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"A structure is not truly solved until it is refined! : 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."

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

For presentation at AGU 2002 workshop - National Museum of Natural History, Smithsonian Institution, Washington D.C., USA, Thursday 30th May 2002; 1:00PM

[AGU 2002, Washington D.C., USA]

This page is located at http://www.ccp14.ac.uk/poster-talks/aca_2002b/


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Table of Contents

A structure is not truly solved until it is refined! : 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.

Notes Free Zone - they are on the web http://www.ccp14.ac.uk/poster-talks/agu2002b/

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)

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)

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)

Brian Toby’s EXPGUI: Profile Screen in EXPGUI with shft

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.

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 (so that atoms cannot shift more than a define absolute amount (Ĺ))

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: 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).

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

Photorealistic rendering of structures GUI WinORTEP / GUI Struplo / WinGX

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

Author: Lachlan Cranswick

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

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

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