Refine crystal orientation and lattice parameters for an sqw or d0d/d1d/...d4d object
>> [rlu_corr,alatt,angdeg] = refine_crystal(w, rlu0, rlu)
>> [rlu_corr,alatt,angdeg] = refine_crystal(w, rlu0, rlu, alatt_init, angdeg_init)
In addition, there are keyword arguments to control the refinement e.g.
>> [rlu_corr,alatt,angdeg] = refine_crystal(..., 'fix_angdeg')
>> [rlu_corr,alatt,angdeg] = refine_crystal(..., 'free_alatt', [1,0,1])
In all cases, further output arguments can be returned:
>> [rlu_corr,alatt,angdeg,rotmat,distance,rotangle] = refine_crystal(...)
This function is used to get a matrix that relates the coordinates of a vector (h0,k0,l0)
as expressed in an initial or reference lattice to the coordinates (h,k,l) in the true lattice.
It does this by taking a set of points (h0,k0,l0) and the corresponding set of true indicies
(h,k,l), and refining the lattice parameters and orientation. The refined lattice parameters
are also returned.
The output from this function can be used to correct the crystal orientation and lattice parameters
in Horace. Type >> help change_crystal_horace for more details.
Input:
------
w sqw object
rlu0 Positions of reciprocal lattice vectors as h,k,l in reference lattice
(n x 3 matrix, n=no. reflections)
rlu True indexes of reciprocal lattice vectors (n x 3 matrix)
Optional input parameter:
alatt_init Initial lattice parameters for start of refinement [a,b,c] (Angstroms)
angdeg_init Initial lattice angles for start of refinement [alf,bet,gam] (deg)
If one or both of alatt_init and angdeg_init are not given, then the corresponding
reference lattice parmaeters are taken as the initial values for refinement.
Keywords (more than one is permitted if not inconsistent)
fix_lattice Fix all lattice parameters [a,b,c,alf,bet,gam]
i.e. only allow crystal orientation to be refined
fix_alatt Fix [a,b,c] but allow lattice angles alf, bet and gam to be refined
together with crystal orientation
fix_angdeg Fix [alf,bet,gam] but allow pattice parameters [a,b,c] to be refined
together with crystal orientation
fix_alatt_ratio Fix the ratio of the lattice parameters as given by the values in
lattice_init, but allow the overall scale of the lattice to be refined
together with crystal orientation
fix_orient Fix the crystal orientation i.e. only refine lattice parameters
Finer control of refoinement of lattice parameters: instead of fix_lattice, fix_angdeg,... use
free_alatt Array length 3 of zeros or ones, 1=free, 0=fixed
e.g. ...,'free_alatt',[1,0,1],... allows only lattice parameter b to vary
free_angdeg Array length 3 of zeros or ones, 1=free, 0=fixed
e.g. ...,'free_lattice',[1,1,0],... fixes lattice angle gam buts allows alf and bet to vary
Output:
-------
rlu_corr Conversion matrix to relate notional rlu to true rlu, accounting for the the
refined crystal lattice parameters and orientation
qhkl(i) = rlu_corr(i,j) * qhkl_0(j)
alatt Refined lattice parameters [a,b,c] (Angstroms)
angdeg Refined lattice angles [alf,bet,gam] (degrees)
rotmat Rotation matrix that relates crystal Cartesian coordinate frame of the refined
lattice and orientation as a rotation of the initial crystal frame. Coordinates
in the two frames are related by
v(i)= rotmat(i,j)*v0(j)
distance Distances between peak positions and points given by true indexes, in input
argument rlu, in the refined crystal lattice. (Ang^-1)
rotangle Angle of rotation corresponding to rotmat (to give a measure
of the misorientation) (degrees)
The output argument rlu_corr, together with the input alatt0 and angdeg0, are sufficient to compute
the other output arguments. That is why Horace functions that use the output of this function will
generally only require rlu_corr.
EXAMPLES
Want to refine crystal orientation only:
>> rlu_corr=refine_crystal (rlu0, alatt0, angdeg0, rlu, 'fix_lattice')
Want to refine lattice parameters a,b,c as well as crystal orientation:
>> [rlu_corr,alatt]=refine_crystal (rlu0, alatt0, angdeg0, rlu, 'fix_angdeg')
% Overloaded methods:
sqw/refine_crystal
sqw/refine_crystal
d4d/refine_crystal
d3d/refine_crystal
d2d/refine_crystal
d1d/refine_crystal
d0d/refine_crystal