Instrument Services, Inc. will be presenting to classes on the use of SIMON 3D software at PittCon97. For information on these or other courses that may be given in the future please contact SIS.

Additional details on SIMION 3D are available on our WEB site at


1. David A. Dahl 43ed ASMS Conference on Mass Spectrometry and Allied Topics, May 21-26 1995, Atlanta, Georgia, 717.

2. S. M. Colby; C. W. Baker; J. J. Manura Proc, 41st ASMS Conf. 1996. (Available at application note #47)

3. X. Tang, R. Beavis, W. Ens, F. Lafortune, B. Schueler and K. G. Standing, Int. J. Mass Spectrom. Ion Processes, 85 (1988) 43.

4. D. Ioanoviciu, Int. J. Mass Spectrom. Ion Processes, 131 (1994) 43.

5. T. Bergmann, T. P. Martin and H. Schaber, Rev. Sci. Instrum., 60 (1989) 347.

6. R. C. King, R. Goldschmidt and K. G. Owens 39th ASMS Conference on Mass Spectrometry and Allied Topics, May 19-24 1994, Nashville, TN, 717.

7. V.V. Laiko and A.F. Dodonov, Rapid Comm. Mass Spectrom. 8 (1994) 720-726