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"Some tricks and hints for using Alan Larson and Bob von Dreele's GSAS and Brian Toby's EXPGUI for Rietveld crystal structure refinement of minerals and polymeric inorganics from powder diffraction data"

by Lachlan M. D. Cranswick (CCP14 Project Secretary)

For presentation at Materials Science and Engineering, Columbia University, room 1128-1134, Mudd Bldg, MC 4701, 500 W. 120th Street, Manhatten, New York, NY 10027, USA, Friday 10am, 28th June 2002

(Local contact: Feng Zhang)

[Materials Science & Engineering @ Columbia University, New York, USA]

This page is located at http://www.ccp14.ac.uk/poster-talks/columbia2002/


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Table of Contents

Some tricks and hints for using Alan Larson and Bob von Dreele's GSAS and Brian Toby's EXPGUI for Rietveld crystal structure refinement of minerals and polymeric inorganics from powder diffraction data.

Hand Written Notes Free Zone they are on the web http://www.ccp14.ac.uk/poster-talks/columbia2002/

Talk Aims

Topics Discussed

An initial point - computer skills

GSAS

GSAS: Some Relevant Background

Brian Tobyís EXPGUI Interface for GSAS

Brian Tobyís EXPGUI: Easy to start a new refinement (1 of 13)

Brian Tobyís EXPGUI: Easy to start a new refinement (2 of 13)

Brian Tobyís EXPGUI: Easy to start a new refinement (3 of 13)

Brian Tobyís EXPGUI: Easy to start a new refinement (4 of 13)

Brian Tobyís EXPGUI: Easy to start a new refinement (5 of 13)

Brian Tobyís EXPGUI: Easy to start a new refinement (6 of 13)

Brian Tobyís EXPGUI: Easy to start a new refinement (7 of 13)

Brian Tobyís EXPGUI: Easy to start a new refinement (8 of 13)

Brian Tobyís EXPGUI: Easy to start a new refinement (9 of 13)

Brian Tobyís EXPGUI: Easy to start a new refinement (10 of 13)

Brian Tobyís EXPGUI: Easy to start a new refinement (11 of 13)

Brian Tobyís EXPGUI: Easy to start a new refinement (12 of 13)

Brian Tobyís EXPGUI: Easy to start a new refinement (13 of 13)

Brian Tobyís 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 Tobyís EXPGUI: Importing crystal structure data

Brian Tobyís EXPGUI: Writing your own importing options

New(ish) Features in Brian Tobyís EXPGUI

Brian Tobyís EXPGUI: Graphically Defining the Background (1 of 3)

Brian Tobyís EXPGUI: Graphically Defining the Background (2 of 3)

Brian Tobyís EXPGUI: Graphically Defining the Background (3 of 3)

Brian Tobyís EXPGUI: Graphically Excluding Regions (1 of 3)

Brian Tobyís EXPGUI: Graphically Excluding Regions (2 of 3)

Brian Tobyís EXPGUI: Graphically Excluding Regions (3 of 3)

Brian Tobyís EXPGUI: If things go beserk: Backtracking through previous runs to when before things went beserk.

Brian Tobyís EXPGUI: Le Bail fitting to get the whole profile fit the data before structure refinement

Brian Tobyís EXPGUI: Why Isnít this Synchrotron data fitting? - 1

Brian Tobyís EXPGUI: Why Isnít this Synchrotron data fitting? - 2

Brian Tobyís EXPGUI: Why Isnít 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 DONíT Use Histogram Weighting

GSAS: If you DO Use Histogram Weighting

GSAS: Atom shift limits (so that atoms cannot shift more than a define absolute amount (Ň))

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 Belmonteís 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 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 Spekís Platon Addsym - finding extra symmetry and exploring symmetry in simple to complex polymeric inorganics

Ton Spekís Platon Addsym - another spectacular example

Ton Spekís Platon Addsym - spectacular example Run Platonís Addsym in default mode

Platonís Addsym - finding extra symmetry in hand- build inorganic models

Platonís Addsym - finding extra symmetry in powder refined structure in triclinic

Summary

Author: Lachlan M. D. Cranswick

Email: l.m.d.cranswick@dl.ac.uk

Home Page: http://www.ccp14.ac.uk

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