Full Year 2014
----------------------
>> 6 December 2014: New version of FullProf. Change in FullProf for calculation of ATZ.
---------------------- Random crashes. New Get_Data.
- The Windows executables of FullProf (wfp2k.exe and fp2k.exe) in the distribution from
the first december were corrupted by linking with a bad version of the CrysFML library
and this produced random crashes of the programs. This has been corrected in the current
version that has been updated to:
**********************************************************'
** PROGRAM FullProf.2k (Version 5.50 - Dec2014-ILL JRC) **'
**********************************************************'
- A change in FullProf has been performed for recalculating ATZ after refinement of
ocupation factors and re-writing the new PCR file. This allows to determine the amount
of different phases automatically when the composition is changing as a function of
temperature (or an external paramter) and a sequential refinement is being performed.
- New changes in Get_Data (see the instructions running Get_Data without arguments).
----------------------
>> 23 November 2014: Correction of a subtle bug in FullProf when Nor=1 and
---------------------- a centre of symmetry was explicitly given in a magnetic phase
- When Nor=1 was selected and a symmetry operation representing a center of symmetry
(e.g. SYMM -x,-y,-z) was present explicitly in the list of operations of a magnetic
phase the preferred orientation was wrongly calculated (half the true value) producing
a change in the value of the magnetic moment that was higher by a factor of sqrt(2).
The bug was introduced in the version of March 2014 as a side effect of large modifications
in the symmetry procedures of the library CrysFML. This has now been corrected.
(Thanks to Peter Georgiev for signaling this bug).
----------------------
>> 18 November 2014: Mixing rigid bodies with special form factors
----------------------
- In the present version of FullProf it is now possible to mix special form factors for
"free atoms" in the rigid body option of FullProf Jbt=4. There is an important change
in the format for free atoms that is incompatible with the previous format. Free atoms
were assumed implicitly as type=2 (N_t=2, anisotropic temperature factors), now the
value of N_t should be provided after the occupation factor, if it is not given then
N_t=0 and the free atom is considered as isotropic. An error in reading old PCR files
will occur but can be easily changed by removing the anisotropic temperature factor
lines (in case of real isotropic model) or by adding the number "2" after the position of
the occupation factor and then keeping the anisotropic temperature factor lines.
The value of N_t can now be used as in Jbt=0: N_t=0 (isotropic), N_t=2(anisotropic)
N_t=4 (special form factor, e.g. SPHS or SASH with isotropic temperature factors) or
N_t=5 (as N_t=4 plus additional lines for anisotropic temperature factors of the object).
In EdPCR only the option N_t=2 is handled.
- Minor changes in WinPLOTR-2006
----------------------
>> 22 October 2014: Interoperation with the program VESTA. Correction of small bugs
----------------------
- The program VESTA has been included in the FullProf toolbar to be invoked directly.
For proper use from the toolbar the executable of VESTA should be entered in the
appropriate place on the toolbar settings. VESTA should be installed previously
and the executable should be searched with the corresponding "Browse" button on the
"Settings" dialog of the toolbar and saved by clicking on "Save settings" button.
The VESTA button on the toolbar operates on CIF files. If there is a file with the
loaded "Code File" and extension "cif" the file is opened directly. You may open
from VESTA the mCIF files generated by FullProf for conmensurate magnetic structures.
VESTA can downloaded from: http://jp-minerals.org/vesta/en/
- Binary files for VESTA (extensions *.pgrid/*.ggrid) are now produced automatically by
Fourier and by FullProf (strain and size shapes) and can be visualized with VESTA.
You may combine volumetric data (density) with structural data by importing structural
data (Edit->Edit Data->Structure Parameters ...) if density data are already loaded
or viceversa (Edit->Edit Data->Volumetric Data ...).
- Changes and corrections in WinPLOtr-2006, Get_Data, Toolbar and FullProf (mCIF file)
have been performed.
----------------------
>> 4 September 2014: New mCIF file generated by FullProf, New Get_Data and mCIF_to_PCR
----------------------
- Get_Data is now able to work with the new files of D20 at ILL. Two new instructions
have been included: normalization with time and a global zero-shift. See the instructions
by invoking in a console get_dat without arguments.
- The magnetic CIF syntax is still evolving. The program mCIF_to_PCR is now able to
read the mCIF files generated by ISOCIF and by the Bilbao Crystallographic Server
applications. The P1 mCIF file generated by FullProf is now according to the latest
syntax of magnetic CIFs.
----------------------
>> 1 July 2014: Protection in Simulated Annealing jobs and new console utilities
----------------------
- Simulated annealing with powders was not working in the last version of FullProf for
non-magnetic crystal structure solution if there was no code (or if it was equal to zero)
after the sigma of integrated intensities in the input intensity file. A protection has
been implemented to avoid NaN is scale factors.
- The Windows executable console program CrysCalc.exe (written by Thierry Roisnel and available
in the CrysFML repository: http://) has now been included in the FullProf Suite. Notice that
there is a "c" as the last character of the executable name, contrary to the existing program
CrysCal.exe that is a GUI for other programs. The documentation of CrysCalc is accessible
via the toolbar of the FullProf Suite or from the command line when executing CrysCalc.
----------------------
>> 19 June 2014: Restoring the use of the old way of invoking TOF data in sequential mode.
----------------------
- The modification performed the 2 April had as a consequence a side effect making the multiple
patterns within a single file (e.g. TOF with multiple banks) not working in sequential mode.
This has been corrected and now the new way of working with different files (X-ray and neutrons)
for each temperature is also working without disturbing the previous protocol.
(the note of 2 April has been changed slightly)
Now the invoking protocole:
[w]fp2k seq tbmo multi_pattern 1 7 y y y y y n
means exactly what is described in note of 2 April.
The protocole:
[w]fp2k seq tbmo my_codefile 1 7 y y y y y n
used for a multiple pattern refinement, means that the names of the data files within the PCR file
have all the same name (for instance my_codefile1.gss for the first temperature) and will be
incremented for the next temperature (e.g. my_codefile2.gss).
----------------------
>> 7 June 2014: Correction of bugs and small improvements.
----------------------
- Simulated annealing with powders was not working in the last version of FullProf. The multiplicity
was set unadvertently equal to 1 always at the moment of reading integrated intensites. This is
now corrected
- Some cuts of the output text concerning lattice translations in BasIreps have been corrected.
- The length of some strings in WinPLOTR-2006 has been augmented in order to avoid crashes when
working on very deep directories giving rise to very long pathes.
- FullProf stops now when incongruent data is input concerning a single pair (k,-k) of propagation
vectors. For instance if the user provides Nvk=1 and k is not equivalent to -k. In this last case
Nvk should be equal to -1
----------------------
>> 15 May 2014: New option for special reflections in FullProf. Magnetic structure factors in
---------------------- single crystal work. Correction of a bug introduced in February 2014.
- When special reflections are used four new items are read: Delta_U/Sig1, code, Delta_Y/Gam2, code.
Delta_U/Sig1 corresponds to an additional contribution to Gaussian strain of the reflection and
Delta_Y/Gam2 corresponds to an additional contribution to Lorentzian size of the reflection.
Sig1 and Gam2 make reference to TOF notation for Gaussian and Lorentzian parameters for the width parameters.
These terms are now taken into account for microstructure calculations. They cannot be refined
simultaneously with D-HG^2 or D-HL. This provides more flexibility for treating complicated situations
in which a series of reflections behave differently than others. For instance for the cases in
which superstructure reflections are broader than fundamental reflections (due to a shorter correlation
length - size effect) and there is no simple way to separated them with a simple formula depending on hkl.
The maximum number of special reflections has been increased to 200 per phase.
An example of line in the PCR file containing few special reflections, for which a single additional
Lorentzian size parameter is used, is given below:
! Special reflections:
! h k l nvk D-HG^2 Cod_D-HG^2 D-HL Cod_D-HL Shift Cod_Shift Del_U/sig1 Code Del_Y/gam2 Code
0 0 1 0 0.0000 0.000 0.00000 0.000 0.00000 0.000 0.00000 0.000 2.59057 31.000
0 0 2 0 0.0000 0.000 0.00000 0.000 0.00000 0.000 0.00000 0.000 2.59057 31.000
1 0 0 0 0.0000 0.000 0.00000 0.000 0.00000 0.000 0.00000 0.000 2.59057 31.000
1 0 1 0 0.0000 0.000 0.00000 0.000 0.00000 0.000 0.00000 0.000 2.59057 31.000
1 0 2 0 0.0000 0.000 0.00000 0.000 0.00000 0.000 0.00000 0.000 2.59057 31.000
1 1 0 0 0.0000 0.000 0.00000 0.000 0.00000 0.000 0.00000 0.000 2.59057 31.000
0 0 3 0 0.0000 0.000 0.00000 0.000 0.00000 0.000 0.00000 0.000 2.59057 31.000
1 1 1 0 0.0000 0.000 0.00000 0.000 0.00000 0.000 0.00000 0.000 2.59057 31.000
. . . .
- In the output file of FullProf, when working with single crytals, the complex Magnetic Structure
Factor and Magnetic Interaction vectors are now output systematically, together with the reflection
indices, observed and calculated intensities (square of the Magnetic Interaction vector), extinction,
etc. This gives rise to lines of more than 270 characters.
- A bug concerning the checking of equivalence of propagation vectors in centred lattices and special
values of the components has been corrected in FullProf. This was a consequence of extensive changes
in CrysFML in February 2014 (see note of 15 February 2014) that neglected the explicit symbol provided
by the user of the lattice centring in FullProf.
----------------------
>> 10 April 2014: Correction of a bug in Get_Data in reading D1B data from the ILL database
----------------------
- An error was introduced in the last version of Get_Data when trying to read very old data from
the ILL database concerning the instrument D1B. The new format was not recognised!. Now this
has been corrected.
----------------------
>> 2 April 2014: Sequential mode for multiple patterns has been implemented in FullProf
----------------------
- Up to now the built-in sequential mode of FullProf was working only with a single
diffraction pattern per temperature. Now the use of the DATA file code name "multi_pattern"
indicates that the actual names of the multiple patterns are specified within the PCR file.
The restrictions for the names of the multiple patterns are the following:
1: The names should be written as a codename finishing with an underscore and an integer
number like "codename_nnn.extension" (without quotes)
2: Each pattern type may have its own codename and number
3: No gap can exist in the sequence of data files. Starting with the integer number "n"
(e.g. codename_n.extension) the program will re-write the PCR file for the next temperature
using the same codename, underscore and extension but replacing the integer "n" by "n+1" and
the constructed name should exist as a valid data file.
- As an example, the command line for invoking the program with initial PCR file "tbmo.pcr"
for seven temperatures should be of the form:
[w]fp2k seq tbmo multi_pattern 1 7 y y y y y n
(see note of 25 September 2013 for a full explanation of the syntax of the command line
invoking FullProf in sequential mode)
The PCR file should contain the appropriate names of the data files. For instance:
.....
!File names of data(patterns) files
TbMo_neutrons_23.dat
TbMo_xrays_48.dat
......
FullProf will re-write the new PCR file with the following names:
.....
!File names of data(patterns) files
TbMo_neutrons_24.dat
TbMo_xrays_49.dat
......
And will finish the last case with the names:
.....
!File names of data(patterns) files
TbMo_neutrons_29.dat
TbMo_xrays_54.dat
......
- If the program is invoked from WinPLOTR/WinPLOTR-2006, or from wfp2k itself, in the place
of the data code file one should write: multi_pattern (lower case)
The starting and final numbers may not coincide with the actual names of the data files,
they are used only for calculating the number of times FullProf will be internally called.
----------------------
>> 20 March 2014: New version of the program FullProf
----------------------
- The current version of FullProf has been updated to:
**********************************************************'
** PROGRAM FullProf.2k (Version 5.40 - Mar2014-ILL JRC) **'
**********************************************************'
- See the notes from the last few months to see the changes.
- FullProf Studio is now able to read CFL files (including those with values accompanied with standard deviations) and
symmetry operators of the Shubnikov types as those now included in FullProf.
- WinPLOTR-2006 allows to export an *.xys file from the pattern on screen, saving the standard deviation after
making a subtraction of a linear background.
- The selective conditions for hkl-size-broadening are now real numbers. This allows the introduction of more complex
conditions when the broadening affect only superstructure reflections.
- FullProf is now able to produce a magnetic CIF file (extension mCIF) for conmmensurate magnetic structures described
in the magnetic cell. This mCIF file can be directly read by FP_Studio and also by the program VESTA.
The program converts the user-description of the magnetic structure, using the crystal cell and propagation vector and MSYM
operators or basis functions, to the magnetic cell with all the magnetic atoms inside that cell. This mCIF file may
be used to determine the Shubnikov group of the used model thanks to the program ISOCIF that can be executed via the Web
at http://stokes.byu.edu/iso/isocif.php
----------------------
>> 28 February 2014: Extensive changes in the programs of the FullProf Suite
----------------------
- A new option for reading symmetry operators for magnetic structures in FullProf has been implemented.
These operators are for commensurate structures and the mix in some sense SYMM and MSYMM operators.
The value Isy=2 is used to inform the program that this kind of operator will be provided. Three forms
are recognized by FullProf, examples of these operators for are given below:
1-> SHUB x+1/2,-y,z -u,v,-w
2-> SHUB x+1/2,-y,z -mx,my,-mz +1
3-> SHUB x+1/2,-y,z +1
The three operator are identical (the +1 indicated that time reversal is not associated to the operator,
a -1 indicates the opposite situation). The keyword SHUB is not strictly needed, it may be replaced by any word
or number but it cannot be omitted. The spaces are significant and serve as separators of the different items.
In the case 1 we provide three items, in 2 four items and in case 3 three items. The complete list of symmetry
operators corresponding to a particular setting of any magnetic space group may be obtained through the Bilbao
Crystallographic Server using the programs MAGSTR or STRUCTURE CONVERT.
Below there is an example of the appropriate PCR section in the form number 2:
!-------------------------------------------------------------------------------
! Data for PHASE number: 2 ==> Current R_Bragg for Pattern# 1: 1.48
!-------------------------------------------------------------------------------
Magnetic structure in C_amcm_2k_mL2-
!
!Nat Dis Mom Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More
3 0 0 0.0 0.0 1.0 1 0 2 0 0 0.000 0 5 0
!
F -1 <--Space group symbol for hkl generation
!Nsym Cen Laue MagMat
128 1 1 1
!
1 x,y,z mx,my,mz +1
2 y+5/8,x+3/8,-z+1/4 my,mx,-mz +1
3 -x+7/8,-y+3/8,z -mx,-my,mz +1
4 -y+1/4,-x,-z+1/4 -my,-mx,-mz +1
5 -x+3/4,-y+1/2,-z+1/4 mx,my,mz +1
........
126 -y+1/8,-x+1/8,z+1/2 -my,-mx,mz -1
127 x+1/8,y+7/8,-z+3/4 mx,my,-mz -1
128 y+3/4,x+1/4,z+1/2 my,mx,mz -1
!
!Atom Typ Mag Vek X Y Z Biso Occ Rx Ry Rz
! Ix Iy Iz beta11 beta22 beta33 MagPh
Gd11 JGD3 1 0 0.50000 0.75000 0.25000 0.00000 0.50000 -0.755 0.755 0.000 #
0.00 0.00 0.00 0.00 0.00 -11.00 11.00 0.00
. . . . .
!-------> Profile Parameters for Pattern # 1
! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model
0.60633E-01 0.23158 0.05930 0.00000 0.00000 0.00000 1
........
------------------------------------------------------------------------------------
- A console program converting mCIF files (as produced by the Bilbao Crystallographic Server or by ISOCIF) to PCR files
has been included in the new FullProf Suite. The console program is called mCIF_to_PCR and will be extended with
a GUI in the near future. Presently the provided PCR file is adequate for a simulation and the user should change
by hand the parameters he(she) wishes.
- The program Mag_Info has been included, as a console application, for obtaining information about magnetic space
groups. In the near future this program will be extended with a GUI and a wizard to create PCR files for magnetic
structures using Shubnikov groups in whatever setting. The program reads the database 'magnetic_data.txt' compiled
by Harold T. Stokes and Branton J. Campbell (Brigham Young University, Provo, Utah, USA) based on data from:
Daniel Litvin,"Magnetic Space Group Types", Acta Crystallographica (2001) A57 729-730.
(http://www.bk.psu.edu/faculty/litvin/Download.html)
----------------------
>> 15 February 2014: Changes in WinPLOTR-2006 and Symmetry Procedures.
----------------------
- WinPLOTR-2006 has been extended to accept new format of input files. In particular the files
having extension .xys (see note of 2 September 2012) can be directly associated to the program
that read them automatically, new keywords that are interpretable by WinPLOTR have been introduced.
These files are of the type xy-sigma (Instr=10) but with more information. One can use these files
for general plotting by adding the Legend_X and Legend_Y texts as well as the Scattering Variable.
The possibility of reading a calculated value has also been included
The header of these files are formed by
of the form x_val y_val sig_val.
- Due to changes in the base library CrysFML many programs have been modified in order to comply with
the changes. Please communicate any misbehaviour that may be due to these changes.
- The Symmetry Procedures program included within the GUI Crystallographic Calculator has been extended in order to
play with space groups in user-defined settings.