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Note 45: Application of SIMION 6.0 to Filament Design for Mass Spectrometer Ionization Sources


By Steven Colby, Christopher W. Baker and John J. Manura


We investigate and analyze methods for improving the source geometry of a quadrupole mass spectrometer. As an example of the techniques employed, the effects of the orientation of a filament wire are explored. Emphasis is placed on the application of a software program, SIMION 3D, for the simulation of ion optics. In order for these results to be of general use, a generic ion source is modeled and the simulation process is described in sufficient detail so that the reader can use these methods on more specific examples.


The results reported in this poster were generated with the ion optics program, SIMION 3D v.6.0. This software was developed by David Dahl at the Idaho National Engineering Laboratory1. The latest version allows for greatly expanded simulation capabilities. These include larger array sizes (10 million points) and three dimensional modeling. The new capabilities of dynamic parameter variation, time varying potentials, and user programming are also employed in the work below.

Fig. 1 - Simulated quadrupole Mass Spectrometer


SIMION was used to model the quadrupole mass spectrometer shown in Figure 1. The simulation was divided into five sections. Each of these was designed and "refined" individually. (Refining is SIMION's method of calculating the potentials on non-electrode points.) The sections are then placed on an Ion Optics Bench (IOB) in their proper positions. The IOB feature allows items to be reused in different simulations. For example, parts of the quadrupole mass filter in this work were taken from an example that is included with the software. The IOB also permits the use of pieces whose symmetries differ. It is often helpful to incorporate elements of symmetry in the simulation, because they dramatically reduce the number of array points required. Likewise, sections of the simulation can have a different number of grid points per unit area. This allows for more accurate simulations where needed, as around the filament, without requiring such high precision everywhere else in the instrument.

The five sections (or instances) used in our experiments were a magnet, the source, the region between the source and the start of the quadrupoles, the quadrupoles, and the volume including the end of the quadrupoles and detector. The source instance consisted of a cylindrical piece (1.5 cm long X 1.0 cm dia.) with a flat plate at one end and a "repeller" on the side facing away from the quadrupoles. The plate included a 2 mm aperture to pass ions into the mass analyzer. Two planes of symmetry along the main axis of the instrument were used to divide the number of points in the calculation by a factor of four. A 2 x 3 mm slit was placed in the source to allow electrons from the filament to enter. (Because of the symmetry used, our simulation included two identical filaments and slits.) The filaments and slits were either oriented parallel or perpendicular to the principal axis of the instrument. The filament was placed 2 mm from the source cylinder. A magnetic instance was placed over the source, so that an appropriate magnetic field was generated between the two filaments. The instance between the source and the quadrupoles included an electrode with another 2 mm aperture. In many actual instruments, an einzel lens is placed in this area. The instance also incorporated a section of the quadrupoles in order to properly model the transition between these two regions of the instrument. The quadrupoles were modeled in two dimensions and then "extruded" along the axis of the instrument in the IOB. The final instance modeled the transition between the end of the quadrupoles and the detector.

Table 1. DC Potentials

Repeller +40.0V

Filament -70.0

Source cylinder 0.0

Lens after source 0.0

Quadrupole axis -8.0

Detector front -100.0

Detector Back -1500.0

Electrons and ions were simulated using SIMION's trajectory calculations. The DC potentials used are shown in Table 1. The potentials of the quadrupoles were varied at a radio frequency of 1.1 MHz in order to pass ions of 100 m/z. Control of the time dependent potentials was accomplished using SIMION's user programming interface. Each simulation was performed using groups of ions. Within each group electrons were assumed to leave a filament at 10 different points covering a linear range of 2 mm. At each of these points five electrons were generated with different angular trajectories. All electrons were given 0.25 eV of kinetic energy. Before the simulation of each group, a random number was generated for use in determining where electrons should turn into positive ions of 100 m/z. This was intended to simulate the electron impact ionization of neutral species. The simulation was repeated a large number of times in order to model the random generation of ions in the region between the two filaments.

Fig. 2 - Example Code Fragment For Simulated Ionization. (click here for full code, 4K)

 seg Other_Actions 
 rcl ionized ; check to see
if we have already ionized 
 x>0 exit ; if yes, don't
do it twice 
 rcl Ion_Px_gu ; Get ion position 
 rcl IonStart - ; subtract
the starting position 
 abs ; take absolute value 
 rcl Ionplace ; recall ionization
 x>y exit ; if we aren't there
yet we leave 
 mark ; otherwise: record
 rcl IonColor ; recall new
 sto Ion_Color ; change the
ions color 
 rcl IonCharge ; recall new
 sto Ion_Charge ; change the
ions charge 
 rcl IonMass ; recall new
 sto Ion_Mass ; change the
ions mass 
 rand 2 * 1 - ; random # between
1 and -1 
 rcl PercentEnergyVar * ;
multiply by the energy variation 
 rcl IonEnergy * ; multiply
by the average energy 
 rcl IonEnergy + ; add to
the average energy 
 ; to get new energy 
 rcl ion_mass ; recall ion
 x><y ; swap x and y 
 >spd ; convert to speed 
 sto speed ; hold in temp
 ; converted new energy to
 360 rand * ; get a random
el angle  
180 rand * ; get a random
az angle 
 rcl speed ; 
 ; now x= speed, y=az, z=el 
 >r3d ; convert to rectangular
3d coordinates 
 sto Ion_Vx_mm ; change the
ions velocity 
 sto Ion_Vy_mm 
 sto Ion_Vz_mm 
 1 sto Ionized ; change boolean
(we have done it) 
 exit ; done 

The conversion of electrons to ions was handled using SIMION's user programming interface. An example of the code used is shown in Figure 2. This fragment illustrates the use of a previously calculated random distance (ionposit) to determine where ionization should occur. Commands are then executed to change the mass, charge, and display color of the particle. Further code then gives the new ion a new kinetic energy and direction. (Ions started with thermal energy +/- 10%.) The section of code shown is executed once every time SIMION calculates a step in the trajectory simulation. The programming language used is designed to compile directly to assembly code resulting in very fast calculations. The complete source code for all user programs used in this simulation is available on the internet2.

Fig. 3 - Sample Simulations (In A and B, Only the source region is shown. Views are along the y-axis).

Fig 3aA

Fig 3bB



Figure 3 shows the simulation of three ion groups. These are intended to show examples of the possible fates of the simulated ions. In the first case (A), ions are formed too close to the electron slit. They are, therefore, drawn back toward the filament. This was the most common path for ions to take. In the second case, ions are generated closer to the center of the source and, therefore, are eliminated by striking the front and side walls. In the final case, ions are formed very close to the center of the source region. Some of these ions reach the detector. However, the randomly directed initial thermal kinetic energy is sufficient to prevent most of these ions from reaching the detector.

Fig. 4 - Location Of ion Impacts For Parallel and Perpendicular Filaments Figure 4

The probabilities of ion elimination occurring in each region of the instrument are summarized in Figure 4. This figure shows the results obtained when the filament was oriented parallel or perpendicular to the principal axis of the instrument. In either case, over 64% of the ions are lost through the filament opening. This is due to both the magnetic and electric fields of the source. The fraction of ions lost through this route is a function of the size and depth of the rectangular opening used to admit electrons into the source. A plot of potential energy contours of the source is shown in Figure 5. Ions are accelerated in directions perpendicular to the red lines shown. It is clear that only in the center region are ions directed towards the exit aperture. Those ions that do move towards the exit are accelerated into the plane of Figure 5 (xz plane) by the magnetic field. As a result, the ions that strike the front plate of the source do so on average below the level of the principal instrument axis. As was shown in Figure 4, those ions that do not travel towards the filament still have only a small chance of reaching the detector. The parallel orientation of the filament decreases the probability of ion detection by approximately 50%. This result was unexpected since a greater fraction of the electrons from the parallel filament pass close to the center axis of the instrument.

Fig. 5 - Potential energy Contours Of the Source Region

Figure 5

Fig. 6 - Screen Capture Showing the Ion Optics Bench and Parameter Variation Menu

Figure 6

Using SIMION's data recording menu, it is possible to determine the starting positions of the ions that reach the detector. This enables us to determine the zone in which detectable ions may be generated. The volumes found were approximately 0.15 x 1.7 x 1.4 mm for the perpendicular filament and 2.2 x 0.11 x 1.2 mm for the parallel filament orientation. This volume (~0.3 mm3) is quite small relative to the volume of the source.

Limitations Of the Simulation

Our goal in this presentation has been to demonstrate methods for instrument analysis and design rather than to characterize a specific instrument. However, as with any computer modeling, there are limitations to these simulations that must be kept in mind when analyzing the results. For example, the user program allows electrons to generate ions before they reach a significant kinetic energy. The system has also not been optimized so the potentials listed in Table 1 are not likely to be the best for ion collection in this system. Likewise, the specific geometry used was not based on an actual instrument or an optimal design. We have also not included the einzel lens found in many commercial instruments. This will certainly have a dramatic influence on the collection efficiency of ions.

Current Work

Our current work involves changes in the user program so that ions will only be generated in a volume slightly larger than the ion acceptance zone. This will dramatically improve the speed of simulations. We will then add an einzel lens before the quadrupoles and attempt to optimize instrument conditions. Optimization will be accomplished using SIMION's variable adjust utility. This option permits the user to change simulation parameters at any point during the trajectory calculations. A sample menu is shown in Figure 6. (This figure shows part of the IOB graphical user interface. Part of the instrument shown has been removed to reveal the interior.) In this example, variables, including percent tune, m/z, and lens potential, can be changed by typing in the appropriate values. The flight of ions is affected immediately.


We have demonstrated the use of SIMION 3D in modeling the source region of a quadrupole mass spectrometer. The software is an excellent tool for the investigation of ion optics within the instrument. We believe that the work of David Dahl will contribute to a large variety of applications.


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