Fullprof精修使用说明-英文.pdf

FullProf users guideFullProfRietveld,Profile Matching&Integrated Intensities Refinement of X-ray and/or Neutron Data(powder and/or single-crystal)HELP FULLPROF/INTRODUCTION:HOW TO GET Fullprofo Purpose authors references documentationo Features of FullProfo Running the programm.input and output files.2-DESCRIPTION OF INPUT FILES DETAILED DESCRIPTION OF CODFIL.PCR FILE 3-MATHEMATICAL INFORMATIONo Calculated profile.Structure factors.o FoiTn/aclor calculations and Refinemenlso Magnetic scatlering calculations.o Backgroundo Peak-shape functionso Monochromator,Lorentz and geometrical correctionso Asymmetryo Preferred orientationo Absorption(and microabsoprtion)o Systematic line shiftso Codewordso Standard deviationso Methods of refinemenlo Agreement factorso Analysis of the refinement 4-ADDITIONAL NOTESo Magnetic refinementso Propagalion vectorso Microstrains and Size effectso HKL-dependenl shifls and asymmelry.o Quantilalive phase analysiso User-supplied paramelers&subroulines for slructure-factor calculation.o Examples of user-supplied subroutines.5-SINGLE CRYSTAL AND INTEGRATED INTENSITY REFINEMENTSo General commenls.o The extinction correction.o Mixed refinements.6-REFERENCES.7-DIMENSIONS OF ARRAYS OF THE STANDARD VERSIONDETAILED DESCRIPTION OF INPUT FILE:CODFIL.PCR(comment lines)http:/sinq.web.psi.ch/sinq/doc/fullprof_old.html(I of 82)2005-11-921:22:35FullProf users guideline 1:Comment2:Job Npr Nph Nba Nex Nsc Nor Dum Iwg Iio las Res Ste Nre Cry Uni Cor2_1:Resolution file3:Ipr Pgl loc Mat Per Lsl Ls2 Ls3 Syo Prf Ins Rpa Sym Hkl Fou Sho Ana4:lambda 1 lambda2 Ralio Bkpos Wdl Clhm muR AsyLim Rpolarz4_1:Bkpos Wdl labscor5:NCY Eps R at R an R pr R gl Thmin Step Thmax PSD Sent。6:2Thela/TOF Background7:Excluded regions(LowT HighT)8:Additional scattering factors8_1:Additional scattering,factors(nain,DfD,dfDD,ilyin)8_2:Additional scattering factors(A 1,B 1,A2,B2,A3,B3,A4,B4,C)9:Number of refined parameters1010 1:Zero Code Sycos Code Sysin Code Lambda Code MORE10 1-1:P0 Cod P0 Cp Cod Cp Tau Cod Tau10 l(bis):Zero Code Dtt 1 Code Dtt2 Code 2sinThet1。2:Background coefficients/codes10.3:Background Tranf coefficients/codes Additional background coefficients/codes10 4:Window for Fourier filtering11:Data for PHASE number:n=Current R Bragg:RbNat Dis Mom Prl Pr2 Pr3 Jbt Irf Isy Str Furlh ATZ Nvk Npr MoreJvi Jdi Hei Sol Mom Ter Brind RMua RMub RMuc Jtyp Vek X Y Z Biso Occ Rx Ry Rzlx ly Iz beta 11 beta22 bela33 MagPhAtom Typ Mag Vek X Y Z Biso Occ Mom beta PhasePhi&Theta of Cone-axis+unused paramsbetal 1 beta22 beta33 betal2 betal3 beta23/Codes11-5-1:Scale Shape 1 Bov Strl Str2 Str3 Strain-ModelScl Sc2 Sc3 Sc4 Sc5 Sc6U V W X Y GauSiz LorSiz Size-ModelUr Vr Wr EtarO XrExtl Ext2 Ext3 Ext4 Ext5 Ext6 Ext7a b c alpha beta gammaPrefl Pret2 Asyl Asy2 Asy3 Asy4Additional Shape parametersAdditional U,V,W parameters for Lambda2AsyP Shift 1 Shift2 Mod A ModShttp:/sinq.web.psi.ch/sinq/doc/fullprof_old.html(2 of 82)2005-11-9 21:22:35FullProf users guide11-5-lbis:TIME OF FLIGHT INPUTScale Extinct Bov Strl Str2 Str3 StrainModelSig2 Sigi SiqO Xt YtZl ZO IsizeModelGam2 Gaml GamO LStr LSiz a b c alpha beta gammaPrefl Pref2 alphO betaO alphl betal Absorption Correction ParametersAsyP Shift 1 Shift2 Mod A ModS11-10-2:5 additional strain parameters11-11:Propagation vectors:11-12:Further parameters:11-13:Additional strain parameters:11-14:Generalized strain parameters:11-15:Soft distance constraints:11-16:Soft moment constraints:12-1:Hard limits for selected parameters:12-1:Nconfg Nsolu Num Ref Nscalef13:Iscale Idif14:2Thi 2Th21.-INTRODUCTION AND GENERAL INFORMATIONSHORT REFERENCE GUIDE OF THE PROGRAMFFFFFF ppppppF1 1 P P fF1 1 P P fFFFF1 1 PPPPPP fFu u 1 1 P r r r ooo f f fFu u 1 1 P r o ofFuuuuu 111 111 P r ooo fProgram:FullProf(Version 3.5 Dec97-LLB-JRC)Juan Rodriguez-Carvejal Laborctoic Leon Brillouin(CEA-CNRS)Tel:[phone],Fax:[phone]Disclaimer:The author is not responsible for erroneous results obtained with FullProf.This guide cannot substitute the lack of knowledge of users on crystallography,magnetism,diffraction physics and data analysis.This short guide is merely a description of the input files with minor explanations on how to proceed.Powder diffraction is becoming more and more powerful but FullProf is not an automatic,(black-box)program,as is usually found in single crystal structure determination.No attempt has been made in order to predict the behaviour of the program against bad input data.The user must check his(her)data before claiming a misfunction of the program.The author acknowledges all suggestions and notification of possible bugs found in the program.IndexThe most recent version of FullProf is always in pub/divers/fullp“of the http:/sinq.web.psi.ch/sinq/doc/fullprof_old.html(3 of 82)2005-11-9 21:22:35FullProf users guideanonymous ftp-area of the LLB unix-cluster.Users interested in create their own subroutines to link with FULLP-library are asked to read the file”fpreadme”in the above mentioned disk-area.To access this area from Internet,one has to type in the local host the following commands:LocalPrompt ftp 132.166.17.100 orLocalPrompt ftp ball.saclay.cea.frAnswer with the word:anonymous,to the Login request and password.Within the ftp prompt,do:From a UNIX host:ftpcd pub/divers/fullp-Go to FullProf areaftpget fpreadme-Obtain the documentftpJbye-Return to hostFrom some VMS-VAX hosts:ftpset def pub/divers/fullp-Go to FullProf areaftpget fpreadmen-Obtain the documentftpex-Return to host工nd。1.1:Purpose,authors,references and documentationFullProf is a program for Rietveld analysis(structure profile refinement)of neutron(CW,TOF,nuclear and magnetic scattering)or X-ray powder diffraction data collected as a function of the scattering variable T(2theta or TOF).The program can be also used as a Profile Matching tool,without the knowlegde of the structure.Single Crystal refinements can also be performed alone or in combination with powder data.FullProf has been developed starting from the program of Wiles&Young,J.Applied Cryst.14,149(1981),(DBW3.2S,Versions 8711 and 8804).The modifications of the code are mainly related with the re-organization of the central routines performing the calculation of profile functions,derivatives,structure factors,and the introduction of many other things.The total source is more than 1 Megabyte(more than 28.000 fortran lines).The format of the main control input file(e.g.a control file created for use with DBW-8711 can be used by FullProf with minor modifications).The input file is accepted as interpreted free format.The source is written in standard FORTRAN 77 language,and is organized as to be easily adapted to different computers.The actual version can be run on VAX,Alpha and Unix computers,Macintoshes and on PCs(Lahey Computer Systems Inc.FORTRAN-compiler,minimum 386/4Mb with coprocessor required).The migration towards genuine Fortran 90 is in progress.Index1.2:Features of FullProf:-Choice of line shape(Gaussian,Lorentzianz modified Lorentziansz pseudo-Voigtz Pearson-VII or Thompson-Cox-Hastings)for each phase.-Neutron(constant wavelength and TOF)and X-ray(laboratory and synchrotron sources)-One or two wavelengths(Kal+Ka2)-Background refinement-Multi-phase(up to 8 phases)-Preferred orientation:two functions available-Absorption correction for a cylinder-Choice between three wheighting schemes:standard least squares,maximum likelihood and unit wheights.http:/sinq.web.psi.ch/sinq/doc/fullprof_old.html(4 of 82)2005-11-9 21:22:35FullProf users guide-Choice between automatic generation of hkl and/or symmetry operators and file given by user.-Magnetic structure refinement(crystallographic and spherical representation of the magnetic moments).Two methods:describing the magnetic structure in the magnetic unit cell of making use of the propagation vectors using the crystallographic cell.This second method is necessary for incommesurate magnetic structures.-Automatic generation of reflections for an incommensurate structure with up to 24 propagation vectors.Refinement of propagation vectors in reciprocal lattice units.-h,k,1 dependence FWHM for strain and size effects-h,k,1 dependence of shift and asymmetry for special kind of defects-Profile Matching.The full profile can be fitted without prior knowledge of the structure(needs only good starting cell and profile parameters)Index-Quantitative analysis without need of structure factor calculations.-Chemical(distances)and magnetic(magnetic moments)slack constraints-Resolution function(for pseudo-Voigt peak shape)may be supplied in a file-Structural or magnetic model could be supplied by an external subroutine for special purposes(rigid body,TLS,polymers,form factor refinements,small angle scattering of amphifilic crystals,description of incommensurate structures in real direct space,etc.)-Single crystal data or integrated intensities can be used as observations(alone or in combination with a powder profile)-Neutron(or X-rays)powder patterns can be mixed with integrated intensities of X-rays(or neutron)from single crystal or powder data.Index1.3:Running the program,input and output files.To run the program the user has to invoke the name of the executable file and press the ENTER/INTRO key.Of course the executable file must be in a directory included in the PATH or an alias should exist.For for doing sequential refinements there is a number of command files that can be used.The command files(scripts)depend on the operating system.A facility is included in FullProf for versions higher that 3.2 that allows sequential of cyclic refinements.Examples:1:Prompt FULLPROF2:Prompt FullProf,FullProf can also be run from a command file.After invoking the execution of the program the following dialog appears in the current window(for the PC version):*PROGRAM FULLPROF(Version 3.5-Dec97-LLB JRC)*火Rietveld,Profile Matching&Integrated Intensity Refinement of X-ray and/or Neutron Data(PC-version)=Give the code of the files(xx for xx.per):http:/sinq.web.psi.ch/sinq/doc/fullprof_old.html(5 of 82)2005-11-9 21:22:35FullProf users guideAfter entering a value for xx,hereafter assumed to be CODFIL,the program prompts the following question(If xx=startingz the program enter in a new dialog to create an example of CODFIL.per file(called starting.per)for making a pattern calculation.The user can modify this generated file to adapt it to his(her)own problem)=Give the name of data file(yy for yy.dat)(or yy.uxd,yy.acq)(=CODFIL):If the user answer with the name of the data file isCODFIL.dat(or CODFIL.uxd).We assume,in the following,the user has attributed the value FILE to the item yy.The file CODFIL.per must be created(from the scratch or by modifying an existing one)with the help of an ASCII editor.This file contents the diffraction conditions and crystallographic information needed by the program.The optional file FILE.dat(or FILE.uxd,FILE.acq)contents the profile intensity of the powder diffraction pattern.For doing sequential refinements the user can run the program usinga command file,or answer CYC to the prompt asking for the code of the files.In the last case another dialog opens:=Code of the starting*.per file(xx for xx.pcr):Here the user should answer with the xx explicit name(let us assume that the code is CODFIL).=Give the code of data files(yy for yynnn.dat,uxd,acq)(=CODFIL):As suggested by the question the name of the data files should have a part that constitutes the code followed by a ordinal number.The user should give here the code.Let us assume that the code is FILEDAT.=Number of the starting*.dat file:46=Number of the last*.dat file:133The user should give the ordinal numbers of the first and last files to be processed.The numbers 46 and 133 are examples.The program works by using the file CODFIL.per to process the file FILEDAT46.dat.The updated CODFIL.per are,then,used to process the file FILEDAT47.datz etc.At the end,when the file FILEDATI33.dat has been processed,the control file contents the parameters adequate to the last treated file.The results of the whole set of treatments are stored in file CODFIL.RPA.IndexInput files:To run the program,you need at least one input filez CODFIL is the code of the control file given by the user.CODFIL.PCR:Input control fileIt must be in the current directory to run the program.This file contains the title and crystallographic data and must be prepared by user with a file editor.http:/sinq.web.psi.ch/sinq/doc/fullprof_old.html(6 of 82)2005-11-9 21:22:35FullProf users guideThere are two different formats for this file:the first on is fr format and closely related to that of the Young&Wiles1s program.The second is based on keywords and commands.(this last format is not available at present)Warning:this file is normally up-dated every time you run the program(see parameter NXT on line 3).In the first stages of a refinement,it is wise to save a copy of this file with a different name.The following files are optional.FILE.DAT:Intensity data file(unit 4):format depends on instrument.If you do not specify the name FILE,the program takes FILE=CODFIL.Not necessary for pattern calculation modes.FILE.BAC:Background file(unit 12).The format of this fileis the following(as that of FILE.DAT for INSTRM=0):first line:2theta(initial)step 2theta(final)following lines:list of intensities in free format.CODFILn.HKL:Set of files with the reflections corresponding to phase nn(n is the ordinal number of a phase).These files are optional and depend on the value of the parameter IRF(n)(see below)If sequential refinements have to be done,this file is called HKLn.HKL 工nd。MYRESOL.工NSTRU:File describing the instrumental resolution function.Any name can be used and its content depend on the value of the paramenter IRESO(see below).GLOBAL.SHP:File providing a numerical table for calculating Indexor CODFIL.SHP:the peak shape and its derivative.The peak shape should be given in a normalized form P(x)where the variable x is chosen to give a FWHM=1 and the area is 1=Integxl,x2 P(x).dx=l.That allows the use of the conventional U,V,W parameters for defining the FWHM as a function of angle.The format of this file is the following:Linel:Any commentLine2:Np8,nupr,(anpr(j)z j=l,nupr)Nq8=Number of pointsnupr=Number of different profiles anpr(j)=Angle to which profile n jn is best adapted The rest of the lines are columns withX,P(X,1),PP(X,1),P(X,2),PP(X,2),P(X,nupr),PP(X,nupr)in free format.PP(X,j)is the derivative of P(Xz j)with respect to X.The profile of a reflection situated between anpr(j)and anpr(j+1)is linearly interpolated between the profiles P(X,j)and P(X,j+1)CODFIL.COR:File with corrections for integrated intensities of profile intensities depending on the value of the variable ICORR.See below.IndexOutput files:Except for*.OUT and*,SUM,their creation depends on the value of a flag which is quoted in parenthesis.The ordinal number on the flag list is given in brackets.http:/sinq.web.psi.ch/sinq/doc/fullprof_old.html(7 of 82)2005-11-9 21:22:35FullPr