Section 3
Contents
1. EX EA E e 2 9 o o Ww Os OO U r2 fr wo ON CO ut2 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 0 00244 0 00244 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 T 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 L225 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 page 3 10 ut3 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 10 0 rm BO oo 44 0 PRP RPP p pmp mp pP p p m pP PPP PPP mI EB p pmP H p pmP dp p m qoeooeooooo0coc oooooocjnooooo0 O Q ut4 0 006 0 006 0 006 0 006 0 006 0 006 0 006 0 006 0 016 0 016 0 02 0 02 0 001 0 001 0 014 0 014 0 014 0 014 0 014 0 014 0 014 0 014 0 014 0 008 0 008 0 008 0 008 0 008 0 008 0 008 0 008 0 008 0 012 0 012 0 012 0 012 0 012 0 012 0 012 0 012 0 012 0 013 0 013 0 013 rt Un OOOOOOOOOOOOOOOOOOOoOoOooooodooooooooooooooooooc 45 1 0 1 04 150 20 1 2 0 1 25 1 0 0 013 0 46 1 0 1 04 150 20 4 2 0 1 25 1 0 0 013 0 47 1 0 1 04 150 20 7 2 0 1 25 1 0 0 013 0 48 1 0 1 04 150 21 0 2 0 1 25 1 0 0 013 0 49 1 0 1 04 150 21 2 2 0 1 25 1 0 0 013 0 50 1 0 1 04 150 19 1 2 0 1 25 1 0 0 013 0 51 1 0 1 04 150 19 5 2 0 1 25 1 0 0 013 0 52 1 0 1 04 150 19 8 2 0 1 25 1 0 0 013 0 53 1 0 1 04 150 20 1 2 0 1 25 1 0 0 013 0 54 1 0 1 04 150 20 4 2 0 1 25 1 0 0 013 0 55 1 0 1 04 150 20 7 2 0 1 25 1 0 0 013 0 56 1 0 1 042. 3 3 Time channels The time channel structure is set up by the ICP and three basic structures are available channel width constant with time channel width proportional to time of flight and width proportional to the square of the time of flight There can be up to five ranges of time of flight each with a choice of structure The constant channel width is the simplest but has the disadvantage that on converting to Q the data becomes squashed into the low Q region with the high Q region having widely spaced points The second choice has the advantage that the channel widths are proportional to the resolution over the whole range since the resolution is constant in At t and 49 09 For this option the distribution of points in Q is still on constant increment but not as bad as the first option The last choice would provide constant increments in Q On LAD we have chosen the second option that is the channel vidth is proportional to time of flight There is only one region staring at 200 us ending at 19500 us just before the next pulse which arrives at 20 ms The constant of proportionality is 0 002 which allows for about ten points across a Bragg peak at the backward angle 150 highest resolution detectors Since the resolution worsens as the scattering angle decreases and the constant does not change vith angle the number of points at the lower angles are higher than necessary The combination of unequal Q increments and the incremen
3. Each spectrum has the same range of time of flight so because each spectrum may have a different flight path the wavelength range will differ Before manipulating spectra they must therefore be rebinnned onto a common wavelength range this also includes the same increment in wavelength the counts are corrected for detector dead time This requires the total frames for the run vhich is taken from the parameter section the error is taken to be the square root of the count The program is in two sections each producing an output file which can subsequently be read into GENIE using the REad command 3 6 2 Monitor files This section creates a file with the extension MON containing the two monitor spectra The incident monitor is just converted to wavelength The transmission monitor is converted to wavelength rebinned to the wavelength range of the incident monitor and divided by the incident monitor spectrum The purpose of dividing by the incident monitor page 3 16 spectrum is to allow for the possibility of variations in moderator temperature leading to changes in the flux wavelength distribution as well as scaling all runs to a same neutron flux It is therefore in a form suitable for calculating the transmission cross section 3 6 3 Detector files This section deals with the detector spectra and creates a file with the extension NRM The spectra can be grouped together in a manner defined ina data file A default
4. MUL and SMO to produce the corrected S Q at each angle as an output file with extension DCS Routine PLATOM calculates the self scattering at each angle creating an output file with extension SLF Routine INTERFERE subtracts the self scattering in the SLF file from the total scattering in the DCS file to yield the interference scattering which is placed in a file of extension INT Routine MERGE combines the individual angles in file with extension INT or DCS to produce a single S Q in a file with extension S0Q page 3 14 Routine STOG transforms S Q to g r and GTOS transforms g r to S Q The diagram below shows the normal sequence of operations and Appendix D summarizes the filename extensions which are produced RAW data files in LADMGR RESTORE Transmission Routines CORAL ANALYSE The operations in brackets are optional and can be skipped if necessary This will typically happen when the inelasticity correction is either not needed or not calculable page 3 15 3 6 PROGRAM NORM Version 4 1 March 1989 3 6 1 Introduction This program NORMalises the RAW data that is it takes detector spectra corrects for deadtime divides by the monitor spectrum converts from time of flight to Q vector combines spectra and outputs results to files The following operations are carried out on all spectra the time of fight is converted to wavelength using the parameters contained in the RAW file
5. angle d is the d spacing of the powder peak These parameters are determined vith calibration experiments of two types The first equation can be used vith neutron absorption resonances which occur at fixed energy or wavelength By measuring many resonances from different foils placed in the incident beam values for and L can be determined Most resonances occur at high energies eV short times of flight so these calibrations give good values for 4 The second equation of course leads to the familiar calibration using standard powders such as Ni A150 and MgO These experiments will give values of 4 and the product LsinO At short times there are either no Bragg peaks or they cannot be resolved so that the value of A by this technique is not as reliable as that from resonances As pointed out in Appendix A the Bragg peaks have an asymmetric page 3 7 shape which varies with scattering angle so the peaks have to be analysed to take this into account The instrument calibrations are carried out by the Instrument Scientists and do not normally need to be repeated by the user Nonetheless it is wise to look for discrepencies between the results from different scattering angles to determine if the supplied calibration is correct The header sections of the RAW data files should contain the correct values On the FEM they are stored in a file called DETECTOR DAT If that file does not contain all the values or if they need changi
6. out the Fourier Transform of S Q to g R and its inverse g R to S Q They are invoked with the GENIE TRANSFORM command Otherwise the required input by the user should be fairly straightforward The command is for example after the GENIE page 3 44 1 f STOG W2 etc Note that for these routines to work correctly it essential for both S Q and g r to oscillate about unity page 3 45
7. the corresponding 2 routines are TCR cylindrical geometry RAW data TFR flat plate geometry RAW data TCM cylindrical geometry data flat plate geometry data To run these GENIE command files the user should go into GENIE and type Gg f ter for example The routines prompt for the sample and background run numbers and then divide sample by background to give the transmission NOTE if the sample is in a container then the correct background to use is the empty container run number NOT the nothing in the beam background The next prompt is for the binning parameters default values or input values Then Function program is entered to calculate the cross section TRANSCYL for cylindrical geometry or TRANSFLAT for flat plate geometry The result is displayed and the routine prompts for a choice of recalculating or outputting the result to an ASCII file suitable for the corrections programs this file has the sample runnumber and page 3 23 extension See section 2 4 for further information on the calculation of the total cross section The program TRANSCYL can take into account 2 concentric cans or 1 can plus a furnace i e there are 4 radii defining 3 annuli The routine will calculate the cross section of annulus 1 and requires the cross sections for annuli 2 and 3 as input The following input is required beam width radius 1 default 0 ie 0 for solid sample
8. the command is aborted CALib This command initiates the changing of the values of the calibration constants The new values must be in the file DETECTOR DAT which must exist in the current directory The new values are displayed as they are read in The command must be issued before both the RUN and BEgin commands The monitor data 15 read during RUN so its parameters will not be changed unless CALib is issued before it There is an error message if the number of detectors is wrong or if the detector numbers are out of sequence and the parameters are not changed The option can be removed with the qualifier N page 3 19 GRoup The group command defines the group structure of the spectra The routine prompt is group gt There will be a request to input a filename A lt CR gt will default to the file G F GROUPS DAT in the LADMGR program area otherwise type the name of the file to be read vith directory if necessary The group structure as in the file is as follows first line number of groups subsequent lines one for each group number of spectra the spectra numbers Up to 25 groups are alloved each vith up to 25 spectra The spectra should be in increasing angle There is one qualifier TYPEIN which allovs the group structure to be typed in directly There vill be prompts for input the structure is similar to that in the file If the group file does not exist or if more than 25 groups are defined ther
9. version called GROUPS DAT is available for LAD in the instrument program directory G F The operations are the individual spectra are read converted to vavelength and normalised to the incident monitor spectrum as outlined above This must be done on the individual detectors in vavelength and not after addition or converting to Q in order to take correct account of the shape of the monitor spectrum the individual detectors are converted into counts per Q each spectrum is rebinned onto a specified Q range and constant Q increment and the spectra vithin a defined group are added The default grouping for LAD creates a file of 14 groups corresponding to the 7 scattering angles on either side The groups are in pairs in increasing angle 3 6 4 Operation The program is a stand alone program similar in operation to GENIE and is started with the command NORM The program prompt is gt The command RUN defines run numbers to be used The command GRoup defines the spectra group structure The command BEGIN starts the program looping over all groups page 3 17 The command CALib initialises reading of the detector table optional The sequence of commands is as follows gt SET DIR or DISK default values on gt SET INST entry to program gt SET EXT gt CAL if required gt GR gt RUN gt BE to begin operation gt to exit program The HELP facility is also available within the program The comma
10. 0 00 set parameters gt U Q V1 change units to Q gt ASS 1235 assign run number for vanadium 2W2 S1 gt Set PAR 2 10 1 150 00 gt U Q V2 gt W3 W1 W2 divide S by V to give S Q gt D W3 display S Q gt L X O 20 change range of X ie Q gt D E display new Q range and with error bars 3 4 2 GENIE command files Operations can be stored as a command file and such a file is provided for calculating the crude S Q i e sample can vanadium with no other corrections The routine is started in GENIE with the command g f SQRAW that is the command file is called SQRAW COM in directory g f It prompts for sample can and vanadium run numbers and page 3 13 for the angle The resulting raw S Q is displayed 3 5 OVERVIEW OF PROGRAMS The package provides a series of stand alone Programs and GENIE routines which are to be run in a particular order Program NORM normalises RAW data and produces output files with extensions MON and NRM TRANSMISSION Routines calculate cross sections from the transmission data with extension MON and creates files with extension Program CORAL calculates the corrections using the files with extension MUT and produces corrections files with extensions ABS MUL or REF Routine VANSM treats the reference or vanadium spectra using files with extensions NRM and REF and creates files vith extension SMO Routine ANALYSE takes the files vith extensions NRM ABS
11. 150 21 0 2 0 1 25 1 0 0 013 0 57 1 0 1 04 150 21 2 2 0 1 25 1 0 0 013 0 58 1 0 1 043 150 34 1 2 0 1 25 1 0 0 012 0 59 1 0 1 043 150 34 4 2 0 1 25 1 0 0 012 0 60 1 0 1 043 150 34 7 2 0 1 25 1 0 0 012 0 61 1 0 1 043 150 34 9 2 0 1 25 1 0 0 012 0 62 1 0 1 043 150 35 3 2 0 1 25 1 0 0 012 0 63 1 0 1 043 150 35 6 2 0 1 25 1 0 0 012 0 64 1 0 1 043 150 35 9 2 0 1 25 1 0 0 012 0 65 1 0 1 043 150 36 1 2 0 1 25 1 0 0 012 0 66 1 0 1 043 150 36 4 2 0 1 25 1 0 0 012 0 67 1 0 1 046 150 57 0 2 0 1 25 1 0 0 008 0 68 1 0 1 046 150 57 2 2 0 1 25 1 0 0 008 0 69 1 0 1 046 150 57 45 2 0 1 25 1 0 0 008 0 70 1 0 1 046 150 57 8 2 0 1 25 1 0 0 008 0 71 1 0 1 046 150 58 0 2 0 1 25 1 0 0 008 0 72 1 0 1 046 150 58 3 2 0 1 25 1 0 0 008 0 73 1 0 1 046 150 58 7 2 0 1 25 1 0 0 008 0 74 1 0 1 046 150 59 0 2 0 1 25 1 0 0 008 0 75 1 0 1 046 150 59 3 2 0 1 25 1 0 0 008 0 76 1 0 1 039 150 88 4 2 0 1 25 1 0 0 014 0 77 1 0 1 039 150 88 8 2 0 1 25 1 0 0 014 0 78 1 0 1 039 150 89 1 2 0 1 25 1 0 0 014 0 79 1 0 1 039 150 89 5 2 0 1 25 1 0 0 014 0 90 1 0 1 039 150 89 7 2 0 1 25 1 0 0 014 0 81 1 0 1 039 150 90 0 2 0 1 25 1 0 0 014 0 82 1 0 1 039 150 90 3 2 0 1 25 1 0 0 014 0 83 1 0 1 039 150 90 55 2 0 1 25 1 0 0 014 0 84 1 0 1 039 150 90 9 2 0 1 25 1 0 0 014 0 The first column is the detector number delta l and 2theta are as defined above Code defines the instrument 150 is LAD the parameters utl ut5 are user defined and in thi
12. IT command for example if the command file is called TEST COM the job is started with SUBMIT TEST 3 6 8 Reading output files The data in the MON and NRM files can be read into a workspace using a standard READ command For example to read the fifth group of NRM into the second workspace type Read W2 1 001234 5 after the prompt gt The following GENIE command files carry out the standard operations similar to SQRAW ie calculating a crude S Q see section 3 4 2 There are 2 versions SQGRP operates on individual groups SQANG operates on angles as in the default grouping The routines prompt for sample can and vanadium run numbers and for the group number or angle as appropriate page 3 22 3 7 TRANSMISSION ROUTINES The transmission cross section of a sample in a t o f experiment and thus the absorption correction cannot be calculated from the individual atomic cross sections eg by assuming a 1 v dependence of the absorption cross section because of the effect of S Q Hence the transmission is calculated from the experimental data for both sample and vanadium see section 2 4 These command files for GENIE calculate the transmission cross section from the monitor data in either the RAW files or in MON files The former is useful for checking the sample during the run whilst the latter is for the subsequent analysis Two forms of sample geometry be treated cylindrical and flat plate So
13. It is of most use for long programs such as those used to calculate the absorption correction and the multiple scattering correction Some useful batch related commands are as follovs SUBMIT VANO1234 COM submit the command file VANO1234 COM to be run by batch SHOW QUE SBATCH show the status of all batch queues DELETE ENTRY 999 RLDESBATCH delete batch job 999 the entry number 999 may be obtained by use of the SHOW QUE command from queue RLDESBATCH for example SHOW SYS BAT shows all the batch jobs currently executing in the current processor and how much CPU time each has used Note that if a job has been submitted to a different CPU from the current one the amount of time in that job can only be obtained by logging on to the appropriate CPU This is not normally possible for HRPD POLARIS and CRISP unless you know the password because these FEM s have limits on who can log on page 3 6 3 3 INSTRUMENT INFORMATION 3 3 1 Calibration On time of flight instrument the data must be converted from stored counts in channels to counts in other units such as wavelength d spacing and Q vector These conversions are determined by two standard equations t m h LA 2d sinO Bragg s equation where t is the time of flight is the origin in time determined by the electronics is the total flight path equal to the sum of the initial a and final 15 flight paths is the vavelength 20 is the scattering
14. M file which is to be run The name must be prefixed by a directory name if the command file does not reside in the current default directory There is an initialisation command file that is automatically read on entering GENIE This sets up values for the number of spectra and their size and the default disk directories The data in Workspaces can be written to binary files for subsequent reading back into workspaces External programs can be run to manipulate data in workspaces these are the FUNCTION and TRANSFORM commands and are used in our programs for example to read in corrections parameters Data in non GENIE type files usually ASCII can be read into workspaces using page 3 12 the Load command The units of x in the workspace can be changed provided that the workspace contains instrument parameters which are input via the SET PAR command The y values of the data in the workspaces are stored in the form of per unit of x eg per microsec or per Care must taken when changing units and dividing for example the correct order is to change unit then divide The option of scaling x to the y unit can be removed with the SET Yunit command 3 4 1 Simple Example of GENIE commands In order to read in a sample and vanadium spectrum divide and display as S Q the following operations are necessary gt ASS 1234 assign run number for sample gt W1 S1 read spectrum 1 into workspace 1 gt Set PAR 1 10 1 15
15. OUTINES PLATOM AND INTERFERE PLATOM is a GENIE function to evaluate the self scattering from the sample This routine uses the approach described by Powles 6 and extended by Howe McGreevy and Howells 20 see section 2 9 which page 3 42 involves an expansion in powers of and derivatives of the detector efficiency and flux distribution The user should decide whether or not this approach is acceptable for his particular experiment It is intended to eventually offer programs implementing other alternative approaches to inelasticity correction The routine PLATOM is executed by entering GENIE and typing Gg NRM file is required for input so to obtain the required Q scale The default directory must be set to that of the file before entering GENIE The GENIE function PLATOM can be applied to a multi component system and requires the following input number of atom species and for each one its fractional concentration these should add to one its atomic weight in atomic mass units C 12 0 its total scattering cross section in barns sample temperature in units of Kelvin used to calculate mean atomic kinetic energy in sample The user should check that the calculation of the self scattering is acceptable by using GENIE plots to check whether the corrected differential cross section oscillates about the calculated self scattering At high Q the differential cross sec
16. SECTION 3 HOW TO RUN THE PROCEDURES page 3 1 3 1 THE ISIS COMPUTING SYSTEM 3 1 1 The computers The current ISIS computing system sometimes referred to as PUNCH PUlsed Neutron Computer Heirarchy is illustrated below and is fully described in the PUNCH User Manual Terminal Cambridge Ring LAD FEM Ethernet R55 uVAX VAX8650 JANET HUB Computer Each instrument is controlled by a Front End Mini FEM computer which in the case of LAD is a Micro VAX 2 The central mainframe referred to as the HUB is a VAX8650 The FEM and the HUB are connected by two network systems the Cambridge Ring and Ethernet The HUB is also the node for other vide area networks such as JANET for UK universities and DECnet EARN and BITNET for world wide access Users will be assigned their own username on the HUB see Local Contact for details for use in analysing data The username vill be of the form 1 where the letters are the initials of the user and the numerals take into account several users vith the same initials The same username may also be used to log on to the LAD FEM page 3 2 3 1 2 Getting started gt gt gt Note any command typed into the computer should be followed by pressing the RETURN key sometimes referred to as Carriage Return CR This will be assumed throughout the manual To log on to the HUB 1 Press the BREAK key on the terminal until the prompt DNS appears 2 Type CALL HUB 3 Pr
17. The programs take up to 15 mins of CPU time especially the cylindrical multiple scattering program so submitting to batch processing is highly recommended Two further command files are available to make this easier and they assume that the filenames have the form LAD runnumber where runnumber is 5 digits the same format as RAW files These commands in ladmgr progs are SUBABS and SUBMUL and assume that the runnumber only has 3 digits When running from the page 3 29 lad area the abbreviations SUBA and SUBM can be used eg SUBA 123 or SUBM 234 All created files will be in the current directory If a program runs out of CPU time the problem is probably due to a step size that is too small Resubmit with a larger step size say a factor two larger This should only occur for samples of large radius eg greater than 10mm The use of CORAL removes all these complications and avoids detailed knowledge of the operating system Do not run two versions of the same option at the same time for example wait for an ABS or MUL program to finish before starting a new version ABS and MUL can be run at the same time If you are logged on at a terminal there will be a message from CORAL when a batch job has finished In the course of setting up the input files to run the corrections programs you will need to specify the capture cross section at 1 8 The value needed should be checked by looking at the measured cross sections sinc
18. are submitted to batch a The collimation to the detector is set to 4cm vide this will be vider than the sample in most cases b The neutron beam height defaulted to 4cm will in general be less than the sample height defaulted to 6cm The neutron beam is centred on the centre of the sample c The profile across the beam is constant and the beam is symmetric about the sample centre For FLAT plate geometry the only parameter is The angle between the incident neutron beam and a line perpendicular to the sample plane The default value is O that is sample perpendicular to the beam It is assumed that the sample is an infinite plate The routine also reads the data file RAW or NRM to obtain the number of angles and their values The angle for each group vill be printed page 3 32 CAn Inputs parameters associated with a can and other annuli such as radiation shields The routine prompt is can gt For CYLINDRICAL geometry the parameters are Outer radius of annulus cm for single can radius 3 For FLAT plate geometry the parameters are Thickness of can at front cm Thickness of can at back default front value COMMON parameters are Number density in atom or mol per Absorption cross section 1 8 in barns File name for cross section data there is NO default file name If the file does not exist an error message appears and the routine is aborted There is one qualifier MANY which is invoked
19. ch wavelength the values of A Ps sc 4c sc cc This is repeated for each bank normally 7 banks for LAD The MUL files have a similar format Using the notation of section 2 8 it is no of wavelengths bank no not necessarily group no scattering angle of bank page 3 39 then for each wavelength the values of A SINGLE A M A TOTAL A 3 9 ROUTINE VANSM This is a GENIE command file that removes the Bragg peaks from the vanadium spectra puts a smooth line through the data and divides by the calibration correction as described in section 2 7 This calibration correction is obtained by combining the results of the single and multiple scattering correction in the file with extension with a vanadium Placzek correction estimated using the program g F N PLAVAN which uses the same formalism as that used for the sample Placzek correction described in section 3 11 The routine reads the vanadium data from the file with extension NRM and smooths using Chebyshev polynomials The Bragg peaks are removed at the same time by ignoring the region around the peaks in the fitting procedure The fitting routine defaults to 10 polynomials but this can be changed if required The routine is run from GENIE by typing G F VANSM The routine just simply for the vanadium run number and a corresponding background run number and automatically loops through the groups It requires a file with extension REF to exist in the cu
20. e is an error message and the command is aborted RUN Defines the run numbers The command is RU runi lt run2 gt Up to 8 runnumbers may be specified The output file will take the name of the first run number specified and will contain a sum over all the runs page 3 20 3 6 6 Example of GROUPS DAT file Standard Groups dat file for LAD corresponding to detector layout on February 1989 P D 11 12 9 10 42 50 33 58 24 67 15 76 O O O 0 0 O e KF KF HL 43 51 34 29 25 68 16 77 44 52 35 60 26 69 17 78 41234 45678 45 53 36 61 27 70 18 79 46 54 37 62 28 71 19 80 47 55 38 63 29 72 20 81 48 56 39 64 30 73 21 82 49 57 40 41 65 66 31 32 74 75 22 23 83 84 number of groups 50 59 10 10 20 20 35 35 60 60 90 90 gas L gas R gas L gas R scintillator scintillator scintillator scintillator scintillator scintillator scintillator scintillator 150 Left 150 gas Right The average angles produced by these groupings are 4 8 ur wur wr 9 69 20 23 35 27 58 08 89 69 and 145 6 page 3 21 3 6 7 Batch operation The program can also be run in batch mode A command file must be created in the following format norm gt gr return gt run nl n2 gt be delta q q max gt ex exit The job is submitted to the batch queue vith the SUBM
21. e the SCATTERING cross section is determined from the TOTAL cross section by means of the relation o a 4 o 2 Therefore IF for some reason the capture cross is LESS than its barn book value e g due to an error in the sample composition then simply using the barn book value could lead to a NEGATIVE scattering cross section in the multiple scattering routines In other words the capture cross section typed into CORAL must be consistent with the total cross section values in the MUT files used Finally note that when running the multiple scattering for a container on its own the multiple scattering run is set up vith the SA command and not the command i e the container must be treated as page 3 30 a sample in this case 3 8 4 Description of commands A full description of the commands now follows page 3 31 BEan Inputs parameters associated with the neutron beam and the instrument The routine prompt is beam gt If neither a SA or VA command has previously been issued an error message is printed and the routine is aborted For CYLINDRICAL geometry the parameters are in cm Incident beam vidth Incident beam height default 4 0 The folloving assumptions are made concerning the beam although the programs are designed to accept more general cases If alternative conditions are known to exist then the input and files must be modified outside of CORAL and before the jobs
22. ess RETURN to make the prompt Username appear 4 the username eg ABCO1 5 In response to the prompt Password type password 6 A short command routine will then be executed setting the system ready for analysing LAD data and then the user will be logged on to the HUB and able to commence data analysis The command routine must be setup by the Local Contact during the first use of the username Periodically the user vill be required to change the password This is done by use of the command SET PASS Once logged on the user 1 will have access to an area of disk space for storing files the directory ABCO1 and sub directories of it In these areas there are full access rights ie read write execute delete The user has limited rights usually read only to areas within LADMGR Initially when the data is collected it is stored in the directory LADMGR DATA on the FEM and automatically transferred to the HUB in the same directory However due to space restrictions the data is archived onto optical disk and deleted within a few days Data files are restored by issuing the command RESTLAD when logged onto the HUB This restores the raw data page 3 3 files to the area LADMGR RESTORE with the restore process taking a maximum of about 10 minutes The data files are held in this area for a period of 3 days Both these areas can be referred to by the logical name inst data for example a directory l
23. f data by the extension name Within the programs the instrument name and leading zeros in a run number need not be specified In all the above cases the file structure is the same There is a header section which contains information supplied by the instrument control program ICP on the FEM There are sections on instrument parameters for example detector angles flight paths spectrum numbers for detectors and monitors run parameters for example date time of start and end number of protons neutrons and frames sample parameters for example title of run dimensions These are followed by arrays containing time of flight which is stored as the time boundaries for the channels as specified by the ICP each spectrum as counts per channel Files are in binary format but ASCII versions of parts of the data can be provided The GENIE program can also create files in binary format but vith a different layout The file starts with a selection of parameters from the RAW data header section such as scattering angle and flight paths and is followed by arrays containing the values of x y and error on y Such binary files will used extensively by our programs with the page 3 5 type of data denoted by the extension Programs are available for converting these binary files to ASCII format 3 2 2 Batch System The batch system enables a program to be run non interactively so as not to tie up the terminal
24. for more than one annulus At present restricted to 2 annuli This would be used for cases involving shields etc When used the routine prompts for the number of annuli and the above set of parameters is repeated for each annulus If not specified the default is one annulus The routine reads the number of wavelengths in the cross section data file and if this differs from that in the sample file an error message is printed page 3 33 GEORmRm The sample geometry can be changed using the SET command The command SET Geom Cyl invokes cylindrical geometry whereas the command SET Geom Flat invokes flat plate geometry On entering the program the default is Cylindrical This command must be issued before any of the SA VA or CA commands OUtput This initiates output of parameters to a file The command option creates a file with the extension AIN or MIN as specified by the option parameter and the name will be that specified in the RUN command If the option is not specified the routine prompts for a value option can take the values Van for vandium corrections Abs for absorption correction Mul for multiple scattering correction The routine prompt is out For CYLINDRICAL geometry the parameter is Step size cm the default values are 0 1 for VAN and MUL 0 02 for ABS For FLAT plate geometry the parameters are for multiple scattering only accuracy default 0 001 number of planes default 100 The name of
25. inner radius for empty can radius 2 outer radius of sample radius 3 default 0 ie no can outer radius of can if can is defined ie non zero value for radius 3 radius 4 default 0 ie no furnace or second can furnace second can outer radius sample number density in atom or mol per if can is defined number density filename for cross section data if furnace is defined furnace number density filename for cross section data The cross section file consists of the total scattering and absorption cross sections at a series of wave lengths A file can be created using the program CSFILE Standard files for vanadium VAN MUT and titanium zirconium TIZR MUT are available in the program directory g f If a cross section data file does not exist there is an error message and the routine is aborted subtlety occurs on LAD associated within the transmission monitor which does not sample the transmitted beam uniformly but instead samples the beam on a square grid with 5mm between elements This means the cross section determined from the transmission monitor page 3 24 readings can be significantly in error particularly if the sample does not attenuate the beam very much or if the sample is much thinner than the beam This effect is also pronounced vhen the transmission of a thin sample container is being measured In such cases the beam vidth can be regarded as an adjustable parameter which
26. is altered until the cross section of the vanadium rod comes out as expected this should then be used as the effective beam vidth for the samples If the container attenuation is so small to make the transmission readings unreliable then one of the standard files should be used for the container cross section The program TRANSFLAT requires the folloving input sample thickness sample number density in atom or mol per MUT files can be read into GENIE with the command LO W1 LAD MUT g F read cs which puts the cross section into workspace 1 A straight line fitting program is available to fit a straight line through the cross section data This is accessed by typing FU wl g F fit line w2 which puts the straight line fit to the data in wl into w2 This is useful for determining the asymptotic values of the measured cross sections page 3 25 3 8 PROGRAM CORAL Version 4 1 March 1989 3 8 1 Introduction The stand alone program CORAL is used to set up a calculation of either an absorption correction or a multiple scattering correction The actual calculations use several minutes of computer time and so they are performed in batch with the program CORAL setting up the necessary input The scheme described in section 2 5 is used to perform the calculations They may be performed for either a cylindrical or a flat plate sample with or without a container The corrections calculated by CORAL
27. isting can be obtained by DIR inst_data Programs and command files are stored in the area LADMGR PROGS which has the logical name g Note a logical name is simply convenient synonym used to stand for a string of characters The user may wish to make use of sub directories to help organise the files within his own area In this case the following commands are useful CREATE DIR ABCO1 ANA create a sub directory named ABCO1 ANA SET DEF ABC01 ANA set the default directory to be ABCO1 ANA This has the effect that subsequently the computer will assume that file is in the directory ABCO1 ANA unless another directory is specified SH DEF show the default directory 3 2 DATA FILES AND BATCH SYSTEM 3 2 1 Data File Structure The data on the FEM can be in 3 locations the DAE the CRPT or disk either as a SAV file or a RAW file On the HUB it is either SAV or The convention used to name files involves 3 parts a filename an page 3 4 extension and a version number For data the filename is constructed from the instrument name 3 characters and a 5 digit run number The type of file is specified by the extension for example SAV or RAW The full name of the raw data file version 1 for run 1234 for example is LADO1234 RAV 1 our programs we continue to use this form of nomenclature so that data for a specific sample can be recognised by its run number and the type o
28. may be performed for either a NRM file or a RAW file although in the recommended sequence of analysis it is a NRM file which is corrected In order to perform either calculation a file containing the total cross section is required In normal use the file calculated by the TRANSmission programs may be used for this The absorption and multiple scattering corrections for a sample may be performed in either order In the case of vanadium the recommended sequence of analysis involves performing only a multiple scattering correction at this stage using the special CORAL command VA page 3 26 The program CORAL uses the following file naming conventions for correcting the run LAD01234 NRM for example Absorption Multiple Scattering Vanadium Correction Correction Correction Created before Batch Job File Containing Commands to Run Batch Job ABS01234 COM MULO1234 COM VANO1234 COM File Containing Input Parameters for Batch Job LADO1234 AIN LAD01234 MIN LADO1234 MIN Created during Batch Job File Containing Log of Batch Job ABS01234 L0G MULO1234 LO0G MULO1234 L0G File Containing Batch Job Result LADO1234 ABS LADO1234 MUL LADO1234 REF Files named CYLMUL IN and CYLMUL OUT are also used during the multiple Scattering calculation but are deleted after successful operation As well as the usual input parameters such as dimensions this program requires a description of the beam profile and the total cr
29. nd Help will provide brief comments on the NORM commands whilst Help GENIE gives information on GENIE commands Xxx AX X AX 3 6 5 IMPORTANT NOTE At the time of writing NORM contains a bug which means it can only be run on one set of data i e one sequence of commands as above On completion it must be exitted and restarted with the NORM command again for each set of files Description of Commands A full description of the commands now follows page 3 18 BEgin This command begins the automatic looping over all the groups as defined by the Group command The routine prompt is begin gt The routine will ask for increment in Q delta q default is 0 02 maximum Q value q max default is 50 Alternatively the two parameters can be included with the command in the form BE delta q q max Each spectrum group will be rebinned at constant delta q where the q values are integer multiples of delta q ie N delta q The minimum rebinned q value is the first multiple of delta q greater than the minimum q value of the raw data The maximum rebinned q value is the last multiple of delta q less than the maximum q value of the raw data or the defined maximum q value whichever is the smaller the CAL command has previously been issued the values of the calibration constants vill be changed There 15 an error message if a run number has not been given or if the groups have not been defined and
30. ng a similar file can be created on the HUB to be used by our programs 3 3 2 Spectrum numbering All detectors and monitors are allocated a spectrum number The physical detectors are mapped to spectrum numbers by software via a file called SPECTRA DAT These can be changed by the user at the start of an experiment but in most cases a standard setup is used The number of spectra and the number of channels per spectrum are defined on the FEM by the ICP and their product defines the storage capacity required and the maximum value is determined by the hardware in the FEM In the data analysis programs the spectra can be further combined for example according to scattering angle This will in general be neccessary to reduce the volume of data and is particularly true for the scintillator modules which have a large number of detector elements Subsequently a combined spectrum from several detectors is treated as though being at the average angle In the case of LAD the detectors occur in groups at scattering angles of approximately 5 10 20 35 58 90 and 150 and the default vay of combining the detectors is based on these groups Two of the spectra are always the monitors one in the incident beam and the second in the transmitted beam page 3 8 The header section of the data files also keeps record of the spectrum numbering and in our programs we make use of this data so that the user does not need to know them 3
31. o the programs is line 1 2 7 1 7 2and 3 7 4and 5 7 6and 7 7 8and 9 10 1 10 2 11 12 13 and so on For FLAT programs is line 1 2 parameters title number of profile values the profile values step size for calculation cm number of detector angles the angle values height of sample position of incident beam edges position of detected beam edges bottom and top of incident beam bottom and top of scattered beam number of annuli in sample na radii of annuli 1 values number density in atom or mo1 absorption c s at 1 8 filename of total scat abs c s data as 10 for next annulus as 11 plate geometry the format for the input data file to the parameters title angle between sample and beam page 3 38 3 accuracy and number of planes calculation 4 number of detector angles 5 the angle values 6 number of cans plus sample 7 thicknesses of sample and can front and back 8 1 number density atom or mol for sample 8 2 absorption c s at 1 8 for sample 9 filename of sample total scat abs c s data 10 as 8 for can 11 as 9 for can 3 8 6 Format of output files The ABS files consist of a tabulation of the absorption factors such as SC for example for every vavelength and scattering angle 3 specified in the input file The format is no of wavelengths bank no not necessarily group no scattering angle of bank then for ea
32. oss section as a function of wavelength This cross section data is in a data file with extension MUT as produced by the TRANSmission program It can also take into account several annuli surrounding a sample eg can and furnace and masked beams e g beam vidth smaller than sample diameter The location of the input run is defined using the SET commands The default directory is set on entry to the instrument data area e g LADMGR DATA for LAD and the default extension is RAW All output goes to the current directory page 3 27 3 8 2 Operation The program is a stand alone program similar in operation to GENIE but without any display options and is started with the command CORAL The program prompt is c The sequence of commands is as follows SET EXT if required default is RAW SET DISK or DIR if required default is LADMGR DATA SET INS if required default is LAD SET GEOM C or F if required default is C RUN lt runnumber gt or V CA if required BE OUT option SUB In the program some of the parameters have fixed values while others are set to default values When a default can be changed its value is printed and RETURN keeps the default otherwise type in the new value The HELP facility is also available vithin the program The command Help on its own will provide brief comments on the CORAL commands whilst Help Genie gives information on Genie commands When running CORAL i
33. rrent directory as produced by the VA command in CORAL The smoothed result is output to a file with extension SMO Spectra from the SMO file can be read using the standard GENIE READ command It is recommended that users check that a satisfactory smooth line has been put through the vanadium data This can be done by displaying the contents of workspaces 1 n n is the number of groups after running VANSM These workspaces contain the difference between the original NRM data for each detector group and the smoothed version page 3 40 original NRM data for each detector group and the smoothed version but BEFORE the calibration correction has been applied The command for this would be D L W5 to display the difference for detector group 5 The user may wish to experiment with fitting Chebyshev polynomials of order other than the default 10 Before running VANSM diagnostic output may turned on by typing in GENIE v19 1 Similarly typing v20 15 sets the polynomial order to 15 for example The ideal polynomial order is selected so that the residual given in the diagnostic output has settled down to a value almost independent of polynomial order Thus suitable procedure for selecting an appropriate polynomial order involves first doing a test fit with diagnostic output a very large 502100 polynomial order 3 10 ROUTINE ANALYSE This GENIE command file takes the spectra data and applies the corrections to produce
34. s case are uti detector type code l gas 2 scintillator ut2 and ut3 parameters to calculate detector efficiency ut4 resolution ut5 Spare The calibration determines L 1 1 is taken to be the nominal value of 10 0m If 1 is not defined in the parameter section of the data files then 12 can be set to L for the purposes of unit conversion to wavelength page 3 11 3 4 OVERVIEW OF GENIE For more details of this program the user should consult the GENIE Manual We will restrict ourselves to comments on the general principles and the more important points in its operation The overall program structure is command driven not by menu However where possible the individual routines called by the commands will include a menu or question answer structure for ease of use Workspaces are used for data manipulation The number of workspaces and their size array length can be chosen by the user However there is a limited memory space available so the product of the number of workspaces and their length must be within this limit There must always be enough space for the graphics area and buffer areas This will normally be set for you Command files be used for repetitive operations and can also include terminal input A command file is program run within GENIE which executes commands from a COM file instead of the user typing in at the keyboard Command files are run in GENIE by typing followed by the name of the CO
35. t is important to type the full sequence of the above commands from RU to BE before typing OUT otherwise errors in the output files can occur Thus if when in SAMPLE or CAN or VANADIUM or page 3 28 BEAM typing error occurs then the whole sequence from RUN inclusive should be typed again to ensure the output files are correct 3 8 3 Hints on running The cylindrical input file format in 3 8 4 is used for both the absorption and the multiple scattering programs The only change neccessary to the parameters is the step size line 4 The MS calculation can have a larger step size than the absorption by up to an order of magnitude Typically for MS use 0 1 and for absorption 0 02 The flat plate input file is also used for both correction programs but line 3 is only nesseccary for the multiple scattering and default values have been set at 0 001 for accuracy and 100 planes The MS program assumes an input file with extension MIN and creates an output file with extension MUL and a lineprinter listing with extension LIS The filename for all three files is the same The corrections programs are called CYLABSTOF CYLMULTOF FLTABSTOF and FLIMULTOF and are in the instrument program directory ie ladmgr progs or logical name g F on LAD There are command files also in ladmgr progs for running the programs called RUNABS and RUNMUL with one parameter the filename All created files will be in the current directory
36. the data file created is also printed If run number has not been given an error message is printed and the routine is aborted The same happens if the option value is incorrect page 3 34 The output filename is defined with the command RUN run number If the runnumber is not specified its value is asked for For the Vanadium it would be the vanadium run number The sample run number is used for absorption and multiple scattering in the sample If a can is present its run number is used for the can multiple scattering SAmple Inputs parameters associated with the sample The routine prompt is sam gt For CYLINDRICAL geometry the parameters are Sample height cm default 6 0 First radius cm default 0 0 for solid rod Second radius cm For FLAT plate geometry the parameters are Sample thickness cm COMMON parameters are Number density in ston or mol per Absorption cross section 1 8A in barns File name for cross section data if only RETURN is typed itdefaults to a file with runnumber and extension eg LADOO123 MUT The routine checks that the data file exists if it does the routine reads the number of wavelengths in the cross section data file and uses that value If the file does not exist it prompts for a value page 3 35 SUbmit The job is submitted to the batch queue to run the corrections programs with the command SUB runnumber If runnumber is not specified the value gi
37. the differential scattering cross section The routine is invoked vith the command Gg F ANALYSE The routine reads sample and can data from the NRM files the smoothed vanadium from the SMO file and corrections from the ABS and MUL files It carries out the folloving operations as described in section 2 8 subtract background from sample divides sample by vanadium subtracts multiple scattering from sample if can is present subtract background from can page 3 41 divide can by vanadium subtract multiple scattering from can apply absorption correction to can subtract can from sample apply absorption correction to sample divide by sample calibration constant This is done on all groups specified and the results written to a file with extension DCS Note that the sequence of operations given above is necessary in order that the corrections be performed properly The ANALYSE routine requires the folloving input option of can or no can sample background and can run numbers range of groups to be used sample calibration constant vhich for CYLINDRICAL samples is the number of atoms or scattering units in the beam x 10724 for FLAT PLATE samples is the product of atomic number density in atoms per and the thickness of the sample cm Spectra from the DCS file can be read using the standard GENIE READ command Note DCS stands for Differential Cross Section 3 11 R
38. tion LAD01234 DCS should tend to the average level given by the self scattering LAD01234 SLF This check may be performed by using GENIE to DISPLAY the self scattering and then to PLOT the differential cross section on top or vice versa For example gt READ W1 LADO1234 DCS 5 gt READ W2 LADO1234 SLF 5 gt D 1 gt P W2 page 3 43 Programming note If the user makes changes to the routine PLATOM COM to suit his own requirements he should be aware that it makes use of the GENIE variable vi8 The GENIE routine INTERFERE is used to calculate the interference or distinct as it is otherwise known scattering by subtracting the self scattering in the SLF file from the differential scattering cross section in the DCS file This routine is invoked by entering GENIE and typing Gg f INTERFERE 3 12 ROUTINE MERGE This GENIE command file combines selected areas of spectra from different groups into one composite S Q as defined in section 2 10 For input it requires the sample DCS or INT file the vanadium SMO file and the vanadium MON file to be present in the user s area The output is in the file with extension 500 Before running this command file the user must determine by plotting the results from ANALYSE or INTERFERE to determine which groups and which Q ranges for each group he or she wishes to merge The routine is invoked by typing Gg F MERGE 3 13 ROUTINES STOG AND GTOS These GENIE functions carry
39. ts in general being smaller than neccessary for liquid and amorphous work means that rebinning of data in Q is alvays required page 3 9 TABLE 3 1 LAD February 1989 Number of 84 5 Det sS E ee ee E E a a N Qo 22 HP rr mE pP B HB d B EIE pm p pmP p pmP pP pm mp P PRP PP PPP e eo mbii J OO i0 O0 Un LO OP o d d od od d o gd dg BR RBS HW WH WH DH LO CO LO CO CO CO fo f NO HE J OY Ui WHE OO I i oo ne en ee cOOOOOOoOOoOoo0oOo0O0O00000000000000000050 Delta 4 Un Example of DETECTOR DAT file detectors Number of user table parameters detector Len2 128 128 128 128 128 128 128 128 H FR HH H H H HB IB Code 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 150 2theta ut1 145 6 1 0 145 6 145 145 145 145 145 145 9 6 9 6 4 8 4 8 180 0 0 01 88 4 88 8 89 1 89 5 89 7 90 0 90 3 90 55 90 9 57 0 57 2 57 45 57 8 58 0 58 3 58 7 59 0 gt lt C OOOOOOOO0oO0O000000000000000000000000000000000000 N32 BO BRO BS PO PO INO PO POP IND INO PO 82 ID IND P2 IND P2 PO IS P2 0829 INO 82 NO 2 EP
40. ven in the RU command is used and the correction option is that defined by the last Output command issued runnumber is specified it refers to a file with that runnumber not that given by the RUn command The routine will ask for the correction option This will normally be used to submit a job using a file created in a previous session on Coral There will be a LOG file with a name of the form ABS runnumber or MUL runnumber with extension LOG The output from the programs will be in files with name LAD runnumber and extension MUL ABS or REF for the VAN Lineprinter output will have extension LIS page 3 36 Inputs parameters associated with vanadium The routine prompt is van gt For CYLINDRICAL geometry the parameters are Beam height cm default 6 0 Vanadium radius cm assumes a solid rod For FLAT plate geometry the parameter is Vanadium thickness cm COMMON parameters are Number density default 0 072 atoms Absorption cross section 1 8A default 5 04 barns File name for cross section data if lt RETURN gt is typed it defaults to file with runnumber and extension MUT eg LADOO123 MUT The routine checks that the data file exists if it does the routine reads the number of wavelengths in the cross section data file and uses that value If the file does not exist it prompts for a value page 3 3 7 3 8 5 Format of data files For CYLINDRICAL geometry the format for the input data file t
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