Full Year 2019
----------------------
>> 27 November 2019 : Correcting a bug in magnetic moment constraints appearing in special cases
----------------------
- In the previous version of the FullProf and Mag_Symm programs there was a bug concerning the calculation
of magnetic moment constrains for some special positions in tetragonal Shubnikov groups: some components
where put to zero unduly. This has now been corrected.
- Cosmetic changes in WinPLOTR-2006 for reading *prof.cif files.
----------------------
>> 21 October 2019 : Correcting a bug when using "mag_only" in Type 3 Shubnikov groups
----------------------
- In Type 3 magnetic space groups only the "pure" magnetic reflections were generated in the
previous version. This is only adequate for Type 4 groups. This has now been corrected.
----------------------
>> 17 October 2019 : Correcting few bugs in simulated annealing for solving magnetic structures
----------------------
- En the previous version, after extensive changes, an error was introduced for the case Jbt=-1
and simulated annealing (other cases Jbt=1, +/-10, 5, etc were not affected). This bug has now
been corrected.
- The PRF file generated after a simulated annealing run on the full profile was not correct
for cases where superspace is not used.
- Some changes have been introduced in the note of 9 October 2019 concerning cases where
superspace is not used in simulated annealing.
----------------------
>> 9 October 2019 : Extensive changes in the new version of FullProf concerning Simulated Annealing and Superspace.
----------------------
- The current version of the FullProf program has been updated to:
**********************************************************
** PROGRAM FullProf.2k (Version 7.20 - Oct2019-ILL JRC) **
**********************************************************
- LeBail fits and Simulated annealing are now totally operable with magnetic superspace groups. Single crystal
data can also be treated provided that the appropriate input integrated intensity file is given. This file
is similar to the *.int file produced by a LeBail fit. The program DataRed will be modified in the near future
to perform single crystal data reduction using the superspace formalism.
- Spherical coordinates for the modulation amplitudes in the superspace formalism for magnetic structures
have been fully implemented. Notice that the symmetry constraints when this option is applied cannot be
automatic. The best is to start a run using crystallographic components and look into the output files
to see how the spherical components have been calculated and apply the appropriate constraints using refinement
codewords.
- Superspace mCIFs files are now generated by FullProf. The name of these files are named as "codfile_ssgN.mcif",
where "codfile" is the name of the PCR file without extension and N indicates the number of the phase.
These files can be read by the program Jmol for visualizing the incommensurate magnetic structures but not
by the program VESTA. The supercell option in P1 with "MULTCELL na nb nc" is still used in this case to produce
a box with all magnetic moments to be visualized with VESTA. FullProf Studio files are not output because the
superspace formalism has not been included in FP_Studio yet.
- Simulated annealing has been extended to work with the full powder diffraction profile, for that it is
necessary to make a previous run using a Lebail fit, putting Ipr=-2 and include the name of the *.spr
file in the next line of the PCR file. Moreover the creation of a cluster of intensities is needed but
it is necessary to make Jvi=13, for the case of superspace description, or Jvi=11 for other cases.
This *.int file is used in the simulated annealing work with the full profile only for reading
the indices of reflections. The information contained in the *.spr file is really what is used in the
process of minimizing the cost function. The PRF file for visualizing the final profile
is identical to that generated using the Rietveld method.
In case of several phases, the calculated profile of the LeBail Fit corresponding to the desired phase
is output to the *.spr file instead of the total observed profile. This is very useful in case of known
impurities (treated using the Rietveld method with fixed positions) to extract an unknown phase or
to extract pure magnetic reflections to solve a magnetic structure. If the use wants to use the calculated
profile even in the case of a single phase in the LeBail fit the value of Jvi should be negative: Jvi=-13
or Jvi=-11.
Example of the relevant parts of a PCR file for preparing the simulated annealing work. We have used
superspace operators to generate only incommensurate magnetic reflections (keyword "mag_only") because we
are treating a difference pattern. Notice that this PCR file generates the profile information in the
file test.pcr and the reflection clusters in the file: test-pm1_ctrl.int
.....................................Start of the example
COMM My Title: LeBail fit to prepare a SAnn work with the full powder profile
! Current global Chi2 (Bragg contrib.) = 999999
! Files => DAT-file: xxxxx.dat, PCR-file: test-pm
!Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut
1 0 1 25 2 0 1 1 0 0 1 0 0 0 0 0 0 0 1
!
!Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 NLI Prf Ins Rpa Sym Hkl Fou Sho Ana
-2 0 1 1 1 0 4 0 0 3 8 0 0 0 0 0 0 ! <=========================
! File name (or filecode) of the *.spr file containing profile points information
test.spr ! <=========================
!
. . . . .
!---------------------------------------------------------------------------------------------------------
! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 0.08 Magnetic R-Factor: 0.00
!---------------------------------------------------------------------------------------------------------
Magnetic Structure of: mag_only
!
!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More
0 0 0 0.0 0.0 1.0 2 0 2 0 0 956.092 1 7 1 ! <=========================
!
!Jvi Jdi Hel Sol Mom Ter Brind RMua RMub RMuc Jtyp Nsp_Ref Ph_Shift N_Domains
13 0 0 0 0 0 1.0000 0.0000 0.0000 0.0000 1 0 0 0 ! <=========================
!
Pmn2_11'(0,0,g)s0ss 31.1.9.2.m124.2 <--Magnetic Super Space group symbol (name & number)
Parent Setting: Pnm2_11'(0,0,g)ss0s (a1,a2,a3,a4;0000)
! Generators
Genr -x+1/2,-y,z+1/2,t,1
Genr x,-y+1/2,z,t+1/2,1
Genr x,y,z,t+1/2,-1
N_qc 1
Q_coeff
1
!-------> Profile Parameters for Pattern # 1
! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model
1.000 0.00000 0.0000 0.00000 0.00000 0.00000 0
0.00000 0.000 0.000 0.000 0.000 0.000
! U V W X Y GauSiz LorSiz Size-Model
0.186772 -0.232957 0.386853 0.227668 0.000000 0.000000 0.000000 0
0.000 0.000 0.000 0.000 0.000 0.000 0.000
! a b c alpha beta gamma #Cell Info
7.232945 5.60301 12.170022 90.000000 90.000000 90.000000
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000
! Pref1 Pref2 Asy1 Asy2 Asy3 Asy4 S_L D_L
1.00000 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
! Propagation vectors:
0.0000000 0.0000000 0.4147567 1 1.0000 <-- Propagation Vector, nharm, sintl_lim 1
0.000000 0.000000 0.000000
. . . . . .
.....................................End of the example
- Examples of LeBail fit, simulated annealing, spherical components, integrated intensity refinements have
been put in the Examples directory of the FullProf Suite distribution. All those files can be identified
by the starting characters (DyMnGe_*) of their names.
----------------------
>> 11 July 2019 : Correction of a bug in WinPLOTR-2006.
----------------------
- In the fitting option of WinPLOTR-2006 the saved file *.pik was not correct for X-ray diffraction
with kalpha-1,2 doublets. The second wavelength was not saved correctly. This has now been corrected.
- In FullProf using Prf=7 for some values of the asymmetry correction the calculation of the profile around
2theta=90 was not correct. This has now been corrected. Remember that one can put S_L /= 0 and D_L=0 and refine
only a single parameters that eliminates the correlation of S_L and D_L when both are used. This is the
recommended way of working (see J.R. Hester, J. Applied Crystallography 46, 1219-1220(2013)).
----------------------
>> 11 June 2019 : Corrections of bugs in the superspace part of the program. Removing JBT=15.
----------------------
- During the Erice School on Magnetic Crystallography (Erice 31 May - 9 June 2019) few bugs have been corrected.
In some circumstance some reflections were not generated. The toolbar was unable to charge properly mCIF files
coming from the magnetic database of the Bilbao Crystallographic Server. The application of constraints was
not properly working in some circumstances, etc. All these bugs have been corrected.
Still to implement: output for FullProf Studio, complete mCIF files in superspace, spherical coordinates for
the modulation amplitudes, etc.
- Examples of superspace options have been included in the distribution.
- The option JBT=+/-15 has been removed. This option was implemented long time ago for handling incommensurate
crystal structures without using superspace and making a rational approximation for the calculation of
structure factors. This option will be fully superseded by the superspace formulation JBT=+/-7. Presently
the displacement modulation amplitudes are put to zero but will be available as soon as the calculation
of the structure factor with integration in internal space is implemented.
----------------------
>> 30 May 2019 : A new version of FullProf handling superspace formalism is now distributed
----------------------
- The current version of the FullProf program has been updated to:
**********************************************************
** PROGRAM FullProf.2k (Version 7.00 - May2019-ILL JRC) **
**********************************************************
- This version of FullProf is able to refine an incommensurate magnetic structure using the formalism
of superspace. Only the magnetic modulations are currently taken into account. To access this
option for a particular phase one has to use Jbt=7 and Isy=2 and a positive number giving the independent
propagation (modulation) vectors (Nvk > 0). An example of PCR file section is given below for the case
of DyMn6Ge6. Before the line starting with "!Atom" a series of text lines should provide the necessary
information for constructing the superspace group. The symbol of the superspace group is used only for
informative purposes because, for the moment, it is not used by FullProf that constructs the
magnetic superspace group for the list of generators. In the provided PCR all the symmetry operators
are provided to facilitate copy and paste from CIF files, however the same result can be obtained
with a single line like:
generators x1-x2,x1,x3,x4+1/6,+1; x1-x2,-x2,-x3,-x4+1/3,-1
or generators x-y,x,z,t+1/6,+1; x-y,-y,-z,-t+1/3,-1
or two lines like:
genr x-y,x,z,t+1/6,+1
genr x-y,-y,-z,-t+1/3,-1
The other fundamental information to be provided is the number of Q_coefficients (N_qc) and the coefficients
themselves (Q_coeff). In the simple case below, (3+d) with d=1, only a propagation vector is given and only a single harmonic
is considered. For a case with two propagation vectors in which mixed satellites occur and harmonic up to order 2 for the
first propagation vector, for instance, we have to write the following lines:
N_qc 4
Q_coeff
1 0
0 1
2 0
1 1
This means that the modulation amplitudes Mcos-Msin-1 correspond to the first Q_coeff [1 0], the
Mcos-Msin-2 to the second Q_coeff [0 1] ... Mcos-Msin-4 to the forth Q_coeff [1 1].
For powder diffraction we can limit the generation of reflections by limiting individually the maximum
sinTheta/Lambda (see the item "! Propagation vectors:").
The keywords appearing in the name of the phase like "VARY xyz mxmymz McosMsin " (or in within a block
COMMANDS - END_COMMANDS) make refine the atom positions of the average structure, homogeneous moment components
and amplitudes of the modulation functions. The program select automatically the refinement codes applying
the necessary symmetry constraints.
The atoms items should be given as in the example below. Notice that that following the label of the
atom and the symbol for selecting the form factors and scattering lengths the number Max_Qcoeff tells the
program how many (Mcos, Msin) amplitudes will be used for this particular atom. After the coordinates,
isotropic temperature factor and occupation factor there is number indicating the type of atom in the usual
way, the last number is for indicating the chemical species in case of bond-valence calculations.
It is assumed by default the presence of an homogeneous magnetic moment corresponding to the propagation
vector k=0. In case the superspace group forbids this k-vector, the program automatically nullifies its value.
The amplitudes of the modulations are given as Mcos and Msin (vectors of three components in Bohr magnetons
with respect to the unitary basis along the a,b,c axes) in the form:
Mcos-Msin-j Mcosx Mcosy Mcosz Msinx Msiny Msinz
ccx ccy ccz csx csy csz
As usual, below each component there are refinement codes attributed automatically by the program.
. . . . . . . . . . . .
!---------------------------------------------------------------------------------------------------------
! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 3.04 Magnetic R-Factor: 4.55
!---------------------------------------------------------------------------------------------------------
DyMn6Ge6 magnetic VARY mxmymz McosMsin xyz
!
!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More
5 0 0 0.0 0.0 1.0 7 0 2 0 0 133584.188 1 7 0
!
P62'2'(0,0,g)h00 <-- Magnetic SuperSpace group symbol
genr x1,x2,x3,x4,+1
genr x1-x2,x1,x3,x4+1/6,+1
genr -x2,x1-x2,x3,x4+1/3,+1
genr -x1,-x2,x3,x4+1/2,+1
genr -x1+x2,-x1,x3,x4+2/3,+1
genr x2,-x1+x2,x3,x4+5/6,+1
genr x1-x2,-x2,-x3,-x4+1/3,-1
genr x1,x1-x2,-x3,-x4+1/2,-1
genr x2,x1,-x3,-x4+2/3,-1
genr -x1+x2,x2,-x3,-x4+5/6,-1
genr -x1,-x1+x2,-x3,-x4,-1
genr -x2,-x1,-x3,-x4+1/6,-1
N_qc 1
Q_coeff
1
!
!Atom Typ Max_Qcoeff X Y Z Biso Occ N_type Spc / Line below:Codes
! Mcosx Mcosy Mcosz Msinx Msiny Msinz / Line below:Codes
! beta11 beta22 beta33 beta12 beta13 beta23 / Line below:Codes
Dy JDY3 1 0.00000 0.00000 0.00000 0.00000 1.00000 1 0
0.00000 0.00000 0.00000 0.00000 0.00000
MagM0-Moment: 0.00000 0.00000 3.86750 <- Homogeneous magnetic moment
0.00000 0.00000 41.00000
Mcos-Msin-1: 7.10154 3.55077 0.00000 0.00000 6.15012 0.00000 <-Amplitudes of Modulated moments
112.00000 111.00000 0.00000 0.00000 111.73206 0.00000
Mn1 MMN2 1 0.00000 0.50000 0.25093 0.00000 6.00000 1 0
0.00000 0.00000 101.00000 0.00000 0.00000
MagM0-Moment: 0.00000 0.00000 -1.03164 <- Homogeneous magnetic moment
0.00000 0.00000 31.00000
Mcos-Msin-1: -2.29552 -1.19523 0.00000 0.37579 -1.19714 0.00000 <-Amplitudes of Modulated moments
91.00000 61.00000 0.00000 81.00000 71.00000 0.00000
Ge1 GE 0 0.66667 0.33333 0.50000 0.00000 2.00000 0 0
0.00000 0.00000 0.00000 0.00000 0.00000
Ge2 GE 0 0.66667 0.33333 0.00000 0.00000 2.00000 0 0
0.00000 0.00000 0.00000 0.00000 0.00000
Ge3 GE 0 0.00000 0.00000 0.34589 0.00000 2.00000 0 0
0.00000 0.00000 51.00000 0.00000 0.00000
!-------> Profile Parameters for Pattern # 1
. . . . . . . . . . . . . . . . . .
! Propagation vectors:
0.0000000 0.0000000 0.1647532 1 1.0000 <-- Propagation Vector, nharm, sintl_lim 1
0.000000 0.000000 0.000000
. . . . . . . . . .
- In the forthcoming months the full implementation of superspace for modulated crystal structures will be
finished. A series of utilities for working with superspace, as well as a complete refurbishment of the
program BasIreps, are planed.
----------------------
>> 27 March 2019 : Correction of a bug in BasIreps. Change in the FullProf Suite distribution
----------------------
- During some time a version of BasIreps unable to read the PIR_data.txt database was in the web site. Now
the current version has been corrected.
- Some files containing databases for magnetic groups, superspace groups, physically irreducible representations
and scattering data have been regrouped on the subdirectory of the FullProf_Suite called "Databases". This
is transparent for the users, however if one wants to replace just an existing executable file by a newer
one, the programs BasIreps, Mag_Info, Mag_SymmCalc, FAULTS will not work because the look for files in the
directory FullProf_Suite/Databases.
----------------------
>> 25 March 2019 : Small Change in BondStr.
----------------------
- In BondStr the atomic radius is now taken always from the Atomic Properties table provided by S. Adams.
in case a species is not defined the covalent radius stored in internal tables of CrysFML is used.
This changes slightly the values of the energy of the previous version but agrees with the values
published in the paper J.Appl.Cryst.(2019),52, 148-157 in which this prescription was used.
----------------------
>> 7 February 2019 : New version of BondStr. Magnetic R-factors in Shubnikov options. Correction of bugs.
----------------------
- The program BondStr and its interface have been updated. The program has been published in
Journal of Applied Crystallography this year and the supplementary information accompanying
the article contains a manual of BondStr. Please use the following reference for citing the
use of the program:
"An investigation of the structural properties of Li and Na fast ion conductors using high-throughput
bond-valence calculations and machine learning", by Nebil A. Katcho, Jesus Carrete, Marine Reynaud, Gwenaelle Rousse,
Montse Casas-Cabanas, Natalio Mingo, Juan Rodriguez-Carvajal and Javier Carrasco,
J.Appl.Cryst.(2019),52, 148-157
- When using the Shubnikov formulation (and also symmetry modes) for refining magnetic and crystal
structures with neutron diffraction, a global R-Bragg factor was output. Now the Nuclear and Magnetic
R-Factors are output, moreover a so called "Pure Magnetic R-Factor" is also calculated for reflections
containing only magnetic contribution. Moreover one can use a d-spacing limit for calculating magnetic
contributions distinct from the usual DLIM instruction. One has to provide the command: MDLIM n_pat d-spacing
within the COMMANDS section. Now the instruction "save_mag_strf" outpus the list of saved magnetic structure
factors and magnetic interaction vectors for all patterns in files with extension *.mstf
Example:
........
!Name of my phase ...
COMMANDS
MDLIM 1 1.8 MDLIM 2 1.8 MDLIM 3 1.9 MDLIM 4 2.0 MDLIM 5 2.2
save_mag_strf
END_COMMANDS
- In the program WinPLOTR-2006 a bug concerning the output of the different colours of reflections
has been corrected.
- Some bugs in the Linux version of EdPCR have been corrected. EdPCR was crashing when opening and clicking in
the profile refinement dialog.
- Correcting a bug in FullProf, only with TOF, when Nor=1 was selected and fixed symmetry operations are provided
by the user. If a symmetry operator representing a centre 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). This has now be corrected.