Earl J. Kirkland

Advanced Computing in Electron Microscopy Earl J. Kirkland 2nd ed. 2010 edition

Marc Notes: Includes bibliographical references and index. Review Quotes: From the reviews of the second edition: It is thirteen years since the first edition of Advanced Computing in Electron Microscopy by E. J. Kirkland appeared. the book contains much guidance in this complex area and the list of references draws attention to many relevant papers that can all too easily be overlooked. (Ultramicroscopy, Vol. 116, 2012) Jacket Description/Back: Advanced Computing in Electron Microscopy, 2nd Edition, brings together diverse information on image simulation. An invaluable resource, this book provides information on various methods for numerical computation of high resolution conventional and scanning transmission electron microscope images. This text will serve as a great tool for students at the advanced undergraduate or graduate level, as well as experienced researchers in the field. This enhanced second edition includes: -descriptions of new developments in the field -updated references -additional material on aberration corrected instruments and confocal electron microscopy -expanded and improved examples and sections to provide stronger clarityReview Quotes: From the reviews of the second edition: It is thirteen years since the first edition of Advanced Computing in Electron Microscopy by E. J. Kirkland appeared. the book contains much guidance in this complex area and the list of references draws attention to many relevant papers that can all too easily be overlooked. (Ultramicroscopy, Vol. 116, 2012)"Table of Contents: 1. Introduction -- 1.1. Computing in Electron Microscopy -- 1.2. Organization of this Book -- 2. The Transmission Electron Microscope -- 2.1. Introduction -- 2.2. Modeling the Electron Microscope -- 2.3. Relativistic Electrons -- 2.4. Reciprocity -- 2.5. Confocal Mode -- 2.6. Aberrations -- 2.7. Aberration Correction -- 2.8. More Aberrations -- 2.9. Further Reading -- 3. Linear Image Approximations -- 3.1. The Weak Phase Object in Bright Field -- 3.2. Partial Coherence in BF-CTEM -- 3.2.1. Aberration Correctors and Partial Coherence -- 3.3. Detector Influence (CTEM) -- 3.4. Incoherent Imaging of Thin Specimens (CTEM) -- 3.5. Annular Dark Field STEM -- 3.5.1. Minimum Probe Conditions -- 3.5.2. Source Size -- 3.5.3. Defocus Spread -- 3.6. Confocal Mode for Weak Phase Objects -- 3.7. Phase and Amplitude Contrast Revisited -- 4. Sampling and the Fast Fourier Transform -- 4.1. Sampling -- 4.2. Discrete Fourier Transform -- 4.3. The Fast Fourier Transform or FFT -- 4.4. Wrap Around Error and Rearrangement -- 4.5. Fourier Transforming Real Valued Data -- 4.6. Displaying Diffraction Patterns -- 4.7. An FFT Subroutine in C -- 4.8. Further Reading -- 5. Calculation of Images of Thin Specimens -- 5.1. The Weak Phase Object -- 5.2. Single Atom Properties -- 5.2.1. Radial Charge Distribution -- 5.2.2. Potential -- 5.2.3. Atomic Size -- 5.2.4. Scattering Factors -- 5.3. Total Specimen Potential -- 5.4. BF Phase Contrast Image Calculation -- 5.4.1. Single Atom Images -- 5.4.2. Thin Specimen Images -- 5.4.3. Partial Coherence and the Transmission Cross Coefficient -- 5.5. ADF STEM Images of Thin Specimens -- 5.5.1. Single Atom Images -- 5.5.2. Thin Specimen Images -- 5.6. Summary of Sampling Suggestions -- 6. Theory of Calculation of Images of Thick Specimens -- 6.1. Bloch Wave Eigenvalue Solution -- 6.1.1. Bloch Waves -- 6.1.2. Periodic Potential -- 6.1.3. Matrix Equation -- 6.1.4. Initial Conditions and the Exit Wave -- 6.1.5. Bloch Wave Eigenvalue Summary -- 6.2. The Wave Equation for Fast Electrons -- 6.3. A Bloch Wave Differential Equation Solution -- 6.4. The Multislice Solution -- 6.4.1. A Formal Operator Solution -- 6.4.2. A Finite Difference Solution -- 6.4.3. Free Space Propagation -- 6.5. Multislice Interpretation -- 6.6. The Multislice Method and FFT's -- 6.7. Slicing the Specimen -- 6.8. Aliasing and Bandwidth -- 6.9. Interfaces and Defects -- 6.10. Multislice Implementation -- 6.10.1. The Propagator Function and Specimen Tilt -- 6.10.2. Convergence Tests -- 6.10.3. Partial Coherence in BF-CTEM -- 6.10.4. Parallel Computing -- 6.11. More Accurate Slice Methods -- 6.11.1. Operator Solutions -- 6.11.2. Finite Difference Solutions -- 7. Multislice Applications and Examples -- 7.1. Gallium Arsenide -- 7.1.1. BF-CTEM Simulation -- 7.1.2. ADF-STEM Simulation -- 7.1.3. Channeling -- 7.2. Silicon Nitride -- 7.3. CBED Simulations -- 7.4. Thermal Vibrations of the Atoms in the Specimen -- 7.4.1. Silicon 111 CBED with TDS -- 7.4.2. Silicon 110 ADF-STEM with TDS -- 7.5. Specimen Edges or Interlaces -- 7.6. Biological Specimens -- 7.7. Quantitative Image Matching -- 7.8. Troubleshooting (What Can Go Wrong) -- 8. The Programs -- 8.1. Program Organization -- 8.2. Image Display -- 8.3. Programming Language -- 8.3.1. Disk File Format -- 8.4. BF-CTEM Sample Calculations for Periodic Specimens -- 8.4.1. Atomic Potentials -- 8.4.2. Multislice -- 8.4.3. Image Formation -- 8.4.4. Partial Coherence -- 8.5. ADF-STEM Sample Calculations for Periodic Specimens -- 8.6. NonPeriodic Specimens -- 8.6.1. Fixed Beam Calculation -- 8.6.2. Scanned Beam Calculation -- 8.7. Program Display -- 8.8. Program Slicview -- A. Plotting Transfer Functions -- A.1. CTEM -- A.2. STEM -- B. The Fourier Projection Theorem -- C. Atomic Potentials and Scattering Factors -- C.1. Atomic Charge Distribution -- C.2. X-ray Scattering Factors -- C.3. Electron Scattering Factors -- C.4. Parameterization -- D. Bilinear Interpolation -- E. 3D Perspective View -- References -- Index. Publisher Marketing: Preface to Second Edition Several new topics have been added, some small errors have been corrected and some new references have been added in this edition. New topics include aberration corrected instruments, scanning confocal mode of operations, Bloch wave eigenvalue methods and parallel computing techniques. The ?rst edition - cluded a CD with computer programs, which is not included in this edition. - stead the associated programs will be available on an associated web site (currently people.ccmr.cornell.edu/ kirkland, but may move as time goes on). I wish to thank Mick Thomas for preparing the specimen used to record the image in Fig.5.26 and to thank Stephen P. Meisburger for suggesting an interesting biological specimen to use in Fig.7.24. Again, I apologize in advance for leaving out some undoubtedlyoutstanding r- erences. I also apologize for the as yet undiscovered errors that remain in the text. Earl J. Kirkland, December 2009 Preface to First Edition Image simulation has become a common tool in HREM (High Resolution El- tron Microscopy) in recent years. However, the literature on the subject is scattered among many different journals and conference proceedings that have occurred in the last two or three decades. It is dif?cult for beginners to get started in this ?eld."