============================================================ XXXXXXX XXXXXXX XXXXXX XXXXX XXXXXXXX XX XX XXXX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XXXXXXX XXXXXXX XX XX XXXXX XX XXXXX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX XXXXXX XXXXX XXXXXXXX XX XX XXXX ============================================================ System of Programs for Powder Diffraction Data Analysis ver. 2.4 Wieslaw Lasocha and Krzysztof Lewinski Department of Crystal Chemistry and Crystal Physics Jagiellonian University Ingardena St. 3, 30-060 Krakow POLAND INTRODUCTION ============ Analysis of the diffraction data routinely includes profile fitting, automatic indexing, and refinement of the unit cell parameters. Although variety of programs for this purpose exists, each one uses proprietary format of the data files, that makes difficult and time consuming preparation of input files. We developed system of programs PROSZKI (pronounce 'proshkee') to make analysis of the powder diffractograms more efficient and comfortable. The package contains separate programs that can be executed independently in any order. The main program in the system, PRMAIN, serves as a shell that enables user to set up global parameters file, interactively create input files for other programs, read output files and automatically transfer some results to the global parameters file (GPF). Programs included in the package enable user to analyze diffraction pattern, determine and refine lattice parameters, and simulate diffraction pattern. Calculations are based on well -known methods. For indexing and refinement of the lattice parameters, user has choice of alternative methods. Preparation of input files is simplified by use of a reasonable set of default parameters. Troublesome questions are reduced to minimum. All input files retain original format enabling use of any program or data file outside the system. INSTALLATION AND HARDWARE REQUIRAMENTS ====================================== The programs are implemented on IBM-compatible computers (minimum PC/XT) with 640 KB RAM. Floating point processor is required for TREOR, POWDER and DICVOL programs, for other programs is not necessary although is used if present. Programs and accompanying files occupy about 2.5 MB disc space. Both color (CGA/EGA/VGA) and monochrome monitor and graphics card (Hercules) can be used. The default directory in which programs should be installed is C:\PROSZKI. If for some reason this directory is inconvinient, you can change both default disk and directory, but the program must be 'mounted' in the new place. After copying all files to the directory, make this directory current, and run program MOUNT_PR. This program changes path which is coded inside the program and allows it to find some additional files, like help file. The mounting procedure can be performed ONLY ONCE. If you have to change the directory again, repeat the mounting procedure with the ORIGINAL copy of PRMAIN.EXE file. Also, using your favorite editor, you have to change directory name in the PROSZKI.BAT file. The PROSZKI.BAT file must be located in the directory which is in MS-DOS search path. HOW TO USE PROSZKI ================== To start the program type 'PROSZKI' at DOS prompt and then enter the name (and optionally path) of your parameters file (without extension '.PAR'). If the program can not find this file you have two options: create it or enter the name again. After program completed reading parameters from the file, it displays the main menu and some additional information. The top line shows the name of the current problem (active parameters file), the bottom line contains information about active keys you can use to select options. In most cases they are: to select option from menu jump to the top/bottom of menu go to the previous menu or exit program display help information The main menu allows you to select one of the following options: Diffraction Pattern Analysis ---------------------------- Pattern decomposition from digitized diffractograms. Indexing -------- You will have choice of four indexing programs utilizing different methods. Lattice Constants Refinement ---------------------------- Two programs with different capabilities for refinement of the unit cell parameters using least squares method. Diffraction Pattern Simulation ------------------------------ Calculation of simulated X-ray or neutron powder diffraction pattern from known crystal structure. Update Parameters ----------------- Access to the global parameters file (GPF). You can enter and modify values of experimental parameters and diffraction lines. Access to DOS ----------- Suspends execution of PROSZKI and allows you to use DOS commands. Useful for printing, file management and editing but execution of external programs is limited by amount of available memory and depends on configuration of your computer. Press key without any command to return to the menu. New Active File --------------- Select this option if you want to start work with another problem or set of parameters. Help ---- Displays short information about available options. Create Input File for Rietveld ------------------------------ This option allows you to create input file in format required by programs DBWS and XRS-82 (not included in PROSZKI). STOP ---- Stops execution of PROSZKI without asking for confirmation. Another menu appears on the screen when you selected program you want to run. It contains the following options: Prepare Input File ------------------ Creates input file using values from the parameters file and asks you to enter some other parameters interactively. Run Program ----------- Starts execution of selected program. Browse Through Results ---------------------- Displays the most important results selected from the output file. Exit to Previous Menu --------------------- Equivalent to key, displays previous menu. TABLE OF EXPERIMENTAL PARAMETERS AND DIFFRACTION LINES ====================================================== All parameters dealing with the same subject are collected in groups. To change value of some parameter, you have to select group it belongs to using and keys and then press . Some parameters can be changed by entering new value, some other by selecting value from menu. If there is already old value in the field, you can accept it by pressing . Program checks for errors (e.g. character instead of number) and illogical values (e.g. negative wavelength). You can also quit by pressing . title Name of your sample and other important information not included in the parameters table (e.g. temperature). The title will be used in all input files created by the program. compound Additional information like chemical formula or alternative name of the sample. radiation Type symbol of the X-ray tube (element) and optionally wavelengths for mean alpha, alpha_1, alpha_2 and beta radiation. For most popular types of radiation (Cu, Cr, Fe, Mo, Co and Ag) wavelengths are preset in the program. You can also select method of monochromatisation (if any) and type of filter. measurement Select type of your diffractometer or conditions camera and specify such a parameter as diameter, 2_theta range, step size (for diffractometer) and systematic shift of the zero position. Using mean alpha wavelength and 2_theta range, program will calculate maximum and minimum values of measurable d_obs. Shift will be used for calculations of d_cor, its value can be determined experimentally or estimated during unit cell parameters refinement (LATCON) or indexing (Visser's program). symmetry From the menu you can select crystallographic system (or 'unknown') and then type in space group symbol and number. Program does not verify correctness of that information, so be careful when typing. Examples of correct space group symbols: P n A 21 , p 63/m , P 3, etc. Negative space group number indicates nonstandard group or rhombohedral axes. lattice If the crystallographic system was parameters specified, only independent parameters and their standard deviations need to be typed. Volume of the unit cell will be automatically calculated. density Molecular weight, number of molecules in the unit cell (integer) and volumes of the unit cell are used to calculate theoretical density of your crystals. Change of the volume will also change calculated density. diff. lines Total number of diffraction lines and number of lines active. Only lines with status "active" are used for preparation of input files for other programs. Table of diffraction lines can be entered from parameters table by selecting option 'diff. lines' and pressing or directly by pressing key. The table can contain up to 100 diffraction lines. For each line we have following parameters: 2_theta observed or calculated Bragg's angle d_obs observed or calculated value of d d_cor d value corrected for zero shift h k l Miller indices I/I100 relative intensity alpha radiation type: 0 - mean alpha 1 - alpha_1 2 - alpha_2 3 - beta st line status: 1 - line active, is used to generate input files for other programs 0 - line inactive, is always ignored. Only POWDER program uses such a line assuming however that this line is extraneous. To enter a new line you have to: - select row - add new empty line AFTER current line using key or - add new empty line BEFORE current line using key - select column and type in value - move cursor and enter value of next parameter - repeat this for each line and parameter The new line always has status=1 (line is active) as a default value. Cursor is positioned in 2_theta column. To delete diffraction line, select it and press . You will be asked to confirm deletion. Insertion or deletion of diffraction line always changes line numbers. To modify existing parameter(s) select it using cursor and enter new value. Every time you enter new value of 2_theta, program automatically calculates d_obs and d_cor. Similarly, if you change value of d_obs, also new values of 2_theta and d_cor will be inserted. You can not change directly d_cor, this parameter is always calculated. Modification of the radiation type (in column 'alpha') changes 2_theta or d, depending on selected mode. In default mode values of d are calculated from 2_theta, alternatively 2_theta can be calculated from d_obs. You can change mode using keys or for 2_theta priority and or for d_obs priority. Active mode is indicated by the asterix in the column's label. This is useful when you are trying to find positions of beta peaks corresponding to strong alpha peaks or find out angular difference between peaks observed and referred in literature by d value. Changes of some global parameters like wavelength or zero correction can affect values in the table of diffraction lines. To recalculate d or 2_theta you can use key. All values will be recalculated depending on current 2_theta/d priority. Relative intensities are not used for any calculations in this version of program, Miller indices are used only for unit cell parameters refinement by LATCON and optionally APPLE. Active keys you can use are: / to change current line / to change column / displays next/previous page deletes current line inserts new line before current line inserts new line after current line returns to the table of experimental parameters or cancels entering of new value , 2_theta priority , d_obs priority , recalculates values of 2_theta or d , zeroes all Miller indices hkl displays HELP information ANALYSIS OF DIFFRACTION PATTERN =============================== The system PROSZKI utilizes version 13 (1985) of NEWPEAK program for analysis of diffraction pattern. This program can use data from powder diffractometer as well as data from Guinier film digitized by a film scanner. To run the NEWPEAK program you have to know following data values: - Start, stop and step size of your experiment. These data should be written to GPF. In case of Guinier data you will be prompted for 2_theta position of the focal line. - FORTRAN format of your diffraction data. Consult FORTRAN textbook for details if your diffraction data file contains additional information besides counts (e.g. 2_theta values). To run, program requires additional file name.FIX containing parameters modifying decomposition procedure. Default values are stored in the file PEAKINP.FIX in the PROSZKI directory. If the file name.FIX does not exist in your current directory, this file is automatically created by PRMAIN. By changing values of parameters stored in the file name.FIX you can modify pattern decomposition procedure. Description of parameters can be obtained by setting INFO=1 in input file. Besides the normal output as offered by the original version of NEWPEAK, the program included in PROSZKI optionally creates additional files for use by external plotting programs. These files contain 2_theta(i)and counts(i) pairs: name.RAW - raw data file name.OBS - smoothed data with subtracted background name.CAL - restored experimental data name.BGR - 'background' determined by the program name.DIF - differences between observed and restored data INDEXING ======== Indexing procedures try to determine a cell that will explain the d-spacing data observed. This procedure requires the material to be a single phase (or as pure as possible) and the experimental data to be very accurate. An indexing algorithm cannot be stated rigorously because of the unpredictable distribution of unobserved lines and the errors of measurements. Therefore, it is expected that various methods may be useful for various powder patterns. Four programs representing four different approaches to indexing problem were included in system PROSZKI. Indexing programs and their classification according to R. Shirley are as follows: - VISSER's ITO-12 deductive, parameters space - TREOR-4 semi-exhaustive, indices space - POWDER exhaustive, indices space - DICVOL exhaustive, parameters space Indexing programs usually provide the user with several answers and a figure-of-merit that is based on the lattice fit. It is up to the user to choose the best solution. Any lattice with an acceptable figure-of-merit needs to be examined further to determine if it explains all the data, including physical property measurements (e.g. density) on the material. In general, exhaustive methods are better down to orthorhombic, but become impractical somewhere between three and five unknown parameters. For monoclinic and triclinic, one should try first deductive programs (which are faster but less tolerant of data errors) then semi- exhaustive ones. Remarks: - Information about symmetry, density and molecular weight can be used by the indexing programs if they were written to the GPF. - With exception of triclinic and monoclinic systems indexing programs try to find lattice parameters in specified or higher symmetry crystallographic systems. Different approach to symmetry is represented by the VISSER program, see description of the program for details. - To use VISSER (ITO-12) program you need at least 20(!!!) interplanar d-spacings. - Program prompts for estimated unit cell parameters range or volume if indexing program can use such information. REFINEMENT OF LATTICE PARAMETERS ================================ The POWDER system enables refinement of lattice parameters with APPLE and LATCON programs. The choice of a given program depends on the data set and the problem to be solved. The most important features of both programs, essential at the choice, are the following: LATCON - offers the possibility of refinement of 2_theta scale displacement - can work with standard and non-standard settings in the monoclinic system APPLE - can work without prior knowledge of hkl indices for particular lines, but requires lattice parameters - both during refinement and generation of reflections can apply systematic absences - can apply different weights for particular reflections - calculates a goodness-of-fit value i.e. de Wolff's figure of merit and a FM criterion - for all standard space groups systematic extinction conditions can be read from a file specially prepa- red for the PROSZKI - For nonstandard space groups special condition can be selected from 'extinction' submenu SIMULATION OF POWDER DIFFRACTION PATTERNS ========================================= The LAZY-PULVERIX program was designed to calculate both the X-ray and neutron powder diffraction patterns. Information about scattering factors and anomalous dispersion correction is stored in the program. List of allowed atoms, ions as well as space group symbols and program limits you can be found in the manual, or in HELP at the 'Prepare input file' level. Running LAZY-PULVERIX please note: - Negative space group number indicates a non- standard space group. In this case you will be prompted for: center of symmetry presence, Bravais lattice type and symmetry cards. - Lattice constants, crystal system and the range of the simulated pattern must be entered through the option 'Update Parameters' before you start 'Prepare Input File'. Zero step size disables line-printer graphics representation of the pattern. - Space group symbols, symmetry cards and atomic coordinations are tested by PROSZKI. Symmetry operators are adjusted if necessary. All space group symbols and element symbols must be specified exactly as shown in manual using CAPITAL letters. - Atomic positions are written to the Lazy input file and to the path\name.ATO file. Subsequent run of 'Prepare Input File' performs editing of the existing file. CREATE INPUT FILE FOR RIETVELD ============================== Although programs for Rietveld refinement are not included in the PROSZKI system, user can create input files in format required by two such programs, DBWS 9006PC (Sakthivel & Young) and XRS-82 (Baerlocher). The most important features of both programs are: DBWS 9006PC - multi-phase capability - choice of preferred-orientation function - accepts data from various sources e.g. multiple- detector neutron diffractometers and synchrotron X-ray data XRS-82 - learned-profile function option - sophisticated use of constrains and restraints - possibility of Fourier map calculations and analysis For each program two files *.DAT and *.INP are created. File DBW.DAT or XRS.DAT contains diffraction data in desired format. Because these data are read from input file for NEWPEAK program, before you will try to use this option, you have to create such a file using 'Prepare input data file' option in NEWPEAK menu. Parameters for Rietveld refinement are in file DBW.INP or XRS.INP. You have to edit this file manually to set e.g. number of refinement cycles and select variables for refinement. To include the atomic positions in *.INP file, first you have to create file name.ATO using option 'Prepare input data file' in LAZY menu, otherwise these positions will be missing. You DO NOT have to run LAZY! EXAMPLES ======== Together with the programs, set of example files is distributed. The KMO.DAT file contains diffraction data for potassium trimolybdate, file KMO.PAR is a 'global parameters file' for this compound. The other KMO.* files are examples of input file and can be used immediately to test all programs. You can also try to create and/or modify input files using following parameters: diffraction data format: (8(f7.0,1x)) start, stop, step: 6.00 96.0 0.02 wavelength: Cu Kalpha0 1.54056 Kalpha1 1.54056 Kalpha2 component was removed by diffractometer software space group: Cmcm (63) cell parameters: 13.663 12.050 7.634 90 90 90 estimated error of line position: less than 0.06 deg. atomic positions: Mo1 0.0000 0.1736 0.2500 Mo2 0.1419 0.0000 0.5000 K 0.8102 0.3287 0.7500 Try the following sequence of programs and procedures: Pattern decomposition Typical half-width of observed diffraction lines is about 0.1 deg. Run the NEWPEAK program, check results using 'browse' option and write diffraction lines to GPF. Indexing You can use any indexing program without specifying additional information. Select the best solution and write it to GPF. Check full output file looking for the information about the lattice type and systematic extinctions. Add symmetry to GPF according to selected lattice parameters. Lattice constants refinement Run the APPLE program first. Repeat refinement using different space groups and compare obtained figure of merit. Select the best results and write them with hkl's to GPF. Simulation of diffraction pattern First write correct space group to the GPF. Use atomic positions of Mo and K to calculate diffraction pattern.