Structure Refinement

Linda Lim

Stanford University

Stanford Synchrotron Radiation Lightsource

Stephens’ Law –“A Rietveld refinement is never perfected,

merely abandoned”

Demonstration: Rietveld Refinement of spinel oxide

Outline

List of programs for Rietveld refinement

Rietveld refinement using GSAS

Fourier method

Summary

References

Selected list of Programs

o CCP14 for a more complete list(http://sdpd.univ-lemans.fr/du-sdpd/nexus/ccp14/web/index3.htm)

GSAS

GSAS-II

Fullprof

DBW

MAUD

Topas from Bruker – not free

Example: MnGa2O4

General purpose: to refine a crystal structure

Specific to this example:

Purpose: to find out the site occupancies of

Mn2+ and Ga3+ in octahedral (oct) and

tetrahedral (tet) sites respectively

Why is it significant?

Anti-site defects may affect conductivity due

to generation/compensation of charges

Inverse Modeling Method 1

Rietveld Method

Data

ModelRefined Structure

40 60 80 100 120 140 160

0

1000

2000

3000

4000

5000

6000

7000

Inte

nsity

Profile

shape

Background

1. Model

Sample: MnGa2O4

Spinel AB2O4

Lattice parameter: 8.450 Å

Space group: F d -3 m

Some options:

- Retrieve crystallographic information from powder diffraction database (.cif file)

- Key in the above information directly into

GSAS

Fractional coordinates

- Relative position of a specific atom in the

unit cell

Multiplicity

- How many of a specific atom in the unit cell

UISO

- Isotropic thermal parameter

2. Profile Shape

From instrument parameter file

Obtain from refinement of calibrant (eg.

LaB6)

Gives the initial values for the profile function

(instrumental only parameters)

Add screenshot for previous slide on how to load data

and instrument parameter file

Powpref genles

Run genles until convergence is achieved

liveplot

First fit!

3. Background

3. Background Choose a suitable background function, then refine

background (powpref genles)

Background has improved

Lstview

Chi-squared value = 253.5

Shows the

output of the

refined

parameters

Refine: Scale

Powpref

genles liveplot

Refine: Scale

Fit has improved!

Refine: Scale

Chi-squared value = 13.59

Refine: diffractometer zero

correction

Powpref

genles liveplot

Refine: Zero

Chi-squared value = 5.543

Refine: Scale

Chi-squared value = 13.59

Before refining zero

Refine: cell

Powpref

genles liveplot

Refine: cell

Chi-squared value = 5.076

Refine: profile

Peak shapes

K. Stone

Thursday afternoon

Refine: profile

Chi-squared value = 4.944

Progress so far

Inverse Modeling Method 2

Fourier MethodData

ModelRefined Structure

40 60 80 100 120 140 160

0

1000

2000

3000

4000

5000

6000

7000

Inte

nsity

Profile

shape

Background

subtract

phases

Integrated

Intensities

Fourier Difference Map

z

x

y

Add constraints

Now, we’re adding Mn in octahedral site

and Ga in tetrahedral site

Add constraintsWe want to see the occupancy of Mn in

octahedral site

Refine site occupancy

Fix site occupancies after each refinement

F= site occupancy

Refine fractional coordinates and thermal parameterConstrain x,y,z,u for Td and Oct sites

respectively.

Refine fractional coordinates and thermal parameter

X= fractional coordinates

U = thermal parameter

Final Parameters

Chi-squared value = 2.835Rp = 0.0382

Fourier difference map

Summary of refinement

parameters Final site occupancies

Final formula

(Mn0.76Ga0.24)tet (Mn0.21Ga1.79)octO3.9

Anti-site defects are present

Atom Site Occupancy

Mn Tet 0.7573

Ga Tet 0.2427

Mn Oct 0.1064

Ga Oct 0.8963

O 0.9742

How do you know when to

stop?

Chi-square, liveplot, R factor look good

Most importantly, it has answered the

scientific question you have

Stephens’ Law –“A Rietveld refinement is never perfected,

merely abandoned”

References

Collaborative Computation Project 14: http://sdpd.univ-lemans.fr/du-sdpd/nexus/ccp14/web/index3.htm

Rietveld mailing list: http://lachlan.bluehaze.com.au/stxnews/riet/using.htm

Brian Toby’s EXPGUI mailing list: http://www.aps.anl.gov/mailman/listinfo/expgui

To download EXPGUI and GSAS as a package: https://subversion.xor.aps.anl.gov/trac/EXPGUI

Powder Diffraction: Theory and Practice (RSC Publishings)

Acknowledgments

Oak Ridge National Laboratory SNS

US Department of Energy

Thank You