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FAULTS: A program for refinement of structures with extended defects

Article  in  Journal of Applied Crystallography · December 2016

DOI: 10.1107/S1600576716014473

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 J. Appl. Cryst. (2016). 49, doi:10.1107/S1600576716014473 Supporting information

Volume 49 (2016)

Supporting information for article:

FAULTS: a program for refinement of structures with extended

defects

Montse Casas-Cabanas, Marine Reynaud, Jokin Rikarte, Pavel Horbach and

Juan Rodríguez-Carvajal
SUPPLEMENTARY INFORMATION
FAULTS: a program for refinement of structures with extended defects

Montse Casas-Cabanasa,*, Marine Reynauda, Jokin Rikartea, Pavel Horbachb,c and Juan Rodríguez-
Carvajalb,*
a
CIC Energigune, Parque Técnologico de Álava, Albert Einstein 48, 01510 Miñano (Spain)
b
Institut Laue Languevin, 71 avenue des Martyrs, 38000 Grenoble (France)
c
Institute for Metal Physics, National Academy of Science, 36 Vernadsky Blvd., 03680, Kiev (Ukraine)
* Correspondence e-mails: mcasas@cicenergigune.com, jrc@ill.eu

1. LiεNi1.02O2 example

Figure SI 1: a) Illustration of the structural model used as starting model for the FAULTS
refinement of the simulated pattern of LiɛNi1.02O2. b) Comparison between the pattern of the
starting model (blue) and the simulated pattern of LiɛNi1.02O2 (red) to be refined with FAULTS.
2. MnO2 example

Figure SI 2: Conventional Rietveld refinement of the XRD pattern of the MnO2 sample starting
from the pyrolusite structure and using spherical harmonics to model an anisotropic size
broadening. Some of the reflections are not or badly indexed, and their intensities and broadening
are poorly simulated.
Table SI 1: Structural description of the pyrolusite and ramsdellite elements used as the starting
model for the FAULTS refinement of MnO2.
Cell
a' = 4.4041 Å b' = 2.8765 Å c’ = 4.4041 Å
α = 90º β = 90º γ = 90º
Pyrolusite-type layers
Atom x/a y/b z/c Occupancy
Layer r1 MnIV+ 101 0 0 0 1.0
OII– 121 0.3046 0 0.3046 1.0
OII– 122 0.6954 0 -0.3046 1.0
OII– 141 0.8046 0 0.1954 1.0
OII– 142 0.1954 0 -0.1954 1.0
Layer r2 MnIV+ 201 ½ ½ 0 1.0
Ramsdellite-type layers
Atom x/a y/b z/c Occupancy
Layer R1 MnIV+ 301 0.0258 ¾ 0.2805 1.0
MnIV+ 302 0.9742 ¼ -0.2805 1.0
OII– 321 0.2162 ¼ 0.0726 1.0
OII– 322 0.7838 ¾ -0.0726 1.0
OII– 341 0.3001 ¾ 0.5887 1.0
OII– 342 0.6799 ¼ -0.5887 1.0
OII– 361 0.8201 ¼ 0.4641 1.0
OII– 362 0.1799 ¾ -0.4641 1.0
Layer R2 MnIV+ 401 0.4742 ¾ 0.2805 1.0
MnIV+ 402 0.5258 ¼ -0.2805 1.0
OII– 421 0.2838 ¼ 0.0726 1.0
OII– 422 0.7162 ¾ -0.0726 1.0
Transition vectors
Transition x/a y/b z/c Type
From layer r1 r1  r1 - - - forbidden
r1  r2 0 0 ½ pyrolusite
r1  R1 - - - forbidden
r1  R2 0 ¼ 0.7805 De Wolff defect
From layer r2 r2  r1 0 0 ½ pyrolusite
r2  r2 - - - forbidden
r2  R1 0 -¼ 0.7805 De Wolff defect
r2  R2 - - - forbidden
From layer
R1  r1 - - - forbidden
R1
R1  r2 0 -¼ 0.7805 De Wolff defect
R1  R1 - - - forbidden
R1  R2 0 0 1.0528 ramsdellite
From layer
R2  r1 0 ¼ 0.7805 De Wolff defect
R2
R2  r2 - - - forbidden
R2  R1 0 0 1.0528 ramsdellite
R2  R2 - - - forbidden
Figure SI 3: Layer description used in the FAULTS refinement of MnO2.
Layer stacking probabilities and stacking models

For the sake of comparison, we have employed the same notations and statistical tools as proposed by
Chabre and Pannetier (Chabre & Pannetier, 1995) to describe the sequence of the two kinds of layers:
- Pr and PR are the respective fractions of single (rutile-type = pyrolusite-type) and double
(ramsdellite-type) chain slabs in a given sample. Then, we have the following equality:
Pr + PR = 1
- Pr∙r and PR∙r are the probabilities of occurrence of a rutile (pyrolusite) chain following a rutile chain
r and a ramsdellite chain R, respectively. In the same way, Pr∙R and PR∙R are the probabilities of
occurrence of a ramsdellite chain R following a rutile chain r and a ramsdellite chain R,
respectively. One can write the following equations:
Pr∙r + Pr∙R = 1 and PR∙r + PR∙R = 1
and one can deduce that:
1 − PR∙R
Pr = Pr ∙ Pr∙r + PR ∙ PR∙r and Pr =
2 − Pr∙r − PR∙R
1 − Pr∙r
PR = Pr ∙ Pr∙R + PR ∙ PR∙R and PR =
2 − Pr∙r − PR∙R
- PrR is the probability of finding a rR or Rr pair at any position in the crystal:
PrR = PRr = Pr ∙ Pr∙R = PR ∙ PR∙r

From the structural model presented in Table SI 1, we simulated the XRD patterns of different models of
stacking, which are described below.

1/ Model 1: “Random sequence”

In the first stacking model explored we used a recursive sequence of layers in which the occurrence of a
layer does not depend on the previous layer. This model, called “Random sequence” by Chabre and
Pannetier (Chabre & Pannetier, 1995), is therefore defined by the following equations:
Pr∙r = PR∙r = Pr and PR∙R = Pr∙R = PR with Pr = 1 − PR
where Pr and PR are the respective amount of pyrolusite layers and ramsdellite layers in the sample.
The stacking rules for this model can be represented with the following chart:

Figure SI 4 shows the evolution of the simulated XRD patterns when varying the value PR from 0 to
100%. This figure is very comparable with the results obtained by Charbre and Pannetier (Chabre &
Pannetier, 1995) with the program DIFFaX (Treacy et al., 1991a). The patterns obtained for PR = 0% and
PR = 100% correspond to the ideal pyrolusite and ramsdellite structures, respectively. As the value of PR
increases, we observe a progressive broadening and vanishing of some reflections of the pyrosulite (e.g.,
(101)r at d ≈ 3.11 Å) while other reflections corresponding to the ramsdellite progressively appear and
get narrower (e.g., (101)R at d ≈ 4.06 Å, (103)R at d ≈ 2.55 Å, (111)R at d ≈ 2.34 Å, (113)R at d ≈ 1.90 Å).
Note also that in the meantime other reflections do not broaden but only progressively shift their position
to go from one structure to the other (e.g., (011)r ≡ (012)R at d ≈ 2.41-2.43 Å, (112)r ≡ (212)R at d ≈ 1.63-
1.66 Å, (202)r ≡ (204)R at d ≈ 1.56-1.62 Å).
Figure SI 4: Evolution of the simulated XRD patterns of the intergrowth of pyrolusite and
ramsdellite layers when varying the amount of ramsdellite elements 𝐏𝐏𝐑𝐑 from 0 to 100% in the
Model 1: “Random sequence”.

PR
1.00
0.99
0.95
0.90
0.80
0.70
0.60
0.50
0.40
0.30
0.20
0.10
0.05
0.01
0.00
2/ Model 2 : Segregated sequence
Conversely to the first model, in the second model, the probability of occurrence of a layer depends on
the previous one. We defined PF the probability of the layer of a given structure type (pyrolusite or
ramsdellite) to be followed by a layer of the other structure:
Pr∙R = PR∙r = PF and thus Pr∙r = PR∙R = 1 − PF
which can be illustrated by the following chart:

The evolution of the XRD patterns obtained when varying the value of PF from 0 to 100% are showed in
Figure SI 5. The very first pattern (PF = 0.0) is the XRD pattern of the pyrolusite structure. The
following five patterns (0.01 ≤ PF ≤ 0.3) correspond to a total or partial segregation between pyrolusite
and ramsdellite domains. As the value of PF increases, these domains are progressively intermixed, and
the structure obtained when PF = 100 % corresponds to the regular alternation of pyrolusite and
ramsdellite layers to produce the ordered sequence r–R–r–R–r–R–…
Figure SI 5: Evolution of the simulated XRD patterns of the intergrowth of pyrolusite and
ramsdellite layers when varying the amount of ramsdellite elements 𝐏𝐏𝐅𝐅 from 0 to 100% in the
Model 2: Segregated sequence.

PF
1.00
0.99
0.95
0.90
0.80
0.70
0.60
0.50
0.40
0.30
0.20
0.10
0.05
0.01
0.00
3/ Model 3: “Ordered sequence #1”
The third model corresponds to one example of the “ordered sequences” described by Chabre and
Pannetier (Chabre & Pannetier, 1995), in which the probability of occurrence of a RR pair is negligible
(PRR ≈ 0). Therefore this model follows the stacking rule:
PR∙r = 1 − PR∙R = 99.99%
The value of Pr∙R was then varied from 0 to 100%, so that to vary the amount of ramsdellite motif (PR )
from 0 to 50%. The stacking of this model can therefore be illustrated by the following chart:

The resulting simulated patterns are shown in Figure SI 6. The pattern calculated for Pr∙R = 0 corresponds
to the pyrolusite structure, while the one obtained when Pr∙R = 100 % is that of the hypothetical structure
of the regular sequence r–R–r–R–r–R–….. As the value of Pr∙R increases, some peaks split and the
diverge from their original position (e.g., (101)r at d ≈ 3.11 Å, (011)r at d ≈ 2.41 Å, (002)r at d ≈ 2.20 Å).
Moreover, the introduction of ramsdellite motifs into the pyrolusite lattice goes with the appearance of a
tiny reflection at d ≈ 4.40 Å (2θλ=Cu ≈ 20º), which is subject to a kind of Warren fall and whose intensity
increases and shape becomes more symmetric until forms the perfectly ordered phase r-R-r-R-r. One can
note that this feature was also present in Model 2: Segregated sequence (Figure SI 5), although is less
obvious.
Figure SI 6: Evolution of the simulated XRD patterns of the intergrowth of pyrolusite and
ramsdellite layers when varying the probability of having a ramsdellite elements after a pyrolusite
one 𝐏𝐏𝐫𝐫∙𝐑𝐑 from 0 to 100% in the Model 3: Ordered sequence #1.

Pr∙R
1.00
0.99
0.95
0.90
0.80
0.70
0.60
0.50
0.40
0.30
0.20
0.10
0.05
0.01
0.00
4/ Model 4: “Ordered sequence #2”
The fourth model is the opposite example of the “ordered sequence” described by Chabre and Pannetier
(Chabre & Pannetier, 1995), and is characterized by the negligible probability of occurring a rr pair in the
ramsdellite framework (Prr ≈ 0). It is therefore defined by the following equation:
Pr∙R = 1 − Pr∙r = 99.99%
Similarly to the previous model, the value of PR∙r was varied from 0 to 100%, so that to vary the amount
of pyrolusite motif in the structure (Pr ) from 0 to 50%. The stacking of this model can therefore be
illustrated by the following chart:

The resulting simulated patterns are shown in Figure SI 7. In this case, the first pattern corresponds to
that of the ramsdellite structure, and, again, the structure obtained when PR∙r = 100 % is the regular
alternation of the two kinds of chains r–R–r–R–r–R–…
Figure SI 7: Evolution of the simulated XRD patterns of the intergrowth of pyrolusite and
ramsdellite layers when varying the probability of having a pyrolusite elements after a ramsdellite
one 𝐏𝐏𝐑𝐑∙𝐫𝐫 from 0 to 100% in the Model 4: Ordered sequence #2.

PR∙r
1.00
0.99
0.95
0.90
0.80
0.70
0.60
0.50
0.40
0.30
0.20
0.10
0.05
0.01
0.00
5/ Intermediate models
In the fifth and sixth models, we fixed the probability of having a ramsdellite layer after a rutile one
(Pr∙R ) to 5 and 10 %, respectively, and we followed the evolution of the patterns of while varying the
probability of maintaining a ramsdellite domain after a ramsdellite slab (0 ≤ PR∙R ≤ 100%):

Model 5 Model 6

These models permit to simulate the effect of how extended are the domains of ramsdellite (one or
several ramsdellite layers). The results of these simulations are presented in Figure SI 8and Figure SI 9,
respectively. The diagrams obtained for PR∙R = 0% and PR∙R = 100% are close to the ones of pyrolusite
and ramsdellite, respectively. These figures show that the XRD patterns of the intergrowth of pyrolusite
and ramsdellite do not suffer from much modification when varying PR∙R between 0 and 50 %, except
that the main reflection (011)r at d ≈ 2.41 Å is progressively split in two peaks as the PR∙R increases. This
means that for pyrolusite structures containing low content of ramsdellite inclusions, it is difficult to
decipher if these inclusions are of the form of single layer of ramsdellite or larger domains of ramsdellite
(several layers).
Figure SI 8: Evolution of the simulated XRD patterns of the intergrowth of pyrolusite and
ramsdellite layers when varying the probability of having a ramsdellite elements after a ramsdellite
one 𝐏𝐏𝐑𝐑∙𝐑𝐑 from 0 to 100% in the Model 5, while the probability of having a ramsdellite layer after a
rutile one (𝐏𝐏𝐫𝐫∙𝐑𝐑) is fixed to 5 %.

PR∙R
1.00
0.99
0.95
0.90
0.80
0.70
0.60
0.50
0.40
0.30
0.20
0.10
0.05
0.01
0.00
Figure SI 9: Evolution of the simulated XRD patterns of the intergrowth of pyrolusite and
ramsdellite layers when varying the probability of having a ramsdellite elements after a ramsdellite
𝐏𝐏𝐑𝐑∙𝐑𝐑 from 0 to 100% in the Model 6, while the probability of having a ramsdellite layer after a rutile
one (𝐏𝐏𝐫𝐫∙𝐑𝐑) is fixed to 10 %.

PR∙R
1.00
0.99
0.95
0.90
0.80
0.70
0.60
0.50
0.40
0.30
0.20
0.10
0.05
0.01
0.00
Table SI 2: Selected distances of the refined model for the MnO2 sample
Pyrolusite-type stacking
r1–r2–r1
MnIV+ 101 – OII– 121 1.85(5) MnIV+ 201 – OII– 121 1.93(3)
MnIV+ 101 – OII– 122 1.85(5) MnIV+ 201 – OII– 121 1.93(3)
MnIV+ 101 – OII– 141 1.88(3) MnIV+ 201 – OII– 122 1.93(3)
MnIV+ 101 – OII– 141 1.88(3) MnIV+ 201 – OII– 122 1.93(3)
MnIV+ 101 – OII– 142 1.88(3) MnIV+ 201 – OII– 141 1.90(5)
MnIV+ 101 – OII– 142 1.88(3) MnIV+ 201 – OII– 142 1.90(5)
Ramsdellite-type stacking
R1–R2–R1
MnIV+ 301 – OII– 321 2.14(5) MnIV+ 401 – OII– 421 2.26(5)
MnIV+ 301 – OII– 321 2.14(5) MnIV+ 401 – OII– 421 2.26(5)
MnIV+ 301 – OII– 322 1.82(7) MnIV+ 401 – OII– 422 1.88(7)
MnIV+ 301 – OII– 341 1.97(7) MnIV+ 401 – OII– 342 1.82(4)
MnIV+ 301 – OII– 361 1.96(5) MnIV+ 401 – OII– 342 1.82(4)
MnIV+ 301 – OII– 361 1.96(5) MnIV+ 401 – OII– 362 1.98(7)
MnIV+ 302 – OII– 321 1.82(7) MnIV+ 402 – OII– 421 1.88(7)
MnIV+ 302 – OII– 322 2.14(5) MnIV+ 402 – OII– 422 2.26(5)
MnIV+ 302 – OII– 322 2.14(5) MnIV+ 402 – OII– 422 2.26(5)
MnIV+ 302 – OII– 342 1.97(7) MnIV+ 402 – OII– 341 1.82(4)
MnIV+ 302 – OII– 362 1.96(5) MnIV+ 402 – OII– 341 1.82(4)
MnIV+ 302 – OII– 362 1.96(5) MnIV+ 402 – OII– 361 1.98(7)
De Wolff defects stacking
r1–R2–r1 r2–R1–r2
Mn 101 – OII– 121
IV+
1.85(5) Mn 201 – OII– 341
IV+
1.84(3)
MnIV+ 101 – OII– 122 1.85(5) MnIV+ 201 – OII– 341 1.84(3)
MnIV+ 101 – OII– 141 1.88(3) MnIV+ 201 – OII– 361 1.98(5)
MnIV+ 101 – OII– 141 1.88(3) MnIV+ 201 – OII– 342 1.84(3)
MnIV+ 101 – OII– 142 1.88(3) MnIV+ 201 – OII– 342 1.84(3)
MnIV+ 101 – OII– 142 1.88(3) MnIV+ 201 – OII– 362 1.98(5)
MnIV+ 401 – OII– 421 2.26(5) MnIV+ 301 – OII– 321 2.14(5)
MnIV+ 401 – OII– 421 2.26(5) MnIV+ 301 – OII– 321 2.14(5)
MnIV+ 401 – OII– 422 1.88(7) MnIV+ 301 – OII– 322 1.82(7)
MnIV+ 401 – OII– 122 1.90(5) MnIV+ 301 – OII– 341 1.97(7)
MnIV+ 401 – OII– 122 1.90(5) MnIV+ 301 – OII– 361 1.96(5)
MnIV+ 401 – OII– 142 1.93(7) MnIV+ 301 – OII– 361 1.96(5)
MnIV+ 402 – OII– 421 1.88(7) MnIV+ 302 – OII– 321 1.82(7)
MnIV+ 402 – OII– 422 2.26(5) MnIV+ 302 – OII– 322 2.14(5)
MnIV+ 402 – OII– 422 2.26(5) MnIV+ 302 – OII– 322 2.14(5)
MnIV+ 402 – OII– 121 1.90(5) MnIV+ 302 – OII– 342 1.97(7)
MnIV+ 402 – OII– 121 1.90(5) MnIV+ 302 – OII– 362 1.96(5)
MnIV+ 402 – OII– 141 1.93(7) MnIV+ 302 – OII– 362 1.96(5)
Figure SI 10: Results of the FAULTS refinement of the MnO2 sample when refining the layer
width instead of the isotropic broadening parameters Dl and Dg. Remark that the reflection (002)r
at d ≈ 2.24 Å (2θCu ≈ 40.0°) is not well modelled.

Figure SI 11: Evolution of the XRD pattern of the pyrolusite with the presence of twinning (twin
plane (011), from ideal pyrolusite (Pt = 0.0) to fully twinned pyrolusite (Pt = 1.0).

Pt
1.00
0.90
0.80
0.70
0.60
0.50
0.40
0.30
0.20
0.10
0.00

To simulate the effect of twinning in the pyrolusite lattice along (011), new layers were defined so that to
have the staking direction perpendicular to the twinning place. The structural model used in FAULTS is
described in Table SI 3 and an illustration of a possible twinning is shown in Figure SI 12.
Table SI 3: Structural model used to described twinned pyrolusite (twin plane (011).
Cell
a'' = 4.4041 Å b'' = 5.2603 Å c'’ = 4.81664 Å
α = 90º β = 90º γ = 90º
Layers
Atom x/a y/b z/c Occupancy
Layer T1 = IV+
Mn 11 0 0 0 1.0
T3
MnIV+ 12 ½ ½ 0 1.0
OII– 111 ¼ ¼ 1/6 1.0
OII– 112 ¼ ½ -1/3 1.0
OII– 121 ¾ ½ 1/3 1.0
OII– 122 ¾ ¾ -1/6 1.0
OII– 131 ¾ ¼ -1/6 1.0
OII– 132 ¾ 0 1/3 1.0
OII– 141 ¼ 0 -1/3 1.0
OII– 142 ¼ ¾ 1/6 1.0
Layer T2 =
MnIV+ 21 0 0 0 1.0
T4
MnIV+ 22 ½ ½ 0 1.0
Transition vectors
Transition x/a y/b z/c Probability Type
From layer
T1  T1 - - - 0 forbidden
T1
T1  T2 0 -0.299 ½ 1-Pt no twinning
T1  T3 - - - 0 forbidden
T1  T4 0 0.299 ½ Pt twinning
From layeT
T2  T1 0 -0.299 ½ 1-Pt no twinning
T2
T2  T2 - - - 0 forbidden
T2  T3 0 0.201 ½ Pt twinning
T2  T4 - - - 0 forbidden
From layeT
T3  T1 - - - 0 forbidden
T3
T3  T2 0 -0.299 ½ Pt twinning
T3  T3 - - - 0 forbidden
T3  T4 0 0.299 ½ 1-Pt no twinning
From layeT
T4  T1 0 -0.201 ½ Pt twinning
T4
T4  T2 - - - 0 forbidden
T4  T3 0 0.299 ½ 1-Pt no twinning
T4  T4 - - - 0 forbidden
 Figure SI 12: Illustration of a possible twinning of the pyrolusite along the twin plane (011).

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