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The MODES User Guide v3

1. 5 1 1 Directory This command opens a new window showing files in the working area There are 5 panes showing those with extensions IPG DIF RES and FQT plus the last pane containing the file header information The display does not update automatically to update click on Rescan MODES Directory of C rawdata si 1332 ipg l siz z060 dif siz4523 res a Fie osi71393ipg Groups 42 PGDD2 si71335 ipg si77061 dif si71386 ipg si78813 dif User CD ATAT si71387 ipg _ i si7 1388 ipg Title BhO lt 2 9ml 210 C 002 Euken Date 09 APR 2008 23 54 49 si 1390 ipg si 1391 ipg Energy range 0 524 to 1 068 meV si 1392 ipg 7 ae 5i71393 ipg Ean a0 ale 4747 z si 1394 ipg History Gopt s si 1395 ipg pa T si71396 ipg e P P 2 aroups 963 1004 zl IPG Files DIF Fies RES Files FOT Files Header info 18 Page 5 1 2 Read Int Read data from file into workspaces There are 2 options 1 block enter workspace name eg w or all blocks 5 1 3 Write Int Write data from workspaces to file There are 2 options 1 block or all blocks 5 1 4 Export Export data from RAW or MODES treated files eg IPG to formats readable by other Data Analysis Programs such as MSLICE or DAVE Data can be cropped in x axis and binning modified Export SPE DAVE BAR Raw ime other Run 77466 Range of Spectra First e63 Last i004 Peas Energy range meV Min 0 88 Max
2. The measured spectrum I Q w is proportional to the four dimensional convolution of the scattering law S Q w with the resolution function R Q w of the spectrometer via I Q w S Q w amp R Q w so S Q w can be obtained in principle by a deconvolution in Q and w The method employed here is based on the Fourier Transform FT technique 6 7 On Fourier transforming the equation becomes I Q t S Q t x R Q t where the convolution in w space is replaced by a simple multiplication in t space The intermediate scattering law I Q t is then obtained by simple division and the scattering law S Q w itself can be obtained by back transformation The latter however is full of pitfalls for the unwary The advantage of this technique over that of a fitting procedure such as SWIFT is that a functional form for I Q t does not have to be assumed On IRIS the resolution function is close to a Lorentzian and the scattering law is often in the form of one or more Lorentzians The FT of a Lorentzian is a decaying exponential exp at so that plots of In I Q t against t would be straight lines thus making interpretation easier In general the origin in energy for the sample run and the resolution run need not necessarily be the same or indeed be exactly zero in the conversion of the RAW data from time of flight to energy transfer This will depend for example on the sample and vanadium shapes and positions and whether the analyser temperature has ch
3. Jo Js 2nd to Sth scattering range as specified Total Total scattering J sum all J Mult Multiple scattering Jms sum Jn from 2 to 5 R1 ratio Ja Jt R1 ratioJi h Ri is the normal output this is the multiple scattering only R can be used to correct for multiple scattering attenuation due to re scattering and absorption all at once The value of R1 or R1 is averaged over the positive amp negative energy values and is printed This is also the form of the data in the ANS file The use of multiple scattering corrections is not straightforward and will depend on the method of data interpretation employed The two cases that have been used most frequently are 1 Corrections to the Elastic Incoherent Structure Factor EISF In this case only the fraction of the scattering that is multiple scattering is used that is the total scattering is reduced by the multiple scattering fraction 2 Fitting of peak shapes In this case the shape of the multiple scattering with energy transfer is important The multiple scattering can change the shape of the sample S Q w and therefore must be applied before the resolution broadening is applied 3 5 Convolution peak fitting 3 5 1 Theory The measured data I Q w is proportional to the convolution of the scattering law S Q w with the resolution function R Q w of the spectrometer via I Q w S Q w R Q w The traditional method of analysis has been to fit the measured I Q w with an
4. The input files have extension FW lt n gt lt m gt To fit choose the extension from the drop down menu enter file number or Browse Read and Plot Choose the nth order polynomial for the fit and when a new window appears enter initial guesses for the coefficients and choose fixed or fit Then Plot Fit The fit values will be store in the output file with extension POLY_LOG 5 7 7 Smooth This routine performs a smoothing operation on a spectrum via one of 2 techniques 1 FFT Smooth transform apply the Weiner filter to truncate the noisy high x values and back transform 2 Maximum Entropy ME Smooth uses same concept as in ResMem section 3 7 2 5 8 Bayes This section contains a set of programs performing analysis using Bayesian methods Several of the routines use a Res file this contains a smooth curve representing the resolution function if the instrument 5 8 1 ResMem EEx Polynomial Fit Ert fozi fw21 d File osi79993 Browse Ey Polynomial Order Plot Fit 4 coeffs Smooth Raw Int Run Spectra First s3 Last i004 EE Energy range me Min 0 62 0 5 Max 0 77 os Incr o 002 _Trnoat Ren This routine creates a PGOO2 RES file from chosen vanadium run It also outputs a VAN file 37 Page e Frame 1 Insert number of runs Insert sample run numbers Insert range of spectra
5. GCL or ICL routines which will be converted to run on as GCL scripts The information in this document has been organized as follows the first section gives an overview of the theory behind converting raw output from the quasielastic spectrometers to physical and accurate quantities using MODES In the next section after a description of how to initialize the program each item on the menu and its functions are described in detail Installation instructions can be found in the appendix 2 General overview Data handling of Quasielastic Neutron Scattering QENS data from instruments such as IRIS and OSIRIS can be divided into two sections Reduction and Analysis Reduction involves taking the raw data in time of flight and converting it into an instrument independent scientific function such as S Q w which depends only on the dynamics of the sample measured The operations include e Converting from time of flight to energy transfer or other unit such as d spacing e Summing of spectra into groups and converting from detector angle to Q value e Correcting for container scattering if necessary e Correcting for absorption from sample and container and multiple scattering In the package the data after these processes are saved in Intermediate file format Subsequent analysis involves operations on Intermediate files which in general are smaller than the original raw files Analysis will be taken to refer to science based interp
6. minimum energy emax maximum energy einc energy increment for SPE format output export_file 1 runnumber where runnumber runnumber for DAVE format ouput export_file 2 runnumber floor where runnumber runnumber floor minimum value for data default 0 0 62 Page
7. with 2 column format i e lt width gt mw Sre lt error in width gt use one line per group it Yes No Plot fit Yes to show plots for each group _Lorenzians Owar or No The start fit wah l PLOT Prob Group fi Lorentzians elastic peak amp up to 3 quasielastic peaks He ie o 0 Water elastic peak amp 3 linked Widths 1 2 3 Intensities 1 2 3 quasielastic peaks If the Plot option is On then after each fit a window appears to allow plotting of the fitted data and or the residuals Lorentzians elastic only 0 or with peaks 1 2 3 Water elastic only 0 or with peaks 2 Next moves on to the next group and Cancel switches off the plotting option and the fitting continues for all groups e Frame 7 selection of Plot options Prob for probability of each Lorentzian as a function of group Plotted as Log no of quasi elastic lines the less negative the value the better the fit the top curve is the best This is very useful to decide how many Lorentzians are appropriate to fit the data Group for fit for chosen group Choose whether the x axis is to be Q or Q Plot Widths amp Intensities for 1 2 or 3 peaks 39 Page e The Log button opens 2 windows that give a summary of the fitted parameters Use the sliders to choose the spectrum number and the number of peaks fitted For each spectrum the parameters thei
8. 34 92 inor Floor a n E E am EE 5 1 5 Import Import data from other Data Analysis Programs such as MSLICE or DAVE 5 1 6 Exit This exits Modes and OpenGenie A warning window will appear for confirmation 5 2 MODES The commands here define various general parameters for use in the program They can be altered at any time The default values given below are those set on start up The values chosen here will affect the way other routines are performed 19 Page 5 2 1 Raw This will change the location ie disk amp directory for the raw data files 5 2 2 Work This will change the location ie disk amp directory for intermediate data that is the area where all the calculations will be performed It does not need to be the area from which the program is started although the user must have access rights to that area The type of file extension and format Genie ipg or Nexus can also be defined 5 2 3 Analyser This defines the analyser crystal and reflection IRIS has Graphite and Mica OSIRIS only has graphite Default PGOO2 5 2 4 Calib This defines whether the detector efficiencies in the files R IS_detector calib or OSIRIS_detector calib previously detector calib are to be used by ICON amp IONIAN Default not used 5 2 5 Geom This defines the shape of the sample flat plate or cylinder and is only needed if absorption and or multiple scattering corrections are to be carried out Defau
9. Res file function for resolution and the RES file created by ResNorm if required Perform the following operations e Frame 1 Choose the file extension from the drop down menu Insert run number or Browse Read and Plot the first group 38 Page e Frame 2 shows the analyser selected in the Quasilines function SEE MODES option Choose energy range for the fit meV Bt fpa ipg Define energy range and binning Run ario Browse E gt a Run to rebin Plot first group if required e Frame 3 choose whether to use a Mn aoo Max 1200 Normalisation file If yes insert RES file name Binning B an Plot or Browse e Frame 4 shows RES file appropriate for selected analyser Read file and Plot if required e Frame 5 choose to apply multiple scattering Res fle PG002 res Read Eor corrections requires a MSC file from MINUS e Frame 6 choose fit parameters options are Elastic peak Yes or No to fit the peak Fit function options Background sloping linear constant Foalyser is PGOOZ Energy range C u ev Normalisation file N Yes MS corrections N Yes Bastic peak Yes No flat or zero Backoond Fix width 1 No or File to fix one of the oe ices Ea three quasielastic peaks with widths as Eee defined in a text file including extension
10. and resolution runs Choose the file extension from the drop down menu Insert sample run number or Browse amp Select Insert resolution run number or use provided one PG002 res Read then Plot Sample S and or Resolution R to check energy range of the first group e Frame 2 The analyser chosen in MODES options is shown Choose energy range and increment step for Fourier Transform Run to rebin energy then Plot Sample S and or Resolution R to check energy range of the first group e Frame 3 Choose whether to apply MS corrections e Frame 4 Choose whether to normalise to 1 Choose type of scale for the y axis Run to perform FFT Insert group number and Plot or Choice for multiple plots A new window will appear Insert X range after using Plot in nanoseconds Insert Y range Choose Symbol Colour amp Line from drop down menus 32 Page Insert group number and Display amp Plot line and P error if required To add further groups change group number and change the Symbol and or Colour and or Line then Plot to add data set to graph N B Display will always clear the graph of all data sets before plotting the desired one whereas Plot will plot the desired data set on top of the ones already plotted e Save as FQT file Et fing ipo Sample Number e5628 Browse Res data Number E Browse Res
11. appropriate set of functions related to the form of S Q w predicted by theory 10 Page In quasielastic scattering the simplest form is when both the S Q w and the R Q w have the form of a Lorentzian a situation which is almost correct for reactor based back scattering spectrometers such as IN10 amp IN16 at ILL The convolution of two Lorentzians is itself a Lorentzian so that the spectrum of the measured and resolution data can both just be fitted with Lorentzians The broadening of the sample spectrum is then just the difference of the two widths The next easiest case is when both S Q w and R Q w have a simple functional form and the convolution is also a function containing the parameters of the S Q w and R Q w functions The convoluted function may then be fitted to the data to provide the parameters An example would be the case where the S Q w is a Lorentzian and the R Q w is a Gaussian For diffraction the shape of the peak in time is a convolution of a Gaussian with a decaying exponential and this function can be used to fit the Bragg peaks The final case is where R Q w does not have a simple function form so that the measured data has to be convoluted numerically with the S Q w function to provide an estimate of the sample scattering The result is least squares fitted to the measured data to provide values for the parameters in the S Q w function This latter form of peak fitting is provided by SWIFT It employs a l
12. data analysis to model fitting is the use of Bayesian methods which involve the direct use of probability theory 11 This technique has now been applied to quasielastic scattering 12 to determine the number and widths of Lorentzian peaks and to tunnelling 13 to determine the number and positions of side peaks A more recent development for quasielastic scattering is the determination of the exponent in a stretched 14 Page exponential 3 7 2 ResMem This program creates a smooth finely interpolated file for the resolution function from coarse and noisy data Smoothness is imposed through an invariant Gaussian interpolant whose width can be optimised A linear background may be subtracted The x binning energy transfer must be constant The User does not normally need to run this program The appropriate resolution files have already been created by the instrument scientists 3 7 3 ResNorm This program creates a group normalisation file by taking a resolution file as defined in section 11 3 and fitting it to all the groups in the resolution data file which has the same grouping as the sample data of interest The routine varies the width of the resolution file to give a stretch factor and the area provides an intensity normalisation factor The output is written to an ASCII file with the name FOROO7 DAT in the following format data file e resolution file amplitude stretch factor Q value Kss repeat for each g
13. e Frame 2 Choose energy range for the fit meV Choose increment for Bin Save the rebinned data as a VAN file e Run and Save creates the file lt analyser gt RES where lt analyser gt is eg PGOO2 as defined in MODES setup 5 8 2 ResNorm This routine fits the Res file to the measured resolution data and creates a RES file containing the stretch factor for the width and the integrated intensity Perform the following operations e Frame 1 Choose the file extension from the drop down menu Insert run number or Browse Read and Plot the first group e Frame 2 shows the analyser selected in the MODES option Choose energy range for the fit meV Define energy range and binning Run to rebin Plot first group if required ResMem Number of Runs fi farsas Range of Spectra First 2 last fs Run Number Energy range me for fit Min 0 33 KE hix o 003 13s 2 Increment ResNorm Ext fipg ipg Foalyser is PGOOZ hin 00 0 Binning pa Energy range htx fio p ev Res file PGOO2 res passat pi e Frame 3 shows appropriate RES file the analyser selected Read file and Plot if required e Fit and Plot group A file with the name run_name RES is created 5 8 3 QL function This runs the QuasilLines program using the
14. function File Pcoo2 res Plot Plot R Fury plot X range 0 0 fo Y range 9 50e 001 foo 1 02e 003 fio Foalyser is PGOOZ Energy range me Min 0 55 fos Max 0 69 fos Increment 0 002 Plot Plot R Symbol Circe 4 Colour Green 4 line OS 4 MS corrections N Yes Normalise to 1 Yes No linear amp Log re _ 5 7 2 Fqt Fit This fits the I q t with a specified function e Frame 1 Insert run number or Browse amp re Fes emt Select Read to read all the groups Plot to see the first group and iow 25 33 Page re Fixes beta check on time range in nanoseconds e Frame 2 Insert Group number and Plot Insert time range amp click on Range to rebin Plot if required Choose the type of fit from the appropriate drop down menu Exponential function requires 2 parameters exp1 ns and Bgd value between 0 and 1 for the form I Q t I Q 0 exp exp1 t Bgd Stretched exp requires 3 parameters exp1 ns Bgd and beta values between 0 and 1 for the form 1 Q t I Q 0 exp exp1 t Bgd A second window titled Parameters also opens upon opening the F Q t Fit window and is also opened when either of the drop down menus are clicked Insert starting value amp choose whether the parameter is to be fitted or stays fixed Click on Fit to close the para
15. graph previously plotted within a session 48 Page References 1 2 3 4 5 6 7 8 9 CJ Carlile Rutherford Laboratory report RL 74 103 1974 A K Soper W S Howells amp A C Hannon RAL Report RAL 89 046 1989 H H Paalman amp CJ Pings J Appl Phys 33 2635 1962 M W Johnson AERE Report R7682 1974 J S Higgins R E Ghosh W S Howells amp G Allen JCS Faraday II 73 40 1977 J S Higgins G Allen R E Ghosh W S Howells amp B Farnoux Chem Phys Lett 49 197 1977 D C Champeney Fourier Transforms amp their physical applications Academic Press E Oran Brigham The Fast Fourier Transform Prentice Hall U P Wild R Holzwarth amp H P Good Rev Sci Instr 48 1621 1977 A Heidemann W S Howells amp G Jenkin Neutron Spin Echo Lecture Notes in Physics 128 Ed F Mezei Springer Verlag 1980 10 V Arrighi J S Higgins AC Burgess amp W S Howells Macromolecules 28 2745 1995 11 D S Sivia Physica B 202 332 1994 12 D S Sivia C J Carlile W S Howells amp S Konig Physica B 182 341 1992 13 D S Sivia amp CJ Carlile J Chem Phys 96 170 1992 Further reading e Information on Open Genie can be found at http www opengenie org Main Page e IRIS User Guide can be found at Manual for IDA the original data analysis program for IRIS data M Telling and W S Howells RAL Report RAL TR2000 004 2000 49 Page Appendix A Installation Instructions for MODES3 1 Installation Start
16. radius outer radius amp number density if sample is a solid cylinder r1 0 r2 outer radius Insert name of MUT file or Browse amp Select e Frame 3 Insert beam width e Frame 4 For annular geometry Insert number of annuli For standard IRIS OSIRIS cells insert 1 Values of r1 r2 and r3 will be inner sample radius outer sample radius and outer sample radius 2xcan wall thickness respectively If your container has more than one annulus for each annulus insert radius number density and name of MUT file or Browse amp Select and 28 Page Continue e Run and Plot the results if required 5 6 3 Create S Q w file Create S q w file This creates an S Q w file to be used as input in the multiple scattering correction program MINUS section 3 4 2 aa number pts ner Qw grid w micro eV number pts incr e Frame 1 Define the Q w grid size e Frame 2 Set an output file name including File the extension Create S Q w file based on one Polynomial Order mama ions i odel of two options Polynomial ora Jump M de MA ae Choose model option and a new window will appear to input parameter values In all cases cea the model will be used to calculate the half width wo such that S Q w is then calculated as S Q w Peakheight wo w0 w The input for the polynomial function has a maximum of 5 parameters c1 to c5 so tha
17. will show the fitted values of the previous fit So if a set of groups is to be fitted when a good first fit is obtained these values may be used as starting values for the next group Alternatively for a given group the fitted values for 1 peak may be used as starting values for a 2 peak fit To fit each group individually enter the Group number To start the fit for all groups click Auto 35 Page 5 7 4 Swift Plot This allows you to plot saved fit parameters from SWIFT e Frame 1 Swift Plot Fit function option Quasielastic Choose the fit function section 5 7 3 Insert sample run number or Browse pee Read to read all groups into workspaces Polly Energy range is given for the data Shift File firsa1762 Energy is in me e Frame 2 Enter the group number and Calc Choose energy range for display and Plot Use Choice to choose colour symbol and line type for the plot similar to that in section 5 7 1 Data energy min Group number Fit energy min 5 7 5 Msd Fit Plot energy min This routine fits a straight line to data in order to calculate the mean squared displacement msd The input files have the extension MSD which were created by the program ELWIN section 5 4 3 In the first window insert the number of run numbers the first run number the variable eg Temperature the variable start value and the increment
18. 1 quasielastic peaks a single Lorentzian would produce a straight line in the plot of In Qt versus t Deviations from a straight line would indicate that either there are more than one Lorentzians or that the shape is not a Lorentzian In the former case it is often difficult to establish any quantitative conclusions as to the number of peaks or their relative gradients 2 inelastic peaks a pair of broadened peaks transforms into a damped cosine function The central elastic peak would add a constant This is the case where the I Q t could become negative and taking the modulus makes the shape less easy to recognise 3 non Lorentzian shape this could be either a stretched exponential form exp at where B can range from 0 to 1 or not of standard function form The former case has been discussed by Arrighi et al 10 4 EISF the transform provides an immediate estimate of the EISF without any arbitrary fitting procedure From the properties of FT the elastic peak 6 function transforms to a constant and the first time coefficient t 0 is the integrated count so the ratio of I Q t at long time to zero time is the EISF provided that I Q t has become constant at long time However bear in mind that due to taking the modulus the long time limit will be scattered around a positive non zero value rather than zero itself when the elastic component is zero 3 7 Bayesian analysis 3 7 1 Introduction An alternative and better method of
19. 1 peak Bastic QE E 2 0E Polly ger Shift 1 peak Plot Fit Plot Res 34 Page Define energy range and increment for fit Run to rebin data to new energy range Plot S ample and Plot R es to plot first group of each file e Frame 3 Choose Group number Choose type of fit function amp number of peaks from drop down menu Plot Fit displays the fit Plot Res displays the residuals Save Fit stores parameters in file and Reset zeroes stored parameters Plot width plots stored fitted half widths A new window will appear to set starting fit parameters for each option These can be set to remain fixed or to be fitted Use Fit to close the window and start the fitting procedure Option 1 Background Origin Elastic height Height and half width meV for each Lorentzian Option 2 Background Origin Elastic height Height and half width meV for each Lorentzian Option 3 Background Origin Height and half width meV for each Lorentzian Option 4 Background Origin Height and half width meV for the elastic peak Height and half width meV for the inelastic peak Parameters Set Parameters Option 2 Fixed Background Fixed Origin Fixed Pk 1 Height Fixed Pk 1 H width me E amp Fixed Pk 2 Height Cc Fixed Pk 2 H width me After the first fit when the parameter window opens it
20. 5 4 5 Bin gt Ascii Bin gt Ascii This routine is used to convert binary files into ASCII versions ex fo men TT E e Choose the extension of the binary file from drop down seca tta case om E menus graphite intermediate files mica intermediate files and data analysis files Dem ed e Insert run number or Browse e Insert filename automatically gives an extension ASC e Run e The asc file created will have some header information plus three columns Energy meV 25 Page S Q w and error in S Q w Data for each group is given one after the other 5 4 6 Ascii gt Bin This routine is used to convert ASCII files into binary files The input format should be three columns corresponding to Energy meV S Q w and error in S Q w Only one Q can be read 5 5 Diff 5 5 1 dVan This is DORIAN for vanadium standard and creates a DVN file in the working area 5 5 2 dNorm This normalizes diffraction data DIF by the measured vanadium standard DVN Creates a DIN file in the working area 5 5 3 dMerge This merges the data from several DIF diffraction files Diffrparis amp aa e Custom into one spectrum Selection Sequence e Frame 1 Use Input default or Custom diffraction parameter file No Runs 2 First Run 40076 e Frame 2 Select range of spectra under either Peas Selection Return to enter Run Number or Sequence Then Read e Fram
21. Data mark Data error Fit Res Backgrd Bastic Peak 1 Peak 2 Peak 3 Fit energy min Plot energy min 42 Page 5 8 10 Jump fit Jump data Two forms of jump motion can be fitted section 3 7 2 the e foz fw21 Chudley Elliott model or the Singwi Sjolander model f Fie far __orowce R Perform the following operations e Choose an option from drop down menu e Insert file name or Browse and Read Jump fit A new window will open to choose the model e Use scroll bar to see x and y values of each point 1 e Choose fit range for groups points Number of points 17 e Choose a model from the drop down menu x 0484 y 45 528 e Plot data with Data and Fit e Plot result as a function of Q or Q iLines General Raw l Int ASCII Ext fipa ipg Run fa1763 Browse Fe Foalyseris PGDO2 Energy range pw eV Mn 558 400 0 Max 680 400 0 Res file P6002 res Stretch No Yes 1 0 Broadening No Yes FWHM broadening 10 0 Keep width fixed No Yes Line shape Gaussian amp Lorentzian Input Refine parameters No Yes File name Read 1 min pt fr max pt pr Chudley Bliot 5 8 11 iLines U m This routine fits for amu RAW IPG and ASCII files where data contains inelastic peaks There are 2 options General for inelastic peaks not necessarily
22. First foes Last i004 Reza Display Options Linear sqrt log Display Options Linear Sort log Plot limits Off On x minf maxf amp S yim max amp Energy zimin max amp 6 Intensity Plot limits Off On x minf max 6 8 yim max amp Energy zimin maxf amp 8 Intensity 5 9 2 Viz This routine provides a colour contour plot and then by using the cursor plots of cuts in the horizontal and vertical direction are produced The cursor can be moved to a different point and new cuts plotted Perform the following operations e Frame 1 is a NoteBook with Tabs to give choice of input same as in CONTOUR section 5 9 1 e Frame 2 Select option for x axis spectrum number angle or Q value e Frame 3 Plot to plot graph Click on position shown by cursors in contour plot to display slices Click middle mouse button scroll wheel to remove cursors before Cancel other routines cannot be run until cursors have been cancelled Options will open a new window and allow changes in colours smoothing etc 45 Page X axis values Angle o Plot commands some sm 5 9 3 Actions Change type DAR Colour table frainbow 0 4 Celltype SQRT 3 cat oh ate Far Line colour Black Line thickness fi 0 Character size fi 5 This window provides a selection of commands for displa
23. Genie commands and the following are MODES commands 5 9 1 Contour This routine provides a colour contour plot Perform the following operations Frame 1 is a NoteBook with Tabs to give choice of input Raw specified spectra from raw data file Insert run number Choose spectral range Read to read data Single specified groups from a single intermediate file Insert run number or Browse extension is chosen using drop down menus Read to read data Selection specified single group from a selection of Intermediate files amp Choose extension from drop down menu Insert number of runs amp a new window will appear Input run numbers and a variable for each e g temp Input a title for the variable amp Continue Insert Group number amp Read to read data Sequence specified group from a selection of Intermediate files in sequence Choose extension from drop down menu Insert number of runs and the number of the first run Input group number and press calculate Read to read data e Frame 2 select option for intensity scaling The sequence from Linear to Log enhances the low count regions e Frame 3 choose limits amp switch On Off e Plot to plot graph 44 Page CONTOUR Raw Single Selection Sequence Ext fipg ipg tqt e mee E CONTOUR Raw Single Selection Sequence Run ai Range of Spectra
24. PT or SSFIT SSLPT LPT OUTPUT Q LPT N A MINUS IPG or IMI MSLPT MSC MSD FIT MSD MST LINE_LOG MUT IPG or DIF MUT POLY FIT FW lt n gt lt m gt POLY_LOG QL FUNCTION RES IPG or JAG or IBG or IMI Q2LPT QL1 QL2 QL3 QL DATA or AM or IBM FW lt n gt lt m gt AM lt n gt lt m gt 57 Page El lt m gt or QWLPT QLW WATI WAT2 WAT lt n gt lt m gt QL PLOT QL N A RESMEM RAW or SAV or s lt m gt VAN lt analyser gt RES RESNORM lt analyser gt RES IPG or IAG or RES IBG or IMI or IAM or IBM S Q w RAW or SAV or s lt m gt SQE SPE STR FUNCTION RES IPG or IAG or IBG or IMI QSELPT QSE SE1 SE2 SE3 or AM or IBM QSB QSS El lt m gt STRETCHED gt BETA SIGMA QSB QSS N A SWIFT RES IPG or IAG or IBG or IMI Q lt n gt _ lt m gt or E lt n gt _ lt m gt or or AM or IBM P lt n gt _ lt m gt or S lt n gt _ lt m gt TRANS TRM 58 Page Appendix D IDA Command Language ICL Glossary 1 ICON 1 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 aco defines the analyser aco energy first spectrum last spectrum analyser code where energy analyser energy first spectrum first spectrum to be grouped last spectrum last spectrum to be grouped analyser code code for reflection analyser code 1 for PG002 2 for PG004 3 for MI002 4 for MI004 5 for MIO06 eg for PGOO2 the defa
25. Read and Plot The plot will be Ln Intensity vs Q The data will be fitted with a straight line where the gradient is the msd There are then 2 options new windows will appear e Manual allows you to fit each run and each group point individually Use the scroll bar to see the values of x and y for each point group Choose the fit range with min pt and max pt numbers Click Fit to start fitting Save the fit parameters for the run Output file with extension LINE_LOG Click Next to fit the next run x O x Run 1 74581 temp 10 Pa ao of points 42 Number of points 42 En ro x 0 036 yo DAG i fio i J iner ce HE EE min pt f1 max pt 42 min pt fr max pt 42 Caneel Pi Bap f MSD intro MSD manual fit Sequence Selection No Runs E First Run fraser Variable text femp Var start 4 36 Page e Auto will fit all runs in one go Use the scroll bar to see the values of x and y for each point group Choose the fit range with min pt and max pt numbers Click Fit to start fitting Plot msd as a function of the variable eg Temperature An output file is automatically created with the msd data with extension WST 5 7 6 Poly Fit This routine fits polynomials up to the 5 order to full width at half maximum values obtained using the BAYES program section 5 8
26. The MODES User Guide v3 S O w o A 0 2 0 1 O 0 1 0 2 Energy Transfer AE E1 E2 meV W S Howells V Garcia Sakai F Demmel M T F Telling and F Fernandez Alonso Quasielastic Neutron Scattering Section Molecular Spectroscopy Group ISIS Pulsed Neutron and Muon Source Rutherford Appleton Laboratory Chilton Didcot OX11 0QX United Kingdom February 2010 1 Page Acknowledgments It is a pleasure to thank all those who have contributed to the development of the MODES package and this latest version of the user manual The development of this package would not have been possible without the help and input of the ISIS Computing Group with special thanks to Freddie Akeroyd Thanks to D S Sivia for providing the Bayesian analysis routines and to the input discussions and comments from all instrument scientists on the IRIS and OSIRIS spectrometers over their lifetime We also thank the user community for innumerable suggestions and for testing the programs We also acknowledge the assistance from the summer student Michael Cole to finalise the present user manual 2 Page Contents 1 Introduction 2 General overview 3 Modes overview 3 1 Calibration 3 2 I Q w 3 3 Diffraction 3 4 Corrections 3 4 1 Absorption 3 4 2 Multiple scattering 3 5 Convolution peak fitting 3 5 1 Theory 3 5 2 Hints on running 3 5 3 Multiple scattering version 3 6 Transform to I q t 3 6 1 Theory 3 6 2 Hints o
27. a irs42893 raw reads the raw data from the given path d s 10 displays spectrum 10 w s 1 saves raw data in spectrum 1 into the workspace w dw displays data in workspace w u lam s 1 changes the x units of spectrum 1 to wavelength u t s 1 changes the x units of spectrum 1 to time 55 Page integrate s 2 integrates counts in spectrum 2 w_int integrate w 1 xmin xmax integrates data in workspace w 1 between xmin and xmax and saves in new workspace w_int w_rebin rebin lin w 0 0 0 01 1 0 perform a linear rebinning of the x axis of workspace w between 0 and 1 with a bin size of 0 01 and save the rebinned data in a new workspace w_rebin writexye s 100 data txt writes data in spectrum 100 into the ascii file data txt in 3 columns x y and error writexye w data txt writes data in workspace w into the ascii file data txt in 3 columns x y and error d w10_T1 displays data in workspace w10_T1 for example containing data for 10 detector at 1 measured Temp d w10_T1 0 5 0 5 0 0 1 constrains the display of data in workspace w10_T1 to an range in x of 0 5 to 0 5 and in y of O to 0 1 a pc Sblack d w10_T1 displays data in workspace w10_T1 in black a pc alter plot colour a pc green p w10_T2 plots data in workspace w10_T2 in green over that already displaye
28. ad_diffm runnumber run sequence number runs where runnumber runnumber run sequence sequence number number runs number of runs this command is repeated number runs times with run sequence increasing from 1 to number runs 4 2 dm_ran defines the d range to be used for each run dm_ran runnumber run sequence d min d max where runnumber runnumber run sequence sequence number d min minimum d for that run d max maximum d for that run runnumber amp run sequence are the same as those in 4 1 4 3 dm_start defines the increment in d spacing amp starts the merging dm_start d increment where d increment increment in d spacing same for all runs 4 4 dm_save int creates an output file if required extension is dim 5 Fury 5 1 sw_read reads the sample amp resolution data sw_read sample run res runn where sample run sample runnumber res runn resolution runnumber 5 2 fugue starts the transforming fugue e min e inc e max unit option ms option where e min minimum energy e inc energy increment e max maximum energy unit option 1 to normalise to unity 0 not normalised ms option 1 for MS corrections 0 no corrections 5 3 fury_int creates an output file if required set extension fqt 61 Page 6 Export 6 1 6 2 6 3 6 4 read_int reads data read_int runnumber where runnumber runnumber export bin defines energy range export_bin emin emax einc where emin
29. amp IONIAN use the parameters from 3 1 to convert the RAW data into I Q w or strictly speaking I 26 w The RAW file will normally contain the standard values of 28 but the user can chose whether to update the detector efficiency or if the spectra need to be normalised to the vanadium The user may also choose how to combine spectra into a smaller number of groups This procedure is carried out for all runs in the experiment Since IRIS can use the Graphite and Mica analysers simultaneously the program will have to be run twice for any run if both analysers are to be used and the output file names extensions differentiate between the two types of analysers Both programs read the monitor spectrum correct for efficiency amp convert to wavelength For each spectrum or group of spectra the spectra are read converted to wavelength normalised to the corrected monitor spectrum and converted to energy transfer The data is then converted to I Q w 3 3 Diffraction IRIS and OSIRIS can also be used for diffraction experiments either dedicated solely to diffraction or for using the diffraction detectors in parallel with quasielastic scattering In this case the detector angles and efficiencies are fixed and the calibration is not necessary Instead of calculating I Q w the reduction routine converts the raw data into d spacing There is a bank of detectors with each detector at a different scattering angle which then give different d spacing
30. ams Appendix D ICL Glossary 48 49 50 55 57 59 5 Page 1 Introduction MODES3 is the latest version of MODES the Graphical User Interface for the old IDA Iris Data Analysis package It is based on OpenGenie with the GUI windows from Tcl Tk The original IDA had a GUI interface GUIDE which submitted old Genie like programs and stand alone FORTRAN programs for batch processing and graphics was provided interactively by old Genie routines The aim of the new package is to provide an integrated one stop interface Much of the data manipulation is performed using OpenGenie routines with Genie Command Language GCL However more complex and involved calculations are easier and more efficiently performed in FORTRAN Thus FORTRAN modules are called by GCL and have been converted to OpenGenie Modules The basic operation consists of a selection of GCL commands referred to as the Ida Command Language ICL In the line mode option there are question and answer routines in GCL which provide parameters for the ICL commands In the Tcl Tk mode menus and graphics are provided and GUls are used to provide the parameters for the ICL commands The package contains the many commonly used functions for the analysis of quasielastic neutron data and should provide the tools necessary for the new users to this technique and become a workhorse for the regular user For the more experienced user there is the option of incorporate their own
31. anged between the runs The procedure takes this into account automatically without using an arbitrary fitting procedure in the following way From the general properties of the FT the transform of an offset Lorentzian has the form cos Wot isin Wot exp Ft thus taking the modulus produces the exponential exp Ft which is the required function If this is carried out for both sample and resolution the difference in the energy origin is automatically removed The results of this procedure should however be treated with some caution when applied to more complicated spectra in which it is possible for I Q t to become negative for example when inelastic side peaks are comparable in height to the elastic peak The interpretation of the data must also take into account the propagation of statistical errors counting statistics in the measured data as discussed by Wild et al 8 If the count in channel k is X then X lt X gt AX where lt X gt is the mean value and AX the error The standard deviation for channel k is 0 7 lt AX gt which is assumed to be given by 0 lt X gt The FT of X is defined by Xj lt Xj gt AX and the real and imaginary parts denoted by xj and xj respectively The standard deviations on Xj are then given by o7 X 1 2 Xo 1 2 Xz and 07 X 1 2 Xo 1 2 Xpj Note that o Xo Xo and from the properties of FT Xor Xx Thus the standard deviation of the first coefficient of the FT is the square roo
32. bles to Tables Modes _tcl to Main Tcl The folders can be anywhere as long as there is a tree structure Modes3 etc eg C Program files Modes3 or G My Programs Modes3 The Open Genie program files are in C Program files CCLRC ISIS Facility Open Genie 1 4 Genie settings Run the program Open Genie settings and set the following The top box of settings Directory Locations do not need changing Click on tick box next to Enable Very Advanced Options to allow changes to The bottom box of settings Startup File Locations Set startup locations to point to your Modes3 folder eg Startup file GCL C Modes3 Main init_sys gcl for ISIS instruments Or C Modes3 Main init_sys_forte gcl for non ISIS instruments Saved Binary Image File keep as default Interface Startup Code TCL C Program Files Modes3 Main modes_interface tcl The locations could also be C Modes3 or G My Programs Modes3 Or olympic babylon5 Public IRIS_analysis Modes3 etc The file init_sys gcl in the folder Modes3 Main needs to be edited In the section for WINNT the variable System root needs to be changed to point to the appropriate Modes3 folder Note in this file there is also a variable System home which is the folder containing the file MODES _user gcl This allows the latter file to be in a different location to the program necessary for example when the program is on the central disk Open GENIE settings Directory Locations For GCL co
33. d with d w10_T1 t logy toggles to log scale on y axis d m w displays data in workspace w with markers d l w displays data in workspace w with lines d e w displays data in workspace w with errors a b 5 alters binning to every 5 c h shows cursor press ctrl x to show x value or ctrl y to show y value press e to exit 56 Page Appendix C Summary of input output files for programs PROGRAM INPUT files OUTPUT files ACORN MUT IPG or IMI ABS ANA DIF or DIN ANALYSE IPG or IMI IBG or IAG or IBM or IAM CALIB IRIS_detector calib or IRIS_detector calib or OSIRIS_detector calib OSIRIS_detector calib DET CONV gt WIDTH Q FW lt n gt lt m gt AM lt n gt lt m gt El lt m gt or WAT1 WAT2 WAT lt n gt lt m gt or SEO SE1 SE2 SE3 DEMON RAW or SAV or s lt m gt DIF DORIAN DMERGE DIF diffr par DIM DNORM DVN DIN DVAN RAW or SAV or s lt m gt DVN ELWIN IPG or IAG or IBG or IMI or ELQ ELF MSD AM or IBM EXPORT RAW or IPG or IAG or IBG or SPE or DASC IMI or IAM or IBM FQT FIT FQT FQT_F lt n gt lt m gt FURY RES IPG or IAG or IBG or IMI FQT or IAM or IBM ICON RAW or SAV or s lt m gt IPG or IMI GRP IONIAN ILINES RAW or IPG or IAG or IBG or ALLPT or ISLPT IMI or IAM or IBM or ASC RES JUMP FIT FW lt n gt lt m gt CEFIT CEL
34. de C Program Files CCLRC ISIS Facility Open GENIE For TCL code C Program Files CCLRC ISIS Facility Open GENIE For MODULE code libraries and include files Advanced C Program Files CCLAC ISIS Facility Open GENIENI T Perform a full build from GCL source Reload any GCL files newer than saved image Startup File Locations Startup file GCL C Modes3 Main init_sys gcl NOTE Saved Binary Image File Normally the default settings will be sufficient to allow Open C Program Files CCLAC ISIS Facilty Open GENIES EAE broeien Interface Startup Code TCL C Program Files Modes3 Main modes_interface tcl Enable Very Advanced Options V 51 Page 1 5 Installing OpenGenie modules Modules in MODES are Fortran routines which are called from the OpenGenie command language GCL and have to be compiled amp linked by OpenGenie to create object files with extension SO If your PC does not have a Fortran compiler then you will have to obtain the SO file from ISIS These are already in the file modes_so zip NB If MODES does not run properly at the end of this installation it might be due to incorrect compilation of the Fortran routines by Microsoft If this is the case download the modes_mod zip file from our ftp site which contains all Fortran modules and the filelink_all gcl This file can be used to compile the Fortran modules To run double click on the file A new window will appear running OpenGenie on comma
35. e 3 Plot Individual run or Combine the runs e Frame 4 Defines Merge parameters d increment MERGE common for all spectra Select opens a new window to dinorement sa define the d range for each spectrum min amp max values calculated from the data are shown Merge mo performs merge Plot shows merged spectrum e Save writes merged spectrum to file with extension DIM 5 5 4 dCor Performs absorption corrections section 5 6 2 5 5 5 dAna Performs multiple scattering and container corrections for diffraction data section 5 6 4 26 Page 5 6 Analyse The routines in this section are used to calculate the absorption and multiple scattering and use them on sample and container data 5 6 1 Mut This creates a cross section file with extension MUT Perform the following operations e Frame 1 Insert run number or Browse amp Select e Frame 2 Insert scattering amp absorption cross sections Run to create file and display graph 5 6 2 Acorn This calculates the absorption corrections A different layout of window appears for each type of sample geometry flat or cylinder depending on which sample geometry has been chosen in the MODES options There MUST be a MUT file for each sample and container used Flat Absorption Sample Parameters Run Number _ browse Thickness cm Flat Can Number density atom A3 Thickness fr
36. e Run e Plot if required Insert the run sequence number then Tab Return or click on Plot button Cex Time Eey No Runs First Run Range of Spectra seqence First 903 Lan i004 Selection No of groups Energy region Options One region Two regions subtract Two regions divide Energy window meV First Mo Max 23 Page 5 4 Int The routines described in this section are the operations performed on the intermediate format data 5 4 1 lonian This is the same as ICON section 5 3 1 but files PG and GRP are created in the working area 5 4 2 Dorian This is the same as Demon section 5 3 2 but a file D F is created in the working area 5 4 3 ElWin This performs elastic window scans by summing over the specified energy range Perform the following operations e Frame 1 is a NoteBook with tabs click on Tab Single specified groups from a single intermediate file Insert run number or press Browse to choose an IPG file from a new window Read data Selection specified groups from a selection of intermediate files Enter extension or choose from drop down menu Enter number of runs and press enter tab new window will appear Enter individual run numbers the variable title the value of the variable and the variable name Continue and Read the data Sequence specified groups from a sequence of intermediate files Enter
37. e following operations e Frame 1 insert sample run number sample thickness number density and angle of can to beam e Frame 2 Insert background or empty can run number e Run to perform calculations e Use trans to plot transmission e Use x sec to plot calculated cross sections For cylindrical geometry perform the following operations e Frame 1 Choose contained and or furnace option e Frame 2 Insert sample run number radii 1 and 2 and number density e Frame 3 If no container insert background run number if container insert empty can run number can radius number density and WUT file e Frame 4 Will appear if a furnace is selected Insert sample run number furnace radius number density and MUT file e Frame 5 Insert beam width e Run to perform calculations e Use trans to plot transmission e Use x sec to plot calculated cross sections 5 6 6 Analyse This routine subtracts the container from the samples and performs absorptions corrections if required With the corrections option off it can be used to compare 2 sample runs e Frame 1 Insert number of runs sample run number or Browse amp Select e Frame 2 Switch Corrections to On Off and switch Container to On Off Trans FlatPlate Sample Geometry is Flat Plate Sample Parameters Run number Thickness cm Number density atom A3 Fagle to beam deg Backgrou
38. east squares algorithm which requires the derivatives of the fitting function with respect to its parameters in order to be faster and more efficient than those algorithms which calculate the derivatives numerically To do this the assumption is made that the derivative of a convolution is equal to the convolution of the derivative as the derivative and the convolution are performed over different variables function parameters and energy transfer respectively this should be correct A flat background is subtracted from the resolution data before the convolution is performed Four types of sample function are available for S Q w Quasielastic this is the most common case and applies to both translational diffusion and rotational modes both of which have the form of a Lorentzian The fitted function is a set of Lorentzians centred at the origin in energy transfer Elastic comprising a central elastic peak together with a set of quasi elastic Lorentzians also centred at the origin The elastic peak is taken to be the un broadened resolution function Shift a central Lorentzian with pairs of energy shifted Lorentzians This was originally used for crystal field splitting data but more recently has been applied to quantum tunnelling peaks The fitting function assumes that the peaks are symmetric about the origin in energy transfer both in position and width The widths of the central and side peaks may be different Polymer a single quasi
39. ectrum to be grouped default for QENS mode on IRIS is 105 112 2 2 demon_first runs demon for 1 run number this can be repeated to create individual output files for each run number specified dem_first runnumber where runnumber run number 2 3 to add runs into one output file the output file will have the run number of the first run dem_first runnumber for first run dem_loop runnumber for each subsequent run to add dem_ave number runs where number runs total number of runs 2 4 demon_int int creates an output file if required the extension will be dif 3 ANALYSE 3 1 sandc reads data for sample amp container sandc sample run can run where sample run runnumber for sample can run runnumber for container 3 2 for subtraction with no corrections subtr factor where factor is the scaling factor for the container so that S S factor C default 1 0 3 3 for subtraction with corrections corr can option factor where can option 1 for no can 2 with can factor is the scaling factor so that S S factor correction C default 1 0 3 4 write_int creates an output file if required set extension outExt where outExt is the extension for the output file the convention is for graphite with input ipg output is ibg for subtr or iag for corr 60 Page for mica with input imi output is ibm for subtr or iam for corr 4 dMerge 4 1 read_diffm reads in input files re
40. eded so is not there e Frame 4 enter the measured resolution file Insert run number or Browse Choose energy range and binning Click Range and Plot group 1 if required The program creates files with extensions QRipt is the full printout of the fitting procedure QL1 the fit parameters for 1 peak QL2 for 2 peaks and QL3 for 3 peaks If the results are plotted then the routine uses the Conv gt width routines section 5 8 4 to create ASCII files of the fitted parameters These have extensions as follows the widths are FWnm where n is the number of peaks fitted and m the peak number the peak amplitudes are AMnm using the same nomenclature for n and m and where m 0 is the elastic peak and the calculated Elastic Incoherent Structure Factors are E n 5 8 6 LPT Output QL output Dek This routine reads Q2lpt data select Function and opens 2 windows that give a summary of the fitted Function Data parameters Use the sliders to choose the spectrum Run 79993 number and the number of peaks fitted For each z eose spectrum the parameters their errors and the Chi no groups fi Rea squared value are given It also reads QRLPT select Data files for when using measured resolution data Coet 5 8 7 Conv gt Width This routine converts fit parameters in the Q files depending on the model to ASCII files The widths and amplitudes intensities can then be plotted Perform the f
41. elastic peak with 3 different forms of shape The theory behind this is described elsewhere 4 5 Briefly polymer theory predicts 3 forms of the I Q t in the form of exp at where b can be 2 3 or 4 The Full Width Half Maximum FWHM then has a Q dependence power law of the form QP The I Q t has been numerically Fourier transformed into I Q w and the I Q w have been fitted with functions of the form of a modified Lorentzian These latter functions are used in the energy fitting 11 Page procedures 3 5 2 Hints on running When running the program the program was originally written for a symmetric energy window that is Emin Emax Using an asymmetric window appears to work but is to be treated with caution the energy increment should not be less than the energy bin in the input data otherwise the result may be unreliable due to the method of rebinning the data Using 100 points provided the previous comment applies provides good results the background and origin parameters can start at zero the elastic peak height is the fraction of the measured resolution peak the quasielastic peak height is the real peak height which can be read directly off a plot This can be the starting parameter if the broadening is greater than the resolution width If the broadening function width of the peak is less than the resolution the start parameter should be the measured sample height multiplied by the ratio of resolution width to esti
42. extension or choose from drop down menu Enter number of runs and number of first run Enter variable text the first value of the variable and the increment Read the data e Frame 2 select energy option eg one region for energy range of elastic line e Frame 3 insert minimum and maximum energies for the integration e Frame 4 plotting runs To plot integrated counts versus Q or Qf select Yes A new window appears when Run is pressed choose either Q or Q choose Next to proceed to next run or Cancel for the program to integrate the counts but not plot To plot integrated counts versus run number variable select No Use the Group button to plot integrated counts of each group Q as a function of variable run 24 Page Elastic Window multi runs T IEE The program creates two ASCII files of the result by run number a file ELQ of intensity and errors as a function of Q and a file MSD of intensity and errors as a function of Q The latter file is then the input into program MSD fit section 5 7 5 In addition when running the Yes option in Frame 4 an extra file ELQ is created where all Q run variable and integrated counts are stored 5 4 4 S Q w Similar to ICON but allows rebinning of data in Q and E Creates SPE files that can be read by MSLICE and SQE files which contain S Q w data Contains the options CONTOUR section 5 9 1 and VIZ section 5 9 2
43. ffraction Mn 105 Max 114 and diffraction e Frame 3 Define time ranges of spectra First TMe s range defines the elastic peak second range First Min Max 650000 defines the background e Click on Run Second e Plot if required to see the results 22 Page 5 3 4 Slice These routines perform integrations over a specified time of flight or energy range for each spectrum Its most frequent use would be to calculate elastic window scans The window is a NoteBook Time or Energy can be chosen by clicking on the appropriate Tab The Energy option is primarily used for analysing data to give the mean squared deviation MSD and will treat a series of RAW files For Time option e Frame 1 Insert run number amp Read Plot displays first spectrum to show time range e Frame 2 Select range of spectra e Frame 3 Define time range option e Frame 4 Define time ranges The second range details only appear when the Two regions option is selected e Run e Plot if required For Energy option e Frame 1 Insert number of runs Insert the number for the first run the program then loops over all the consecutive runs starting with that run e Frame 2 Select range of spectra under either Sequence or Selection e Frame 3 Define energy range option e Frame 4 Define energy ranges in meV The second range details only appear when the Two regions option is selected
44. fon WorkSpace umie 3 Yrange 0 00e000 fo 3 43e002 Pa Spectra from a to a Be Pa X label by ttt CS S Y label bks me Command He Be pa af Eeo Symbol al 3 Colour ce 4 Command SAE Be uap Display Plot Error Line ol a 5 9 5 ASCII This window is for plotting data which are in ASCII files It is of most use in plotting the results from QL FUNCTION and QL DATA fits Perform the following operations e Choose the type of ASCII file x y or x y error and the extension e Insert the run number or Browse then Read e Insert required X amp Y range for plotting e Insert required X amp Y labels and main Title e Choose Symbol Colour and Line type from drop down menus make sure you select each of them before the next step e Display for first plot Display always clears the screen for a new plot and the X and Y ranges will be fixed for overplotting e Error to add error bars e Line to add a line e In order to do multiple plots change filename Read change Symbol and or Colour and Plot and Error or Line if required e After the Read command the maximum amp minimum values of x and y as calculated from the data are displayed in blue 47 Page 5 10 Select 5 10 1 Select limits Allows you to set the limits on the x and y axes of the active plot 5 10 2 Select picture Allows you to re plot any
45. g events up to 5 for each neutron Single scattering is 1 The relative intensities of the various orders of multiple scattering could first be checked with low statistics and better statistics obtained with fewer scattering events In most cases 3 ought to be sufficient e Sample geometry infinite plate finite plate or cylinder e Sample thickness width amp height in cm for plate or sample radius amp height in cm for cylinder e Angle of plate sample to beam perpendicular is zero e Incident or analysing wavelength is obtained from the ICON file e Sample temperature K e Sample number density atoms A e Absorption cross section barns e Bound scattering cross section barns 9 Page The Q w grid and the S Q w are defined by Number of Q points amp increment A e Number ofw points amp increment eV e Option for scattering cross section in file or constant e If constant scattering cross section barns e Form of S Q w input input file calculate n peaks from diffusion constants cm s calculate n peaks with width as a 5 order polynomial in Q ie up to Q The number of angles and their values are obtained from the CON file The line printer output LPT gives the input parameters the table of S Q w values and the width parameters For each angle there is a table giving for each energy the following hh single scattering assuming no absorption amp no other scattering Ji first scattering
46. i This variation replaces the choice of several Lorentzians with a single function with the shape of a stretched exponential p x exp 2n ok This in the energy to time FT transformation is og E exp t t So is identified with 27 h t The model that is fitted is that of an elastic component and the stretched exponential and the program gives the best estimate for the B parameter and the width for each group of spectra 3 7 6 Jump fits One of the models used to interpret diffusion is that of jump diffusion in which it is assumed that an atom remains at a given site for a time t and then moves rapidly that is in a time negligible compared to t hence jump In the Chudley Elliott form the jump takes place to a new site at a point distance L from the original site The fitted function is of the form AE A 1 sin QK QK where AE is the FWHM of the Lorentzian The fit parameters are then A is h nt K is L In the Singwi Sjdlander form the fitted function is AE A 1 exp r Q 4 Getting started With MODES3 installed see Appendix A for installations instructions click on the icon on your desktop to start the program and choose IRIS 1 of OSIRIS 2 The main MODES window will appear as shown below This is a modified version of the Open Genie Tcl Tk window Menus in black are OpenGenie while those in blue are MODES commands Note that some of OpenGenie menus have extra Modes commands Many of the com
47. ing cross sections for the inelastic flight paths The absorption corrections use the formulism of Paalman and Pings and involve the attenuation factors Aj where i refers to scattering and j attenuation For example Ass is the attenuation factor for scattering in the sample and attenuation in the sample plus container If the scattering cross sections for sample and container are 2 and 2 respectively then the measured scattering from the empty container is 2 Ac_ and that from the sample plus container is Isc YAssc ZAcse Thus 2s Ise Ac sc Ac c As sc In the package the program Acorn calculates the attenuation coefficients A j and the routine Analyse uses them to calculate 2s which we identify with S Q w 3 4 2 Multiple scattering Multiple scattering is calculated using the Monte Carlo program MINUS derived from DISCUS by M W Johnson 3 The program requires a sample S Q w and can handle both plate and cylindrical geometries The S Q w can either be calculated using a suitable model such as a set of Lorentzians with specified Q dependence of the widths or a tabulated set of data The following parameters are required e Number of neutrons for calculation default 1000 larger values give better statistics e 2 integers to start the random number generator Need not be changed but if the statistical accuracy needs to be checked several runs should be performed with differing random numbers e Number of multiple scatterin
48. lders directories For MODES3 edit the file MODES _user gcl so that user rawdsk user rawdir define where the RAW files are and user workdsk user workdir define where you create all the other files 2 extra folders can be defined as user dir3 amp user dir4 NB The folder containing MODES_user gcl must be the same as that defined in init_sys gcl as System home 53 Page TextPad C Modes3 MODES_user gcl File Edit Search View Tools Macros Configure Window Help Osh BS6R8 22382 MODES_user gcl PROCEDURE user var GLOBAL user Path definition for RAW files tuser rawdsk C user rawdsk user rawdsk rawdata Filabozzi IRIS_May087 rawdata Filabozzi OSIRIS_Jun09 osiris rawdata test rawdata Befiltertests 0SI_emptybin_emptycryo ravdata Mukho Mukho_sept_097 user rawext raw Path definition for default WORK area user workdsk C user workdir rawdata user workdir rawdata Filabozzi IRIS_May08 tuser workdir yaudata Filabozzi OSIRIS_ Jun093 osiris user workdir rawdata test tuser workdir raudata Befiltertests OSI_emptybin_emptycryo user workdir rawdata Mukho Mukho_sept_09 user workext ipg Other directories user dsk3 C 7 user dsk4 C user dir3 QENS IRIS user dir4 QENS OSIRIS printn Loading user parameters from MODES _user gcl ENDPROCEDURE user_var For Help press F1 MODES u
49. lt flat plate 5 2 6 Log output If set to ON this option creates a file with the name lt program name gt _ lt date gt _ lt time gt log which contains some of the information that is in the header file as it appears in Directory section 5 1 1 together with the ICL commands used 5 3 Raw The routines described in this section are the operations performed on the raw data 5 3 1 Icon This combines spectra into groups and converts from time of flight to energy transfer An intermediate file is NOT created this version is best used for checking data during the run The program requires the files RIS_detector calib or OSIRIS_detector calib in order to read the angles 20 Page e Frame 1 Insert number of runs If there is more than 1 run pressing Return will open a new window to either use Calculate to set a sequence of run numbers or input each Run Number in Selection Select extension SAV RAW or Other and enter into Other box If more than 1 run has been selected choose whether the runs are kept separate ie a file for each run or added ie only 1 file created e Frame 2 Insert range of spectra Default values given are those for the analyser selected e Frame 3 Select grouping scheme creates files with grp extension If All Spectra Together is chosen all spectra will be added together pglop1 grp created If Several Groups is chosen a new window appear
50. main window the name of the selected file will appear in the appropriate box Brows e Geni SE ipg Files firs23605 pg 17 Page In order to make the package more user friendly the following features have been implemented e Within a window all the command buttons except the first one will be disabled on start up and will appear with just the text in light grey If the command invoked by a button is successful then the next button s will be enabled and will change to its appropriate colour If there is an error a message will appear and the subsequent buttons will remain disabled e When plotting a workspace array the routine checks if the input value is valid e Many routines check on the consistency of the data by checking on parameters in the intermediate file header The following checks are carried out analyser in file is consistent with analyser defined for program when manipulating more than one file eg analyse the reflections must be consistent 5 Toolbar This section describes the commands that appear across the top of the window Those in black are standard OpenGenie commands and are described in the manual Those in blue are Modes commands and are described here There are extra choices on the OpenGenie commands File Display amp Select and the additions are also described here 5 1 File The commands above the separator line are OpenGenie commands and the ones below are MODES commands
51. mands especially in Modes will create new windows These will contain some of the following Tcl Tk elements 16 Page e Text message e Input box for text or numbers input MUST be terminated with a Return or Tab In many cases this changes the focus to the next appropriate input box e Radio button round to provide a choice of options e Button rectangular to invoke an action These are colour coded Red dangerous operation Green normal operation Blue plot commands Yellow browse function e Menu button rectangular with a drop down menu of commands Combo box input box with a drop down menu e NoteBook this is a pane with overlayed pages the page required is selected by clicking on the appropriate Tab at the top of the pane Open Genie running MODES 3 your WiSH is my command File Edit Select Operations Display Options MODES Raw Int Analyse Function Bayes Inst OSIRIS Analyser PGO02 Help Log Off Calib Off Geom FlatePlate be 0 047477744807 ba 1 33050847458 W Clear before Plot Hardcopy icture 0 Many routines make use of the Browse window which opens when the yellow Browse button is clicked The main pane of the window then shows a list of files with the specified extension that exist in the working area Click on the required file and its name then appears in the box at the bottom of the window Click on Select and the window will close and in the
52. mated broadening For example if the broadening is a quarter of the resolution then multiply the height by 4 This is to take into account the reduction in height on convoluting when the area remains constant the parameter width is the HWHM of the scattering function The printed output will show this and also give the FWHM when fitting more than 1 peak it is best to start off fitting 1 peak in order to obtain estimates for peak heights and background and origin When increasing the number of peaks it may be useful to constrain some of the parameters in order to obtain a fit and these parameters can then be used as starting parameters for a full parameter fit when fixing parameters the routine asks how many to fix The background and origin are the first to fix 3 5 3 Multiple scattering version This version uses the MS corrections previously calculated by the program MINUS and stored in the ANS file The calculated sample function is corrected for MS and then fitted to the experimental data A full analysis should be an iterative process with steps as follows 1 2 3 use SWIFT without MS corrections to obtain first estimates for widths which are then used to generate S Q w in MINUS use SWIFT with MS corrections to obtain a new set of widths and use them to calculate S Q w again in another run of MINUS repeat step 2 until widths do not change within the errors on the widths 12 Page 3 6 Transform to I Q t 3 6 1 Theory
53. meter window and start the fitting procedure Plot fit to see the fit Save fit to save results if required Auto to automatically fit all Groups Exp plots the saved values of exp1 as a function of Q Beta plots the saved values of beta as a function of Q for the stretched exponential function 5 7 3 Swift This performs a convolution fit that is it convolves a specified function with the measured resolution data and fits the result to the measured sample data Four options are available 1 A set of quasielastic peaks 2 Anelastic peak with quasielastic peaks 3 Polymer shapes 4 Anelastic peak with a set of inelastic peaks Perform the following operations e Frame 1 Choose the file extension from the drop down menu Insert sample run number or Browse Insert resolution run number or Browse or enter resolution file name Read to read all groups into workspaces Plot S ample and Plot R es to plot first group of each file e Frame 2 The analyser chosen in MODES options is shown Et fipg Sample Number ipg Fe en Number _ Browse rco02 res BE s rr Res data Res function File Analyser is PGOO2 0 33 fo 3 Max fo 003 Rn Plot Plot R Energy range me 1 35 IE Min Increment MS corrections BN Yes Group number Fit function option Quasielastic
54. n use 3 7 Bayesian analysis 3 7 1 Introduction 3 7 2 ResMem 3 7 3 ResNorm 3 7 4 Quasi lines 3 7 5 Stretched quasi 3 7 6 Jump fits 4 Getting started 5 Toolbar 5 1 File 5 1 1 Directory 5 1 2 Read 5 1 3 Write 5 1 4 Exit 5 2 MODES 5 2 1 Raw 5 2 2 Work 5 2 3 Analyser 5 2 4 Calib 5 2 5 Geom 5 3 Raw 5 3 1 Icon 5 3 2 Demon Page o CONN DD O 10 13 14 16 18 18 19 20 3 Page 5 3 3 5 3 4 5 4 Int 5 4 1 5 4 2 5 4 3 5 4 4 5 4 5 5 4 6 5 5 Diff 5 5 1 5 5 2 5 5 3 5 5 4 5 5 5 5 6 Analyse 5 6 1 5 6 2 5 6 3 5 6 4 5 6 5 5 6 6 5 7 Function 5 7 1 5 7 2 5 7 3 5 7 4 5 7 5 5 7 6 5 7 7 5 8 Bayes 5 8 1 5 8 2 5 8 3 5 8 4 5 8 5 5 8 6 5 8 7 5 8 8 5 8 9 5 8 10 5 8 11 5 9 Display 5 9 1 Calib Slice lonian Dorian ElWin S Q w Bin gt Ascii Ascii gt Bin dVan dNorm dMerge dCor dAnal Mut Acorn S Q w file Minus Trans Analyse Fury Faqt fit Swift Swift Plot MSD fit Poly fit Smooth ResMem ResNorm QL function Str function QL data LPT output Conv gt Width Stretch gt beta sigma QL Plot Jump fit iLines Contour 23 26 27 32 37 44 4 Page 5 9 2 Viz 5 9 3 Actions 5 9 4 Choice 5 9 5 ASCII 5 10 Select 5 10 1 Select limits 5 10 2 Select picture References amp Further reading Appendix A Installation instructions for MODES3 Appendix B Frequently used GCL commands Appendix C Summary of input output files for progr
55. nd line mode There will be diagnostic information for each module and then to end the program and close the window type Exit lt return gt 1 6 Startup OpenGenie has its own menu in the main Programs menu There are 3 programs Open Genie settings used to setup Modes section 3 above Open Genie line mode Open Genie Tcl mode the version for running Modes3 On installing OpenGenie a shortcut will be created called OpenGenie this will start the program in the line mode option To run Modes3 a new shortcut needs to be created for the Tcl version in the shortcut creator Browse to the OpenGenie program folder eg C Program Files CCLRC ISIS Facility Open GENIE and select the program tkgenie32 exe then in the target input box add the options k I at the end eg C Program Files CCLRC ISIS Facility Open GENIE tkgenie32 exe k I and optionally change the short cut name in the General tab to eg Modes3 When starting MODES there will be a question in the startup Genie window asking for the instrument and stating 1 IRIS 2 OSIRIS BUT if you start using the Start Program menu it will just prompt with Instrument 2 Installation Startup on Linux Mac This is broadly similar to the PC setup The Linux distributions are available in both 32bit and 64bit formats Install OpenGenie from its website http www opengenie org Main_ Page 52 Page Download MODES3 from the directory Modes3 Linux ftp nd rl ac
56. nd or Can Run number Trans Cylinder Sample Geometry is Cylinder Container and or Fumace No container Container Fumace Sample Parameters Run number Radius 1 cm Radius 2 cm Number density atom A3 Can Parameters Run number Radius 3 cm Number density atom A3 Cross section file Fumace Parameters Run number Radius 4 cm Number density atom AG Cross section file Beam width em 31 Page e Frame 3 Insert Container run number or Browse s a meas fe e Frame 4 Inset scaling factor for the subtraction ee rg aS default 1 e Read and Run to subtract the data Sample Number of Runs ft e Plot options Run Number 36736 Browse S amp C to plot sample amp container together S to plot subtracted Corrections N Yes Container No Yes For simple subtraction ie no corrections an BG file is created from IPG or IBM from MI For Container corrected data an JAG file is created from JPG or Run Number fairer IAM from IMI el Scale factor in subtraction fos 5 7 Function Single Pea Run These are a set of routines for performing various PLOT jE functions such as fitting data 5 7 1 Fury This converts the S Q w to I Q t using a Fast Fourier Transform routine Perform the following operations e Frame 1 Choose sample
57. ollowing operations 41 Page e Choose an option from drop down menu choice Conv gt Width of 1 2 or 3 Lorenztian peaks water or stretched exponential 1 Lorentzian e Insert file name or Browse and Read e Choose whether to plot Q or Q In x axis File fosizaaes Browse Read e Plot Width Intensity EISF or beta Plot versus o ov 5 8 8 Stretched gt beta sigma This routine converts fit parameters from the STR cance FUNCTION search beta QSB and sigma QSS to ASCII files They can be plotted by first Reading the data and then Plotting the group TEETE DER 5 8 9 QL Plot a This routine plots the fits saved in QL files File firs35756 Browse _ Read Perform the following operations PLOT Group fi e Frame 1 Choose the number of Lorentzians used in the fit from the drop down menu Cancel Insert run number or Browse and Read Energy range of data will be displayed e Frame 2 Choose group number to display and press Calc Energy range used for fit will be displayed Choose energy range for plot and Plot Data plus all fit curves will be plotted Press choice to change axis ranges colour and type of fit curves A new window will appear QL Plot Conv plot 3 Lorentzians l Data energy min Energy 0 40 Intensity 0 00 Symbol E 4 Colour E 4 Group number line T 3
58. ont cm Thickness back cm Cross section file Number density atom AS 0 0 tame tr l me e Angle of sample to beam Container and or Fumace For flat plate geometry perform the following operations e Frame 1 Insert sample run number or Browse amp Select Insert sample thickness amp number density 27 Page Insert name of MUT file or Browse amp Select e Frame 2 Insert angle of sample to beam e Frame 3 Select container No or Yes If Yes a new window will appear for the can parameters Insert thickness of front and back Insert number density Insert name of MUT file or Browse amp Select Cylinder Absorption mB Container and or Fumace Sample Parameters Cylinder Can Run Number Browse anulus 1 Radius 1 cm foo Radius 3 em Radius 2 em br Number density atom A3 foo Cross section file Number density atom A3 Pouse Fanulus 2 Cross section file Radius 4 em wane _tome i Number density atom AG Beam width feo Cross section file Browse Containter and or Fumace Continue Number of can annuli fil E E o For cylindrical geometry perform the following operations e Frame 1 Select container option No Yes e Frame 2 Insert sample run number or Browse amp Select Insert sample inner
59. r errors and the Chi squared value are given The program creates files with extensions for Lorentzians Q2 pt is the full printout of the fitting procedure QL1 the fit parameters for 1 peak QL2 for 2 peaks Spectrum Number and QL3 for 3 peaks If the results are l plotted then the routine uses the LU Conv gt width routines section 5 8 4 to Number of create ASCII files of the fitted O Z parameters These have extensions as follows the widths are FWnm where n is the number of peaks fitted and m the peak number the peak amplitudes are Log Listing AMnm using the same nomenclature J spenum 1 Qe 0 7758 Angle 48 5434 for n and m and where m 0 is the elastic i Peaks 2 Chi squared 2 F 1 4261 peak and the calculated Elastic PARAMETER ERROR Incoherent Structure Factors are Eln Background min 8 308E 05 2 146 05 Water QW pt is the full printout of the Background max 3 774604 2 19605 fitting procedure QLW the fit Bastic line Position 0 92 0 11 parameters If the results are plotted _ Bastic line Intensity 1 4069 E 02 5 926E 04 then the routine uses the Conv gt width routines section 5 8 4 to create ASCII Line 1 Width 474 24 18 14 files of the fitted parameters These Line 1 Intensity 2 3948E01 2 777603 have extensions as follows the widths are WAT1 and WAT2 and the amplitude as WATnm where n is the number of peaks fitted and m the peak number Line 2 Wvidth 55 63 4 16 Line 2 Inten
60. retation of the reduced data In 6 Page quasielastic scattering this is dominated by methods for measuring the peak shapes and widths and relating these to some theoretical model for the dynamics This can take the form of e Fitting quasielastic peaks using a convolution method e Calculating peak parameters using Bayesian techniques e Performing transformations from S Q w to I Q t e Fitting peak widths using jump diffusion models e Fitting I Q t to models In the package all these operations are controlled from the main OpenGenie window MODES comprises the OpenGenie program package and the MODES package itself The programs run on several computer operating systems VMS UNIX and MS Windows MODES3 is available for users to use on their home institute computers Details of the installation procedures are given in Appendix A 3 MODES overview 3 1 Calibration This procedure determines the instrument parameters required such as flight paths scattering angles and detector efficiencies The flight paths and scattering angles on IRIS and OSIRIS are fixed and have been determined by the instrument scientists Detector efficiencies are measured using a vanadium standard by instrument scientists at the beginning of each cycle or by the user as part of the experiment This vanadium run also serves to determine the energy resolution and provide an absolute cross section calibration One or two ranges can be specified and would normally corre
61. roup 3 7 4 Quasi_Lines The model that is being fitted is that of a 6 function elastic component of amplitude A O and Lorentzians of amplitude A j and HWHM W j where j 1 2 3 The whole function is then convolved with the resolution function The 6 function and Lorentzians are intrinsically normalised to unity so that the amplitudes represent their integrated areas For a Lorentzian the Fourier transform does the conversion 1 x o7 exp 2n ok If x is identified with energy E and 2nk with t h where t is time then 1 E h t exp t t and o is identified with h t The program estimates the quasielastic components of each of the groups of spectra and requires the resolution file RES file and optionally the normalisation file created by ResNorm A summary of the fitted parameters for one and two Lorentzians per group is written to files with the following structure for each spectrum lt Q gt A max W max a 0 a 1 w 1 a 2 w 2 15 Page var a 0 a 0 var a O a 1 var a 1 a 1 var a O w 1 var a 1 w 1 var w 1 w 1 var a O a 2 var a 1 a 2 var w 1 a 2 var a 2 a 2 var a O w 2 var a 1 w 2 var w 1 w 2 var a 2 w 2 var w 2 w 2 Here A max and W max are the scale factors by which the a and w parameters need to be multiplied to obtain the amplitudes A j and HWHMs W j var is the variance Routines are provided for converting these to the simpler width versus Q form 3 7 5 Stretched_Quas
62. s for the same time of flight and several runs may be carried out at different wavelength bands in order to extend the d spacing range There is therefore a routine to merge several data sets into one spectrum spanning the whole d spacing range 3 4 Corrections A complete set of runs will normally contain in addition to the samples and vanadium the background instrument empty empty sample environment equipment eg cryostat furnace and empty containers The first and most important set of corrections is that for absorption self scattering and neutron absorption This usually incorporates the container correction If necessary multiple scattering corrections may then be applied but the calculation requires some knowledge of the inelastic scattering and is therefore an iterative procedure 8 Page 3 4 1 Absorption The main correction to be applied to neutron scattering data is that for absorption both in the sample and its container when present For flat plate geometry the corrections can be analytical and have been discussed for example by Carlile 1 The situation for cylindrical geometry is more complex and requires numerical integration These techniques are well known and used in liquid and amorphous diffraction and are described in the ATLAS manual 2 The routines used here have been developed from the corrections programs in the ATLAS suite and take into account the wavelength variation of both the absorption and the scatter
63. s to define the selection enter the number of spectra per group constant or the number of groups variable pglop2 grp created Individual Spectra is chosen for no grouping pglop3 grp created Nuniber of Runs fi Et sa aR RAW aR Other I Run Number Runs kept separate i Runs added Range of Spectra First 963 Last 1004 Group Files Options B Al Spectra Together Several Groups Seleslin Mus uf yiuups Group tile 5 Individual Spectra s Detailed balance W no WW res Tempe ezo Selection can be used to make groups of non consecutive spectra pglop4 grp created If Group file is chosen a new window appears with a list of grp files click on the one required its name appears in the box click on Select The format of a user created grp file is groups 5 2 first spectra last spectra first gp 2 last gp This method is recommended when restarting MODES to maintain consistency During a session MODES remembers the options and groups from previous usage e Frame 4 allows for detailed balance corrections at the sample temperature e Click on Run e Each group can then be plotted change group number and Return or click on Group button 21 Page 5 3 2 Demon This combines all the diffraction spectra into 1 group and converts from time of flight to d spacing in A An intermediate file is NOT created this version is best used for checking data d
64. ser gcl can be opened using any text editor In the example given above the raw data with extension raw is read from the Z irisdata directory and the reduced files will be stored in the working directory C rawdata test The user may store a number of directories and edit the file by commenting out adding a at the beginning of the relevant line the directories not being used NB Note the use of rather than in the syntax of the file 54 Page Appendix B Frequently used GCL commands It is useful in many occasions to use the command line to perform certain action in Open Genie such as displaying or over plotting a number of data sets For this the Open Genie Scratch Pad can be used This can be found in the File menu as Open Genie Console Open Genie Scratch Pad printn Welcome to Open Genie Run Run Selected Help Clear Close Cth lt GOUT th lt GINF th lt ERR th lt DBG ass 2 Wnsdata Wrs42893 raw Default input 2 irisdata irs42893 raw th lt OUT th lt INF th lt ERR _th lt DBG Search Help Alternatively the Actions GUI 5 9 3 may be used with the Genie commands inserted into the Command box and Executed Here are some common examples of Open Genie commands COMMAND DEFINITION pwd shows path to working directory sh def shows path definitions ass c irisdat
65. sity 3 7947 E02 1 585603 5 8 4 Str Function This is similar to QL function section 5 8 3 but allows the data to be fit to a Stretched Exponential function The frames are the same except for e Frame 6 does not have the option to input a Width file e Frame 6a enter the size of the search grid for the stretched exponential parameters Beta stretching exponent and Sigma width 2 To start click Search the program will test fits 40 Page with different combinations of beta and sigma A new window will appear with option for plotting the results Contour and Viz to plot grid showing the correlation between the beta and sigma parameters Beta plots the distribution of beta parameters that fit the data Sigma plots the distribution of sigma parameters that fit the data e Frame 7 same as in section 5 8 3 but now Plot Width amp Beta amp Int In stretched exponential model the fit is with either an elastic peak only 0 or with a quasielastic peak with stretched form 1 The program creates files with extensions QSE pt is the full printout of the fitting procedure and QSE for the fit parameters Creates also SEO elastic intensity SE1 width SE2 beta and SE3 peak intensity 5 8 5 QL data This is similar to QL function section 5 8 3 but allows the data to be fitted using a measured resolution data The frames are the same except for e Frame 3 is not ne
66. spond to a region around zero energy transfer about the width of the resolution elastic component and a region out in the wings at high energy transfer background For the 1 region option examples include the elastic component alone or the full time range corresponding to an integral over all energies within the observable window For the 2 region option there are a further 2 options a the integrated elastic component is the elastic region sum minus the background region sum This is the option used for the vanadium calibration b the background region divided by the elastic region This is useful for checking on the stability of the detectors On the instrument control computers there is a file called detector dat in the instrument tables directory which contains a table of angles and detector efficiency for each detector spectrum This is kept up to date by the instrument scientists The Instrument Control Program ICP which runs the data acquisition reads this file and writes the values to the header block of the RAW file The purpose of calibration program CALIB is two fold firstly to provide a correct version of the 7 Page detector angles in the user s area secondly to store the vanadium intensities if the user wishes to normalise the data The default copy of this data file called R S_detector calib or OSIRIS_detector calib is edited and written into the user s area 3 2 Conversion to I Q w The procedures ICON
67. symmetrical Symmetric for similar peaks on each side of the elastic peak eg Tunnelling Perform the following operations e Frame 1 Choose the input file from the tabs In each case enter run number or Browse and Read e Frame 2 shows the analyser selected in the MODES option and the input energy range Choose the energy range for fitting Run and Plot if required e Frame 3 shows RES file appropriate for selected analyser Read file Stretch allows you to stretch the width of the resolution file The default is 1 0 This will perform an operation that is similar that in QL when using the normalisation file created by RESNORM which finds the most appropriate stretch factor Broadening of elastic peak inelastic peaks If Yes then enter value of FWHM and Plot if required Keep width fixed if Yes choose Gaussian or Lorentzian e Frame 4 input parameters for the refinement If No then specify number of inelastic peaks to fit If Yes enter ascii filename and Read The format of the ascii 43 Page file should be first line with background at lowest amp highest energy then 1 line for each peak with parameters peak centre position amp height e Frame 5 Run and Plot In Symmetric as above except in Frame 4 where you should specified number of pairs of peaks 5 9 Display The commands above the separator line are Open
68. t of the integrated intensity of the spectrum In practice apart from the first few coefficients the error is nearly constant and close to Xo A further point to note is that the errors make the imaginary part of I Q t non zero and that although these will be distributed about zero on taking the modulus of I Q t they become positive at all times and are distributed about a non zero positive value When I Q t is plotted on a log scale the size of the error bars increases with time coefficient and for the resolution 13 Page will reach a point where the error on a coefficient is comparable to its value This region must therefore be treated with caution For a true deconvolution by back transforming the data would be truncated to remove this poor region before back transforming If the truncation is severe the back transform may contain added ripples so an automatic back transform is not provided 3 6 2 Hints on use When running the program e the program was original written for a symmetric energy window that is Emin Emax It will accept an asymmetric window and appears to work in this mode but caution is recommended e the energy increment should not be less than the energy bin in the input data otherwise the result may be unreliable due to the method of rebinning the data Using 100 points provided the first point applies provides good results A discussion of the analysis has been present in 9 Some examples of usage are
69. t the half width is wo c1 c2Q c3Q c4Q csQ Two Jump Models are available a Chudley Elliott Input parameters A and K such that wo A 1 0 sin QK QK b Singwi Sjolander Input parameters A and R2 such that wo A 1 0 exp R Q 5 6 4 Minus This calculates the multiple scattering corrections based on Monte Carlo calculations section 3 4 2 e Top Frame Indicates which sample geometry has been chosen in MODES options e Frame 1 Insert sample run number or Browse amp Select then Read e Frame 2 Is a Notebook with tabs Click on tab Dimensions are those for the sample For flat plate insert thickness width height and angle to beam For cylinder insert radius 1 outer diameter of the sample and height For annular insert radius 1 and 2 inner and outer sample diameters respectively and height Scatter insert temperature of run amp number density cross sections for absorption and bound scattering for sample e Frame 3 Is a Notebook with tabs Click on tab Calc parameters for Monte Carlo routine 29 Page Insert number of scatterings for single scattering 1 Insert random number starting values values to start random number generator Insert number of neutrons for the simulation Q w grid same as in section 5 5 3 Q w similar to that in section 5 5 3 Here you can insert scattering cross section and choose the form of S Q w Input diffusion coefficient in
70. uk pub ida Modes3 Linux and create files in the same tree format see section 1 3 Use the appropriate SO files 32 or 64 Linux does not have a Geniesettings program so instead you should create a command script file to run For example to run the Tcl Tk option for IRIS create a file itkgen say with 1 bin csh setenv HOME_DIR lt home path gt setenv MODES_ROOT lt root path gt setenv GENIE_PROG MODES setenv GENIE_USER_INSTR IRIS setenv GENIE_GCL_INIT S MODES_ROOT Main init_sys gcl setenv GENIE_TCL_INIT S MODES_ROOT Main modes_interface tcl setenv GENIE_USER_MODES_DIR S MODES_ROOT Main setenv GENIE_USER_LIBRARY_DIR S MODES_ROOT Main Mod setenv GENIE_USER_OGLIB_DIR S MODES_ROOT Lib setenv GENIE_USER_TABLES_ DIR S MODES_ROOT Tables IRIS setenv MODES_HELP S MODES_ROOT Lib setenv GENIE_BGD white genie k l where lt root path gt is the directory for the program and lt home path gt the directory for MODES user gcl The program is then started with the command itkgen Change the instrument with GENIE_USER_INSTR and for the command line version use genie l 5 Work area This is the folder directory where the created files are stored It is usually on the C disk or if using XP Vista it might have to be C Documents and Settings lt user gt My Documents Many folders may be created The folder Modes3 contains 2 files MODES_user gcl amp FORTE_user gcl to define these fo
71. ult values are 1 8450 3 53 1 map defines the grouping map group option number groups number spectra where group option coding for type of grouping number groups number of groups number spectra number of spectra in group grps_out creates output file of grouping scheme optional the filename format is PG or MI analyser code OP amp group option with extension grp grps_in reads in the grouping scheme Can be used instead of map grps_in filename where filename is the name of the file amp it assumes the extension is grp det bal sets of the detailed balance correction det_bal option temp where option 0 for off 1 for on temp temperature in K when on ic_first runs icon for 1 run number this can be repeated to create individual output files for each run number specified ic_first runnumber where runnumber run number to add runs into one output file the output file will have the run number of the first run ic_first runnumber for first run ic_loop runnumber for each subsequent run to add ic_ave number runs where number runs total number of runs write_int creates an output file if required the extension will be ipg or imi according to analyser code 59 Page 2 DEMON 2 1 dif defines the spectral range dif first spectrum last spectrum where energy analyser energy first spectrum first spectrum to be grouped last spectrum last sp
72. units of 10 cm s Enter a parameter file containing diffusion coefficients for polynomial function section 5 5 3 Input S Q w file name created in section 5 5 3 e Frame 4 Choose whether you want an output file e Run to start calculation and Plot to see the results Minus mE Sample Geometry is Flat Plate Sample Geometry is Flat Plate Sample Geometry is Cylinder Run number faseze Browse aad Run number 25628 Browse Read Run number e5628 Browse Read Dimensions Scatter Dimensions Scatter Dimensions Scatter Thickness cm a Width em feo Height em fo Fogle to beam deg fas Temperature K d iat Solid Annular Number density atom AS Radius 1 cm foo Sig Absorption bams JE Radius 2 em 00 Sig Bound bams Height em Bo Qw grid Q w Cale Qw grid Cale Qw grid S Q w Sig Scat Q A 1 e Diffusion coeff number pts incr amp Parameter file w micro e number pts iner amp 0 w file Number scatterings E Random numbers z4 e5789 Number neutrons frooo frooo Output file No Yes Output fle No Yes Output file No Yes me me mm 5 6 5 Trans This calculates the transmission and cross sections using the monitor spectra Top Frame indicates which sample geometry has been chosen in MODES options 30 Page For flat geometry perform th
73. up on a PC 1 1 OpenGenie install from the ISIS website http www opengenie org Main Page 1 2 Getting MODES files and quick installation To install MODES on your computer you need to e Download the pre zipped folder Modes3 Windows zip from the ISIS anonymous ftp site ftp nd rl ac uk pub ida and place this file in your desired location on your computer e g C e Unzip Modes3 Windows zip On most PC s this task can be achieved by right clicking on Modes3 Windows zip and selecting WINZIP gt Extract to here This operation should generate a Modes3 folder containing all requisite files and directories We recommend placing the Modes3 folder at the top level of your drive i e C Modes3 e Proceed to section 1 4 of this Appendix 1 3 Manual installation of PC folders directories If a pre zipped version of MODES is not available the following zip files are needed and can be copied by ftp from the ISIS anonymous ftp site ftp nd rl ac uk pub ida Modes3 Windows modes_gcl zip contains gcl code files modes _lib zip contains files for Library modes_main contains main Modes files modes_so contains compiled modules extension SO modes_tables contains various settings files modes _tcl contains tcl code files Create the following tree structure on disk C Modes3 gt Lib Main gt Gcl Mod Tcl Tables Copy contents of Modes _gcl zip to Main Gcl Modes lib zip to Lib Modes_main to Main 50 Page Modes_so to Main Mod Modes_ta
74. uring the run The program requires the file IRIS_detector calib or OSIRIS_detectors calib in order to read the angles and a diffr par to define the time of flight to d spacing correspondence This parameter file would have been provided by the instrument scientist but the option is given to input a custom file e Frame 1 Same as in ICON e Frame 2 Use Default or Custom diffraction parameter file e Frame 3 Define range of spectra for diffraction detectors on IRIS 105 gt 114 is the range for the quasielastic setup and 3 gt 12 is the range for the diffraction setup e Click on Run e Plot if required 5 3 3 Calib This routine reads the raw file of a vanadium run and calculates the area of the elastic peak for each Number of Runs farri Run Number Et sav RAW Gone Runs kept separate Diffr par file is Spectra Range 105 gt 112 3 gt 10 input Values T Cefauk Custom Runs added spectrum When run the default ima IRIS_detector calib or OSIRIS_detector calib is then Run Number 35624 Check edited and the new version created in the working area In the past it used detector calib Spectral range e Frame 1 Insert number of runs and run number if more than one is chosen a new window will Graphite Mn 3 Max 53 appear to enter individual run numbers Press Moa Mn 54 Max 104 Check to plot e Frame 2 Gives detector numbers for PG Mica Di
75. ying data It is of most use during an experiment to check on progress of a run Perform the following operations e Frame 1 is for monitor 1 spectrum Insert run number amp click Run for Raw data Click on DAE for current data in the DAE To plot the spectrum in time of flight click on Time amp Plot To plot the spectrum in wavelength click on Lambda amp Plot e Frame 2 is a NoteBook with Tabs for workspace manipulation Focus sums the specified range of spectra Insert name of workspace amp choose unit from drop down menu Insert range of spectra amp Exec to run amp Plot Rebin rebins the specified workspace the value shown is that previously defined Insert name of workspace amp choose unit from drop down menu Plot the result e Frame 3 is for up to 3 OpenGenie commands Type the command in the box amp click on Exec to run Specify the range From is minimum to is maximum by is increment Truncate increment is not required the range becomes maximum to minimum Linear the increment specified is the linear step Log the increment specified is the logarithmic step J 46 Page Actions ASCII plot un o Read amp Plot ASCII files Monitor 1 Tine Lambaa Plot xy ext fes xye ext at 4 Filename detector_cc fes __trowse Rea FOCUS REBIN UNIT X range 10 fr ono

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