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# | optional comments | ||
NbHkl | d | 0 | classical phase, the hkl lines are generated |
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>0 | classical phase but the hkl lines are read | ||
-1 | reserved for amorphous sample (not yet implemanted) | ||
-2 | parasitic lines | ||
-3 | quasi-crystals (icosahedral or dodecaedral) pattern fitting | ||
-4 | magnetic superstructures | ||
-5 | incommensurate modulated structures | ||
nTransit | d | number of phase transitions to take into account in the scale factor | |
Temp_Orig | d | Origin of Temp in the phase variable expansion | |
Title | s | Title of the phase |
# | optional comments | ||
Order | % | kind of block | |
---|---|---|---|
Scale | @ | Scale factor for the phase | |
B_global | @ | Overall isotropic Thermal factor |
# | optional comments | ||
Order | % | kind of block | |
---|---|---|---|
the following group of lines is repeated nTransit times | |||
T_c | @ | Origin Temp | |
T_a | @ | Activation Temp | |
Exponant | @ | Overall isotropic Thermal factor |
SymGrp | s | this name must be known in the symetry part of the the file or in the symetry file | |
---|---|---|---|
nOrien | d | 0 | No orientation functions in this phase of the sample |
>0 | Number of functions used for the prefered orientation of the sample, common to all experiments | ||
<0 | Same as above but there are |nOrien| functions for each experiment. | ||
nProf | d | Number of functions used for describing the line profile | |
nAtom | d | Number of independant atoms to be read | |
nBloc | d | Number of rigid blocks to be read | |
uncoherent | d | reserved | |
nBond | d | Number of Temp used in bond restraints |
# | optional comments | ||
Order | % | kind of block | |
---|---|---|---|
Center | @ | Relative sample position error | |
A | @ | Cell lengths | |
B | @ | ||
C | @ | ||
Alpha | @ | Cell angles | |
Beta | @ | ||
Gamma | @ |
# | optional comments | ||
nSize | d | 1 | ratio of symmetry groups size |
---|---|---|---|
order | d | 0 | ratio of vector superstructure |
x_super | f | superstructure vector of the modulation vector expressed on the basic-cell | |
y_super | f | ||
z_super | f | ||
SymName | s | name of the group describing the symetry of magnetic components |
The next group is read 2 times and it contains the informations for generating lines.
nHkl | d | 0 | h, k, l index will generated |
---|---|---|---|
>0 | lines index will be read | ||
... | d |
# | optional comments | ||
nSize | d | 1 | size of the modulation (reserved) |
---|---|---|---|
nSteps | d | 0 | integration mode using defaults for incommensurate |
>0 | number of integration steps for incommensurate | ||
superstructure order for commensurate superstructure | |||
nSat | d | 0 | number of sets of hkl lines used to described the pattern |
x_super | f | superstructure vector or commensurate part of the modulation vector expressed on the basic-cell | |
y_super | f | ||
z_super | f | ||
SymName | s | name of the complementary group describing the symetry |
The next group is read nSat times and it contains the informations on the complementary Miller index of each set of lines. The basic structure (m=0) must be in the first set, all lines in the same set have to follow the same extinction conditions.
nHkl | d | 0 | h, k, l index will generated |
---|---|---|---|
>0 | lines index will be read | ||
nInd | d | 0 | number of indices to used in the group |
hkl_sat | d | nInd * nSize values of indices along the outer dims | |
... | d |
The following block contains the incommensurate wavevector, it is read only if the phase has been defined as incommensurate, nbHkl=-5.
# | optional comment | ||
Order | % | kind of block | |
---|---|---|---|
x_vector | @ | component of the incommensurate modulation vector on the reciprocal super-cell | |
y_vector | @ | ||
z_vector | @ |
The following values are read only if nOrien is not zero.
# | optional comments | ||
c_Orien | d | the eff_nOrien reference number of the orientation functions used in describing the sample prefered orientation | |
---|---|---|---|
... | d | ||
# | optional comments | ||
Order | % | kind of block | |
the following group is repeated eff_nOrien times. | |||
coef | @ | coeficient of the function | |
theta | @ | angle of the polar axis of the function with z | |
phi | @ | angle of the projection of the polar axis on xy with x |
The following values are read only if nProf is not zero.
# | optional comments | |||
c_Prof | d | the nProf reference number of the orientation functions used in line profile description | ||
---|---|---|---|---|
... | d | |||
# | optional comments | |||
Order | % | kind of block | ||
the following group is repeated nProf times. | ||||
Wl_C | @ | width of the Lorentz component | /cos(theta) | |
Wg_C | @ | width of the Gauss component | /cos(theta) | |
WlT | @ | width of the Lorentz component | *tan(theta) | |
WgT | @ | width of the Gauss component | *tan(theta) | |
theta | @ | angle of the polar axis of the function with z | ||
phi | @ | angle of the projection of the polar axis on xy with x | ||
# | optional comments | |||
Order | % | kind of block | ||
the following group is repeated first MaxAssym times then nProf times. | ||||
A0 | @ | constant asymetry term | ||
AT | @ | asymmetry term | *tan(theta) |
The following values are read only if nAtom is not zero. The variables read for each atom depend on the value declared for case just after its name and chemical kind.
# | optional comments | ||
name | c7 | name of the atom | |
---|---|---|---|
kind | c7 | identification of the scattering coefficients | |
case | d | 0 | default |
+1 | use and read anisotropic thermal factor (Beta ij) | ||
+2 | use and read magnetic moment (reserved) | ||
4, | use and read modulation coefs for order 1 | ||
8 | use and read modulation coefs for orders 1, 2 | ||
12 | use and read modulation coefs for orders 1, 2, 3 | ||
16 | use and read modulation coefs for orders 1 to 4 | ||
32 | use and read anharmonic thermal factors ( Cijk ) | ||
64 | use and read anharmonic thermal factors ( Dijkl ) | ||
128 | use and read anharmonic thermal factors ( Eijklm ) | ||
256 | use and read anharmonic thermal factors ( Fijklmn ) | ||
# | optional comments | ||
Order | % | kind of block | |
X | @ | coordinates | |
Y | @ | ||
Z | @ | ||
T | @ | occupancy (taking into account the site multiplicity) | |
the following variable is read only if case is even | |||
B | @ | isotropic thermal factor | |
the 6 following variables are read only if case is odd | |||
B11 | @ | anisotropic thermal factor "Beta" used in the thermal factor :
T = exp -(B11 h^2 + B22 k^2 + B33 l^2 + 2 (B12 hk + B13 hl + B23 kl)) in release up to 1.16, the thermal factor was written without the factor in the diagonal terms, this was modified to agree with the ITC, vol B page 18 formula 1.2.10.3b. Normalized Uij are calculated on last cycle together with the equivalent isotropic factor | |
B22 | @ | ||
B33 | @ | ||
B12 | @ | ||
B13 | @ | ||
B23 | @ | ||
the 3 following variables are read only if case is declared as magnetic | |||
Kx | @ | ||
Ky | @ | ||
Kz | @ |
The following table is read only if the atom is declared as modulated (case == 4..17 ), 8 variables are read for each required order
# | optional comments | ||
Order | % | kind of block | |
---|---|---|---|
S_x | @ | Fourier coefficients of the expansion of the displacement | |
C_x | @ | ||
S_y | @ | ||
C_y | @ | ||
S_z | @ | ||
C_z | @ | ||
S_t | @ | Fourier coefficients of the expansion of the occupancy | |
C_t | @ |
The following table is read only if the atom is declared as anharmonic
(case == 32, 33, 64, 65 ,96, 96....), such expansion can take some
signification only for simple phases; the expansion can 3th, 4th,
5th or 6th order to allow its use one high symetrical sites, at the times one order
only is allowed for each atom.
Gram-Charlier expansion is not normalized: the thermal factor To is replaced by
T=To(1 + i sum(i<=j<=k) Cijk Hi Hj Hk + sum(i<=j<=k<=l) Dijkl Hi Hj Hk Hl + i .... )
the following block is read only if case == 32 or 33
# | optional comments | ||
Order | % | kind of block | |
---|---|---|---|
Chhh | @ | 9 unormalized 3th order coefs of Gram-Charlier expansion,
order just written not checked! | |
Ckkk | @ | ||
Clll | @ | ||
Chhk | @ | ||
Chhl | @ | ||
Ckkh | @ | ||
Ckkhl | @ | ||
Cllh | @ | ||
Cllk | @ |
# | optional comments | ||
Order | % | kind of block | |
---|---|---|---|
Dhhhh | @ | 15 Unormalized 4th order coefs of Gram-Charlier expansion | |
Dkkkk | @ | ||
Dllll | @ | ||
.... | @ | Dhhhk, Dhhhl, Dkkkh, Dkkkl, Dlllh, Dlllk
Dhhkk, Dhhll, Dkkll, Dhhkl, Dkkhl, Dllhk |
# | optional comments | ||
Order | % | kind of block | |
---|---|---|---|
Ehhhhh | @ | 21 Unormalized 5th order coefs of Gram-Charlier expansion
order just written not checked! | |
Ekkkkk | @ | ||
Elllll | @ | ||
.... | @ | Ehhhhk, Ehhhhl, Ekkkkh, Ekkkkl, Ellllh, Ellllk
Ehhhkk, Ehhhll, Ekkkhh, Ekkkll, Elllhh, Elllkk Ehhhkl, Ekkkhl, Elllhk Ehhkkl, Ehhllk, Ekkllh |
# | optional comments | ||
Order | % | kind of block | |
---|---|---|---|
Fhhhhhh | @ | 28 Unormalized 6th order coefs of Gram-Charlier expansion
order just written not checked! | |
Fkkkkkk | @ | ||
Fllllll | @ | ||
.... | @ | Fhhhhhk, Fhhhhhl, Fkkkkkh, Fkkkkkl, Flllllh, Flllllk
Fhhhhkk, Fhhhhll, Fkkkkhh, Fkkkkll, Fllllhh, Fllllkk Fhhhhkl, Fkkkkhl, Fllllhk Fhhhkkk, Fhhhlll, Fkkklll Fhhhkkl, Fhhhllk, Fkkkhhl,, Fkkkllh, Flllhhk, Flllkkh Fhhkkll |
The following blocks are read only if nBloc is not zero.
# | optional comments | ||
Order | % | kind of block | |
---|---|---|---|
the lines are read for each block | |||
X | @ | cell coordinates of the origine of an orthogonal repear which characterize the block | |
Y | @ | ||
Y | @ | ||
theta | @ | Eulerian angles of the block | |
phi | @ | ||
psi | @ |
Then for each block we have to read the number of atoms and their coordinates.
nAtom | d | number of atoms inside the block | |
---|---|---|---|
nAtom atomic description as for independant atoms | |||
name | c7 | name of the atom | |
kind | c7 | identification of the scattering coefficients | |
case | d | as for independant atoms | |
Order | % | kind of block | |
X | @ | coordinates on the orthogonal repear | |
Y | @ | ||
Y | @ | ||
T | @ | occupancy (taking into account the site multiplicity) | |
B | @ | isotropic thermal factor | |
.......... | next atom inside the block |
The following block is read only if nb_Hkl is positive. In case of modulated structure, we will found here all the requested blocks with their n_Hkl non zero.
# | optional comments | ||
Order | % | 0 | if nAtom is not zero, there is no intensities to read |
---|---|---|---|
% | if nAtom is zero, kind of intensities expansion | ||
nbHkl group of h, k, l | |||
h | d | Miller index of the line | |
k | d | ||
l | d | ||
Intens | @ | raw integrated intensity, only if needed |
Even if there is no atom ( pattern matching), a symetry group is mandatory, one can use the trivial (P1) group in this case. The raw intensities can be taken out the hkl file using the observed values. However they are not calculated using the same assumptions : the hkl file contains sums of counts, the other values are refined using the mean square procedure. It is possible to copy in the .k files the values from the hkl file here using a small program (xhkl2k), in this case the block has to be identified using the specific comments #BEGINHKL2K and #ENDHKL2K.
If n_Bond n_Distdnumber of bond lengths restraint n_Angle@number of angular restraint the following value is read n_Bond times Tempd value of the Temp parameter for which the restraints are calculated.
The following block is then read n_Dist times.
# | optional comments | ||
n_coord | d | number of bond using the following length | |
---|---|---|---|
sigma | f | weigth for this length used in the penality function | |
Order | % | kind of block | |
Dist | @ | expected value of the bond length | |
n_coord times, the description of the bonds | |||
Atom0 | c7 | name of the origin atom | |
Atom1 | c7 | name of the end atom | |
Sym | s | string defining the sym operation between the Atom1 and the position of its equivalent in the bond ( can be x,y,z) |
A similar block is then read n_Angl times, calculations are possible but the refinement is not implemented.
# | optional comments | ||
n_coord | d | number of bonds using the following angle | |
---|---|---|---|
sigma | f | weigth for this length | |
Order | % | kind of block | |
Angle | @ | expected value of the angle between bonds | |
n_coord times, the description of the bonds | |||
Atom0 | c7 | name of the origin atom | |
Atom1 | c7 | name of the first end atom | |
Sym | s | string defining the sym operation for Atom1 | |
Atom2 | c7 | name of the second end atom | |
Sym | s | string defining the sym operation for Atom2 |
This block is read only if NbHkl in the phase header specifies a
parasitic crystalline phase :
( NbHkl = -2).
nProf | d | Number of functions used for describing the line profile | |
---|---|---|---|
nDist | d | Number of independant Bragg distancesto be read |
If nProf is non zero, the line profile block is read using the same mode already defined for the known crystalline phases. However the following differences have to be considered : we can not define a polar axis and the function reference number has to be set to 0 (isotropic). Obviously the value of theta and phi can not be refined.
Then the lines can be read.
# | optional comments | ||
Order | % | 0 | kind of the block |
---|---|---|---|
nDist group of Dist and Intens | |||
Dist | @ | distance according to Bragg law | |
Intens | @ | raw integrated intensity |
This block is read only if NbHkl in the phase header specifies a
quasicrystalline crystalline phase :
( NbHkl = -3) with icosaedral or dodecaedral symetry. It allows
only some pattern matching. The distances are calculated using the simplified formula:
Q = (n + m T)A*2 + l B*2
then in the icosaedral system A has to be multiplied by sqrt(2(2+Tau)), and
l and B have to be set to zero
nProf | d | Number of functions used for describing the line profile | |
---|---|---|---|
nDist | d | Number of independant Bragg distancesto be read | |
# | optional comments | ||
Order | % | kind of block | |
Center | @ | Relative sample position error | |
A | @ | the pseudo cell lengths | |
B | @ |
If nProf is non zero, line profile block is read using the same mode defined for the known crystalline phases. However the following differences have to be considered. The polar axis definition is dummy and it is reasonnable to set to 0 (isotropic) the reference number of the function. However other values can be checked.
Then the lines can be read.
# | optional comments | ||
Order | % | 0 | if nAtom is not zero, there is no intensities to read |
---|---|---|---|
% | if nAtom is zero, kind of intensities expansion | ||
nDist group of m, n, l | |||
m | d | pseudo index of the line | |
n | d | ||
l | d | ||
Intens | @ | raw integrated intensity |
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