Analytical

Contents

Release 4.5, June 2000

      How to Use This Book

Who should use this book

How to find information

Other Cerius² books

Electronic information sources

Typographical conventions

1.      Diffraction-Crystal

Models for Diffraction-Crystal

Simulating crystal diffraction patterns

To calculate and display the diffraction pattern of a crystal

Calculate Crystal Diffraction control panel

Specifying the radiation parameters

To change the radiation parameters

Xray Preferences control panel

Neutron Preferences control panel

Electron Preferences control panel

Specifying the temperature factors

To specify the temperature factors

Temperature Factors control panel

Setting the display variables

Powder pattern display variables

To set the powder pattern display variables

To set the powder instrument variables

To set the instrumental broadening variables

To set the preferred orientation variables

Display Powder Diffraction control panel

Powder Instrument control panel

Instrumental Broadening control panel

Preferred Orientation control panel

Fiber pattern display variables

To set the fiber pattern display variables

To set the parameters for plotting simple fiber patterns

To set the parameters for plotting realistic fiber patterns

Display Fiber Diffraction control panel

Scans Preferences control panel

Simple Preferences control panel

Realistic Preferences control panel

Single crystal pattern display variables

To set the single crystal pattern display variables

Display Single-Crystal Diffraction control panel

Redisplaying the diffraction pattern

To redisplay after changing the display variables or region

Comparing with experimental data

To compare with 1D experimental data

To compare with 2D experimental data

1-D Experimental Data control panel

2-D Experimental Data control panel

Listing and saving the data

To list or save the simulated diffraction data

Output Preferences control panel

2.      Diffraction-Amorphous

Models for Diffraction-Amorphous

Simulating amorphous diffraction patterns

Scattering calculation/display types

Isotropic display

Anisotropic display

To calculate an amorphous diffraction pattern

Calculate Amorphous Diffraction control panel

Specifying the radiation

To change the radiation parameters

Xray Preferences control panel

Neutron Preferences control panel

Electron Preferences control panel

Point Preferences control panel

Setting the display variables

To set isotropic display preferences

To set meridional display preferences

To set cylindrical display preferences

To set Legendre display preferences

Isotropic Preferences control panel

Meridional Preferences control panel

Cylindrical Preferences control panel

Legendre Preferences control panel

Setting model-size corrections

To set model-size corrections for isotropic scattering

To set model-size corrections for cylindrical scattering

To set model-size corrections for Legendre scattering

Model-Size Corrections control panel

Calculating radial distribution functions

To calculate a default RDF

To alter RDF parameters and redisplay an RDF

To calculate isotropic scattering from the current RDF

Calculate RDF control panel

Broadened RDF control panel

Reduced RDF control panel

Calculating cylindrical distribution functions

To calculate a default CDF

To alter CDF parameters and redisplay an CDF

Calculate CDF control panel

Broadened CDF control panel

Reduced CDF control panel

Using experimental data

References

3.      Diffraction-Faulted

The DIFFaX algorithm

Using Diffraction-Faulted

Models for DIFFaX

File naming conventions used in DIFFaX

Running a DIFFaX job

Specifying the control file

Dump file

Symmetry Dump

Diffraction intensities

To run a DIFFaX job

DIFFaX Interface control panel

Setting the control parameters

Control Parameters control panel

Specifying diffraction parameters

Instrumental broadening

None

Gaussian

Lorentzian

Pseudo-Voigt (Gaussian and Lorentzian)

Selecting the diffraction point group

Setting the diffraction parameters

Diffraction parameters control panel

Layer Specification

Layer Creation

Layer sequencing

Setting the layer specification parameters

Layer Specification control panel

Specifying the stacking parameters

Setting the stacking parameters

Stacking Parameters control panel

4.      Rietveld (DBWS)

DBWS-9006 documentation

Models for Rietveld (DBWS)

Loading the experimental data

Running a Rietveld (DBWS) refinement

To run a Rietveld (DBWS) refinement

To run a Rietveld (DBWS) analysis (no refinement)

To run a Rietveld (DBWS) calculation

To set the refinement preferences

Rietveld (DBWS) Run control panel

Rietveld (DBWS) Refinement control panel

Specifying the simulation variables

To specify the simulation variables

DBWS Radiation control panel

DBWS Range control panel

DBWS Peak Profiles control panel

Specifying the refinable variables

Background variables

To specify the background variables

DBWS Background control panel

Model-specific variables

To specify the model variables

DBWS Model Variables control panel

Atomic variables

To specify the atomic variables

DBWS Atomic Variables control panel

Specifying the file controls and run mode

To specify the file controls and run mode

To recover results from a background job

DBWS File Controls control panel

Performing Quantitative phase analysis

To perform quantitative phase analysis using Rietveld DBWS

Phases - Quantitative Phase Analysis control panel

References

5.      Rietveld (GSAS)

GSAS documentation

Interfacing with the GSAS programs

GSAS File Controls control panel

Loading the experimental data

Writing model data to a GSAS experiment file

Models for Rietveld (GSAS)

Single or multiple phases

Rigid body constraints

.EXP template file defaults

To write model data to a GSAS experiment file

GSAS Phases control panel

GSAS Rigid Bodies control panel

Writing diffraction data to a GSAS powder data file

To write experimental diffraction data to a GSAS powder data file

GSAS Datasets control panel

Running a Rietveld (GSAS) refinement

To refine a crystal model with Rietveld (GSAS) and GSAS

Displaying the refinement results

To display the refinement results

Calculating and displaying Fourier maps

To calculate Fourier map files

To display a Fourier map file

Fourier - 3D Surfaces control panel

Fourier - 2D Sections control panel

GSAS Files control panel

References

6.      Powder Indexing

About Powder Indexing

Input and output files in Powder Indexing

The experimental powder pattern

To load the experimental powder pattern

1-D Experimental Data control panel

Preparing data for finding peaks

To find peaks using the automatic search command

To pick peaks by hand and edit the peak table

Peaks control panel

Automatic Peak Search control panel

Running TREOR90 and DICVOL91 from Powder Indexing

To Run TREOR90

To Run DICVOL91

Run Indexing control panel

TREOR90 Preferences control panel

DICVOL91 Preferences control panel

Analysis and Refinement of TREOR90 output with PIRUM

To view output files, create a new model, and run PIRUM

To run a PIRUM refinement

TREOR90 Analysis control panel

DICVOL91 Analysis control panel

TREOR90 and DICVOL91 Files control panel

PIRUM Preferences control panel

References

7.      EXAFS

About EXAFS and Excurve: overview of procedures

Models in EXAFS

Using experimental data

To read in and display an experimental data set

EXAFS Experimental Data control panel

Setting up shell and energy parameters for the EXAFS calculation

To set shell parameters from the model

To enter shell parameters by hand

To save shell parameters to file

To load shell parameters from file

EXAFS Parameters control panel

EXAFS Model Calculation control panel

Load EXAFS Parameters control panel

Save EXAFS Parameters control panel

Calculating atom energy potentials and phaseshifts

To calculate all atom phaseshifts the easy way

To calculate atom energy potentials

To calculate and display phaseshifts

To save phaseshifts to file

To load phaseshifts from file

EXAFS Potentials control panel

EXAFS Phaseshifts control panel

EXAFS Excited Atom Parameters control panel

EXAFS Potential Parameters control panel

EXAFS Phaseshift Plot Options control panel

Save EXAFS Phaseshifts control panel

Load EXAFS Phaseshifts control panel

Calculating an EXAFS spectrum (single scattering)

To calculate a single scattering EXAFS spectrum

Run EXAFS control panel

EXAFS Calculate Preferences control panel

Setting plot options

To set plot options

EXAFS Plot Options control panel

Calculating an EXAFS spectrum (multiple scattering)

To calculate a multiple scattering EXAFS spectrum

EXAFS Multiple Scattering Preferences control panel

Calculating a surface/single-crystal EXAFS spectrum

To calculate an EXAFS spectrum for a surface/single crystal

EXAFS Surface/Single Crystal Preferences control panel

Refining shell and energy parameters

Refinement constraints and restraints

Refinement constraints

Refinement distance restraints

To refine shell and energy parameters

To apply distance restraints for parameter refinement

To apply constraints for parameter refinement

EXAFS Refinement Preferences control panel

EXAFS Refinement Restraints control panel

EXAFS Refinement Constraints control panel

Scanning parameters to aid refinement

To perform a 1D parameter scan

To perform a 2D parameter scan

EXAFS Scan Preferences control panel

Fourier transforms in EXAFS

Forward Fourier transforms

Reverse Fourier transforms

To set up calculation of the forward Fourier transform

To calculate the reverse Fourier transform

EXAFS Fourier Transforms control panel

EXAFS FT Window Parameters control panel

EXAFS Reverse Fourier Transforms control panel

References

8.      LEED/RHEED

Using LEED

The LEED simulation

Procedure to calculate a LEED pattern

To alter the display properties of a LEED pattern

To set atom-specific temperature factors

LEEDiffraction control panel

Using RHEED

The RHEED simulation

Procedure to calculate a RHEED pattern

To alter the display properties of a RHEED pattern

RHEEDiffraction control panel

References

9.      HRTEM

Simulating HRTEM experiments

To perform an all-in-one simulation

Creating slices from crystal models

Calculating projected potentials

Calculating phase transfer functions

To create slices and calculate the projected potentials

To calculate a phase-transfer function from a .prj file

Create Slices control panel

Prj Preferences control panel

Ptf Preferences control panel

Propagating the beam through a slice sequence

To propagate the electron beam through the sample

Crystal Propagation control panel

Microscope parameters

To load microscope parameters from a file

To set up microscope parameters by hand

To plot the CTF for your microscope

Microscope Parameters control panel

Propagating the beam through the microscope

To propagate the beam through the microscope

To calculate a defocal series

Microscope Propagation control panel

Displaying .prj, .ptf, .dif, and .pic files

To display the contents of .prj, .ptf, .dif, and .pic files

HRTEM Display control panel

Analysis

To Display a Pendellosung plot

Pendellosung control panel

To display an experimental data file

HRTEM Experimental Data control panel

To use image analysis tools

HRTEM Image Analysis control panel

References

10.      DLS-UI

A note about the scope of this documentation

Overview

Design of the Cerius² DLS user interface

DLS-UI controls: initializing and running

DLS constraints

Load/save atom pair constraints

Fixed atom constraints

Unit cell parameters

Refinement options

Advanced features

DLS Controls control panel

DLS Set-up Atom Pair Constraints control panel

DLS Load/Save Atom Pair Constraints control panel

DLS Fixed Atom Constraints control panel

DLS Unit Cell Constraints control panel

DLS Refinement Options control panel

DLS Edit Atom Pair Table control panel

11.      IR/Raman

The vibrational spectrum calculation

Calculating the vibrational spectrum

IR/Raman Calculate control panel

Vibrational spectrum analysis

Analyzing the vibrational spectrum

IR/Raman Analysis control panel

Experimental data

Loading experimental data

IR/Raman Experimental Data control panel

A.      Data File Formats

1D diffraction data

XY-GRAPH

SIEMENS

NEW PHILIPS

PHILIPS

RAW

ILL

MAC SCIENCE

RIGAKU

SCINTAG

STOE

1CAM

2CAM

3CAM

2D diffraction data

Contour

1USER

2USER

SAXII - Siemens GADDS system format

GSAS data files

EXAFS data file