Constraining sublattices with different space groups in diffpy-cmi

[Sandra Skjærvø]

Hi,

I have a structure that can be divided into two sublattices (oxygens in one and cations in another), and I want to give those two sublattices different spacegroup constraints using ConstrainAsSpacegroup. I know this is possible in PDFgui by simply marking the atoms of the sublattices separately and adding contraints. How can I do this in CMI? Do I need to define the sublattices as separate structures, or can I use the methods in class DiffpyStructureParSet directly?

I hope I have provided enough info, but if not, let me know.

Thanks in advance!

Sandra

[Mikkel Juelsholt]

Hi Sandra

If you have not figured this out yet, I know a slow and dirty way to do it. 

If you load in your structure in a P1 space group, then you can manually write the symmetry constraints. 

For example I have this code with a hexagonal structure where I want to break the symmetry of some atoms and not of others. I have written something like this: 

# Add the structural paramters using space group constaints for the crystal

# Ignore the ADP-s which will be set later.

phase_crystal = pdfgenerator_crystal.phase

sgpars_crystal = phase_crystal.sgpars

#Set unit cell parameters

for par in sgpars_crystal.latpars:

    recipe.addVar(par, name=par.name+'_s', tag='cell')

# Constrain a and b so we keep the hexagonal unit cell

recipe.constrain('a_s','b_s')

    

#Load in the atomif postions and name them

for par in sgpars_crystal.xyzpars:

    lclabel = par.par.obj.GetName().lower()

    lcsymbol = lclabel.rstrip(string.digits)

    # name the variables

    name="{}_{}".format(par.par.name, lclabel)

    tags = ['xyz', 'xyz_' + lclabel, 'xyz_' + lcsymbol]

    recipe.addVar(par, name=name, tags=tags)

    

#  Manually add the symmetry relations between the 6 W atoms that is generated from expanding the structure into P1. 

recipe.newVar('xw1')

recipe.constrain('x_w1','xw1')

recipe.constrain('y_w1','xw1')

recipe.constrain('x_w2','-xw1+1')

recipe.constrain('y_w3','-xw1+1')

recipe.constrain('x_w4','-xw1+1')

recipe.constrain('y_w4','-xw1+1')

recipe.constrain('x_w5','xw1')

recipe.constrain('y_w6','xw1')

I hope this makes sense. 

Mikkel