Home

Koltsov S. Manual Saint Petersburg 2006

1. G To add the tube to the new project user has to fill in following data 33 Working Origin s Working Origin s PA Scaling and Special Angle PA Offset gu Workbench Coords Orientation Orientation LU 0 000 A 0 000 1 00000nn gu Az 0 0000 x 5 Oyt 0 000 Y 0 000 x k DL k El gt D H nn KSE 0 000 z 0 000 Rt D Hun Here user has to set up coefficient mm gu as 0 1 This coefficient is exactly reverse to coefficient of resizing Now you have the tube with length 40 mm and the scale is 10 points per one millimeter 34 Chapter 1 5 Symmetry and mirror of 3D project Here we shall discuss the problem of symmetry As it was shown above there is a possibility to set up a type of symmetry and of mirror in SIMION Using of those parameters allows reducing total number of points per millimeter and reducing the number of electrodes actually created in Virtual Device Example Let us create a simple electrode short tube some kind of a lens We will set up the following parameters of the project and the tube 21 22 xl x Length of X axis units 100 X bottom EN Potential lo Length of Y axis units hon Toto o Name tube 4 bottom lo Color green Length of axis unit 100 Inner Radius EN Mobile pomts Name of project New project Outer Radius 30 There are not mobile po Numbers ofpoints 1000000 Length 40 Picture 22
2. Picture 11 Now you can see the following picture in workbench picture 12 Tree of mobile points L gt z ale rel Picture 12 Now we will add four rods a quadrupole to our project Pick up F and specify the following parameters picture 13 A center o o _ Potential H Y center nu Name rood 4 center 50 C XZplane Color Rose color Radius 10 Mobile points Length a 8 Repeat adding rods 3 times with the following parameters Y center 20 Name rod2 Z center 20 Name rod3 Z center 0 Name rod4 At last you will get the following project pictures 14 15 f AY plane There are not mobile po Adler egen SE E ren ET amer Fe BOOSH Droe Ream Mente marohi Seen Of Geen pekt Lage ga Si Mee Step O0e t Soep ONE St gt Clipping sen ry j Ge mg d DA i CG ay l Picture 15 10 Picture 14 Step 3 Transformation of project to SIMION To transform a 3D project into geometry file GEM file you need just topress button Then specify the folder and the file name for example my skimmer Virtual Device will create file my_skimmer gem Run SIMION open geometry file and you will see the following picture in SIMION workbench pictures 16 17 xGgat S Picture 16 Picture 17 To change parameters of geometrical object it is necessary just to pick up appropriate pictogram from tree of object mode Edit object
3. Picture 27 Virtual Device workbench _ a ob oe r Friii Ea N e Picture 29 SIMION workbench Mirror XYZ 36 Chapter 1 6 Mobile points The main purpose of mobile points is simplification of working with very complicated projects How mobile points can make life easier Actually position of geometrical object center or bottom is defined relatively to zero of system of coordinates If user adds mobile point to project then user can specify position of geometrical object according to that mobile point while position of mobile point is automatically settled up according to zero of system of coordinates Example load project tof_parts mirrors vds All electrodes in this project are related to mobile points point 1 See picture 30 20 3D iew Workbench and PRG files l JD x File Additional Parameters PRG e m E FF lf Ae ee ORAE A Rotation Step Z D I Step amp 0 1 Step 0 1 Distance step 0 1 Axises Grid ei Moving Step 1 Step 1 Step afi Clipping step 1 E X bottom D p Symmetr Potential 1 Y bottom 3 c XYplane Xisbi 84 0 Z bottom Jo Z split bau X length h92 Pr Name mi Z length 432 T Color length e green Mobile points point 1 OK Picture 30 Now choose pictogram points 1 and change X position to zero Add mobile points x Tree of mobile points X position o position o o Z po
4. Now you can judge how easy it is to create a complicated 3D project for SIMION investigations Chapter 1 3 Description of geometrical objects Object BOX This object presents itself box with the following parameters Set geometrical sizeof Boxe x X center bo Potential oO Rotation around X oO center lo Name Noname Rotation around bo Z center o o Rotation around zZ oO X length 2 fio Color of object po length 2 fio Mobile points po Z length 2 10 OK X Y Z center position of center of box X Y Z length 2 half a width along the axes Potential it is potential in volts Name it is just the name of the object It is better to give different names to different electrodes this is a suggestion Name does not play any role Color of object here user can specify color of object Color of object is not used in SIMION Rotation around X Y Z here user can specify angle of rotation around the axes Angle is in degrees Mobile point here user can set connection between the geometrical object and the mobile point if a mobile point was added to the project Details of using mobile points see in chapter 1 4 Example 11 X center 50 Potential 0 RotationaroundX bs Y center En Name box Rotation around be Z center 50 Rotation around Z La X length 2 f Color of object gren Y length 2 p0 Mobile points There are not mobile po Zlengthi2 20 R
5. 1 Geometrical object It is single electrode with certain number geometrical parameters which completely define size of electrode and its position in space 2 Project Project presences itself a combination of geometrical objects inside of 3D volume 3 Mobile point When user set up geometrical object it is necessary to set up position of center of geometrical object This position can be settled relatively to crossing of axis x 0 y 0 z 0 relatively to some point x y z This point has name mobile point Refences 1 Dahl David A SIMION version 7 user s manual 2000 2 Ky3ema A C Casna O P Heprkos M A Anann3upyromtue CHCTeMbI MarHUTHbIXx Macc ClIeKTpoMeTpos Kneg HayKosa mymkKa 1987 3 Koltsov S High transmition electron optics with quasi mirror intermediate stage Ph thesis 2000 Sank Petersburg 4 Vonuxos OK Ytxuu K I Uenapyxun B B Pacuer semMeHTOB 3JIEKTPOCTaTH4eCKUX 9JIEKTPOHHO ONTHYeCKHX CHCTeM yueOHoe Nocobue JlenuHrpan 1984 5 Archangelsky A Examples of programming in Delphi version 5 7 Delphi for professionals Moscow publisher Binom 2003 64
6. Institute for Analytical Instrumentation Russian Academy of Sciences Koltsov S Manual Saint Petersburg 2006 Contents NO ee 3 MAIN MENU OF VIRTUAL DEVICE ggegvweresdekegteg r eege ANEN 4 CHAPTER 1 CAD PROG RA EE 4 BEER Lag CR Dr NC E BEEN 4 CHAPTER 1 2 HOW TO CREATE 3D PROJECT ccccccceccscecccececcececcececescecescscesescesescecescecessscesescess 7 CHAPTER 1 3 DESCRIPTION OF GEOMETRICAL OBJECTS ccccecoccecaccececcececcscececceceseececeseececceceses 11 CHAPTER E D SEB CR EE 30 CHAPTER 1 5 SYMMETRY AND MIRROR OF 2DPROIECT 35 CHAPTER Os NIOBICE RO RE EE 37 CHAPTER 1 7 SCIENTIFIC CALCULA TOR ee EE 38 CHAPTER LS SCREEN RESOLUTION EE 43 CHAPTER 2 SIMION DATA ANALYSIS esesesesecesecccesesecececeoecocococccocococococococococososocosocosecsoso 44 CHAPIFR2 l LOADAN D EE EN NEE 44 EEE IE EE 45 CHAPTER 2 3 HISTOGRAMS RESOLVING POWER 47 CHAPTER 2 4 TABLE MANIPULATION ccceccccecscecccecccececescececcecscscecescecescecessecesesceceececaseeceees 54 CHAPTER 3 CREATION OF TONS DAS NB KEES 57 3 GER ER CBR a EEN 57 CHAPTER A CREATION OF SPECIAL ION DISTRIBUTION DISK 59 CHAPTER 5 CREATION OF SPECIAL ION DISTRIBUTION CONICAL KRAN RIED 61 CHAPTER 6 MAIN PARAMETERS OF MASS SPECTROMETERS ENERGY PUN ADIN E NEE 62 TERMINOLOGY covevssesiccssgusatesedecdescsgeestevesesseeccseesiocetassbeccsegssesasusssecsdoossecogasdesccseastesvaseousecssesseosess 64 MRE Re EE 6
7. Step OD Step OI Step 1 Clipping set Seting up resolution defaul 1280 x 960 16 bpp 1280 x 1024 16 bpp 512 x 384 32 bpp 43 Chapter 2 SIMION data Analysis Chapter 2 1 Load and Save data SIMION allows saving results of simulation in txt file Therefore there is possibility to develop users software for analysis Virtual Device gives such possibility to user It allows unfolding SIMION data into a table if SIMION data are saved in txt file in the following format example of this format is in file my_rec rec 4 e yey yy ion nl Events TOF Mass Charge Instance En Instance Mn mal aa aa Uhen to Record These Data Elements Ion s Start Toni s Every Time Step Ion s Splat A11 Markers ce Format to Use For orded Data 0 Leading Spaces Form Feed Before Each lon potter Each Fly n Picture 31 Important note User has to remember that only two events are allowed The first event is event of ion birth The second event is event of ion death For example Ion s Start and Ion s Splat It is not important what kind of death is User can change Width and Precision Buttons To load data from file in SIMION format see format above it is necessary to press button Open SIMION data The each row in table picture 32 presents one ion with two events The first event birth takes columns from 1 to 28 and second event death takes columns from 29 to 57
8. parameter Button E allows save picture in file bmp format ET ee ee ee ee ee ee ee ee ee ee ee ee ee eee eee ees ee See TE See ee ee eo mm ail mm sl zm mm zm mm mm zm d em zm zm mm zm zm mm e sm zm cb LEET Oase Picture 45 Chart of m z versus The Inversion allows change axes For example see picture 46 52 123 4 5 6 7 8 9 10 111213 14 1516 17 1819 20 21 22 23 24 25 26 27 28 29 30 31 32 33 Time of fligth B M Inversion meata gt ea Picture 46 Chart of m z versus Inversion of axes TOF to m z this option allows transforms specter of time of flight TOF to ratio mass charge see picture 47 Transformation can be done in following step 1 Load data from file This data can be done by saving data in histogram window 2 Set up parameters of transformation This transformation based on following relation between mass charge ratio and TOF m z a TOF b User has to specify two points in TOF specter and related points in m z terms 3 Press button Transformation data and Virtual Device calculate coefficient a and b and make transformation of data see picture 48 Data transformation time of flight to mq 0 0000 time of flight Transform data Time 1 EE miq l 221 5 a Load data Close W Time 2 13 mig 2 443 b Picture 47 Window of transformation of data in time to data in m z 53 Data transformation time of flight to m q 500 0000 1 000 0000 mig transform data Time
9. 15 Resolution 11 3066300642934 Peak 13 30 20976 30 25976 30 20976 Width of peak 0 0500000000000007 Resolution 0 165509424768686 eal 30 20976 30 25976 30 20976 width of peak 0 0500000000000007 Resolution 0 165509424768686 Peak 14 30 30976 0 30 43476 Width of peak 30 30976 Resolution 99 5892854091835 8 0000 10 0000 12 0000 14 0000 16 0000 18 0000 20 0000 22 0000 24 0000 26 0000 26 0000 30 0000 32 0 x Type interpolation Number points per division Threshold Picture 40 Results of calculation of resolution Resolving power This option allows to calculate resolving power for mass specters m m Ax Formula R Here user has to specify approximation of both peaks and m m d d masses which corresponds to peaks Calculation of resolving power can be done in next steps 1 Load data from file To do it just press button Load data This data can be created by saving data in histogram window 2 Specification of type of interpolation regression see picture 42 Type of interpolation Normal distribution or Eckerly function Here user cans chouse type of interpolation for peak The difference between Normal distribution and Eckerly function 1s just constant The parameters Gradient tolerance convergence tolerance Max number of 49 iteration Optimization method defines quality of approximation It is necessary to notice that optimization method strongly influence on results of approximation Ca
10. 3D view in SIMION Axis of symmetry here user can specify the axis of axial symmetry OK Format of file The format of file with data consists of several columns Examples of such files are placed in examples_vds axial object For example my axial object x txt 0 505025 80 505050 100 50 50 35 120 50 50 15 150 50 505 The first column is data along X axis the second column is data along Y axis and the third column is data along Z axis The last column is radius For example Axial object Thickness E Potential o Name Ae Axis of File hmy_axial_ object_x txt Load Data Ce Color of object Dragon E Mobile pomts There are not mobile points Discritization 100 _OK 25 Results SO Wiese Wrarkehemehi and PR files ell j Ps GoMvegdfbeseter PRI osm t EC BOSSE ne OG Rotation Sept D I Step rb Step rb Distance step 0 1 Axises Gi SY epee seal peel cere Wester EL EH Lp D af ug ge Til rte i IE gi pirit et GL e d Lu et Bei S Workbench i in Virtual Device Workbench in SIMION Object Sphere This object defines sphere with the following geometrical parameters Set geometrical size of the Sphere x rb Potential o C leftside_ C left side Yemen ebe Z G rie St KEE Color ino color Y cut vie left side
11. 79 423784 2344 08 230588 2565 73 454 111 2360 1 248 696 2279 74 167 599 2379 16 26685 2418 7 305 421 2396 86 283 352 2280 01 166 872 2281 76 168 416 2564 56 453 491 2254 11 140 643 236182 248 642 FIRA S I S171 Picture 33 Menu for Space and Phase Distribution Total number of ions 6328 100 Save data Number of ions in acceptance 0 0 0 Picture 34 Example Phase Distribution X center 100 X width 10 Vx center 10 Wa feidh 10 Y center 100 Y width 10 Vy center 10 Wy width 10 Z center 100 Z width 10 Va center 10 Va widih 10 Eoad Save Apply D fiw ZX _D fitr ZY D file XY Ghose Picture 35 Size parameters of Detector Acceptance Chapter 2 3 Histograms Resolving power This part of Virtual Device allows quickly create Histograms of ion exit parameters event o death and calculate resolution resolving power See picture 36 On SIMION Data Analysis me x Open Save SIMION data Space and Phase distribution Histograms Resohwing power Table manipulation 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 11K NQ o oOo Gr Gr OG e e acd GO ea 0 Gr OI OG 0 md be be bei be be bei bei be bei be be bei be be bei bg th ra Picture 36 Histogram Resolving power window Histograms This button run chart where user can b
12. C right side e none _ OK X Y Z center those parameters define position of center of sphere Radius defines the radius of inner surface of sphere Thickness here user can set up thickness of electrode The outer surface of sphere is defined as inner radius plus thickness Potential potential in volts Name name of object Color of object here user can specify color of object It is not used in SIMION Mobile point here user can set connection between geometrical object and mobile point if mobile point was added to project X Y Z cut view here user can specify half and quarter of sphere When None is selected a whole sphere is drawn Left right sides selects parts of sphere to be cut of along appropriate axis Example 1 full sphere x A cut vie Z cut vie X center W Potential lo C left side C left side Cor Popi center ep Name sphere right side right side 4 center ep Color green Ce none e none Y cut vie Radius ES Mobile points left side right side Thickness E There are not mobile poini none 26 Results O Fas ssheansey Seated ae EE ser GES Ee gt See soe e E ee SE EE eject N Ea a Q Ki ER O ve e Gei 0 F 5 z D m Ts 5 2 La 5 de i left 5 Kai pl L T Gi right side none a Kai j L KN CG green Mobile points 5 There are not
13. Data for SIMON syMetry planar E vm wee cesur e Fel AO ec Eer Mirror none Rotation Step Z w Step X 0 1 Step 0 1 Distance step bi Axises Grid Gi Type field Electrostatic ts heer Be a ce Magnetic scale factor D OR Picture 21 Picture 23 Virtual Device workbench DIER ag The part of the tube stretching beyond the boundary of the grid is cut off by SIMION Now we will change only the mirror parameter Let us set it up the following value Mirror Y it does not influence the picture in Virtual Device workbench but the picture in SIMION workbench will be different J L Picture 24 SIMION workbench Mirror none 35 Picture 24 SIMION workbench Mirror Y A ER i m B mT ee Datars Pepe Picture 25 SIMION workbench Mirror YZ Therefore user can create a complicated geometry just by changing the mirror parameter Here is another example of such geometry Size of project X 200 Y 100 Z 100 Picture 26 Virtual Device workbench a S zt ANE testers TUR S Des S008 aale ae aes et dr CO J Er Picture 28 SIMION workbench Mirror YZ Now you can see how the mirror parameter influences 3D geometry in SIMION eau E Fel amp EOCESOE DHL ep Rotation Senf D I Step X 0 1 Step 0 1 Distance get Axises Grid J Moving Stop Xj 1 Step OH 1 Sep NL Clipping step 1 ll x
14. ETT rE TT am i Sri D Workbench in Virtual Device Workbench in SIMION 13 Object Tube This object presents itself as a tube with the following parameters Set geometrical size of the Tube l Ka Potential lo Mame Ino name Color Mobile points Outer Radius E Length EN X Y Z bottom position of bottom of tube Inner Radius inner radius of tube Outer Radius outer radius of tube The difference between outer radius and inner radius is thickness of tube Length length of tube Symmetry this option defines plane of bottom of tube Potential it is potential in volts Name it is just a name of object Color of object here user can specify color of object Color of object is not used in SIMION Mobile point here user can set connection between the geometrical object and the mobile point if a mobile point was added to the project For example Set geometrical size of the Tube a A bottom 50 bottom 50 4 bottom o Color gold C XZ plane S Inner Radius Go Mobile points Outer Radius P C SR plane There are not mobile po Length 70 Results I ell El amt fof amp BSOCSCOE reg Moving Step Dt Sep Or Sep Or Clipping geph 1 DZ kat F Is SE ei e SR C Bag i S b S Ae Lees erz e i ma I EISE Workbench in Virtual Device Workbench in SIMION 14 A Object Solid cone This object presents itself as a s
15. Load data from file To do it press button Load data This data can be created by saving data in histogram window 2 Set up type of interpolation User can set up linear or cubic interpolation 3 In case of small number of points per peak user can add additional points between points from file To add points user has to set up number points in number points per division 4 Specify level of threshold This parameter specified level where resolution will be calculated 5 To calculate resolution under above discussed parameters just press button Calculation The results of calculation presented in picture 40 The red color in specter 1s approximation of specter linear or cubic approximation The black points are points which inserted in specter between data points Virtual Device finds all peaks calculate the width of peaks at threshold left right center of peak and calculate resolution of each peak 48 according with formulaR 100 Calculated data presented in window Results Button allows save picture in file bmp format Calculation of resolution n for electron spectroscopy 0 0000 x Type interpolation Number points per division Threshold Picture 39 Window for calculation of resolution Calculation of resolution for electron spectroscopy ea 26 48476 29 63476 27 85976 Width of peak 3 15 Resolution 11 3066300642934 Peak 12 26 48476 29 63476 27 85976 uh Width of peak 3
16. any role for creation of 3D geometry in Virtual Device but SIMION does not accept geometry file with total number of cell more than 50 000000 x esL ra ns Geer File Length of X axis units ho Length of axis units ho TS o EEE iH TR 100x 100 100z Length of Z axis unit ba ES Name of project New project Picture 5 Geometrical size of project in SIMION Numbers of points 1000000 Data for SATON Warning a a Symmetry planar The size of project is bigger then Simion can accepts Mirror ane bi Type field Electrostatic Magnetic scale factor OK Picture 4 Geometrical size of project in Virtual Device Picture 6 Step 2 To create add geometrical objects to project user can choose appropriate pictogram from the toolbar or from the dropdown list For example let us build a system which consists of an orifice a conical skimmer and a quadrupole four rods Set up geometrical size of project as is shown on picture 4 Orifice is a circular plate with hole Pick up pictogram tube You will see the following window picture 7 Set geometrical size ofthe Tube x A center oO o Potential Oo center oO o Name no name 4 center o o Color i Inner Radius 10 Mobile points Outer Radius 15 po Length Bo OK Picture 7 Setting geometrical parameters of tube Specify all parameters as is shown on picture 8 The details of all parameters of different geometrical objects are descr
17. following parameters v v 4 center o Mobile points OK There are not mobile pa X Y Z center position of box center X Y Z length length of box along axes Symmetry this option defines plane of bottom of box Potential it is potential in volts Diameter this parameter defines diameter of hole If diameter exceeds length of box then diameter is automatically reduced Name it is just a name of object Color of object here user can specify 17 color of object Color of object a not used in SIMION Mobile point here user can set connection between the geometrical object and the mobile point if a mobile point was added to the project For example Potential o Diametr Bo Name box with hole X length 4000020 C XAplane Colar red length wm C ZY plane Mobile points OE There are not mobile po Results aa vs P EZ AO A ee SE ep Rotation Seep D I Step Get Sep GE Distance step 0 1 Arben Grid Ch ag sp etc Set E Week Coeter EEN BEN E Cees fps ff coer aaa D Sa Sep eae ie A Deel lf eat Fe ses k be Let Lack rr eee te oe a Lt CH s 8 en Let L A a H FLT j tef Am d jl H Le a Kiel e de s du bel Bee LI v f Lef de ell Us El EST i k7 gt rie EE EE zl T EE Ta wm E ae eal a mg e w lt EE EE eg E SE BC s Workbench in Virtual Device W
18. it is just a name of object Color of object here user can specify color of object Color of object is not used in SIMION Mobile point here user can set connection between the geometrical object and the mobile point if a mobile point was added to the project Discritization this parameter defines how cone can be made in SIMION Actually cone as a geometrical primitive does not exist in SIMION language But it can be built as a number of slices with different radiuses Therefore discritization is number of slices This parameter influences only 3D view in SIMION 16 For example Set geometrical size of the cone with hole X X bottom 50 Length Potential 0 Y battom bn en Name no name Z bottom o C XZplane Color blue gt First Radius imer 10 Mobile points First Radius outer s CBN Plane there are not mobile j second Radius inner 5S Discritization 100 second Radius outer S Results D view Wikherich and PER fled Fie Ackitional mani PE cau et F ef A eec PHOS eget EE Rotation Sept TET Step Ck 0 1 Step DUR Distance ap Aber Grid ch Ree Moving Step DI Step rh Sep Gr Chipping step 1 E TE ey are e a Se sl eal A f Kb ed mm ke pe Workbench in Virtual Device ae ba Ach bebe Bref Workbench in SIMION Discritization 100 Ga Object Box with hole This object presents itself as a box with hole with the
19. making plot of ions in ZY plane Button Distrib In ZX plane this option allows making plot of ions in ZX plane Button Phase distrib Vx X this option allows making plot of ions phases along X axis Button Phase distrib Vy Y this option allows to make plot of ions phases along Y axis Button Phase distrib Vz Z this option allows to make plot of ions phases along Z axis Example of ions phase distribution is presented on picture 34 The red rectangle on picture 34 is window parameters of which are defined in window of detector acceptance see picture 35 User can easily evaluate how many ions inside of detector acceptance Virtual Device automatically calculates total number of ions in distribution and how many ions inside of detector acceptance Detector Accept This option allows set up rectangle which can be used for estimation number of ions in different planes and number of ions in phase diagrams see picture 35 User has possibility to save data of detector acceptance to txt file Buttons D filtr ZX D filtr ZY D filtr XY allows deleting all ions which are out side of rectangle It is filtration inside of window 45 Ca SIMION Data Analysis Jl x Open Save SIMION data Space and Phase distribution Histograms Resolwing power Table manipulation Close rer 0 By Columns kreeg JE rieszg Ke error Column 227288 159 486 225095 138 939 2204 37 912791 2154
20. mm mm mm mm mm mm mm mm mm mm mm mm 15 0000 20 0000 25 0000 30 0000 Time of flight micro sec 10 0000 Delta time 0 1 E Marks Insensity ve S Intens 54 9027777200 Substr time 0 C Normolyzed TOF 36 0217240200 Recalculate Save data Close Picture 38 Creation of envelop of histograms Button Normolyzed makes chart where intensity is in range 0 1 Button Recalculate to refresh drawing after choosing new exit parameter just press this button Button Save data allows saving chart as txt file with two columns intensity and exit parameter Button allows save picture in file bmp format Button Substr time energy X Y Z and so on allows subtract delta value from appropriate exit parameters This feature can be useful for example for estimation of time of flight Button Delta time energy X Y Z and so on This value specifies quality of histogram With this big value you will get a very rough histogram When user moves mouse over window Virtual Device calculate position of mouse and show the intensity and value of exit parameter at mouse position Button Resolution 100 this button allows to calculate resolution of peaks in specter The way of calculation of resolution is described in chapter Main parameters of mass spectrometers Resolution in electron spectroscopy The calculation of resolution can be done in following steps see picture 39 1
21. mobile point Sphere ial fo Name sphere l 3 5 Y S E Es X z aon l N my Ge O S f Lei a S o i a E 5 L S E SE a A eg pa oe Mls lo le eco Hi ER H o op o L I es s t ZE H Bee ul e o E ja Cl 2 aaya ES T 5 BS ss S 7 E e d o o Go A Ce S WC yag d x S 3 5 He 8s 2 5 DH SS G z 2I SIMION In Workbench Example 3 Quarter sphere Set geometrical size of the Sphere i X center ep Potential o center s0 Name sphere Z center ep Color green x X cut vie re left side C right side C none Z cut vie left side right side e none Y cut vie C left side Radius 23 Mobile points iene cite Thickness 5 There are not mobile point C none o Results Oh View Workieench and PRG Bien i Pie Additonal Paneneters PRG csmt Fe f BOCCCE ATOA Rotation StepZ D I Step GK Stepko Gecke d Ades Grid Le Maring Step GH Sen Ch Sen dr Clipping step 1 Lab tat f i ep mb ee Ee ee a Gr reen zg Ce A i D d Let Ei id ue i aa d gw e e e Era Dee i S ie a Ze Workbench in Virtual Device EE Ouarter sphere ee Bn e ee e Tee Te ee Tee Te ege Te Tee Tage Tag Tee ol teg En Dn rann E Workbench in SIMION Object Real grid This object defines parameters of real grid as a single object The grid presents i
22. radius of hole Outer Radius radius of segment Symmetry defines plane of segment Length defines thickness of segment in the plane of symmetry Potential potential in volts Name name of object Color of object here user can specify color of object Color of object 1s not used in SIMION Mobile point here user can set connection between the geometrical object and the mobile point if a mobile point was added to the project Segment center degrees this parameter defines 20 position of segment center This position is in degrees Segment diverg degrees this parameter defines divergence angle of segment For example Set geometrical size of the Segment of disc withhole se X centr bn Potential 0 centr 50 o Name segment Z centr Oo o o Color lgoldmetal Inner Radius 10 Mobile points There are not mobile segment diverg degree So If you add four segments to a project with parameters as in example above and the following parameters first segment Segment center degree 0 second segment Segment center degree 90 third segment Segment center degree 180 fourth segment Segment center degree 270 then you will get the following project Results EE omaj far crn fara eae Seeger Taal E View Workbench and PRD fies ami Pi Mp ASHirnagi come TEL BOOCSS Gren Rotation Sept Step OO bi Step OK Distance swp Auer Grid A Moving St
23. u lf Ke Bo Energy ev La Making many disks Mex ff Min TS Ste Radius of disk Symmetry of the beam jo XY plane Direction of the beam positive axis Number of ions fee oes C XZplane C negative axis il YZ plane Save data Angle step degree so Color of trajectories ___Loaddata fo Black Generate ION File OK Picture 58 Parameters of disk 59 X Y Z those parameters define center of the disk Radius of disk defines radius of disk Radial step defines step along radius Angle step degree this parameter defines the number of lines that can be drawn For example 90 means that lines will rotate with step 90 degree therefore total number of lines in disk will be 4 Mass charge Energy parameters which define type of ions Symmetry of the beam this parameter defines directions of beam Actually it is setting up azimuth and elevation angles Color of trajectories this parameter defines color of trajectories in SIMION Direction of the beam this parameter defines direction of axis along which ions will fly Save data this button allows saving current parameters into txt file Load data this button allows loading parameters from txt file to window Generate JON File this button generates list of ion based on current parameters in window Making many disks this parameter allows creating many disks where one of parameters is changing from disk to disk Max Min Step those
24. 1 9 5 mio l 221 5 a PrE Close 7 2 Time 2 13 miq 2 443 b Picture 48 Result of transformation from TOF to m q Ion mobility This option is discussed in Simulation of ion movement in gas and related problems Chapter 2 4 Table manipulation This chapter covered discussion about manipulation of data in table picture 49 On SIMION Data Analysis O sl 118 09 Eeer 118 09 118 09 11809 118 09 118 09 118 09 118 09 118 09 118 09 11809 Picture 49 Table manipulation window 54 Max Min Average of column To calculate maximum minimum and average value of data in column user has specify the number of column Press this button and type number of column in following window Max Min Average x Column number The results will be presented in next window Results Gy SIMION Data Analysis E ioj x Open Save SIMION data Space and Phase distribution Histograms Resolwing power Table manipulation Max Min Average of column Close 7 29435 73358 747261 Max alue 2721 89 Min value 118 09 Max min 2603 8 Average 1092 64713766396 Resolution average max min 0 419635585553 Resolution 100 average max min 41 963558 7 56946 7 16163 6 79171 7 12607 7 28113 709784 703648 7 06688 7 27893 7 29472 6 79404 734652 7 12458 bei bei bei bet e
25. 2E 3 Please take attention that separator for numerical number is a dot Usual mathematical restrictions are present For example user can not calculate sqrt 1 If user makes a syntax error in description translator shows the list of errors and defines where those errors occur position Zooming chart to zoom in a chart locate mouse on some part of the chart press left mouse button and move mouse to the left and down It will indicate a rectangle then release left 42 mouse button The area inside the rectangle will be zoomed in To zoom out locate mouse on some part of the chart press left mouse button and move mouse to the right and up Chapter 1 8 Screen resolution There is possibility to tune resolution of screen inside Virtual Device To do it just pick up video from main menu Setting resolution inside it allows changing resolution Restore default mode restores default resolution of your computer When user picks up Setting resolution Virtual Device checks all possible variations of videos of your computer and creates a list of modes So user can choose an appropriate mode from the list The length of list varies from computer to computer An example of such list is presented on the following picture 3D iew Workbench and PRG files Mla E3 Fie Additional Parameters PRG video 5_Calculater c m E F Ff A OW We ATO Rotation Step Z 0 5 Step OR Step Gr bz Distance get Axises Grid Moving
26. 3180 Recalculate L Save data Close Picture 50 Let us delete ions from table with mass charge ratio more then 1000 amu Do to it press button Filter and set up parameters as it show on picture 51 Column nomber 3 Minimum o Maximum 1000 OK Picture 51 Filtration data window Now press OK then run Histogram window and you will see following results picture 52 histograms M U x Histogra 10 0000 7 0000 80000 9 0000 10 0000 11 0000 12 0000 13 0000 14 0000 16 0000 17 ee 18 0000 19 0000 Time of flight micro sec Deltatime 0 1 Bens ity vs v Intens 15 6676923100 Substr time 0 WITT TOF 20 7036130700 Se luet Picture 52 Histograms after filtration 56 Compare specter on pictures 50 and 52 you can estimate the effect of filtration Tranform to ion list This option allows transforming exit parameters of ions death event to list of ion This list of ions user can use as initial ion distribution in SIMION simulation Export to Excel this option can be useful for those users who like to use Microsoft Excel software for data analysis Chapter 3 Creation of ions list This part of Virtual Device allows creating the list of 1ons This part is almost similar to the corresponding part of SIMION except energy distribution Parameters position of ions X Y Z azimuth angle elevation angle masses charge are appropriate parameters of ions see picture 53 Energy distribut
27. 4 Introduction Virtual Device is an Add on software to SIMION v 7 Virtual Device covers several features which are not fully developed in SIMION such as fast creation of 3D geometry CAD program fast analysis of results of simulation in SIMION and fast creation of different ions distributions CAD program The main idea of CAD program allowing fast creation of 3D geometry is following It is known that ion optic often consists of typical electrodes like lenses or rods therefore it is possible to create specific users ion optics only by using standard components However SIMION itself provides possibility to create any desirable shape of electrodes because there is special language and any user can develop his her own geometry by using this language On the one hand this gives the user a very powerful tool but on other hand specific skills are required CAD program is based on the idea that a user can use finite number of electrodes to recreate specific geometry and each typical electrode can be represented as a bit of program in SIMION language The CAD program has a number of well defined 3D geometrical objects like sphere cone or bar and each geometrical project coupled with bits of program in SIMION language User can graphically recreate specific 3D geometry as a combination of standard electrodes by setting geometrical parameters of each electrode Therefore total geometry can be transformed into a program in SIMION language GEM fi
28. 4159 Exp 0 5 S gr b0 120 75678223173 bi 0 455826570100562 midle 11 9132714856 Resolwing power 14 5347743306355 10 0000 25 0000 30 0000 x Interpolation Type Throshalas First peak Second peak Load data Close Boo Minimum r Minimum i Maximum 10 5 Maximum IER L Mass 1 500 Mass 2 600 Picture 43 Results of calculation of resolving power Example of results of resolving power calculation First peak Function y BORIS Exp 0 5 Sqr X B2 B1 b0 44 959248464339 b1 0 322677006022181 b2 7 2999845373 1304 One side 6 46757515636707 Second side 8 13239391194106 Middle 7 29998453415406 Second peak Function y BORIS Exp 0 5 Sqr X B2 B1 b0 48 232083486332 bl 0 455826569442327 b2 11 7003229921036 One side 11 Second side 12 8265429712 Middle 11 9132714856 Resolving power 14 5347748062745 Tof vs Energy of start This option allows creating chart with time of flight versus energy of start Example of such chart is presented on picture 44 Marks This option allows switching off on marks Button allows save picture in file bmp format 51 Time of flight vs energy at start x Energy at start ev Picture 44 Chart of ion distribution TOF versus energy of start m z vs This option allows estimate mass charge ratio first parameter versus different parameters second parameter See picture 45 Dropdown list allows specifying the second
29. Button Append SIMION data this button allows to add data from SIMION file to existing data Button Save data this option allows to save data from table to txt file Button Load data this option allows loading data from txt file to table Button Append data this option allows adding data from txt file to data in table 44 Button Split and Save data this option allows splitting data from table and save splits into different txt files Button Clear table this button clear table n SIMION Data Analysis Joj xj Open Save SIMION data Space and Phase distribution Histograms Resolwing power Table manipulation 2 Load data Append Data Clear table Append SATON Data Save data Split and Save data H 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 118 09 158 gt Gu OG O O GO eG OG aq ae GO a a a a amp zt bei bei bei bei bei bei bei bei bei bei bei bet bet Lu D I 118 N9 Picture 32 Open Save data Chapter 2 2 This part of Virtual Device gives possibility quickly makes plots of ion distribution in different planes and make plots of phase distribution of ions along axes see picture 33 Button Distrib In XY plane this option allows making plot of ions in XY plane Button Distrib In ZY plane this option allows
30. ION 0 3D Yiew Workbench and PRG files loj x File Additional Parameters PRG egw et Fel AO ec SE e M Rotation Step D I Step GH Step VE Distance step 0 1 Axises Grid EL Moving Step KI Step Oth Step rh Clipping sep Picture 1 Workbench in Virtual Device Gs mr E EE A Oz OO e amp Ee s This toolbar has a number of geometrical objects To add a new object into project user can just press on one of those pictograms but there is another way of adding of geometrical objects to project The picture on pictogram presents geometrical type of geometrical object except any axial object see chapter 1 3 G S setting up geometrical size of project and all necessary parameters for SIMION M P setting up mobile point Rotation Step 4 bi Step XX 0 1 Step oi Distance step 0 1 EE EE changing step of rotation of the project and step of moving of the project in space Axis Grid Mises Git EI This toolbar allows switching on of drawing of axis and grid and also saving picture from workbench window into file bmp format E E Seve i seme E Clipping step 1 This toolbar allows changing the step of moving of the project in space The next window toolbar is intended for rotating and moving 3D geometry picture 2 To avoid numerical pressing on mouse button during rotation of project user can only place cursor on one of buttons of rotation press left mouse button and pr
31. angle step degree El angle step desree Kc Load data Color of trajectories Generate TON File E OK Picture 61 Parameters of conical distribution X Y Z these parameters define position of the point source in space Az Angle degree El angle degree define divergence of azimuth and elevation angles Az Angle step degree El angle step degree define steps of changing of azimuth and elevation angles Mass amu Charge elem u Energy ev these parameters define type of ions Symmetry of beam Direction of beam define direction of ions in space Save data Load data allow storing loading current parameters in txt file from txt file Generate JON file this option generates list of ions based on parameters in window Number of ion it just shows how many ions were stored in file JON 6l Example 1 Set up parameters as is shown on picture 62 2 Create an empty project in SIMION 3 Load ions to SIMION and run ions You will see the following picture see picture 63 Special distribution conical distribution E ID x Distribution of ions The conical distribution Center of distribution Particle X Booo Mass amu co Ke o Charge elem u QP along X axis Zo o oo Fnergy ev QP irecti Az angle degree Elev angle degree Az angle step degree EL angle step degree ____Save data ho Load data Color of trajectories lo Black C along Z axis positive axis C
32. bei bei bet bet bet e bei bet bei TAIAP1 Window Results gives following data example Max value 2721 89 Min value 118 09 Max min 2603 8 Average 1092 64713766396 Resolution average max min 0 419635585553408 Resolution 100 average max min 41 9635585553408 This window also gives possibility allows quickly estimate resolution which calculated from different formulas Data transf This option allows changing the value in table It can be done by following operation multiplication division addition subtraction To change data user has to fill out following option Operation Ge Wlultiplication C Division C Addition C Subtraction Column Value hb Execute 55 For example you like to recalculate time of flight column 31 from microsecond to second 1 chouse Multiplication set up Column 31 set up Value 0 000001 Press Execute Filter This option allows deleting data from table which does not satisfied to some criteria Therefore it is some kind of data filtration For example Load data from file Agilent Agilent7 txt To do it use Button Load data This file contains data of 7 peaks which corresponds to different time of flight different mass charge ratio Histograms of those peaks are presented on picture 50 Histograms Fi it Delta time fl L ensity vs z Intens 26 0555555600 M Histogram Substr time 0 Normolyzed TOF 9 681124
33. cts invisible without removing it from project For this it is necessary first to choose mode Suppress Unsuppress and second to pick up appropriate pictogram in the tree of project Then this geometrical object will become invisible in the workbench The modes Edit object C Delete object C Suppress Unsuppress Tree of objects points It is the box equivalent to the toolbox with a number of geometrical objects This box can No objects drop down with the list of objects Therefore user can add new objects to project by choosing Tree of abjects points an object from the dropdown list It 1s the second e way of adding new objects into project Set geometrical size Set geometrical size G S setting up Add mobile points geometrical size of project and all necessary parameters for SIMION Add mobile points M P setting up mobile Solid cone point Cone with hole Box with hall Buttons N Can New project This button allows creating a new project or clear old project It means hat the user deletes all geometrical objects from the project if they existed in the project et Load old project from file to workbench ES Save project to file Add a project from file to the project which already exists in the workbench Load project created in previous versions from file to workbench OREK Close CAD program EI convert 3D project to geometrical file GEM By pressing this button use
34. entific calculater 41 Syntax Operation and functions At the moment user can use the following functions and operations notation Operation functions arccos x Arccosines results in radians arctg x Arctangents results in radians cos x Cosine argument in radians exp x exponent In x natural logarithm sin x Sine argument in radians sqrt x tg x Tangents argument in radians Opening bracket Closing bracket subtraction multiplication division assignation Constants Pi E base of natural logarithm Formal rules l Zs There is no difference between upper and lower cases for example Sin sin SIN are equivalent The description of formulas can occupy as many lines as is necessary User can continue description to a new line at any position Numbers have to be unbroken User can use identifier For example Pi is one of identifiers It is possible to set up user s identifiers Comments have to be placed in brackets at any position of description but not inside a number or inside an identifier If description of very complicated formulas consists of many expressions then those expressions have to end by semicolon see examples in the catalogue described above User can use variables If variable 1s not defined in description then it 1s supposed that this variable is zero Numerical constant can be written in the following formats 5 5 1 4E10 4
35. eometry to geometry file save as PA arrays and load PA file with coefficient 0 5 User will get project in SIMION in millimeters however with large number of points per millimeter Hint 6 How are millimeters in Virtual Device related to points in SIMION The relation between millimeters in Virtual Device and points millimeters in SIMION is quite simple For example We would like to create a tube in millimeters in Virtual Device and we like to have this tube in SIMION with the millimeters points ratio 0 1 It means 1 millimeter is presented by 10 points cells in SIMION We can do it in several steps A Let us make the following tube x X bottom ep EE Potential o bottom s0 XY plane Name ino name Z bottom s0 Color Dragon C XZ plane s Inner Radius 10 Mobile points Outer Radius fis SIE There are not mobile po Length The length is 40 mm we supposed that is in millimeters We would like to have this distance also in SIMION B Then we have to enlarge 3D project by resizing coefficient of resizing 10 1 or we can set up parameters of tube by hand C After resizing it is necessary transform our 3D project to a GEM file D Create new project in SIMION by loading GEM file and save result as tube PA I Empty memory in SIMION and create a new project in SIMION F Add tube PA to the new project You can do by pressing button Add in Pas See the following picture
36. ep GI Step OO Sep Gr Chipping step 1 o E CA ee KO Sood Workbench in Virtual Device es a Set geometrical size of the Cross x X center io Color no color Y center io Mobile points There are not mobile points Z center io Rotation around 1 tube io Length a Rotation around 2 tube lo Potential 0 Drawing quality Imer Radius 1 tube 10 Inner Radius 2 tube 10 Outer Radius 1 tube jis Outer Radius 2 tube E OK X Y Z center center of crossing of tube Length length of both tubes Potential it is potential in volts Name name of object Color of object here user can specify color of object Color of object is not used in SIMION Mobile point here user can set connection between geometrical object and mobile point if mobile point was added to project 21 Inner Radius Tube 1 Outer Radius Tube 1 radiuses of the first tube The difference between outer and inner radiuses is thickness of the first tube Inner Radius Tube 2 Outer Radius Tube 2 radiuses of the second tube The difference between outer and inner radiuses is thickness of the second tube Rotation around Tube 1 Rotation around Tube 2 those parameters define angle of rotation around tubes Potential potential in volts Example Set geometrical size of the Cross E x X center Bo Color lgld y center Bo 2 Mobile points there are not mobile po
37. er csu e r r Eo cz eec Gre Rotation Step Step GZ Step VS Distance step 0 5 Axises Grid Moving Step GEI Step 1 Step Z 1 Clippingstep 1 You will get a window of calculator It is not just an ordinary calculator here user can type complicated formulas and quickly create graphs The results of calculation can be stored in text files and hereinafter used in creation of electrodes with axial symmetry axial objects Actually shape of graphs is used as profile of an electrode with axial symmetry The calculator window has the following parts 1 on the left there 1s white space where user can type formulas examples of formulas are in the directory Virtual 38 Device examples_scientific_calculator 2 A blue white chart in the middle is chart where user can see results of calculation as a graph 3 to the right there is option to save results in text format This format is one used for creation of objects with axial symmetry Scientific Calculator Calculation of shape of electrode with axial symmetry uniform sealing x H uniform sealing y H gt X axis Position 0 Xmm X max H N points 100 Save results Close e as Si button to load formulas from text file wm button to run calculation User has to type function in the following format y f x therefore X min and X max define the range of x N points defines how many points will be used in calculation in
38. esults Keen Een eur tt Ce D e teot _peeoe Workbench in Virtual Device Workbench in SIMION It is necessary to notice that default direction of axes in Virtual Device is different from direction of axes in SIMION User can rotate axes in Virtual Device to get the same direction of axes in SIMION 12 Object Cylinder This object presents itself as a solid cylinder with the following parameters Es Potential 0 Name noname Color E Radius io o o Mobile points OK Length EN X Y Z bottom position of bottom of cylinder Radius radius of cylinder Length length of cylinder Symmetry this option defines plane of bottom of cylinder For example if ZY plane was choosen than cylinder will be along X axis Potential it is potential in volts Name it is just a name of object Color of object here user can specify color of object Color of object is not used in SIMION Mobile point here user can set connection between geometrical object and mobile point if a mobile point was added to the project AY plane For example Set geometrical size of the cylinder Ka Potential 0 Name cylinder Z bottom 0 C XZplane Color Dragan ts Mobile pomts There are not mobile po C Y plane Results cme ref amp OFees Dror Pemi soni MM enn lon lennon al Antia mt 9 He waer CH iy ER L i lb Kn d wh wl ben Ba GC Gd HE
39. f saving see picture 31 Run ions Since our ions will fly in an empty space the initial energy distribution will not change 5 Load results of simulation into Virtual Device To see the energy distribution it 1s necessary to create a graph of energy versus number of ions To do this just point out mouse on the table and twice press quickly left mouse button You will see a window where user can make charts with any column versus any column Set up the number of the column for the bottom column 29 number of ions and the left axes column 56 exit energy and press redraw You will see the following Gauss distribution see picture 57 Does ase ha eee oe ee oe ee ee EEEEE EA a aaa aiaa aaa a a Oe a ee er ee R wn rr ae H H lte Ka a Get Joint ge ve ee Wine Ltd et Ve eeler eegenen a a Dt at lge Rn w bet ed Odre Eet Ae We L t mer 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 X axis Left Axis Bottom Axis Number of column 56 Number of column 29 Title ly axis Title Ix axis Redraw Save picture M Marks Picture 57 Results of simulation of Gauss energy distribution Chapter 4 Creation of special Ion distribution disk This part of Virtual Device allows creating ion distribution which presents itself as crossing of many lines see 58 Special distribution disk Distribution of ions The Disk Center of Disk Particle X So Mass amu SC Bo Charge elem
40. herefore total number of points can be estimated from estimation of hole For example we would like to estimate number of points for a system of lenses Example A Symmetry Planar Mirror none The lens of system of lenses is about 50 mm the hole diameter of lenses is 2 mm and outer diameter of lenses is 30 mm The total volume is 30 30 50 45000 mm This volume corresponds to X Y Z 50 000 000 points Suppose we like to use 100 points for diameter It means 2mm 100 points therefore 30 mm 1500 and 50 30 2500 If we base on this estimation then total number of points will be 1500 1500 2500 5625 000 000 Obviously this value is much above 50 000 000 Therefore number of points which can be used in hole is a very important parameter Example B Symmetry Planar Mirror YZ The total number of points can be reduced if we use mirror type symmetry For example let us discuss the same geometrical system of lenses We have supposed that axis of axial symmetry is X axis Geometry can be made only for region X gt 0 Y gt 0 Z gt 0 The region Y lt 0 Z lt 0 is automatically calculated by SIMION if we specify Mirror YZ In that case the total number of points will be 1500 2 1500 2 2500 1406250000 Compare this results with results in example A above we can conclude that by using mirror we reduce total number by four times Hint 3 If you have unintentiously deleted working window and view of project window You can
41. ibed in chapter 1 3 Set geometrical size of the Tube ka X center 80 Potential lo Y center ap Name orifice 4 center 50 Color green Imer Radius 10 Mobile points Outer Radius ep There are not mobile po op Picture 8 Now press OK and you will see the following picture in workbench picture 9 File Additional Parameters PRG as MP P EZ A ee BLOW Tree of mobile points There are not mobile points 4 el se SER Picture 9 Now we will add conical skimmer Choose E or cone with hole from dropdown toolbar and specify geometrical parameters as following picture 10 Set geometrical size of the cone with hole x X center a Length Potential Oo Y center 50 fo Name skimmer 4 center a Color red First Radius inner E Mobile points First Radius outer 20 There are not mobile z Second Radius inner bk Discritization 100 Second Radius outer gS symumnetr C XY plane C XZ plane Y plane Picture 10 Setting parameters of cone with hole Now we will add an electrode which looks like orifice Repeat instructions for orifice and set up the following parameters picture 11 Set geometrical size of the Tube z X center bn Potential 0 center 50 o Name jorifice2 4 center 50 o Color Dragon gt Inner Radius 20 Mobile points Outer Radius 50 There are not mobile po Length 2
42. int here user can set connection between geometrical object and mobile point if mobile point was added to project Example Set geometrical size of the ideal conical grid X bottom 50 Y bottom en Z bottom bn First radius lo second radius 20 Length 30 Potential o Name conical gri Mobile points Results T Mi Ara Warthe k ad Mhi Bea Ze Rang fy BCE e E EE My ome rr G e Dio Sas fe tiere e wees ECE ele Alig FESCH Cader Frist Rare omg e in Virtual Device x Workbenc Workbench in SIMION This grid is almost invisible in SIMION 23 a Object 3D sentence This object allows adding 3D letters to workbench This object 1s not supported in SIMION Set position of 3D text fit doesn t work in SE E eg mer ep X Y Z center these parameters define position of first letter in sentence Size this parameter defines the size of sentence Sentence here user can type letters Rotation around Z Y X those parameters define angles of rotation around axes angles are in degrees Color this parameter defines color of object For example Set position of 3D text it doesn t work in Simion A centre 30 Rotation around z 15000 4 centre en Rotation around y Oo centre en o Rotation around x Bo oo Size 80 Color of object Dragon Sentence V D v 17 Re
43. ion l Ss No type You have to specify max min and the step of energy In that case you will produce a number of ions n max min step Energy will be in range min to max Random value You have to specify max min e max e min The program will calculate linear function f a e b where b e min a e_max e min 1000 Then the program will run a cycle from e min to e max and energy of ions will be E a random 1000 b Total number of ions will be 1000 Gauss distribution User has to specify A sigma EO max min and step In this case max and min means maximum and minimum of Gauss wings in terms of energy energy axis Value A means center of Gauss distribution and sigm ol dispersion As you know maximum of Gauss distribution is about 1 To get Gauss distribution on a higher level Eo it is necessary to multiply Gauss by Eo Program will run a cycle from min to max with step ei current energy in circle on ei A Fe Number of ions is max 200 energy axis Energy distribution will be E min step LOT BER Position of ions X axis Energy distribution ev Distribution of charge in units Minimum Maximum Step Minimum Maximum Step Minimum Maximum Step 50 s0 H 3 D H H H 0 Type of distribution Type of particle Protons C Electrons Position of ions Y axis 8 i C Random value Minimum Maximum Step C Gaussian distribution Ei a fl pa si RE A 0 Suz Eo 100 Position of
44. ions Z axis Minimum Maximum Step Distribution of masses in amu Bo Bo D Minimum Maximum Step 100 Don d Distribution of azimuth angle degrees m proton l amu Minimum Maximum Step m electron 0 000548579903 amu 0 lo d Number of ions 0 number of ion Distribution of elevation angle degrees Minimum Maximum Step Color of trajectories Saye Load 0 lo d 0 Black E Generate JON file Close Picture 53 Creation of list of ions in Virtual Device Save this option stores current parameters in txt file Load this option loads parameters from txt file to window Set up list of ions Generation JON file this option generates list of ions based on parameters and stores it to file in SIMION format 57 For example Gauss distribution Set up parameters as is shown on picture 54 Es Set up list of ions loj x Fosition of ions X axis Distribution of charge in units Minimum Maximum Step EE EE Type of distribution Type of particle i Random value Protons Minimum Maximum Step Gaussian distribution C Electrons C 50 50 il pane A fo s o5 Eo hon PE Distribution of masses in amu Minimum Maximum Step Fosition of ions Z axis Minimum Maximum Step eg 50 fi Distribution of azimuth angle degrees Minimum Maximum Step m electron 0 000548579903 amu i Wu aaae ELLE d g p g 0 0000 500 0000 1 000 000 Numbe
45. lculation of resolving power x Interpolation Type Calculation Threshold First peak Second peak Load data Close 5S Minimum 6 Minimum ja Maximum 105 Maximum 13500 Mass 1 em Mass 2 em Picture 41 Window for calculation of resolving power Gradient tolerance Type of interpolation Normal Distribution 1 5e 08 i Convergence tolerance Cptinuzation method 1 00e 06 Quasi Newton optimization method e Wax number of iterations 2000 OF i Picture 42 Window for specification of type of regression 3 Set up threshold This parameter defines the level where resolving power calculates 4 Set up peaks which will be used for calculation of resolving power Minimum Maximum defines left and right wings of peak Mass 1 2 parameters defines masses which correspond to both peaks 5 Calculation of resolving power To calculate resolving power just press button Calculation The results of calculation are presented on picture 43 The red color is approximation of peaks The results of calculation are in window Results Button allows save picture in file bmp format 50 Calculation of resolving power x First peak a Function b0 B1 sqrt 2 3 134159 Exp 0 5 S qr b0 112 562716909121 bi 0 322677041313192 b2 7 29998450900873 one side 6 46757506762619 second side 8 13239395481021 midle 7 2999845112182 Second peak Function b0 B1 sqrt 2 3 13
46. le The advantage of this way of creation is the following 1 Very quick creation of 3D geometry 2 Very simple way of rearranging of geometry shifting moving electrodes relatively to each other 3 Automatic transformation of 3D geometry into geometrical file GEM file The disadvantage of this way of creation is only one not any 3D geometry can be created into Virtual Device due to finite number of electrodes But this limitation can be overcome by increasing the number of typical electrodes At this moment total number of typical electrodes 1s 14 which covers about 90 95 of typical ion optics schemes Analysis of results of simulation SIMION gives possibility to save results of simulation into a txt file and format of this file is open see SIMION manual Therefore user can write his her own software to analyze results of simulation or use some well known mathematical software Actually there are several standard procedures often used in ion optics building ion distribution in different planes phase distribution in different planes creation of histograms of specific ion optics parameters for example time of flight calculation of resolution of energy analyzers and mass spectrometers Virtual Device gives possibility to make such standard procedures as ion distribution phase distribution in different planes calculation of histograms of exit parameters therefore definition of shape of peak transformation of time of flight into
47. m rn Ae e SE Workbench in Virtual Device Workbench mm SIMION Discritization 100 So user can see the difference in pictures SIMION workbench for different values of discritization Therefore user has to remember about this parameter When user defines value of discritization it means that user defines the thickness of slice The thickness of slice has to be less than or equal to length of cell It is because roughness of geometry is completely defined by length of i cell Workbench in SIMION Discritization 5 T Object Cone with hole This object presents itself as a cone with hole with the following parameters Set geometrical size of the cone with hole 4 Ka Potentia Name no name o Mobile points First Radius inner 10 e ZY plane First Radius outer GO There are not mobile second Radius inner E Discritization 10 second Radius outer S OF X Y Z bottom position of bottom of cone First Radius inner First Radius outer outer radius defines radius of cone at one end of cone inner radius defines radius of hole at the same end of cone Second Radius inner Second Radius outer outer radius defines radius of cone at the second end of cone inner radius defines radius of hole at the second end of cone Length length of cone Symmetry this option defines plane of bottom of cone Potential it is potential in volts Name
48. mass charge terms and calculation of mass resolution It 1s also possible to transform data to Excel format Initial ion distribution SIMION provides creation of initial ion distribution but until recently some key features have not been realized in SIMION At this moment SIS has developed new format of creation of ion distribution But this feature is available only online Virtual Device gives possibility to create initial ion distribution as it was realized in version 7 and to create some specific ion distribution for example Gauss distribution of energy Main menu of Virtual Device The main menu looks as following irtual Device Y 17 close software Sa run program to create 3D model Si create ions distribution analyze SIMION data Ee rz create special ion distribution disc create special ion distribution point source A about author To run any part of software it is necessary just to click the appropriate button by mouse left mouse button Chapter 1 CAD program Chapter 1 1 Menu This part of software covers creation of 3D project and transformation it to GEM file It consists of three windows Workbench The first one is workbench where user can see 3D geometry Below there is an example of 3D geometry picture 1 You can rotate 3D geometry by moving mouse with left button pressed The grid shows the size of the project All parts that are beyond the grid will be cut by SIM
49. metrical object from object This window also Tree of objects points contains a tree of the project and a tree of mobile points No objects Tree of project When user ER iC New project adds new geometrical object to project a new item CR New project a gt Eko appears in the tree of d S VE project The pictogram in Seka es tree shows what kind of etl object the user has added to 3 E skimmer 1 project The tree shows total F number of geometrical objects in the project type of object the tree can also be used for editing deleting and suppressing objects see modes of working Tree of mobile points The tree of mobile points shows how many mobile points the user is using in the project This tree can also be used for editing and deleting mobile points Picture 3 Working window The three modes of working with project User can work with project in three modes The first mode Edit object is the mode where user can add and edit parameters of geometrical object To edit an object user has to pick up appropriate pictogram in the tree of project The second mode Delete object is the mode where user can delete object from project from tree To delete geometrical object from project it is necessary first to choose mode Delete object and second to pick up appropriate pictogram in the tree of project The third mode is Suppress Unsuppress It is the mode where user can make one of geometrical obje
50. negative axis Picu 63 It is necessary to note that creation of ions along Y axis is complicated due to an internal problem of SIMION v 7 This problem was resolved in version 8 Chapter 6 Main parameters of mass spectrometers energy analyzers Let us discuss briefly the main mass spectrometers parameters relevant to different ways of 10n separation Dispersion This parameter defines how mass spectrometer can effectively separate ions according to mass charge ratio Suppose we have mass specter which was got by scanning a 62 parameter For example parameter can be magnetic field or accelerating voltage The increment of as function of mass can be presented as the following series we suppose charge 1 2 Am a A a gege m m where is often called dispersion when Ao is a distance between two peaks m and Am 2 A If we take the first term of the series then dispersion can be expressed as follows D m Am where Axis distance between two peaks It is necessary to note that some scientists regard dispersion as Ax only From our point of view is not a good definition because Ax becomes A SCH RER SSC function of 2 therefore it is necessary to specify ratio TT each time when dispersion 1s m m discussed Our definition 1s more convenient because the value of dispersion depends only on geometrical and physical parameters of mass spectrometers Resolution resolving power in mass spec
51. nts Z center en Rotation around 1 tube o o Length bo Rotation around 2 tube o Potential E Drawing quality Inner Radius 1 tube T Imer Radius 2 tube P Outer Radius 1 tube 15 Outer Radius 2 tube 18 Results Be algi x Lf ermal Santer kx KE Fig adioa Peamter PRG Eanna SE py Ce cereal jose FEL BOCOOG DRLO ie Bonge Sept Step OO H Sep Or D Distance step 0 1 Axises Grid EY Moving Step Or Step Oth Step Zi Chipping sefi Workbench in Virtual Device Workbench in SIMION Drawing quality this parameter defines quality of drawing of cross in Virtual Device only and it does not influence results of transformation of cross to SIMION User can set up drawing quality of cross according of users video card The high value of drawing quality leads to decreasing of velocity of redrawing of cross during rotation 22 E Object Ideal conical grid This object presents itself as an ideal conical grid with the following parameters Set geometrical size of the ideal conical grid xj X bottom lo symmetr lo SR Zooo ien Mobile points 10 There are not mobile GR sc ox X Y Z bottom these parameters define position of bottom of conical grid First second radiuses radiuses of both ends of conical grid Length length of conical grid Symmetry this parameter defines plane of bottom Potential potential in volts Name name of object Mobile po
52. oject starts rotate around axis with some step Steps of rotation can be settled up in toolbar is described above This toolbar also gives possibility of to change point of view Type of view Clipping view allows cutting off a part of 3D geometry and seeing geometry from the inside Clipping plane is invisible which is always parallel to the screen By pressing mouse button on buttons of Clipping view user can move clipping plane forward back compared with the plane of screen When the clipping plane crosses a geometrical object a part of an object situated between the clipping plane and the plane of the screen will be cut off Step of moving of the clipping plane can be settled up in toolbar described above Clipping step View of project Ka Rotation around A Rotation around XS Rotation around Distance 40 lait lt q 189 ai P Move Gi Move CO Move 4 Type of view Clipping View Klak ak lt gt Picture 2 Toolbar for rotation moving and clipping of project To move project in space in workbench window it is necessary to press buttons Move X Y Z It can be done by left mouse button Step of moving can be set up in a toolbar described above x Working Window picture 3 This window gives The modes possibility to create project to save project to file to PERE load project from file to transform project to ei Grieg e geometrical file to add geometrical object to project to Suppress Unsuppress delete geo
53. olid cone with the following parameters x Faa bottom 0 C XZ plane Color no color First Radin f0 X Y Z bottom position of bottom of solid cone First Radius Second Radius radiuses of both ends of the cone Length length of cone Symmetry this option defines plane of bottom of cone Potential it is potential in volts Name it is just a name of object Color of object here user can specify color of object Color of object is not used in SIMION Mobile point here user can set connection between the geometrical object and the mobile point if a mobile point was added to the project Discritization this parameter defines how a solid cone can be made in SIMION Actually a solid cone as a geometrical primitive does not exist in SIMION language But it can be build as a number of slices with different radtuses Therefore discritization is the number of slices This parameter influences only 3D view in SIMION C AY plane For example Set geometrical size of the solid cone E KOU X bottom 50 SC Potential o bottom Er Name solid cone Color jred 5 Mobile points Points M C XZ plane C AY plane Second Radius 10 Length 60 Diseritization 100 Results merely RH KEIER Py EECH aiaj Dms oanet FFs A AS ge ne w coe E Rotates Step 0 1 Sump DOE Swap DEL Dinance step 0 1 Arbes Grid A REISER 23 peters SS See e265 E E EE r
54. orkbench in SIMION Object Ideal plane grid This object presents itself as a box with thickness of one cell According to SIMION rules any object with thickness about one cell will be regarded as ideal grid Ideal grid is described by the following parameters Ideal plane grid E Ka SE A center pn Potential b o o ose center oO o Name no name Z center oO o Mobile pomts X length 2 ho po Y length 2 jio ok C XZ plane C ZY plane Symmetry this option defines plane of grid If XY plane is chosen then user has to specify length along X and Y axes If XZ plane is chosen then user has to specify length along X and Z axes If ZY plane is chosen then user has to specify length along Z and Y axes X Y Z center position of grid center Potential it is potential in volts Name it is name of object Mobile 18 point here user can set connection between the geometrical object and the mobile point if a mobile point was added to the project For example Ideal plane grid A center 50 o Potential oO o center en o Name lideal grid Z center 50 o Mobile points Zlength 2 bn Wiere are not mobile po C XZ plane ZY plane Results heresy Ma Y Mekbech Yy Catur kW premejo e er Workbench in Virtual Device Workbench in SIMION e Object Box with split This object presents itself as a box with split with the following paramete
55. ou will get the following results Scientific Calculator Calculation of shape of electrode with axial symmetry example of calculation Y sinis exp x 5 uniform scaling x 1 fio uniform scaling jlo a Position 0 Xmin 0 X max fio N points 100 Save results Close Now save results in some txt file launch a new axial object and load data from your txt file Remember that you have to specify axial symmetry for axial object as Z axis because you have saved results of calculation in Scientific calculator with Z axis of symmetry Do not forget to set up correct parameters for SIMION project as is shown on the following picture Length of X axis units 100 Length of axis units 100 Length of Z axis units Jon Name of project New project Number of points 1000000 Data for SIMIION Symmetry planar Mirror w YS Field type Electrostatic Magnetic scale factor i If you do all correctly you will get the following picture in Virtual Device and it is equivalent in SIMION bow Work ben h amd DE ee een GE Sat cal fl EE Cal enn L t pe E le cam FEI OS ee E Rotation Step D Step QO 05 Step DK Distance ant 5 Axises Grid Moving Step X 1 Step Dir Sep OK Clipping step 1 To create such electrodes I spend about several minutes How many hours do you spend to do the same There are more examples in directory Virtual Device examples_ sci
56. parameters define the number of disks that will be created and which parameter will be changing from disk to disk Example 1 Set up the following parameters and press Generate JON File Virtual Device will generate a distribution which presents itself as a series of crosses where ion mass varies from 1 to 500 with a step 100 amu Special distribution disk O x Distribution of ions The Disk Conter of Dist Paytisla Making many disks Mass X Bo Mass amu id Max il Ke 50 Charge elem u H Min 500 Z 50 Energy ev f i Radius of disk Symmetry of the beam SEN Io 40 0000 500000 egen b 50 0000 Xaxi Z axi lo XY plane Direction of the beam a BE positive axis Number of ions Radial step XZ plane b negative axis mm mm EEEE D YZ plane Save data Angle step degree CC 150000 f g bo Color of trajectories ___Loaddata fee engl i 50 0000 lo Black i i Z axis OK Picture 59 Ion distribution cross Example 2 Set up parameter Angle step degree 10 and press Generate JON File Virtual Device will generate the following distribution as disk see picture 60 This distribution is 5 disks where the first disk is ions with mass 1 amu the last disk is ions with mass 500 amu Special distribution disk Radius of disk en Radial step Angle step degree pe Dist
57. r expresses 3D geometry of the whole project in SIMION language Chapter 1 2 How to create 3D project The creation of 3D project can be split into several steps 1 Setting geometrical size of project and all necessary parameters for SIMION 2 Creation of electrodes 3 Transformation of 3D geometry into GEM file Step 1 Setting initial parameters of project can be done in the following way Press button or choose Set geometrical size from dropdown list of tree of objects points You will see a window picture 4 which is equivalent to window in SIMION picture 5 Length of X axis length of project along X axis Length of Y axis length of project along Y axis Length of Z axis length of project along Z axis Name of project this name is just a name of project and it is not used in SIMION Symmetry defines the type of symmetry Planar means 3D volume see SIMION manual Mirror here user can set up type of mirror For example none means 3D volume does not have any symmetry The details of types of symmetry are discussed in chapter 1 4 Type field defines what kind of field can be used electrostatic or magnetic field Magnetic scale factor default value zero When user has settled up geometrical sizes along the axes Virtual Device calculates total number of cells If total number of cells exceeds the value 50 000000 then Virtual Device warns you about it see picture 6 This warning does not play
58. r of ions 1002 number of ion Minimum Maximum Step Color of trajectories Save I Rea E Generate JON file Picture 54 Generation of Gauss distribution epecce eee ne fee gee eee eer ee GK EN EEN p f 4 ms Ee ee ees ee ee leee eebe zs eeee be e bass fa sm zm zm ais ms zm zm zs cb TILLIT ease de eeeeeeelle e se ee a dia n ee d e m proton 1 amu ll te Aea belated tated de Distribution of elevation angle degrees 1 Press button Generation ION file and specify file where ions have to be stored for example gaus ion ion 2 Now you have to create an empty project without electrodes see picture 55 Max PA Size 1 020 000 Pts Picture 55 Creation of new project in SIMION 4 Load list of ions from file gaus 1on ion You can do it by pressing button Load ION in Defines Ions Individually See picture 56 Define Ions Individually Time of Birth 0 00000000e 00 usec Ion s Mase 1 000000000e 02 amu Ion s Charge 1 000000000e 00 Units First x 5 000000000e 01 mm First y 5 000000000e 01 mm First z 5 G00000000e 01 mm Azimuth 0 000000000e 00 Deg Elevation 0 000000000e 00 Deg Ion s KEO 2 4788 76028e 00 eU CHNP 1 000000000e 00 Color 1 Draw Marker Steps 1 000e 00 usec Color 1 Picture 56 Load list of ions 58 4 Specify files where results of simulation have to be stored Do not forget about format o
59. restore those windows by choosing Additional Parameters view all See picture 19 3D iew Workbench and PRG files mr Ae eet PDX ef peice Le T Step Oth Step Gr Distance step 0 1_ Axises Grid Gi Moving Step 1 Step Gr Step 1 Clipping step 1 Picture 19 Hint 4 User can automatically set up the same potential for electrodes which have the same color For example you have 10 electrodes with some color say red Then choose Additional Parameters Set Potentials by color See picture 20 Picture 20 31 Then you will see the following window picture 21 Specify color for example red and value of potential By pressing Set potential user automatically sets up value for all electrodes with red color Set potential Ka Color ino color Set Potential o Set poten tential Picture 21 Hint 5 Resize project It is intuitively clear that it is more convenient to create a 3D project in millimeters But SIMION deals with points To make users life easier option Resize project was developed User can change the size of geometrical object by setting coefficient of multiplication Geometrical parameters position of center bottom length and so on will be changed by multiplication by this coefficient For example ID Ai a1 Fle E Se ame Tec eeeees Enter ratio new value old value T Results 32 Now user can transform 3D g
60. ribution of ions The Disk Center of Disk Particle X Bo Mass amu fo SC 50 Charge elem u il Z Bo o Energy ev fo Symmetry of the beam XY plane C XZ plane C YZ plane Color of trajectories Making many disks Max 00 Mis Step ho Direction of the beam e positive axis negative axis Save data Load data A 40 0000 50 0000 60 000C Picture 60 Ion distribution disk Z axis Number of ions Picture inside the window shows ion distribution as it looks in SIMION 60 This kind of distribution can be very useful in ion optics investigation where user would like to investigate how first image transforms to second image If ions distribution during the transformation in 10n optics does not change then this ion optics is ideal Chapter 5 Creation of special ion distribution conical distribution This part of Virtual Device allows creating ion distribution which presents itself as conical distribution see picture 61 Ions start from a point source and fly under two angles according to axis Special distribution conical distribution ID x Distribution of ions The comecal distribution Center of distribution C along Z axis K o Mass amu i e DE o Charge elem u i asa cams Ke o Energy ev i Direction of the beam D positive axis Az angle degree Elev angle degree C negative axis D D S Save data Az
61. rs Box with a split o ax Potentia xeos yems Mobile points There are not mobile po OK X Y Z bottom position of bottom of box X Y Z length length of box along axes Symmetry this option defines plane of bottom of box Potential it is potential in volts 19 Split those parameters define radius of splits along appropriate axes If radius exceeds length then radius is automatically reduced Name it is just a name of object Color of object here user can specify color of object Color of object is not used in SIMION Mobile point here user can set connection between the geometrical object and the mobile point if a mobile point was added to the project For example Box witha split X bottom bn Potential 0 Y bottom 50 X split bn Z bottom 50 Y pli po X length CS Name box with split length so oo Color Z length fo Mobile points There are not mobile po 7 OK Results 9 view Workbeera hh and PRG ikes ell Sl Pie Addtional Poraneters Pa came Cel 6OCOSG Greg Rotation Step Step Dr bh Step Dr Distance step 0 1 Axes Grid ei Moving Step ON Set O Se Gr Clipping step 1 mg Ir S Je ed eh da de A SE SE eben Ae at e Workbench in Virtual Device with the tollowing parameters X centr io 0 no name Mobile points X Y Z bottom position of bottom of segment Inner Radius
62. shape txt Now create a new axial object see any axial object and load data from fresh baked file my_shape txt you will get axial object with the following surface 39 This electrode is quite small because sin x is range 1 1 To increase all data proportionally just change uniform scaling x and y to 10 and save results you do not need to recalculate Load the new data into your axial object and you will get the following results left picture 3D iew Workbench and PRG files LI x File Additional Parameters PRG video S_Calculater c m E FT Ff AO we BLO Rotation Step Z J Step X 0 5 Step Gr bz Distance step 0 5 Axises Grid Moving Step OCH Step lt Step 1 Clipping step 1 Length of X axis units Won Length of Y axis units 100 Length of Z axis units 100 Name of project New project Number of points 1000000 Data for SIMICORN Symmetry planar Mirror YZ 5 Field type Electrostatic Magnetic scale factor po As you can see the uniform scaling coefficients are just scaling coefficients Now specify parameters for SIMION project as is shown on the right picture above then create gem file and load this file to SIMION As a result you will get the following picture ER WEE fe Le i 40 Example 2 Now load formulas from file my example txt Specify X range as 0 10 specify axis of symmetry as Z axis uniform scaling coefficients as 10 Y
63. sition bie Name point 1 z OH Points E point 1 You will see that all electrodes will be automatically shifted Therefore mobile point allows changing positions of all electrodes associated with mobile point at the same time If you do not use mobile points then you have to change positions of all electrodes step by step by hand 37 D 3D view orkbench and PRG files File Additional Parameters PRG cs mr EE ff A D Z D ee EF SIE M Rotation Step D I Step Ob Step 0 1 Distance step 0 1 Axises Grid E Therefore you can evaluate how useful mobile points are Chapter 1 7 Scientific calculator Introduction The main purpose of scientific calculator is to increase speed of development of electrodes with axial symmetry Some electrodes profiles can be described by analytical expressions Virtual Device provides possibility of fast building of such electrodes The creation of electrodes is based on translation of arithmetic expression which is just a text to code which can be executed by computer The are many possibilities of translation but we base on so called reverse Polish writing We shall not go into details of how this algorithm works The details of algorithm used in Virtual Device are published in 5 To run calculator pick up S_Calculator Calculator as is shown on the following picture 10 3D view Workbench and PRG files File Additional Parameters PRG video 5_Calculat
64. sults 3D iew Workbench and PRG files File Additional Parameters PRG as MP P EZ AO ge BLOW 24 E Object Any axial object This object gives possibility to create a geometrical object with axial symmetry where shape profile of electrode is given Axial object eee x Axis of symme ie E ae Color of object of object Color of object no color D Mobile Mobile points Mobile points There are not mobile point Discritization 10 File here user can specify the file where shape of electrode is stored The format of file is discussed bellow The file describes inner surface of electrode Thickness here user can set up thickness of electrode The outer surface of electrode is defined as inner surface plus thickness Color of object here user can specify color of object Color of object is not used in SIMION Mobile point here user can set connection between geometrical object and mobile point if mobile point was added to project Potential potential in volts Name name of object Discretization this parameter defines how this geometrical object can be made in SIMION Geometrical object with axial symmetry can be build as a number of slices with different radiuses Each slice is presented as a round electrode with a hole Radius of the hole is defined by data from file The outer radius is radius of the hole plus thickness Therefore parameter discretization is a number of slices It influences only
65. the given range Button Close closes the window Position shows the position of cursor in area of formulas That can be very useful when user has made mistakes Scientific calculator reminds about error and names the position where error occurs button to save formulas in text file It is necessary to note that user has to use function y f x because this part of code interpreter of code was imported to Virtual Device According to axial symmetry it means X axis is axis of symmetry Y Z axes of radius To have access to other axes of symmetry we just add possibility of changing axis of symmetry when data will be written to file For example user types a function y f x but chooses Z axis as axis of symmetry to the right of calculator window Therefore X axis will be substituted by Z axis The example of that is shown below The best way to learn how to use Scientific calculator 1s just to repeat several examples Example 1 type the following expression Y sin x 3 and set up range of X 0 10 p Press button and you will get the following chart Scientific Calculator Calculation of shape of electrode with axial symmetry example of calculation A Ve simdvlci ECKE EWECH ETC EE uniform sealing x lo uniform scaling Get i 0 1 4 k Position 0 Xmm g X max j10 N points on Save results Close Save data press button Save results and specify file name for example my_
66. trode is missing you can inform the author kol sergei yandex ru and your electrode will be added to Virtual Device 29 Chapter 1 4 Useful hints This chapter covers some useful hints and suggestions Hint 1 The quality of 3D geometry in SIMION is strongly dependent on the number of points per millimeter Therefore it is better to set up as many points as possible But there is limitation for total number of points maximum number 50 000 000 in version 7 This limitation can be overcome in two ways First way User can set up a 3D project with different number of points per millimeter It 1s better to first create a geometry with rough grid and then with precise grid within the former Two instances will overlap each other For example Two cones with different density The cone with precise grid is placed at tip of the cone with rough grid Picture 18 Two cones with different density of points per millimeter Second way Sometimes 3D geometry can be splitted up for several instances which do not overlap Therefore user can set up about 50 000 000 points for each instance In this case total number of points can be much more then 50 000 000 points Hint 2 When setting number of total points it is necessary to take into account how many points are in the most narrow hole or split If it is supposed that ions have to come through a hole then field in this region has to be calculated very carefully T
67. trometry It is supposed that ion with mass m corresponds to position x and m Am corresponds to x Ax Ax can be expressed in terms of dispersion Ax D E We can resolve two peaks if Ax gt d where d is width of peak at base m of peak we suppose that both peaks are equal Therefore resolution of the mass spectrometer can be expressed in the following way R m Actually assumption about equality of peaks is not true Therefore we have to m D take into account the difference in width of peaks Resolution in this case can be expressed as follows R E m m d d d d the widths of peaks at base 2 Resolution is often defined at level 50 or 10 of intensity of peak Therefore d d are widths of peaks at those levels see picture 39 where m m masses of ions which correspond to two peaks 15 0000 16 0000 17 0000 18 0000 19 0000 20 0000 Picture 39 Resolution in electron spectroscopy The definition of resolution in electron spectroscopy is slightly different from definition in mass spectrometry Resolution can be expressed as follows in percent R 100 where AE is width of peak at level 50 of intensity of peak E is energy of peak center of peak 3 4 But in principle it is possible to use other threshold level It is necessary to note that in electron spectroscopy resolution R 100 is used but in mass spectrometry resolving power is used R A m 63 Terminology
68. tself as a number of wires Set geometrical size of the real plane grid E E x Potential o Name noname 4 center lo C XZ plane Color Mobile points Length 20 There are not mobile poin Radius of wire D Distance 3 OK X Y Z center position of center of grid Length X Y Z defines sizes of grid Radius of wire defines the radius of wire Distance defines the distance between wires Potential potential in volts Name name of object Color of object here user can specify color of object It is not used in SIMION Mobile point here user can set connection between geometrical object and mobile point if mobile point was added to project 28 For example X center 50 Potential 0 center 50 Name real grid 4 center 50 Color Dragon Grid in plane Length Cx 40 Mobile points Length 40 iere are not mobile ponts Radius of wire p Distance 3 Results Hs Yere i Wrk ie Rotation Sept D I Step Gr Step Dr Distance get Anise Grid AL Kee Sek eech pack eech b ze Workbench in Virtual Device Real grid Workbench in SIMION Real grid The advantage of real grid is the following The real grid can be arranged as a single fast adjustment electrode therefore user can quickly change potential on grid Dear User at this moment there are 14 geometrical objects If you feel that some important type of elec
69. uild histogram of exit parameter see picture 37 Histograms 40 0000 24 30 0000 feu li ef 20 0000 JI ei IST k 10 0000 ut CC i LL ug i J l al 10 0000 Deiane L P 54 9027777200 V Histogram Substr time jo l Normolyzed 36 0817240200 Reealeulate Save data Close Picture 37 Creation of histograms User can set up exit parameter from dropdown list intensity vs As definition as it show on picture 36 Virtual Device calculate intensity of time of flight Marks this allows switching on off labels grin numbers in blue rectangle Histogram allows to switch between histograms red lines and envelope curve of histogram grin lines see picture 38 47 eee ee eee eee eee ee eee ee ee ee ee ee e mmm mm mm mm mm mm mm mm ee ee ee ee r ee en ee ee ee ee a aaa er 1 elek gie Aaler ie Bertels wane nn en EE ECKE DEET ET UL 4 s a 4 pb oo ee er ner qh ee Ee ee a ae ee ee ee ee ee ee en Je A 1 ee an en eee l eee a ate ed VC aed weit bester Die ett Kegel tee Uu ote adie egent a aad eet CH aetna alee Wett ted ied litle 1 task 3 br degen vor wien et Jet Cp edo Cl Use le bale sm eesessesedsessssseagssszbkeesseadsssssssssleassseszbassdssssssessbkasssssesssglsessssessstsesesdhlsssessssessshsebsseseesseessssssmssm em mm zm mm mm zm mm mm zm mm olu o o o o o o o kub ee o vm mm zm zm mm em zm mm mm zm mm mm mm mg wm wm zm mm mm mm

Koltsov S. Manual Saint Petersburg 2006

Contents

Download Pdf Manuals

Related Search

Related Contents