Programs (downloads, links and basic instructions)

Here you will find information on the programs we use in our group - links to download sites and some starting points or links to fantastic getting started guides.

Programs

VESTA -  http://jp-minerals.org/vesta/en/ Free software crystal structure visualisation

LAMP -  http://www.ill.eu/instruments-support/computing-for-science/cs-software/all-software/lamp/ For large datasets – brilliant for in situ synchrotron X-ray diffraction and neutron diffraction datasets from the Australian Synchrotron and ANSTO

CMPR - https://subversion.xor.aps.anl.gov/trac/CMPR Fantastic plotter of diffraction patterns, allows indexing and manipulation to other formats

Rietveld analysis software 

The site with everything structural: http://www.ccp14.ac.uk/

GSAS+EXPGUI - http://www.ccp14.ac.uk/solution/gsas/ Commonly used in our group

Fullprof - https://www.ill.eu/sites/fullprof/

Jana2006 - http://jana.fzu.cz/

Rietica - http://www.rietica.org/

Note there are tutorials for each of these - get your hands dirty with them =).

A great one for GSAS is available at: http://www.scribd.com/doc/85039972/Gsas-Workshop

Further tutorials and information on GSAS can be found on: http://www.aps.anl.gov/Xray_Science_Division/Powder_Diffraction_Crystallography/

 

Other software

Battery tester software is available from the directory on the control PC.

Origin, arguably produces the best figures for publications and reports (e.g. thesis) - UNSW Science has a site-wide license which you can obtained from Ray Arnold.


Below are some introductory and common commands for LAMP, GSAS and CMPR.

LAMP

You will have files saved as XXX_LAMP.hdf

To open these locate the directory on the initial start up screen and set this as the working directory.

It is nice to work in classical layout - under layout - click extend to classical

To view and manipulate files - click file - import file workspace.

In the new window - place the first desired file in W1 and click get the file

Continue with files and change workspaces to W2, W3 and so on for other files as required.

When finished click done, which will close this window.

In the main window you can scroll through these patterns by clicking the arrows next to the workspace identifier.

Various plotting features are available where limits on x, y and z can be set and 3D plots can be made. You can plot in space under (below) or in a new screen (beside).

Common commands that can be used include the following (insert them into space next to 'DO' button and click 'DO' to action these commands):

W4=total(W3,2) - this is totalling in 2-dimensions. If W3 only had one collection in it will give a 1D diffraction pattern or a conventional diffraction pattern. If W3 had multiple collections in it - a 2D collection of diffraction patterns will be shown.

  • You can use Superplot (from tools) to scroll through the individual patterns in the 2D plot, by selecting the workspace (W4 in this case) and scrolling up or down (found below the workspace selection bar)

W20= - this plots W12 first then W13 and then W14 in one 2D plot. One after the other.

W5=W4(*,32:96,*) - this takes the middle 50% of the detector or 2D data and outputs it. You can change the numbers to give the section of the detector you want. The detector is 128 units in height. This is a method to remove (or minimise) the curvature of peaks in the collected diffraction patterns.

Wom_gsas_save,w4,"name" - this outputs a .gsa file. If the data is 2D then it will output a sequence of files labelled name_1, name_2 and so on. Note the first thing in "name" has to be a letter (e.g. 11330 will not work, but a11330 will)

STR_FIT (tools) is useful for single peak fitting routines.

 

For synchrotron XRD data into LAMP - stacking datasets for a contour plot the following might be useful:

w60= - adjust according to the number of workspaces.

 

CMPR

Select file format - For GSAS converted files GSAS-raw data

It will give .gsas you can manually type in .gsa

Navigate to the file using the right hand side options - double clicking on files will choose them and plot them

Click the plot tab and select the files you want plotted - you can use Ctrl to select specific ones

Write tab will let you write the files in the selected format - txt for Excel and Origin manipulations

Remember to choose the directory you want these saved and to SELECT the file you want written.

 

GSAS 101

You need to put in a folder the following files:

XXX.EXP                                                                   - main refinement file + change file name - I like to start off with a seed file and I can send this to you.

xxx.gsa or xxx.gsas                                                - data file

Echidna.prm or XRD.prm or similar                          - instrument file

Double click the .exp file (or on windows 7+ open the .exe and locate the file)

Then click "expedt" - giving you a dos command window. In this window if you press 'enter' you will get details about what each command does

You need to upload the datafile so enter 'y' then 'p' then 'h' then 'r' then '1' and then type the full name of the file (no spaces)

It will ask you whether this is the correct file 'y'

Then enter the instrument file name

Then the number '1' and follow this with 't' (which sets max 2theta)

Then keep typing 'x' to get out of the menu

Back in the GUI it should ask whether you want to load the changes 'yes'

Navigate around the tabs - it is a file where you are using histogram 2 - histogram one is turned off and if you have synchrotron or lab XRD data you can turn it on.

Turn off all the refinement flags for the phases - click the phase and uncheck boxes around 'refine cell'

Replace a phase with the phase you are interested in from the .cif file or insert manually and check this phase's box in the histogram tab - you can add more than one phase if you wish

In scaling tab you click on scale factor and phase fractions.

Then click 'powpref' to load above changes and 'genles' to run the refinement and liveplot to see what is happening.

From now on in you can change/alter other things such as background in the histrogram tab (change the type of background used, insert background manually, or increase # parameters used to model background) or cells/atomic positions (X) / atomic displacement parameters (Uiso) in phase tab or GW, GU, GV and other factors in the profile tab. Sometimes you need to reset the profiles to default values if the peakshapes you are refining are too broad. Play with these concepts and see what happens. If you get stuck don't worry about it too much. You can re-start.

Remember to change 1 or a couple of things and refine and probably allow only small changes - damping to 8 or 9.

 

Enjoy and may the force be with you...