Bibliography

Bibliography#

The list of references cited in the user guide are given below.

[Bar18]

J. Barthel. Dr. probe: a software for high-resolution stem image simulation,. Ultramicroscopy, 193:1–11, 2018.

[Car20]

Miguel A. Caro. Amorphous carbon films generated through simulated deposition with GAP from 1eV to 100eV. 2020. URL: https://doi.org/10.5281/zenodo.3778153, doi:10.5281/zenodo.3778153.

[FMF+10]

B. D. Forbes, A. V. Martin, S. D. Findlay, A. J. D'Alfonso, and L. J. Allen. Quantum mechanical model for phonon excitation in electron diffraction and imaging using a born-oppenheimer approximation. Phys. Rev. B, 82:104103, 2010. URL: https://link.aps.org/doi/10.1103/PhysRevB.82.104103, doi:10.1103/PhysRevB.82.104103.

[HKRA19]

F. S. Hage, D. M. Kepaptsoglou, Q. M. Ramasse, and L. J. Allen. Phonon spectroscopy at atomic resolution. Phys. Rev. Lett., 122:016103, Jan 2019. URL: https://link.aps.org/doi/10.1103/PhysRevLett.122.016103, doi:10.1103/PhysRevLett.122.016103.

[JN13]

Lewys Jones and Peter D. Nellist. Identifying and correcting scan noise and drift in the scanning transmission electron microscope. Microscopy and Microanalysis, 19(4):1050–1060, 2013. doi:10.1017/S1431927613001402.

[Kir10]

Earl J. Kirkland. Advanced computing in electron microscopy. Springer, 2 edition, 2010. ISBN 978-1-4419-6532-5.

[LMB+17]

Ask Hjorth Larsen, Jens Jørgen Mortensen, Jakob Blomqvist, Ivano E Castelli, Rune Christensen, Marcin Dułak, Jesper Friis, Michael N Groves, Bjørk Hammer, Cory Hargus, Eric D Hermes, Paul C Jennings, Peter Bjerre Jensen, James Kermode, John R Kitchin, Esben Leonhard Kolsbjerg, Joseph Kubal, Kristen Kaasbjerg, Steen Lysgaard, Jón Bergmann Maronsson, Tristan Maxson, Thomas Olsen, Lars Pastewka, Andrew Peterson, Carsten Rostgaard, Jakob Schiøtz, Ole Schütt, Mikkel Strange, Kristian S Thygesen, Tejs Vegge, Lasse Vilhelmsen, Michael Walter, Zhenhua Zeng, and Karsten W Jacobsen. The atomic simulation environment — a python library for working with atoms. Journal of Physics: Condensed Matter, 29(27):273002, 2017.

[LBL16]

Ivan Lazić, Eric G.T. Bosch, and Sorin Lazar. Phase contrast stem for thin samples: integrated differential phase contrast. Ultramicroscopy, 160:265–280, 2016. doi:https://doi.org/10.1016/j.ultramic.2015.10.011.

[LD14]

Ivan Lobato and Dirk Van Dyck. An accurate parameterization for the scattering factors, electron densities and electrostatic potentials for neutral atoms that obey all physical constraints. Acta Crystallographica Section A, 70:636–649, 2014.

[MPS21]

Jacob Madsen, Timothy J. Pennycook, and Toma Susi. Ab initio description of bonding for transmission electron microscopy. Ultramicroscopy, 231:113253, 2021. doi:https://doi.org/10.1016/j.ultramic.2021.113253.

[Men19]

B.G. Mendis. An inelastic multislice simulation method incorporating plasmon energy losses. Ultramicroscopy, 206:112816, 2019. URL: https://www.sciencedirect.com/science/article/pii/S0304399119301627, doi:https://doi.org/10.1016/j.ultramic.2019.112816.

[MHJ05]

J. J. Mortensen, L. B. Hansen, and K. W. Jacobsen. Real-space grid implementation of the projector augmented wave method. Phys. Rev. B, 71(3):035109, 2005.

[Oph17]

Colin Ophus. A fast image simulation algorithm for scanning transmission electron microscopy. Advanced Structural and Chemical Imaging, 2017.

[Pen99]

Lian-Mao Peng. Electron atomic scattering factors and scattering potentials of crystals. Micron, 30(6):625–648, 1999.

[SML+19]

Toma Susi, Jacob Madsen, Ursula Ludacka, Jens Jørgen Mortensen, Timothy J. Pennycook, Zhongbo Lee, Jani Kotakoski, Ute Kaiser, and Jannik C. Meyer. Efficient first principles simulation of electron scattering factors for transmission electron microscopy. Ultramicroscopy, 197:16–22, 2019.

[VdBJK15]

W. Van den Broek, X. Jiang, and C.T. Koch. Fdes, a gpu-based multislice algorithm with increased efficiency of the computation of the projected potential. Ultramicroscopy, 158:89–97, 2015. doi:10.1016/j.ultramic.2015.07.005.

[VD09]

D. Van Dyck. Is the frozen phonon model adequate to describe inelastic phonon scattering? Ultramicroscopy, 109(6):677–682, 2009.

[DaskDTeam16]

Dask Development Team. Dask: Library for dynamic task scheduling. 2016. URL: https://dask.org.