FAULTS manual

Montse Casas Cabanas (CIC energiGUNE), Marine Reynaud (CIC energiGUNE)

Jokin Rikarte Ormazabal (CIC energiGUNE), Pavel Horbach (ILL)
and Juan Rodriguez Carvajal (ILL)

September 2018
Contents

1 The FAULTS program 1

1.1 Download and installation . . . . . . . . . . . . . . . . . . . . 2
1.2 Program specifications . . . . . . . . . . . . . . . . . . . . . . 2
1.3 Input files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3.1 The input control file: CFILE.flts . . . . . . . . . . . 4
1.3.2 Experimental pattern files . . . . . . . . . . . . . . . . 26
1.3.3 Background: CFILE.bgr . . . . . . . . . . . . . . . . 29
1.3.4 Secondary phases: CFILE.sub and CFILE.hkl . . . 29
1.3.5 Crystallographic Information File as an input:
CFILE.cif . . . . . . . . . . . . . . . . . . . . . . . . . 30
1.4 Output files . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
1.4.1 Calculated profile: CFILEn.dat . . . . . . . . . . . 31
1.4.2 Calculated SADP: CFILEn.sadp . . . . . . . . . . . 31
1.4.3 Observed and calculated profile: CFILEn.prf . . . . 31
1.4.4 Crystallographic structure files: CFILE.fst,
CFILE flts.cif and CFILE flts.vesta . . . . . . . . 32
1.4.5 Progress report: CFILEn.out . . . . . . . . . . . . . 32
1.4.6 Final report: CFILE new.flts . . . . . . . . . . . . 32
1.5 Running FAULTS . . . . . . . . . . . . . . . . . . . . . . . . 33

i
2 Example 36
2.1 Stacking faults in LiNiO2 . . . . . . . . . . . . . . . . . . . . 36
2.2 Analysis of simulated data . . . . . . . . . . . . . . . . . . . . 39

3 Frequent errors 43
3.1 Input control file .flts . . . . . . . . . . . . . . . . . . . . . . . 43
3.2 Input experimental data files . . . . . . . . . . . . . . . . . . 44
3.3 Other remarks . . . . . . . . . . . . . . . . . . . . . . . . . . 45

ii
Chapter 1

The FAULTS program

FAULTS is a Fortran90 program to refine X-ray Powder Diffraction (XRD)

and Neutron Powder Diffraction (NPD) patterns of crystal systems with
any type of coherent planar defect. This program is based on the DIFFaX
program [1, 2] and on the library CrysFML (Crystallographic Fortran
Modules Library) [3, 4].

The DIFFaX program (Diffracted Intensities From Faulted Xtals)

calculates diffraction intensities from defective layered crystals. This tool
has been widely used to interpret the diffraction data of one-dimensionally
disordered systems and it is based on an algorithm that exploits the
recursive nature of the patterns found in randomized stacking sequences to
compute the average interference wavefunction scattered from each layer
type occurring in a faulted crystal (mathematical details can be found
in references [5, 6]). However, approximate or merely qualitative results
sometimes are not sufficient for a thorough microstructural characteriza-
tion, a computerized comparison of the DIFFaX calculated intensities with
experimental data has been developed. The resulting code is the FAULTS

1
program [7, 8]. Note that FAULTS, as DIFFaX, can also simulate 2D
diffraction patterns and diffuse streaks in reciprocal space for single crystals.

The program is distributed in the hope that it will be useful, but with-
out any warranty of being free of internal errors. The authors acknowledge
all suggestions and notification of possible bugs found in the program.

1.1 Download and installation

FAULTS can be obtained either as part of the FullProf Suite [9, 10, 11]
at www.ill.eu/sites/fullprof/, for Windows, Linux or MacOS, or
as a separate program for Windows by downloading the compressed file
FAULTS.zip at www.cicenergigune.com/faults/.

In case the user chooses to install FAULTS with the FullProf Suite, the
program FAULTS can be launched directly from the FullProf Suite Tool-
bar or by opening a terminal and invoking the program as: Faults myin-
putfile.flts. If FAULTS is downloaded as a separate Windows program, it
should be launched from a command-line window (e.g., cmd.exe or Power-
Shell), after having copied the standard scattering factor data file data.sfc
into the working folder.

1.2 Program specifications

Conventionally, crystals are thought in terms of unit cells, atoms in the
asymmetric unit and a determined symmetry space group. Nevertheless,
to use FAULTS, as in the case of DIFFaX [12], one needs to think of

2
crystals in terms of atomic sheets, or layers, which can be interconnected
via stacking operations occurring with a certain probability. By means
of this description, planar defects can be described as different layer
types and/or transition vectors. Frequently, the plane of layers will not
coincide conveniently with any of the unit cell faces of the parent crystal.
Then, a transformation of atom coordinates to a new cell system is required.

The structural information as well as the refinement details are read by

FAULTS from a free format input data file, with .flts extension. Each value
used to describe the structure is associated to a refinement code that allows
the possibillity of restrictions. The user must be aware of the way he(she)
can control the refinement procedure: the number of parameters to be re-
fined, fixing parameters, making constraints, etc. The experimental XRD
or NPD patterns can be read from many different formats and background
subtraction can be achieved by linear interpolation or polynomially after
applying the scale factor. Impurities or other phases are treated as back-
ground as well, and their pattern information must be given by the user.
Another major feature of FAULTS is the implementation of a more adequate
isotropic size broadening treatment which takes into account the Gaussian
and Lorentzian contributions to the FWHM in addition to the considera-
tion of a finite number of layers per crystallite already present in DIFFaX
[1, 2, 12]. The refinement is carried out using a Levenberg Marquardt fit.
The quality of the agreement between observed and calculated profiles is
given by the R-Factor and Chi2 agreement factors that are calculated at
the end of each refinement cycle and are defined as follows:
Profile factor:
P
i=1,n | yi − yic |
Rp = 100 P
i=1,n yi

3
where yi is the profile intensity and yic is the number of calculated counts
at the i th step.
Reduced Chi square:
 2
Rwp
Chi2 =
Rexp

being Rωp and Rexp the Weighted Profile Factor and the Expected Weighted
Profile Factor respectively, which are defined as:

"P #1/2
i=1,n wi | yi − yic |2
Rwp = 100 P 2
i=1,n wi yi

and

 1/2
n−p
Rexp = 100 P 2
i wi yi

where n-p is the number of degrees of freedom and wi = 1/σi2 , with σi2
referring to the variance of the “obserbation” yi .

1.3 Input files

1.3.1 The input control file: CFILE.flts

The input control file is a free format file that contains all the structural data
and the type of calculation to be done. This file must be written by the user.

The FAULTS input file is similar to the one used in DIFFaX

[12], although there are some differences that should be taken into

4
account to avoid errors. The DIFFaX2FAULTS convertor, which per-
mits to convert DIFFaX input files into FAULTS ones, is available at
www.cicenergigune.com/faults/ and within the FullProf Suite at
www.ill.eu/sites/fullprof/.

Free format means that the input file is not case sensitive and that the
different sections do not have to follow a concret sequence, however, a space
is needed between each item and all the section headings and subsection
keywords must be present. Each line must not exceed 132 characters,
taking into account the blank spaces. When the program is run, mistakes
will normally generate error messages. Empty lines as well as lines starting
with the exclamation symbol (! ) in the first column are considered as
comments and are ignored by the program. Also, comments can be placed
at the end of a line if they are in braces ({}). The use of tabulator to
introduce blank spaces when editing the file should also be avoided, since
some editors do not consider it as blank spaces and they can generate
unpected errors of the program.

An example of input control file can be found in figures 1.1, 1.2 and 1.3,
and an example of input file is provided along with the program. The differ-
ent section headings that constitute the input control file appear in orange
color, comments appear in italics (and of course after a ! symbol), subsec-
tion keywords in red, parameters in blue and refinement codes in green. The
latter are codewords that allow the control of the refined parameters. As
in the FullProf program [10, 11], these are the numbers Cx that are entered
for each refined parameter. A zero codeword means that the parameter is
not being refined. For each refined parameter, the codeword is formed as:

5
 Cx = sign(a)(10p + |a|)

where p specifies the ordinal number of the parameter x and a is the factor
by which the computed shift (the parameter variation in each refinement
cycle) will be multiplied before use.

Below, each section, which has to begin with the corresponding heading,
is explained in more detail.

Title section

The document must begin with this section. TITLE heading must be fol-
lowed in the next line by the title chosen by the user.

Instrumental and size broadening section

The first line must contain the heading INSTRUMENTAL AND SIZE
BROADENING. The data that follow describe the type of radiation and
the instrumental conditions as well as the parameters needed for size
broadening, which are refinable parameters. To refine the parameters that
constitute this section it is not necessary to recalculate the diffraction
pattern in each cycle, so, for computational economy it is strongly recom-
mended to refine them separately.

• Radiation type: The line must begin with the keyword radiation,
followed by one of the different three options, which are X-RAY, NEU-
TRON and ELECTRON (the latter for the simulation of selected area
diffraction patterns -SADP-).

6
 TITLE
LiNiO2 ideal structure

Instrumental And Size Broadening

!Type of Radiation
Radiation X-Ray
! lambda1 lambda2 ratio
Wavelength 1.5406 0.0 0.0
!Instrumental aberrations zero sycos sysin
Aberrations 0.0000 0.0000 0.0000
0.00 0.00 0.00
!Instr. broadening u v w x Dg Dl
Pseudo-Voigt 0.11 -0.0036 0.009 0.7000 479.26 459.87 Trim
0.00 0.00 0.00 0.00 0.00 0.00

Structural
SPGR R -3 m
! a b c alpha beta gamma
Avercell 2.8659 2.8659 14.253 90 90 120.0
! a b c gamma
Cell 2.8659 2.8659 14.253 120.0
11.00 11.00 1.00 0.00
! FullProf Studio commands
FST_CMD SEQ 9 1 2 3 1 2 3 1 2 3
FST_CMD CONN Ni O 0.0 2.3
FST_CMD box -2 2 -2 2 -0.01 1.01
FST_CMD stack_vect 0 0 0.5
!Laue symmetry
Symm unknown
!Number of layer types
Nlayers 3
!Layer width
Lwidth infinite

Layer 1
!Layer symmetry
LSYM none
!Atom name number x y z Biso Occ
Atom Ni3+ 1 0.000 0.000 0.000 0.8 1.0
0.00 0.00 0.00 1.00 0.00
!Atom name number x y z Biso Occ
Atom O2- 2 1/3 2/3 -0.075 1.0 1.0
1.00 0.00 0.00 0.00 0.00
!Atom name number x y z Biso Occ
Atom O2- 3 2/3 1/3 0.075 1.0 1.0
0.00 0.00 0.00 0.00 0.00

Figure 1.1: Example of input control file, corresponding to the ideal

structure of LiN iO2 .
 !Atom name number x y z Biso Occ
Atom Li1+ 4 2/3 1/3 -0.167 0.8 1.0
0.00 0.00 1.00 1.00 0.00

Layer 2 = 1

Layer 3 = 1

Stacking
!Stacking type
Recursive
!Number of layers
infinite

Transitions
!Layer 1 to layer 1
LT 0.00000000 0.000000 0.000000 1/3
0.000000 0.000000 0.000000 0.000000
FW 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00
!Layer 1 to layer 2
LT 1.00 2/3 1/3 1/3
21.000000 0.000000 0.000000 0.000000
FW 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00
!Layer 1 to layer 3
LT 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
FW 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00
!Layer 2 to layer 1
LT 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
FW 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00
!Layer 2 to layer 2
LT 0.00000 0.000000 0.000000 0.0000
0.000000 0.000000 0.000000 0.000000
FW 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00
!Layer 2 to layer 3
LT 1.00 2/3 1/3 1/3
31.000000 0.000000 0.000000 0.000000
FW 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00
!Layer 3 to layer 1

Figure 1.2: Cont. Example of input control file, corresponding to

the ideal structure of LiN iO2 .
 LT 1.00 2/3 1/3 1/3
41.000000 0.000000 0.000000 0.000000
FW 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00
!Layer 3 to layer 2
LT 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000
FW 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00
!Layer 3 to layer 3
LT 0.00000 0.000000 0.000000 0.0000
0.000000 0.000000 0.000000 0.000000
FW 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00

Calculation
Lma
Corrmax 30
Maxfun 2400
Tol 0.100000E-04
Nprint 0

Experimental
!Filename Scale factor code
FILE LiNiO2_ ideal.dat 1.0 0.00
Excluded_Regions 0
FFORMAT free
!Linear interpolation
Bgrinter sim.bgr
!Polynomial Number of coefficients
Bgrcheb 2
!Polynomial coefficients
1.00000 0.20000
0.0 0.0
!number of pattern backgrounds
Bgrnum 1
!Pattern file Filename Scale factor code
Bgrpatt phase2.sub 0.026000 1.00 phase2.hkl

Figure 1.3: Cont. Example of input control file, corresponding to

the ideal structure of LiN iO2 .
• Wavelength: In addition to λ1 , FAULTS reads also the value of λ2
and the intensity ratio I2 /I1 (although in the case of monochromatic
radiation it is only necessary to introduce λ1 ). λ unit is Å and this
line must begin with the keyword wavelength.

• Aberrations: Keyword aberrations followed by values for the instru-

mental aberrations (zero, sycos and sysin) must be given. As they
are refinable, refinement codes must be entered in the next line. The
parameters sycos and sysin relate to systematic 2θ shifts having a
cosθ and sinθ dependency, respectively, that originate from different
physical and/or geometrical problems depending on the diffraction
geometry (see FullProf manual for more details [11]).

• Profile parameters: Instrumental and size broadening are treated

differently than in DIFFaX. In both cases, the calculated pattern is
convoluted with a profile function (indicated by the keyword Gaussian,
Lorentzian or Pseudo-Voigt) that takes into account both instrumen-
tal and size effects. The FWHM of the Gaussian (HG ) and Lorentzian
(HL ) components of the peak profile have an angular dependence given
by:

2 4ln2λ2 180 2
HG = U tan2 θ + V tanθ + W + 2 cos2 θ ( π )
πDG

2λ 180
HL = Xtanθ + ( )
πDL cosθ π
U, V, W and X, which must be introduced by the user, are refin-
able parameters that constitute the instrumental resolution function
(IRF). It is always advisable to know their values a priori and fix them
during the refinement (although U and X can be refined to account

10
 for strains). They must be followed by DG and DL , which are the
parameters that are used to model the isotropic size broadening due
to a finite size of the crystallites ( ≤ 1 µm). They are also refinable.
If the sample is not affected by size broadening, DG and DL can take
any value ≥ 5000 Å.

• TRIM keyword: As in DIFFaX [12], the optional keyword trim,

which has to be put in the same line as the profile parameters, tells
the program to ignore intensity information close to the origin when
simulating the instrumental broadening for a powder diffraction pat-
tern. The peak at the origin is usually many orders of magnitude more
intense than any other peak of the diffraction pattern, and the back-
ground that is generated by the tail of this peak, when broadened,
can easily swamp peaks close to the origin. When trim is specified,
the unbroadened pattern that is written to file retains the data at the
origin, whereas the broadened data that is written to file suppresses
the peak at the origin. It is generally desirable to specify trim when-
ever the powder pattern angular range includes the origin. trim has
no effect if the powder pattern angular range requested by the user
does not include the origin.

Structural section

This section must begin with a first line containing the heading STRUC-
TURAL.

• Cell parameters: The keyword which this line has to begin

with is cell. The value of c, perpendicular to the a-b plane (and
therefore parallel to the stacking direction), is needed to provide a
reference scale along the stacking direction with which to define the

11
 z-component of the stacking vectors. c does not have to correspond
to any special periodic dimension along the stacking direction for any
of the layers. However all the layers must share the same dimensions,
a, b and γ. These are all refinable parameters and the units are Å for
a, b and c, and degrees for γ.

• Laue symmetry: In this case the keyword is symm. There are 12 op-
tions : -1, 2/M(1) , 2/M(2), MMM, -3, -3M, 4/M, 4/MMM,
6/M, 6/MMM, AXIAL and UNKOWN. Axial constraints the
program to integrate only along 00l (useful in turbostratic structures)
and if UNKNOWN is specified the program will establish the symme-
try by randomly sampling the reciprocal space. In this case, the user
can specify a percentage of tolerance on intensity deviations for this
search. Otherwise the program tests the user option and, if it is not
consistent with the cell parameters, it is automatically changed.

• Number of layer types: The keyword is nlayers. It is the number

of different layer types needed to describe the structure. If two layers
are structurally identical but their stacking vectors are different, they
are considered as two different layer types.

• Layer caracteristic width: Unlike in DIFFaX, this line is com-

pulsory, and it must begin with the keyword lwidth. Then the layer
characteristic width is especified, in Å. There are two possible formats
for this line: width along a and width along b, both refinable values,
or infinite. For example,

12
 !layer width
Lwidth 120.00 300.00
0.0 0.0

or

!layer width
Lwidth infinite

• Optional generation of the Bragg positions of the average

cell: In case the cell parameters defined for the FAULTS refinement
are different from the original cell (the cell from which the disordered
model comes from; for instance, in the case of a monoclinic or triclinic
average cell), the user can ask the program to generate the Bragg po-
sitions corresponding to the average cell in the output file CFILEn.prf
(see section 1.4.3). To do so, the user has two options:
(1) either he(she) indicates manually the space group (after the key-
word SPGR) and the cell parameters a, b, c, α, β, γ (after the keyword
Avercell ) of the average cell by adding the following optional lines in
the Structural section:

!Average cell parameters (for Bragg positions in .prf file)

Avercell 3.12 4.15 4.60 90.00 118.79 90.0
!Average space group (for Bragg positions in .prf file)
SPGR C 2/m

(2) or, by means of the keywords CalcAverCell and SPGR, he(she)

asks the program to calculate the average cell from a sequence of layers
that he(she) specifies with the following optional lines in the Structural
section:

13
 !Number of stacking vectors needed to calculate the average cell
CalcAvercell 2
!Specific sequence to calculate the average cell
12
!Average space group (for Bragg positions in .prf file)
SPGR C 2/m

Note that the average cell parameters and space group are only used
for the Bragg positions calculation for the .prf file and are not taken
into account for the pattern calculation during the refinement or sim-
ulation.

• Optional commands for generation of a .CIF file and visual-

ization of the structure with FullProf Studio and VESTA: To
simplify the construction of the structural section and to avoid errors,
it is recommended to regularly draw the structure with the help of
a visualization program, such as FullProf Studio [13, 14] or VESTA
[15, 16]. For this, the program describes the stacking of layers in a
big artificial box containing all the atoms of the layers that are asked
to be painted by the user. To do so, the user should ask the program
to generate the output files .fst, .cif and .vesta (see section 1.4.4)
suitable for FullProf Studio and VESTA, respectively , by entering an
optional line beginning with the keyword FST CMD, followed by the
keyword SEQ, the number of layers and the sequence of the layers to
be drawn; for example:

!Commands for structural visualization output

FST CMD SEQ 5 11231

14
 Then the user can add as many optional lines as needed, each of
them beginning with the keyword FST CMD, followed by the required
FullProf Studio commands (see the FullProf Studio manual for more
details [14]). As examples:
- to control respectively the drawing of Ni-O bonds (of length between
0.0 and 2.3 Å) and NiOx polyhedra, the user may add the following
line:

FST CMD CONN Ni O 0.0 2.3

- to fix the limits of the volume of the big artificial box to be considered
for the plot, the user may add the following line:

FST CMD BOX -2.0 2.0 -2.0 2.0 0.0 0.99

(note that the upper limit of the box along z should be smaller than
1 to avoid periodicity artifacts in structure visualization programs)

- to fix the position of the first layer in the big artificial box,
the user may add the following line :

FST CMD stack vect 0 0 0.5

(make sure to choose the z component of this vector so as to include

all the atoms of the first and last layers within the visualization box in
order to avoid periodicity artifacts in structure visualization programs;
x and y components are usually 0)

Layers section

• Layer number: The layers have to be described with the header

LAYER followed by the ordinal corresponding number. If two layers

15
 are structurally identical it will be enough to write LAYER j = i
where i and j are the ordinal numbers that correspond to each layer
(a blank space is necessary between the number of layer and the =
symbol). Then, for layer j the rest of the section can be avoided.

• Layer symmetry: The keyword lsym must be followed by one of

the two options: NONE or CENTROSYMMETRIC. If the latter
is specified, only the asymmetric half of the atom coordinates need
to be entered, and the program will create another identical atom in
(-x,-y,-z) per each atom described in the layer. Take care to halve the
occupancy in case of the atoms located at any inversion center.

• Atomic data: For each atom the keyword atom must be written,
followed by a specific 4 characters name. The first two characters cor-
respond to the atomic symbol and the last two represent the valence.
If the symbol has only one character, contrary to DIFFAX, there must
not be a space between the symbol and the charge (Ex. F1-, Ni2+).
Some atoms do not require any valence (ex. C). Below is the list of
the names accepted by FAULTS (this list is found in the standard
scattering factor data file data.sfc):
H ; H. ; D ; H1- ; He ; Li ; Li1+ ; Be ; Be2+ ; B ; C ; C. ; N ; O ; O1-
; O2- ; F ; F1- ; Ne ; Na ; Na1+ ; Mg ; Mg2+ ; Al ; Al3+ ; Si ; Si. ;
Si4+ ; P ; S ; Cl ; Cl1- ; Ar ; K ; K1+ ; Ca ; Ca2+ ; Sc ; Sc3+ ; Ti
; Ti2+ ; Ti3+ ; Ti4+ ; V ; V2+ ; V3+ ; V5+ ; Cr ; Cr2+ ; Cr3+ ;
Mn ; Mn2+ ; Mn3+ ; Mn4+ ; Fe ; Fe2+ ; Fe3+ ; Co ; Co2+ ; Co3+
; Ni ; Ni2+ ; Ni3+ ; Cu ; Cu1+ ; Cu2+ ; Zn ; Zn2+ ; Ga ; Ga3+ ;
Ge ; Ge4+ ; As ; Se ; Br ; Br1- ; Kr ; Rb ; Rb1+ ; Sr ; Sr2+ ; Y ;
Y3+ ; Zr ; Zr4+ ; Nb ; Nb3+ ; Nb5+ ; Mo ; Mo3+ ; Mo5+ ; Mo6+
; Tc ; Ru ; Ru3+ ; Ru4+ ; Rh ; Rh3+ ; Rh4+ ; Pd ; Pd2+ ; Pd4+ ;

16
 Ag ; Ag1+ ; Ag2+ ; Cd ; Cd2+ ; In ; In3+ ; Sn ; ; Sn2+ ; Sn4+ ; Sb
; Sb2+ ; Sb5+ ; Te ; I ; I1- ; Xe ; Cs ; Cs1+ ; Ba ; Ba2+ ; La ; La3+
; Ce ; Ce3+ ; Ce4+ ; Pr ; Pr3+ ; Pr4+ ; Nd ; Nd3+ ; Pm ; Pm3+
; Sm ; Sm3+ ; Eu ; Eu2+ ; Eu3+ ; Gd ; Gd3+ ; Tb ; Tb3+ ; Dy ;
Dy3+ ; Ho ; Ho3+ ; Er ; Er3+ ; Tm ; Tm3+ ; Yb ; Yb2+ ; Yb3+ ;
Lu ; Lu3+ ; Hf ; Hf4+ ; Ta ; Ta5+ ; W ; W6+ ; Re ; Os ; Os4+ ; Ir
; Ir3+ ; Ir4+ ; Pt ; Pt2+ ; Pt4+ ; Au ; Au1+ ; Au3+ ; Hg ; Hg1+ ;
Hg2+ ; Tl ; Tl1+ ; Tl3+ ; Pb ; Pb2+ ; Pb4+ ; Bi ; Bi3+ ; Bi5+ ; Po
; At ; Rn ; Fr ; Ra ; Ra2+ ; Ac ; Ac3+ ; Th ; Th4+ ; Pa ; U ; U3+ ;
U4+ ; U6+ ; Np ; Np3+ ; Np4+ ; Np6+ ; Pu ; Pu3+ ; Pu4+ ; Pu6+
; Am ; Cm
After the name, the atom will be identified by an ordinal number.
Then the atomic coordinates x, y, z will be detailed as well as the
atomic displacement factor and finally the occupation, which has to
take a value between 0 and 1. If the layer is centrosymmetric, the atom
located in the centre of symmetry will have 1/2 for full occupancy. All
the parameters are refinable. They can be written as real numbers or
as fractions, which ensures maximum machine precision (except for
the atomic displacements, which cannot be given as a fraction).

Stacking section

The first line of this section must start with the heading STACKING.

• Stacking type: There are two possibilities: EXPLICIT and RECUR-

SIVE. For an explicit sequence of layers, the diffracted intensities will
be calculated for a unique layer sequence that will be specified in the
next line. For a recursive sequence of layers, the diffracted intensities
are to be calculated for a statistical ensemble of crystallites, each with

17
 a distinct stacking sequence, but weighted by the probability that such
a sequence will occur.

• Explicit sequence: If the stacking type is explicit, there are three

possibilities. One of them is SPECIFIC, in which the user has to
introduce a stacking sequence, up to 5000 layers. The list can occupy
more than one line, and between each layer type there must be a
space. Each line must not exceed 132 characters, taking into account
the blank spaces. For example,

EXPLICIT
SPECIFIC
1121312

corresponds to a crystallite that consists of 7 layers of three different

types. However, care has to be taken not to write a forbidden
transition (with a zero stacking probability). If this happens, the
program will stop and give an error message.

Another possibility is the RANDOM M option which tells the

program to generate a sequence of M layers (with a maximum of
5000). The probability that a specific layer-to-layer transition will
occur in the sequence will be weighted by the transition probabilities
listed in the TRANSITIONS section, described next.

Finally, the program can also generate semi-random sequences of two

different layer types, that is to say, the user can control certain parts of
the sequence. To do so, the option SEMIRANDOM M must be used,
where M is the number of layers (also with a maximum of 5000). Below

18
 this line, the user can specify parts of the sequence by the keyword
SEQ followed by the position of the first layer in the sequence, the
position of the final layer and the two types of layers that will be
alternated. For example,

EXPLICIT
SEMIRANDOM 60
SEQ 11 20 1 3

will generate a random sequence of layers but from layer 11 to layer 20

the sequence will be 1 3 1 3 1 3 1 3 1 3. If the sequence is incompatible
with the last layer of the sequence that is generated automatically (due
to the stacking probabilities), in this case layer number 10, this layer
would be eliminated and the fixed sequence would move a position,
starting in layer 10. If that was still not compatible with the stacking
probabilities this process would be repeated until the program found
a compatible sequence.

• Recursive sequence: In this case, the user can indicate the mean
number of layers the crystallites contain. Any number larger than M
≥1022, will be treated as infinite. Alternatively, an infinite number
can be specified by the keyword INFINITE. If the latter is chosen,
the refinement code underneath must be eliminated. If the number
of layers is lower than 1022, the program will apply a line broaden-
ing due to a finite size in the stacking direction. This value (which
can be refined) will have no physical meaning, but it is the only way
to introduce a certain anisotropy in size broadening. However, if the
crystallites induce a purely isotropic size broadening (represented by
DG and DL , that will be lower than 5000) this value should be INFI-

19
 NITE as size broadening has already been taken into account in the
Instrumental and size broadening section.

Transitions section

First line must contain the heading TRANSITIONS. This section contains
as many subsections as different layers constitute the system; and each
subsection will contain as many lines (without taking into account the re-
finement codes) as different layers constitute the system. Each subsection
refers to the transitions of layer i to the rest of layers, including itself. Each
line must contain, after the keyword LT: the stacking probability αij , that
will be a value comprised between zero (forbidden transition) and 1 (unique
possible transition) and the stacking vector Rx , Ry , Rz , relative to a, b and
c respectively. A set of anisotropic Debye-Waller type factors ( C11 , C22 ,
C33 , C12 , C23 , C31 ) is specified after the stacking vector, in a separate line
and beginning with the keyword FW. These factors are equivalent to spec-
ifying an ellipsoidal error spread for the stacking vectors and are useful for
modeling systems where there is some coherence between nearest neighbor
layers, but no long-range coherence, as in the case of liquid crystals or pil-
lared clays. If the stacking probability αij is zero, everything on the line
after it is ignored and set to zero. All the parameters constituting this
section are refinable parameters and can be written as real numbers or as
fractions.
TABLE. For the long period structures, where number of layers is too high,
one can optionally put transition parameters in form of a table. To do this,
put the command TABLE followed by one of next keys: ALPHA (for prob-
abilities), A or B or C (for x,y,z-coordinate of stacking vector, respectively),
FW11, FW22, FW33, FW12, FW13, FW23 (for anisotropic Debye-Waller
factors). Table could contain the blank lines between the rows and com-

20
ments in form of ”!” and ({}). Row in the table corresponds to parameters of
”FROM”-layers. Respectively column corresponds to parameters of ”TO”-
layers. For instance, αij should appear on j-row and i-column.
WARNING: Standard setting using LT and FW keywords should also be
present, but it can be left as zeros. If TABLE appears after standard LT
and FW section, corresponding parameters would be overwritten by data
from tables.

Calculation section

First line must contain the heading CALCULATION. This section contains
the type of calculation the program is asked to perform. There are two
options: SIMULATION and LMA. The first one corresponds to the pat-
tern calculation, and thus no parameter will be refined. The second option
indicates that the refinement is to be done by means of the Levenberg Mar-
quardt fit. Depending on the calculation type, the next lines must contain:

• Simulation: In order to simulate a powder diffraction pattern the

user has to specify the keyword Powder followed by the values of
2θmin , 2θmin and the step (in degrees). Optionally, a scale factor and
an offset value can be specified on the same line to simulate a pattern
with background and noise generated from a Poisson distribution. For
example,

CALCULATION
SIMULATION { type of optimization }
POWDER 5.0 90.0 0.02 ScaleF 1.00 Bckg Level 150.00

If a selected area diffraction pattern is to be simulated, SADP key-

word must be followed by the values of i plane, l upper, loglin and

21
brightness parameters, also used in DIFFaX. The i plane parameter
refers to the plane in reciprocal space to view. Choosing 1 views the
plane containing h0l spots; 2 the plane containing 0kl spots; 3 the
plane containing hhl spots and 4 the plane containing h-hl spots. The
l upper parameter corresponds to the maximum value of l to go out
to. The maximum values of h and k will be automatically defined
by this l value, since the calculated diffraction pattern will be square.
The intensity data can be plotted on a linear or logarithmic scale, by
defining loglin to be 0 or 1 respectively. In linear mode, the value of
brightness refers to an intensity scaling factor. A brightness factor of
1 means that the intensity range (excluding the zero order beam) will
be compressed so as to fit within the range 0 to 32767 and a birghtness
factor of 10 means that the intensity range will be fitted within the
range 0 to 327670, but all values above 32767 will be saturated, and
will be set equal to 32767. The file created is an unsigned 16 bit image
of size 256 x 256 with a *.sadp extension. To display the file a specific
software like ImageJ can be used [17].
For example:

CALCULATION
SIMULATION { type of optimization }
SADP 1 4.0000 1 50.0000 { i plane, l upper, loglin, brightness }

For the streak simulation the user should put the STREAK keyword
followed by the next values: adapt quad, h, k, l0, l1 and dl. Optionally,
one can put UNBROADEN keyword on the next line for calculating
unbroadened streak data. Scale factor is equal to one for the streak
calculations. Data is written in free format and can be visualized using
WinPLOTR. For example:

22
 CALCULATION
SIMULATION { type of optimization }
STREAK 1 1 0 -5 5 0.01 { adapt quad, h, k, l0, l1, dl }
UNBROADEN

• LMA: The user has to specify the maximum correlation parameter

(which defines the minimum correlation used to build the correla-
tion matrix that will be given in the output file; keyword Corrmax ),
the maximun number of function evaluations (keyword Maxfun), the
tolerance (i.e. convergence criterion; keyword Tol ) and the print con-
trol parameter (keyword Nprint). Each of these parameters must be
placed in a new line. For example,

CALCULATION
LMA
Corrmax 30
Maxfun 2400
Tol 0.1E-04
Nprint 0

If the print control parameter Nprint is set to 0, the values of the

agreement factors at the end of each evaluation are displayed in the
FAULTS window (see subsection 1.5) during the refinement process.
If Nprint is negative, the FAULTS windows displays the previous and
new values of the refinable parameters at each evaluation step, in
addition to the agreement factors, at the end of each evaluation.

Finally, whatever the kind of calculation to be performed (SIMULA-

TION or LMA), the user can add an optional line with the instruction

23
Replace Files at the end of the Calculation section to make the program
replace existent output files by the ones generated at the end of a new run,
instead of creating new files.

Experimental section

This section is only necessary in case a refinement is to be done. The sec-

tion must begin with a first line containing the heading EXPERIMENTAL,
followed by:

• Filename: In this line, which must begin with the keyword file, the
user indicates the file name of the experimental intensity data file,
which must not exceed 20 characters, extension included (*.dat or
other ; see section 1.3.2). After that, the scale factor and its refinement
code must be given, in the same line.

• Excluded regions: Optionally the user can exclude some regions of

the experimental data. To do so, Excluded Regions must be written,
followed by the number of excluded regions. In the next lines, 2θ min
and 2θ max of each excluded region must be specified (in a separate
line per excluded region). If these are not detailed, the program will
use the whole 2θ range of the experimental data. WARNING: For
now, only one region can be excluded. Another option to avoid error
of the program is to directly remove the data not used at the lowest
and highest angles from the experimental data file.

• File format: In this line the user writes a code to tell the program
which is the format of the intensity data file, that depends on the
instrument. The possibilities (which are detailed in the next subsec-
tion 1.3.2) are: D1B, D20, NLS, G41, D1A, D2B, D1AOLD, D1BOLD,

24
 DMC, SOCABIM, XYSIGMA, GSAS, PANALYTICAL, TIMEVARI-
ABLE and FREE. The line must begin with the keyword Fformat.

• Background file: To determine the background, three different pos-

sibilities are available, and at least one of them must be present. First,
the background can be modeled by linear interpolation. To do so, the
user must write the keyword Bgrinter followed by the name of the file
(extension included) that contains background data. This file should
contain a list of pairs of values: scattering variable \ intensity (see
subsection 1.3.3). Note that background points are not refinable pa-
rameters. For example,

!Linear interpolation
Bgrinter Sim.Bgr

If the background is to be treated as a polynomial, the keyword is

Bgrcheb and the number of coefficients must be specified after it. In
the following line the polynomial coefficients must be entered. These
are refinable parameters, so the user must remember to write their
refinement codes below them. For instance,

!Polynomial Number of coefficients

Bgrcheb 2
!Polynomial coefficients
1.00000 0.20000
1.0 1.0

Finally, a third background subsection is available in order to deal

with possible secondary phases. In case the sample to be analysed

25
 has secondary phases, these will give extra peaks in the experimen-
tal pattern. In order to take them into account, FAULTS program
can treat them as background. Thus, a file containing the diffraction
pattern in free format (see section 1.3.4) must be provided for each
secondary phase present in the experimental pattern. For now, this
option works only if the general background is treated as a Chebichev
polynomial (it doesn’t work with the background modeled by linear
interpolation). The information about the secondary phases must be
given as follows: first the number of pattern backgrounds is to be
specified, preceded by the keyword Bgrnum; then the user must write
in a separate line the keyword Bgrpatt followed by the filename, scale
factor and its refinement code. Optionally, the name of an *.hkl file
can be given after the scale’s factor refinement code so that the Bragg
reflections of each additional phase appear in the calculated *.prf file.
A separate line will be written for every given pattern. Note that
the 2θ range and step size of the diffraction patterns provided for the
secondary phases should be identical to that of the experimental data
to be refined with FAULTS. For example,

!Number of pattern backgrounds

Bgrnum 1
!Pattern file Filename Scale factor Code hkl file
Bgrpatt phase2.sub 0.026000 1.00 phase2.hkl

1.3.2 Experimental pattern files

The experimental intensity data file can have different formats that depend
on the instrument. The files FAULTS is able to read are the following:

• D1B o D20 (Ins=3 in FullProf ): These are the data file from

26
 D1B and D20 diffractometers (ILL) and have a *.dat extension.
Line 1-3: comments
Line 4: 2θ min, step (deg.) + other parameters
Line 5: number of points in the data file (npts)
Lines1 : npts pairs D Y1 D Y2 ... D Y10 (where D is the detector number and Y
the measured intensity )

• NLS (Ins=4 in FullProf ): Data file from N.L.S.(Brookhaven)

synchrotron radiation with *.dat extension.
Line 1:2θmin, step size, 2θ max (deg.)
Lines1: pairs of lines with 10 items like
Y1 Y2 ... Y10 (intensities)
S1 S2 ... S10 (sigmas)

• G41 (Ins=5 in FullProf ): Data file from G41 multidetector neu-

tron diffractometer at LLB with *.dat extension.
Line 1-3: comments
Line4: npts
Line 5:2θmin, step size, 2θ max (deg.)
Lines1: Y (one column)

• D1A o D2B (Ins=6 in FullProf ): ”Multicounters diffractometers

data with *.dat extension.
Line 1: Comments
Line 2: step size (deg.)
Line 3: 2θmin
Line 4: Comments
Lines1: D Y1 D Y2 ... D Y10

• D1AOLD o D1BOLD (Ins=1 in FullProf ): These are the data

file from D1B and D20 diffractometers (ILL) (old format).

27
 Line 1:2θmin, step size, 2θ max (deg.)
Lines1: npts pairs D Y1 D Y2 ... D Y10

• DMC (Ins=8 in FullProf ): These are files from DMC diffrac-

tometer from Paul Scherrer Institute with *.dat extension.
Line 1-3: comments
Line 4: 2θmin, step size, 2θ max (deg.)
Lines1: Lines1: pairs of lines with 10 items like
Y1 Y2 ... Y10 (intensities)
S1 S2 ... S10 (sigmas)

• SOCABIM (Ins=9 in FullProf ): Thee are XRD files with *.uxd

extension generated by Socabim software.
Line 1-29: comments
Lines1: Y1, Y2, ..., Yn.

• XYSIGMA (Ins=10 in FullProf ): Files with *.dat extension

Line 1: keyword XYSIGMA
Line 2-6: comments
Lines1: X, Y, S

• GSAS (Ins=12 in FullProf ): data file for the GSAS analysis data
program.
Line 1: text
Line 2: npts
Lines1: intensities (diverse formats)

• TIMEVARIABLE (Ins=11 in FullProf data from variable time

data collection.

28
 Line 1: 2θmin, step size, 2θ max (deg.)
Lines1: T1 I1 T2 Y2 ... T10 I10 (T = time)

• FREE (Ins=0 in FullProf ): free format files generally with *.dat

extension. Up to 7 lines of comments are accepted, the first real
numbers are 2θmin , step size and 2θmax (deg.), and the npts following
lines are the intensity values.

1.3.3 Background: CFILE.bgr

If the user chooses to treat the background as a linear interpolation between

N given points, he/she should provide a file which contains the list of points
that will be used to calculate the background at each value of the scattering
variable. The user can create such a file from the experimental data using
the program WinPLOTR [18, 19] of the FullProf Suite [9, 11]. The extension
of this file is usually *.bgr, but can be any other. In this file, comments be
added if they are written after a ! symbol. Example:

! background: positions intensity:

!————————————–
10.0 40.6745
15.0 74.8976
45.0 74.759
...

1.3.4 Secondary phases: CFILE.sub and CFILE.hkl

To take into account secondary phases, it is necessary to provide one or

several files CFILE.sub in free format (see subsection 1.3.2) that contain
the calculated profile of these phases. The extension of such files is usually

29
*.sub, although the program accepts any kind of extension. These files
can for instance be generated by the program FullProf [9] at the end of
a refinement or a simulation when the option Ipr=2 or Ipr=3 is activated
(for more details about this option, please refer to the FullProf Manual
[11]). Moreover, the user can optionally provide a file CFILE.hkl for each
CFILE.sub file, which contains the list of the hkl reflections for each phase.
The user can create such a file by activating the option hkl=5 when carrying
out a refinement or a simulation with the program FullProf [9, 11]. Example:

>Phase no.: 1 CFILE 19 reflections, N&T: 0 0.00

! SPGR: R -3 m; CELL: 2.860 2.860 14.227 90.0 90.0 120.0

h k l Mult S.Factor 2T
0 0 32 2474.23438 18.7107
1 0 16 1799.86182 36.8334
...

1.3.5 Crystallographic Information File as an input:

CFILE.cif

WARNING: This part is under testing.

Crystallographic Information File can be put as an input file to Faults pro-
gram in order to create a CFILE.flts template. This possibility is only
accesible from command line. User have to provide a name of .cif file fol-
lowed by overall number of layers in structure, number of actual layers and
chemical symbol of zero atom. Program define the layer as ensemble of
atoms with equal z-coordinate. Zero atom is an atom, which would be sit-
uated at (0,0,0) coordinate in each layers. It will be used by program to
calculate transitions vectors. Zero atom should be present at each layer.
Example: CFILE.cif 14 1 Mn.

30
1.4 Output files
Once the program has finished, FAULTS will create the following output
files, depending on the users requirements. These files will be saved to the
same directory as the input data files.

1.4.1 Calculated profile: CFILEn.dat

If a powder pattern simulation is to be done, the program writes the cal-

culated profile in a *.dat file that is written in free format (see subsection
1.3.2).

1.4.2 Calculated SADP: CFILEn.sadp

If a selected area diffraction pattern simulation is to be done, the program

writes the calculated pattern in a *.sadp file. It contains an unsigned 16-
bit image of size 256x256. To display this file, a specific software such as
ImageJ can be used [17].

1.4.3 Observed and calculated profile: CFILEn.prf

If the user is performing a refinement, the program creates a file with the
experimental pattern, the calculated one with the best fit, their difference
plot and the Bragg reflections. This file is to be fed into a visualisation
program, such as WinPLOTR [9, 18]. It is essential to plot frequently
the observed and experimental patterns. The examination of the difference
pattern is a quick and efficient method to detect blunders in the model or in
the input file controlling the refinement process. It may also provide useful
hints on the best sequence to refine the whole set of model parameters for
each particular case.

31
1.4.4 Crystallographic structure files: CFILE.fst,
CFILE flts.cif and CFILE flts.vesta

If the user has specified FST CMD commands for the drawing of the struc-
tural model, the program creates 3 output files: a file CFILE.fst to be
fed into the visualization program FullProf Studio [13, 14], a second file
CFILE flts.vesta to be opened with the visualization program VESTA
[15, 16], and a short Crystallographic Information File CFILE flts.cif
which can be read with other visualization programs.
Details on the format of the file CFILE.fst can be found in the FullProf
Studio manual [14].
It is highly recommended to regularly draw the structure during the
construction of the structural model as well as during the refinement.

1.4.5 Progress report: CFILEn.out

When the user run a simulation or a refinement with FAULTS, an *.out file
is generated, which contains information about different steps of the calcu-
lation. If a refinement is done, the last part of the file contains information
about the refinement process: the values the refinable parameters have taken
during refinement, the values of the agreement factors for each evaluation
and the best values of each parameter obtained during refinement.

1.4.6 Final report: CFILE new.flts

When the refinement is finished a *.flts file is generated. It contains the

information of the refinement’s final result. Its format is similar to the
input file, with the same structure (section headings, keywords, parameters,
refinement codes), but with the refined values for the refinable parameters.
Thus, this file can be used as the input file in case the user wants to continue

32
the refinement process. If the file is used as input file directly, at the end of
the refinement it will be overwritten.

1.5 Running FAULTS

The program is invoked from a terminal (or a DOS window) and it will
appear as in figure 1.4.

Figure 1.4: FAULTS layout when invoked

Once the user enters the name of file CFILE.flts, if a refinement is to

be done, the layout of the program will appear as in figure 1.5. During
the refinement process, depending on the option chosen by the user (see
the comments on keyword Nprint in the Calculation subsection page 21),
the terminal will display the values of agreement factors at the end of each
evaluation, and optionally the list of previous and new refinable parameters
at each evaluation step.

33
 Figure 1.5: FAULTS layout during refinement

Once the refinement has finished, the list of the best values obtained
for the refinable parameters is displayed (see figure 1.6). The user can then
open the CFILEn.prf to see the goodness of the refinement.

34
35
Figure 1.6: FAULTS layout at the end of the refinement
Chapter 2

Example

2.1 Stacking faults in LiNiO2

Lithium nickel oxide has been intensively studied as a positive electrode
material in Li-ion batteries [20]. As other lithium transition metal oxides,
it crystallizes in an O3-type layered structure consisting in three NiO2 slabs
per unit cell, with an ABCABC oxygen stacking sequence, and lithium ions
located in the octahedral sites of the interlayer spaces (see figure 2.1). In
order to explain the significant broadening of the (10l ) and (01l ) diffraction
lines, DIFFaX simulations have been used for this material with the hypoth-
esis of the existence of O1 stacking faults in the structure at low lithium
concentrations (Li Ni1.02 O2 ,  ≤ 0.3) [21]. These stacking faults represent a
break in the normal stacking sequence of the structure, with a local ABAB
oxygen stacking sequence.
The ideal structure can be described with three layers, each one contain-
ing a NiO2 slab and a lithium interslab. The three layers are structurally
identical, but shifted with respect to each other, resulting in transition vec-
tors ~t12 =~t23 =~t31 =(2/3 1/3 1/3) and a stacking probability of 1 for each

36
Figure 2.1: a) Ideal structure of lithium nickel oxide (LiNiO2 ) with
O3 stacking, and b) defective structure with O1 stacking faults
(Li Ni1.02 O2 ).

transition. O1 defects require the definition of a new type of layer, struc-

turally different, since these defective layers do not contain any lithium (see
figure 2.2). Therefore, three more layers are defined in the faulted structure,
structurally identical between each other but different from the previous
ones, and new transitions are allowed in order to describe the defects (see
figure 2.3).

37
38
Figure 2.2: a) Schematic representation and atomic coordinates of the layers required for
describing stacking faults for Li0.05 Ni1.02 O2 in the FAULTS program. b) Graphic represen-
tation of the different transition possibilities from layer 1 and transition vectors.
Figure 2.3: Possible layer transitions for Li Ni1.02 O2 containing O1-
type stacking faults, where αij is the probability transition from
layer i to layer j.

2.2 Analysis of simulated data

By means of the stacking description described above, FAULTS has been
used to simulate a diffraction pattern with the parameter’s values described
in table 2.1. The obtained simulated XRD pattern for Li Ni1.02 O2 ( ≤
0.3) has then been used to analyse and test out the program. This are also
the example files (LiNiO2 simul.flts and LiNiO2 refine.flts) included with
the program. The refinement has been done by means of the Levenberg
Marquardt minimization algorithm, restraining the program to a maximum
of 2400 function evaluations and a criterion of convergence 0.1e-4. As an

39
 Refined parameter Simulation Initial value Final value(Std dev.)
a,b 2.81540 2.86540 2.81510(10)
c 13.363000 13.26300 13.3638(7)
Scale 1.00000 1.00000 1.010(3)
zO1 ,zO3 0.07133 0.17133 0.0716(2)
zO2 ,zO4 -0.07133 -0.17133 -0.0716(2)
α12 ,α23 ,α31 0.8580 1.0000 0.8569(10)
α14 ,α25 ,α36 0.1420 0.0000 0.1431(10)
α42 ,α53 ,α61 0.8580 1.0000 0.842(6)
α44 ,α55 ,α66 0.1420 0.0000 0.158(6)

Table 2.1: Starting and final values of the parameters refined in the
analysis of simulated data.

example of the refinement process, the initial values of the refined parame-
ters, which have been chosen far enough from the correct ones not to bias
the result, and the final refined values are also shown in table 2.1. A visual
comparison between the calculated and the simulated powder patterns and
their difference is shown in figure 2.4. Starting Rp and Chi2 values were
45.62% and 186.38 respectively and reached a final value of 4.86% and 1.03
respectively. The values of the refined parameters are very close to those
used in the simulation and lead to a XRD pattern practically identical to
the one obtained with the values of these parameters used in the simulation
(see figure 2.4).
An example of the evolution of a and b cell parameters and of Chi2 and
Rp throughout a run of 12 iteration cycles is shown in 2.5.

40
41
Figure 2.4: Comparison of the X-ray diffraction patterns corresponding to the FAULTS
analysis of the simulated data: simulated pattern (dotted curve) and calculated pattern
using the FAULTS refinement (continuous curve). The diagram underneath shows the
difference between them. The ticks show the position of the Bragg reflections of the R-3m
average unit cell (the one used to describe the ideal O3 structure of Li Ni1.02 O2 ).
Figure 2.5: Evolution of the functions Rp and Chi2 and of the cell
parameters a and b, versus the cycle number.

42
Chapter 3

Frequent errors

This part of the manual is a tentative of compiling frequent mistakes

made by new users of FAULTS. This list is far from being exhaustive.
It is only intended to help beginners in starting working correctly with
FAULTS and doesn’t dispense the user of a carefull reading of the en-
tire manual. The authors would be grateful if users could notify them
about other possible sources of errors not reported below or about pos-
sible bugs in the program (faults*at*cicenergigune.com or fullprof*at*ill.fr).

First of all, the users should always read carefully the messages written
by FAULTS in the command window and in the output file .out. Most of
the errors can be identified from these messages.

3.1 Input control file .flts

• Tabs are not allowed in the input files of FAULTS. Only spaces can
be used.

43
 • All the non-optional sections and keywords have to be present in the
.flts input file.

• Contrary to the .pcr input files used in FullProf, a missing refinement

code will not be considered as zero but will produce an error, so all
the refinement codes have to be present in the .flts input file.

• Contrary to the .pcr input files used in FullProf, empty lines can be
used in the .flts input file.

• The combination of the profile parameters U, V, W, X should not

lead to a profile function with negative values (no negative Gaussian
and/or Lorentzian FWHM). The user can check this by calculating the
2 and H ) with the formula given
Gaussian and Lorentzian FWHM (HG L
in page 10 using the program WinPLOTR [18, 19] (Menu Calculations
=> I.R.F. (U,V,W,X,Y,Z)) or any spreadsheet.

• In refinement mode, at least one parameter should be refined.

3.2 Input experimental data files

The user should make sure that his/her experimental data file complies with
the following points:

• Make sure to comply with the description of each file type.

• No intensity can be zero o negative.

• Empty lines should be avoided.

• If secondary phases are to be included, the 2θ range and step size of

these sub-patterns should be identical to those of the experimental
data file to be refined.

44
3.3 Other remarks
• The way of working with FAULTS requires especial care of the user.
Before starting to do refinements it is advisable to make simulations
in order to start with an initial model that is not too far from the
experimental diffraction pattern.

• If the structural model is complicated, the first calculations can take

time, so the user should make sure that he/she lets the program some
minutes before concluding that it is blocked. Keep in mind that the
derivatives are calculated numerically by calling two times the total
function per free parameter and this calculation may be expensive in
CPU-time.

45
Bibliography

[1] Treacy M.M.J., Newsam J.M. and Deem M.W. A general recursion
method for calculating diffracted intensities from crystals containing
planar faults. Proc. R. Soc. Lond. A, 433:499-520, 1991.

[2] Treacy M.M.J., Newsam J.M. and Deem M.W. DIFFaX. Available at:
http://www.public.asu.edu/~mtreacy/DIFFaX.html.

[3] Rodrı́guez-Carvajal J. and Gonzalez-Platas J., Crystallographic For-

tran 90 modules library (CrysFML): a simple toolbox for crystal-
lographic computing programs. IUCr CompComm. Newsletter, 1:50-
58, 2003. Available at: http://www.iucr.org/iucr-top/comm/ccom/
newsletters/.

[4] Rodrı́guez-Carvajal J. and Gonzalez-Platas J., CrysFML repository.

Available at: http://forge.epn-campus.eu/projects/crysfml/
repository/.

[5] Treacy M.M.J., Deem M.W., and Newsam J.M. DIFFaX Manual, 2005,
Chap 8: How DIFFaX works (p48). Available at: http://www.public.
asu.edu/~mtreacy/DIFFaX$_$manual.pdf.

[6] Hendricks S. and Teller E. X-ray interference in partially ordered layer

lattices. J. Chem. Phys., 10:147-167, 1942.

I
 [7] Casas-Cabanas M., Rodrı́guez-Carvajal J., Palacı́n M.R., Z. Kristal-
logr. Suppl., 23:243-248, 2006.

[8] Casas-Cabanas M., Rikarte Ormazabal J., Reynaud M., Rodrı́guez-

Carvajal J., in preparation.

[9] Rodrı́guez Carvajal J., FullProf Suite. Available at: http://www.ill.

eu/sites/fullprof.

[10] Rodrı́guez Carvajal J., Physica B.(1993), 192, Recent advances in mag-
netic structure determination by neutron powder diffraction. Physica
B., 192:55-69, 1993.

[11] Rodrı́guez Carvajal J., FullProf Manual. Available at http://www.

ill.eu/sites/fullprof/php/tutorials.html.

[12] Treacy M.M.J., Deem M.W., and Newsam J.M. DIFFaX Man-
ual, 2005. Available at: http://www.public.asu.edu/~mtreacy/
DIFFaX$_$manual.pdf.

[13] Rodrı́guez Carvajal J. and Chapon L., FullProf Studio. Available at

http://www.ill.eu/sites/fullprof/index.html.

[14] Rodrı́guez Carvajal J. and Chapon L., FullProf Studio Manual. Avail-
able at http://www.ill.eu/sites/fullprof/index.html.

[15] Momma K. and Izumi F. VESTA3 for three-dimensional vizualization

of crystal, volumetric and morphology data. Journal of Applied Crys-
tallography, 44:1272-1276, 2011.

[16] Momma K. and Izumi F., VESTA (Visualization for Electronic and
STrcutural Analysis). Available at http://jp-minerals.org/vesta/
en/.

II
[17] http://imagej.nih.gov/ij/index.html

[18] Roisnel T. and Rodrı́guez Carvajal J., WinPLOTR: A windows tool for
powder diffraction pattern analysis. Mater Sci Forum, 378(3):128-123,
2000.

[19] Roisnel T. and Rodrı́guez Carvajal J., WinPLOTR: A graphic tool for
powder diffraction. Available in the FullProf Suite or as an independant
program at http://www.cdifx.univ-rennes1.fr/winplotr/.

[20] Whittingham M. S., Lithium Batteries and Cathode Materials. Chem-

ical Reviews, 104:4271-4301, 2004.

[21] Croguennec L., Pouillerie C., Mansour A. N. and Delmas C., Structural
characterisation of the highly deintercalated Lix Ni1.02 O2 phases (with
x≤0.30). Journal of Materials Chemistry, 11:131-141, 2000.

III