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 (can’t 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. Meetsma’s 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 earth’s 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 DON’T 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 Spek’s Platon Addsym - finding extra symmetry and exploring symmetry in simple to complex polymeric inorganics
Ton Spek’s Platon Addsym - spectacular example
Ton Spek’s Platon Addsym - spectacular example Run Platon’s Addsym in default mode
Platon’s Addsym - (1 of 2) finding extra symmetry in inorganics and minerals - P1 triclinic starting structure.
Platon’s Addsym - (2 of 2) finding extra symmetry in inorganics and minerals - P1 triclinic starting structure.
Platon’s Addsym - finding extra symmetry in hand- build inorganic models
Platon’s Addsym - finding extra symmetry in powder refined structure in triclinic
Summary
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