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The SIMION Manual (Partial Copy)

Each copy of the SIMION software comes with a ~450 page manual on core topics plus supplemental documentation on additional topics. In SIMION 2019 and above, the manual is in electronic format, and earlier versions (8.1 and prior) were in print format. The following is an abridged copy of that manual (first two chapters) with table of contents and online search.


This following does a full-text search on the SIMION manual:


Summary Table of Contents

  • Contents / Abstract / Acknowledgements
  • Chapter One - SIMION Overview
  • Chapter Two - SIMION Basics (this sample chapter is a good starting point, giving a short overview of SIMION)
  • Chapter Three - Roadmap and Directions
  • Chapter Four - Creating, Loading, and Saving Potential Arrays
  • Chapter Five - Modifying Potential Array Geometries
  • Chapter Six - Refining and Fast Adjusting Potential Arrays
  • Chapter Seven - Creating a Workbench
  • Chapter Eight - Flying Particles
  • Chapter Nine - Advanced Strategies and Further Directions
  • Appendix A - Hardware and Software Requirements
  • Appendix B - Installing/Troubleshooting SIMION
  • Appendix C - SIMION's GUI
  • Appendix D - Sample Runs
  • Appendix E - Printing
  • Appendix F - Files used by SIMION
  • Appendix G - Text Editing
  • Appendix H - Computational Methods
  • Appendix I - Geometry Files (GEM Files)
  • Appendix J - CAD Import (STL Files)
  • Appendix K - FLY2 Particle Definition Format
  • Appendix L - User Programming
  • Appendix M - Command Line Interface
  • Appendix N - Changes between SIMION 8 and Earlier Versions
  • Appendix O - Index

Full Table of Contents

1.1 Introduction 1-1
1.2 The Simulation Trap 1-1
1.3 Computer Requirements/Installation 1-2
1.4 Note to Users of Prior SIMION Versions 1-2
1.5 Structure of this Manual 1-2
2 SIMION Basics 2-1
 2.1 Introduction 2-1
 2.2 Basic Ion Optics Concepts 2-2
 2.3 The Potential Array 2-7
 2.4 The Role of the Subdirectory in SIMION Projects 2-14
 2.5 The SIMION Main Menu 2-14
 2.6 Building Your First Simulation from Scratch 2-16
 2.7 Summary 2-30
3 Roadmap and Directions 3-1
 3.1 Introduction 3-1
 3.2 A Brief Contextual Overview of SIMION 3-1
 3.3 Potential Arrays and How to Create, Refine, and Use Them 3-7
 3.4 Housekeeping Issues 3-10
 3.5 File Compatibility With Earlier SIMION Versions 3-12
 3.6 SIMION Web Site 3-12
4 Creating, Loading, and Saving Potential Arrays 4-1
 4.1 Introduction 4-1
 4.2 Creating New Potential Arrays 4-4
 4.3 Saving Potential Array Files 4-7
 4.4 Loading Potential Array Files into PA Memory 4-8
5 Modifying Potential Array Geometries 5-1
 5.1 Introduction 5-1
 5.2 Changed Arrays are Flagged 5-1
 5.3 Accuracy of Potential Arrays 5-1
 5.4 Defining Solid or Grid Boundaries 5-4
 5.5 The Modify Function 5-6
 5.6 Geometry Files 5-33
 5.7 STL 3D CAD File 5-34
6 Refining and Fast Adjusting Potential Arrays 6-1
 6.1 Introduction 6-1
 6.2 Refining Potential Arrays 6-1
 6.3 Running Refine 6-7
 6.4 Fast Adjusting .PA and .PA0 Files 6-11
7 Creating a Workbench 7-1
 7.1 Introduction 7-1
 7.2 The Ion Optics Workbench 7-1
 7.3 Accessing SIMIONs View Function 7-12
 7.4 Controlling the View 7-14
 7.5 Controls on the Bottom 7-31
 7.6 The Eight View Control Tabs 7-31
8 Flying Particles 8-1
 8.1 Introduction 8-1
 8.2 Chapter Organization 8-1
 8.3 SIMIONs Unit System 8-1
 8.4 Defining the Ions to Fly 8-2
 8.5 Flying Ions 8-11
 8.6 Data Recording 8-19
 8.7 Flying Ions with User Programs 8-28
9 Advanced Strategies and Further Directions 9-1
 9.1 Introduction 9-1
 9.2 Doing more with Array Instances 9-1
 9.3 Workbench User Programs 9-5
 9.4 Geometry Files 9
A Hardware and Software Requirements A-1
 A.1 SIMION System Requirements A-1
B Installing/Troubleshooting SIMION B-1
 B.1 Installing/Troubleshooting SIMION B-1
 B.2 Installation of SIMION B-1
 B.3 General Troubleshooting B-3
 C.1 Introduction C-1
 C.2 Memory C-2
 C.3 Mouse and Keyboard Usage C-2
 C.4 Command bar C-2
 C.5 Help C-3
 C.6 File Memos C-3
 C.7 Printing, Clipboard, and Image Export C-3
 C.8 Multitasking with SIMION C-5
 C.9 GUI Objects C-5
 C.10 Viewing Windows C-6
 C.11 Adjusting User Preferences C-8
D Sample Runs D-1
 D.1 Launching SIMION for the First Time D-1
 D.2 Your Maiden Voyage With SIMION D-2
 D.3 Your Second Voyage With SIMION D-4
 D.4 Your Third Voyage With SIMION D-5
 D.5 Other Adventures D-7
E Printing E-1
 E.1 Introduction E-1
 E.2 Printer Output Destinations E-2
 E.3 Requesting a Printout E-4
 E.4 The Annotate and Print Screen E-4
 E.5 The Print Options Screen E-5
 E.6 Annotation Options E-14
 E.7 Exporting SIMION Graphics to Other Windows Programs E-22
F Files used by SIMION F-1
 F.1 Introduction F-1
 F.2 Files Found in Project Directories F-1
 F.3 Temporary Ion Trajectory Files F-5
 F.4 Important Files in the C:\FILES.GUI Subdirectory F-5
 F.5 The Format Used with SIMION .PA Files F-7
 F.6 Ion Definition File (.ION) Format F-8
G Text Editing G-1
 G.1 Introduction G-1
 G.2 Choosing a Text Editor G-1
 G.3 How to Designate an Alternate Text Editor G-2
 G.4 Setting Environment Variables G-2
H Computational Methods H-1
 H.1 Introduction H-1
 H.2 The Structure of the Potential array H-1
 H.3 The Relaxation Method H-2
 H.4 Over-Relaxation H-2
 H.5 Dynamically Self-Adjusting Over-Relaxation H-2
 H.6 Planar 2D Symmetry Refining Equations H-3
 H.7 Planar 3D Symmetry Refining Equations H-4
 H.8 Cylindrical 2D Symmetry Refining Equations H-4
 H.9 Skipped Point Refining H-4
 H.10 Array Doubling H-5
 H.11 Fast Voltage Adjustment Method H-6
 H.12 Trajectory Algorithms H-7
 H.13 Instance Selection Rules H-7
 H.14 SIMIONs Unit System H-7
 H.15 Electrostatic Force Computation H-8
 H.16 Electrostatic Forces Outside Instances H-9
 H.17 Magnetic Force Computation H-9
 H.18 Charge Repulsion Forces H-10
 H.19 Relativistic Corrections H-13
 H.20 Numerical Integration Method H-13
 H.21 Adjustable Time Steps H-13
 H.22 Edge Detection and Boundary Approach H-15
 H.23 How Trajectory Quality is Controlled H-16
 H.24 Pseudo-Random Number Generation H-16
I Geometry Files (GEM Files) I-1
 I.1 Introduction I-1
 I.2 Geometry Language Rules I-3
 I.3 Geometry Instructions I-10
 I.4 Developing, Testing, and Using Geometry Files I-29
J CAD Import (STL Files) J-1
 J.1 Introduction J-1
K FLY2 Particle Definition Format K-1
 K.1 Overview K-1
 K.2 Basic Syntax K-2
 K.3 Multiple Particles per Beam K-3
 K.4 Sequences K-4
 K.5 Distributions K-7
 K.6 Pupils K-11
 K.7 Additional Examples K-12
 K.8 Programming (Advanced) K-13
 K.9 Reference K-13
L User Programming L-1
 L.1 Introduction L-1
 L.2 Workbench User Programs L-12
 L.3 User Programming in Lua L-28
 L.4 Built-in Function Reference L-33
 L.5 User Programming in PRG (Old SIMION 7 Language) L-42
 L.6 Compatibility Notes L-67
M Command Line Interface M-1
 M.1 Basic Usage M-1
 M.2 SIMION Return Value M-1
 M.3 SIMION Options M-1
 M.4 SIMION Commands M-3
 M.5 SIMION Environment Variables M-8
N Changes between SIMION 8 and Earlier Versions N-1
 N.1 Differences Between SIMION 8.1 and 8.0 N-1
 N.2 Differences Between SIMION 8.0 and 7.0 N-1
 N.3 Differences Between SIMION 7.0 and 6.0 N-4
O Index O-1

Citations: The manual may be cited more or less like "D. Manura, D. Dahl. SIMION (R) 8.1 User Manual (Adaptas Solutions, LLC, Palmer, MA 01069, <>, January 2008)." depending on your required citation format. The manual is published by Adaptas Solutions, LLC, Palmer, MA 01069 and can be sourced through the web site. There have been five revisions of the SIMION 8.x manual, but the page numbers are identical plus or minus a page. If you prefer a direct URL for the manual alone, you may use this address: .

Errata: see the "SIMION 8 Manual - Changes and Errata" at the bottom of the change log.

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