Manual for Powder Indexing Software Conograph
Contents
1. M Space group Extinction rule 1 312 628 45 bca 72 bca hk0 h k 2n 0kl k l 2n 2 304 805 46 cab 74 cab hkO h k 2n Cancel 3 290 297 46 bca 74 bca Okl k Iz2n 4 284 817 No condition 5 277 796 45 cab 72 cab hOl h l 2n hkO h k 2n lattice constants 6 257 954 hOol h l 2n Fig 8 1 Determination of space group candidates 8 1 9 Other GUI operations 9 1 Configuration parameters Select the Menu gt File gt Preferences as follows snograph BIE Run Help New Project N Open Project 0 Open Recent Output All Lattices Save Project a5 Preferences 8t Then the following Environment variables settings dialog box is displayed Preferences Axis Monoclinic a axis b axis c axis Axis Rhombohedral Hexagonal axis Rhombohedral axis Number of threads 96 OK The lt Number of threads gt is used when running parallel computing The number to which this parameter can be set depends on the computer The initial value is set to the number of threads the computer has 1 The higher the value the2. M Warning The unit cell have very similar computed lines as the following the solution might not determined uniquely from peak 1 3 32781 1 92149 3 32836 90 108 471 90 Monoclinic P Volume 20 0661 M20 176 914 2 6 65581 1 281 3 84299 90 125 259 90 Monoclinic B Volume 26 7548 M20 184 248 Diffraction pattern ed Lattice Constants Smoothed curve e Monoclinic P 3 33 1 92 3 33 90 109 90 V Error 1 A Monoclinic B 6 66 1 28 3 84 90 125 90 M 284 8171 Peak position es 7 M position M Mwu 777 0723 e d E S WT Mrev 6 8261 t i r i SES dedo Msym 1944 204 gt NN 25666 e 4 VOL 80 2645 t T P d MN T UE MBN do E T I oo eee Pee LES acm S S Ee 0 10000 20000 30000 40000 50000 Output histogram data offset interval I Fig 5 12 Check uniqueness of solutions 5 12 6 Refining lattice parameters and zero point shift The method for refining lattice parameter candidates obtained by indexing and zero point shift for angle dispersion methods is explained in the following sections The refinement is conducted using linear non linear least squares methods 6 1 Method for refinement execution 6 1 1 Refinement of lattice parameters selected from the list To refine the lattice parameters and zero point shift select the lattice parameters and
3. Estimate zero point shift estimated and a list of candidates appears 4 3 peakl peak 2 ratio of sin If one of the estimated values is selected two peaks used for estimation are highlighted 13801 0 0846 B 21 20012 0 0423 When one of the estimated values is selected and OK is clicked the 0 20 40 q selected value is entered Diffractometer parameters Time of flight Angle dispersig Wavelength 1 81958 A Zero point shift A28 Fig 4 4 Estimation of zero point shift 4 2 Advanced indexing parameters The recommended values for the parameters in this frame are set automatically when a project is created Although in general the values need not be changed it should be noted that when they were determined the most difficult cases of powder indexing were considered Hence improvement particularly in computation time may be obtained by changing these parameters as described in Section 10 2 Search parameters Bravais lattice available multiple choice Volume of primitive cell A3 AUTO Vol AUTO D W Tricrinic Tetragonal P Number of zones used for search AUTO 2 7 Monadinic E 7 Tetragonal I Number of enumerated primitive cells AUTO 3 Iv Monodinic B Rhombohedral W Orthorhombic P W Hexagonal Tolerance level for errors of sums of q values 1 0 times 4 BI Ortho Id Hexannna I Or
4. vi Name affiliation e mail address to allow us to contact you Depending on the contents of the problem we may request the input output files and other information We seek your cooperation in this regard 12 1 References 1 2 3 4 5 6 7 C Dong F Wu H Chen Correction of zero shift in powder diffraction patterns using the reflection pair method J Appl Cryst 32 pp 8501 853 1999 A D Mighell A Santoro Geometrical Ambiguities in the Indexing of Powder Patterns J Appl Cryst 8 pp 3721 374 1975 R Oishi Tomiyasu A method to enumerate all geometrical ambiguities in powder indexing and its application submitted R Oishi Tomiyasu Robust powder auto indexing using many peaks J Appl Cryst 47 2014 pp 5931 598 R Oishi Tomiyasu Reversed de Wolff figure of merit and its application to powder indexing solutions J Appl Cryst 46 2013 pp 12771 1282 P M de Wolff A simplified criterion for the reliability of a powder pattern indexing J Appl Cryst 1 pp 1081 113 1968 E Wu A modification of the de Wolff figure of merit for reliability of powder pattern indexing J Appl Cryst 21 pp 5301 535 1988 12 2
5. is selected a backup file is created in the folder as the auto generated files backup dat file which stores all the lattice parameter candidates that were obtained by indexing or exist in the Stored Lattice Constants frame mograph MAI Run Help New Project N Open Project 0 Open Recent P Output All Lattices Save Project 5 Preferences a Fig 7 3 Saving a project This file is also outputted when a project containing a data set of lattice parameters is closed this occurs when the application is closed or another project is opened By using the backup file the condition at the time of saving backup dat can be reproduced when Conograph is started in the next session When the project is opened in the next session the user is asked whether s he wishes to open the backup file if it exists in the project folder The existing backup file is overwritten whenever either of the above events occurs in the opened project 7 2 8 Space group determination In the stages described thus far only the systematic absences caused by the Bravais lattice type were considered during computation of the figures of merit However additional extinction derived from the space group may have happened If the Determine Space Group button in the Refine Lattice Constants frame is clicked the value of the de Wolff figure of merit M is recomputed by using the reflection conditions of each space group with the Bravais lattice type select
6. iu 06 light green and peak positions Tetragonal P de Wolff figure of merit M M 3 0 Orthorhombic F 44 used for refinement dark green Orthorhombic I l 284 8 Min Max of lattice constants Orthorhombic C 51 1716 57 0 sa bcs 1000 Orthorhombic P 7 88 Monoclinic B 840 88 Relative error tolerance to search Monoclinic P f 1311 63 for duplicated solutions Triclinic 19 44 0 03 Selected Bravais lattice Orthorhombic l Peak Search Output ETTN List of Indexing Soludgns Refine Lattice Constants Stored Lattice Constants Fig 5 2 Screenshot immediately after indexing execution The lattice with the largest de Wolff FOM Section 5 3 is automatically selected and its information is displayed in the MSelected Lattice ConstantsO frame In the Diffraction Pattern frame the peak positions of the selected lattice are displayed with a light green tick mark From these the peak positions used for refinement Chapter 6 are selected and displayed with a dark green tick mark 5 2 5 3 Sorting filtering lattice parameters The lattice parameter candidates obtained by indexing can be sorted and filtered using parameters in the Criteria for lattice parameters in candidate list and Advanced thresholds for l
7. 28 60069929 818 28 60069929 Fig 2 3 yint yerr 0 85962 0 79216 0 75064 0 40015 0 36920 0 39202 Example of XY format 0 05899 0 05643 0 05470 0 01698 0 01634 0 01686 Fig 2 4 Example of IGOR format 10 0000 0 0200 19 22 17 Fig 2 5 Example of Rietan format 2 4 2 2 Opening a project To open an existing project select File gt Open project as shown below nograph Run Help Mew Project N Open Project 20 Open Recent Output A artices Preferences amp earn Then the file folder selection dialog box is displayed You can specify a project folder in the dialog box Fig 2 3 shows the status of the software immediately after a project is opened and the diffraction pattern file and parameter setup file inp xml are loaded In the Diffraction pattern frame red square in the figure the measured diffraction pattern and errors only when there is an error in the diffraction pattern file are displayed KEL Indexing Advanced Indexing Parameters Log Notd v Diffraction pattern v Error Peak Search Parameters v Smoothed curve v A Peak position Number of data points to use for smoothing peaksearch at each point bd Peck pasion Number of Points End of Interval indexing 9 MAX offset interval delete Mee errem ee eee Full screen 40000 50000 TOF Output histogram data Range of peak sea
8. Monoclinic P 0 Triclinic 0 gt lt Information on the selected candidates gt lt SelectedLatticeCandidate number 140153 gt lt CrystalSystem gt Cubic F lt CrystalSystem gt lt a b c angstrom alpha beta gamma deg gt lt LatticeParameters gt 5 4354e 000 5 4354e 000 5 4354e 000 9 0000e 001 9 0000e4 001 LatticeParamters lt A B C D E F angstrom 2 ReciprocalLatticeParamters 3 3848e 002 3 3848e 002 3 3848e 002 0 0000e 000 0 0000e 000 lt ReciprocalLatticeParamters gt lt A B C D E F angstrom 2 first given by peak positions gt InitialReciprocalLatticeParamters 3 4129e 002 3 4129e 002 3 4129e 002 0 0000e 4000 0 0000e 000 lt InitialReciprocalLatticeParamters gt lt VolumeOfUnitCell gt 1 5861e 002 lt VolumeOfUnitCell gt lt FigureOfMeritWolff name Fw20 gt 7 6120e4000 lt FigureOfMerit Wolff gt lt NumberOfLattices InNeighborhood gt 213 lt NumberOfLatticesInNeighborhood gt lt Number of pairs of hkl and h k l up to the 20th reflection gt lt NumberOfMillerIndicesInRange gt 2 7750e 001 lt NumberOfMillerIndices InRange gt lt EquivalentLatticeCandidates gt lt LatticeCandidate number 13034 gt lt CrystalS ystem gt Cubic I CrystalS ystem gt lt LatticeParamters gt 4 1917e4000 4 1917e 000 4 1917e 000 9 0000e 001 9 0000e 001 lt LatticeParamters gt lt ReciprocalLatticeParamters gt 2 8457e 002 2
9. Peak Search Output frame Fig 3 3 Whether or not peaks are used is represented visually in the Diffraction Pattern frame as shown in Fig 3 4 FEST M List of Indexing Solutions Refine Lattice Constants Stored Lattice Constants p Tp leight FWHM Use for indexing g Position Click to switch the order ascending descending 4 3841 0800000 0 1735176 21 7241100 i 5 4004 5330000 0 1609938 23 1921000 v 6 4058 4620000 0 1760591 22 3059300 a 7 4152 7050000 0 1760708 23 6546600 Data can be selected by dragging 8 4188 8400000 0 1617476 21 6177300 and copied using Ctrl clicking 9 4291 7320000 0 1502431 23 7250000 KA 10 4360 5550000 0 1864202 24 0960600 v 11 4404 0580000 0 2063731 23 8925800 v 12 4477 1680000 0 164382 36 25 7943900 if Fig 3 3 Input peak positions Marker displays switches by interlocking with ON OFF check box 200 outlined markers represent NOT used vif 1 t t 4 t 10000 TOF peaks t of Indexing Solutions FWHM e E OESUTGqU RESTE NS ae 25 2622000 25 8538200 191 26 3370700 902 26 3075800 530 27 7066000 Fig 3 4 Representation of NOT used peaks in the Diffraction Pattern frame A peak can be inserted manually at the mouse pointer position by double clicking on the diffraction pattern Its height is automatically decided by interpolation The specific values of the peak position and the full width at half maximum
10. from the equation 3q2 q4 393 q5 450 E att Hal Ate SS dded under supposition of extinction rules 111 Button to cut short Eouttea ticubwi indexing search indexing search Peru rias i seene c eBdruples q1 q2 q3 q4 from 76 topographs The number of nodes q1 q2 q3 q1 q2 q4 generated from quadruples q1 q2 q3 q4 538 Finding combir k Rs ess sometimes takes several minutes Progress of indexing search is displayed in the Log Note frame Fig 5 1 Screenshot during indexing execution 5 1 5 2 When indexing is complete When indexing is complete the screen shown in Fig 5 2 appears Advanced Indexing Parameters Log Note iW Diffraction pattern wi Error i Smoothed curve iV amp Peak position peaksearch Search parameters Quick search Exhaustive search amp peak reed Number of peaks used for search AUTO 2 offset 0 2 Diffractometer parameters l Time of flight Angle dispersion Conversion parameters TOF c c d cid cd cud c d 9 03976 9965 02 5 88424 te a nm i b a BENE NE 10000 0 2 0 0 0 0 Full screen Information about the Output histogram data lattice with the largest de Bravais lattice Number of solutions M NN Wolff FOM and lattices Cubic F 1754 53 Cubic I of the same Bravais types Cubic P aja Hexagonal ele i Na LE A SOc A lt i som gd Peak positions of selected lattice AUTO 1 sNeals AUTO 1 Tetragonal
11. i TOF Output histogram data Number of peaks used for computation of FOM 20 Sorting criteria de Wolff figure of merit M Bravais lattice TNE M Mwu Mrev Msym NN voL Cubic F 277 96 208 63 6 36 1769 09 85 160 52 Thresholds for indexing solutions Cubic I Cubic P Upper lower thresholds for number of computed Hexagonal lines between 1st and 30th observed lines Rhombohedral f 1857 38 AUTO s Neal s AUTO Tetragonal I 1542 79 Tetragonal P 19 75 de Wolff figure of merit M M 3 0 Orthorhombic F 1326 73 Orthorhombic I 1944 21 Min Max of lattice constants Orthorhombic C 1910 52 0 sabes 1000 Orthorhombic P 7 88 Monoclinic B a 1047 76 Relative error tolerance to search Monoclinic P 1311 63 for duplicated solutions Triclinic 231 60 s 0 03 Selected Bravais lattice Fig 1 1 Conograph user interface 1 1 2 Creating new project opening existing project Fig 1 1 shows a screenshot of the Conograph UI immediately after the application is started To conduct peak searches or indexing it is necessary to create a new project or open an existing project This chapter explains the procedures for both operations Conograph Peak Search Indexing Advanced Indexing Parameters Log Note E Diffraction pattern v Error v Smoothed curve V A Peak position Number of data points to use for smoothing peaksearch at each point J Peak Search Parameters Peak position index
12. lt FittingResults gt lt SelectedLatticeCandidate gt lt Candidates for Cubic F gt omitted lt ConographOutput gt Fig 11 6 Example of index xml 2 2 11 6 lt ZCodeParameters gt lt ConographOutput gt lt TypeOfReflectionConditions gt lt Candidates gt lt SpaceGroups gt 45 bca 72 bca lt SpaceGroups gt lt ReflectionConditions gt hkO h k 2n 0k1 k I 2n lt ReflectionConditions gt lt FigureOfMeritWolff name M20 gt 3 126279e 002 lt FigureOfMerit Wolff gt lt IndexingResults gt lt q obs q err q cal peak pos peak width pos cal hkl fix_or_fit gt 1 016473e 001 9 594352e 004 1 015807e 001 3 132270e 004 1 480559e 002 3 133298e 004 1 0 1 1 2 708116e 001 2 274422e 003 2 707887e 001 1 917970e 004 8 059404e 001 1 91805 1e 004 0 2 0 3 724714e 001 2 575261e 003 3 724523e 001 1 635279e 004 5 655483e 001 1 63532 1e 004 2 1 1 1 Omitted 2 539049e 000 2 019023e 002 2 539077e 000 6 265138e 003 2 488311e 001 6 265 104e 003 3 4 5 l 2 707958e 000 2 205347e 002 2 707998e 000 6 066813e 003 2 467594e 001 6 066769e 003 2 6 0 1 lt IndexingResults gt lt Candidates gt Omitted lt TypeOfReflectionConditions gt lt ConographOutput gt Fig 11 7 Example of out xml 11 7 12 Addendum 12 1 Request for citation Please cite the following when research findings obtained using Conograph are mentioned in academic manuscripts R Oishi Tomiyasu MRobust powder au
13. or more sal aaa PONE A new row is inserted immediately End of Interval above the selected row Peaksearch parameters Number of data points to use for ar 100 MAX means an upper limit is not set Range of peaksearch 0 0 MAX Ka Ka Lower threshold for peak heights c 40 usec times error values of intensities 0 563758 Select a wavelength EZ 1 732850 from list 00 2 293606 oe 1 544358 Fe 1 930042 1 939960 Mo 30 709300 0 713590 Remove Ka peaks Yes a No Ka Ka wave length A 1 54056 1 54435 select Fig 3 1 Setting peak search parameters 3 To conduct a peak search click the Run button gt or select Menu gt Run gt Run peak search eoe raph _ Peaksearch Ini File Run Peak Search Run Auto indexing Refine and Store eaksearch Parameters When the peak search is completed the screen appears as follows sktop sample sample1 auto generated files ESS Indexing Advanced Indexing Parameters Log Note D 1 M Diffraction pattern M Error IV smoothed curve v A Peak position 2 Number of data points to use for smoothing peaksearch esc DONE V Peak position Number of Points End of Interval indexing 9 MAX Peak Search Parameters offset interval delete Full screen Range of peak search 40000 50000 0 0 MAX Output histogram data EALANT a Best M List of Indexing Sol
14. p 3 16352 790 5548 mLEGLOMAE i 4 13559 380 70 Information here can be copied by 3 ea SIY specifying a range by dragging and then 6 11071 930 P M 8 peu 88mg 7 10439 340 pressing Ctrl C Fig 6 1 Screenshot during refinement execution The peak positions to be used for refinement can be selected manually from the Use for refinement column in the Refine lattice constants frame The color of a tick mark changes from dark green l to light green according to a change in the corresponding flag Peak Search Output Best M List of Indexing Solutions Stored Lattice Constants CONSU M e E T M 284 8171 Bravais lattice Orthohombic I ine c dg zOrtnonomsic ss Determine Miller indexing Mwu 777 0723 Spcae Group 5 Mrev 6 8261 Lattice constants a b c A B 194 A o B Y Undo Refine Msym 1944 204 3 84260 3 84339 5 43478 90 0 90 0 90 0 NN 157790 VOL 80 2645 Refine amp store zero point shift 428 deg 0 0 lattice constants Check uniqueness Input position Estimated error from FWHM Computed position Miller index Use for refinement teal 1 31322 700 148 05590 31332 979 1 0 1 v 2 19179 700 80 59404 19180 509 0 2 0 vi 3 16352 790 mkh Hl 1 1 4 13559 380 0 4 E 134 43 060 Peaks to be used for refinement are checked 2 3 6 11071 930 48 55326 11072 002 1 3
15. the checkbox if lattice parameter candidates of the Bravais type are A Yes NOT necessary 5 Indexing After executing a peak search and setting diffractometer parameters indexing can be started 5 1 Indexing execution To start indexing and obtain a list of lattice parameter candidates click the ARun indexingO button gt or select Menu gt Run gt Run auto indexing the values of the input parameter are stored in the pks histogramlIgor and inp xml files from the auto generated files folder ograph File LS Help Run Peak Search Run Auto indexing D bi m Refine and Store Peaksearch While the indexing is being executed the progress is outputted in the Log Note frame Fig 5 1 The Skip button Ifl can be used only when searching a solution and when it is clicked the solution search is aborted and the program shifts to subsequent processing On the other hand the Cancel button m can be used at any time and when it is clicked the indexing is discontinued lt MaxPrimitiveUnitCellVolume gt is set to 61 521 MaxNumberOfMillerIndicesInRange gt is set to 128 MinNumberOfMillerIndicesInRange is set to 12 The range of d value sqrt the minimum of q values sqrt the maximum of q values 0 318822 1 67623 The number of threads is set to 8 Finding Ito relations 2 q1 q2 q3 g4 Number of q1 q2 q3 q4 satisfying 2 q1 q2 q3 q4 201 Number of q q2 q3 q4 detected
16. the observation errors of y values in the second column can be input in the third data column If the third column is empty the roots of the y values are used as the observation errors In the file LF CR LF and CR can be used as a line feed code and spaces and tabs as a delimiter The project is created by clicking the OK button after providing the project information A folder named auto generated files is created in the project folder and used to store all the automatically outputted files This folder contains all the files necessary for using Conograph Thus it contains a copy of the diffraction data file specified in Fig 2 2 and parameter set up files Fig 11 16 When the specified project folder already exists and contains the auto generated files folder as a subfolder the following dialog box appears 2 2 The popact heidar airway mann Boe pma be RO eee M peer n Cam oo If you select Yes all the files originally present in the auto generated files folder are deleted and cannot be retrieved 2 3 tof yint 7 00000 4942 7 01697 4956 7 03395 5084 omitted 89 66605 89 68303 89 70000 IGOR WAVES O tof BEGIN 8 92 00000 8808 00000 8824 00000 omitted 199536 00000 199664 00000 199792 00000 END 3900 15 16 30 15 26 25 26 23 20 omitted 8 12 4 9 13 7 6 12 8 6 11 1 yerr 10 29935988 10 39886363 71 30217388 818 28 60069929 818
17. then click the Refine amp store lattice constants button in the Refine Lattice Constants frame or by selecting Menu gt Run gt Refine amp store lattice constants Peak Search Output Best M List of Indexing Solutions Stored Lattice Constants M 284 8171 Miller indexing Mwu 777 0723 l Mrev 6 8261 Lattice constants a b c B v Unde Msym 1944 204 id NN 25666 VOL 80 2645 Bravais lattice Orthohombic I Determine Spcae Group 3 84260 3 84339 5 43478 90 0 90 0 90 0 Refine amp store zero point shift A28 deg 0 0 lattice constants Check uniqueness Input position Estimated error from FWHM Computed position Use tor refinement 1 31322 700 148 05590 31332 979 1 0 1 v 2 19179 700 80 59404 19180 509 0 2 0 v 3 16352 790 56 55483 16353 209 2 1 1 v 4 13559 380 51 78934 13559 342 0 0 4 v 5 12443 050 49 92759 12443 274 1 2 3 iw 6 11071 930 48 55326 11072 002 1 3 2 v 7 10439 340 48 00951 10438 898 0 3 3 v Fig 6 1 shows a screenshot when the refinement is being executed The refined lattice parameters are saved and displayed in the Stored Lattice Constants frame Advanced Indexing Parameters 7 Diffraction Pattern lt MaxNumberOfPeaks gt is set to 20 zMaxNumberOf TwoDimTopographs is set to 100 lt MaxNumberOfLatticeCandidates gt is set to 64000 MinPrimitiveUnitCell olume is set to 5 lt MaxPrimitiveUnitCellVolume gt is set to 61 521 MaxNumbe
18. 00 4004 5330000 0 1609938 23 1921000 4058 4620000 0 1760591 22 3059300 4152 7050000 0 1760708 23 6546600 4188 8400000 0 1617476 21 6177300 4291 7320000 0 1502431 23 7250000 4360 5550000 0 1864202 24 0960600 4404 0580000 0 2063731 23 8925800 4477 1680000 0 1638236 25 2943900 4524 8110000 0 1536584 24 2384700 4604 6750000 0 1816902 24 3246700 4654 5730000 0 1989797 23 7283300 Lower threshold for peak heights c 5 0 use c times error of intensities lt Remove Ka peaks Yes No Ko Ka wave length A 1 54056 1 54439 select on ow Bw MJ e amp amp 444eeeeeee Fig 2 7 Screenshot immediately after opening a project after peak search Further when a backup file exists the project is opened loading indexing results saved in the backup file 3 Peak search 3 1 Peak search execution After opening the project first a peak search must be performed in order to obtain peak positions for indexing A peak search is performed using the Peak search frame ST indexing Peak Search Parameters Number of data points to use for smoothing at each point Number of Points End of Interval 9 MAX add delete Range of peak search 0 0 MAX Lower threshold for peak heights c 5 0 usec times error of intensities Remove Ka peaks Yes No Ko Ko wave length A 1 54056 1 54439 select Fig 3 1 explains the operations available in the Peak search frame Enter an odd number 5
19. 2 7 10439 340 48 00951 10438 898 0 3 3 6 2 6 1 2 Refining lattice constants entered by user This section explains the method for refining lattice parameters specified manually by the user In this case although indexing execution is not required for refinement a peak search is required for obtaining peak positions The diffractometer parameter Wavelength of diffractometer or Conversion Parameters can be inputted from the Indexing frame When the angle dispersion is selected it is also possible to enter an initial value of the zero point shift from the Refine lattice constants frame normally it is not necessary to set the initial value to a value other than 0 Stored Lattice Constants Peak Search Output Best M List of Indexing Solutions Bravais lattice Orthohombic I Determine M 284 8171 ti Miller indexing Mwu 777 0723 Spcae Group Mrev 6 8261 Lattice constants a b c A B j 20 A o B Y Undo Refine Msym 1944 204 3 84260 3 84339 5 43478 90 0 90 0 NN 157790 VOL 680 2645 Refine amp store zero point shift A20 deg D 0 lattice constants Check uniqueness Input position Estimated error from FWHM Computed position Miller index Use for refinement 1 31322 700 148 05590 31332 970 1 0 11 if If the Miller indexing button is clicked the Miller indexing of peaks is performed using the Bravais lattice and lattice parameters entered Subsequently the Miller indices assig
20. 326 11072 002 1 3 2 10439 3400 48 00951 10438 898 0 3 3 vi Ch u d li BJ EA Fig 5 6 Selected Lattice Constants frame Table 5 3 Information displayed in Selected Lattice Constants frame Value of the de Wolff FOM M of the selected lattice Value of Wu FOM M of the selected lattice Value of Reversed FOM M of the selected lattice Value of Symmetric FOM M of the selected lattice 5 Value of NN of the selected lattice i e the number of lattices that are found during indexing execution and judged to be identical with the selected lattice Unit cell volume A of the selected lattice All the lattice parameters saved during the execution of powder indexing are displayed in Lattice Constant Frame Fig 5 7 It is possible to check peak positions of all the solutions in Lattice Constant Frame by scrolling them using the up and down arrow keys or the mouse wheel By clicking the name of a Bravais type in Lattice Constant Frame the solution with the largest FOM specified in Indexing Frame is selected Bravaislattice M Mwu M By clicking here the solution with the largest FOM Cubic F among solutions with the same Bravais type is selected Cubic I Cubic P j 30 17 71 05 4 85 146 33 78 29 80 79 80 20 69 15 47 2 52 54 23 53 51 61 51 61 4 07 3 20 1 92 7 84 1 36 48 36 48 32 6 7 78 7 17 2 04 15 90 8 36 48 36 48 16 1
21. 5 69 14 54 2 45 38 47 18 27 47 29 83 7 82 7 96 2 16 15 87 78 22 49 79 97 51 17 02 24 62 7 42 126 69 273 23 aT ol 6 24 80 22 72 5 09 176 15 33 13 75 14 30 29 130 01 135 29 80 51 6 e 15 31 77 5 39 140 88 18 13 76 14 90 20 79 37 70 5 44 113 01 L7 13 76 14 90 Scrolling using arrow keys or mouse wheel Fig 5 7 List of lattice parameter candidates obtained by indexing It should be noted that the values of the FOM are occasionally improved greatly by refinement Fig 5 8 The operations necessary for refinement are explained in Section 6 1 1 Advanced Indexing Parameters Log Note Diffraction Pattern Initial value of lattice parameters Reduced unit cell parameters 4 7521 4 7521 12 9704 90 90 120 Optimizing lattice parameters by linear least squares 1 Initial M20 27 6254 Initial de Wolff FOM M20 of optimized solution 266 635 2 Initial M20 266 635 The de Wolff FOM was improved M20 was not improved Refinement is stopped if there is no further improvement Optimized unit cell parameters 4 76098 4 76098 12 9954 90 90 120 Optimized zero point shift 0 147583 Refined lattice parameters Reduced unit cell parameters 4 76098 4 76098 12 9954 90 90 120 and zero point shift Niggli reduced parameters Fig 5 8 Message outputted in Log Note frame during refinement execution While the refinement is being execu
22. 8457e 002 5 6913e 002 0 0000e 000 0 0000e 000 lt ReciprocalLatticeParamters gt lt FigureOfMerit Wolff name Fw20 gt 1 3537e 000 lt FigureOfMerit Wolff gt lt NumberOfLatticesInNeighborhood gt 213 lt NumberOfLattices InNeighborhood gt lt LatticeCandidate gt Omitted lt EquivalentLatticeCandidates gt Fig 11 5 Example of index xml 1 2 11 5 9 0000e 001 0 0000e 000 0 0000e 000 9 0000e 001 0 0000e 000 lt IndexingResults gt lt q_obs q_cal peak_pos pos_cal closest hkl is the difference between q obs and q cal small compared to q err 4 1501e 002 1 0154e 001 4 9066e 004 3 1339e 004 1 1 1 0 1 0159e 001 1 0154e 001 3 1332e 004 3 1339e 004 1 1 1 l 2 1784e 001 2 7079e 001 2 1387e 004 1 918 1e 004 0 2 2 0 Omitted 2 2680e 000 2 2678e 000 6 6286e 003 6 6288e 003 7 3 3 2 4367e 000 2 437 1e 000 6 3952e 003 6 3947e 003 6 6 0 lt IndexingResults gt lt FittingResults gt lt q obs q err q cal peak pos peak width pos cal hkl fix_or_fit gt 4 1501e 002 1 2834e 004 1 0154e 001 4 9066e 004 1 7914e 002 3 1339e 004 1 1 1 0 1 0159e 001 4 0706e 004 1 0154e 001 3 1332e 004 1 4806e 002 3 1339e 004 1 1 1 l 2 1784e 001 8 7727e 004 2 7079e 001 2 1387e 004 1 0149e 002 1 918 1e 004 0 2 2 0 omitted 2 2680e 000 7 2533e 003 2 2678e 000 6 6286e 003 2 4936e 001 6 6288e 003 7 3 3 l 2 4367e 000 8 1458e 003 2 437 1e 000 6 3952e 003 2 5146e 001 6 3947e 003 6 6 0 l
23. Criteria for lattice constants displayed in list Hevnann Rhombohedral 251 28 475 49 7 30 1834 89 260 3 84 3 84 3 84 60 0 60 0 60 0 Tetragonal I 249 83 398 22 6 18 1542 79 222 3 84 3 84 5 44 90 0 90 0 90 0 are classified according to the Bravais Tetragonal P 5 06 4 60 3 91 19 75 2 2 72 2 72 3 14 90 0 90 0 90 0 type and sorted according to the Orthorhombic F 223 64 577 20 5 93 1326 73 68 5 43 5 43 5 44 90 0 90 0 90 0 Orthorhombic I GEEZIEERNEZEASEALICERNE CLE WS OC ER L NER LRERCERETIORETGRETD AS Orthorhombic 280 50 427 41 6 81 1910 52 6 3 84 5 43 1 92 90 0 90 0 90 0 Orthorhombic P 4 03 3 11 1 95 7 88 0 2 70 3 14 3 84 90 0 90 0 90 0 Manaclinic R 22n 33 A20 an A 765 10n4A7 7A 65 300 543 213 Qn n 1ns5 5 ann specified sorting criteria Fig 5 3 Sorting criteria and thresholds for lattice parameters in candidate list 5 3 An explanation of the parameters and their recommended values are listed in Table 5 1 The recommended values are set up automatically in the text box when a project is created Table 5 1 Thresholds for lattice parameters displayed in candidate list Contents Recommended value D Number of n peaks used for calculation of figures of merit FOM The first n 20 smallest q values are used This parameter can be larger than the number of peaks contained in the diffraction pattern because it is automatically reduced 3 Only lattice cand
24. E 002 END WAVES O dphase 1 xphase 1 yphase_1 h_1 k_1 1 1 BEGIN 3 138130E 000 3 133851E 004 0 000000E 000 2 717700E 000 2 713443E 004 0 000000E 000 0 1 921704E 000 1 918059E 004 0 000000E 000 0 omitted 6 405680E 001 6 394727E 003 0 000000E 000 2 8 6 405680E 001 6 394727E 003 0 000000E 000 6 6 END X Display yint vs tof X AppendToGraph yphase 1 vs xphase 1 X ModifyGraph mirror left 2 X ModifyGraph mirror bottom 2 X ModifyGraph rgb yint 0 65535 65535 X ModifyGraph offset yphase_1 0 0 mode yphase_1 3 marker yphase_1 10 msize yphase_1 3 mrkThick ypha se 1 20 6 rgb yphase 1 2 3 52428 1 Fig 11 4 Example of histogramlgor 11 4 lt ConographOutput gt lt Information on the best M solution for each Bravais type TNB total number of solutions of the Bravais types M de Wolff figure of merit Mwu Wu figure of merit Mrev reversed de Wolff figure of merit Msym symmetric de Wolff figure of merit NN number of lattices in the neighborhood VOL unit cell volume Bravais Lattice TNB M Mwu Mrev Msym NN VOL Cubic F 25 7 6120e 000 213 1 5861e 002 Cubic 17 2 1801e 000 246 2 0063e 001 Cubic P 0 Hexagonal 4 2 1261e 000 43 1 3385e 001 Rhombohedral 20 4 6341e 000 149 1 0755e 002 Tetragonal I 14 3 3966e 000 633 8 0329e 001 Tetragonal P 0 Orthorhombic F 0 Orthorhombic I 0 Orthorhombic B l 2 6029e 000 8 5 7058e 001 Orthorhombic P 0 Monoclinic B 0
25. FWHM can be edited in the Peak Search Output frame Fig 3 5 Advanced Indexing Parameters Log Note D Double click on the screen peaksearch e e a 2 Peak is inserted at the mouse position T a 15 2 3 Peak is inserted according to its position and highlighted FWHM becomes the same as the value of nearest peak i Parameters of peaks can be edited To delete select entire row and press Delete key J e i Full screen 260 7280 Output histogram data pking Solutions Refine Lattice Constants Stored Lattice Constants HM Use for indexing 3l 6781 597 0 171130 25 34650 v 32 7062 586 0 571042 25 26220 vw 252 582 0 6969071 25 26220 34 7595 798 0 5023191 26 33707 v 35 7829 247 0 2503902 26 30758 v Fig 3 5 Manual insertion of a peak 3 5 4 Parameters used for indexing The parameters used in indexing are located in three frames Fig 4 1 1 Indexing frame a Search parameters and diffractometer parameters b Sorting criteria and thresholds for lattice parameters displayed in the list can be changed after indexing 2 Advanced indexing parameters frame 3 Peak Search Output frame Immediately after a new project is created the values recommended for the respective parameters are set Basically it is not necessary to change the values except for the diffractometer parameters The parameter in ite
26. Indexing execution is completed The application is closed or another project is started File gt Output all lattices Fig 7 1 is selected onograph File Run Help New Project N Open Project 360 Open Recent b Output All Lattices Save Project 36S Preferences 36 Fig 7 1 Output all lattices From the lattice parameter candidates obtained by indexing the lattice constant information displayed on the GUI is indicated in the index xml file for the format refer to Fig 11 5 and 10 7 If the name of the diffraction data file is histogramlgor the name of the output file becomes index xml The same file is always overwritten at the time of the above events 7 2 Igor text file and index2 xml file When the Output histogram data button Fig 7 2 is clicked the histogramlgor file is outputted in the project folder In this file 1n addition to the contents of the input diffraction data file the Miller indices and the peak positions of the lattice parameters that show tick marks in the Diffraction Pattern frame are saved Output histogramlgor file containing Miller indices and Output histogram data their corresponding peak positions tick marks Fig 7 2 Output of Igor file 7 1 At the same time information about the lattice parameters outputted in the histogramlgor file is outputted as the index2 xml file 7 3 Backup file When File gt Save project Fig 7 3
27. Manual for Powder Indexing Software Conograph Oct 2015 Contents IEEE Oe Eos DIPENDE Tm 1 1 2 Creating new project opening existing project ssssessssseseseseeeeeeenne nennen ener nenas 2 1 Dols CCMEAUI AMC apr n 2 1 PP EEE 6 0G 2s 01 0 e ene mee M M 2 5 ME cet Gch eneeeeenr gee errr eee reerrrr errr TT ret rrr rere rer rt rr rrr rT rrr rT 3 1 ils Peak oce 3 1 3 2 Checking peak search results 2 221220 sdacessordcosanessannidcoshepsanntdoannensaeneandanhea lt cdeaniasnaenceanientanies 3 3 3 3 Removing and adding peaks manually cprsssccrscessccrecsnreeecsmasetessermacmassneeveraavonnyueienevanacs 3 4 Ai Paranee u ed Tor 1G CX UMS serere rier eE EE EEE E EEA 4 1 4 1 Search parameters and diffractometer parameters cccccccsesecceeseceeeeceeeeseeeseeeeeseeeesees 4 2 4 2 Advanced indexing PparamMeters ccceccccseeccccseccccseecccseeeceeeseesseseeeseseeseeeeesseseeseeseeeaensesges 4 5 a INC E E EE EE S 5 1 o MEME AO a O 5 1 s When indexine MIHI TM 5 2 Dads SOMME IGF ING latice paraineteTS srra n 5 3 5 4 Find plausible indexing SO ULIOnS x ecccic ccescececevc cece cece tia eene oett eoe ae tee oae ee ee eoe aee dentes 5 6 2 9 Decideth correct lattice parate S sevesssevcsnesonnnsvensnessvenseieseensenpdeerseessenneevdeneiebaiewieesien 5 10 6 Refining lattice parameters and zero point shift eeeesssesssssesessee
28. These parameters are used for indexing Relative error tolerance to search for duplicated solutions z 0 03 Fig 4 1 Input parameters of powder indexing 4 1 4 1 Search parameters and diffractometer parameters In the Search parameters area the search method and number of peaks used for powder indexing can be specified There are two search method options Quick search when the size of the unit cell is small or for cases with high symmetry Exhaustive search for all cases Search parameters la Quick search Exhaustive search Number of peaks used for search AUTO 2 Fig 4 2 Search parameters Since the basic algorithms of the two search methods are the same the two methods can return the same result if you adjust the parameters used for the quick search Powder indexing with Quick search is successful in many cases However Memory efficient search should be used in more difficult cases Powder indexing with Memory efficient search occasionally takes more than 10 minutes In the Diffractometer parameters area the time of flight or angle dispersion method can be selected Except for the zero point shift the parameter values are unique to t
29. ange gt 1 0 Use the threshold 1 Use a constant times the error of y value as a threshold gt lt UseErrorData gt 1 lt UseErrorData gt lt When UseErrorData is 0 it is used as the threshold for peak search Otherwise Threshold times the error of y value is used as a threshold gt lt Threshold gt 5 0 lt Threshold gt lt 0 Threshold is applied to estimated y values of peak tops when the background of the histogram is removed 1 Threshold is applied to actual y values of peak tops gt lt UseBGRemoved gt 0 UseBGRemoved lt 0 deconvolution is not applied deconvolution is applied Alpha2Correction 0 lt Alpha2Correction gt Waves Kalphal WaveLength gt 1 54056 Kalphal WaveLength gt lt Kalpha2WaveLength gt 1 54439 lt Kalpha2WaveLength gt lt Waves gt lt PeakSearchPSParameters gt lt ZCodeParameters gt Fig 11 3 Example of inp xml 2 2 IGOR WAVES O tof yint yerr BEGIN 1850 00 2 871904E 001 3 359009E 003 1854 00 2 834581E 001 3 337111E 003 1858 00 2 848073E 001 3 351369E 003 Omitted 49564 0 9 989611E 002 1 378697E 002 49588 0 1 010892E 001 1 386346E 002 END WAV ES O peak peakpos height FWHM Flag BEGIN 3 148311E4 003 1 535192E 001 3 749774E 001 2 3 340909E 003 1 676432E 001 2 429063E 001 3 3 697289E 003 1 661457E 001 2 063853E 001 Omitted 49 3 133224E 004 2 968128E 000 1 480559E 002 50 4 906641E 004 1 092195E 001 1 791403
30. attice parameters in candidate list areas of the Indexing frame The lattice parameters listed in the drop down menu of the Lattice Constants frame are sorted and filtered using the parameters in the areas of Fig 5 3 After indexing sorting and filtering can be redone at any time by changing the values of these parameters Threshold for making a list of result Number of peaks used for figure of merit 20 D Sorting criteria Sorting criteria de Wolff figure of merit M J oe Sorting criteria for lattice parameters For details refer to Table 5 1 and Table Advanced threshold for making a list of result 5 2 Upper lower thresholds for number of computed lines between 1st and 30th observed lines AUTO Neal AUTO Criteria for lattice constants displayed in list de Wolff figure of merit M M 3 0 3 Thresholds that limit lattice parameters to be Min Max of lattice constants displayed For details refer to Table 5 1 The d Pe iiia lattice parameters are re filtered whenever the Relative error tolerance to search o Enter key is pressed or the mouse cursor is moved for duplicated solutions 0 03 6 to another text box Peak Search Output Selected Lat Const Refine Lat Const Stored Lat Bravais lattice M Mwu Mrev Msym NN a b c amp B Y Cubic F 277 96 208 63 6 36 1769 09 85 5 43 5 43 5 43 90 0 90 0 90 0 Cub List of powder indexing solutions Lattice parameters that satisfy N
31. be detected in a peak search If cx error value of intensity is used as in the default setting a peak at peak position x is detected if and only if it has a peak height greater than the threshold x Err y where Err y is the value of the error in intensity at x The peak height used here is obtained by subtracting the estimated background value from y Our recommended threshold value is within the range of 36 10 10000 eon Soo 4000 200 Fig 10 1 Example of peak search results in radiation beam data 2 Number of data points used for differential calculation gt This parameter can be used to avoid background noise being picked up as peaks If it has a small value the smoothing curve is fit more finely to local irregularity because the number of data points for computing each y value of the smoothing curve is set to this value Fig 10 2 shows an example 10 1 0 40 0 40 0 35 0 35 0 30 wide ea 0 30 0 25 0 25 0 70 0 70 38 90 92 294 096 098 100 8 amp 8 90 92 394 396 98 100 x10 x10 Fig 10 2 Number of data points gt 5 Fig 10 3 Number of data points gt 25 10 2 10 2 Powder indexing It has been confirmed that a search using the recommended parameter values provides correct solutions in an extremely wide range of cases in particular in memory efficient search 4 Nevertheless if good results are not obtained they may be improved by changing some of the parameters In the following the parameters t
32. ck the information displayed in Best M frame in terms of the following two points 1 Which Bravais types include a solution with a fairly large de Wolff FOM M lattice for 5 6 example M gt 10 1 Among all the lattices of such a Bravais type does the same lattice obtain the maximum value in almost all FOM including the de Wolff FOM This is because different FOM have complementary properties refer to Table 5 2 and therefore a lattice that has obtained the maximum values for M M and M has a high possibility of being the true solution By clicking on a set of lattice parameters in Best M Frame Fig 5 5 the tick marks in the Diffraction Pattern frame are automatically updated and information about the parameters is displayed in the Selected Lattice Constants frame Fig 5 6 Table 5 3 Stored Lattice Constants Peak Search Output BestM List of Indexing Solutions Refir a Lattice Constants M 284 8171 Miller indexing O Mwu 777 0723 3 Mrev 6 8261 Undo 4 sym 1944 204 3 84260 3 84339 5 43478 90 0 90 0 90 0 NN 25666 B VOL 80 2645 Bravais lattice Orthohombic I 7 Determine 5pcae Group Lattice constants a b c B Y Refine amp store zero point shift A20 deg 0 0 lattice constants Check uniqueness Use for refinement M Input position Estimated error fram FWHM Computed position Miller index 13559 342 0 0 4 12443 274 1 2 3 11071 930 48 55
33. e computed lines and the observed lines Z should be compared In addition the lattice parameters may not be determined uniquely from the peak positions Fig 5 10 This phenomenon occurs infrequently in low symmetry cases and consistently in high symmetry cases and is known as geometrical ambiguity 2 Therefore it should be checked in respective cases whether or not the uniqueness of solutions holds by using Conograph6 Check Uniqueness button Fig 5 12 Cubic F 5 43 5 43 5 43 90 90 90 Orthorhorbict 1 28 3 84 5 43 90 90 90 OrtharhambiclO 3 94 5 43 1 92 90 90 90 MN T a m 40x10 time of flight Fig 5 10 Example of distinct lattice parameters with identical peak positions The peak positions of all the lattices that have been refined can be displayed as tick marks on the Diffraction Pattern frame This allows the peak positions of several lattice parameters to be compared simultaneously In order to hide tick marks of some of the lattices untick the corresponding check boxes labeled Plot or the corresponding lattice can be deleted in the Stored Lattice Parameters frame The methods for changing the display of tick marks are shown in Fig 5 11 and Table 5 4 5 10 Indexing Parameters Log Note Esluicissi icd T E Diffraction pattern f Error f Smoothed curve D v amp Peak position peaksearch 60000 f Peak position indexing 40000 2 offset 4300 0 Intensi
34. e unit cell gt 0 gt MinPrimitiveUnitCell Volume AUTO MinPrimitiveUnitCell Volume lt Maximum of the volume of primitive unit cell 20 gt MaxPrimitiveUnitCellVolume AUTO MaxPrimitiveUnitCell Volume lt Maximum number of quadruples q1 q2 q3 q4 taken from selected topographs gt MaxNumberOfTwoDimTopographs AUTO lt MaxNumberOfTwoDimTopographs gt lt Maximum number of seeds of 3 dimensional topographs gt lt MaxNumberOfLatticeCandidates gt AUTO lt MaxNumberOfLatticeCandidates gt lt Output for each crystal system 0 No 1 Yes gt lt OutputTriclinic gt 1 lt OutputTriclinic gt lt OutputMonoclinicP gt 1 lt OutputMonoclinicP gt lt OutputMonoclinicB gt 1 lt OutputMonoclinicB gt lt OutputOrthorhombicP gt lt OutputOrthorhombicP gt lt OutputOrthorhombicB gt 1 lt OutputOrthorhombicB gt OutputOrthorhombicI 1 lt OutputOrthorhombicl gt lt OutputOrthorhombicF gt lt OutputOrthorhombicF gt lt OutputTetragonalP gt lt OutputTetragonalP gt lt OutputTetragonall gt 1 lt OutputTetragonall gt lt OutputRhombohedral gt 1 lt OutputRhombohedral gt lt OutputHexagonal gt 1 OutputHexagonal lt OutputCubicP gt 1 lt OutputCubicP gt lt OutputCubicl gt 1 lt OutputCubicl gt lt OutputCubicF gt 1 lt OutputCubicF gt Fig 11 2 Example of inp xml 1 2 11 2 lt Parameters for output gt lt Relative resolution to judge whe
35. ed 3 Improve results of peak search or change the Use for Indexing flags in Peak search output frame Impurity peaks greatly affect the sorting results Because of this it is desirable to reduce the number of impurity peaks as far as possible at least in the range of the first to n th peaks when the parameter Number of peaks used for computation of FOM gt is set to n 10 4 11 Input output text file formats The formats for the input output text files cntl inp xml inp histogramlgor and index files are shown in this section lt ZCodeParameters gt lt ConographInputFile gt lt Control parameters for calculation gt lt ControlParamFile gt HRPOO0675 BS bin04f inp xml lt ControlParamFile gt lt Peak position data gt lt PeakDataFile gt HRP000675 BS bin04f_pks histograml gor lt PeakDataFile gt lt Output file gt lt OutputFile gt hrp000675 bs bin04f index lt OutputFile gt lt ConographInputFile gt lt PeakSearchInputFile gt lt ControlParamFile gt HRPOO0675 BS bin04f inp xml lt ControlParamFile gt lt HistogramDataFile gt lt FileName gt HRP000675 BS bin04f histogramIgor lt FileName gt lt XY general IGOR IGOR Rietan Rietan gt lt Format gt IGOR lt Format gt lt When IsErrorContained equals 1 input errors in the 3rd column of the histogram gt lt IsErrorContained gt lt IsErrorContained gt lt HistogramDataFile gt lt Outf
36. ed in the frame and a window as in Fig 8 1 appears The M values of all the space groups are listed up in the window and it is possible to check which space group fits well to the observed peaks Peak Search Output Best M List of Indexing Solutions Eu Stored Lattice Constants Bravais lattice Orthohombic I Determine Miller indexing c Bi A iT Lon eue OU Mrev 6 8261 Lattice constants a b c A a B y Msym 1944 209 i i Undo Refine 3 84260 3 84339 5 43478 90 0 a0 90 0 SSS NN 64150160 l VOL 80 2645 Refine amp store zero point shift A28 deg 0 0 lattice constants Check uniqueness Input position Estimated error from FWHM Yo mputed position Miller index Use for refinement 1 31322 700 148 05590 31332 979 1 0 1 vf Peak positions of space group candidates are displayed Determine Ypace Group e 4 1 45 72 v Diffraction pattern T 2 46 74 Fi Error I 4 3 46 74 Vf Smoothed curve zd A 4 Nocondition v A Peak Pon b A peaksearc 4 v Peak position E A indexing gt aa t f j 4 M offset 0 301 uL e n eG See d h NUN UE EL l I By clicking here information M t T TE about the space groups displayed vp HHHH in the plot area is output in a 1 0 10000 20000 t 1 1 spgroup xml file Fig 11 7 and a histogramlIgor file Fig 11 4 30000 TOF
37. eeeeen nennen 6 1 6 1 Method for refinement execution essssssssssssseseeeeeeenn nennen nennen nenne nnne nnne 6 1 6 1 1 Refinement of lattice parameters selected from the list eeesssssesssss 6 1 6 1 2 Refining lattice constants entered by USEF cccecccccsesecceeececaececeseceaeseesseeeesaseeas 6 3 62 Undo DUltON peer eee eee ene PEC HEC Er HIM Es E I Ero tutu entre tr eee EIU 6 5 FEE S leidet 7 1 el eS AU E A A N E 7 1 7 2 gor text file and index2 xml file cab cecscsestscseeseseatscstacseccaeccetacsescadeqateestaneuensacsnenesenetenesets 7 1 To MC UU MM T EEO E 7 2 Oe PAC SPO D Cele NAL RO cece gece eese aede ERE TEUER RUE EU d UR EU ER RETE UOS 8 1 MEG 8 elena OU Wo cine m Te 9 1 91 Configuration parameters sessar sass saaacesa bates gaa nseasaeceasseceusnaneusaacesasesesasacesacetesaaes 9 MEE BEP CIN NR 9 10 Parameters that can be changed to obtain better results eeeseeeeeeeeesreeeeeee 10 1 I0 1 Ped SCOEC ieu mp ERR MINIME E MIENNE MEET 10 1 10 25 PONE Inee XIllg Seen ORD ot ee net em eI o UN OD REED DEED ere COR el ee Peter E EA 10 3 10 2 1 Conduct a more exhaustive search ccccccccoccccsccoeccccccsccscscscscscececscececscscecncs 10 3 10 2 2 Enhance compute Speed uiu e i RAE M EUER LEA ER LL dae Sc oes crane teas deus ean easenns 10 3 10 2 3 Improve the efficacy of fi
38. greater is the speed however the computational cost also becomes high It is advisable to set a small value if you want to run another application simultaneously The used configuration parameters are stored in the auto generated files inp xml file The values of the configuration parameters when the application is closed are stored in the software setup file and are reset when the next session starts 9 2 Help menu From the Help menu you can select Manuals 9 l Manual When Manual is selected the user manual i e this manual appears 10 Parameters that can be changed to obtain better results 10 1 Peak search In peak search it is recommended that diffraction peaks are collected as uniformly as possible on the basis of peak height Filtering diffraction peaks manually including removal of overlapped peaks is unnecessary and not desirable unless there is valid prior information In order to obtain such a peak search result only the following parameters need to be adjusted 1 lt Threshold for peak height gt 2 lt Number of data points used for smoothing histogram gt In addition in cases of characteristic X ray data that contain a2 peaks the a2 peaks must be removed prior to powder indexing Fig 3 1 The following are notes related to the adjustment of the parameters 1 and 2 1 lt Threshold for peak height gt This parameter is used as a lower threshold for magnitudes of intensities to
39. gures of merit eesseesseeeem m 10 4 e Loo V6 DISP MF US BI SECO BIET m 11 1 te S IURE 12 1 DL KEJU oe aO a 12 1 Ms BUT E eE Du E E N 12 1 Acknowledgments We would like to express our gratitude to the professors of Ibaraki University Tokyo Institute of Technology and the High Energy Accelerator Research Organization for providing powder diffraction data for this project We would also like to thank the staff of the Visible Information Center Inc for their cooperation in developing the GUI This software was developed with the support of the Grant in Aid for Young Scientists B No 22740077 and funding from Ibaraki Prefecture J PARC 23D06 1 Overall configuration Conograph was developed by the High Energy Accelerator Research Organization for running two command user interface CUI programs for powder indexing and peak searching through operations on a graphical user interface Fig 1 1 shows a screenshot of the Conograph user interface Conograph Users stamura Desktop sample sample1l Advanced indexing Parameters Log Note Search parameters Quick search Memory efficient search Number of peaks used for search AUTO Diffractorneter parameters Time of flight _ Angle dispersion Conversion parameters TOF co cu d a c d c d a cud c d 9 03976 9965 02 5 88424 LL LIBE 10000 20000 0 0 0 0 4 4 s Full sereen C tor
40. he respective diffractometer Fig 4 3 Fig 4 4 and Table 4 1 Entering O deg for the zero point shift is normally effective More precise values can be estimated by executing refinement after indexing Diffractometer parameters D Time of flight Angle dispersion Conversion parameters TOF cg cad cod cad cad csd 9 03976 9965 02 5 88424 Tactometer parameters D Time of fight Angle dispersion Ditt Wavelength 1 54056 A Zero point shift A28 0 0 deg 4 6 Estimate zero point shift Fig 4 3 Diffractometer parameters Top Time of flight method Bottom Angle dispersion method Table 4 1 Diffractometer parameters Selects FTime of flight or FAngle dispersion Conversion parameters represented as polynomial coefficients from zero to fifth order 3 Wavelength A Peak shift parameter e20 degrees Estimates zero point shift by using the reflection pair method The zero point shift can be estimated by conducting the reflection pair method 1 Fig 4 3 In the reflection point method the zero point shift is estimated by using two peak positions that have a ratio of d values equal to two fold As shown in Fig 4 3 the one that appears to be correct can be selected from various candidates Diffractometer parameters Time of flight Angle dispersion Wavelength 1 81958 A When button is clicked the zero point shift is Zero point shift A28 0 0 deg
41. idates with a de Wolff FOM M greater than this value are 3 displayed Lower and upper thresholds of lattice parameters a b c A Lee 5 Relative resolution of d 1 d value Used for deciding whether two lattices 0 03 are identical If the lattice parameters are specified it is possible to calculate the number of AUTO peaks that exist in the range from the first to the n observed peaks Lower and upper thresholds of the number Immediately after indexing is executed lattice parameters in the list are sorted according to the de Wolff FOM Mj By using the Sorting criteria drop down menu Fig 5 4 it is possible to change the sorting criteria for the lattice parameters refer to Table 5 2 Ev de Wolff figure of merit M om Wu figure of merit Mwu Reversed de Wolff figure of merit Mrev Symmetric figure of merit Msym Fig 5 4 Sorting criteria for lattice parameters Among the aforementioned five FOM the de Wolff FOM gives preference to the lattice parameters with high symmetry and has the best efficiency However another FOM occasionally might be more effective than the de Wolff FOM particularly if the powder diffraction pattern contains impurity peaks 5 The first four FOM 6 9 in Table 5 2 are defined in such a way that the values become close to 1 if there is no correlation between the observed and computed lines A lattice satisfying M gt 10 M gt 10 M gt 3 or M gt 30 i
42. ile gt HRP000675 BS bin04f pks histogramlIgor lt Outfile gt lt PeakS earchInputFile gt lt ZCodeParameters gt Fig 11 1 Example of cntl inp xml lt xml version 1 0 encoding UTF 8 gt lt ZCodeParameters gt lt ConographParameters gt lt Parameters for the histogram gt lt Q tof l angle dispersion gt lt IsAngleDispersion gt 0 lt IsAngleDispersion gt lt Conversion parameters for tof a polynomial of any degree gt lt ConversionParameters gt 0 1 0 lt ConversionParameters gt lt Peak shift parameters for angle dispersion Z deg Ds deg Ts deg 2 d sin theta0 Wlength 2 theta 2 theta0 Z Ds cos theta0 Ts sin 2 thetaQ gt lt PeakShiftParameters gt 0 lt PeakShiftParameters gt lt Wave length angstrom for angle dispersion gt lt WaveLength gt 1 54056 lt WaveLength gt lt Parameters for search gt lt SearchLevel gt lt Q quick search suitable for lattices with higher symmetries l exhaustive search suitable for lattices with lower symmetries gt 0 lt SearchLevel gt lt Number of reflections for calculation gt lt MaxNumberOfPeaks gt AUTO lt MaxNumberOfPeaks gt lt The critical value c to judge if linear sums of Q equal zero abs Xsigma 1 Q 1 lt c Err lt sigma_1Q_ i gt lt Critical ValueForLinearSum gt 1 lt Critical ValueForLinearSum gt lt Minimum of the volume of primitiv
43. ing Number of Points End of Interval 9 offset interval delete D Full screen 0 4 0 6 0 8 1 Range of peak search TOF 28 Output histogram data 0 0 MAX List of Indexing Solutions Refine Lattice Constants Stored Lattice Constants FWHM Use for indexing Lower threshold for peak heights c 5 0 use this c Remove Ka peaks Yes No wave length A select Fig 2 1 Screenshot immediately after opening Conograph 2 1 Creating a new project To create a new project first select File gt New project as shown below iograph Open Project 0 Open Recent P f E Www AN Leettices 1 1 Enn wem gn Y EYI Proqppct Preferences e In the dialog box for creating projects you can specify the diffraction data file and project folder as shown in Fig 2 2 2 1 Select diffraction data file New Project Project folder Browse Cancel OK New project Histogram data path E _ sample sample 1 Synchrotron sample1_pks histogramigor Project folder EX sample sample 1 Synchrotron As the project folder a folder containing diffraction data is inputted automatically This setting can be changed if necessary Fig 2 2 Dialog box for creating new project The diffraction data file can be formatted in three types of format XY Fig 2 3 IGOR Fig 2 4 and Rietan Fig 2 5 For the XY and IGOR formats
44. k position T indexing offset 0 2 Q 4 MM i interval 0 2 BITE il S E 1 chem 0 10000 20000 30000 40000 50000 gt TOF Output histogram data Peak Search Output iy List of Indexing Solutions Refine Lattice Constants Stored Lattice Constants Bravais lattice Number of solutions M Mwu Mrev Msym NN Cubic F 1 275 75 206 96 6 38 1754 53 54 Cubic I Cubic P 0 Hexagonal 0 Rhombohedral 8 231 80 438 51 7 38 1692 56 185 Tetragonal I T 238 06 376 17 6 11 1455 10 145 Tetragonal P 2 4 41 3 97 3 72 16 44 1 Orthorhombic F 9 205 46 532 29 5 98 1226 92 47 Orthorhombic 14 1944 21 Orthorhombic C 35 251 72 384 11 6 82 1716 57 51 Orthorhombic P 1 4 03 3 11 1 95 7 88 Monoclinic B 21 174 76 337 12 4 81 840 88 51 Monoclinic P g 188 41 478 83 6 96 1311 63 8 Triclinic 3 9 35 10 72 2 28 19 44 17 Selected Bravais lattice Orthorhombic l Best M 284 8174 3 8426 3 8434 5 4348 90 000 90 000 90 000 Among all the lattices with Best Mwu 777 0728 3 8426 3 8434 5 4348 90 000 90 000 90 000 a Hisce deep Best Mrev 6 8581 3 8428 3 8444 5 4346 90 000 90 000 90 000 ype Best Msym 1944 2054 3 8426 3 8434 5 4348 90 000 90 000 90 000 the candidate with the best Largest NN 135 3 8426 3 8434 5 4348 90 000 90 000 90 000 FOM value is displayed The lattice can be selected by clicking on it Fig 5 5 Best M frame In order not to spend much time searching for plausible solutions you should che
45. m 3 above is introduced in Section 3 3 The criteria and thresholds in item 1b are introduced in Section 5 3 because they can be changed even after indexing In the current section the remaining two types of parameters are explained Search parameters r Bravais lattice available multiple choice Volume of primitive cell A AUTO sVolsz Triclinic v Tetragonal P Monoclinic P Tetragonal I Number of enumerated primitive cells AUTO Monoclinic B v Rhombohedra Number of zones used for search AUTO Search parameters Quick search Memory efficient searc Q Tolerance level for errors of sums of q values 1 0 times v Orthohombic P v Hexagonal Number of peaks used for search AUTO wq 1 9 v Orthohombic C v Cubic P Decoder mei m Ee EID v Orthohombic I v Cubic I i i X i v i Time of flight Angle dispersion Orthohombic F Cubic F Threshold of minimum distance 2 0 Conversion parameters between lattice points s 1 2 3 4 5 Lt A pt on Tas elute baal a Maximum number of soutions 1000 0 0 0 0 0 0 for each Bravais lattice Criteria for indexing solutions Number of peaks used for computation of FOM 20 Use for indexing Sorting criteria de Wolff figure of merit M hresholds for indexing solutions Upper lower thresholds for number of computed lines between 1st and 20th observed lines AUTO s Neal s AUTO de Wolff figure of merit M Mz 3 0 Kee Min Max of lattice constants 0 sabes 1000
46. ned to peaks are displayed Peak Search Output BestM List of Indexing Solutions Stored Lattice Constants d bir a z M 284 8171 Bravais lattice Orthohombic I Determine Miller indexing UNO EEE Spcae Group A Mrev 6 8261 Lattice constants a b c a B A a B y Undo Refine Msym 1944 2041 3 84260 3 84339 5 43478 90 0 90 0 90 0 NN 157790 Ranne estore VOL 80 2645 zero point shift 426 deg 0 0 lattice constants Check uniqueness Input position Estimated error from FWHM Computed position Miller index Use for refinement 31322 700 148 05590 31332 979 1 0 1 vf 19179 700 80 59404 19180 509 0 2 0 vf 16352 790 56 55483 16353 209 2 1 1 13559 380 51 78934 13559 342 0 0 4 12443 050 49 92759 12443 274 1 2 3 11071 930 48 55326 11072 002 1 3 2 10439 340 48 00951 10438 898 0 3 3 The refinement of the lattice parameters is performed using the assigned Miller indices If required it is possible to manually specify which peak positions are to be used for refinement by using the flags in the rightmost column refer to Table 6 1 for the meaning of the other columns When the Refine amp store lattice constants button is clicked lattice parameters are refined and appended in the Stored Lattice Constants frame 6 3 Table 6 1 Information about peaks in Refine lattice constants frame Contents Peak positions of the considered diffraction pattern These values calculated from the f
47. o be changed in order to conduct a more exhaustive search Section 10 2 1 enhance computing speed Section 10 2 2 and improve the efficacy of the figures of merit Section 10 2 3 are explained 10 2 1 Conduct a more exhaustive search 1 Searching method in Indexing frame Quick search gt Exhaustive search 2 lt Number of peaks used in the search gt Indexing frame AUTO a number greater than 48 When AUTO is entered 48 peaks are used for powder indexing unless the diffraction pattern contains only a smaller number of peaks However even this number of peaks may be insufficient if a dominant zone exists In such cases increasing the number is effective 3 Tolerance level for errors of sums of q values Advanced Indexing parameter frame 1 i In cases of characteristic X rays or reactor sources better results may be yielded if a large value is used 10 2 2 Enhance computing speed 1 Increase lt Number of threads gt File gt Preferences The simplest method is to increase the number of threads used 2 Search parameters Indexing parameters frame Exhaustive search Quick search 3 Bravais lattice Advanced Indexing Parameters frame untick If you have prior information about the Bravais type the information can be used to reduce the time required in the stage after Bravais lattice determination 4 Increase values of Volume of primitive cell or Thresholds of minimum dis
48. rOtMillerIndicesInRanges is set to 128 lt MinNumberOfMillerindicesinRange gt is set to 12 Check Uniqueness Checking coincidence of computed lines Warning The unit cell have very similar computed lines as the following the solution might not determined uniquely from peak positions 1 3 32791 1 92149 3 32836 90 108 471 90 Monoclinic P Volumez20 0661 M20 176 914 2 6 65581 1 281 3 84299 90 125 259 90 Monoclinic B Volume 26 7548 M20 184 248 Refine Optimizing lattice parameters by linear least squares Log reporting the 1 Initial M20 z 284 817 BU was not lop rod results of refinement Peak Search Output Best M List of Indexing Solutions Stored Lattice Constants M 284 8171 Miller indexing Mwu 777 0723 Mrev 6 8261 Bravais lattice Orthohombic I 5 Determine Spcae Group Lattice constants a b c a B vm 19 A B v Undo Refine Msym 1944 204 3 84260 3 84339 5 43478 90 0 90 0 90 0 MN 157790 After refinement VOL 2 80 2645 these values are Kane m store zero point shift A20 deg 0 0 lattice constants Check uniqueness _ cmd Check uniqueness updated using the Input position Estimated error from FWHM Computed position Miller index Use for refinement obtained lattice 1 31322 700 148 05590 31332 979 1 0 1 M arameters 2 19179 700 80 59404 19180 509 0 2 0 f
49. rch 20000 30000 0 0 MAX BSS eens BestM List of Indexing Solutions Refine Lattice Constants Stored Lattice Constants Height FWHM Use for indexing Lower threshold for peak heights Cm 5 0 use c times error of intensities Remove Ka peaks Yes No i Ka Ka wave length A 1 54056 1 54439 select Fig 2 6 Screenshot immediately after opening a project prior to peak search 2 5 If a peak search has been performed in the opened project and the file pks histogramlgor exists the indexing frame is displayed as shown in Fig 2 7 In addition to the diffraction pattern the peak positions Z and a smoothed diffraction pattern are displayed Conograph Users stamura Desktop sample samplel auto generated files ZLEFE indexing Advanced Indexing Parameters Log Note Diffraction Pattern Peak Search Parameters Number of data points to use for smoothing at each point Number of Points End of Interval 9 MAX t i Full sereen Range of peak search 10000 40000 50000 Output histogram data 0 0 MAX CARAT Best M List of indexing Solutions Refine Lattice Constants Stored Lattice Constants Position Height FWHM Use for indexing 3151 9200000 0 1593156 37 4977600 3341 9950000 0 1686752 24 2906400 3696 8450000 0 1680182 20 6385300 3841 0800000 0 1735176 21 72411
50. s in general likely to be the correct solution However sometimes several distinct lattices may obtain large FOM values simultaneously To select the most appropriate lattice parameters all the plausible solutions should be checked using the methods described in Sections 5 4 and 5 5 5 4 Table 5 2 Sorting criteria for lattice constants displayed in list Sort in descending order by the de Wolff FOM M 6 computed by using the method described in 5 to increase the numerical stability The de Wolff FOM possesses these properties a Insensitive to existence of unobserved computed lines according to extinction rule b Sensitive to existence of un indexed observed lines such as impurity peaks c When almost identical lattices belong to different Bravais types the lattice with higher symmetry normally obtains a higher value Sort in descending order by Wu FOM M 7 In terms of a and b it is similar to the de Wolff FOM in terms of c it is opposite that is a lattice with a lower symmetry is more likely to obtain a high value Sort in descending order by Reversed FOM M5 5 M is computed by exchanging the roles of observed peak positions and calculated peak positions in the definition of the de Wolff FOM Because of this it has properties that are opposite to those of the de Wolff FOM a Sensitive to existence of unobserved computed lines b Insensitive to existence of un indexed observed lines c Tends to
51. select a lattice with lower symmetry As in the case of the de Wolff FOM if there is no correlation between observed lines and computed lines the value becomes close to one Sort in descending order by Symmetric FOM M M M 5 According to its definition it has properties between 0M and BM As in a number of statistical quantities such as chi squares or R factors the value remains the same after observed lines and computed lines are exchanged Sort in descending order by NN number of lattices judged to be almost identical among all the solutions by using the relative resolution in 5 5 5 4 Find plausible indexing solutions Several of the FOM introduced in Section 5 3 can extract a small number of candidates with high compatibility with inputted peak positions from multiple powder indexing solutions However none of the FOM is sufficiently effective when two lattices that belong to different Bravais types are compared In order not to miss plausible solutions in addition to their values of FOM their Bravais types should be checked By using Best M Frame Fig 5 5 it is possible to compare the best FOM values of the solutions in each Bravais type By clicking the name of a Bravais types the solutions with the largest FOM are displayed Advanced Indexing Parameters Log Note Dici iv Diffraction pattern v Error V Smoothed curve v Peak position e Bi peaksearch e f iW Pea
52. tance between lattice points Advanced Indexing Parameter frame If you have prior information about these parameters the information can be used to reduce the time required for powder auto indexing 10 3 10 2 3 Improve the efficacy of figures of merit 1 Zero point shift Indexing frame 0 deg more accurately estimated value For diffraction patterns with a large zero point shift 220 gt approximately 0 17 the FOM values sometimes become small The results may be improved by conducting powder indexing using the estimated value of the zero point shift The zero point shift can be estimated by using one of the following methods a The reflection pair method 1 b After conducting powder indexing once refine the zero point shift and lattice parameters with relatively larger M and M for instance M gt 3 orM gt 10 approximately and re execute indexing using the obtained zero point shift In both methods it is necessary to test several candidate values 2 Number of peaks used for computation of FOM gt Indexing frame 20 gt a number greater than 20 The value 20 frequently used for this parameter might be insufficient if a problem called dominant zone occurs If a dominant zone is found when refining the lattice constants and zero point shift a warning message and the number of peaks required appear in the Log Note frame In that case set this parameter to a value greater than the number display
53. ted a warning concerning dominant zones may appear in the Log Note frame Fig 5 9 When this warning appears it may be considered that the FOM did not work efficiently Therefore it is advisable to increase the Number of peaks used for computation of 5 8 FOM gt in the Criteria for lattice constants in the list area Fig 5 3 according to the warning Next verify that there is no warning when refinement is executed again l ERHI MEETA BE TS T 2 Initial M10 66 9228 M10 was not improved Optimized unit cell parameters 27 4571 29 7438 51 5464 90 90 90 Optimized zero point shift 0 0158915 Reduced unit cell parameters 27 4571 29 743851 5464 90 90 90 Optimizing lattice parameters by linear least squares Warning appears that number of peaks used for 1 Initial M5 395 685 MS of optimized solution 25673 3 computation of FOM should be increased to more 2 Initial MS 25673 3 than 23 M5 was not improved Optimized unit cell parameters 12 4677 51 554 14 8786 90 90 90 Optimized zero point shift 0 0155809 Reduced unit cell parameters 12 4677 51 55414 8786 90 90 90 Warning A dominant zone exists This is resolved by increasing the parameter lt MaxNumberOfPeaksForFOM gt to a number more than 7 Fig 5 9 Log message reporting that a dominant zone is found 5 9 5 5 Decide the correct lattice parameters Before drawing a conclusion as to which solution for the lattice constants is correct th
54. tern Are there many diffraction peaks that have not been detected Has noise including small peaks that may not be diffraction peaks been detected as a peak The aforementioned problems during peak search can be resolved by adjusting some of the peak search parameters and re executing peak search for parameter adjustment refer to Section 10 1 The graph magnification in the Diffraction Pattern frame is changed by using the mouse wheel or rubber band rectangular range selection using left drag A parallel shift of the display area is achieved by using Ctrl left drag or center drag The shortcut menu that appears when you right click on the graph is shown in Fig 3 2 Its components and their descriptions are listed in Table 3 de Auto scale 1 Undo 2 Copy image to clipboard 8 Save image 4 Fig 3 2 Shortcut menu Table 3 1 Shortcut menu Adjusts scale to fit entire graph Returns to the previous display status Copies graph contents onto the clipboard Saves graph contents in an image file 3 3 3 3 Removing and adding peaks manually This section introduces a method for modifying peak search results using the GUI operations However even if the results are not satisfactory you should attempt to adjust the peak search parameters first before proceeding to the following operations Peaks used in indexing can be selected using the check boxes that appear in the Use for indexing column in the
55. ther two lattices are equivalent or not If the relative difference of two lattice parameters is within this value only that with a better figure of merit is output gt Resolution 0 05 lt Resolution gt lt Maximum number of false unindexed peaks gt lt MaxNumberOfUnindexedPeaks gt 20 lt MaxNumberOfUnindexedPeaks gt lt Number of reflections to calculate figure of merit gt lt MaxNumberOfPeaksForFOM gt 20 lt MaxNumberOfPeaksForFOM gt lt Output the candidates with better FOM than the following value gt lt MinFOM gt 3 lt MinFOM gt lt Number of hkl among input reflections gt lt MaxNumberOfMillerIndicesInRange gt AUTO lt MaxNumberOfMillerIndicesInRange gt lt MinNumberOfMillerIndicesInRange gt AUTO lt MinNumberOfMillerIndicesInRange gt lt Minimum and maximum of the unit cell edges a b c angstrom gt lt MaxUnitCellEdgeABC gt 1000 lt MaxUnitCellEdgeABC gt lt MinUnitCellEdgeABC gt 0 lt MinUnitCellEdgeABC gt lt ConographParameters gt PeakSearchPS Parameters lt ParametersForSmoothingDevision gt lt NumberOfPointsForSGMethod odd number gt lt NumberOfPointsForSGMethod gt 9 lt NumberOfPointsForSGMethod gt lt EndOfRegion gt lt The maximum point of smoothing range gt MAX lt EndOfRegion gt lt ParametersForSmoothingDevision gt lt PeakSearchRange gt Begin 0 0 lt Begin gt End MAX End lt PeakSearchR
56. thorhombic C Cubic P Minimum Mwu 1 9 a W Orthorhombic I Cubic I 9 Minimum Mrev 1 0 6 W Orthorhombic F Cubic F Threshold of minimum distance between lattice points 2 0 7 Maximum number of solutions for each Bravais lattice 1000 Fig 4 5 Advanced indexing parameters A description of the parameters and their recommended values are listed in Table 4 2 Table 4 2 Advanced indexing parameters Contents Recommended value D Lower and upper limit of primitive cell volume _ AUTION sd Lower and upper limit of primitive cell volume Maximum value from four q values 1 d qi q2 q3 q4 acquired from AUTO selected topography that satisfies Ito equation Maximum number of powder indexing solutions to be enumerated before AUTO Bravais lattice determination Reference value to determine whether linear sum of q 1 d value is equal to zero including Ito formula Lower thresholds for the Wu FOM M the reversed FOM M5 and the distance between two closest points in the crystal lattice If a solution has HI 3 D values below these thresholds it is deleted and cannot be retrieved after indexing is executed If a solution has a rank below this number when all the solutions with the 1000 same Bravais types are sorted in the order of the de Wolff FOM M it is deleted and cannot be retrieved after indexing is executed 9 Untick
57. to indexing using many peaks J Appl Cryst 47 2014 pp 5931 598 The methods and figures of merit of Conograph are also introduced in the following papers R Oishi Tomiyasu NA method to enumerate all geometrical ambiguities in powder indexing and its application submitted R Oishi Tomiyasu MDistribution rules of systematic absences on the Conway topograph and their application to powder auto indexingO Acta Cryst A69 2013 pp 6031 610 R Oishi Tomiyasu PReversed de Wolff figure of merit and its application to powder indexing solutions J Appl Cryst 46 2013 pp 12771 1282 R Oishi Tomiyasu PRapid Bravais lattice determination algorithm for lattice parameters containing large observation errors Acta Cryst A68 2012 pp 5251 535 R Oishi M Yonemura T Ishigaki A Hoshikawa K Mori T Morishima S Toru T Kamiyama fiNew approach to indexing method of powder diffraction patterns using topographsO Zeitschrift f r Kristallographie Supplements 30 2009 pp 151 20 12 2 Bug report Please send the following information to the e mail address conograph bug lists osdn me All comments will be considered and reflected at the time of Conograph version upgrading 1 OS used including 32 bit and 64 bit 1 Conograph version used indicated in the GUI Help menu iii Particulars of problem iv Details of conditions when problem occurred v Possibility of recurrence does it occur always or sometimes
58. ty 20000 T 3 interval 4300 0 0 1 11 I T a a NN m WE BE E EE HUER a a IEEE i l l i 1 i i l l i i i Full screen 0 20 40 60 28 Output histogram data Fig 5 11 Diffraction Pattern frame Table 5 4 Diffraction Pattern frame Displays hides switch Height y coordinate of the position of tick marks displayed at the top Press Enter key to reflect the change This height can be increased or decreased by locating the cursor in the text box and rotating the mouse wheel Space between tick marks and tick marks immediately below Enlarges the Diffraction Pattern frame to full screen If the peak positions of a solution accord well with the observed lines in the diffraction patterns select the solution and click the Check Uniqueness button Then all the lattices with almost the same peak positions as the currently selected lattice are generated 3 If such lattices exist a window appears as shown in Fig 5 12 The available operations in the window are the same as in the Diffraction Pattern frame By clicking the MOutput histogram dataO button a histogram file that contains the peak positions of all the lattice parameters displayed is outputted 5 11 lispersion Check Uniqueness Checking coincidence of computed lines I c d 24 itions 0 0 e 0 9 Check Uniqueness Orthorhombie I 3 84 3 84 5 43 90 90 90
59. ull widths at half maximum of peaks are used as weights for least squares method Peak positions of the selected lattice constants computed by 5 using the Miller indices in column 4 and diffractometer parameters 4 Miller indices used for refining lattice parameters BN Checked if the peak position is used for refining lattice parameters 6 4 6 2 Undo button By clicking the Undo button it is possible to restore the lattice parameters and the zero point shift to the values that existed before you keyed in the numbers in the text boxes or executed refinement Fig 6 2 This Undo cannot be applied successively and therefore only the last values of the parameters can be retrieved Peak Search Output BestM List of Indexing Solutions Bravais lattice Orthohombic I Determine Mis coals EE Mwu 777 0728 Spcae Group Mrev 6 8261 Lattice constants a b c a B Y Msym 1944 205 Undo Edit NN 135 3 84260 3 84339 5 43478 90 0 5 43478 VOL 380 2645 Refine amp store zero point shift A20 deg 0 0 lattice constants Check uniqueness FWHM Computed position Miller index Use for refinement 05590 31332 979 1 0 1 V Input position Estim 1 31322 700 Peak Search Output Be TS stored Lattice Constants JO Sunipq SUIX PUI IJN Bravais lattice Ortho E M 284 8179 M
60. utions Refine Lattice Constants Stored Lattice Constants Position Height FWHM Use for indexing Lowe te estos toc pee tee ce 3151 9200000 0 1593156 37 4977600 v 3341 9950000 0 1686752 24 2906400 3696 8450000 0 1680182 20 6385300 3841 0800000 0 1735176 21 7241100 4004 5330000 0 1609938 23 1921000 4058 4620000 0 1760591 22 3059300 4152 7050000 0 1760708 23 6546600 4188 8400000 0 1617476 21 6177300 4291 7320000 0 1502431 23 7250000 4360 5550000 0 1864202 24 0960600 4404 0580000 0 2063731 23 8925800 4477 1680000 0 1638236 25 2943900 4524 8110000 0 1536584 24 2384700 4604 6750000 0 1816902 24 3246700 4654 5730000 0 1989797 23 7283300 c 5 0 use c times error of intensities Remove Ka peaks Yes No Ka Ka wave length A 1 54056 1 54439 select v O 4 DUM 4 UN M IAAAAAAAAAAAAAAKR In the Diffraction Pattern frame a smoothed diffraction pattern and peak positions Z are displayed Simultaneously they are stored in the file auto generated files folder _pks hstogramlgor If the peak search results found at the end of the _pks histogramlgor file Fig 11 4 are modified using a text editor the results are loaded on the application when the same project is reopened 3 2 3 2 Checking peak search results To obtain appropriate peak search results for indexing you should check whether the following problems occur in particular for the low angle peaks by magnifying the graphical display of the diffraction pat
61. wu 777 0744 ae Group Mrev 6 8261 Msym 1944 209 NN 25165824 VOL 80 2645 Lattice constants a b c a B 3 84260 3 84339 5 43478 0 0 90 0 90 0 Refine amp store zero point shift A20 deg 0 0 lattice constants Check uniqueness Input position Estimated error from FWHM Computed position Use Tor refinement 1 31322 700 148 05590 31332 979 1 0 1 v n S Stored Lattice Constants L Peak Search Output Best of Indexing Solutions fixus M 284 8179 Der DOE ler indexing Mwu 777 0744 pcae Group Mrev 6 8261 Msym 1944 209 NN 64150160 Bravais lattice Orthohombic Lattice constants a b c a b o Refine 3 84260 3 84339 5 43478 90 0 90 0 VOL 80 2645 Refine amp store zero point shift A20 deg 0 0 lattice constants Check uniqueness Input position Estimated error from FWHM Computed position Miller index Use r miia 1 31322 700 148 05590 31332 979 1 0 1 v Fig 6 2 Undo button 6 5 7 Result output There are three types of output files index xml index2 xml histogramlgor and a backup file all are text files except for the backup file The respective output files are explained in the following sections 7 1 ndex xml The auto generated files index xml file is outputted in the project folder if either of the following events occurs
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