Win/MacHREM Win/MacHREM TDS CIF Win/MacHREM User Guide 2
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- ゆうりゅう いくのや
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1 TM V2.5 Windows/ PowerMacintosh
2 Win/MacHREM Win/MacHREM TDS CIF Win/MacHREM User Guide 2
3 Preferences MultiGUI ImageGUI DFOutGUI ImageBMP SpotBMP FAQ MultiGUI ImageGUI DFOutGUI Support/Update WEB: Win/MacHREM User Guide 3
4 Win/MacHREM Win/MacHREM Win/MacHREM Windows/PowerMacintosh Win/MacHREM 1. Win/MacHREM Windows/Macintosh GUI Win/MacHREM GUI 2. Win/MacHREM Win/MacHREM User Guide 4
5 3. Windows Macintosh PICT Win/MacHREM FFT Option STEM Option Win/MacHREM Win/MacHREM GUI GUI GUI WORKSHEET Save Save As... Execute 1. MultiGUI GUI File Execute Multislice Win/MacHREM User Guide 5
6 2. ImageGUI GUI File Execute 3. ImageBMP Image Tableau K. Ishizuka and N. Uyeda: A New Theoretical and Practical Approach to the Multislice Method: Acta Cryst. A33 (1977) K. Ishizuka: Contrast Transfer of Crystal Images in TEM: Ultramicroscopy 5 (1980) K. Ishizuka: Multislice Formula for Inclined Illumination: Acta Cryst. A38 (1982) : 22 (1987) K. Ishizuka: A practical approach for STEM image simulation based on the FFT multislice method, Ultramicroscopy 90 (2001) Win/MacHREM Windows/Macintosh Window GUI Win/MacHREM User Guide 6
7 WinHREM WinHREM CD-ROM WinHREM 2.5 Setup.exe WinHREM 2.5 WinHREM 2.5 ( Windows\Program Files WinHREM WinHREM 2.5 MacHREM MacHREM CD-ROM MacHREM 2.5 OS X MacHREM 2.5 Win/MacHREM Data WinHREM MacHREM Utilities Programs Resources GUI Documents Win/MacHREM User Guide 7
8 Windows NOTE USB USB 1. CD-ROM 2. HASP4Driver hdd32.exe 3. Setup type Typical OS USB Macintosh 1. HASP_Driver_Unified_Installer aksusb Installer Mac OS X, Mac Classic 2. USB Win/MacHREM User Guide 8
9 GUI WorkSheet File Edit Help Data SnO 2 W 8 Nb 18 O 89 SnO2 WNbO SnO2 WNbO 1. MultiGUI 2. Data SnO2.WS1 TIPS Win/MacHREM User Guide 9
10 3. Title SnO2 test calculation 4. File Save As SnO2test TIPS.WS1 6. File Execute Multislice Win/MacHREM User Guide 10
11 MULTI.EXE Execution completed. Congratulations! NOTE WinHREM Input/Output MacHREM MacHREM File Edit File Save Print TIPS File Exit Win/MacHREM User Guide 11
12 Windows Command +. Mac OS File Exit NOTE MacHREM MacHREM 7. MultiGUI File Exit (Quit) 1. ImageGUI 2. Data SnO2.WS2 NOTE MultiGUI SnO2test WS2 Default.WS2 TIPS Win/MacHREM User Guide 12
13 3. Title SnO2 test calculation 4. File Save As SnO2test TIPS.WS2 6. File Execute IMAGE.EXE Win/MacHREM User Guide 13
14 Execution completed. Congratulations! NOTE WinHREM Input/Output MacHREM MacHREM File Edit File Save Print TIPS File Exit Windows Command +. Mac OS File Exit NOTE MacHREM MacHREM 7. ImageGUI File Exit (Quit) Win/MacHREM User Guide 14
15 SnO2 1. ImageBMP 2. Data SnO2test.AUX.AUX 3. Generate Slice 10 Defocus 500 A (under) Diaply Range (0<->1) x (0<->1) Win/MacHREM User Guide 15
16 4. Display Range a b 5. Generate 2 x 2 6. File Save File Print 7. File Close TIPS Shift 8. ImageBMP File Exit (Quit) Slice Defocus Win/MacHREM User Guide 16
17 Select TIPS All Select TIPS All Select TIPS Image Tableau Slice, Defocus Slice, Defocus Option Win/MacHREM User Guide 17
18 TIPS Atom Overlay Setup NOTE File Print Win/MacHREM User Guide 18
19 SnO2 1. SpotBMP 2. Data SnO2test.DF.DF 3. Generate Win/MacHREM User Guide 19
20 4. Show Index Spot Shape Peak Generate 5. SpotBMP File Exit (Quit) Win/MacHREM User Guide 20
21 MultiGUI ImageBMP MultiGUI Output Control Export Data for Gray Scale Map.AUX NOTE ImageGUI.AUX ImageBMP AUX Image Selection Win/MacHREM User Guide 21
22 Potential Wave Function S how Generate Win/MacHREM User Guide 22
23 SpotBMP DFOutGUI 1. DFOutGUI 2. Data SnO2.WS3 NOTE MultiGUI SnO2test WS3 Default.WS3 3. File Save As SnO2test Win/MacHREM User Guide 23
24 TIPS.WS3 5. File Execute DFOUT.EXE Execution completed. Congratulations! Normalized Kinematical scale TIPS: Kinematical Structure Factor Output Range Win/MacHREM User Guide 24
25 [-π, +π] π/2 NOTE WinHREM Input/Output MacHREM MacHREM File Edit File Save Print TIPS File Exit Windows Command +. Mac OS File Exit NOTE MacHREM MacHREM 6. DFOutGUI File Exit (Quit) Win/MacHREM User Guide 25
26 ImageBMP ImageBMP NOTE Image Tableau Shift Win/MacHREM User Guide 26
27 NOTE Image Tableau MultiGUI SnO2 1. MultiGUI 2. Data SnO2.WS1 SnO2 3. Options ModelView TIPS Win/MacHREM User Guide 27
28 a, b, c TIPS Projection Control Win/MacHREM User Guide 28
29 TDS TDS Debey-Waller factor TDS MultiGUI Edit Preferences Preferences Atomic Scattering factor Weikenmeier-Kohl Factor Include TDS absorption CIF MacHREM/WinHREM CIF (Crystallographic Information File) Import/Export Win/MacHREM User Guide 29
30 NOTE MacHREM/WinHREM CIF MacHREM WinHREM CIF Import/Export MacHREM WinHREM NOTE MultiGUI Atom Parameters Edit Export Atom Parameters Import MacHREM WinHREM MacHREM/WinHREM K. Ishizuka: Multislice Formula for Inclined Illumination: Acta Cryst. A38 (1982) <hk0> <hk0> MultiGUI Edit Preferences Preferences Crsytal Setteing <110> I (a,b,c) a a II, III, V VI <100> b a II V Win/MacHREM User Guide 30
31 NOTE MultiGUI MacHREM/WinHREM 10 MultiGUI MultiGUI Atom Parameters Edit Import Options DIFFUSE TIPS OK Win/MacHREM User Guide 31
32 File File Execute DIFFUSE DIFFUSE.EXE Execution completed. Congratulations! NOTE WinHREM Input/Output MacHREM MacHREM File Edit File Save Print TIPS File Exit Windows Command +. Mac OS File Exit NOTE MacHREM MacHREM MultiGUI File Exit (Quit) ImageBMP.ED ImageBMP.ED Win/MacHREM User Guide 32
33 ImageBMP Show Generate Win/MacHREM User Guide 33
34 Win/MacHREM 1. GUI File Save As... NOTE File Save Win/MacHREM User Guide 34
35 1. GUI 2. Default Untitled File Save As... Preferences GUI Preferences Preferences Units, Defocus sign Preferences GUI 1. MultiGUI ImageGUI Edit Preferences 2. Apply 3. Close Cancel Preferences Close Preferences Cancel Apply Preferences NOTE Apply Cancel Preferences Apply TIPS Close Apply Win/MacHREM User Guide 35
36 Units, Defocus sign GUI 1. Angstrom nm s d* s d* mrad Win/MacHREM User Guide 36
37 2. I c b a II Range Slice thickness 5. Field width Blank lines 6. Weikenmeier-Kohl TDS Debye-Waller Factor GUI WinHREM/MacHREM Default.ws1 Win/MacHREM User Guide 37
38 1. GUI 2. Default Win/MacHREM User Guide 38
39 MultiGUI Win/MacHREM User Guide 39
40 1. Title 2. Cell Parameters Angstrom nm cosine cosine 3. Symmetry Operation Select Edit Select Select Space Group View Edit Elements Edit Win/MacHREM User Guide 40
41 Edit International Tables for Crystallography, ;. 4. Atom Parameters Import Edit Import Import Data Base MultiGUI Text Data Separator Win/MacHREM User Guide 41
42 Parameter Sequence None Select Edit No of Atoms Edit Edit No Name Ag C(1) O-2 x, y, z Occupancy Thermal Overall Thermal Factor Overall Thermal Factor 5. Phase Grating Setup Deviding a cell into multislice Calculation Win/MacHREM User Guide 42
43 7. Acc Voltage 8. Incident Beam Direction [001] 9. Unitary Test Limit Cycle 10. Dynamical Structure Factor Range Cycle 11. Potential Distribution 12. Wave Function Cycle 13. Numerical Map 14. Half-tine Map Win/MacHREM User Guide 43
44 ImageGUI Win/MacHREM User Guide 44
45 1. Title 2. Optical Parameters Spherical aberration coeff. Defocus spread Beam convergence Aperture radius position 3. Simulation Mode 1 First order/envelope 2 Second order/tcc 4. Slice thicknesses Defocus values 20 Preference 6. Microscope Images 7. Structure Factor 8. Numerical Map 9. Half-tine Map Win/MacHREM User Guide 45
46 DFOutGUI Numerical Output Normalized Kinematical scale 2. Graphical Output 3. Export Data for Graphical Application Win/MacHREM User Guide 46
47 4. Output Range 5. Indices of Reflections 10 2 Win/MacHREM User Guide 47
48 ImageBMP Image Selection Win/MacHREM User Guide 48
49 Display Range pixel/angstrom 1 Angstrom Image Selection Slice All Select Defocus All Select NOTE Preferences Under-focus Image Tableau Options Win/MacHREM User Guide 49
50 Survey Survey Reverse Contrast Atom Overlay Setup Generate Generate Win/MacHREM User Guide 50
51 Image Selection Potential All Projection Wave Function All Show Win/MacHREM User Guide 51
52 SpotBMP Display Range Radius Resolution Win/MacHREM User Guide 52
53 1/Angstrom 2. Display setup Type Show Index Spot shape Spot radius Background Color 3. Survey Survey 4. Slice All 5. Generate Win/MacHREM User Guide 53
54 Generate Win/MacHREM User Guide 54
55 MultiGUI Win/MacHREM User Guide 55
56 ImageGUI Win/MacHREM User Guide 56
57 DFOutGUI Win/MacHREM User Guide 57
58 FAQ Frequently asked Questions Q and A MultiGUI Q A 1. Atom Parameters Edit 2. x,y,z Name X Y Z Occupancy Thernmal Overall Thermal Factor 3. OK NOTE NOTE Export WinHREM User Guide / FAQ 58
59 Q Occupancy A Occupancy Occupancy Q... A 3 0, 0, 120 TIPS Q A Q A Q A WinHREM User Guide / FAQ 59
60 Q A Preferences Dynamical Calculation Range Q [011] [111] A [011] (001) [011] (011) [011] K. Ishizuka, Acta Cryst. A3 8 (1982) Q A c [0, 0, 1] NOTE Laue Ewald TIPS t = d a+ d b+ d c * * * = ra + r b + r c Laue r 1,r 2 r 1,r 2 a, b r = d a + d ba + d ca r = d ab + d b + d cb WinHREM User Guide / FAQ 60
61 Q A TIPS Q A Preferences MultiGUI Q A Mott f s { Z f s } s ; s= sinθ λ e ()= () x 2 International Tables for x-ray Crystallography, Vol. IV Q A Q A Thermal WinHREM User Guide / FAQ 61
62 WORKSHEET Overall Thermal Factor TIPS WORKSHEET Overall Thermal Factor Q A sin exp θ 2 B λ _ Bragg Q Unitary test A FFT Unitary test Unitary test Unitary test Limit 1 Q A WinHREM User Guide / FAQ 62
63 Q A 3 Q A NOTE Q A International Tables for Crystallography, ;. x, y, z; y, x, z. Q A Q A x,y,z, WinHREM User Guide / FAQ 63
64 .atm Q A x,y,z WinHREM User Guide / FAQ 64
65 ImageGUI Q A Aperture radius) s d* 2s = d* 2s d* Q Simulation A Simulation Mode Mode Envelope TCC/Transmission Cross-coeffocient TCC Envelope Q Simulation A Second Mode First Order(envelope) Second order(tcc) order(tcc) First Order(envelope) Second order(tcc) MultiGUI Preferences Dynamical calculation/range MultiGUI WinHREM User Guide / FAQ 65
66 DFOutGUI Q A HOLZ/Higher Order Laue Zone Q A 0 π - π/2 Q A WinHREM User Guide / FAQ 66
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