SIMION 2024 Supplemental Documentation¶
This “Supplementary Documentation” covers SIMION topics in addition to those in the SIMION User Manual. Content is organized in a wiki-like format. Note: this online version of the documentation is abridged from the full documentation included in SIMION. See the “Help > Browse Documentation” menu in SIMION for the full version of this documentation.
Starting points
For new users
SIMION® - What is SIMION?
SIMION brochures: six-page PDF brochure | two-page PDF flyer - provide general background
Examples (view 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
For users of older versions of SIMION, what changed:
SIMION Advances - all major changes
SIMION® 8.2 - changes from 8.1 to 8.2 (2019)
SIMION® 8.1 - changes from 8.0 to 8.1
SIMION® 8.0 - changes from 7.0 to 8.0
SIMION Software Change Log - very detailed list of differences between SIMION versions
Major resources:
SIMION Info - latest online copy of a subset of this documentations
Installation
SIMION® Quick Start Notes - start here
Background Topics
Accuracy - warnings about simulations
Light Optics - how does electron optics compare to light optics
practical matters
Basic Physics
Chapter 2 “SIMION Basics” in SIMION User Manual
Electric fields
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
Potential Array | Potential Array File Types (Comparison) | Writing PA0 Files
Defining geometries
Chapter 4 “Creating, Loading, and Saving Potential Arrays” of SIMION User Manual
Modify screen - Chapter 5. Modify in SIMION User Manual
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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 | Converting from 3D CAD (STL) Format to PA Format
Refining geometries
Chapter 6 “Refining and Fast Adjusting Potential Arrays” in SIMION User Manual
Electrode Surface Enhancement / Fractional Grid Units - [8.1]
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
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SIMION Example: contour - field plotting library
Defining particles
Chapter 8.4 “Defining the Ions to Fly” in SIMION User Manual
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
Data recording, Analysis, Postprocessing
Chapter 8.6 “Data Recording”
Test Plane | SIMION Example: test_plane | SIMION Example: test_sphere
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
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SIMION Example: tune - optimization of voltages
SIMION Example: geometry_optimization - optimization of geometries
User Programming
Appendix L “User Programming” in SIMION User Manual
Various areas involving 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 the book Programming in Lua, 2nd Ed.
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
Performance Topics
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 - Assemble SIMION geometry files and analyze SIMION data
Matlab / Octave
Fluent, ANSYS, COMSOL, Computational Fluid Dynamics (CFD)
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.
Space Charge
The mathematical equation, Poisson Equation
System Components/Types
Focusing/optics
Energy analyzers/electrostatic deflectors
Cylindrical Mirror Analyzer (CMA) - cylindrical mirror analyzer
Parallel Plate Analyzer - parallel plate analyzer
Hemispherical Deflection Analyzer (HDA) - hemispherical deflection analyzer
Other application
Magnetic
More Advanced Physics/Math
Previous Courses
The ASMS beginner course (ASMS Short Course on SIMION) explored the examples. The advanced course explored programming and GEM files especially. See ASMS Courses. Advanced course notes: ASMS Course Notes.
The 2013 CPOTS course CPOTS2013 outline covered many things SIMION and non-SIMION.
Hi-Res isotopic ration MS course - HIPIRMS course