User Manual for OPENGENIE muon data analysis suite
Contents
1. C Parameter 1 Ao Parameter 2 Parameter 3 B Parameter 4 C lee Gkt 4 4 2 1 0 exp Parameter 1 Ao Parameter 2 o Parameter 3 C Lkt G t A 4 2 1 At exp 2 C Parameter 1 Ao Parameter 2 Parameter 3 C 2 2 2 Gktlor G t A t 21 0t Jexp z Jexp 40 C Parameter 1 Ao Parameter 2 o Parameter 3 Parameter 4 C Gktslo t A 2 4 Jexp exp a C Gaussosc Lorosc Additional functions Parameter 1 Ao Parameter 2 o Parameter 3 Parameter 4 p Parameter 5 C G t A cos t p expl or C Parameter 1 Ao Parameter 2 o Parameter 3 o Parameter 4 Parameter 5 C G t A cos t exp At C Parameter 1 Ao Parameter 2 o Parameter 3 Parameter 4 Parameter 5 C Additional function can be added by Comfunc This can auto generate the function for you but requires Compaq visual fortran This creates so files which can be loaded into Opengenie The Comfunc script will auto load the so file created Loaded additional functions To load function module to fit your data with Module load lt funcname so gt Batch fitting In order to batch fit a set of data then type Fitit The first run must have been already fitted Plotting fit results parameters Firstly a file must be created with two columns First run number second x axis parameter e g Temperature or Fiel2. 03 26 03 27 02 28 02 29 01 30 01 31 08 32 08 3301 12 34 01 35 02 36 02 37 03 38 03 39 04 40 04 4 05 42 05 43 06 44 06 45 07 46 07 47 08 48 08 49 07 50 07 51 06 52 06 53 05 54 05 55 04 56 04 57 03 58 03 59 02 60 02 6101 62 01 63 08 64 08 taud dat 2 5023159E 03 8 8687800E 03 2 5076472E 04 1 4882313E 02 6 1632111E 03 5 7040760E 03 4 6056886E 03 1 1012390E 04 phase dat 59 9817 62 5343 45 6286 101 088 112 891 108 478 83 3170 T3 34 0910 Longitudinal grouping 64 GROUPED IN 2 NO OF HISTOS 1X 12 NO OF GROUPS 1X P2 64 02 GROUPING OF HISTOS HISTO NO 1X 12 GROUP NO 1X 12 GROUP ZERO MEANS IGNORE HISTO 01 02 02 02 03 02 04 02 05 02 06 02 07 02 08 02 09 02 10 02 11 02 12 02 13 02 14 02 15 02 16 02 17 02 18 02 19 02 20 02 21 02 22 02 23 02 24 02 25 02 26 02 27 02 28 02 29 02 30 02 31 02 32 02 33 01 34 01 35 01 3601 37 01 38 01 39 01 40 01 14 4101 42 01 43 01 4401 45 01 46 01 47 01 48 01 49 01 50 01 51 01 52 01 5301 5401 5501 56 1 57 01 5801 5901 60 01 6101 62 01 6301 64 01 taud dat 0 00250232 0 00886878 phase dat 78 1690 117 213 15
3. i e use the v or fit new2 commands Static dipole fields with a hopping muon This program simulates longitudinal SR data with a field distribution for static nuclear dipole with a hopping muon The command is Zsimdgkt The results can be viewed analysed as if the data was real i e use the v or fit_new2 commands Static dilute atomic moments with a hopping muon This program simulates longitudinal uSR data with a field distribution for static dilute atomic moments with a hopping muon The command is Zsimdlkt The results can be viewed analysed as if the data was real i e use the v or fit_new2 commands Static dipole fields from a crystal structure This program simulates longitudinal SR data with a field distribution for static dipole fields from crystal structure The command is Zsimxtal The results can be viewed analysed as if the data was real i e use the v or fit_new2 commands The program will ask for an atom file which should be in the format of LattA LattB LattC Numof Atom Atomxpos Atomypos Atonzpos Appendix A Example files for maxent Transverse groupings Stdgrp par 64 GROUPED IN 8 NO OF HISTOS 1X 12 NO OF GROUPS 1X P2 64 08 GROUPING OF HISTOS HISTO NO 1X 12 GROUP NO 1X 12 GROUP ZERO MEANS IGNORE HISTO 01 01 02 01 03 02 04 02 05 03 06 03 07 04 08 04 09 05 10 05 1106 12 06 13 07 14 07 15 08 16 08 17 07 18 07 19 06 20 06 2 05 22 05 23 04 24 04 25
4. User Manual for OPENGENIE muon data analysis suite Contents TAT OCU eio NODE 3 boh a AN dg adv adt f tu de 3 Data Q ss Al PIN A oen le nr a 3 Setting the data directory dii ta ei Li 3 Getting the Run information seas 3 3 Converting NeXus files to ascii entender dads 4 a NTN 4 ie 4 Viewing multiple runs gt 4 Viewing data and dead 5 Viewing multiple runs 5 Colour 5 Viewing the logs in the data file 6 Exporting data fits and plots RE 6 6 Writing datato TESS 6 7 6 Find secs i 6 Fitting data from convert ascii output 6 Preloaded Functions oeque renta tora onde 7 Additional TSN 8 Loaded additional functions tenet st 8 Plotting fit results parameters sn sonne diner de ibtd 8 as Ass 9 Maximum Entropy analysis 9 NK 10 Static dipole fields ooa e enga ovine atus 10 Static dilute atomic moments 10 Static dipole fields with a hopping MUON 10 Static dilute atomic moments with a hopping 10 Static dipole fields from a crystal 11 Appendix uos ois nte uoo m uquna a es E
5. d C has 12 Example files for maxent av 12 Transverse Qroupihigs se o ed reu NE 12 Longitudinal grouping reto erectus ett 14 Introduction This document aims to explain how to reduce analysis uSR data using the OPENGENIE routines Installation 1 Install OpenGENIE from ISIS website http www isis rl ac uk OpenGENIE 2 Download and unpack muon openGENIE files 3 Edit opengenie_startup gcl and replace lt your_install_dir gt with the directory you unpack the muon openGENIE files 4 type load lt your_install_dir gt opengenie_startup gcl You need to type this every time you start OpenGENIE Data reduction Setting the data directory Type at the OPENGENIE command prompt Datadir lt data directory gt Getting the Run information At the opengenie prompt type Headers This will create a text file called headers txt and open a text editor Optaining Alpha To obtain Alpha type T2Ofitg for a Gaussian envelope Or T2Ofitl for a lorentzian envelope Alpha will be given at the end Converting NeXus files to ascii To convert data into xye format and fit using the opengenie fit routines then Convert_ascii2 The defaults are read from the first Nexus data file Typing zero will read the current run if data directory is the MuSR disk For Opengenie analysis use the rumda output option This will write files to the working directory called r lt runnumber gt dat rumbda opt
6. d Then use the Opengenie script Plotpara2 This will plot all the variables as a function of the second column in the dependent parameter file see above These plots can be made larger by clicking on the plot Crtl x will exit this script After viewing the data these results can be written to a file using Writeres This will write the results to a file called results dat Extra Scripts Maximum Entropy analysis The maximum entropy analysis is available However in the current working directory there must be 1 a stdgrp file called stdgrp par which contains detector groupings 2 a deadtime file called taud dat which contains the deadtimes for each group 3 a phase file called phase dat which contains the phase of each detector group Examples of these files are given in Appendix A Running the maxent will generate a file called lt runnumber gt max Simulations There are several simulation programs that have been written and can be ran within OpenGenie Static dipole fields This program simulates longitudinal SR data with a field distribution for static nuclear dipole The command is Zsimsgkt The results can be viewed analysed as if the data was real i e use the v or fit_new2 commands Static dilute atomic moments This program simulates longitudinal uSR data with a field distribution for static dilute atomic moments The command is Zsimslkt The results can be viewed analysed as if the data was real
7. e Black Viewing the logs in the data file To view the logs stored in the data file type Plotlog Exporting data fits and plots Rebinning data To rebin the data ready to be written to a statistically group data set ready for importing into another plotting package then Rebin lin lt xmin gt lt xmax gt bin size us Or newwksp Rebin lin dataw xmin xmax bin size us gt Dataw can of course be replaced by fitw Writing data to files Workspaces such as dataw and fitw can be written to disk using Writexye dataw filename dat Writexy fitw filename fit The data will of course all ready exist in the ungrouped from after converting to acsii and then fitting Printing plots Select print from the plot window Fitting data Fitting data from convert ascii output To fit data type fit new2 This will use the least squares fitting routine within OpenGenie It will ask you for start time stop time number of variables initial starting parameters whether to vary the parameters and the function to be fitted This will create a fit and par file If you wish to fit using an old par file then fit_new2 fo Or if you wish to fit your data using a par file which is the results from another data file then fit_new2 f Preloaded Functions There are some preloaded functions installed listed below Lor G t A exp At C Parameter 1 Ao Parameter 2 Parameter 3 C Slo G D A
8. ion or musr run number dat for general output Data visualisation Viewing dafa To view the data V The data will be shored in a workspace called dataw This can be manipulated with the usual Opengenie commands such as Adjusting the xmin xmax ymin and ymax d m dataw O 16 O 0 3 Adjusting the data binning a b bin size To view the short time data then after typing v typing short will view the data from O to 3 us with a data binning of 1 Viewing multiple runs To view multiple runs if the runs are in a sequence i e every run or every n runs Mulp If not then use MuPlot not fully implanted yet Which asks for the run numbers to plot Viewing data and fit To view the data Vf The data will be shored in a workspace called dataw and the fit will be stored in fitw This can be manipulated with the usual Opengenie commands such as Adjusting the xmin xmax ymin and ymax d m dataw O 16 0 0 3 p l fitw Adjusting the data binning a b bin size To view the short time data and fit then after typing v typing shortf will view the data and fit from O to 3 us with a data binning of 1 Viewing multiple runs To view multiple runs if the runs are in a sequence i e every run or every n runs Mulpf If not then use MuPlotf not fully implanted yet Which asks for the run numbers to plot Colour of plot In order to change the colour of the plot type any of the following Blue Red Yellow Green Purpl
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