xnd top | Next file | Previous file |
---|
@PHASE | key identifier | ||
---|---|---|---|
NATURE | d | 0 | classical phase, the hkl lines are generated |
>0 | classical phase but the hkl lines are read | ||
-1 | Radial expension for background | ||
-2 | Parasitic lines | ||
-3 | Quasicrystal (icosahedral or dodecaedral) pattern fitting | ||
-4 | magnetic superstructures | ||
-5 | incommensurate modulated structures | ||
-6 | incommensurate modulated structures with magnetic lines | ||
-7 | reserved for amorphous sample (not yet implemanted) | ||
TRANSIT | d | 0 | number of phase transitions to take into account in the scale factor |
ORIG | f | 0 | Origin of Temp in the phase variable expansion |
TITLE | s | Title of the phase |
@SCALE | key identifier of the variable block | |
---|---|---|
Scale | $ | Scale factor for the phase |
B_global | $ | Overall isotropic Thermal factor |
@TRANSIT | key identifier of the variable block | |
---|---|---|
the following group of lines is repeated nTransit=@PHASE(TRANSIT) times | ||
T_c | $ | Origin Temp |
T_a | $ | Activation Temp |
Exponant | $ | Exponant |
If the @CRYSTAL key is not found a 1.1 crystal header is assumed.
@CRYSTAL | key identifier | ||
---|---|---|---|
SYMGRP | s | this name must be known in the symetry part of the the file or in the symetry file | |
ATOM | d | 0 | Number of independant atoms to be read |
ORIEN | 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. | ||
PROF | d | 0 | Number of functions used for describing the line profile In case of modulated structure, a negative value means that the profil depend on the set of lines. |
BLOCK | d | 0 | Number of rigid blocks to be read |
BOND | d | 0 | Number of Temp used in bond restraints |
SETS | d | 0 | Number of lines sets, incomensurates ... or profile dependence ... |
@CELL | key identifier of the variable block | |
---|---|---|
Center | $ | Centering error for this phase (s/R in reflexion) |
A | $ | Cell lengths |
B | $ | |
C | $ | |
Alpha | $ | Cell angles |
Beta | $ | |
Gamma | $ |
This block is a small implementation of some magnetic structures, it is just
to allow user to get rid of some magnetic lines when studying complex phases.
User have to provide at less two SET : one for magnetic lines and one for
the other.
@MAGNET | key identifier | ||
---|---|---|---|
SYMGRP | s | At the time the symmetry is not checked and user must provides a triclinic group in which the operations concern only the moment of the atom in the same order than the standard symmetry group. |
In this case, the cell parameters and then the coordinates have to be expressed
using the super-cell in which the rational part of the modulation vanishes,
this cell is associated with the so-called "big indices". Nevetheless the coordinates of this rational
part (centering in the superspace) are still expressed referring to the basic-cell associated
with the "small indices". When there is no 4D centering, the two metrics are coincident.
User have to provide at less two SET : one for base lines and one for the other.
@MODUL | key identifier | |||
---|---|---|---|---|
SYMGRP | s | name of the complementary group describing the symmetry | ||
SIZE | d | 1 | size of the modulation (reserved) | |
ORDER | d | 0 | incommensurate | use default (25)integration steps |
<=0 | opposite of number of integration steps | |||
>0 | reserved for commensurate | |||
CENTER_X | f | 0.0 | projection along X,Y, Z of the 4D centering vector | |
CENTER_Y | f | 0.0 | ||
CENTER_Z | f | 0.0 | ||
COMPO | d | 0 | Not a composite structure | |
>0 | Number of the first atom belonging to the second cell | |||
COMPO_SYM | s | symmetry of the second cell. The reserved name SWAP_COMPO can be used, it exchanges the modulation and the symmetry along z between the two cells; in this case there is no complementary group to read. | ||
COMPO_SYM4 | s | name of the complementary group of the second cell |
Keys are scanned from SET_0 to SET_(@CRYSTAL(SETS)-1).
For incommensurates or composites, the LOOP is requested, it allows to specify
the lines to be used and the 4th indices. The value of the string must be consistent
with known for the sudied case.
The ALLOW and DENY strings synthax remains the c ones knowing only "+-*/%" operators
for integers and logical comparisons operators.
@SET_n | key identifier | ||||
---|---|---|---|---|---|
LINES | d | 0 | generated lines (default) | ||
>0 | number of lines to read | ||||
ALLOW | s | string rules | "ALLOW = 'H%2==0 && (K+2*L)%3==1'" | ||
DENY | s | string rules | "DENY = 'H%2==0 && (K+2*L)%3==1'" | ||
LOOP | s | magnetic lines | "LOOP='MAGNET'" | ||
incomensurate | base lines | "LOOP='HKL,M=0'" | |||
sattelites lines | "LOOP='HKL,M=1,-1..'" | ||||
composites | common lines | "LOOP='HKL=0,M=0'" | |||
1st layer lines | "LOOP='HKL,M=0'" | ||||
2nd layer lines | "LOOP='HKL=0,M'" | ||||
sattelites lines | "LOOP='HKL,M=1,2..'" | ||||
AUTO | d | 0 | pattern matching | ||
1 | allows to create intensity variable at cycle 1 |
@VECTOR | key identifier of the variable 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 | |
@ORIEN | key identifier of the variable 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=@PHASE(PROFIL) is not zero.
If nProf < 0, there are nProf functions for each set of lines (incommensurate case,...)
# | optional comments | ||
c_Prof | d | the abs(nProf) reference number of the orientation functions used in line profile description | |
---|---|---|---|
... | d | ||
# | optional comments | ||
if nProf < 0 the @PROF_n keys ares read nSets=@CRYSTAL(SETS) times else the @PROF key read (nProf > 0). | |||
@PROFxx | key identifier of the variable block | ||
the following group is repeated abs(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 | ||
@ASSYM | key identifier of the variable block | ||
# | optional comments | ||
the following group is repeated first MaxAssym=@MODES(ASSYM) times then abs(nProf) times. | |||
A0 | $ | constant asymetry term | |
AT | $ | asymmetry term | *tan(theta) |
The following values are read only if nAtom=@CRYSTAL(ATOM) is not zero. The @COORD variables read for each atom depend on the value declared for case just after its name and chemical kind.
# | optional comments | ||
@ATOM | key identifier of the variable block | ||
---|---|---|---|
NAME | c7 | name of the atom | |
CHEM | 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 | ||
4 | use and read modulation coefs | order 1 | |
8 | orders 1, 2 | ||
12 | orders 1, 2, 3 | ||
16 | orders 1 to 4 | ||
32 | use and read anharmonic thermal factors | Cijk | |
64 | Dijkl | ||
128 | Eijklm | ||
256 | Fijklmn | ||
512 | free rotator (reserved for R is read as B22) | ||
# | optional comments |
@COORD | key identifier of the variable block | |
---|---|---|
X | $ | coordinates |
Y | $ | |
Z | $ | |
T | $ | occupancy (taking into account the site multiplicity) |
the following variable is read only if case=@ATOM(CASE) is even | ||
U | $ | isotropic thermal factor |
the 6 following variables are read only if case=@ATOM(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=@ATOM(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
@MODUL | key identifier of the variable 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, 97....), 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 lines sets, several block may be read if @SET_n::LINES >0 n_Hkl non zero.
@LINES | key identifier | |||
---|---|---|---|---|
h | d | Miller index of the line | ||
k | d | |||
l | d | |||
m | d | Only for 4D modulated structures | ||
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. A procedure introduce in the 1.2 release allows xnd to minimise the generated intensities : in the sets the key-word AUTO with value 1, creates the variable at the end of cycle 0, they are then minimised at cycle 2...
If n_Bond in the phase header is positive, we read here restraints on the bond lengths and angles. This block can also be used to calculate these value giving it a neglectible weight in the refinement procedure. There is first a header to read and then the parameters
n_Dist | d | number of bond lengths restraint | |
---|---|---|---|
n_Angle | d | number of angular restraint | |
the following value is read n_Bond times | |||
Temp | d | 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 distances to 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 |
This block is read only if NbHkl in the phase header specifies a
simple radial distribution :
( NbHkl = -1).
For such a simple distribution
d(r)=SIGMA(1,n) Nr(i) Delta(r-Dist(i)), which can be used to model the background (D Simeone@saclay.cea.fr), it can be shown that the scattering amplitude is a sum of
S(i,q)=sin(q Dist(i))/q Dist(i), then the scattered intensity can be expressed as
y=scale*LP*(SIGMA(1,n) S(i,q))^2.
nDist | d | Number of peaks in the function |
---|
# | optional comments | ||
Order | % | 0 | kind of the block |
---|---|---|---|
nDist group of Dist and Nr | |||
Nr | $ | scattering power | |
Dist | $ | distance |
xnd top | Next file | Previous file |
---|