XRFCOMBI User Manual
Contents
1. Data from fitfiles generated by the Pymca software from spectra measured under the same conditions for samples having the same qualitative composi tion can be processed in a single batch by importing them in xrfcombi using this button All previous steps except Enter intensities should have been carried out before the import One has to make sure that the file containing the list of the fitfiles to be processed should be in the xrf bin data di rectory It should have the name fitfilelist py and the format as generated by Pymca Also make sure that the references to the fitfiles in this list are correct no forward but backslashes between subdirectories 3 3 6 Results The button Results of the ANALYZE SAMPLE menu bar gives access to the various calculation methods as described in the Anal Chim Acta pa pers and a calculation method that includes the contribution of scatter to the intensities of the measured lines SMPLX SCATTER The latter cal culation method should only be used if the calibration has also been carried 16 out including the contribution for scatter Only in case the calibration is carried out with the pure element concerned as the only standard this is not necessary Choose the wanted calculation method The calculation results are avail able when the Results button returns from its raised state to the flat state and then can be inspected with the View item of the Results menu or printed with the Print item N B Only t2. ment number of atoms information and entering a new number of elements for the new compound creates fresh entries for the symbol number of atoms items When the last new compound has thus been defined and been entered in the list with OK ADD TO FILE the entry form can be dismissed 3 1 2 Sample Clicking the Sample button in the SIMULATION MENU starts the def inition of the composition of the sample for which the intensities have to be calculated This action opens two windows the COMPOUND SELEC TION window figure 5 and the DEFINE SAMPLE window figure 6 Continue by entering the requested data for NAME and THICKNESS aan RETA no DISMISS eee Figure 5 List box with compounds to select in their boxes Next click on the names of those compounds listed in the COMPOUND SELECTION listbox that should be included in the sam ple These compounds will appear automatically as entries in the DEFINE SAMPLE entry form When all necessary compounds have been selected dismiss the COMPOUND SELECTION box Then adjust the fractions of the compounds in the DEFINE SAMPLE form to the right values either by overwriting the fractions shown or just entering them in their boxes Now click on the OK ADD TO FILE button If you plan to do calculations on a sample with the same compounds but with different contents or with a different thickness do not dismiss this entry form to be able to use it later Figure 6 Entry form for definition of Sample
3. without having to select all compounds again The boxes HOMOGENEOUS PARTICULATE VOID FRAC TION and VOID SIZE are not yet used in the program so don t bother with them Now the lines for which the intensities have to be calculated should be entered Start this process by clicking on the Lines button of the SIMU LATION MENU This opens the DEFINE LINES entry form figure 7 This entry form is also used in other places in the program where more data is needed than for the simulations that we are dealing with now so not all entries need to be filled It suffices to enter the data on Element symbol only Line line type ka kb1 kb2 lal la2 lb1 etc kV the voltage the x ray tube is operated on in kV when the line is measured and to set the ra diobutton FILTER ON When the latter button is red the calculations are performed for the presence of an aluminium filter of 300 um in the primary beam we have only this one filter Pressing OK ADD TO LIST enters this line into the list and when all lines have thus been entered pressing CLOSE FILE writes this list to a diskfile that is used in the calculations After all lines have been entered the form can be dismissed At this stage sufficient data has been entered to start the simulation calcu lations by clicking on the Simulate button of the SIMULATION MENU A DropDown Menu opens and a choice between calculations with or with out scattering has to be made by click on one of the entries
4. toplayer 4 Line 4 same structure als line 2 but now for the 3rd layer from the top etc An example of simsampl dat is given below 005 Cu 0 8 Zn 0 2 01 Cu 0 1 Al 0 1 Zn 0 8 10 0 BaTi03 1 0 3 2 0 0 3 0 0 1 This files describes a sample with a toplayer of 0 0005 g cm2 Cu Zn con sisting of 80 Cu and 20 Zn a middle layer of 0 001 g cm2 Cu Al Zn 10 10 80 on a substrate of 10 0 g cm2 pure bariumtitanate The file deflines dat should contain the data on the fluorescence lines for which the relative intensity will be calculated It can be built by hand using an ascii editor but it can also be constructed using xrfcombi gt Simulate gt Lines Its structure is as follows e Line 1 Element symbol line symbol kV setting e Line 2 Element symbol Line symbol kV setting e etc An example for the file deflines dat Cu ka 50 0 Zn ka 50 0 Al ka 50 0 Ba lal 50 0 Ti ka 50 0 18 Using these files with simmul produces Rel int Cu ka is 9 691811e 02 Rel int Zn ka is 1 469369e 01 Rel int Al ka is 2 873800e 04 Rel int Ba lal is 3 212512e 01 Rel int Ti ka is 7 387456e 02 4 2 xrfmul The program xrfmul can be used to calculate the composition and thickness of the layers of a multilayersample if sufficient measurement data is provided This program needs 2 data files in de bin data directory 1 sample dat and 2 lines dat The structure of the sample dat file is as follows Line 1 number of layers of the sa
5. 10 D ompomd Figure 16 Entry form for sample composition unknowns unknown massthickness should be given as question marks Concentrations that are known i e the Li2B407 content should be given as fractions and are kept fixed during the calculations When this form has been completed for a sample to be analyzed the button Enter of this form should be pressed to copy the data to the TABLE OF CONCS As soon as the data of the last sample has been entered this form can be dismissed by clicking on its Done button The next step is to inspect the TABLE OF CONCS for errors cor recting them if there are any and copying them to a system file used in the 15 calculations by clicking on its OK button As was mentioned above only one sample has to be provided if the insities are imported from Pymca fitfiles 3 3 3 Define Lines The definition of the characteristics of the measured lines proceeds exactly as in the calibration section It is stressed here that entering multiple lines for one element is only possible for the calculation methods that use the simplex algorithm XRFSLMPX SMPLX GICAL and SMPLX SCATTER The other calculation methods don t converge if multiple lines for one element are used 3 3 4 Enter intensities The procedure to enter the measured intensities is also the same as in the calibration menu If intensities are to be imported from Pymcea fitfiles this step can be skipped 3 3 5 Import Intens from Pymca
6. Table of measured intensities the entry box shrinks and can be dismissed After checking the contents of the TABLE OF INTENSITIES and cor recting the mistakes this table can be dismissed by clicking its OK button The data is now written to a file which is used in the calibration calculations 12 3 2 5 Results The calibration results can now be obtained by clicking on the Results menubutton of the CALIBRATION MENU bar This opens a pull down menu with which the right type of calculations can be started or the results can be inspected and printed The button Normal calibration starts a calibration procedure that uses the normal relative intensities based on the intensities of the pure elements With the button Gi factor calibration the calibration method from the paper Non destructive analysis of small ir regularly shaped homogeneous samples by X ray fluorescence spectrometry M Bos et al in Anal Chim Acta 412 2000 203 is carried out It is very well possible to perform the calibration calculation in both ways The results are kept in different files i e listio dat resp listgi dat the list of calibra tion constants listio dat that the system uses in the analyzing phase If scatter corrections are wanted in the analyzing phase the calibration should be carried out using the menu choices Calibrate gt Results gt Scatter calibration 3 2 6 File The CALIBRATION MENU bar has a File menubutton that gives ac cess to some
7. line ka rel int 0 0738746 1 Z 56 line lat rel int 0 321251 2 Z 13 line ka rel int 0 00028738 3 Z 30 line ka rel int 0 146937 4 Z 29 line ka rel int 0 0969181 Line nr 0 RXI found 0 0738745 RXI meas 0 0738746 Line nr 1 RXI found 0 321251 RXI meas 0 321251 Line nr 2 RXI found 0 00028738 RXI meas 0 00028738 Line nr 3 RXI found 0 146937 RXI meas 0 146937 Line nr 4 RXI found 0 0969183 RXI meas 0 0969181 Layer 0 has 2 compounds and a massthickness of 0 0005 g cm2 Compound Cu wfract 0 8 Compound Zn wfract 0 2 Layer 1 has 3 compounds and a massthickness of 0 001 g cm2 20 Compound Al wfract 0 0999999 Compound Cu wfract 0 100001 Compound Zn wfract 0 8 Layer 2 has 1 compounds and a massthickness of 10 g cm2 Compound BaTi03 wfract 1 Ssq is 1 43745e 15 It is stressed that the calculations with xrfmul and simmul do not include scatter contributions 21
8. maintenance functions via a dropdown menu The last item on this menu Quit calibration closes the calibration menu bar All files used in the calibration calculations can be archived by clicking on the Save Calib Data entry of this menu The entry Load Calib Data restores archived cal ibration to the standard files which then can be edited by hand if necessary so that a recalculation of calibration constants can be performed Finally the calibration constants can be inspected graphically via the gnuplot program by clicking on the Plot Calib Data entry of the File menubutton 3 3 Analyze The button Analyze on the main menu bar figure 1 opens the ANALYZE SAMPLES menu bar see figure 14 This bar shows a number of buttons that give access to the entry forms that should be filled out to enter data on the qualitative composition of the sample Compounds in Sample the 13 file Compounds in sample Enter Cones Define Lines Enter intensities Results Help Figure 14 Analyze menu bar quantitative composition of the sample for those components of which the concentration is known together with the indication of the quantities to be calculated from the measurements i e unknown concentrations and maybe the massthickness of the sample Enter Concs the definition of the lines that were used in the measurements Define Lines and the intensities of the measured lines Enter intensities As an alternative for Enter intensities th
9. the various calibration samples is started by clicking on the Enter Concs button of the CALIBRATION MENU bar This action opens an entry form ENTER CONCS sce figure 10 and a table TABLE OF CONCS see figure 11 that gives an overview of Figure 10 Entry form for concentrations of compounds in sample the composition of the standard samples entered thus far The entry form should be filled with a sample identification Sample ID the massthickness in g cm2 of the sample and the fractions of its constituents If all entries have been entered correctly the Enter button should be pressed to copy the data for this particular sample to the table where it appears automatically When all standard samples have been treated the Done button of the entry form can be clicked The next step is to check the contents of the table TABLE OF CONCS If there are mistakes then correct them by clicking on the pertinent box and 10 Figure 11 table of entered sample compositions type the correct value When all is ok then click on the OK button of the table 3 2 3 Define Lines With the Define Lines button the same entry form as used in the Simu late menu is opened to indicate which X Ray Fluorescence Lines haven been measured see figure 7 Now however we are dealing with specific mea surements so all information should be entered correctly In our laboratory we we either measure with a large mask or a small one or we measure in cups closed w
10. PA ahai hia a abe Figure 8 Menu bar for calibration Data is needed on the composition of the standard samples used for the calibration and on the measured fluorescence lines and their intensities En try forms for this data can be opened by clicking on the buttons Define Sample the compounds composing the sample Enter Concs the frac tions of these compounds in the standard Define Lines the nature of the lines used in the calibration and Enter intensities the measured intensi ties for all measured lines for all samples The data should be entered in a specific order Define Sample gt Enter Concs gt Define Lines gt Enter intensities 3 2 1 Define Sample Clicking on the Define Sample button of the CALIBRATION MENU bar opens the listbox COMPOUND SELECTION see figure 5 contain ing all the compounds that the system knows of and a box SAMPLE COMPOUNDS that shows the compounds entered thus far see figure 9 Compounds are entered into the sample by clicking on their name in the listbox COMPOUND SELECTION There is no error correction possi bility On an error just dismiss the SAMPLE COMPOUNDS box and start again by clicking on the Define Sample button of the CALIBRA TION MENU When all compounds that are needed have been entered dismiss both boxes lt o Lstt of compounds in sample series ira ih renee nnen Figure 9 Window showing compounds in sample 3 2 2 Enter Concs The entry of the composition of
11. Simulate no o anmain rnme ANALYZING X TAL TTT cere er riranin Jehan beainiar ee UR 200 ee syne Pee Cete re rena ad OK ADD TO LIST CLOSE FILE 1 maaar er en Figure 7 Entry form for definition of lines scatter and Simulate with scatter When the calculations are ready the results can be inspected by openening the Viewer dropdown menu on the SIMULATION MENU bar and clicking on the View Results Simula tion item This dropdown menu also gives the opportunity to inspect all data files used for the calculation to check for entry errors The results can also be printed by opening the Print dropdown menu and choosing Print results If the DEFINE SAMPLE entry form was not dismissed earlier it is now possible to repeat the calculations for a different composition or thickness just by changing the pertinent data in this entry form writing it to file by clicking on OK ADD TO FILE button of this DEFINE SAMPLE MENU form and clicking the Simulate button again followed by Viewing or Printing When done with all the needed simulations dismiss the DEFINE SAM PLE entry form and dismiss the SIMULATION MENU by clicking on the Dismiss Sim Menu button on its bar 3 2 Calibrate The button Calibrate opens the menu bar for the calibration process see figure 8 File _ Define Sample Define lines Enter Cones Enter intensities 2 penine sample Del Results Help riihi eri
12. XREFCOMBI User Manual M Bos Herikebrink 87 7544 ES ENSCHEDE NETHERLANDS July 2009 1 INTRODUCTION The first version of this manual described the installation and use of the set of programs described in the papers M Bos J A M Vrielink Anal Chim Acta 378 1998 291 and M Bos J A M Vrielink W E van der Linden Anal Chim Acta 412 2000 203 It now contains additional information con cerning corrections for double photon interactions concerning scatter The user interface is written in Tk Tcl Menu buttons give access to the various programs and some utilities to simplify data entry Data transfer between the various programs is performed by temporary ascii files that can be inspected and edited by any plain ascii text editor The calculation methods XRFSMPLX XRFROUS SMPLX SCATTER and SMPLX GICAL handle concentrations of sam ple components in terms of chemical compounds directly and produces results in terms of the concentrations of chemical compounds All other programs start with a conversion of the initial estimate of the sample composition to an estimated elemental composition refine this elemental composition and produce the result also as an elemental composition The choice of the program to use for calculating analytical results should be governed by the guidelines given in the abovementioned papers In March 2004 the program xrfcombi was extended with the incorpo ration of second order processes comprising one scatte
13. e intensities can be imported from socalled fitfiles from the ESRF program Pymca for batch processing of spectra measured under the same conditions and samples containing the same compounds In this case Enter intensities should be skipped To use this facility the form ENTER CONCS has to be filled out only once These entries should be dealt with in the order given The Results button gives access to the various calculation methods and with the File button data that has been entered can be archived or saved data can be retrieved and or edited Details for the various entry forms are given below 3 3 1 Compounds in sample The first thing to do in an analyzing session is clicking on the Compounds in sample button of the ANALYZE SAMPLES menu bar and this produces the same COMPOUNDS SELECTION listbox with compounds from which the samples can be composed as was used in the calibration menu figure 5 Clicking on the names of the wanted compounds enters them in the SAMPLE COMPOUNDS table see figure 15 Both windows should be dismissed before continuing 3 3 2 Enter Concs The Enter Concs button of the CALIBRATION MENU bar opens an entry form and a table The entry form ENTER CONCS shows entries for the sample identification the massthickness and the concentration of the 14 Figure 15 Table of sample compounds constituents of the sample see figure 16 Unknown concentrations or an ENET AET vite Pe A a an eee ee a Massthickn a
14. hat shows the list of all known compounds and an entry form to define new compounds see figure 4 If the list contains all the wanted compounds the entry form can be dismissed If not this entry form should be filled out starting with the name of the compound to be defined in the FORMULA NAME box Next the density of the compound should be entered in the density box This quantity is not yet used in the calculations so at the moment this value is not important but in the future it will be used to convert mass thickness to normal thickness so it is better to enter FORMULAINAME TOZ Figure 4 Entry form for definition of Compounds the correct value here Anyhow a value should be entered otherwise the format of the complist dat file will be disturbed In this release all compounds should be defined in terms of number of atoms of the elements present in the compound so the radiobutton AT should be on red If WT is chosen the program refuses to accept the entry for now Entering the number of different elements present in the compound in the box NR_ELEMENTS opens a number of entries in which the symbols of these elements should be entered followed by the number of atoms of the element in the compound When the information is entered correctly then click the OK ADD to FILE button and proceed to the next com pound to be defined overwriting the info in the FORMULA NAME and density box Clicking in the box NR ELEMENTS removes the old ele
15. he method SMPLX SCATTER includes scatter contribu tions and should be used with the corresponding calibration method 3 3 7 File The File menu button of the ANALYZE SAMPLE menu bar gives access to utilities for editing storing and retrieving the system files that are used in the calculation of the results The Quit item dismisses the ANALYZE SAMPLE menu bar 4 MULTILAYERS Apart from the user interface xrfcombi and its associated prgrams that can be run from it the bin directory contains 2 standalone programs simmul and xrfmul that deal with multilayers Both programs can only be run from the commandline and rely on the presence of some data files in the bin data directory to provide the needed input data 4 1 simmul simmul needs the following datafiles in the bin data directory 1 sim sampl dat and 2 deflines dat The first contains the structure and quan titative composition of a multilayer sample the second contains the names of the lines for which the relative fluorescence intensities will be calculated The file simsampl dat should contain the following data 1 Line 1 number of layers of the sample 17 2 Line 2 number of components of toplayer massthickness of toplayer followed by n times a name of a compound from the list complist dat and its fraction in the toplayer n stands for the number of compounds that the toplayer consists of 3 Line 3 same structure as line 2 but now for the layer beneath the
16. inss SEDER ECT ctinetintreionmanneiinee ermine o T y huaman Figure 2 Entry form for spectrometer data it should be filled out by mouse clicking on the entry and typing the pertinent data in the entries box When done the To File button should be clicked and the window can be dismissed Depending on the task that has to be performed one can now make a choice with the buttons Simulate Calibrate and Analyze Help is not implemented yet In the Simulate Calibrate and Analyze tasks one can define samples or standard samples in terms of already defined compounds The definitions of these compounds are kept by the system in the file complist dat New entries in this list can only be made via the Simulate gt Compounds menu 3 1 Simulate The simulation menu is meant to calculate relative intensities for given lines belonging to elements of a sample with known composition Clicking on the Simulate button of the main menu bar produces the simulation menu figure 3 via which composition data and the wanted lines can be given Lines Simulate Distiiss Swn Menu viewer Print Help arara ir arimana manii aamini aana naina ae ninina mana Figure 3 Bar for Simulation Menu 3 1 1 Compounds Now the first thing to do is to check whether the systems knows all the compounds of which the sample has to be composed This can be performed by clicking the Compounds button that produces two windows one named COMPOUNDS t
17. ith a mylar film The choice can be indicated by clicking on the correct radiobutton Furthermore we have the choice between four analyzing crystals The choice is indicated to the system by clicking on one of the radiobuttons LIF 200 GE PE or PX1 The only thing the system does with this data is to mark calculated calibration constants as belonging to these specific conditions in the file listio dat so that in the analyzing phase the correct calibration constants can be found for a given set of measurement conditions So if you don t find your wanted conditions concerning masks and analyzing crystals here just pick one and be consistent in using it 11 3 2 4 Enter intensities The final thing to do before the calculations can be started is to enter the measured intensities for all standard samples The process is started by clicking on the Enter intensities button of the CALIBRATION MENU bar This opens and entry form ENTER INTENSITIES in which the intensities measured for the indicated sample should be given see figure 12 Clicking on the Enter button of this form copies the data to the TABLE EGOS EAA I Sample ID Calibration standard noz PU oe Arka S00 Ber ae nes Ge ka 50 g o Fe ka oth a Bea ee eae AAA A SAE MASAMA ARESA ESAE EAAS BSAA SAAT PAAA te terior A A IE E AAAA AA A Figure 12 Entry form for measured intensities OF INTENSITIES figure 13 Ifall standard samples have been treated Figure 13
18. mple Line 2 number of compounds of toplayer massthickness of toplayer followed by eiher 0 or 1 name of compound 1 fraction of compound 1 in toplayer followed by either 0 or 1 name of compound 2 in toplayer etc line 3 same structure as line 2 but for layer beneath toplayer e etc massthicknesses and fractions followed by a 0 are refined those followed by a 1 are kept fixed For the quantities to be refined an estimate should be given An example for the same multilayer as given in the example for simmul 3 2 0 0001 O Cu 0 5 O Zn 0 5 0 3 0 0001 O Al 0 33 0 Cu 0 33 O Zn 0 8 1 1 10 0 1 BaTi03 1 0 1 19 This setup determines the thickness and composition of the toplayer and the thickness of the second layer and its Al and Cu content The Zn content is fixed at 80 and so are the thickness and composition of the substrate BaTiO3 The measurement data should be put in the file lines dat in the format e Line 1 Element Symbol Line symbol kV setting relative intensity e Line 2 same structure for next fluorescence line For the same example Ti ka 50 0 7 387456E 2 Ba lal 50 0 3 212512E 1 Al ka 50 0 2 8738E 4 Zn ka 50 0 1 469369E 1 Cu ka 50 0 9 691911E 2 The relative intensity given in this file for each line should be calculated by hand from the measured intensity by dividing by the slope of the correspond ing calibration line Running xrfmul with both these files in the bin data directory pro duces O Z 22
19. ring event and one photoelectric absorption based on the work of G Tirao and G Stutz X Ray Spectrom 32 2003 13 For the rayleigh scattering thr RTAB database from L Kissel is used http www phys llnl gov Research scattering Compton scattering is handled by a closed equation based on the Thomas Fermi model The test version xrfeombi022 of July 2009 offers the possibility to import intensity data from socalled fitfiles produced by the program Pymca that was developed at ESRF V A Sole E Papillon M Cotte Ph Walter and J Susini Spectrochim Acta Part B 62 2007 p 63 Apart from the user interface xrfcombi and its associated programs that can be run from it the bin directory contains 2 standalone programs simmul and xrfmul that deal with multilayers Bug reports and suggestions for improvement of the programs can be sent by e mail to m bosQmisc utwente nl 2 INSTALLATION 2 1 Linux The software is available as a gzipped tar archive xrfecombi021b tgz and can be unpacked in a user directory by the command tar xvzf xrfcombi020 tgz To function the software needs an installed version of Tk Tcl The pro gram wish of this package should be reachable via usr XR11R6 bin wish If this is not the place of wish the first line of the script combiscat bin xrfcombi should be adapted to point to the place of wish The package gnuplot should be available if one wants to use the plot option in the File menu of the calibration step
20. to display calibration lines The printing of results is routed via the standard unix printer of the lpr command So attention has to be paid to the printcap file 2 2 W95 W98 W2000 XP Vista The software is available as a zipped archive and can be unpacked in a user directory To function the software needs an installed version of Tk Tcl for Windows The package gnuplot should be available if one wants to use the plot option in the File menu of the calibration step to display calibration lines The printing of results is routed via a utility program Iprint exe which copies the output to be printed in plain ascii to the port LPT1 If no printer is connected to this port the program will hang 3 USING THE PROGRAM Once installed the program can be started in its working directory com biscat bin Linux or xrf bin Windows by typing xrfcombi Linux or xrfgo Windows after which the main menu bar see figure 1 shows up sentra p renin EAA ne We rresecnnnn Fle Simulate Calibrate Spectrometer Analyze Help Figure 1 Main menu of XRFCOMBI The first thing to do now is to set the spectrometer characteristics by clicking on the Spectrometer button with the left mouse button Now a data entry form SPECTROM PARAM appears G 2 and all items of mhiannan Aine AARAA AA a EAE me i f H Sample take off angle aege h T wid P E S AE E E E VEE ANA EN ATAA RE MARADNA AAAA A To File y PW1480 Para zo Des
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