MALTS user manual
Contents
1. in both the x and y directions In general a larger matrix size will allow for better image simulation If you select a value smaller than the number of meshes in the x and y directions the box will turn yellow until the problem is rectified X mesh size this is the size of the mesh used in the x direction in the micromagnetic simulation Ideally this should be small for optimal image simulating It is also recorded in the text file as xstepsize Y mesh size this is the size of the mesh used in the y direction in the micromagnetic simulation Ideally this should be small for optimal image simulating It is also recorded in the text file as ystepsize Z mesh size this is the size of the mesh used in the y direction in the micromagnetic simulation It is also recorded in the text file as zstepsize Value multiplier this is recorded at the start of the text file as valuemultiplier File output name this is what the LTEM image file will be saved as MALTS saves both a screenshot of the user interface and the Lorentz image as image files into its directory To avoid overwriting change this name every time you run MALTS Do not use the same name as that of the data file since this will cause the data file to be overwritten Beam divergence radians defocus um spherical aberration coefficient mm and accelerating voltage kV are all experimental values corresponding to the specific LTEM e2. 32734 580266 80271826743 96 173117055506623 550794 74146465107 574438 51588814100 85 082799420955782 201759 0307 3102739 569584 15067805746 70 394895298924851 563806 35524621536 967558 260847387757 75 305460121731329 564158 46558096912 567228 16032361682 r0 077822524308360 564897 05566149 706 560472 09036531821 8 035910384374588 53608226 13631697360 563133 24149159901 101 65357092679196 574190 97978480917 557050 00026011048 126 260944091604697 582453 49693705235 548404 868115576057 156 62993400176802 0 00000000000000000 0 00000000000000000 0 00000000000000000 242315 035733604578 588127 871053409760 960 474857904613799 561927 70176292601 5609418 28431707912 89 096723808863297 5600795 60572341358 564572 994387083609 85 587832513555796 567896 51890189026 563465 64864963759 81 307799524956451 205978 92458165622 505391 70089094520 84 188587988215488 563560 93014684040 267801 96380671114 88 934078696475211 560076 62458070740 565293 94557696686 100 981869456030041 573519 37120444782 557741 44283380092 11 46882400568512 0 00000000000000000 0 0000000000000 0000 0 00000000000000000 0 000000000000000 00 0 00000000000000000 0 00000000000000000 562513 0625010602352 568839 53132906579 960 273887348171954 581209 01450564922 549723 03251571928 96 494011913267201 572820 602311842642 558459 06252301077 96 000716582065948 574141 54864631745 5357100 95416536101 94 79479
3. 35057477760 5696 76 35870912834 561666 126136977235 95 279534645907901 559902 97593885812 571409 35200734565 99 8606899060025115 329353 019107370607 571947 12878931127 103 25280925490836 0 00000000000000000 0 00000000000000000 0 0000000000000 0000 0 00000000000000000 0 000000000000000 00 0 00000000000000000 0 00000000000000000 0 00000000000000000 0 000000000000000 00 0 00000000000000000 0 0000000000000 0000 0 00000000000000000 0 00000000000000000 0 00000000000000000 0 00000000000000000 504402 42069839290 5606965 51592620621 106 11435872178689 580908 40293728083 550041 28586963180 105 99877 301724659 5377176 86860727204 553955 603927134487 109 83705893407384 553810 28092747717 577316 34261435096 115 27973959094388 0 00000000000000000 0 00000000000000000 0 00000000000000000 0 0000000000000000 0 00000000000000000 0 00000000000000000 0 00000000000000000 0 0000000000000 0000 0 00000000000000000 ALAARE 15 0 h Segment Figure 3 Text to be deleted at the end of the text file before computation is highlighted in blue NAME OF DATA FILE example BEAM DIVERGENCE radians 0 01e 3 DEFOCUS microns 1600 SPHERICAL ABERRATION COEFFICIENT mm TILT AXIS degrees from x axis ANGLE OF TILT degrees NUMBER OF MESHES IN X DIRECTION NUMBER OF MESHES IN Y DIRECTION NUMBER OF MESHES IN Z DIRECTION X MESH SIZE nm Y MESH SIZE nm Z MESH SIZE nm 20 MEA
4. 46637 5380388 71211018378 169 17900515029 IN X DIRECTION DOOOCOOOOOOO00 0 OOO00000000000000 0 OOOOROOROORO JETE ee RR RR A vrei Ooo00OROOR00000 0 OooOROOROOROOROOR 0 00000000000000000 0 00000000000000000 564455 14738008485 566913 023125314429 103 96876382065231 55 7490 53435751610 573763 27329194895 101 60255596153871 5534554 22552721272 576001 70943068032 102 17299934033372 555997 27058092352 573210 41061093961 109 32848695904734 556836 753384851708 574395 84609872801 119 15098414465105 556232 03448914329 574983 39532659180 137 50189994003676 5539705 90466531343 571602 37568196817 156 19703281060507 568694 23584745964 562660 49932310684 169 16071020319313 0 00000000000000000 0 00000000000000000 0 0000000000000000 569443 93277215795 561901 76541132736 116 002636812069000 5603912 033605973895 5674535 20520881557 100 48677144935574 560107 31144719548 Figure 2 Example file from OOMMF 1 to show which parameters to enter into the MALTS GUI red Text to be deleted at the start of the text file before computation is highlighted in blue Ej example Notepad File Edit Format View Help 5307292 989379609003 88 405264977273390 565919 23538447788 505451 50734709984 108 90391286331705 5606191 61459721311 565178 76651972590 132 04181886405237 201002 98835446511 570329 39835299784 156 30632001462881 559658 08371105720 971649 20887195563 106 45625568648789 550718 102493
5. MALTS USER MANUAL Introduction MALTS Micromagnetic Analysis to Lorentz TEM Simulation is a generalised tool to simulate Lorentz Transmission Electron Microscopy LTEM contrast of magnetic nanostructures It works in conjunction with the open access software Object Oriented Micromagnetic Framework OOMMEF 1 or MuMax 2 which computes the magnetisation state of the object of interest MALTS then computes the magnetic and electric phases accrued by the transmitted electrons via the Aharonov Bohm expressions The transfer and envelope functions are used to simulate the progression of the electron wave through the microscope lenses The final contrast due to all these effects is determined by Fourier Optics For further details of how the computation is performed please see 3 Although the MALTS software was developed in MATLAB the standalone executable exe file can be used on a computer which does not have MATLAB installed so long as the correct version and platform of MATLAB Compiler Runtime MCR is downloaded If you would like to acknowledge the use of MALTS please cite 3 Step by step instructions for operation Use the micromagnetic solver OOMMF or MuMax to compute the magnetisation state of the object desired Load the omf file computed by OOMMEF or MuMax in the mmDisp screen of the OOMMF software Go to File then Save As and select text in the middle at the top Specify a file name and location and press ok Open the fil
6. N INNER POTENTIAL OF MATERIAL V 26 ACCELERATING VOLTAGE kV 300 300 250 200 E gt 150 100 50 50 100 Permalloy 26V Cobalt 25V SIZE OF MATRIX iron 25V Nickel 24V 64 v FILE OUTPUT NAME VALUE MULTIPLIER exampleoutput 1 ELECTRIC COMPONENT LTEM PROFILE cmin 200 250 300 lt a ie cmax lt a ie Figure 4 the Graphical User Interface for MALTS Shown here is a simulation for the example text file shown in Figures 2 and 3 of LTEM Fresnel mode contrast for a uniformly magnetised nanodisc of dimensions diameter 50nm thickness 20nm 1 Donahue M J and Porter D G OOMMEF User s Guide Version 1 0 Interagency Report NISTIR 6376 National Institute of Standards and Technology Gaithersburg MD Sept 1999 http math nist gov oommf 2 Vansteenkiste A and Van de Wiele B MUMAX A new high performance micromagnetic simulation tool JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS 2011 323 2585 2591 3 Walton S K Zeissler K Branford W R and Felton S MALTS A tool to simulate Lorentz Transmission Electron Microscopy from micromagnetic simulations Appendix treatment of tilt in MALTS Consider a LTEM simulation with a single mesh in the z direction If the sample is tilted by angle of tilt degrees about the x axis the electron beam will no longer see the same sample dimensions and instead see its projection on the xy plane The sample will appear thicke
7. _OOMMF rectangular mesh ee 0 Segment count 1 Begin a Begin Heacer Title NewOOMME examp e Oxs _TimeDr iver Magnet i zat ior 00 3004892 omf Desc Oxs vector field MJ source file E NewOOMMF Iter MIF Desc Iteration 4892 tate id Stage 0 Stage iteration 4892 Desc Stage simulation time 2 72908e 009 Total simulation time 2 72908e 009 s meshtype rectangular meshunit m 2 5090000000000001e 009 ybhase 2 5000000000000001Le 009 zbase 1e 00 3 xstepsize 5 0000000000000001e 009 ystepsize 5 0000000000000001e 009 zstepsize 2e 008 xmodes 104 ynodes 104 znodes 1 xmin 0 ymin 0 zmin 0 xmax 4 9999999996099998e 006 ymax 4 99999994579099998e 008 zmax 2e 008 valueumit A Valuemultiplier 1 ValueRangeMinMag 799999 45599999988 ValueRangeMaxMag 600000 0G 00000012 End hoader Begin Data Text i VeQHOO000000000G 0 o000Q000000000000 0 000000000000000E NUMBER OF MESHES 0 00000000000000000 737 592316 1528256266 24 2 44023 50204 sig 3298379240092 ds 1080920811 NUMBER OF MESHES 2 34 N Z DIRECTION VALUE MULTIPLIER 0 0990000000 IN Y DIRECTION _ oo00000000000000 0 00000000000 OOoOoDoOOO0O0000000 0 00000000000000000 O 00008D00000000000 0 00000000000000000 549243 272006526487 581662 97297300 93406775931 583047 85103849613 126 89440459335 98852888052 132 63918608511617 556077 699634591 N UMBER OF MESHES 604 503269729 549099 14244790154 581799 02649462 E 6005998
8. e that you have just saved in a text editor Make a note of the value of multiplier written in the pretext then delete any text before up to and including Begin Data Text and after starting from End Data Text the main numerical data This is shown in blue in the example Save this edited text file in the same directory as your MALTS software Start the executable exe file under Windows to reach the user interface The headings correspond to the following Name of data file this is the name of the text file that you have just saved from the mmDisp Number of meshes in X direction this corresponds to the total length in x divided by the mesh size used in the micromagnetic simulation This should be an integer It is also recorded in the text file as xnodes Number of meshes in Y direction this corresponds to the total length in y divided by the mesh size used in the micromagnetic simulation This should be an integer It is also recorded in the text file as ynodes Number of meshes in Z direction this corresponds to the total length in z divided by the mesh size used in the micromagnetic simulation This should be an integer It is also recorded in the text file as znodes If the incorrect number of meshes has been inputted the boxes are highlighted in yellow to alert the user to change them Size of matrix the user can select any value for this providing that it exceeds the number of meshes
9. olid blue line represents the untilted profile and the dotted blue line represents the tilted profile d the sample is rotated back to its initial configuration The dotted blue line represents the profile of the sample having been tilted about the dashed black line axis Now consider a simulation in which there are multiple meshes in the z direction Exactly the same method as above is used for each individual mesh However the meshes are not stacked directly on top of each other with respect to the electron beam after tilting and are instead shifted with respect to each other by a distance shift zmesh sin tiltangle The direction of the shift depends on the sign of the angle of rotation This shift is achieved in MALTS via a linear interpolation method in the y or y if the tilt axis is not the x axis direction shift required due to tilt z mesh size angle of tilt Figure 5 when multiple meshes are tilted they are no longer stacked directly on top of each other Instead they are shifted with respect to each other
10. r in the z direction z_thicker z_init cos angle of tilt and compressed in the y direction y_compressed y_init cos angle of tilt MALTS achieves this compression by resizing the matrix in the y direction via a bicubic interpolation method eee PPPan a a Figure 3 compression in the y direction on rotation about the x axis by an angle of 30 degrees The solid blue line is the untilted sample profile and the dotted blue line is the tilted sample profile The dashed black line represents the x axis i e the axis of tilt If the sample is tilted about an axis in the xy plane tilt axis degrees away from the x axis the sample is rotated by tilt axis degrees so that its tilt axis is aligned with the x direction The compression is then performed in the y direction and the sample is then rotated back to its initial configuration by tilt axis degrees a 7 Ca A A yY A Cai a X a at ett hae 5 te rs r o To a e Pig a i lt e ea a Pas a Ps bed r va a r 2 a a Pi T Pd Pia A Ki as Gi 7 kd e Pa te a Pid annas n i Figure 4 a the dashed black line indicates the axis of tilt and the solid blue line represents the untilted sample profile b the sample is rotated such that the tilt axis is now in the x direction c the sample is then compressed in the y direction The s
11. xperiment The mean inner potential V is specific to the material and typical values are cited on the user interface for ease of use The default values are typical experimental values Tilt axis degrees from x axis and Angle of tilt degrees enable the user to simulate LTEM contrast when the sample is tilted see Figure 2 Angle of tilt degrees X al Axis of rotation degrees from x axis Figure 1 geometry for tilting the sample The grey scale adjusters alter the colour limits to specified minimum and maximum values Values less than cmin map to cmin and values greater than cmax map to cmax Those values between cmin and cmax are mapped linearly in grey scale The Lorentz TEM image button on the right hand side simulates a Lorentz TEM image White contrast means more intensity reaching the screen black contrast less intensity The Electric Component LTEM image buttons enables the computation of an LTEM image with only electric and no magnetic contrast Equally if a magnetic component LTEM image is required just set the mean inner potential to zero The Profile button shows the outline of the structure considered If this looks wrong but there are no yellow warning boxes this could mean that the number of meshes in the x and y directions are the wrong way around Example iE example Notepad NAME OF DATA FILE Z MESH SIZE m a E e File Edit Format View
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