xnd 1.1: phases description in the input file.

Introduction

• the phase header and the common blocks
  • Scale Factor block.
  • Phase Transition block.
• Known crystalline phases
  • Cell parameters block.
  • Supplementary header for magnetic structures.
  • Supplementary header for modulated phases.
  • Prefered orientation block.
  • Line profile block.
  • Atoms.
  • Rigid Bodies.
  • HKL list and intensities.
  • Restraints.
• Parasitic lines
• Quasicrystal lines

Phase Header and common blocks

Phase Header

Scale factor block

Phase transition block

Known crystalline phases.

Crystalline phase header

Cell parameters block.

Supplementary header blocks for magnetic structure.

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

Supplementary header blocks for modulated phases.

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	@

Preferred orientations blocks.

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

Line Profile blocks.

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)

Atoms.

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	@

the following block is read only if case == 64 or 65

	#		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

the following block is read only if case == 128 or 129

	#		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

the following block is read only if case == 256 or 257

	#		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

Rigid Bodies.

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

Hkl list and intensities.

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.

Restraints.

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

Parasitic lines

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

Quasi crystal lines

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