xnd: 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.
  • Using explicit sets of lines.
  • Incommensurate vector.
  • Prefered orientation block.
  • Line profile block.
  • Atoms.
  • Rigid Bodies.
  • HKL list and intensities.
  • Restraints.
• Other phases
  • Parasitic lines
  • Quasicrystal lines
  • Radial expension for background

Phase Header and common blocks

Phase Header

@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 factor block

Phase transition block

Known crystalline phases.

Crystalline phase header

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 parameters block.

Supplementary header blocks for magnetic structure.

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.

Supplementary header blocks for modulated phases.

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

Using explicit sets of lines.

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

Incommensurate wavevector.

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
@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

Line Profile blocks.

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)

Atoms.

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