-
Notifications
You must be signed in to change notification settings - Fork 2
/
main.tex
639 lines (590 loc) · 29.5 KB
/
main.tex
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
\documentclass[12pt,letterpaper,final]{amsart}
\usepackage[utf8]{inputenc}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{mathtools}
\usepackage[bookmarks=true, colorlinks=true]{hyperref}
\usepackage{setspace}
% Graphics
\usepackage{graphicx}
\usepackage{epstopdf}
\DeclareGraphicsRule{.eps}{pdf}{.pdf}{`epstopdf #1}
\pdfcompresslevel=9
\setlength{\voffset}{0in}
\setlength{\hoffset}{0in}
\setlength{\oddsidemargin}{0in}
\setlength{\evensidemargin}{0in}
\setlength{\marginparwidth}{0in}
\setlength{\textwidth}{6.5in}
\setlength{\parskip}{1ex}
\doublespacing
\raggedright
\usepackage[numbers,sort&compress]{natbib}
% Front matter
\author{Joel Vincent Bernier}
\title{A general geometric model for parameterizing diffraction measurements}
% some macros
\newcommand{\mbm}[1]{\ensuremath{\mbox{\boldmath$#1$}}}
\newcommand{\tvecd}{\ensuremath{\mbm{\mathrm{t}}_d}}
\newcommand{\tvecs}{\ensuremath{\mbm{\mathrm{t}}_s}}
\newcommand{\tvecc}{\ensuremath{\mbm{\mathrm{t}}_c}}
\newcommand{\rmatd}{\ensuremath{\mathsf{R}_d}}
\newcommand{\rmats}{\ensuremath{\mathsf{R}_s}}
\newcommand{\rmatc}{\ensuremath{\mathsf{R}_c}}
\newcommand{\amat}{\ensuremath{\mathsf{A}}}
\newcommand{\bmat}{\ensuremath{\mathsf{B}}}
\newcommand{\gvec}{\ensuremath{\mbm{\mathrm{G}}}}
\newcommand{\ghat}{\ensuremath{\hat{\mbm{\mathrm{G}}}}}
\newcommand{\bhat}{\ensuremath{\hat{\mbm{\mathrm{b}}}}}
\newcommand{\dhat}{\ensuremath{\hat{\mbm{\mathrm{d}}}}}
\newcommand{\ehat}{\ensuremath{\hat{\mbm{\mathrm{e}}}}}
\newcommand{\eye}{\ensuremath{\mbm{\mathrm{I}}}}
\newcommand{\vmat}{\ensuremath{\mbm{\mathrm{V}}}}
\newcommand{\defgrad}{\ensuremath{\mbm{\mathrm{F}}}}
\newcommand{\detpt}{\ensuremath{\mbm{\mathrm{x}}}}
\newcommand{\ghati}{\ensuremath{\hat{G}_{i}}}
\newcommand{\bhati}{\ensuremath{\hat{b}_{i}}}
\newcommand{\dhati}{\ensuremath{\hat{d}_{i}}}
\newcommand{\ghatj}{\ensuremath{\hat{G}_{j}}}
\newcommand{\bhatj}{\ensuremath{\hat{b}_{j}}}
\newcommand{\dhatj}{\ensuremath{\hat{d}_{j}}}
% points
\newcommand{\Pzero}{\ensuremath{\mathrm{P0}}}
\newcommand{\Pone}{\ensuremath{\mathrm{P1}}}
\newcommand{\Ptwo}{\ensuremath{\mathrm{P2}}}
\newcommand{\Pthree}{\ensuremath{\mathrm{P3}}}
\newcommand{\Pfour}{\ensuremath{\mathrm{P4}}}
% coordinate axes
\newcommand{\Xl}{\ensuremath{\hat{\mbm{\mathrm{X}}}_l}}
\newcommand{\Yl}{\ensuremath{\hat{\mbm{\mathrm{Y}}}_l}}
\newcommand{\Zl}{\ensuremath{\hat{\mbm{\mathrm{Z}}}_l}}
\newcommand{\labframe}{\ensuremath{\left\{\Xl\Yl\Zl\right\}}}
\newcommand{\Xb}{\ensuremath{\hat{\mbm{\mathrm{X}}}_b}}
\newcommand{\Yb}{\ensuremath{\hat{\mbm{\mathrm{Y}}}_b}}
\newcommand{\Zb}{\ensuremath{\hat{\mbm{\mathrm{Z}}}_b}}
\newcommand{\beamframe}{\ensuremath{\left\{\Xb\Yb\Zb\right\}}}
\newcommand{\Xd}{\ensuremath{\hat{\mbm{\mathrm{X}}}_d}}
\newcommand{\Yd}{\ensuremath{\hat{\mbm{\mathrm{Y}}}_d}}
\newcommand{\Zd}{\ensuremath{\hat{\mbm{\mathrm{Z}}}_d}}
\newcommand{\detframe}{\ensuremath{\left\{\Xd\Yd\Zd\right\}}}
\newcommand{\Xs}{\ensuremath{\hat{\mbm{\mathrm{X}}}_s}}
\newcommand{\Ys}{\ensuremath{\hat{\mbm{\mathrm{Y}}}_s}}
\newcommand{\Zs}{\ensuremath{\hat{\mbm{\mathrm{Z}}}_s}}
\newcommand{\sampframe}{\ensuremath{\left\{\Xs\Ys\Zs\right\}}}
\newcommand{\Xc}{\ensuremath{\hat{\mbm{\mathrm{X}}}_c}}
\newcommand{\Yc}{\ensuremath{\hat{\mbm{\mathrm{Y}}}_c}}
\newcommand{\Zc}{\ensuremath{\hat{\mbm{\mathrm{Z}}}_c}}
\newcommand{\crysframe}{\ensuremath{\left\{\Xc\Yc\Zc\right\}}}
% vector components
\newcommand{\labcomps}[1]{\left[#1\right]_l}
\newcommand{\beamcomps}[1]{\left[#1\right]_b}
\newcommand{\detcomps}[1]{\left[#1\right]_d}
\newcommand{\sampcomps}[1]{\left[#1\right]_s}
\newcommand{\cryscomps}[1]{\left[#1\right]_c}
\newcommand{\rcpcomps}[1]{\left[#1\right]_*}
% cross-references
\newcommand{\figref}[1]{Figure~\ref{#1}}
\newcommand{\eqnref}[1]{Equation~\ref{#1}}
\newcommand{\secref}[1]{\S~\ref{#1}}
% miscellaneous
\newcommand{\ie}{{\em i.e.}}
\newcommand{\eg}{{\em e.g.}}
\newcommand{\cf}{{\em cf.}}
\newcommand{\xray}{X-ray}
\newcommand{\xrays}{X-rays}
\newcommand{\gx}{\ensuremath{\gamma_x}}
\newcommand{\gy}{\ensuremath{\gamma_y}}
\newcommand{\gz}{\ensuremath{\gamma_z}}
\newcommand{\crysdir}{\ensuremath{\mathbf{h}}}
\newcommand{\sampdir}{\ensuremath{\mathbf{s}}}
\newcommand{\hkls}{\ensuremath{hkl}}
\newcommand{\bhkls}{\ensuremath{\bar{h}\bar{k}\bar{l}}}
\newcommand{\cella}{\ensuremath{\mathbf{a}}}
\newcommand{\cellb}{\ensuremath{\mathbf{b}}}
\newcommand{\cellc}{\ensuremath{\mathbf{c}}}
\newcommand{\dalfa}{\ensuremath{\alpha}}
\newcommand{\dbeta}{\ensuremath{\beta}}
\newcommand{\dgama}{\ensuremath{\gamma}}
\newcommand{\cellParams}{\ensuremath{\left\{ a,b,c,\dalfa,\dbeta,\dgama \right\}}}
\newcommand{\cellParamsRef}{\ensuremath{\left\{ a_0,b_0,c_0,\dalfa_0,\dbeta_0,\dgama_0 \right\}}}
\newcommand{\rcella}{\ensuremath{\mathbf{a}^*}}
\newcommand{\rcellb}{\ensuremath{\mathbf{b}^*}}
\newcommand{\rcellc}{\ensuremath{\mathbf{c}^*}}
\newcommand{\ralfa}{\ensuremath{\alpha^*}}
\newcommand{\rbeta}{\ensuremath{\beta^*}}
\newcommand{\rgama}{\ensuremath{\gamma^*}}
\newcommand{\rcellParams}{\ensuremath{\left\{ a^*,b^*,c^*,\ralfa,\rbeta,\rgama \right\}}}
\newcommand{\cellVol}{\ensuremath{v}}
\newcommand{\cellVolExpr}{\ensuremath{\dotp{\cella}{\crossp{\cellb}{\cellc}}}}
\newcommand{\strain}{\mbm{\epsilon}}
% CONVENIENCE
\newcommand{\coe}{\ensuremath{\cos\eta}}
\newcommand{\sie}{\ensuremath{\sin\eta}}
\newcommand{\cob}{\ensuremath{\cos\theta}}
\newcommand{\sib}{\ensuremath{\sin\theta}}
\newcommand{\cop}{\ensuremath{\cos\phi}}
\newcommand{\sip}{\ensuremath{\sin\phi}}
\newcommand{\cow}{\ensuremath{\cos\omega}}
\newcommand{\siw}{\ensuremath{\sin\omega}}
\newcommand{\cox}{\ensuremath{\cos\chi}}
\newcommand{\six}{\ensuremath{\sin\chi}}
\newcommand{\coxsq}{\ensuremath{\cos^2\chi}}
\newcommand{\sixsq}{\ensuremath{\sin^2\chi}}
\newcommand{\sitx}{\ensuremath{\sin{2\chi}}}
\newcommand{\nZ}{\ensuremath{n_0}}
\newcommand{\nO}{\ensuremath{n_1}}
\newcommand{\nT}{\ensuremath{n_2}}
\newcommand{\nZO}{\ensuremath{n_0n_1}}
\newcommand{\nZT}{\ensuremath{n_0n_2}}
\newcommand{\nOT}{\ensuremath{n_1n_2}}
\newcommand{\hgZ}{\ensuremath{\hat{G}_0}}
\newcommand{\hgO}{\ensuremath{\hat{G}_1}}
\newcommand{\hgT}{\ensuremath{\hat{G}_2}}
\newcommand{\hbZ}{\ensuremath{\hat{b}_0}}
\newcommand{\hbO}{\ensuremath{\hat{b}_1}}
\newcommand{\hbT}{\ensuremath{\hat{b}_2}}
% MATH OPERATORS
\newcommand{\rmat}[2]{\ensuremath{\mathsf{R}\left(#1,\;#2\right)}}
\newcommand{\sub}[2]{\ensuremath{#1_#2}}
\newcommand{\dotp}[2]{\ensuremath{#1\cdot#2}}
\newcommand{\crossp}[2]{\ensuremath{#1\times#2}}
\newcommand{\modulus}[2]{\mathop{\mathrm{mod}\left(\frac{#1}{#2}\right)}}
\newcommand{\skewMat}[1]{\ensuremath{
\left[
\begin{array}{rrr}
0 & -#1_2 & #1_1 \;\\
#1_2 & 0 & -#1_0 \;\\
-#1_1 & #1_0 & 0 \;
\end{array}
\right]}}
\newcommand{\skewOp}[1]{\ensuremath{\mathrm{skew}\;#1}}
\newcommand{\symmMat}[1]{\ensuremath{
\left[
\begin{array}{ccc}
#1_0 & #1_5 & #1_4 \\
& #1_1 & #1_3 \\
\multicolumn{2}{l}{\text{\smash{\raisebox{0.35ex}{\;Sym.}}}} & #1_2 \\
\end{array}
\right]}}
\newcommand{\outerProdMat}[1]{\ensuremath{
\left[
\begin{array}{rrr}
#1_0^2 & #1_0#1_1 & #1_0#1_2 \\
& #1_1^2 & #1_1#1_2 \\
\multicolumn{2}{l}{\text{\smash{\raisebox{0.35ex}{\;\;Sym.}}}} & #1_2^2 \\
\end{array}
\right]}}
\newcommand{\EyeMinusOuterProdMat}[1]{\ensuremath{
\left[
\begin{array}{rrr}
1 - #1_0^2 & -#1_0#1_1 & -#1_0#1_2 \\
& 1 - #1_1^2 & -#1_1#1_2 \\
\multicolumn{2}{l}{\text{\smash{\raisebox{0.35ex}{\;\;Sym.}}}} & 1 - #1_2^2 \\
\end{array}
\right]}}
% --------------------- Document ---------------------
\begin{document}
\maketitle
\begin{abstract}
A complete and general geometric model for parameterizing diffraction
measurements with one or more planar detectors is presented. It includes provisions for describing both mono- and poly-chromatic schemes for {\em collimated} incident beams (\ie\ negligible beam divergence), although extensions to divergent sources are discussed. Detectors are modeled as polygonal planar bodies, and their shapes and placements in the reference frame are completely arbitrary. The mapping that takes an admissible reciprocal lattice vector in the crystal frame to pixel coordinates in a specific detector frame is of the form $\mathbf{A}(\mathbf{x})\cdot\mathbf{x} =
\mathbf{y}$. Application to the rotation method, including the effects of non-perpendicularity of the rotation axis to the incident beam wave vector, is presented in detail.
\end{abstract}
\newpage
\section{Background \& Motivation}
With many different measurement schemes, the rise of HEDM, and multi-panel instruments, it bears merit to revisit a generic geometric model suitable for implementation in data reduction software... standardization, {\em blah, blah, blah}
\section{Coordinate Systems}
A single-detector diffraction measurement schema is illustrated in
\figref{F:diffraction_schema}. For generality we utilize five
fundamental coordinate systems:
\begin{itemize}
\item the {\bf laboratory} frame, \labframe;
\item the {\bf beam} frame, \beamframe;
\item the {\bf detector} frame(s), $\detframe_i$;
\item the {\bf sample} frame, \sampframe; and
\item the {\bf crystal} frame, \crysframe.
\end{itemize}
\subsection{Laboratory Frame}\label{S:laboratory}
The laboratory frame is intended to provide a global reference frame
that is stationary during the measurement. The incident beam has a
non-negligible physical extent in the lab frame, typically possessing
a rectangular or circular cross-section. For clarity, we restricting
our focus to sources that may be described using plane waves. With
regards to the geometric construction, it is useful to define the beam
direction as the unit incident wave vector,
$\bhat\equiv\frac{\mbm{k}_i}{\|\mbm{k}_i\|}$. The centroid of the
beam cross-section is defined to coincide with the origin of
\labframe, labeled \Pzero.
\subsection{The Beam Frame}
When working with the geometry of diffraction, it becomes very useful
to associate detector-relative cartesian coordinates -- and
diffraction vectors \dhat\ -- with a Bragg angle, $2\theta$, and
azimuth, $\eta$. Noting that the Bragg condition is axisymmetric
about the incident wave vector, a natural frame in which represent
these spherical angles has the origin at the diffracting element, and
incident beam aligned with one of the basis vectors. In the present
notation, the Bragg angle (see \eqnref{E:braggCondition}) is defined
as
\begin{equation}
2\theta \equiv \arccos{\left( \bhat \cdot \dhat \right)},
\end{equation}
where \dhat\ is the unit vector representing the direction of the
diffracted beam
\begin{displaymath}
\dhat \equiv \frac{\Pfour-\Pthree}{\|\Pfour-\Pthree\|}.
\end{displaymath}
To define an azimuth, a reference direction, \ehat, must be specified.
The definition of a reference azimuth vector is arbitrary, however
\ehat\ and \bhat\ cannot be collinear. The standard setting has
$\labcomps{\ehat}=\left[1\;0\;0\right]^T$. The components \bhat\ in
the laboratory frame are parameterized by spherical angles $(\phi,
\gamma)$:
\begin{equation}
\labcomps{\bhat} = -\begin{Bmatrix}
\sin\phi \cos\gamma \\
\sin\phi \sin\gamma \\
\cos\phi
\end{Bmatrix}.
\end{equation}
The standard setting has $\phi=\gamma=0$. The basis vectors defining
the beam frame in the standard setting are
\begin{equation}
\beamframe = \left[ \ehat,\; -\bhat\times\ehat,\; -\bhat \right].
\label{E:etaFrame}
\end{equation}
The components of a unit diffraction vector in the beam frame are
\begin{equation}
\beamcomps{\dhat} = \begin{Bmatrix}
\sin2\theta \cos\eta \\
\sin2\theta \sin\eta \\
-\cos2\theta
\end{Bmatrix},
\end{equation}
and the azimuth of a diffracted beam is obtained as
\begin{equation}
\eta = \arccos{\left(\ehat \cdot \left( \eye - \bhat \otimes \bhat \right)\cdot\dhat\right)}.
\end{equation}
Lastly, the components of a reciprocal lattice vector, \gvec, are
simply
\begin{equation}
\beamcomps{\gvec} = \frac{2\sin{\theta}}{\lambda}\begin{Bmatrix}
\cos\eta \cos\theta \\
\sin\eta \cos\theta \\
\sin\theta
\end{Bmatrix}
\end{equation}
where $\lambda$ is the \xray\ wavelength.
\subsection{Detector Frame}\label{S:detector}
A typical detector element has a planar active area with a rectangular
shape. A complete instrument may contain several independent
detectors with unique orientations and placements in the lab frame. A
cartesian coordinate system \detframe\ is attached to each independent
detector element as follows: the origin \Pone\ is coincident with the
centroid of the active surface, and \Zd\ represents the plane normal.
The \Xd,\Yd\ directions are typically aligned with the horizontal and
vertical pixel-relative directions on each panel. The coordinates of
points in each independent detector coordinate system, \detframe\, are
related to coordinated in \labframe\ via a simple affine
transformation:
\begin{gather}
\labcomps{\detpt} = \rmatd\cdot\detcomps{\detpt} + \labcomps{\tvecd}
\end{gather}
where $\tvecd = \Pone - \Pzero$ and the notation
$\labcomps{\detpt}$ indicates the components of $\detpt$ in
\labframe. Because only planar detectors are considered, the
components of a detector-relative point are of the form
$\detcomps{\detpt}=[x\; y\; 0]$.
\subsection{Sample Frame}\label{S:sample}
The sample frame provides a basis in which to represent a uniquely
oriented and located specimen. For the arbitrarily defined
sample-relative vector $\mathbf{S}$, coordinates in \sampframe\ are
connected to \labframe\ via the affine transformation
\begin{equation}
\labcomps{\mathbf{s}} = \rmats\cdot\sampcomps{\mathbf{s}} + \labcomps{\tvecs}
\end{equation}
where $\tvecs=\Ptwo-\Pzero$. In the case of the rotation method, this
is frame is the oscillation frame. Without loss of generality, the
oscillation axis is fixed to \Ys. It may be canted with respect to
\Yl\ by the angle $\chi$\footnote{the canting angle $\chi$ is
typically very small for an HEDM schema, although some special cases
might require it to be set to some non-zero value. Including this
degree of freedom in the model also allows for it to be quantified
via calibration.}. The oscillation angle itself is represented by
$\omega$. The full model has a sufficient number of degrees of
freedom to preclude the need for a third rotational degree of freedom
for \sampframe.
\subsection{Crystal Frame}\label{S:crystal}
The crystal frame represent a local RHON coordinate system attached to
the lattice of a single-crystal domain in the sample. In the context
of far-field HEDM, the origin of \crysframe, labeled \Pthree,
represents the centroid of the crystallite. For a crystal-relative
vector $\mathbf{c}$, the components are transformed as
\begin{align}
\sampcomps{\mathbf{c}} &= \rmatc\cdot\cryscomps{\mathbf{c}} + \sampcomps{\tvecc}\\
\labcomps{\mathbf{c}} &= \rmats\cdot\rmatc\cdot\cryscomps{\mathbf{c}} + \rmats\cdot\sampcomps{\tvecc} + \labcomps{\tvecs}
\end{align}
where $\tvecc=\Pthree-\Ptwo$. The formulation of diffracted beam vectors for a given unit cell is discussed in \secref{S:diffraction}.
%%
\begin{figure}[htb]
\centering
\includegraphics[width=0.85\textwidth]{new_geometry.pdf}
\caption{A single-detector diffraction schema illustrating the four
fundamental coordinate systems and the 5 generic points
\Pzero-\Pfour\ used to create the transfer function taking
reciprocal lattice vector components to detector-relative
components. For completeness, the reciprocal lattice vector
\gvec\ and Bragg angle $2\theta$ associated with \Pfour\ are
shown. The azimuthal angle, $\eta$, of \ghat\ about \bhat\ is not
shown; however, the reference azimuth is, denoted by the unit
vector \ehat. }
\label{F:diffraction_schema}
\end{figure}
%%
\newpage
\section{Diffraction}\label{S:diffraction}
\subsection{Convention for writing components of crystal lattice vectors}\label{S:conventions}
In order to insert the geometry of diffraction into the coordinate
system hierarchy described above, it is necessary to etablish a
convention for describing the crystal lattice. The crystal lattice
itself may be parameterized by its primitive vectors \cella, \cellb,
and \cellc. They share a common origin at a lattice site and are
subject to the following conditions:
%%
\begin{equation}
\begin{array}{rcl}
\|\cella\| &=& a\\
\|\cellb\| &=& b\\
\|\cellc\| &=& c\\
{1 \over bc}\dotp{\cellb}{\cellc} &=& \cos\dalfa\\
{1 \over ca}\dotp{\cellc}{\cella} &=& \cos\dbeta\\
{1 \over ab}\dotp{\cella}{\cellb} &=& \cos\dgama
\end{array} \label{E:lattParams}
\end{equation}
%%
The six scalar cell parameters \cellParams\ represent a convenient
parameterization of the reference unit cell, which typically
correspond to an unloaded state at a reference temperature. Crystal
symmetry operations (excluding triclinic) generate equivalences among
cell parameters; however once a crystal is deformed, the reference
symmetry is broken and all six parameters must be considered as
independent. The treatment of strained crystals in the context of the
reference crystal symmetry is discussed in detail below. For writing
components of crystal-relative vectors and tensors in \crysframe, a
convention must be chosen to register the lattice vectors. The
convention employed herein is consistent with that proposed by
\cite{Nye:crysBookAppB}. Explicitly stated, $\cella\parallel\Xc$ and
$(\crossp{\cella}{\cellb})\parallel\Zc$, as depicted in
\figref{F:lattice}.
%%
\begin{figure}[ht]
\centering
\includegraphics[width=0.6\textwidth]{unitCell.pdf}
\caption{The convention for describing the
reference (read: unstrained) lattice has $\cella\parallel\Xc$ and
$\rcellc\parallel\Zc$. Note that a triclinic
primitive cell is depicted for generality. The crystal orientation, \rmatc,
takes components in the crystal frame, \crysframe, to the sample
frame, \sampframe.}
\label{F:lattice}
\end{figure}
%%
The reciprocal lattice, which forms a dual basis to the direct
lattice, is a very useful concept in diffraction. The reciprocal
lattice vectors are defined\footnote{this is the so-called
``crystallographer's convention'' where the prefactor of $2\pi$ is
omitted.} as follows:
%%
\begin{align}
\rcella = {1 \over v}\crossp{\cellb}{\cellc}\\
\rcellb = {1 \over v}\crossp{\cellc}{\cella}\\
\rcellc = {1 \over v}\crossp{\cella}{\cellb}
\end{align}
%%
where $\cellVol = \cellVolExpr$ represents the volume of the primitive
cell, and \rcellParams\ are the reciprocal lattice parameters defined
analogously to the direct lattice parameters in \figref{F:lattice} and
\eqnref{E:lattParams}. With \crysframe\ define with reference to
\cellParams\ and \rcellParams, we define the change-of-basis matrix,
\amat, which takes components in the direct lattice frame to the
\crysframe as
%%
\begin{align}
\amat &\equiv \cryscomps{\cella\;\cellb\;\cellc} \label{E:amatrix}\\
&= \begin{bmatrix}
a & b\cos{\gamma} & c\cos{\beta} \\
0 & b\sin{\gamma} & -c\cos{\alpha^*}\sin{\beta} \\
0 & 0 & c\sin{\alpha^*}\sin{\beta}
\end{bmatrix}. \nonumber
\end{align}
%%
Note that an identity from \citet{Neustadt:a05876} is employed to
simplify the components for \amat. Analogously the change-of-basis
matrix, \bmat, that takes vector components in the reciprocal lattice
frame to the crystal frame is defined as
%%
\begin{align}
\bmat &\equiv \cryscomps{\begin{matrix} \rcella & \rcellb & \rcellc \end{matrix}} \label{E:bmatrix}\\
&= \frac{1}{\cellVol}\begin{bmatrix}
bc\sin{\ralfa}\sin{\dbeta}\sin{\dgama} & 0 & 0 \\
-bc\sin{\ralfa}\sin{\dbeta}\cos{\dgama} & ac\sin{\ralfa}\sin{\dbeta} & 0 \\
-bc(\cos{\ralfa}\sin{\dbeta}\cos{\dgama} + \cos{\dbeta}\sin{\dgama}) & ac\cos{\ralfa}\sin{\dbeta} & ab\sin{\dgama}
\end{bmatrix}, \nonumber
\end{align}
%%
Assume that a reciprocal lattice vector, \gvec, satisfies a Bragg condition. The unit vector aligned with its associated diffracted beam, \dhat, is then
\begin{align}
\dhat &= \mathsf{R}\left(\pi, \ghat\right)\cdot\left(-\bhat\right) \nonumber\\
&= \left(2\ghat\otimes\ghat - \eye\right)\cdot\left(-\bhat\right) \nonumber\\
&= \left(\eye - 2\ghat\otimes\ghat\right)\cdot\bhat \label{E:dhat}\\
& \mbox{where } \ghat\cdot\bhat = -\frac{\lambda}{2}\|\gvec\| = -\sin{\theta}, \label{E:braggCondition}\\
& \dhat\cdot\Zd < 0, \label{E:intersectsDetector}
\end{align}
$\ghat=\gvec / \|\gvec\|$, and \bhat\ is the unit vector aligned with the beam propagation direction. \eqnref{E:braggCondition} is the Bragg condition for \xrays\ having wavelength $\lambda$, and \eqnref{E:intersectsDetector} is the geometric condition ensuring that \dhat\ can intersect the detector plane. Note that there is an additional condition that must be satisfied in the instrument for \Pfour\ to be observable; it must also lie within the physical extent of the detector element. Application of this condition is, however, quite straightforward and not explicitly stated in this document.
%
\subsection{Representing crystal orientation and strain}
A reciprocal lattice vector, \gvec, is typically representend by its components in the reference (read: undistorted) reciprocal lattice frame, $\rcpcomps{\gvec}=[h\; k\; l]$. The change-of-basis matrix, \bmat, that takes components in the reciprocal lattice to \crysframe\ was given by \eqnref{E:bmatrix} above (\secref{S:conventions}). The effects of both finite distortion and rotation of a crystal lattice with respect to \sampframe\ are captured using a deformation gradient tensor, \defgrad, as presented in \cite{Bernier:2011uq}. The tensor \defgrad\ acts on the {\em direct} lattice vectors, and takes undistorted lattice vectors in the reference crystal frame, \crysframe, to reoriented and distorted lattice vectors in the sample frame, \sampframe. Using the polar decomposition,
\begin{equation}
\defgrad = \vmat \rmatc,\; \forall\; \vmat \in Sym^{3\times3},\; \rmatc \in SO^3,
\end{equation}
where \rmatc\ is the crystal orientation and \vmat\ is the ``left'' stretch tensor. \citet{Edmiston2012} have shown that
$\defgrad^{-T}=\vmat^{-1}\rmatc$
can be applied analogously to reciprocal lattice vector components written in \crysframe.
Given the reciprocal lattice vector \gvec, with components $\rcpcomps{\gvec}=[h\; k\; l]$ in the reciprocal lattice frame, the fully distorted and orientend components in \labframe\ are then derived as
\begin{align}
\labcomps{\gvec} &= \rmats \sampcomps{\gvec} \nonumber\\
&= \rmats \sampcomps{\defgrad^{-T}} \cryscomps{\gvec} \nonumber\\
&= \rmats \sampcomps{\defgrad^{-T}} \bmat \rcpcomps{\gvec} \nonumber\\
\Aboxed{ &= \rmats \sampcomps{\vmat^{-1}} \rmatc \bmat \rcpcomps{\gvec} }\label{E:gvecLab},
\end{align}
The three crystal orientation degrees of freemdom are wrapped up in \rmatc, while the six that represent strain are contained in \vmat.
Functionally, the orientation degrees of freedom can be decoupled from the strain (and position) degrees of freedom in the initial analysis. This ``orientation indexing'' procedure essentially consists of testing discrete orientations $\mathsf{R}(\phi, \mbm{n})$, for a set of feasible \gvec\ and checking for intensity at the associated detector points \Pfour. For the rotation method, the oscillation angle $\omega$ must be calculated for each feasible \gvec\ as well; this will be discussed in \secref{S:oscill}.
\section{Parametric ray-plane intersection and the transform function}\label{S:transform}
The coordinates of the points $\Pzero-\Pfour$ (see \figref{F:diffraction_schema}) in the lab frame are
\begin{align}
\labcomps{\Pzero} &\equiv \begin{bmatrix} 0 & 0 & 0 \end{bmatrix} \\
\labcomps{\Pone} &= \labcomps{\tvecd} \\
\labcomps{\Ptwo} &= \labcomps{\tvecs} \\
\labcomps{\Pthree} &= \rmats\sampcomps{\tvecc} + \labcomps{\tvecs} \\
\labcomps{\Pfour} &= \rmatd\detcomps{\detpt} + \labcomps{\tvecd}
\end{align}
Using the parametric equations for a plane (\eqnref{E:plane}) and line (\eqnref{E:line}), we may obtain a system of equations linking \dhat\ and \Pfour.
\begin{gather}
\Zd \cdot (\Pfour - \Pone) = 0 \label{E:plane}\\
\Pfour = \Pthree + u\dhat \label{E:line}
\end{gather}
Substituting for \Pfour\ and rearranging to solve for the scale parameter $u$ yields
\begin{align}
\Zd \cdot (\Pthree - \Pone + u\dhat) &= 0 \nonumber\\
\Zd \cdot (\Pthree - \Pone) &= -u\Zd \cdot \dhat \nonumber\\
\implies u &= \frac{\Zd \cdot (\Pone - \Pthree)}{\Zd \cdot \dhat
}
\end{align}
Finally, inserting this result into \eqnref{E:line} with some rearrangement yields
%\begin{equation}
% \detcomps{\Pfour} = \rmatd^T\cdot\labcomps{ \rmats\tvecc+\tvecs-\tvecd
% - \frac{\left(\rmatd\Zl\right)\cdot\left(\rmats\tvecc+\tvecs-\tvecd\right)}
% {\left(\rmatd\Zl\right)\cdot\dhat}\cdot\dhat },
%\end{equation}
%or in component form:
\begin{equation}
\boxed{\detcomps{\Pfour} = \rmatd^T \cdot \left[ \labcomps{\Pthree - \Pone}
- \frac{\mathrm{dot}\left(\labcomps{\Zd}^T,\; \labcomps{\Pthree - \Pone}\right)}
{\mathrm{dot}\left(\labcomps{\Zd}^T,\; \labcomps{\dhat}\right)}\labcomps{\dhat} \right] }, \label{E:Pfour}
\end{equation}
where $\labcomps{\dhat}$ is obtained from \eqnref{E:dhat} and \eqnref{E:gvecLab}.
% as
%\begin{align}
% \dhati &= \left(\delta_{ij} - 2\ghati\ghatj\right)\cdot\bhatj
%\end{align}
%%
\section{Solving for the oscillation angle, $\omega$}\label{S:oscill}
For a monochromatic schema using the rotation method, the action of the oscillation in a canted configuration is represented by the rotation \rmats\, where
\begin{align}
\rmats &= \rmat{\chi}{\Xl}\rmat{\omega}{\Yl} \label{E:rmats} \\
&= \left[\begin{array}{rrr}1&0&0\\0&\cox&-\six\\0&\six&\cox\end{array}\right]
\left[\begin{array}{ccc}\cow&0&\siw\\0&1&0\\-\siw&0&\cow\end{array}\right] \nonumber\\
&= \left[\begin{array}{ccc}
\cow & 0 & \siw \\
\six\siw & \cox & -\six\cow \\
-\cox\siw & \six & \cox\cow
\end{array}\right] . \nonumber
\end{align}
From \eqnref{E:gvecLab} we have
\begin{equation}
\sampcomps{\gvec} = \sampcomps{\defgrad^{-T}}\bmat\rcpcomps{\gvec} \label{E:ghatInSamp}
\end{equation}
By writing the Bragg condition (\eqnref{E:braggCondition}) in terms of lab-frame components by multiplying by the normalized components $\sampcomps{\ghat}$ above by \rmats\ leads to relation of the form
\begin{align}
a \siw + b \cow &= c \label{E:trig}\\
&\equiv R\sin{\left(x+\alpha\right)} \label{E:identity}\\
\mbox{where } R\equiv\sqrt{a^2 + b^2} &\mbox{, and } \alpha\equiv\mathrm{atan2}(b, a),
\end{align}
and
%%
\begin{align}
a = \sampcomps{\hgT}\labcomps{\hbZ} &+ \six\sampcomps{\hgZ}\labcomps{\hbO} - \cox\sampcomps{\hgZ}\labcomps{\hbT}\\
b = \sampcomps{\hgZ}\labcomps{\hbZ} &- \six\sampcomps{\hgT}\labcomps{\hbO} + \cox\sampcomps{\hgT}\labcomps{\hbT}\\
c = -\sin{\theta} &- \cox\sampcomps{\hgO}\labcomps{\hbO} - \six\sampcomps{\hgO}\labcomps{\hbT}
\end{align}
%%
These yield the solutions
\begin{equation}
\omega = \left\{
\begin{array}{r}
\arcsin{ \left( \frac{c}{\sqrt{a^2 + b^2}} \right) } - \alpha \\
\pi - \arcsin{ \left(\frac{c}{\sqrt{a^2 + b^2}}\right) } - \alpha \\
\end{array}
\right. \label{E:omegas}
\end{equation}
which are either unique (both sides of the diffraction cone), a double root (tangent to the diffraction cone -- typically not considered) or do not exist ($|\frac{c}{\sqrt{a^2 + b^2}}| > 1$, can't intersect diffraction cone).
\section{Summary}\label{S:summary}
The complete procedure for finding the detector coordinates of all reflections for a specifically oriented, strained crystal at the the position \Pthree\ consists of the following procedure:
\begin{enumerate}
\item Generate $[h\; k\; l]$ up to the relevant order (determined by geometry and wavelength of the \xrays) \\
\item Calculate the set of reciprocal lattice vector components in \sampframe\ using \eqnref{E:ghatInSamp} \\
\item Calculate the set of oscillation angles, $(\omega_0,\; \omega_1)$, for each unique $[h\; k\; l]$ using \eqnref{E:omegas}\\
\item Calculate the set of unit diffraction vector components in \labframe\ using \eqnref{E:rmats}, \eqnref{E:gvecLab}, \eqnref{E:dhat} for each valid oscillation angle pair in $(\omega_0,\; \omega_1)$\\
\item Calculate $\detcomps{\Pfour}$ from \eqnref{E:Pfour}.
\end{enumerate}
\begin{appendix}
\section{Tilt parameterization}
\subsection{Tait-Bryan angles}
Passive convention.
\begin{align}
\rmatd &= \rmat{\zeta}{\Zl}\rmat{\psi}{\Yl}\rmat{\phi}{\Xl} \label{E:rmatd} \\
&= \begin{bmatrix}
\cos{\zeta} & -\sin{\zeta} & 0 \\
\sin{\zeta} & \cos{\zeta} & 0 \\
0 & 0 & 1
\end{bmatrix}
\begin{bmatrix}
\cos{\psi} & 0 & \sin{\psi} \\
0 & 1 & 0 \\
-\sin{\psi} & 0 & \cos{\psi}
\end{bmatrix}
\begin{bmatrix}
1 & 0 & 0 \\
0 & \cos{\phi} & -\sin{\phi} \\
0 & \sin{\phi} & \cos{\phi}
\end{bmatrix} \nonumber\\
&= \begin{bmatrix}
\cos{\zeta} & -\sin{\zeta} & 0 \\
\sin{\zeta} & \cos{\zeta} & 0 \\
0 & 0 & 1
\end{bmatrix}
\begin{bmatrix}
\cos{\psi} & \sin{\psi}\sin{\phi} & \sin{\psi}\cos{\phi} \\
0 & \cos{\phi} & -\sin{\phi} \\
-\sin{\psi} & \cos{\psi}\sin{\phi} & \cos{\psi}\cos{\phi}
\end{bmatrix} \nonumber\\
&= \begin{bmatrix}
\cos{\zeta}\cos{\psi} & \cos{\zeta}\sin{\psi}\sin{\phi} - \sin{\zeta}\cos{\phi} & \cos{\zeta}\sin{\psi}\cos{\phi} + \sin{\zeta}\sin{\phi} \\
\sin{\zeta}\cos{\psi} & \sin{\zeta}\sin{\psi}\sin{\phi} + \cos{\zeta}\cos{\phi} & \sin{\zeta}\sin{\psi}\cos{\phi} - \cos{\zeta}\sin{\phi} \\
-\sin{\psi} & \cos{\psi}\sin{\phi} & \cos{\psi}\cos{\phi}
\end{bmatrix} \nonumber
\end{align}
\end{appendix}
\bibliographystyle{abbrvnat}
\bibliography{hedm}
\end{document}