Table of Contents
Tricks and hints for using Alan Larson and Bob von Dreele's GSAS, and Brian Toby's EXPGUI, for combined X-ray / Neutron refinement and restrained Rietveld refinement of large polymeric inorganics and minerals.
Hand Written Notes Free Zone they are on the web
Talk Aims
Topics Discussed
An initial point - computer skills
GSAS
GSAS: Some Relevant Background
Brian Toby’s EXPGUI Interface for GSAS
Brian Toby’s EXPGUI: Easy to start a new refinement (1 of 13)
Brian Toby’s EXPGUI: Easy to start a new refinement (2 of 13)
Brian Toby’s EXPGUI: Easy to start a new refinement (3 of 13)
Brian Toby’s EXPGUI: Easy to start a new refinement (4 of 13)
Brian Toby’s EXPGUI: Easy to start a new refinement (5 of 13)
Brian Toby’s EXPGUI: Easy to start a new refinement (6 of 13)
Brian Toby’s EXPGUI: Easy to start a new refinement (7 of 13)
Bob von Dreele’s comments on Damping
Brian Toby’s EXPGUI: Easy to start a new refinement (8 of 13)
Brian Toby’s EXPGUI: Easy to start a new refinement (9 of 13)
Brian Toby’s EXPGUI: Easy to start a new refinement (10 of 13)
Note from Bob von Dreele on POLA
POLA for your Diffractometer and graphite monochromator
Another way: POLA, IPOLA and diffracted beam graphite monochromator
Brian Toby’s EXPGUI: Easy to start a new refinement (11 of 13)
Brian Toby’s EXPGUI: Easy to start a new refinement (12 of 13)
Brian Toby’s EXPGUI: Easy to start a new refinement (13 of 13)
Note from Bob von Dreele on shft
Brian Toby’s EXPGUI: Profile Screen in EXPGUI with shft
Estimated Standard Deviations (ESD) vs Standard Deviations
Unit-cell “a-axis” parameter of monoclinic zirconia collected repetitively and refining zero offset
Rietveld ESD on Unit cell parameter vs the standard deviation from multiple packings and measurements
Unit-cell “a-axis” parameter of monoclinic zirconia collected repetitively and refining sample displacement
Rietveld ESD on Unit cell parameter vs the standard deviation from multiple packings and measurements
Brian Toby’s EXPGUI: Writing your own importing options
New(ish) Features in Brian Toby’s EXPGUI
Brian Toby’s EXPGUI: Graphically Defining the Background (1 of 3)
Brian Toby’s EXPGUI: Graphically Defining the Background (2 of 3)
Brian Toby’s EXPGUI: Graphically Defining the Background (3 of 3)
Brian Toby’s EXPGUI: Graphically Excluding Regions (1 of 3)
Brian Toby’s EXPGUI: Graphically Excluding Regions (2 of 3)
Brian Toby’s EXPGUI: Graphically Excluding Regions (3 of 3)
Brian Toby’s EXPGUI: If things go beserk: Backtracking through previous runs to when before things went beserk.
Brian Toby’s EXPGUI: Le Bail fitting to get the whole profile fit the data before structure refinement
Brian Toby’s EXPGUI: Why Isn’t this Synchrotron data fitting? - 1
Brian Toby’s EXPGUI: Why Isn’t this Synchrotron data fitting? - 2
Brian Toby’s EXPGUI: Why Isn’t this Synchrotron data fitting? - 3
GSAS and example ceramic / polymeric inorganic problem
GSAS and example ceramic / polymeric inorganic problem: chronic peak overlap
Will be concentrating on HOW to using GSAS for this type of problem
Nuances and People Involved in this structure
Is GSAS the only effective program for large restrained inorganic Rietveld Refinements(?)
GSAS : YES! - at present the only effective Rietveld system for these types of large problems
GSAS - relevant newish features
GSAS scales up!: to the point of refining protein data
GSAS: Individual Histogram Weighting
GSAS: Individual Histogram Weighting
GSAS: Individual Histogram Weighting (using Sum(w*d**2) as a guide)
GSAS: If you DON’T Use Histogram Weighting
GSAS: If you DO Use Histogram Weighting
GSAS: Atom shift limits
GSAS: Rod Hill and Ian Madsen VCT data collection
VCT for Refinement (1 of 4) Variable Count Time data (as collected - CAD4 style)
VCT for Refinement (2 of 4) Variable Count Time data (normalised as FCT)
VCT for Refinement (3 of 4) Variable Count Time data (normalised as FCT)
VCT for Refinement (4 of 4) Variable Count Time data (displayed as VCT)
Getting Madsen and Hill VCT data into GSAS ESD format
Getting ASCII x,y,weight data into GSAS ESD format
Setting up a Restrained Rietveld refinement of > 300 atom polymeric inorganic structures in GSAS
Restrained refinement in GSAS: setting up an EXCEL spreadsheet
GSAS: setting up an EXCEL spreadsheet: Example Atom Co-ordinates
GSAS: setting up an EXCEL spreadsheet: ConTEXT freeware text editor and column editing
GSAS: setting up an EXCEL spreadsheet: Input for Crystals to generate GSAS bond restraints lists
GSAS: Getting > 1600 bond restraints in a GSAS happy format In Crystals running the script to generate the list of restraints
GSAS: Getting > 1600 bond restraints in a GSAS happy format Use a column able editor such as ConTEXT to change to desired bond lengths and ESDs
GSAS: Getting > 1600 bond restraints in a GSAS happy format Use Scott Belmonte’s COUE software to convert the Crystals restraints into GSAS format
GSAS: setting up an EXCEL spreadsheet: Dual Occupancy Atom Constraints (in expedt: k l a k)
GSAS: setting up an EXCEL spreadsheet: Total Cell Content Restraints (in expedt: k l s c)
GSAS: setting up an EXCEL spreadsheet: Charge Balance Restraints (in expedt: k l s c)
GSAS: importing all these macro files into GSAS
GSAS: turning off /on histograms, restraints, atoms in EXPGUI
GSAS: turning off /on histograms, restraints, atoms in EXPEDT
GSAS: using restraints as diagnostics
GSAS: spiraling in on the minimum and final structure
GSAS: lessening the tedium: batch file control of the refinement : ( fully ordered model)
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: script to increase the refined angular range)
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: changing the bond restraint weighting)
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: only refining on neutron data)
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine heavy metal framework atoms)
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine light metal framework atoms)
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine interstitial metal atoms - less vacancies)
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine oxygens)
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine UISO)
GSAS: lessen the tedium: batch file control of the refinement : (Create a Batch File to follow your desired command sequence)
GSAS : If the refinement is not happy
GSAS : “wall paper bubble effect trying to keep all bonds physically reasonable
GSAS : Combined refinement on both XRD and Neutron in C1 (bond length problems - “bubbles” - to stomp on) (which imply problems with the model or symmetry).
JANA Single Crystal and Powder Diffraction Refinement
Despite a good fit : model can still have problems : wrong chemistry was defined and structure not physically reasonable.
WinGX and Platon for validation of the structure and looking for higher symmetry
WinGX for Windows single crystal suite Validation and Structure Checking
Void checking using Platon
Graphically interacting with programs that are GSAS EXP file friendly
Ton Spek’s Platon Addsym - finding extra symmetry and exploring symmetry in simple to complex polymeric inorganics
Ton Spek’s Platon Addsym - another spectacular example
Ton Spek’s Platon Addsym - spectacular example Run Platon’s Addsym in default mode
Platon’s Addsym - finding extra symmetry in hand- build inorganic models
Platon’s Addsym - finding extra symmetry in powder refined structure in triclinic
Summary
|