Skip to main content Accessibility help

Building a Library of Simulated Atom Probe Data for Different Crystal Structures and Tip Orientations Using TAPSim

  • Markus Kühbach (a1), Andrew Breen (a1), Michael Herbig (a1) and Baptiste Gault (a1)


The process of building an open source library of simulated field desorption maps for differently oriented synthetic tips of the face-centered cubic, body-centered cubic, and hexagonal-close-packed crystal structures using the open source software TAPSim is reported. Specifically, the field evaporation of a total set of 4 × 101 single-crystalline tips was simulated. Their lattices were oriented randomly to sample economically the fundamental zone of crystal orientations. Such data are intended to facilitate the interpretation of low-density zone lines and poles that are observed on detector hit maps during Atom Probe Tomography (APT) experiments. The datasets and corresponding tools have been made publicly available to the APT community in an effort to provide better access to simulated atom probe datasets. In addition, a computational performance analysis was conducted, from which recommendations are made as to which key tasks should be optimized in the future to improve the parallel efficiency of TAPSim.


Corresponding author

*Author for correspondence: Markus Kühbach, E-mail:


Hide All
Amdahl, GM (1967). Validity of the single processor approach to achieving large-scale computer capabilities. AFIPS ‘67 (Spring) Proceedings of the April 18–20, 1967, Spring Joint Computer Conference, vol. 30, pp. 483485.10.1145/1465482.1465560
Araullo-Peters, VJ, Breen, A, Ceguerra, AV, Gault, B, Ringer, SP & Cairney, JM (2015). A new systematic framework for crystallographic analysis of atom probe data. Ultramicroscopy 154, 714.
Araullo-Peters, VJ, Gault, B, Shrestha, SL, Yao, L, Moody, MP, Ringer, SP & Cairney, JM (2012). Atom probe crystallography: Atomic-scale 3-D orientation mapping. Scr Mater 66, 907910.
Brannon, R M (2002). A review of useful theorems involving proper orthogonal matrices referenced to three-dimensional physical space. Tech. rep., Sandia National Laboratories. Available at
Breen, AJ, Babinsky, K, Day, AC, Eder, K, Oakman, CJ, Trimby, PW, Primig, S, Cairney, JM & Ringer, SP (2017). Correlating atom probe crystallographic measurements with Transmission Kikuchi Diffraction Data. Microsc Microanal 23, 279290.
Ceguerra, AV, Breen, AJ, Stephenson, LT, Felfer, PJ, Araullo-Peters, VJ, Liddicoat, PV, Cui, XY, Yao, L, Haley, D, Moody, MP, Gault, B, Cairney, JM & Chang, CST (2013). The rise of computational techniques in Atom Probe Microscopy. Curr Opin Solid State Mater Sci 17, 224235.
Chandra, R, Dagum, L, Kohr, D, Maydan, D, Mcdonald, J & Menon, R (2001). Parallel Programming in OpenMP, 1st ed. San Francisco: Morgan Kaufmann.
de Cougny, HL, Devine, KD, Flaherty, JE, Loy, RM, Ozturan, C & Shephard, MS (1994). Load balancing for the parallel adaptive solution of partial-differential equations. Appl Numer Math 16, 157182.
de Cougny, HL & Shephard, MS (1999). Parallel refinement and coarsening of tetrahedral meshes. Int J Numer Methods Eng 46, 11011125.
Devaraj, A, Perea, DE, Liu, J, Gordon, LM, Prosa, TJ, Parikh, P, Diercks, DR, Meher, S, Kolli, RP, Meng, YS & Thevuthasan, S (2018). Three-dimensional nanoscale characterisation of materials by Atom Probe Tomography. Int Mater Rev 63, 68101.
Downs, RT & Hall-Wallace, M (2003). The American mineralogist crystal structure database. Am Mineral 88, 247250.
Eaton, HC & Lee, L (1982). The simulation of images in the field ion microscope: Specimens of arbitrary crystal structure and orientation. J Appl Phys 53, 988994.
Felfer, P, Scherrer, B, Demeulemeester, J, Vandervorst, W & Cairney, JM (2015). Mapping interfacial excess in atom probe data. Ultramicroscopy 159, 438444.
Fryxell, B, Olson, K, Ricker, P, Timmes, FX, Zingale, M, Lamb, DQ, Macneice, P, Rosner, R, Truran, JW & Tufo, H (2000). Flash: An adaptive mesh hydrodynamics code for modeling astrophysical thermonuclear ashes. Astrophys J Suppl Ser 131, 273334.
Gault, B, Haley, D, De Geuser, F, Moody, MP, Marquis, EA, Larson, DJ & Geiser, BP (2011 a). Advances in the reconstruction of Atom Probe Tomography data. Ultramicroscopy 111, 448457.
Gault, B, Loi, ST, Araullo-Peters, VJ, Stephenson, LT, Moody, MP, Shrestha, SL, Marceau, RKW, Yao, L, Cairney, JM & Ringer, SP (2011 b). Dynamic reconstruction for Atom Probe Tomography. Ultramicroscopy 111, 16191624.10.1016/j.ultramic.2011.08.005
Gault, B, Moody, MP, Cairney, JM & Ringer, SP (2012). Atom Probe Microscopy, 1st ed. New York: Springer.
Geiser, BP, Larson, DJ, Gerstl, SSA, Reinhard, D, Kelly, TF, Prosa, TJ & Olson, JD (2009). A system for simulation of tip evolution under field evaporation. Microsc Microanal 15, 302303.
Geuser, FD, Lefebvre, W, Danoix, F, Vurpillot, F, Forbord, B & Blavette, D (2007). An improved reconstruction procedure for the correction of local magnification effects in three-dimensional atom-probe. Surf Interface Anal 39, 268272.10.1002/sia.2489
Gražulis, S, Chateigner, D, Downs, RT, Yokochi, AT, Quirós, M, Lutterotti, L, Manakova, E, Butkus, J, Moeck, P & Le Bail, A (2009). Crystallography Open Database—an open-access collection of crystal structures. J Appl Crystallogr 42, 726729.
He, MR, Kim, SKSG, Felfer, PJ, Breen, AJ, Cairney, JM & Gianola, DS (2016). Linking stress-driven microstructural evolution in nanocrystalline aluminium with grain boundary doping of oxygen. Nat Commun 7, 11225.
Jägle, EA, Choi, PP & Raabe, D (2014). The maximum separation cluster analysis algorithm for atom-probe tomography: Parameter determination and accuracy. Microsc Microanal 20, 16621671.
Kelly, TF, Miller, MK, Rajan, K & Ringer, SP (2013). Atomic-scale tomography: A 2020 vision. Microsc Microanal 19, 652664.
Kingham, DR (1982). The post-ionization of field evaporated ions: A theoretical explanation of multiple charge states. Surf Sci 116, 273301.
Kühbach, M & Breen, A (2018 a). Milling of single-crystalline tips supplementary material: Zenodo open source data repository. Tech. rep. GmbH, Düsseldorf: Max-Planck-Institut für Eisenforschung. Available at
Kühbach, M & Breen, A (2018 b). Milling of single-crystalline tips: Zenodo open source data repository. Tech. rep. Düsseldorf: Max-Planck-Institut für Eisenforschung, GmbH. Available at
Kühbach, M & Breen, A (2018 c). Single-crystalline Al tips: Zenodo open source data repository. Tech. rep. Düsseldorf: Max-Planck-Institut für Eisenforschung, GmbH. Available at
Kühbach, M & Breen, A (2018 d). Single-crystalline Mg tips: Zenodo open source data repository. Tech. rep. Düsseldorf: Max-Planck-Institut für Eisenforschung, GmbH. Available at
Kühbach, M & Breen, A (2018 e). Single-crystalline W tips: Zenodo open source data repository. Tech. rep. Düsseldorf: Max-Planck-Institut für Eisenforschung, GmbH. Available at
Kühbach, M & Breen, A (2018 f). Single-crystalline Zr tips: Zenodo open source data repository. Düsseldorf: Tech. rep. Max-Planck-Institut für Eisenforschung, GmbH. Available at
Larson, DJ, Gault, B, Geiser, BP, De Geuser, F & Vurpillot, F (2013). Atom Probe Tomography spatial reconstruction: Status and directions. Curr Opin Solid State Mater Sci 17, 236247.
Larson, DJ, Geiser, BP, Prosa, TJ, Gerstl, SSA, Reinhard, DA & Kelly, TF (2011). Improvements in planar feature reconstructions in atom probe tomography. J Microsc 243, 1530.
Lefebvre, W, Vurpillot, F & Sauvage, X (2016). Atom Probe Tomography: Put Theory into Practice, 1st ed. Amsterdam: Academic Press.
Loseille, A, Menier, V & Alauzet, F (2015). Parallel generation of large-size adapted meshes. Procedia Eng 124, 5769.
Marquis, EA & Hyde, JM (2010). Applications of atom-probe tomography to the characterisation of solute behaviours. Mater Sci Eng R 69, 3762.
Miller, M (1996). Atom Probe Field Ion Microscopy. Oxford, UK: Clarendon Press.
Momma, K & Izumi, F (2008). VESTA: A three-dimensional visualization system for electronic and structural analysis. J Appl Crystallogr 41, 653658.
Momma, K & Izumi, F (2011). VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data. J Appl Crystallogr 44, 12721276.
Momma, K & Izumi, F (2014). VESTA: a Three-Dimensional Visualization System for Electronic and Structural Analysis — The VESTA Manual, August 6, 2014. Tech. rep. Czech and Slovak Crystallographic Association (CSCA). Available at
Moody, MP, Tang, F, Gault, B, Ringer, SP & Cairney, JM (2011). Atom probe crystallography: Characterization of grain boundary orientation relationships in nanocrystalline aluminium. Ultramicroscopy 111, 493499.
Moore, AJW (1981). The simulation of FIM desorption patterns. Philos Mag A 43, 803814.
Müller, EW (1956). Field desorption. Phys Rev 102, 618624.
Oberdorfer, C (2014 a). Numeric simulation of atom probe tomography. PhD Thesis, Westfälische Wilhelms-Universität Münster, Münster, Germany.
Oberdorfer, C (2014 b). TAPSim How-to. Tech. rep. Institute of Materials Physics, University of Münster.
Oberdorfer, C, Eich, SM, Lütkemeyer, M & Schmitz, G (2015). Applications of a versatile modelling approach to 3d atom probe simulations. Ultramicroscopy 159, 184194.
Oberdorfer, C, Eich, SM & Schmitz, G (2013). A full-scale simulation approach for atom probe tomography. Ultramicroscopy 128, 5567.
Oberdorfer, C, Withrow, T, Fisher, LJYK, Marquis, EA & Windl, W (2018). Influence of surface relaxation on solute atoms positioning within atom probe tomography reconstructions. Mater Charact 146, 324335.
Owen, SJ, Brown, JA, Ernst, CD, Lim, H & Long, KN (2017). Hexahedral mesh generation for Computational Materials Modeling. 26th International Meshing Roundtable, (IMR26 2017), vol. 203, 167179.
Sanchez, A (2018). Scatplot scatter plot with color indicating data density. Tech. rep. Available at
Shoemake, K (1992). Uniform random rotations. Graphics Gems III, Kirk D, ed., pp. 124132. London: Academic Press.
Vurpillot, F, Bostel, A & Blavette, D (1999 a). The shape of field emitters and the ion trajectories in three-dimensional atom probes. J Microsc 196, 332336.
Vurpillot, F, Bostel, A, Menand, A & Blavette, D (1999 b). Trajectories of field emitted ions in 3d atom-probe. The European Physics Journal 6, 217221.
Wei, Y, Gault, B, Varanasi, RS, Raabe, D, Herbig, M & Breen, A (2018). Machine-learning-based atom probe crystallographic analysis. Ultramicroscopy 194, 1524.
Yao, L (2016). A filtering method to reveal crystalline patterns from atom probe microscopy desorption maps. MethodsX 3, 268273.
Yao, L, Ringer, SP, Cairney, JM & Miller, MK (2013). The anatomy of grain boundaries: Their structure and atomic-level solute distribution. Scr Mater 69, 622625.


Type Description Title
Supplementary materials

Kühbach et al. supplementary material
Kühbach et al. supplementary material 1

 PDF (2.3 MB)
2.3 MB
Supplementary materials

Kühbach et al. supplementary material
Kühbach et al. supplementary material 2

 Unknown (32 KB)
32 KB
Supplementary materials

Kühbach et al. supplementary material
Kühbach et al. supplementary material 3

 Unknown (30 KB)
30 KB


Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed