Full Year 2008
----------------------
>> 10 December 2008: New output for fou=6,-6. New option for Bac=-4. Bugs
----------------------
- Putting fou=6 the program outputs an hkl file with the following items
h k l Aobs Bobs Sigma(Fobs), where Aobs=Fobs*cos(Phase) and Bobs=Fobs*sin(Phase)
Putting fou=-6, the output is: h k l Acal Bcal Sigma(Fobs)
- The number of coefficients for the Fourier cosinus series treating the background
has been increased up to 18. Just a double line (values/codes) has to be added
in the PCR file.
- Correction of bugs in the SUM files when writing for hel=2
- Correction of a bug in EdPCR. When importing a CIF file the default
PCR file for calculated pattern was not giving a sensible 2theta range
and step, now fixed.
----------------------
>> 8 October 2008: New option for output of symmetry modes
----------------------
- If the value of p_mode(1)=2 (see note of 29 August 2008) the other
values are not needed. The program interprets this value as and indication
to output in the FST and OUT files the structures corresponding to
single irreducible representations (Irrep). All modes corresponding to
a single Irrep are combined in the FST file.
- The atom labels with more than 4 characters were not read properly.
This bug is now fixed.
----------------------
>> 30 September 2008: New IRF files added to the IRF_files directory
----------------------
- The directory IRF_files has been re-organised and new IRF files have
been included into the subdirectories. Please read the information file
readme_irf.inf inside the IRF_files folder.
----------------------
>> 21 September 2008: New version of XLENS (Version 14) and new command in PCR file
----------------------
- A new version of the program XLENS (version 14) is now distributed within the
FullProf Suite. The format of the POW file generated by FullProf when jview=12
is the same as before version 13. The new format (not yet operational in version
14) will be accessible with jview=-12.
In FullProf a new command has been added in order to create the proper CDR file
The command to be provided in the PCR file has the following format:
CONTENT El1 n1 El2 n2 El3 n3 ....
where ni (integer) is the number of atoms of the chemical species Eli (Chemical
symbol of the element). This command should appear, as other commands, between
the kewywords COMMANDS and END COMMANDS, after the name of the current phase.
CONTENT is only useful when doing a Le Bail fit in order to generate the POW and
CDR files for XLENS.
----------------------
>> 4 September 2008: New version of FullProf Studio
----------------------
- A new version of FullProf Studio (version 2) has been produced incorporating the possibility
of representing the elliptical envelope of helical structures. The manual has been also updated
and some additional examples (*.fst files) have been added to the "examples" directory of the
FullProf suite.
----------------------
>> 29 August 2008: New version of FullProf. Use of symmetry modes with AMPLIMODES.
----------------------
- A new version of FullProf has been produced incorporating the possibility
for refinement (powder, single crystals, simulated annealing) of amplitudes
of symmetry modes. The present version is:
**********************************************************'
** PROGRAM FullProf.2k (Version 4.40 - Aug2008-ILL JRC) **'
**********************************************************'
- The length of the label of an atom has been increased to 6 characters. This implies a small
change in the format of the PCR files that is transparent to the user.
- In the present version of FullProf the refinement of a crystal structure can be done
in terms of symmetry adapted modes. FullProf uses the output of the program AMPLIMODES
from the Bilbao Crystallographic Server (http://www.cryst.ehu.es/cryst/amplimodes.html)
The free parameters, instead of atom positions, are the amplitudes of symmetry modes.
The provided atom positions should not be refined. They are given as a reference of the high
symmetry (HS) phase described in the low symmetry (LS) frame.
This option is accessible by putting the variable JBT=6.
The input is exactly the same as for JBT=0, except that no refinement codes are allowed for
atom positions. This is taken into account by the program when Aut=1 (automatic mode).
If Aut = 0 it is the responsibility of the user to nullify the refinement codes of the atom
positions.
Extra input:
- The number of further parameters should be equal to the number of independent symmetry
modes (N_modes). This is, in principle, less or equal to the number of free position
parameters allowed to be refined in the conventional description of the low symmetry phase.
- After the conventional atom list (before providing the scale factor, etc ...) the
keyword: V_MODES followed by an integer (N_vector_modes) should be given. In general
N_vector_modes >= N_modes.
- A set of N_vector_modes lines should be given. In each line one should provide
the number of the concerned mode, the atom label (up to 6 characters) to which the vector
makes reference (atoms of the asymmetric unit), the label of the irreducible representation
to which belong the mode (up to 6 characters), the three components of the polarisation
vector referred to the low symmetry conventional crystallographic basis and a numeric coefficient
(normally 1.0) used for normalisation purposes.
- The above set of lines must be followed by the keyword A_MODES and the number of effective
independent modes (N_modes).
- The integer value N_modes can be optionally followed, in the same line, by a set of N_modes
integers, p_modes(1:N_modes), of values 0 or 1 for indicating the program to output files for
FullProf Studio of individual modes. If nothing is given the program assumes p_modes(1:N_modes)=0.
The files contain single modes virtual structures (codefil_n_mode_j.fst for codefil.pcr,
n:number of the phase, j: number of the mode when p_mode(j) = 0) corresponding to the presence
of a single mode. In the case of p_mode(j)=1 the codefil_n_mode_j.fst file contain the structure
of the high temperature (described in the low symmetry frame) together with an arrow description
of the atom displacements corresponding to the single mode j.
- A set of N_modes lines containing the name of the amplitude parameter (normally of the form
Qj_Label_Irrep, with j=1:N_modes) the value of the amplitude and its refinement code.
FullProf uses this extra information for calculating the effective fractional coordinates of
each atom in the asymmetric unit of the LS phase. The component k of the vector position for
the atom j, rLS(k,j), is calculated using the expression:
rLS(k,j) = rHS(k,j) + U(k,j)
U(k,j) = Sum{m=1,N_modes} ( Q(m) * vect(k,m,j) * coeff(m) )
Where rHS(k,j) is the k-component of the vector position of atom j given the list of atoms and
correspond to the high symmetry phase referred to the low symmetry basis. Q(m) is the amplitude of
the mode numbered "m", vect(k,m,j) in the k component of the polarisation vector of the
mode m for the atom j and coeff(m) is a constant coefficient provided by the user for normalisation
purposes.
In the general case coeff(m)=1, but if several symmetry modes, for instance from m=i+1
to m=i+n, belong to the same representation, Dv, we can define a vector of amplitudes for the form:
VQ = {Q(i+1), ...Q(i+n)} that may be treated as a single parameter.
If one knows the ratios between the amplitudes, so that VQ= Qv {r1,r2 .... rn} and {r1,r2,....rn} is
normalized to 1.0, the coefficients coeff(m) can be identified to the ratios. Then using the same
amplitude Qv for all the modes of the representation the coefficients are: coeff(i+j)= rj.
Of course the values of the refined amplitudes depend on the numerical values used for the components
of the polarisation vectors as well as the values provided for coeff(m). The final displacement vectors
U(k,j) in fractional units are independent of the particular values used for coeff(m) because the
amplitude Q(m) will change consequently in order to keep the appropriat product Q(m)*coeff(m).
The program generates always CFL and FST files containing the conventional description of the final
crystal structure together with single mode FST files. The standard deviations of the atoms positions
are calculated using the propagation error formula neglecting the correlation between the refined
amplitudes of the modes. The example of LaMnO3 treated using this formulation has been included
in the examples directory of the FullProf Suite (files LMO_Modes_Pbnm.pcr, LMO_Modes_Pnma.pcr, to
be used with the data file lamn_3t2.dat and file Lamn_san.pcr to be used with Lamn_san.int and
Lamn_san.spr).
The relevant portion of the PCR file corresponding to the default example given in the Web page of the
AMPLIMODES program is given below. Notice that the first amplitude (concerning only the Ba atom) is fixed
to zero because the origin is floating along z due to the polar nature of the space group.
. . . . . . . . . . . . . . . . . . . . . . . . . . .
!-------------------------------------------------------------------------------
! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 0.79
!-------------------------------------------------------------------------------
BaTiO3 FIX xyz
!
!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More
4 0 0 0.0 0.0 1.0 6 0 0 0 5 967.370 0 7 0
!
A m m 2 <--Space group symbol
!Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes
Ba1 BA 0.00000 0.00000 0.00000 0.47643 0.25000 0 0 0 1 # color grey conn TI O 0.0 2.2
0.00 0.00 0.00 151.00 0.00
Ti1 TI 0.50000 0.00000 0.50000 0.24156 0.25000 0 0 0 2 # color green poly Ti1
0.00 0.00 0.00 161.00 0.00
O1_2 O 0.00000 0.00000 0.50000 0.58601 0.25000 0 0 0 3 # color cyan
0.00 0.00 0.00 171.00 0.00
O1 O 0.50000 0.25000 0.25000 0.51687 0.50000 0 0 0 3 # color cyan
0.00 0.00 0.00 181.00 0.00
! Polarisation Vectors of Symmetry Modes for each atom
V_MODES 8
! Nm Atm Irrep Vx Vy Vz Coeff
1 Ba1 GM4- 0.000000 0.000000 0.176512 1.00000
2 Ti1 GM4- 0.000000 0.000000 0.176512 1.00000
3 O1 GM4- 0.000000 0.062406 0.062406 1.00000
3 O1_2 GM4- 0.000000 0.000000 0.124813 1.00000
4 O1 GM4- 0.000000 -0.088256 0.088256 1.00000
4 O1_2 GM4- 0.000000 0.000000 0.000000 1.00000
5 O1 GM5- 0.000000 -0.062406 -0.062406 1.00000
5 O1_2 GM5- 0.000000 0.000000 0.124813 1.00000
! Amplitudes of Symmetry Modes
A_MODES 5 1 1 1 1 1
Q1_GM4- 0.000000 0.000000
Q2_GM4- 0.098947 21.000000
Q3_GM4- -0.085383 31.000000
Q4_GM4- -0.120367 41.000000
Q5_GM5- -0.006086 51.000000
!-------> Profile Parameters for Pattern # 1
! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model
4.0008 0.00000 0.00000 0.00000 0.00000 0.00000 0
11.00000 0.000 0.000 0.000 0.000 0.000
! U V W X Y GauSiz LorSiz Size-Model
0.176029 -0.197814 0.091459 0.000000 0.030062 0.000000 0.000000 0
. . . . . . . . . . . . . . . . . . . . . . . . . . .
---------------------
>> 19 June 2008: New version of XLENS (Version 13)
----------------------
- A new version of the program XLENS (version 13) is now distributed within the
FullProf Suite. There is a change in the format of the POW file generated
by FullProf in order to fit the changes in XLENS. Beware this change makes the
use of older versions of FullProf incompatible with the new XLENS format.
See documentation
----------------------
>> 30 April 2008: New version of the FullProf Suite for Windows, Linux and MaC OS.
----------------------
- The complete FullProf Suite has been uptdated and some programs modified slightly
in order to simplify the use of different Fortran compilers (g95, gfortran, Intel,
Lahey-Fujitsu and AbSoft) in different platforms (Windows, Linux and MacOS).
The Web page of the FullProf Suite has been simplified.
Please communicate any error found in the use of the different programs.
Warning:
In the Mac OS version some GUIs are not yet working but all the console programs are
OK. In particular GBond_Str and GBasIreps crash. The corresponding console programs
Bond_Str and BasIreps work without problem.
- Strong changes in WinPLOTR-2006 for reading 2D detectors and improving OpenGL access.
- A GUI for XLENS is now distributed within the FullProf Suite.
- New documentation for some programs: DataRed and XLENS
- Internal changes in FullProf for improving the output of PRF files, handling
polarised neutrons data treatment, etc.
The new version of FullProf has been updated to:
**********************************************************'
** PROGRAM FullProf.2k (Version 4.30 - Apr2008-ILL JRC) **'
**********************************************************'
----------------------
>> 22 March 2008: Modifications in CIF output and in WinPLOTR. New version of FullProf.
----------------------
- An output in CIF format with calculated distances and angles are now produced
by FullProf when CIF file (Rpa=-1) and distance/angle calculations are asked (Jdi=3).
- The Windows version of WinPLOTR is able now represent distances as a function of
temperature after a sequential refinement. A new item in the dialog box of WinPLOTR
opened when the button CYC is pressed asks for a visualisation of the distance results
at the end of the sequential FullProf refinement.
- Some minor improvements, and correction of small bugs, have been introduced in
WinPLOTR-2006, FullProf and EdPCR
- Internal changes improving the detection of bad input data have been introduced
in the new version of FullProf that has been updated to:
**********************************************************'
** PROGRAM FullProf.2k (Version 4.20 - Mar2008-ILL JRC) **'
**********************************************************'
----------------------
>> 14 February 2008: SEQ files can now be rewritten
----------------------
- The SEQ file generated during a sequential refinement when Rpa=-2 has the
attribute: position="append". The subsequent sequential refinements using the
same name code for the PCR file were adding the new results at the end of the
previous SEQ file. This behaviour can be changed (complete rewrite of the
file) by putting Rpa=-3. The program changes to Rpa=-2 once the paremeters
of the first file have been output to the SEQ file. The final PCR has the
value Rpa=-2, if one wish to restart from the scratch another refinement
do not forget to put by hand Rpa=-3.
- The keyword "cyc" for invoking the sequential refinement by FullProf can now
be replaced by the more appropriate "seq" keyword. Both keywords are case
insensitive.
----------------------
>> 7 February 2008: Bugs of WinPLOTR-2006 and FullProf corrected
----------------------
- The latest version of WinPLOTR-2006 was wrong when reading PRF files with Prf=-3
and the number of reflections was smaller than the number of points in the pattern
(the normal case!). I introduced the bug the 18 January 2008 to allow the automatic
handling of k_search from WinPLOTR-2006. This produced an "access violation" error.
Moreover, FullProf was not exporting the cell parameters and space group to the
PRF when Prf=-3.
These two issues are corrected now.
----------------------
>> 2 February 2008: Changes in WinPLOTR. Bug corrected when more than one Z-matrix
----------------------
- The Windows version of WinPLOTR is now able to open several SEQ files in order to
plot heterogeneous data. This is particularly useful when the analysis of diffraction
data as a function of temperature uses different phases for different temperature
intervals. The user can open a SEQ file, select the parameters he/she wants to plot
and then open another SEQ file, select the parameters, and so on. At whatever moment
the "Select Files" item in the "File" menu can be invoked for selecting parameters to
to be plotted. WinPLOTR can also export the data as multicolumn files of extension *.xyy
or *.xyn that can be read by external programs like KaleidaGraph, Origin, SigmaPlot,
Excel, etc.
- A bug has been corrected in the Z-matrix option of rigid body description. The program
showed an "access violation" error when more than one Z-matrix was used in a single
phase. Now the simulated annealing option with different Z-matrices works properly.
The other formulations of rigid bodies were not affected.
----------------------
>> 20 January 2008: Changes in Bond_Str and GBond_Str.
----------------------
- The program Bond_Str can now calculate a Bond-Valence Map if the instruction
"MAP nx ny nz ATName drmax" is included in the CFL file. This can be done
by using the new string field in the GUI GBond_Str reserved to this command.
The integer values nx,ny and nz represent the number of divisions along a,b,c
for the calculation grid. ATName is the chemical symbol of the ion used as
a point probe (it must be in the list of chemical species of the given asymmetric
unit) and drmax is the maximum distance for calculating the bond-valence sums.
The resulting map can be visualised by GFourier. These calculations correspond
to those performed by the program VALMAP (J. Gonzalez-Platas et al. J. Appl.
Cryst xxxxxxxxxx).
- A bug in the CFL file output by the latest version of FullProf (for doing distance,
angle and BVS calculations) has been corrected.
This bug was a side effect of a change (with a copy/paste mistake) in the library
CrysFML. The automatic calculation of distances was impossible.
----------------------
>> 18 January 2008: Changes in *.prf files to run k_search from WinPLOTR-2006
----------------------
- The output files *.prf have now in the first line (title) information about
the cell parameters and space group of the first phase. This information is used
by WinPLOTR-2006 in order to prepare an input file for the program "k_search".
WinPLOTR-2006 has now a new item in the menu Calculation/Peak Detection. The
new item is called "Satellite Detection" and is enabled when a PRF file is on
the screen. Selecting this option the program is instructed for searching peaks
in the difference diagram yobs-ycalc, so that satellites can be dectected. After
removing spurious satellites and manually introducing undetected peaks the whole
can be saved as a k_search input file. The program can then be run automatically.