New Features
·
The
current version of the program FullProf is 2.50 Oct2003
·
Some
actions have been included to control local divergence of some parameters. Now
instead of fixing the diverging parameter to an arbitrary value, the parameter
is fixed to the previous value but the multiplier associated with its
refinement codeword is divided by two in order to make more successful the
refinement in the next cycle. A warning is always output. This allows a better
control by the user of the refinement process.
·
The
refinement flags concerning different patterns are now output explicitly even
if the user has not given zero values. Now the output of the NPATT line adopts
the following aspect:
NPATT 3
1 1 1 <- Flags for patterns
(1:refined, 0: excluded)
When using using zero flags for some
patterns remember that the weighting factor of each pattern is changed by the
programa, so that the sum of weights of all considered patterns is equal to 1.
If one wants to re-start with more patterns, check the weighting factors before
running the program.
·
The
resolution function of the different banks corresponding to a TOF
diffractometer can now be included in a single file. One has to repeat the name
of the file for each pattern in the PCR file. The different bank information
has to be separated by the keyword "END" (without quotes) withint the
IRF file. Now the intrumental parameters + refined shifts are output as
comments in the PCR file when an IRF file is used in TOF.
The keyword TOFRG is now used for
limiting the TOF read in the input data file. Only the points satisfying:
TOF_min <= TOF <= TOF_Max, are used in the program. Examples of IRF files
will be provided in the subdirectory "IRF-files" of the FullProf
suite directory.
·
New
modes for treating preferred orientation have been included. Putting NOR=2 the
user can give several (up to a maximum of 5 per phase) preferred orientation
directions (POD) and refine the corresponding March-Dollase parameter and the
fraction of crystallites having a particular preferred orientation direction.
The fraction corresponding to the last POD cannot be refined: it is calculated
from the other values in such a way as to get a sum equal to 1.
·
If
NOR=3 the Multi-axial March-Dollase model for preferred orientation adapted for
high pressure anvil cells in which the incident beam is in the same direction
as the external force producing the high pressure and perpendicular to the
image plate collecting the data. A numerical integration is performed to
calculate the value of corresponding to expressions (4),(5) and (6)
of the paper: "Observation and
Modelling of Preferred Orientation in Two-Dimensional Powder Patterns"
Journal of Synchrotron Radiation 3, 112-119 (1996). by N. G. Wright, R. J. Nelmes, S. A.
Belmonte and M. I. McMahon
The input in the PCR file
corresponding to both models is similar. If the program detect that NOR=2 or
NOR=3 a line containing the number of POD (NPOD) is read after the pair of
lines following the text
"! Pref1
Pref2 Asy1 Asy2
Asy3 Asy4"
or the text:
"! Pref1
Pref2 alph0 alph1
beta0 beta1 " for TOF,
or the text:
"! alph0t
beta0t alph1t beta1t " in case of using the function NPROF=10 for TOF.
If NOR=3 a second integer is read in
the same line that corresponds to the number of steps for the numerical
integration (is not given the program uses NOrstep=20)
It follows a set of NPOD lines
containing the following information:
Indices of the POD direction (3 real numbers), March-Dollase parameter
and refinement code (2 real numbers) and Fraction of crystallites and code for
the current POD.
Example:
For NOR=2
....
! Pref1
Pref2 Asy1 Asy2
Asy3 Asy4 S_L
D_L
0.00000
0.00000 0.00000 0.00000
0.00000 0.00000 0.00000
0.00000
0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00
! March-Dollase multi-axial model for preferred
orientation (naxes)
2
! Pref-hkl MD-r Code(MD-r)
Fraction Code(Fract.)
1.00
0.00 1.00 1.3807
91.000 0.6246 101.000
2.00
1.00 1.00 0.6107
111.000 0.3754 0.000
.......
For NOR=3
....
! Pref1
Pref2 Asy1 Asy2
Asy3 Asy4 S_L
D_L
0.00000
0.00000 0.00000 0.00000
0.00000 0.00000 0.00000
0.00000
0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00
! March-Dollase-Wright multi-axial model for
preferred orientation
!
(naxes, N_Int_steps)
2 30
! Pref-hkl MD-r Code(MD-r)
Fraction Code(Fract.)
0.00 0.00 1.00
1.1102 61.000 0.7200
71.000
2.00
1.00 0.00 0.7107
81.000 0.2800 0.000
....
Bugs
·
A
new version of the program EdPCR has
been included in the FullProf Suite. The latest version had a bug: the change
of profile function was disabled.
Bugs
·
A
bug concerning the scale factors in single twinned single crystal refinements
was introduced in the May2003 version that was still in the latest version.
Contrary to the precedent versions the refinement of several scale factors was
diverging systematically (another editing error!). The bug has been corrected.
Bugs
·
Sorry!
a copy/paste error was introduced in the latest version (24 September) of
FullProf interrupting the reading of reflections in the second run of a Le Bail
fit before the end of the file. Now this bug is corrected.
New Features
·
A
new format for data files has been implemented INSTRM=14. It corresponds to the
multibank format for TOF diffractometers existing at ISIS. The format is the
following:
1.
The
first line is considered as a title
2.
All
following lines starting by the symbol # are considered as comments
3.
A
line starting with the keyword BANK indicates that follows a series of lines
containing three items: scattering variable (TOF/2theta/Energy), profile
intensity and sigma. Internally the intensity and sigma are multiplied by a
factor 1000. This is because the normalization procedures used at ISIS produce
quite small numbers and FullProf expects "counts" as input for
profile intensities.
The user can change this factor
putting the keyword "fac_y" followed by the desired factor (a real
number) in one of the comment lines before the keyword BANK. Remember that if
the final intensities are too small numbers (order of unity) the calculation of
RBragg factors may be in error. If within the line containing the keyword BANK
there is the keyword RALF, the input intensity and sigma values are divided by
the steps according to:
4.
If
all banks are to be used, in the PCR file one has to repeat the name of the
data file a number of times equal to the number of banks (number of patterns).
If the user experiences that the generation of reflections takes long time,
this is certainly due to too short times of flight, included in the data file,
that do not contain useful information. This can be overcome just putting in
the line containing the name of the phases the instructions 'DLIM n_pat
d-spacing' See the end of the note of 20 January 2003
for details.
Bugs
·
Several
small bugs of the latest version have been corrected:
1.
The
new format for INSTRM=10 was incompatible to some older versions
2.
The
CIF file generated for powder work was corresponding to single crystal work and the profile file was not
output. Now when RPA=-1 two CIF files are generated
3.
Some
format errors have been corrected in the generated CIF files.
New Features
·
The
current version of the program FullProf is 2.45 Jul2003
·
Some
changes have been introduced for treating the background:
1.
The
polynomial background of 12 coefficients, for constant wavelength case, has
been changed so that the last three coefficients correspond to inverse powers
of 2theta. The ,
and
coefficients correspond to the powers
,
and
respectively. The background for the case
Nba=-3 corresponds to the formula:
2.
Now
there is the possibility to include several previously calculated profiles as
contributing, through a linear combination, to the background of a powder
diffraction pattern. The individual profiles are read in input files named
"filedat_n.bac". Where "filedat" is the code of the data
file corresponding to a diffraction pattern and the index "n" is the number of the
contributing profile. The format of these files should correspond to INSTRM=0
and must have the same number of points as the observed powder diffraction
pattern. At present a maximum of 10 user-given profiles can be used as an
additional contribution to the background calculated using whatever function
available previously. The additional contribution to the background is
calculated as:
This is useful for complicated
backgrounds or for adding calculated thermal diffuse scattering to a powder
diffraction pattern. To use this new option the flag MORE in the same line as
the variable "Zero" must
be 2 or 3. In this last case (MORE=3) Microabsortion coefficients are read
first, then a line containing in the first position the number of profiles and
the coefficients of the linear combination is read. An additional line is read
for the refinement codewords of the coefficients.
An example of the relevant part of a
PCR file is the following:
............................
!
!
Zero Code Sycos
Code Sysin Code
Lambda Code MORE
0.00000 0.00 -0.29309 0.00
0.00025 0.00 0.000000 0.00
3
!
! Microabsorption coefficients
for Pattern# 1
! P0
Cod_P0 Cp Cod_Cp
Tau Cod_Tau
0.6950
0.00 0.6413 0.00
0.0452 0.00
!
! Num. and coeff. of profiles
contributing to background of Pattern# 1
1
1.2310
51.0000
............................
For using only microabsoprtion
coefficients MORE=1 and for using only
additional background contributions MORE=2. To use this option with TOF neutron diffraction MORE=2.
Bugs
·
A
bug in the program BasIreps was introduced in the last version providing the
wrong number of generators of the space group. This has been corrected and new
output is available concerning the general expressions of the Fourier
coefficients. The Fourier coefficients are written in terms of symbolic free
parameters.
·
The
values of the weight fraction of the phases when using (JBT=-3, IRF=2) for
quantitative analysis was not written in the output files. This has been
corrected. Now the written hkl-files
(h,k,l,M, Struct-Fact ...) when Hkl=5 contain the value of ATZ. This ensures
that the used ATZ-values agree with those used for calculating the structure
factors.
New Features
·
New
documents have been written to explain the use of multipolar refinements in
flipping ratio refinement of single crystals and to detail the peak shape
functions used for TOF powder diffraction.
·
Reorganization
of the TOF peak shapes and derivatives. The refinement of the instrumental
parameters is now much more stable. Some internal changes make differences with
respect to previous versions for the values of the profile parameters. The new
peak shape (thanks to Laurent Chapon!) consisting in the convolution of a
pseudo-Voigt function with the Ikeda-Carpenter function is now working. The TOF
peak shapes used in FullProf and the meaning of each refinable parameter is now
documented in the note: TOF_FullProf.PDF
Bugs
·
A
bug in the program Fourier was introduced in the last version that was
appearing with non-centrosymmetric structures. This has been corrected. The
direct access to GFourier help-file is now working.
·
The
interface program EdPCR is being modified and corrected extensively in order to
include most of the capabilities of FullProf. There are still many things to be
included and corrected but we intend to make so easy the manipulation of the
PCR files that even experienced user will find advantageous the use of EdPCR
for doing modifications in their PCR files. We have modified the creation of
simple templates and simplified the creation of a new PCR file from the
scratch.
New Features
·
The
current version of the program FullProf is 2.40 May2003
·
Different
PANalytical formats and extensions are automatically recognized for INSTRM=13.
·
New
keywords have been introduced for IRF files. The interface program EdPCR is now
able to write an IRF using a template. A subdirectory called IRF-files will be
created on installing the FullProf suite where several examples of IRF files
can be found.
·
The
program makes automatically constraints when two atoms occupy the same
crystallographic position. This apply only for working in automatic mode.
·
Some
modications in the profile matching modes have been performed. Now the case
jbt=3 works as stated in the manual (jbt=-3 was already working well!). The
case jbt=2 and several atoms were given, the program was starting
"always" from the calculated structure factors of the known part of
the structure. Now only for the first run (irf=0) the atoms are important. This
option serves to bias the distribution of overlapped intensities according to
the known atom positions.
·
Single
crystal simulations (flipping ratios ...) are now possible by putting JOB=2,3
and CRY=4. The program generates reflections according to the provided ,
angles. The wavelength and other
characteristics of the simulation are provided at end of the PCR file.
In the example below, the used
wavelength is 0.711 angstroms, itypd=2 means that the program will calculte
flipping ratios from the model given in the same file. Polarp and Polarm are
the efficiency of the flipper for neutrons "up" and "down"
respectively, UB_mat=1 means that the program will read the orientation matrix
just below the current line. If itypd=0,1 the program will calculate structure
factors and the output *.int file will contain squares of structure factors (itypd=0)
or simply the modules of structure factors (itypd=1).
Example:
COMM Simulation of Flipping
ratios
! Files => DAT-file:
flipr-sim, PCR-file: flipr-sim
!Job Npr Nph Nba Nex Nsc Nor
Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut
3
0 1 0
0 0 0
0 0 0
0 0 0
0 4 0
0 0 0
!
!Ipr Ppl Ioc Mat Pcr Ls1 Ls2
Ls3 NLI Prf Ins Rpa Sym Hkl Fou Sho Ana
0
0 1 0
1 0 0
0 0 1
0 0 0
0 0 0 0
!
!NCY Eps
R_at R_an R_pr
R_gl Thmin Step Thmax
PSD Sent0
1
0.01 1.00 1.00
1.00 1.00 10.0000
0.1000 89.9000 0.000
0.000
!
. . . . . . . . . . . . . . . . . . . . . . .
. . . . .
. . . . . . . . . . . . . . . . . . . . . . .
. . . . .
Tail of the PCR file adapted for single crystal
simulations.
. . . . . . . . . . . . . . . . . . . . . . .
. . . . .
! x-Lambda/2 +
Not yet used parameters
0.03000
0.00000 0.00000 0.00000
0.00000
0.00 0.00 0.00 0.00 0.00
! Parameters for Single X-tal
calculations
! Lambda itypd
ipow Polarp Polarm
UB_mat
0.7110
2 0 0.89000
0.89000 1
! UB_matrix
-0.017950
0.000610 0.188620
-0.042370
-0.173200 -0.003470
0.127620
-0.031460 0.012250
Bugs
·
Bug
correction: the output SHELX *.ins files for profile matching mode contains now the symmetry operators.
·
Some
modications in the profile matching modes have been performed. Now the case
jbt=3 works as stated in the manual (jbt=-3 was already working well!). The
case jbt=2 and several atoms were given, the program was starting
"always" from the calculated structure factors of the known part of
the structure. Now only for the first run (irf=0) the atoms are important. This
option serves to bias the distribution of overlapped intensities according to
the known atom positions.
New Features
·
A
new option for treating the profile parameters of special reflections has been
included in FullProf. This option works with Constant Wavelength and Time of
Flight diffraction patterns. The user may select few reflections from the
pattern to treat them in a special manner: an additional Gaussian and
Lorentzian broadening with respect to the values calculated with the resolution
parameters, as well as the shift with respect to the calculated position (from
cell parameters) can bi fitted. This situation may be found in cases of
defective materials for which the law governing the shifts and broadening is
not known in advance, or in cases of instrumental defects(slight change of
wavelength accross the pattern, etc).
At present 50 reflections per phase
and per pattern is the maximum allowed.
For using this option for a given
phase and a given pattern the user should provide the value of the variable
"Nspec_ref(iphase,n_pat)" representing the number of reflections to
be treated as "specials". This variable is given immediately after
the variable Jtyp(iphase,n_pat)"
The program expect to read (in case
of Nspec_ref /= 0) a list Nspec_ref lines containing:
hkl, nvk, D-HG^2, code, D-HL, code, Shift, code
where nvk is the number of the
propagation vector (if relevant), code
is the refinement code for the parameter. The list starts at the end of
the profile parameters for a given pattern.
The meaning of the parameters is the
following:
The Gaussian for a special reflections is calculated as:
is treated as a free parameter.
The Lorentzian for a special reflections is calculated as:
is treated as a free parameter.
The position of a special
reflections is calculated as:
Shift is treated as a free
parameter.
Example:
Case of PCR file corresponding to
the format used with a single pattern
!-------------------------------------------------------------------------------
! Data for PHASE number: 1
==> Current R_Bragg for Pattern#
1: 1.06
!-------------------------------------------------------------------------------
Myphase
!
!Nat Dis Ang Pr1 Pr2 Pr3 Jbt
Irf Isy Str Furth ATZ Nvk Npr More
6 0 0
0.0 0.0 1.0 0 0
0 0 0
5050.20 0 7 1
!
!Jvi Jdi Hel Sol Mom Ter Brind
RMua RMub RMuc
Jtyp Nsp_Ref
0
0 0 0
0 0 1.0000
0.0000 0.0000 0.0000
1 3
!
P 3 1 c <--Space group symbol
. . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . .
! Pref1
Pref2 Asy1 Asy2
Asy3 Asy4 S_L
D_L
0.00000
0.00000 0.07373 0.01902
0.00000 0.00000 0.00000
0.00000
0.00
0.00 251.00 241.00 0.00
0.00 0.00 0.00
! Special reflections:
! h
k l nvk
D-HG^2 Cod_D-HG^2 D-HL
Cod_D-HL Shift Cod_Shift
1
0 1 0
0.00000 0.000 0.04417
551.000 -0.01236 561.000
2
0 0 0
0.00000 0.000 0.03056
571.000 -0.00274 581.000
3
0 1 0
0.00000 0.000 0.00759
591.000 -0.00119 601.000
Bugs
·
A
bug concerning the generation of reflections when particular propagation
vectors of the form k=2H in centred cells has been corrected. In very special
cases some reflections were not generated and it was necessary to put nvk=-1 to
get all reflections generated. However this had, as a consequence, a bad
calculation of the magnetic moment amplitude. The workaround was to create an hkl
file to be read (irf=1) and putting back nvk=1. Now this is no more needed.
New Features
·
A
new automatic installation of the FullProf suite is available. The programs FullProf (fp2k, wfp2k), GFourier,
Fourier, WinPLOTR, EdPCR, BasIreps,
ITO, DICVOL91, TREOR, SuperCell, etc ... as well as the corresponding documentation and examples are
distributed in a single executable
installer.
·
Patterson
calculation when using profile matching modes (JBT=2,3) can be performed automatically using Fou=4 and
the program GFourier.
·
A
new value for the IRESO variable for the instrumental resolution function has
been implemented. When IRESO=-1 the program expects to read the following
variables:
U-inst V-inst W-inst
ETA-inst X-inst Y-inst
The program takes the values of FWHM
and ETA a pseudo-Voigt function (NPRO=5) deduced from the above values as:
and calculates for each reflection
the Gaussian (HG-inst) and Lorentzian (HL-inst) components of the corresponding
Voigt function using the De Keijser formula (J.Appl.Cryst. 1982, 15, 308-31).
These are added quadratically for the Gaussian and linearly for Lorentzian
components of the T-C-H (NPRO=7) pseudo-Voigt of the sample.
·
Instrumental
resolution function (IRF) files have been implemented for TOF patterns. At
present it is available for profile functions NPROF=9 (Res=5) and NPROF=10
(Res=6). When an IRF file is read, all the corresponding refinable parameters
read in the PCR file are additive, so that the refined parameters are shifts
with respect to the instrumental values.
The format of the IRF files is the
following:
First line: considered as a TITLE
All empty lines and lines starting
with "!" or "#" are considered as comments. The rest of
lines contain the following keywords and real values. The order of keywords is
irrelevant but the keywords should be written in upper case characters.
D2TOF Dtt1 Dtt2
TWOTH 2ThetaBank
SIGMA Sig-2 Sig-1
Sig-0
GAMMA Gam-2 Gam-1
Gam-0
ALFBE alph0 beta0
alph1 beta1
ALFBT alph0 beta0
alph1 beta1
Below there are two examples of IRF
files
Example of IRF file for RES=5,
NPROF=9
-----------------------------------
file starts in the next line
Instrumental resolution function of
TOF of GPPD at IPNS (Argonne)(from NBS-Si)
! Test of the IRF
for TOF in FullProf. RES=5
! This is a comment
# This is also a
comment
# IRF valid for
profile function number 9 in Fullprof
! Dtt1 Dtt2
D2TOF 7476.910
-1.540
! 2ThetaBank
TWOTH 144.845
! Sig-2
Sig-1 Sig-0
SIGMA 0.000
49.020 5.987
! Gam-2
Gam-1 Gam-0
GAMMA 0.000
7.642 0.000
! alph0 beta0 alph1 beta1
ALFBE 0.000000
0.042210 0.597100 0.009460
Example of IRF file for RES=6, NPROF=10
---------------------------------- file starts
in the next line
Instrumental resolution function of TOF of GPPD
at IPNS (Argonne)
! Test of the IRF for TOF in
FullProf. IRESO=6 Jason Hodges' TOF vs d
# IRF valid for profile
function number 10 in Fullprof
# Dtt1
D2TOF 7478.332
# Dtt1t Dtt2t
x-cross Width
D2TOT 7459.7754
19.9522 1.2640 2.3630
# TOF-TWOTH of the bank in degrees
TWOTH 144.845
# Sig-2
Sig-1 Sig-0
SIGMA 0.000
33.000 0.000
# Gam-2
Gam-1 Gam-0
GAMMA 0.000
0.000 0.000
# alph0 beta0 alph1 beta1
ALFBE 1.470500
2.483000 -0.853300 9.298000
# alph0t beta0t alph1t beta1t
ALFBT 7.387000
27.180000 4.012400 4.733000
·
A
new keyword has been introduced to modify the behaviour of the program in
relation with the generation of reflections. In one writes in the line
containing the name of the phase the word DLIM followed by the number of the
pattern and the value of a d-spacing, only the reflections having a d-spacing
greater than the provided value are used in the refinement of the data.
Example:
!---------------------------------------------
My phase name DLIM 2 2.14 DLIM 3 1.5
!Nat Dis ....
The reflections of pattern number 2
are limited to d-spacing greater than d=2.14 angstroms and those of pattern
number 3 to d-spcing greater than 1.5 angstroms. This may be useful for
magnetic structure refinement when using a diffraction pattern going far in Q
(for instance in TOF case).
Bugs
·
Some
minor bugs in the generation of CIF files have been corrected. In particular, related coordinates of type
(x,2x,z) or (x,-x+1/4,z) were output with numerical values corresponding to
(x,x,z).
·
Correction
of some bugs in calculating the background for polynomial and Debye-like
refinements before starting the refinement cycles. This was without
consequences in the refinement. This bug was introduced when the refinement of
the linearly interpolated background was implemented.