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ECM 2001 Talk - New features in existing powder diffraction software - to help battle ever more complex crystallographic problems

by Lachlan M. D. Cranswick

For IG_9.1: Crystallographic Computing: Advanced Computational Tools for Small Molecules and Materials (Monday, 27th August 2001) - ECM 2001 - Krakow / Cracow - Poland - 25th August to 1st September 2001

This page is located at http://www.ccp14.ac.uk/poster-talks/ecm2001/


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Table of Contents

SIG_9.1: Crystallographic Computing: Advanced Computational Tools for Small Molecules and Materials (Monday, 27th August 2001) New features in existing powder diffraction software to help battle ever more complex crystallographic problems.

Talk Aims

Notes Free Zone - they are on the web http://www.ccp14.ac.uk/poster-talks/ecm2001/

A snapshot of programs (canít do justice to all the updates in freely available software)

New features in Chekcell and Rietica

Why Bother - Volume of Oxygen in the Earth's Outer Core

New Features in Chekcell and Rietica: What do we need from the diffraction data?

Problems that need to be overcome by (Crysfire); Chekcell and Rietica

Problems that need to be overcome by (Crysfire); Chekcell and Rietica

Problems that need to be overcome by (XFIT, Crysfire, Refcel, UNITCELL); Chekcell and Rietica

Chekcell - Jean Laugier and Bernard Bochu http://www.ccp14.ac.uk/tutorial/lmgp/

Routine operation of Chekcell (1 of 5)

Routine operation of Chekcell (2 of 5)

Routine operation of Chekcell (3 of 5)

Routine operation of Chekcell (4 of 5)

Routine operation of Chekcell (4 of 5)

Chekcell: Major new feature of Chekcell Porting and integration of Ton Spek and A. Meetsmaís Le Page

Chekcell: GUI Cell transformation

Chekcell: result of using Le Page

1. Chekcell: indexing unknown cells from unexpected phase transitions in high pressure experiments

2. Chekcell: re-indexing lost cells (maybe transformed) from big pressure jumps in high pressure experiments due to racing a synchrotron beam-dump.

3. Chekcell: re-index again (big jumps due to trying to beat a synchrotron beam dump)

Chekcell / LePage Summary:

Rietica Rietveld for Mass Le Bail fitting to get cell vol. Example of 3 phase setup : KClO3; KClO4, B2-KCl

Rietica Rietveld for Mass Le Bail fitting : Rietica Database of Structure

Rietica Rietveld for Mass Le Bail fitting At simplest: 3 step process after initial setup has been done

Rietica Rietveld for Mass Le Bail fitting 1 of 10

Rietica Rietveld for Mass Le Bail fitting 2 of 10

Rietica Rietveld for Mass Le Bail fitting 3 of 10

Rietica Rietveld for Mass Le Bail fitting 4 of 10

Rietica Rietveld for Mass Le Bail fitting 5 of 10

Rietica Rietveld for Mass Le Bail fitting 6 of 10

Rietica Rietveld for Mass Le Bail fitting 7 of 10

Rietica Rietveld for Mass Le Bail fitting 8 of 10

Rietica Rietveld for Mass Le Bail fitting 9 of 10

Rietica Rietveld for Mass Le Bail fitting 10 of 10

Rietica Rietveld for Mass Le Bail :Graphing up the results

New Rietica Macro Language - RIET BASIC

1. Rietica and Le Bailing : Short-term non-linearities of an Energy Dispersive Detector(?)

2. Rietica and Le Bailing : Short-term non-linearities of an Energy Dispersive Detector(?)

Chekcell and Rietica: results of the volume of Oxygen and the earthís other core

GSAS for large restraint Rietveld refinements of polymeric inorganics

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

People Involved in this structure

GSAS: Some Relevant Background

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 new features

GSAS: Individual Histogram Weighting

GSAS: Individual Histogram Weighting

GSAS: Individual Histogram Weighting (use Sum(w*d**2) as a guide)

GSAS: If you DONíT Use Histogram Weighting

GSAS: If you DO Use Histogram Weighting

GSAS: Rod Hill and Ian Madsen VCT data collection

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: 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

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 (bond length problems - bubbles - to stomp on) May be problems with overlapping impurities (possible impurity problems only found during the refinement).

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

Ton Spekís Platon Addsym - spectacular example

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

Platonís Addsym - (1 of 2) finding extra symmetry in inorganics and minerals - P1 triclinic starting structure.

Platonís Addsym - (2 of 2) finding extra symmetry in inorganics and minerals - P1 triclinic starting structure.

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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