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Micron
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A R T I C LE I N FO A B S T R A C T
Keywords: A new computer program, TEMUC3, has been developed for unit-cell determination of crystal phases using
Computer software electron diffraction data. A graphic user-friendly interface was designed for the following operations, (i) a re-
Electron diffraction ciprocal lattice is reconstructed from a tilt series of electron diffraction patterns; (ii) a Niggli cell is generated
Lattice reconstruction from the two electron diffraction patterns in a tilt series; iii) a Niggli cell is generated from three electron
Niggli cell
diffraction patterns, in which each pair shares a common reflection vector; (iv) a conventional unit-cell is
Unit-cell refinement
converted from a Niggli cell; (v) a unit-cell is refined from a set of reflections. The application of TEMUC3 is
further elucidated in three examples. A brief discussion on the generation of a primitive cell from electron
diffraction data and the cell reduction in reciprocal and direct space is presented.
1. Introduction cell had been widely used in X-ray crystallography (e.g., Santoro and
Mighell, 1970). The concept was also used in electron diffraction ex-
Determination of unit-cells for unknown crystalline phases is a basic periments for unit-cell determination of crystalline phases (Kuo, 1978).
requisite for materials characterization and the first step of ab initio A modified cell reduction method was adopted in a computer program
structure determination. Electron diffraction technique as a counterpart package by Li (2005) and later by Zhao et al. (2008). A cell reduction
of X-ray diffraction technique has been extensively used in material approach was recently described by Yang et al. (2017) for unit-cell
characterization and crystal structure determination. Electron crystal- determination from three specially related SAED patterns. The relation
lography has the following important complements to X-ray crystal- among the three SAED patterns allows the angle between each pair of
lography (Zou et al., 2011): (i) crystals are millions of times smaller them to be calculated accurately.
than those for X-ray diffraction studies; and (ii) it is possible to focus the A general 3D reciprocal lattice reconstruction method was discussed
electrons to form an image. by Fraundorf (1981) and a computer program with a visual 3D re-
A selected-area electron diffraction (SAED) pattern can be viewed as ciprocal space for this purpose was developed by Zou et al. (2004). An
a two-dimensional (2D) section of a three-dimensional (3D) reciprocal algorithm for unit-cell determination of crystalline phases from a col-
lattice. A series of reciprocal planes can be obtained using a double tilt lection of randomly oriented SAED patterns was developed by Jiang
holder for a transmission electron microscope (TEM). Due to the fea- et al. (2009,2011). Electron diffraction tomography technique (Kolb
tures of the SAED technique, it is natural to determine the unit-cell for et al., 2007, 2008) and the diffraction rotation technique (Zou et al.,
an unknown crystalline phase from a tilt series of SAED patterns. This is 2011) have recently attracted major interest. The diffraction rotation
considered as a traditional method, which was documented originally technique aims to collect a complete data set of diffraction patterns in a
in the book by Vainshtein (1964) and recently in the book by Zou et al. fashion similar to X-ray crystallography.
(2011). However, this method is troublesome in the application to In this paper, the development on a new computer program,
crystalline phases in monoclinic and triclinic systems. TEMUC3, is described for unit-cell determination of crystalline phases
A crystal lattice can be characterized by a unique choice of a re- using electron diffraction data. Application examples and discussions
duced cell and there are 44 primitive Niggli reduced cells corre- are given for the further elucidation.
sponding to 14 Bravais lattices (Niggli, 1928). The importance of the
Niggli cell is due to its uniqueness and the possibility that it can be used
for determining the Bravais type of the lattice (Gruber, 1973). Niggli
⁎
Corresponding author at: 855N 16th Street, N201 NANO, Lincoln, NE, 68588-0298, United States.
E-mail address: xzli@unl.edu.
https://doi.org/10.1016/j.micron.2018.10.010
Received 6 July 2018; Received in revised form 31 October 2018; Accepted 31 October 2018
Available online 02 November 2018
0968-4328/ © 2018 Elsevier Ltd. All rights reserved.
X.-Z. Li Micron 117 (2019) 1–7
Fig. 2. Geometry for generating a primitive cell from two SAED diffraction
patterns and the angle between them. Plane-1 and plane-2 are the two SAED
patterns and the angle between them is φ. A primitive cell is defined by a*, b*,
c* and α* = ∠ COQ (or ∠ POB), β* = ∠ TOQ (ω1), γ* = ∠ TOC (ω2).
SAED patterns and then to refine the lattice parameters. A general al-
gorithm of least-squares refinement was described in the previous paper
(Li, 2005). For the purpose of application, the refinement of lattice
parameters is better to carry out for seven crystal system separately.
The data set of reflection vectors are indexed within error tolerance and
then the lattice parameters can be refined using the lengths of reflection
vectors.
Fig. 1. A flow chart of the Niggli cell reduction procedure in TEMUC3.
The data set for unit-cell determination of crystalline phases in The graphic user interface of TEMUC3 consists of a menu system, a
TEMUC3 is a tilt series of SAED patterns or three SAED patterns, in display panel and multiple dialogs. Each of the dialog is designed for a
which each pair shares a common reflection vector. A reflection vector single task. The panel and dialogs can be activated from the menu
is a vector from the incident beam to a reflection spot. The basic pro- system and used in various combinations for the following modules, (i)
cedures for unit-cell determination of crystalline phases using SAED the traditional method for lattice reconstruction, (ii) two methods for
data are (i) a reciprocal lattice (or primitive cell), (ii) a direct lattice (or generation of primitive cells and then conventional unit-cells and (iii)
primitive cell), (iii) a cell reduction if necessary, and (iv) a refinement refinement of lattice parameters. Fig. 3 shows the menu system of
of lattice parameters. TEMUC3, the icons of a display panel and single task dialogs are shown
The reconstruction of a reciprocal lattice from a tilt series of SAED in the graphic menu bar.
patterns is straightforward. Assuming there is one reflection vector on In the implementation of the reciprocal lattice reconstruction
each SAED pattern perpendicular to the common reflection vector in a method, a panel is used to display the reflection data from a tilt series of
tilt series, a 2D lattice can be reconstructed on the basis of these re- SAED patterns together with an adjustable lattice and a control dialog is
flection vectors and their tilt angles. A 3D lattice is then obtained by the used to adjust the data and the lattice to fit them together. In this way, a
combination of the 2D lattice and the common reflection vector. In 3D lattice is obtained and then forwarded to the next dialog for further
SAED experiments, it is usually to select shortest reflection vector processing.
among all the observed reflections to be the common reflection vector In the implementation of the Niggli cell reduction method, two
in a tilt series of SAED patterns for unit-cell determination, dialogs are designed to generate primitive cells from two different date
A flow chart of the Niggli cell reduction procedures in TEMUC3 is sets, one from two SAED patterns and the tilt angle between them (Li,
shown in Fig. 1. In the first step, a primitive cell can be generated in two 2005) and the other from three SAED patterns, in which each pair
methods, either (i) from two SAED patterns with a common vector and shares a common reflection vector (Yang et al., 2017).
a tilt angle between them (Li, 2005) or (ii) from three SAED patterns The reciprocal lattice or primitive cell is then forwarded into a
with a common reflection vector among each pair of the patterns (Yang dialog for conversion of the lattice or primitive cell into direct space,
et al., 2017). Fig. 2 shows the geometry to generate a primitive cell meanwhile the scale factor on the SAED patterns is used for unit con-
from two SAED diffraction patterns. Assuming three vectors, a*, b*, c*, version. The next step is to make the cell reduction and the metric
span a primitive cell, where a* and b*, span the plane-1 and a* and c* symmetry search for a conventional unit-cell. The final step is the re-
span the plane-2. The angle between plane-1 and plane-2 is φ. Thus the finement of the lattice parameters using the lengths of reflection vectors
angles of the primitive cell are α* = ∠ COQ (or ∠ POB), β* = ∠ TOQ only. The refinement is formulated under the constraints of seven
(ω1), γ* = ∠ TOC (ω2). The geometry to deduce a primitive cell from
three SAED patterns was described in the published paper by Yang et al.
(2017).
The second step is to transform the primitive cell from reciprocal
space to direct space. The third step is to make a cell reduction. An
algorithm developed by Krivy and Gruber (1976) was used in TEMUC3.
The fourth step is to convert from a Niggli cell to a conventional unit-
cell. The procedure proposed by Clegg (1981) was used in TEMUC3. Fig. 3. Menu system of TEMUC3. Icons of a display panel and multiple dialogs
This procedure overcomes the problem by directly comparing the re- are shown in the graphic menu bar, which can be activated and combined for
duced cell to 44 forms of the Niggli cell. The final step is to index the unit-cell determination in various modules.
2
X.-Z. Li Micron 117 (2019) 1–7
Fig. 4. Experimental SAED patterns of a new compound in CoFeCrGe alloy, (a–e) a tilt series of SAED patterns and (f) a separate one in 4-fold symmetry. Zone axes
and reflection indices were calculated after the determined lattice parameters.
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X.-Z. Li Micron 117 (2019) 1–7
Fig. 5. Experimental data set of a new compound in CoFeCrGe alloy with a 2D lattice (a) before and (b) after fitting in TEMUC3.
reflection vectors in the first column are the common one among the tilt Table 2
series of SAED patterns. SAED data of the Al5Co2 phase in Fig. 6. The angle between SAED patterns of A
Referring to the flow chart in Fig. 1, the following procedure was and B is 18.5° and the angle between SAED patterns of B and C is 18.4°. Scale
used for unit-cell determination: (i) a primitive cell was directly gen- bar on SAED patterns is 2 nm−1 / 84 pixels.
erated from two SAED patterns and the tilt angle between them; (ii) the SAED pattern V1 (pixel) V2 (pixel) Angle (º)
primitive cell was converted from reciprocal space to direct space; (iii)
the primitive cell was then converted to a Niggli cell by reduction and A 63.4 138.2 62.7
B 84.0 84 67.9
was then converted to a conventional unit-cell. The results are given in C 63.4 127.7 75.6
Tables 3 and 4, using the SAED patterns in Fig. 6(a–b) and (b–c), re-
spectively.
Table 5 lists the average results of the calculated lattice parameters the processing procedures in TEMUC3 and those in Yang et al (2017).
and the original data for comparison. It shows a slight difference be- Fig. 7 shows the simulated SAED patterns from the Mg4Zn7 phase, in
tween them due to the decimal round up when input data were pre- which the common reflection vectors for each pair of them were
pared for unit-cell determination. The zone axes and the reflection in- marked. Table 6 lists the lengths of the common reflection vectors for
dices in Fig. 6 were calculated using the calculated lattice parameters of the three SAED patterns in Fig. 7. A primitive cell was generated from
the hexagonal Al5Co2 phase. The refinement step was skipped since the three SAED patterns and then go through the similar procedure in
simulated data was used. section 4.2. The intermediate results are listed in Table 7. The calcu-
lated and original lattice parameters are listed in Table 8 for compar-
ison. As explained above, a slight difference between them is mainly
4.3. Cell reduction (ii) on the Mg4Zn7 phase
due to the decimal round up during the preparation of the input data.
The Mg4Zn7 phase (Yarmolyuk Ya et al., 1975) was used as an ap-
plication example for the cell reduction method by Yang et al. (2017).
The same set of diffraction patterns was also used as an example of the
cell reduction (ii) in TEMUC3. The example is used for comparison of
Fig. 6. Simulated SAED patterns from the Al5Co2 phase, the two basic reflection vectors were marked.
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X.-Z. Li Micron 117 (2019) 1–7
Table 3 Table 6
The intermediate stages for the unit cell determination of the Al5Co2 phase from SAED data of the Mg4Zn7 phase, lengths and angles of the basic vectors V12, V23,
SAED patterns A and B in Table 2. V31 of the SAED patterns in Fig. 7. Scale bar on SAED patterns is 2 nm−1 / 84
pixels.
Primitive cell in reciprocal space (pixel, º)
SAED pattern V12 (pixel) V23 (pixel) V31 (pixel) Angle (º)
a* b* c* α* (º) β* (º) γ* (º)
63.4 138.2 84.0 17.572 67.9 62.7 a 81.9 — 33.1 78.3
b 81.9 30.1 — 87.6
Unit cell in direct space before cell reduction (nm, º) c — 30.1 33.1 77.8
Fig. 7. Simulated SAED patterns from the Mg4Zn7 phase, the two basic reflection vectors were marked. Each pair in the three SAED patterns shares a common
reflection vector.
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X.-Z. Li Micron 117 (2019) 1–7
is collected. Lattice parameters can be calculated from the data set with
computer software (Kolb et al., 2007; Zhang, 2010). This method may
require much longer experimental time. Therefore, if the determination
of unit-cell is the only requisite task, the traditional method is more
efficient.
One of the advantages in the Niggli cell reduction method is it can
be applied to all seven crystal systems. The cell reduction method i in
TEMUC3 requires an accurate measurement of the tilt angle between
two SAED patterns. In the approach proposed by Yang et al. (2017), the
tilt angles can be calculated directly from electron diffraction data. Of
course, the benefit comes from the burden of the work load on the
experimental work. This approach was adopted in TEMUC3 as the cell
reduction method ii.
An algorithm was provided for unit-cell determination from ran-
domly oriented electron diffraction patterns (Jiang et al., 2009,2011).
This method was applied to the samples which is sensitive to the
electron beam or crystalline particles. Since a set of electron diffraction
patterns are collected from randomly oriented samples, the patterns
must be obtained from a single phase. It will be challenging to use this
method if a small amount of second phase exists in samples.
Tilt angles in a tilt series of SAED patterns are important for the Acknowledgements
initial stage of unit-cell determination. Once the lattice parameters
were approximately determined, the set of SAED patterns can be in- The author would like to thank A. Sarella and J. Doyle for their help
dexed with error tolerance. Only the lengths of the reflection vectors to improve the manuscript.
are used for the refinement of lattice parameters. Therefore, even the
tilt angles are hardly obtained accurately in electron diffraction ex-
periments, the measurement of lattice parameters are limited only by Appendix A. Supplementary data
the error on lengths of the diffraction vectors. The accurate of mea-
surement on digital graphics can be achieved down to subpixel (Li, Supplementary material related to this article can be found, in the
2018). online version, at doi:https://doi.org/10.1016/j.micron.2018.10.010.
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X.-Z. Li Micron 117 (2019) 1–7
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