GENERAL STRUCTURE ANALYSIS SYSTEM Allen C. Larson & Robert .

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LAUR 86-748 GENERAL STRUCTURE ANALYSIS SYSTEMAllen C. Larson & Robert B. Von DreeleLANSCE, MS-H805Los Alamos National LaboratoryLos Alamos, NM 87545Copyright, 1985-2004, The Regents of the University of California.This software was produced under a U.S. Government contract (W-7405-ENG-36)by the Los Alamos National Laboratory, which is operated by the University ofCalifornia for the U.S. Department of Energy. The U.S. Government is licensed touse, reproduce, and distribute this software. Permission is granted to the public tocopy and use this software without charge, provided that this notice and anystatement of authorship are reproduced on all copies. Neither the Government northe University makes any warranty, express or implied, or assumes any liability orresponsibility for the use of this software.To cite GSAS please use the following (or equivalent):A.C. Larson and R.B. Von Dreele, General Structure Analysis System (GSAS), LosAlamos National Laboratory Report LAUR 86-748 (2004).

9/26/04TABLE OF CONTENTSPage iGSAS Introduction .1GSAS Installation .1GSAS Installation for Microsoft Windows from ftp files: .1GSAS Installation on Linux for Intel PC from ftp files: .4GSAS Organization .6BIJCALC - Thermal Motion Analysis.6CAD4RD - Input Enraf-Nonius Single Crystal Data.6CLLCHG - Unit Cell Transformation Routine.6DISAGL - Bond Distance and Angle Computation .6EXPEDT - GSAS Editor .6EXPNAM – Selection of Experiment Name .7FITSPEC - Fitting of Incident Spectra .7FORSRH - Fourier Peak Search .7FORPLOT - Fourier Map Display.7FOURIER - Fourier Map Calculations .7GENLES - General Least Squares .7GEOMETRY - Calculate Molecular Geometry.8GSAS2CIF – Prepare Crystallographic Information File .8GSAS2PDB – Prepare Protein Data Base File .8HKLSORT - Reflection Lister for Publication .8HSTDMP - Powder Pattern Lister.8ISTATS - Intensity Statistics .8ORTEP - Crystal Structure Plotting.9P3R3DATA - Input Siemens P3R3 Single Crystal Data .9POLFPLOT – Pole Figure Plotting.9POWPLOT - Powder Pattern Plotting .9POWPREF - Powder Data Preparation .9PROFTEST - Display of Powder Profile Shapes and Derivatives .9PUBTABLES - Preparation of Tables for Publication .10RAWPLOT - Plotting of Powder Patterns .10RCALC - Analysis of Structure Factor Residuals .10REFLIST - Reflection Data Lister .10REF2ASC - Conversion Of Reflection File to ASCII .10REF2BIN - Conversion of ASCII Reflection File to GSAS Binary.10RDUCLL - Cell Reduction Routine .10SCABS - Single Crystal Absorption Calculations.11SCMERGE - Single Crystal Data Sort and Merge.11SPCGROUP - Interpretation of Space Group Symbols.11SXTLDATA - General Input of Single Crystal Data .11UNIMOL - Assembling of Unique Molecules.11VRSTPLOT – Preparation of Virtual Reality Crystal Structure File.11Utility Routines in GSAS (Unix only) .11ATOM - Display of Atomic Scattering Factor Data .12ELST, DLST, SLST, TLST - List File Utilities .12PEXP, TEXP, DEXP, SEXP, LSEXP, EDEXP - Experiment File Utilities.12NEXT - Experiment Selection Utilities .12

9/26/04TABLE OF CONTENTSPage iiProgram Execution in GSAS .12GSAS Program and File Layout.13Training Exercises - Introduction .14General Instructions .15Macro capability in GSAS.16File Names in GSAS.16Neutron TOF Powder Data - Nickel Powder .17Introduction to EXPEDT .17Starting GSAS .17Running EXPEDT .19Preparation of Powder Data - Program POWPREF.36Plotting of Powder Data - Program POWPLOT .36Introduction.36Running POWPLOT .37Setup for Least Squares - Program EXPEDT.42Introduction.42Running EXPEDT .42Refinement of Powder Data - Program GENLES .51Plotting of Results - Program POWPLOT .52Introduction.52Running POWPLOT .52Suggestions for Further Work on "NICKEL" .59Background coefficients .60Zero .60Atom parameters .60Profile coefficients.60Other parameters.60Neutron CW Powder Data - Yttrium Iron Garnet .61Powder Data Setup and Atom Data Entry .61Powder Data Preparation and Refinement .63Fourier Setup and Calculations.67Fourier Map Display.71Distance-Angle Setup and Calculations .75X-Ray Powder Diffraction – Fluoroapatite .76Powder Data Setup and Atom Data Entry .76Powder Data Preparation and Refinement .77Drawing the Structure of Fluoroapatite with VRSTPLOT .84Single Crystal X-Ray Data – Oxonium Hexafluoroantimonate .90Processing Single Crystal Data .90Absorption Correction Setup and Calculations .100Intensity Statistics .103Data Merge .104Patterson Calculations.105Map Search and Structure Solution.107Atom Insertion and Structure Refinement.108Anisotropic Refinement and Structure Results .112

9/26/04TABLE OF CONTENTSPage iiiStructure Drawing .114Mathematical Basis.122Introduction.122Structure Factors .122Solvent Scattering Factor .125Single Crystal Extinction.125Total Powder Diffraction Profile Intensity.127Incident Intensity Function.127Background Functions .129Diffuse Scattering Function .131Scale Factors – Sh and Sph .132Bragg Intensity - Yph .132Intensity correction factors .133Extinction in powders .133Powder absorption factor.134Preferred orientation of powders: March Dollase function.136Preferred orientation of powders: spherical harmonics function .137Reflection multiplicity .140Angle dependent corrections.140Reflection d-spacing and lattice parameters .141Profile peak shape function.141Neutron time of flight .141Neutron and X-ray 2!.142Energy dispersive X-ray .142Profile functions .143TOF profile functions .143TOF profile function 1.143TOF profile function 2.144TOF profile function 3.147TOF profile function 4.149Interpretation of TOF powder profile coefficients .153Strain broadening .153Particle size broadening .154CW profile functions.156CW profile function 1 .156CW profile function 2 .156CW profile function 3 .158CW profile function 4 .160Interpretation of CW powder profile coefficients.162Strain broadening .162Particle size broadening .163Energy dispersive profile function .165Reflection peak widths.165Least Squares Theory .165Minimization function .165Single crystal diffraction data.166

9/26/04TABLE OF CONTENTSPage ivPowder diffraction data.167Soft restraints data.168Bond angle restraints.169Unit cell contents restraints.169Bond distance restraints .169Torsion angle restraints.170Planar group restraints .170van der Waals repulsion restraints .171Hydrogen bond restraints .171Chiral volume restraints.171Coupled torsion angle pseudopotential restraints .172Positive pole figure restraints .172Rigid body calculations.173Least Squares Calculations .175File Structures in GSAS .179Introduction.179File Name Conventions.179EXPNAM.EXP - The Experiment File .179Overall data records .179Crystal structure records .183Histogram/phase records.188Histogram records .189All diffraction histogram types .189Powder histogram records .190Single crystal histogram records .195Restraint histogram records .197Bond distance restraints .197Bond angle restraints.197van der Waals and hydrogen bonding restraints.198Chiral volume restraints.198Planar group restraints .199Torsion angle restraints.199Coupled torsion angle pseudopotential restraints .200Positive pole figure restraints .200Unit cell contents restraints.201Single crystal instrument data records .201Constraint records .202ORTEP records.203Rigid body records.204SCD instrument records.206The last record.211Handling of EXPNAM.EXP File by GSAS.211EXPNA

A.C. Larson and R.B. Von Dreele, General Structure Analysis System (GSAS), Los Alamos National Laboratory Report LAUR 86-748 (2004). 9/26/04 TABLE OF CONTENTS Page i

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