SIMION Learning/Training

This is a proposed outline of topics to study when learning SIMION.

• Starting points
  • For new users
    • SIMION brochures: six-page PDF brochure 8.0 | two-page PDF flyer 8.1 - provide general background
    • Screenshots
    • Read the first two chapters of the SIMION manual, available online. SIMION User Manual
    • A Tour of the SIMION Demo - try out the demo version and follow along
    • Screencasts
  • For users of older versions of SIMION, what changed:
    • SIMION Advances - all major changes
    • SIMION® 8.1 - changes from 8.0 to 8.1
    • SIMION® 8.0 - changes from 7.0 to 8.0
    • SIMION® Roadmap (8.2 and Beyond)
    • SIMION Software Change Log - very detailed list of differences between SIMION versions
  • Major resources:
    • Frequently Asked Questions (FAQ)
    • SIMION User Manual
    • SIMION Info - latest online copy of a subset of this documentations
  • Installation
    • SIMION® Quick Start Notes - start here
    • License for SIMION
    • System Requirements | Linux | Mac OS
• Background Topics
  • Accuracy - warnings about simulations
  • Light Optics - how does electron optics compare to light optics
  • practical matters
    • Electric Arc
    • Ground Chamber
• Basic Physics
  • Chapter 2. SIMION Basics in SIMION User Manual
  • Lorentz Force Law
  • Electric fields
    • Coulomb’s Law | Gauss’s Law
    • Laplace Equation | Poisson Equation
    • Dirichlet Boundary Conditions | Neumann Boundary Condition
    • First Uniqueness Theorem
    • Maxwell Equations
    • Earnshaw’s Theorem
    • Pseudopotential
• Bird’s Eye View / Files Composing Simulations
  • A Tour of the SIMION Demo - try out the demo version and follow along
  • Chapter 2.6 Building your First Simulation from Scratch in SIMION User Manual
  • Chapter 3 Roadmap and Directions in SIMION User Manual
  • ION File / FLY File / FLY2 File
  • GEM Geometry File
  • Potential Array | Potential Array File Types (Comparison) | Writing PA0 Files
  • Workbench .IOB File
  • Lua
• Defining geometries
  • Chapter 4 of SIMION User Manual
  • Geometry Input Methods
  • Potential Array | Potential Array File Types (Comparison)
  • Modify screen - Chapter 5. Modify in SIMION User Manual
  • GEM Geometry File
    • Read appendix in SIMION User Manual on GEM files.
    • View example GEM files SIMION Example: geometry
    • Explore new GEM2 syntax GEM Geometry File (advanced)
  • Manipulating SIMION Potential Arrays Programmatically (advanced)
  • SL Tools | SL Tools Tutorial
• Refining geometries
  • Chapter 6. Refining in SIMION User Manual
  • Refine
  • Anisotropically Scaled Grid Cells in SIMION [8.1]
  • Electrode Surface Enhancement / Fractional Grid Units - [8.1]
  • PA Antimirroring
  • Additional Fast Proportional Scaling Solutions - [8.0.3]
  • Multiple PAs
  • Poisson Solver in SIMION
  • Magnetic Potential
• Putting PA’s in a Workbench
  • Chapter 7.1-7.2 The Ion’s Optics Workbench of the SIMION User Manual
  • Visualization and field plotting
    • Chapter 7.3. Accessing SIMION’s View Function
    • Chapter 7.4. Controlling the View
    • Chapter 7.5. Controls on the Bottom
    • Chapter 7.6. The Eight View Control Tabs
    • Plotting Fields
      • SIMION Example: contour - field plotting library
• Defining particles
  • Chapter 8.4 Defining the Ions to Fly in SIMION User Manual
  • Particle Initial Conditions
  • ION File
  • FLY File
  • FLY2 File
  • Monte Carlo Method
• Calculating Particle Trajectories (Fly’m)
  • Chapter 8.5 Flying Ions in SIMION User Manual
  • Chapter 8.6 Flying Ions with User Programs in SIMION User Manual
  • Appendix H Computational Methods in SIMION User Manual
  • Particle Trajectory Calculations
  • Time Step Size
• Data recording, Analysis, Postprocessing
  • Chapter 8.6 Data Recording
  • Trajectory Data Recording
  • Markers
  • Emittance
  • Test Plane | SIMION Example: test_plane | SIMION Example: test_sphere
  • SIMION Example: count_transmission
  • SIMION Example: lens_properties
    • beam_minmax_diameter, confusion_disc - beam measurement
    • particle_distance_traveled
    • surface_plot
    • pq, snell
    • zoom_afocal, zoom_lens_curve - aberration coefficients
  • (Mass) Spectrum
  • Optimization
    • SIMION Example: tune - optimization of voltages
    • SIMION Example: geometry_optimization - optimization of geometries
  • Movie Files
  • Data Import/Export
  • Importing and Exporting Field and Potential Array Data
  • Engineering Tolerance
• User Programming
  • Appendix L User Programming in SIMION User Manual
  • Cookbook of SIMION User Programming Examples.
  • Questions: What level of experience do you have programming (in Lua or languages other than Lua)? What techniques the need that require user programming? Many things in SIMION are helped by user programming.
  • Preprocessing (GEM/FLY2)
  • Postprocessing (data recording/excel/gnuplot)
  • Fly’m itself (time dependent voltages, collision models, test planes, etc.)
  • For an intro to Lua (separate from SIMION), there’s Perhaps the book Programming in Lua, 2nd Ed and perhaps other resources.
  • Time-Dependent Field - programming different types of wave forms.
  • Reference material
    • Programming API for SIMION - Lua, C++, Perl, and Python programming libraries reference. In particular,
      • Lua Variables - tips on variable visibility and scope
      • simion.pas - manipulate PA’s programmatically
      • Calling External Programs
      • Command Line Interface
• Performance Topics
  • Accuracy
  • Time Step Size
  • Calculation Time
  • RAM and Memory
  • Multiple PAs
  • 64-bit CPU support
  • Max Electrodes
  • Scaling a PA
  • Multiple PAs
  • Multicore CPU support
  • Graphics Card
  • SIMION on Amazon EC2
  • Intel Xeon Phi
  • Running SIMION on HPC Clusters
  • Kinetic Energy Error
• Working with Other Programs
  • Editing SIMION Text Files - SciTE, VIM, and Emacs text editors.
  • Excel, gnuplot, Origin
  • Using Poisson Superfish with SIMION, Using QuickField with SIMION
  • Virtual Device - Easily assemble SIMION geometry files and analyze SIMION data
  • Matlab / Octave
  • Fluent, ANSYS, COMSOL, Computational Fluid Dynamics (CFD)
  • CAD
• Additional physics
  • Collision models Ion-Gas Collisions
    • The main ones are HS1, SDS, and Drag. SDS is based on Drag but Drag was recently extended to do more of that SDS does (diffusion) from more first principles.
    • Computational Fluid Dynamics (CFD) importing gas flows from various CFD programs (latest field_array example). Computational Fluid Dynamics (CFD) Some of this is outside SIMION scope and no so much my expertise.
    • Mobility Equation
  • Space Charge
    • The mathematical equation, Poisson Equation
    • Space Charge
    • Poisson Solver in SIMION
  • Magnets
    • Biot-Savart Law
    • Permeability
    • Magnetic Potential
    • Magnetic Sector
    • SIMION Example: mfield_adjust | SIMION Example: icr | SIMION Example: field | SIMION Example: solenoid | SIMION Example: helmholtz_coil | SIMION Example: magnetic_potential | SIMION Example: magnetic_sector
  • Dielectrics, Resistive Electrodes
• System Components/Types
  • Grid
  • Lens
  • Cylindrical Mirror Analyzer (CMA) - cylindrical mirror analyzer
  • Parallel Plate Analyzer - parallel plate analyzer
  • Hemispherical Deflection Analyzer (HDA) - hemispherical deflection analyzer
  • Magnetic Sector
  • Ion Trap [ Penning Trap | Paul Trap | Electrostatic Trap ]
  • Quadrupole Mass Filter
  • Quadrupole Deflector
  • Cyclotron
  • Particle Guns
  • Helmholtz Coil
  • Velocity Map Imaging (VMI)
  • Detectors
  • Ion Funnels
  • Mass Spectrometry
• More Advanced Physics/Math
  • Pseudopotential
  • Mathieu Equation and Stability Diagram
  • Transfer Matrix
  • Paraxial Approximation
  • Emittance
  • Thermionic Cathode
  • Fast Fourier Transform (FFT)

Previous Courses

• Very old course outline: ASMS Course Notes (beginner and advanced courses). ASMS Courses As seen user programming and GEM files were big parts. The beginner course notes explored the examples.
• The 2013 CPOTS course CPOTS2013 outline covered many things SIMION and non-SIMION.
• Hi-Res isotopic ration MS course - HIPIRMS course

TO DO

• Perhaps add a “theory” page better outlining the lay of the land on gas flow physics).