Tabulated variation
of Alpha/Beta decay parameters in TOF
New Features
·
A
table with the values of the decay parameters Alpha and Beta as a function of
d-spacing can now be given in the Instrumental Resolution Function file for TOF
when Res=5 using the profile function Npr=9. The program calculates the value of Alpha and Beta for each
reflection by linearly interpolating the list of given values. A maximum of 100
points is allowed. The keyword for introducing the list is: LISTALFBET followed
by the number of points (NPo). After this line the program reads NPo lines
containing three real values: the d-spacing Alpha and Beta. This procedure
allows the treatment of moderators that cannot be modelled easily using a
back-to-back exponential, convoluted with a pseudo-Voigt function, having a
dependence of their decay parameters of the form:
Alpha=Alpha0+Alpha1/dsp
and Beta=Beta0+Beta1/dsp^4
An example is given below:
............. omitted lines
!
Gam-2 Gam-1 Gam-0
GAMMA
0.000 4.937 0.000
!
alpha beta
LISTALFBET
24
0.4277
0.580207 0.935069
0.4508
0.550432 0.762171
0.4709
0.526999 0.644441
0.4878
0.508716 0.562862
0.5023
0.494028 0.503393
0.5206
0.476688 0.439694
0.5437 0.456394
0.373471
0.5671
0.437566 0.319440
0.5903
0.420400 0.275896
0.6206
0.399880 0.230396
0.6609
0.375457 0.184648
0.7043
0.352329 0.148817
0.7809
0.317792 0.106979
0.8554
0.290103 0.081954
0.9017
0.275216 0.071148
1.0412
0.238344 0.050993
1.1044
0.224713 0.045555
1.2098
0.205134 0.039299
1.3526
0.183477 0.034180
1.5618
0.158896 0.030199
1.6313
0.152131 0.029381
1.9128
0.129738 0.027355
2.7052
0.091739 0.025649
3.1237
0.079448 0.025400
END
Shift to these values can always be fitted
provided the shifts verify the dependency versus d-spacing described above for
the function Npr=9. The parameters that can be refined are
D_Alpha0,D_Beta0,D_Alpha1,D_Beta1, where the prefix "D_" stands for
the shifts.
Change of the name
of integrated intensity cluster files
·
The
name of the file containing generated integrated intensity clusters after a run
of FullProf in which More=1 and Jvi=11 (useful for simulated annealing) has
been changed to avoid incompatibility with WinPLOTR. When WinPLOTR runs
FullProf, after selecting a PCR (or NEW) file, looks for input data files
(*.dat, *.hkl, *.int ...) if it finds a file with the extension "int"
having the same code (with a numeric suffix) as the PCR file will send to
FullProf a wrong input data file. The name is now of the form:
"codefile"n_cltr.int. Where "codefile" stands for the name
of the PCR file and "n" is the number of the phase. The suffix
"_cltr" (cluster) indicates that the file has been generated by
FullProf. It can be changed (if wished) for using the file as input for
Simulated Annealing.
Correction of bugs
in magnetic phases in EdPCR Program
Bug
·
Long
standing bugs in the edition of magnetic phases have been corrected in EdPCR.
In particular the writing in bad fields (anisotropic thermal parameters) of
magnetic parameters. The edition of symmetry operators and basis functions of
irreducible representations of the propagation vector group has also been
corrected.
The bug consisting in the modification of the
number of propagation vectors when passing through the constraints windows has
also been fixed. There are still other bugs that will be corrected
progressively. Workarounds are always possible by editing the PCR file using the
text editor of EdPCR.
Note: In some cases EdPCR quits suddenly
(giving or not an error message) after clicking in a button. This normally
occurs on XP when EdPCR has been invoked from WinPLOTR. We do not know what is
the cause of this extrange behaviour. If the user experiments this problem, a
workaroung is to invoke EdPCR by clicking on it, from a link on the desktop or
from the command line. Please inform me in what circumstances this behaviour
occurs
Improvements in
running FP_CYC from WinPLOTR
New Features
·
Several
changes and additions have been performed for running FullProf in sequential
mode. Additional information, in particular for plotting the behaviour of
individual reflections coming from Le Bail fits of many files treated in
sequential mode, can be found in the news of WinPLOTR.
1.
Concerning
"fp2k", the argument giving the code for the data (datcode) files
(can be now extended with an extension (ext) that may be different of
".dat". For instance the third argument can be of the form
"datcode.xy", where ext=".xy" is the extension of the data
files. The extension can also be given in the dialog box of WinPLOTR.
2.
Two
kind of formats for the names of the data files are now accepted. In the first
one the names of the data files are of the form:
"datcode<n>ext", where "<n>" is an integer
number and "ext" is the extension of the data files (by default
".dat"). The length of the names is variable. The second format for
the names has a fixed length and it is of the form: "datcode<000xxx>ext",
where <000xxx> is an integer with zeroes on the left to complete a fixed format. This
format can have a maximum of 9 digits, the program determines the format
automatically from an analysis of the existing first file.
For instance, invoking FullProf from the
command line (or from WinPLOTR) as:
> fp2k cyc my_pcr
datcode.uxd 23 268 y
n y
The program will select ".uxd" as
extension of the data files. Moreover the program will determine if the file
"datcode23.uxd" exist or not. In the case the file is found, the
program assumes that the length of the names is not fixed (first format) and will treat the
files from "datcode23.uxd" up to "datcode268.uxd" even if
there is some lacking files in between. In the case the file is not found the
program will try to find files with names of the form
"datcode00...23.uxd", once a file, for instance
"datcode0023.uxd", is found the program assumes that all the other
files have the same length, so the final file must be
"datcode0268.uxd". The from the last sequence "y n y", the
program will save the ".prf" and ".mic" and will discard
".hkl" files.
Basis vectors of
IrReps and Fp_Studio
New Features
·
The
current version of FullProf has been updated to:
**********************************************************
** PROGRAM FullProf.2k (Version 3.40 -
Nov2005-LLB JRC) **
**********************************************************
·
In
the current version of FullProf the FST file generated when the magnetic structure
is described using basis vectors of the irreducible representations of the
propagation vector group is now adequate for visualising the magnetic
structure. FullProf converts the basis functions provided by BasIreps to
Fourier coefficients readable by Fp_Studio. This is done even in the case where
the MSYM-like representation of the symmetry is not appropriate.
·
A
convergence condition has been implemented for Le Bail fits. Until now no
convergence condition was applied as soon as a phase was treated using
abs(Jbt)=2, so that the program runs for the prescribed number of cycles even
if no improvement was produced. At present,
the convergence condition is that the programs stops doing cycles if the
difference between successive Chi2 values is less than 1.0E-3.
Bug in magnetic
structure factor when using Isy=-2
Bug
·
A
bug has been corrected when using magnetic incommensurate structures
calculations and basis functions coming from symmetry analysis with BasIreps.
The bug was only for the case of using Isy=-2: numeric form of complex basis
vectors. Internally the calculation of the Fourier coefficients was done using
the complex conjugate of the basis vectors instead of the basis vectors
themselves. This has been corrected in the current version of FullProf. This
error does not affect the case of Isy=1,-1: direct use of Fourier coefficients
and MSYM operators deduced from the same basis functions (alphanumeric symbols
describing Fourier coefficients in BasIreps). Of course for Isy=-2 but with no
complex components the calculation was correct in the previous version.
·
The
FST file for FullProf Studio when JBT=5 was wrong. A phase factor was with the
wrong sign in generating the Fourier coefficients. This has been corrected in
the current version of FullProf.
Warning
Remember
that, when a magnetic structure is described in two different phases (for
instance if there are two propagation vectors), the user must edit the FST file
and merge the two magnetic phases in a single one. Otherwise the propagation
vector of the first phase is attributed wrongly to the second phase.
Manual for flipping
ratio refinements
New Features
·
The
current version of FullProf has been updated to:
**********************************************************
** PROGRAM FullProf.2k (Version 3.30 -
Jun2005-LLB JRC) **
**********************************************************
·
Some
improvements for the output of *.fst files have been introduced. The output was
not complete when using numeric form for symmetry operators and pure magnetig
phase in single crystal refinements.
·
A
manual describing the use of FullProf for flipping ratio refinements has been
included in the FullProf Suite. The document is called Flipping_Ratios_in_FullProf.pdf and it is included in the
"docs" subdirectory of the FullProf_Suite directory.
Correction of a
recent bug in generated sub-profiles
Bug
·
In
the current version of FullProf there was an error in generating sub-profiles.
This does not affected any important calculation, only the output of the
profiles corresponding to the different phases (for plotting purposes) was
wrong. This was due to an internal re-arrangement. Now the *.sub files are
correct. Sorry!
·
The
output CIF file, containing the profile and structure factors for powder
patterns, has also been improved and corrected.
Correction of a bug
in generation of atom multiplicities
Bug
·
In
the current version of FullProf there was an error in calculating
multiplicities of atom sites in some particular circumstances. This affected
only quantitative analyses if ATZ was generated automatically. This error was
introduced in the latest version due to an internal change in the libraries:
the setting up of an "epsilon" value was not properly done due to the
move of a particular subroutine to another module. The bug has been fixed.
Sorry!
Correction of a bug
in satellite option of rigid bodies
Bug
·
In
the current version of FullProf there was an error, appearing only in some ircumstances,
for the satellite groups in rigid bodies. ometimes the second reference atom
was not properly detected. This was due to a change from the function nearest
integer (NINT) to integer (INT).This has been corrected now coming back to the
correct expression.
New version of
Bond_Str
New Features
·
The
current version of FullProf has been updated with a new internal version of the
program Bond_Str. The stand-alone program Bond_Str has also been updated and a
new GUI is also available. In the previous version the calculation of
bond-valence sums were performed using the worse bond-valence parameter of the
file "bvpar.cif". This was an error of mine! When there were several
(d0,B0) sets corresponding to the same cation-anion species I selected the last
set ... just the worse! as written in the header of the "bvpar.cif"
file. This has been corrected in the current new version.
·
A
small program to prepare Rigid body objects for FullProf is now provided within
the FullProf suite. See note of
d:\my_prompt>
mol_tpcr myfile
where "myfile.cfl" is a previously
existing file in wich the molecule(s) to be read is(are) written. The main use
of this program is to prepare internal coordinates of a rigid group when one
knows a crystal structure where this group is present. The internal coordinates
are independent of the crystal structure and can be ported to a new unit cell
for purposes of solving a new crystal structure by positioning known groups.
An example of such a file, it can be used for
testing purposes, is given below
------------------ start File: urea.cfl
-------------------------------------------
!
! Example of molecule given in a crystal
!
!
CELL
5.584001 5.584001 4.688990
90.0 90.0 90.0
!
MOLEX
8 Urea F
!
Xc Yc Xc Phi
theta Chi TypeAngles TypeThermal
0.00000 0.50000
0.32811 0.0 0.0
0.0 P ISO
0
0 0 0 0
0 !Refinement codes
!Atm Spe x
y z N1
N2 N3 Biso
Occ
Ur1 C
0.00000 0.50000 0.32811
0 0 0
0.50000 1.00000
Ur2 O
0.00000 0.50000 0.59574
0 0 0
0.50000 1.00000
Ur3
N 0.14466 0.64466
0.17816 0 0
0 0.50000 1.00000
Ur4
N -0.14466 0.35534
0.17816 0 0
0 0.50000 1.00000
Ur5
H 0.14261 0.64261 -0.03550 0 0 0
0.50000 1.00000
Ur6
H 0.25589 0.75589
0.28398 0 0
0 0.50000 1.00000
Ur7 H
-0.14261 0.35739 -0.03550 0 0 0
0.50000 1.00000
Ur8 H
-0.25589 0.24411 0.28398
0 0 0
0.50000 1.00000
! x(P1) y(P1)
z(P1) x(P2)
y(P2) z(P2) x(P3)
y(P3) z(P3)
XYZ_Frame
0.00000 0.50000 0.59574
1.00000 0.50000 0.32811
0.00000 0.50000 0.32811
!
------------------ End File: urea.mol
-------------------------------------------
The meaning of the keyword CELL and other
parameters are obvious from the given names.
The keyword MOLEX must be followed by the
number of atoms in the molecule, the name of the molecule and the kind of
coordinates provided below (F: for fractional coordinates with respect the the
given cell, C: cartesian, Z: for Z-matrix or S: for spherical coordinates )
The parameters Xc, Yc, Zc are the fractional
coordinates of the origin of the internal Cartesian system with respect to the
given unit cell.
The angles Phi,Theta and Chi are Euler angles
(two types, P: Phi and Theta are the polar spherical angles of the Z-axis of
the Cartesian internal frame with respect to the Cartesian frame attached to
the unit Cell, E: conventional Euler angles).
The keyword "XYZ_Frame" is followed
by the fractional coordinates of three points in the unit cell. These three
points will serve to position the molecule in the crystal and to calculate the
centre and Euler angles. The origin of the Cartesian internal system will be
put in the third given point. The z-axis is parallel to the vector P1-P3, the
x-axis lies within the plane (P1-P3,P2-P3), and the y-axis completes the direct
frame.
The numbers N1,N2,N3 are integers defining the
connectivity of the molecule as it is conventional in the Z-matrix formulation.
If all of them are put to zero, the program will generate automatically a
connectivity table taking the first atom as the origin, the second along
"x" and the third in the x-y plane. This internal Cartesian frame
will be put
New version of
FullProf. User given Form-factors and ADPs
New Features
·
The
current version of FullProf has been updated to:
**********************************************************
** PROGRAM FullProf.2k (Version 3.20 -
Feb2005-LLB JRC) **
**********************************************************
·
The
note of
·
A
new option for atomic types has been added. Putting n_t=5 for an atom or object
(SASH,...), it is supposed that the form factor is like that of n_t=4 but
additional ADP are read after the normal reading for n_t=4. This allows the use
of anisotropic temperature factors in calculating flipping ratios or structure
factors of complex object described by different kinds of form factors. Two
additional lines (one with beta11, beta22, ... and the other with the
corresponding codes) are read for an atom after the reading of form factor
coefficients.
·
The
calculation of errors in microstructural parameters are now propagated in order
to give the estimated errors of size and strain values along different
crystallographic directions. The sigmas appear in files *.siz and *.str that
can be obtained by putting JVI=5.
Bug
·
A
bug concerning the absorption correction of powder patterns treated in
integrated intensity mode has been corrected. The absorption correction when
IRF=4 and IPOW=2 was not applied. This has as a consequence that, in cases of
non-negligible absorption, the magnetic moments obtained when using simulated
annealing were lower than those obtained when using the Rietveld method. Now
the INT file generated after a Le Bail fit (Jbt=2 and Jvi=11) includes the muR
coefficient for absorption correction.
A new section in
the PCR file for putting commands
New Features
·
A
bug concerning restraints has been corrected. If there was no distance
restraints, angle restraints were not applied. Now angle restraints are applied
even if no distance restraint is given.
·
New
commands to facilitate the refinement strategy are available. Using the
automatic mode (Aut=1) and the COMMANDS instruction explained in the note of 15
January, the new extensions of VARY and FIX are as follows. Within an
instruction VARY of an instruction FIX individual parameters of selected atoms
are allowed.
The available structural parameters are
"x_", "y_", "z_", "xyz_" and
"b_". The names of the selected atoms must be identical to those
given in the list of the asymmetric unit (The instructions are case sensitive).
As usual the instructions are applied as they appear. For instance a FIX
instruction after a VARY may suppress a refinement code. For instance the list of commands,
appearing just after the phase name, given below
COMMANDS
VARY
xyz_Fe xyz_O1
VARY
x_Mn1 z_O27 y_Ho1 b_Al
FIX
b_Mn1 x_C23
END COMMANDS
tells to the program that it should refine all
positional parameters of atoms Fe and O1, the "x" coordinate of Mn1,
the "z" coordinate of O27, the "y" coordinate of Ho1 and
the temperature factor(s) of atom Al. If Al is anisotropic all beta-parameters
compatible with the site symmetry are refined. The instruction FIX avoid the
refinement of the thermal parameters of Mn1 and the "x" coordinate of
atom C23.
Introduction of
some facilities to treat layered structures
New Features
·
A
section for commands has been introduced in the PCR file. A part of using the
string containing the name of the phase for passing keywords and command, it is
now possible to include up to 20 commands per phase. These commands are given
starting with keywords. The command section for each phase starts after the
name of the phase with the word COMMANDS and ends few lines below with the
words END COMMANDS. In the middle one can give commands/keywords instructing
the program for different purposes (VARY,DLIM, etc...). This works only in the
automatic mode.
·
(Updated,
Among the available commands, the keywords
LAYER_A, LAYER_B and LAYER_C are used to tell the program that the current
phase will be treated as a single layer, so the reflections (H00),(0K0) or
(00L), respectively, will be suppressed and the atom coordinates will be given
in angstroms along the corresponding direction.
Considering an artificial (quasi-empty)
supercell cell with a very long axis in the perpendicular direction to the
layer, the 3D diffraction pattern approach to that of the single layer
diffraction pattern without need of integrating the rods in reciprocal space.
To eliminate the ripples a long axis together with a special broadening is
enough. The method is based in the idea developed by K. Ufer et al.(Z.
Kristallogr. 219, 519 (2004)) making the method perfectly compatible with the
Rietveld method.
The keywords LAYER_A, LAYER_B and LAYER_C must
be followed by the order of the supercell used, as in:
COMMANDS
LAYER_C 15
.....
END COMMANDS
This means that corresponding supercell
parameter (as given in the unit cell line) is c=15*cs, being cs the c-parameter
of the subcell. This is needed to conserve the (0,0,l=L/15) reflections that
are treated separately. This option is still at a testing stage. A complete
account will be given as soon as possible.
The program
Bond_Str is now available as stand alone application
New Features
·
A
program for calulating distance and angles of a crystal structure as well as
the bond valence sums for all ions is now available within the FullProf Suite.
The program can also be obtained independently of the whole package just from
the following ftp area:
ftp://ftp.cea.fr/pub/divers/Bond_Str
http://valmap.dfis.ull.es/fullprof
There are two programs: Bond_Str.exe and
GBond_Str.exe. The first one performs the calculations and the second one is
just a GUI for running the first or to import files. The calculation is the
same as that already performed within FullProf, however the advantage of the program is
that it can be used to read CIF files and make the calculations without running
FullProf. The input file can be a CIF file or a CFL file. For details read the
manual Bond_Str.pdf or Bond_Str.htm.