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Crystallography Software Guide

GSAS II is a free crystallography software developed at Argonne National Lab that can be used for analyzing powder and single crystal X-ray and neutron diffraction data from laboratory X-rays to synchrotron sources. It has a Python-based graphical user interface with two main windows for refinement and plotting. The software guides users through the process of data analysis with step-by-step tutorials and videos and allows for background fitting, unit cell refinement, structure solution, and Rietveld refinement. GSAS II exports results and allows users to simulate diffraction patterns.

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172 views52 pages

Crystallography Software Guide

GSAS II is a free crystallography software developed at Argonne National Lab that can be used for analyzing powder and single crystal X-ray and neutron diffraction data from laboratory X-rays to synchrotron sources. It has a Python-based graphical user interface with two main windows for refinement and plotting. The software guides users through the process of data analysis with step-by-step tutorials and videos and allows for background fitting, unit cell refinement, structure solution, and Rietveld refinement. GSAS II exports results and allows users to simulate diffraction patterns.

Uploaded by

Nostalgia Blue
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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General Structure Analysis

System (GSAS) II Introduction


GSAS II

• FREE Crystallography Software


– Argonne National Lab
– Bryan Toby & Robert Von Dreele
• Python based
• Powders to Single Crystals
• X-Rays and Neutrons
• Lab X-Rays to Synchrotron
• Constant Wavelength to Time of Flight
Opening Screens

2 Screens open
• Refinement
• Plots
Help Button
Tutorials

Red = Click
Blue = FYI
Tutorials
Tutorials
Step by Step and VIDEOS

Files should automatically


download when adding
tutorial
VIDEOS
Day 1 - screenshots
Raw Data

1. Ensure proper directory


2. Choose view any file
3. Select the .XRA data
X-Ray Source Data
Select .PRM for Source Data

For real lab data, you can hit cancel and it


will use a “standard” set up for CuKα
Fields appear since data is loaded
Second Window
Adding Phase
Select Phase .EXP file
Click through screens then apply to the
Data
Fitting Background

Select Background
1. Select background function
2. Number of Coeff.
Refine

1. Click Calculate/Refine
2. Save the temporary file
Save to file that doesn’t matter
Calculated data is added to pattern
Issue falls on peak displacement
Changing Shown Data
Refine Unit Cell
Once complete click Calculate/Refine
Checking Rwp
Issue now is the general peak width
2

Click phase fraction & domain size then


calculate
Draw
Structure
2

Clicking refine top menu brings possible


1 controls. Click coordinates and thermal
parameters then refine.

Rwp ~ 9%
Producing Plot
GSAS Plot
Export Data to Plot
Data Output
Day 2 - screenshots
Add phases , then simulate data
Choose .prm file and phases to model

• After these two steps are completed, a PWDR


tree will be added to GSAS window.
Set phase fractions
The scattering contribution for each phase is set from the
product of the histogram scale factor multiplied by the
phase fraction for each phase.
Turn off optimization and adjust scale factor
Refine to run the simulation
Simulated pattern for neutron
This data can be simulated for any experiment you would
consider – neutron and x-ray wavelengths
Indexing – read in raw data
Indexing is useful if you have an unknown phase and want
to start trying to determine space group.
The .prm file will
automatically load
since the .prm file
has same name
as the data file.
Set limits – include all major peaks
Find all the peaks
If your data is high quality, auto search can usually be enough to find all major
peaks and enable a good first indexing.
Peaks are indexed
Refine peak positions + intensities
Refine peak width based on .prm file
Prepare index peak list
Run autoindexing
Need to choose symmetry of cells you wish to consider
– start w/ highest symmetry
Indexing
Indexing results – bad
Indexing results - good
Links/Take Away

• https://subversion.xray.aps.anl.gov/trac/pyGSAS
– GSAS II Home
• https://www.aps.anl.gov/Education/Powder-
Diffraction-Educational-Materials
– Powder Diffraction Education Materials
• Plenty of Tutorials
• Plottable Data
• User Friendly

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