1 spurion SPURION- program to calculate spurious processes from ICP-like buffers or data files. To run on Jazz: "Jazz:~ % spur" To view documentation (html, latex, PS, PDF) based on the help files, www.ncnr.nist.gov/resources/spur 2 Version This help file is spurion.hlp and associated documentation generated from this file is ../doc/spurion.tex ../doc/spurion/spurion.html documents the following version of SPURION: **************************************************************************** * spur_020430_$(g77,sgi). V0.4.13 April, 2002. Used on 2002-04-30 11:39:1 * * Written by Jeff Lynn, the dark ages, ca. 1970 * * Graphical version written by Carl Adams, Feb. 2001 * * Modified by Tanya Riseman, Nov, 2001 - March, 2002 * **************************************************************************** Help file spurion.hlp last modified April 30, 2002 by Tanya Riseman. 2 Authors SPURION was written by Jeff Lynn, the dark ages, ca. 1970 (original punch-card version) Carl Adams, 1997 - 2000 (graphics and Bragg Intensities) NIST center for Neutron Research. Now at St. Xavier University. Tanya Riseman, 2001-2002 (debugging, Scan graphics, menus) NIST center for Neutron Research. Ext 8379. Room E010. The LAZY and PULVERIX subroutines was originally written by K. YVON, circa 1977-1989 LABORATOIRE DE CRISTALLOGRAPHIE AUX RAYONS X UNIVERSITY OF GENEVA 24 QUAI ERNEST ANSERMET, CH 1211 GENEVA, SWITZERLAND TEL 022 219355 ADAPTED TO B6700 AT UCSD, HANS F. BRAUN, 7 FEB. 1979 ADAPTED TO CDC 7600 AT BNL, D. E. COX, DEC. 1984 modified 3.87 to prepare CPDF/PROFIL input file by P.ZOLLIKER The HELP subroutine was written by Paul Kienzle, 1997 University of Birmingham Birmingham, UK 2 Disclaimer Although the SPURION program has been tested by its authors no warranty is made as to the accuracy and functioning. Although the LAZY_PULVERIX has been extensively tested by its authors no warranty is made as to the accuracy and functioning. The values of wavelengths, scattering factor constants and the equivalent positions used by the program are part of the output and the user is advised to compare them with the values given in the international tables for crystallography. 2 Help The help file spurion.hlp has a hierarchical tree structure. It is an ASCII file, based on the VMS help facility. The first column should be reserved for a number character (1-9), indicating the depth of the help topic. The name of the help topic follows the depth number. If the character in the first column is "!", the line is ignored as a comment. 1. Type '?' to get a list of help topics at your current level. 2. Type 'thistopic' to get the help for one of the help topics. 3. Type 'thistopic subtopic subsubtopic' to skip down the tree quick, if you remember the path. 4. Type carriage return to go up a help level. Eventually you will return to the calling program SPURION. 5. You may truncate the help topic to the shortest unique set of characters. The help routine needs the environment variable MSRHELP to be set in order to find the help file spurion.hlp, which is probably in the same directory as the source code. At the shell level, depending on the OS (VMS or Unix) and the UNIX shell being used: On VMS, "assign MSRHELP:" On Unix,"setenv MSRHELP " or "export MSRHELP=''" 2 PGPLOT By now you should have two plots "pages" for a default scan: 1. A "lattice" page of reciprocal space in the scattering plane of the spectrometer showing the Q, ki, and kf for the first and last points of the scan. 2. A "scan" page showing the data (if the scan information is from a data file) and all the important spurions. If not, you may have problems with the PGPLOT environment variables. They are set in a script file (/usr/local/bin/spur on Jazz or runspurion_linux) that sets environment variables and then runs the SPURION program: On jazz.ncnr.nist.gov (OS is SGI): (This is the up-to-date public version) #! /bin/sh PGPLOT_DEV='/xserver' PGPLOT_ENVOPT='I' PGPLOT_XW_WIDTH='0.7' export PGPLOT_DEV PGPLOT_ENVOPT PGPLOT_XW_WIDTH PGPLOT_DIR='/usr/user2/cpadams/pgplot/' PGPLOT_FONT=' /usr/user2/cpadams/pgplot/grfont.dat' MSRHELP='/usr/local/lib/spur' export PGPLOT_DIR PGPLOT_FONT MSRHELP /usr/local/bin/spur.bin On a Linux machine such as Tanya Riseman's desktop computer: (This is the current development version) PGPLOT_DEV='/xserver' PGPLOT_ENVOPT='I' PGPLOT_XW_WIDTH='0.7' export PGPLOT_DEV PGPLOT_ENVOPT PGPLOT_XW_WIDTH PGPLOT_DIR='/usr/local/share/pgplot/' PGPLOT_FONT='/usr/local/share/pgplot/grfont.dat' MSRHELP='/home/tanya/for/spuriondir/src_0204/' export PGPLOT_DIR PGPLOT_FONT MSRHELP /home/tanya/for/spuriondir/bin/spur_020430_g77 If you are porting or modifying SPURION, you may get copies of the the PGPLOT library and documentation from the official PGPLOT web site: http://www.astro.caltech.edu/~tjp/pgplot/ 2 Overview By now you should have two plots "pages" for a default scan: 1. A "lattice" page of reciprocal space in the scattering plane of the spectrometer showing the Q, ki, and kf for the first and last points of the scan. 2. A "scan" page showing the higher order spurions energies vs.scan point. Using the command "dm", you may read in scattering information from a q-buffer (.buf) or from the header of a data file (.bt*) to replace the default values that the q-buffer variables are initialized with. Information about the crystal structure and the Bragg peak intensities are inferred from a Lazy-Pulverix input file (.lpi) that you can enter with the command "dm". The default is a square lattice and no information about the Bragg intensities, which is the case when the Lazy-Pulverix information is missing. 2 Lattice_plot In the "lattice" plot, the inner and outer shaded area represents regions of reciprocal space that cannot be accessed for 0.lpi) has been read in, the "lattice" plot will show the structure and indicate which peaks are strong, weak and (optionally) absent. Consult this help file under INPUTFILES command for information about the LPI files. The Sf(Q=0)^2 value is shown and should be equal to the sum of scattering lengths in the unit cell squared. Sfq^2 values and systematic absences are calculated with no Lorentz or thermal factors. Look at the output file .struct if you wish to verify that the generated atoms are in the correct positions in the unit cell. If there are errors when reading the LPI file, you can find diagnostic information in the file .log. ! If the number of unique Sfq^2 values is not too ! large they will be listed here as well (or use the f command to obtain the ! value directly). ! If you encounter problems consult the Lazy-Pulverix (LPI) documentation. ! You can disable the Sfq^2 calculation with the c command or by ! renaming LPI. Truncated scaling is such that any points above or below this ! range will be plotted as the extremum value. A future version should have the ! capability of changing the scaling type and the range. ! In the future there should be a way that an ICP buffer can be read ! directly into SPURION but at present the best way to do this is to open an ! emacs editor in jazz with name mybuffer.buf for example. Then drag your mouse ! over the opened buffer in the ICP window and use the middle-button paste to ! copy it into the emacs window. Left justify the file using your backspace ! key, save it, and then open it with SPURION. If you have already ran this ! buffer to create a .btx file then SPURION can open the .btx file, and the w ! command can create a buffer if you wish. 2 Scan_plot The "scan" plot shows has two basic plots: 1. The experimental intensity vs scan point (if a data file *.bt* was used) with the positions of likely spurions optionally super-imposed. In the case of those higher order spurions which intercept Bragg peaks, the Sf^2 of the Bragg peak is used a relative "intensity" for the spurion. a. Higher order spurions are yellow. b. Elastic spurions are red c. Aluminum spurions from the sample holder are green. d. Incoherent spurions from the monochromator/analyzer are cyan/blue. 2. The energy of the higher order spurions vs. scan point. Higher order spurions which intersect Bragg peaks are indicated in yellow. Elastic spurions (dE = 0) are in red. Both horizontal axes are in terms of the "scan" point, that is, the sequential order of the scan. If the scan is a temperature scan, a temperature axes will appear on the top of the top most plot. Between the two plots, the angle A4 appears, and perhaps the Q values and/or the energies of the scan is either of them vary. 2 MainMenu Summary of SPURION program main menu commands. 3 MENUsnapshot The first line is the executable's name, version number and today's date. The second line is where serious warnings appear, related to inconsistencies in the q-buffer. This warning line also appears in red on both the "lattice" page and the "scan" page. The third line are the input files which have been successfully read in. Each row of the menu has a 2 character option command, a description, a logical indicating if the option is in use, a logical indicating if the option is the one most recently selected and a short string indicating what numerical values are in use related to the option. The two logicals should not be needed by the user. Snap shot of main menu: Command ("q" to quit)? spur_020430_$(g77,sgi). V0.4.13 April, 2002. Used on 2002-04-30 11:39:19 SPUR_DEFAULT.buf SPUR_DEFAULT.lpi SPUR_DEFAULT. dm: Start over with defaults or new files F F S s : Toggle plot higher-order scattering spurions F F i : Toggle plot incoherent scattering spurions T F mon= 0 ana= 0 a : Toggle plot aluminum Ewald spheres F F o : Toggle plot u and v orientation vectors F F nabsent= 0/ 0 l : Toggle label Q, Ki and Kf wavevectors F F g : Toggle overlay grid on lattice plot T F o: 1.000 1.000 mm: Modify Q, E, and other Q-buffer values F F t : Change the rlv, energy spurion tolerances F F 0.050 A^-1 1.00 meV b : BUMP! change maximum A4 F F 115.00 degs f : Sf^2 for an (hkl) reflection F F ( 0, 0, 0)= 0.0 z : Zoom spurion energy plot (0,0,0,0 for auto) F F 0 0 0.0 0.0 r : Rescale plot (reverse xmin and xmax for left) F F Right handed spectm sm: Presentation of structure factors menu F F n : Toggle display of notes next to plot T T pw: Printout/ change graphics device F F bw: Write out Q-buffer to a file F F no bufout yet gw: Generate spectrometer angles-ICP dry run F F no icp yet h : HELP!! T F QQ: to quit F F Command ("QQ" to quit)? h 3 dm_DefaultMenu dm: Start over with defaults or new files The "dm" command allows you to read in new q-buffer information from either a q-buffer (.buf) or from a data file (.bt#), or continue to use the current q-buffer values in memory, or start all over with the program's default values. This is the purpose of the first question in the dialog. Next, you may optionally select lazy-Pulverix information which defaults to none used, the current selected file, a new file with the same base name as the q-buffer or data file (.lpi) or a file with an arbitrary name. The output file names are automatically based on the q-buffer name (.buf) or data file read in (.bt#). If no file is read in, the base name becomes = "SPUR_DEFAULT". 4 Inputfiles Input file names will be of the form .buf (Q buffer from experiment) or .bt# (ICP triple axis data file, #= 0 - 9) .lpi (Lazy Pulverix input file, optional) For more information about the q-buffer file, see the help topic "Inputfiles BUF". For more information about the data file, see the help topic "inputfiles BT". For more information about the LPI file, see the help topic "inputfiles LPI". 4 Outputfiles Output file names will be of the form .struct (Structure information) .spur (Spurion information) .log (Log file, in case program fails) .debug (Temporary debugging info) Optional output file names will be of the form .bufout (Optional output Q buffer from this program) ! .lpiout (Optional output Lazy-Pulverix input file) .icp (Optional ICP dry run, contains spect angles) _bw.ps (Optional B&W postscript file, lattice plot) _cl.ps (Optional color postscript file, lattice plot) _scbw.ps (Optional B&W postscript file, scan plot) _sccl.ps (Optional color postscript file, scan plot) The output file names are automatically based on the q-buffer name (.buf) or data file read in (.bt#). If no file is read in, the base name becomes = "SPUR_DEFAULT". 4 Dialog Dialog: What sort of q-buf info do you want to input? d: default values set by program c: current values in program b: q buffer file .buf 0-9: ICP triple axis data file .bt# h: HELP!! Enter q-buf choice (d,c,b,0-9, h): b What sort of q-buf info do you want to input? d: default values set by program c: current values in program b: q buffer file .buf 0-9: ICP triple axis data file .bt# h: HELP!! Enter q-buf choice (d,c,b,0-9, h): b 3 s_Spurion s : Toggle plot higher-order scattering spurions SPURION will calculate the Q-positions of scattering processes resulting from n*ki-m*kf where n and m range from 1 to 4. These spurions correspond to higher order reflections from the monochromator and analyzer. On the "Lattice" page: The higher order spurions are shown with yellow and red dots. Red dots correspond to elastic scattering (dE = 0) and yellow inelastic on the "Lattice" page. Any spurions that match non-absent Bragg reflections are shown with arrows. Consider the amount of higher-order scattering from monochromator and analyzer, the E of the spurious process, and the relative Bragg peak intensity which contributes the spurious process. The match to the Bragg reflections is governed by the spatial tolerance factor, which you can change with the "t" command. The elastic scattering has dE=0 to within the energy tolerance, which you can also change with the "t" command. On the "Scan" page: Those higher order spurions which match within q-tolerances of a Bragg peak are indicated by yellow symbols on the "Scan" page. The intensity plotted is proportional the the Sf^2 of the Bragg peak on the top plot, if Bragg peak intensities are available. The bottom plot shows the energy of the higher order spurions vs. scan point. All elastic spurions and those inelastic spurions which are within tolerance of Bragg peaks are written to the screen. All spurions are written out to the output file .spur. 3 i_Incoherent i: Toggle plot incoherent scattering spurions ??? Check colors in code! SPURION will calculate the Q-positions of scattering processes ki-|ki|*kf/|kf| and |kf|*ki/|ki|-kf. These are processes where the scattering from the sample is elastic and either the monochromator or analyzer is scattering incoherently but with directions governed by A3 and A4. (Imagine you are using vanadium as a MON or ANA. Not such a smart idea!) Shown with cyan dots or blue dots with arrows if it matches a non-absent Bragg peak. Spurions are written to .spur. The amount of incoherent scattering from MON and ANA and the relative Bragg peak intensity determine the strength of this spurious process. This process can be verified experimentally by changing A1 or A5 with A2 or A6 held constant. In addition, I know that I have performed experiments with Si MON/ANA Xtals and Al powder scattering at the sample contributed to this process. Check this manually by the positions of Al Ewald spheres relative to the cyan dots. The matching of Bragg reflections is governed by the q-tolerance factor, which you can change with the t command. On the "Scan" page: Those incoherent spurions which match within q-tolerances of a Bragg peak are indicated by cyan symbols for the monochromator and blue symbols for the analyzer on the top plot of the "Scan" page. 3 a_Aluminum a : Toggle plot aluminum Ewald spheres SPURION calculates the Al Ewald spheres and compares their radii in reciprocal space to |Q|. The spheres are plotted in green or in red if it matches a Q in the scan. ! The initial execution of this command will plot ! those spheres closest to Q and the next will plot all of the spheres. ! The Al powder line ! positions are also given for an Ei that matches the fixed-E although these ! values may not have much meaning if the scattering is not elastic. Repeated ! use of this command toggles between nearby and all spheres. The matching is controlled by the tolerance factor which may be changed by the t command. Any spurions are saved in .spur. Aluminum is face-centered cubic so only h,k,l all even or all odd reflections will be present and the calculation uses lattice parameter a=4.04096 A. On the "Scan" page: Those aluminum spurions which match within q-tolerances of a scan point Q are indicated by green symbols on the "Scan" page. 3 o_Orientation o : Toggle plot u and v orientation vectors The orientation vectors, whose (hkl) are given in the axes labels, are plotted in magenta. Bug: the arrowhead size is often too large. 3 l_Labelwave l : Toggle label Q, Ki and Kf wavevectors Label the ki, -kf, and Q wave vectors and state the energy transfer. You can either overwrite the plot (blotting out the graphics below) or just overlay the labels. Carl Adams: I have done my best to try and get the labels in sensible places with reasonable sizes but what you see is what you get. Let me know what kind of problems you encounter. 3 g_Grid g : Toggle overlay grid on lattice plot Plots a dashed line grid over the reciprocal lattice plot on the "LATTICE" page, with your choice of u- and v- step size give in rlu's. You have the choice of the grid being Cartesian-style or using the u and v orientation vectors. 3 mm_ModifyMenu mm : Modify Q, E, and other Q-buffer values One of the most powerful SPURION commands. With the "mm" command you can nearly any of the q-buffer parameters in memory, thereby modifying the scan conditions of the q-buffer and see how the spurions are affected. The modifications do not take effect until you exit this sub-menu. Note: any inconsistent modifications should produce warnings and errors, including bright red warnings on the bottom of the plots and at the top of the main menu. There are no guarantees that all possible inconsistencies will be caught. However, most errors should be correctable by reentering this modify menu. Summary of modify sub-menu commands. 4 MENUsnapshot The first line is a description of the sub-menu. The second line are the input files which have been successfully read in. Each row of the menu has a 2 character option command, a description, a logical indicating if the option is in use, a logical indicating if the option is the one most recently selected and a short string indicating what numerical values are in use related to the option. The two logicals should not be needed by the user. Snap shot of the modify sub-menu: Modify buffer parameters. SPUR_DEFAULT.buf SPUR_DEFAULT.lpi SPUR_DEFAULT. lp: Lattice: parameters a, b, c F F 3.14 3.14 3.14 A la: Lattice: angles aa, bb, cc F F 90.0 90.0 90.0 Dg ec: Energy: at center of scan F F 0. meV es: Energy: step F F 1. meV fe: Energy: value of fixed (MON) or (ANA) F F 14.6999998 meV mo: Energy: toggle MON or ANA with E-fixed F F (ANA) is fixed dm: Energy: lattice spacing of MON F F 3.35400009 A da: Energy: lattice spacing of ANA F F 3.35400009 A qc: Space: qh qk ql at center of scan F F (1.10,1.10,0.00) qs: Space: qh qk ql step F F (0.00,0.00,0.00) u : Orient: u=(hkl) of scattering plane F F ( 1, 1, 0) v : Orient: v=(hkl)' of scattering plane F F ( 0, 0, 1) t0: Temp/H: start temperature T0 F F 300. K ts: Temp/H: temperature step inc-T F F 0. K np: Time: number of scanned (E,Q,T) points F F 5 h : HELP!! F F q : to quit F F Command ("q" to quit)? 4 lp_latticeparms lp: Lattice: parameters a, b, c 4 la_latticeangles la: Lattice: angles aa, bb, cc 4 ec_energycenter ec: Energy: at center of scan 4 es_energystep es: Energy: step 4 fe_fixedenergy fe: Energy: value of fixed (MON) or (ANA) 4 mo_MonOrAnaFixed mo: Energy: toggle MON or ANA with E-fixed Either the monitor or the analyzer has fixed energy. This command toggles which one is fixed. 4 dm_lattcSpacingMON dm: Energy: lattice spacing of MON 4 da_lattcSpacingANA da: Energy: lattice spacing of ANA 4 qc_qcenter qc: Space: qh qk ql at center of scan 4 qs_qstep qs: Space: qh qk ql step 4 u_uScatteringPlane u : Orient: u=(hkl) of scattering plane 4 v_vScatteringPlane v : Orient: v=(hkl)' of scattering plane 4 t0_tempStart t0: Temp/H: start temperature T0 4 ts_tempStep ts: Temp/H: temperature step inc-T 4 np_pntsInScan np: Time: number of scanned (E,Q,T) points 4 h_Help h : HELP!! 4 q_Quit q : to quit sub-menu 3 t_Tolerance t : change the tolerance for spurions Change the q and energy tolerance factors used in the "s" higher order spurions, "i" incoherent spurions, and "a" aluminum spurion calculations. ! If a spurion comes within q_tol of an allowed Bragg reflection the ! user is informed and the spurion is recorded. The default value is 0.05 AA^-1 The user should keep in mind what the instrumental resolution really is, and modify the values accordingly. Ideally, eventually this program will automatically calculate reasonable resolutions. Currently the program uses either 0.05 AA_1 or the q step size for the q tolerance and either 1 meV or the energy step size for the energy tolerance. Dialog: Current rlv tolerance 0.050 AA^-1. Enter new value. 0.05 Current energy tolerance 1.000 meV?. Enter new value. 1. 3 b_bump b : BUMP! change maximum A4 Change the maximum for the spectrometer's angle A4. Defaults to 115 degrees. 3 f_Flection f : Sfq^2 for an (hkl) reflection in the scattering plane Given that the intensity scaling of the reflections is quite rough use the f command to give Sfq^2 directly. No Lorentz or thermal factors are included. At present only those Sfq^2 which are in scattering plane can be calculated. The value is printed to screen and also appears in the "notations" section of the "lattice" plot and on the main menu. If the requested h,k,l is accidentally not in the scattering plane, a list of the possible q values is printed out. While SPURION is in the testing phase pay close attention to the atomic positions and scattering lengths given in .struct when comparing this value of Sfq^2 to those given by other programs or procedures. Inform Tanya Riseman or Carl Adams of discrepancies. ! !4 bug ! !(BUGGY!!) Range too limited. Many arrays getting stomped on? ! main: post cmd_spurion: nspurtot= 0 !h k l of desired reflection? 1 0 1 ! Possible reflections: !Sf^2( -1, -1, 0)= absent !Sf^2( 0, 0, -1)= absent !Sf^2( 0, 0, 0)= absent !Sf^2( 0, 0, 1)= absent !Sf^2( 1, 1, 0)= absent 3 z_ZoomScanPlots z : Zoom spurion energy plot (0,0,0,0 for auto) On the "lattice" page, select horizontal range for scan points (min=0, max=# of scanpoints) and the vertical range for the higher order spurions' energies. Enter xmin_npts, xmax_npts, ymin_e, ymax_e separated by spaces or commas. Use zeros to have the program use the full range by default. 3 r_rescaleLattcPlot r : rescale plot (reverse xmin and xmax for left) At the prompt enter xmin,xmax,ymin,ymax separated by spaces or commas. You may switch to a left-handed coordinate system and spectrometer by making xmin larger than xmax. 3 sm_StrucFactorMenu sm: Presentation of structure factors sub-menu Modify the presentation of the reciprocal lattice plot on the "LATTICE" page. Note: If no lazy-Pulverix input file (*.lpi) is being used, this sub-menu is of no use. Summary of structure factors sub-menu commands. 4 MENUsnapshot The first line is a description of the sub-menu. The second line are the input files which have been successfully read in. Each row of the menu has a 2 character option command, a description, a logical indicating if the option is true/false, a logical indicating if the option is the one most recently selected and a short string indicating what numerical values are in use related to the option. The two logicals should not be needed by the user. The first logical is used to remember the presentation options. Snap shot of the structure factors sub-menu: Modify display of Bragg intensities ceb.buf ceb.lpi ceb. s : Toggle display Bragg intensities T F Sf^2 not shown n : Toggle rep. intensities by circles/numbers F F circles c : Toggle rep. intensities by color/grey scale T T color z : Rel. circle size F F 1. u : Toggle circle size uniform or vary with Sf^2 F F uniform l : Toggle show/hide sorting labels F F ABC..cba labels a : Toggle display/hide systematic absences F F hide absences g : Toggle bunching sort by S^2= base^n or +- tol F F sort by +- tol t : Select sorting tolerance (+- tol) F F 0.007 = tol b : Select sorting base: (base^(n-1) < S^2 < base^n F F h : HELP!! F F q : to quit F F 4 s_DisplaySf s : Toggle display Bragg intensities Can stop displaying the Bragg peak intensities Sf^2 as if there was no lazy- Pulverix input file. 4 n_NumbersOrCircles n : Toggle rep. intensities by circles/numbers Label the Bragg peak intensities Sf^2 on the Lattice plot by either numbers or by circles. 4 c_colorOrGrey c : Toggle rep. intensities by color/grey scale Represent the relative intensity by either a grey scale or a blue-green color scale. Affects both circles and numbers. 4 z_circleSize z : Rel. circle size A scaling factor for the size of the circles plotted. 1 is the default size. Greater than 1 makes larger circles. Only affects circles, not numbers. 4 u_uniformCircles u : Toggle circle size uniform or vary with Sf^2 Circles can be draw with a uniform size or with their radii proportional to the Bragg peak's intensity. Only affects circles, not numbers. 4 l_sortingLabels l : Toggle show/hide sorting labels The intensity values are sorted. They are optionally noted in a key on the right hand size of the page if the main menu item "n" notations is selected. The individual intensities are optionally labeled on the plot by a code 'ABC...cba" with the largest intensity labeled by "A" and the smallest by "a". This command toggles whether the labels are shown on the plot. 4 a_absences a : Toggle display/hide systematic absences Systematic absences are optionally marked off by green crosses. 4 g_logSorting g : Toggle bunching sort by S^2= base^n or +- tol Different Bragg peaks will have the same intensities SF^2, such as (1,0,1) and (1,0,-1). However, Lazy-Pulverix does not return exactly the same values. We want to label intensities which are nearly the same by the same label. Therefore, we sort the intensities, and those which are within tolerance (+- tol) of each other are deemed to be identical. This is called the "linear" sorting scheme. This command toggles between the default sorting scheme described above and one based on a log scale, base b. The log-sorting scheme bunches all intensities which are between base^n and base^(n+1) and gives those intensities a common label. This is useful when there are many different intensities and one wants to quickly identify those which are large or small quickly. This is called the logarithmic sorting scheme. 4 t_sortingTol t : Select sorting tolerance (+- tol) This is only used when using a normal "linear" sorting scheme has been selected. See the help option g_logSorting (for command "g"). ! ! ??? Fill in formula 4 b_sortingBase b : Select sorting base: (base^(n-1) < S^2 < base^n This is only used when using a "logarithmic" sorting scheme has been selected. See the help option g_logSorting (for command "g"). 4 h_help h : HELP!! 4 q_quit q : to quit sub-menu 3 n_Notations n : Toggle display of notations next to plot Notations are optionally placed on the "Lattice" and (eventually) the "Scan" pages. Notations include 1. q-buffer information, shown on the "Lattice" page. 2. Which important main menu items have been selected, shown on the "Lattice" page. 3. The labels and intensity circles (grey or colored) for the Bragg peak intensities, shown on the "Lattice" page. What is shown will depend on selections made in the "sm" sub-menu (presentation of structure factors). ! 4. The Lazy-Pulverix input file, shown on the "Scan" page. 3 pw_Printout pw: printout/change graphics device This is the printout command. You can change the graphics device from the default X-server to either black and white postscript or color postscript for either the "lattice" page or the "scan" page. The generated PS file have a name based on the q-buffer or data file's name. Unfortunately, PGPLOT can only process one PS file at a time, so you must ask for both the "lattice" and the "scan" pages separately. Currently, you can run other commands after this "pw" command, and they will appear in the PS file. Consequently you MUST close the PS file by either selecting another "pw" device number (like 0=XSERVE) or by quiting the program. Otherwise, the PS file will not be properly ended. If using gray scale, remember that for the white on black X-window, white is most intense but for black on white postscript black is most intense. Colors will come out as black on back and white printers. dialog: Device # =0 for XSERVE (screen, no printout) =1 for XWIN (screen, no printout) =2 for B&W postscript file: _bw.ps = lattice plot =3 for color postscript file: _cl.ps = lattice plot =4 for B&W postscript file: _scbw.ps = scan plot =5 for color postscript file: _sccl.ps = scan plot Apologies: PGPLOT can only process one PS "window" at a time. To properly close a PS file, a new device must be selected or quit program. Enter device number (0-5) !3 obsolete_Circlesize ! ! c : change circ size (- to toggle grayscale, ! 0 tog struc calc) ! ! By default SPURION gives the relative intensity of the Bragg ! reflections using a grayscale with the indicated linear/log scaling and ! ranges. White is the most intense and black the least intense on the X-win ! display but the opposite in the ps file. NO Lorentz or thermal factors are ! included! Giving a negative value for the circle size will scale the circle ! diameter with the intensity. A circle size of zero disables the calculation ! of Sfq^2 and systematic absences. See the full help for details of this ! calculation. !3 obsolete_Units ! ! u : toggle rlu - AA^-1 units ! ! Default units are reciprocal lattice units given by the lengths of the ! u and v orientation vectors. However notice that the dimensions on the plot ! are really inverse Angstroms so Ewald spheres appear as circles and the ! reciprocal lattice symmetry is preserved. The u command toggles between rlu ! and AA^-1 units given on the axes depending on whether you are trying to ! identify the reflections or trying to determine the lengths of wavevectors. 3 bw_qbufferWrite bw: Write out Q-buffer to a file Outputs the q-buffer variables to .bufout, in same format as input q-buffers *.buf. 3 gw_Genangles gw: generate spectrometer angles Another powerful calculational command that reproduces the dry run of ICP. Outputs to .icp. Tanya: I can change the formating of .icp to assist it s usage as input to another program, if desired. Carl Adams: While SPURION is still in the testing phase it probably makes sense to confirm that it agrees with ICP (at least within 0.005 degrees). If there are discrepancies contact Tanya Riseman or Carl Adams ASAP and we will fix the problem. DO NOT BELIEVE the output of SPURION if it does not agree with ICP!! I have included a few things in SPURION to check the validity of the buffer with warnings when appropriate but it may miss things that ICP does not. Matt Woodward: The numbers look OK. 3 h_Help h : HELP!! Give either a general help/description of SPURION or give details of SPURION commands. Reproduced in the file spurion.hlp Details of the behavior of the help() routine: The help file spurion.hlp has a hierarchical tree structure. It is an ASCII file, based on the VMS help facility. The first column should be reserved for a number character (1-9), indicating the depth of the help topic. Type '?' to get a list of help topics at your current level. Type 'thistopic' to get the help for a one of the help topics. Type 'thistopic subtopic subsubtopic' to skip down the tree quick, if you remember the path. Type carriage return to go up a help level. Eventually you will return to the calling program SPURION. You may truncate the help topic to the shortest unique set of characters. ! If it is not unique, all commands which start with it, ! will be shown. 3 q_Quit q : to quit ! Note at this time SPURION cannot update the changes you may have made ! to the buffer using the m command. Just hitting or an unused command ! causes you to close the graphics device, output files, and quit SPURION. This ! may seem a bit overzealous but SPURION starts and runs so quickly I find it ! practical Also remember that the output files are overwritten every time so ! rename them if you have result you would like to keep. Remember that the output files are may be overwritten if the same base file name is reused, so rename them if you have result you would like to keep them. 2 Background This help section discusses background information. 3 Spectrometer 3 Bragg 2 Inputfiles Input file names will be of the form .buf (Q buffer from experiment) .lpi (Lazy Pulverix input file) ! The files required by SPURION are an input "buffer" file ! (sample.buf or by default qbuffer.buf), with the same format as the header ! of a blah-blah format data file and a Lazy-Pulverix file (LPI) 3 BT .bt# (ICP triple axis data file, #=0-9) Works for BT2 presently. *** Expand ************** ???? 4 example The header portion of a data file (pross007.bt2): 'PROSS007.BT2' '12-AUG-2001 12:43' 'Q' 1175000. 6 'NEUT' 105 'RAW' Filename Date Scan Mon Prf Base #pts Type PrOsS PrOs4Sb12 =20 60 20 40 2 0 0 0 1 0 0 0.000 0 0 1 Collimation Mosaic Xstal Orientation 6.283 6.283 6.283 90.000 90.000 90.000 Lattice Parameters in real space 11.000 -0.250 14.700 3.354 3.354 6.00000 0.00000 E center Delta E EA fixed M-dsp A-dsp Tmp strt Tmp inc 1.800 0.000 0.000 0.0000 0.0000 0.0000 0.0000 Q (hkl scan center) Delta Q (hkl) Hfield Q(x) Q(y) Q(z) E T-act min Counts 1.8000 0.0000 0.0000 24.0000 8.00510 5.95 21 1.8000 0.0000 0.0000 23.7500 8.02280 5.97 26 ... 1.8000 0.0000 0.0000 -2.0000 7.90630 6.36 12 3 BUF This section describes the required format of a input q-buffer file. *** Expand ************** ??? The program is now better at being able to read in .buf files which have had spaces removed or added in the course of hand editing. (Hopefully no editing will be necessary after the file created using cut-and paste between windows). The overall ICP format is required, particularly the colons ":" and equal signs "=" after labels. 4 example Qbuffer No: 3 Comment: EuMnP Xtal Lattice: a: 4.1396 b: 4.1396 c: 4.1396 aa: 90.000 bb: 90.000 cc:90.000 Energy: EC: 5.0000 ES: 1.000 FE: 14.700 (ANA) dM= 3.3542 dA= 3.3542 Space: HC: 1.0000 KC: 1.0000 LC: 0.0000 HS: 0.0000 KS: 0.0000 LS: 0.0000 Orient: (h k l): 1, 1, 0 Angl: 0.000 (h k l)': 0, 0, 1 Temp/H: T0:1.2000 Inc-T.00000 Wait: 0 Err:.50 Hld0: 0 Hld: 0 Field Time: Monit: 110000 Prefac: 1 M-typ:TIME #pts: 11 AMON POLA FKEY 3 LPI This section describes the required format of a lazy PULVERIX input file LPI. The original lazy-PULVERIX has rather strict fixed format requirements for the LPI. We have relaxed them, so that the output from the WWW application Lazy can be read, plus additional relaxations so that hand editing is not so dangerous. The input of the LPI file is now case insensitive. Where there is free formating reads allowed, parameters may be separated by spaces, commas or tabs. Blank parameters are indicated by a comma, e.g. ' ,'. Only the first 2 characters of each command are inspected, but the read routines expect all the characters to be present, followed by a space, then followed by the command's parameters. Adapted from http://barns.ill.fr/dif/icsd/lazy_reference.html 4 Title Sample title (Required) The title is the remainder of the line after the first 6 characters 'TITLE ' Include for example the chemical formula and diffraction conditions. This title will be used to label the plot. 4 COndit Experimental conditions (Optional) The CONDIT line is NOT essential. example: CONDIT CUA1 1.59460 3 80.0 N 2GN N FORMAT(3A2,4X, A4, F8, F3, F5, 1X,A1, I2, A2, 1X,A1) 'CONDIT', SYMWL, WL, TL, TH, NORM, IMAGE, SYMLP, IANO 5 CONDIT Columns 1- 6 CONDIT PUNCH CARD LABEL *CONDIT* 5 SYMWL Columns 11-14 SYMWL SYMBOL FOR WAVELENGTH ADJUST TO THE LEFT OF THE FIELD. EXAMPLE CUA1 = COPPER K ALPHA1 RADIATION. THE LIST OF ALLOWED SYMBOLS IS GIVEN AT THE END OF THIS DESCRIPTION. WAVELENGTHS FOR WHICH NO SYMBOL EXIST MUST BE GIVEN EXPLICITLY IN COLS 15-20. IF LEFT BLANK CU K ALPHA RADIATION IS ASSUMED. NEUTRON DIFFRACTION LEAVE COLUMNS 11-14 BLANK AND GIVE VALUE OF WAVELENGTH IN COLUMNS 15-20. Example: CUA1 is the characteristic wavelength symbol Cu-Ka1. 5 WL Columns 15-20 WL WAVELENGTH IN ANGSTROM NEED NOT BE GIVEN IF SYMWL IS SPECIFIED Example: 1.5946 is the wavelength value - only needed if CUA1 blank. If no value is given, CUA1 is assumed. W A V E L E N G T H S (VARIABLE *SYMWL* ON CONDIT CARD) THE LINES CONTAIN THE SYMBOLS FOR K ALPHA1, K ALPHA2 AND THE WEIGHTED AVERAGE OF THE K ALPHA RADIATION FOR CHROMIUM, IRON, COPPER, MOLYBDENUM AND SILVER. THE WAVELENGTHS IN ANGSTROM ARE GIVEN IN PARENTHESES CRA1 (2.28970) CRA2 (2.29361) CR (2.2909) FEA1 (1.93604) FEA2 (1.93998) FE (1.9373) CUA1 (1.54056) CUA2 (1.54439) CU (1.5418) MOA1 (0.70930) MOA2 (0.71359) MO (0.7107) AGA1 (0.55941) AGA2 (0.56380) AG (0.5608) 5 TL Columns 21-25 TL LOWER THETA -LIMIT OF CALCULATION Example: 3 is the minimum theta angle. If blank, 0.0 is assumed. 5 TH Columns 26-30 TH UPPER THETA -LIMIT OF CALCULATION IF LEFT BLANK TL=0 AND TH=89 DEGREES. FOR GUINIER CAMERAS TH IS 45 DEGREES Example: 80.0 is the maximum theta angle. If blank, 89.0 is assumed. (or 45.0 for Guinier cameras). 5 NORM Columns 32 NORM TABULAR REPRESENTATION OF THE POWDER PATTERN. BLANK INTENSITIES NORMALIZED TO 1000 A INTENSITIES NOT NORMALIZED N NO TABULAR REPRESENTATION OF THE POWDER PATTERN Example: N means no tabular listing of the pattern, blank means normalize strongest line to 10000, and A means no normalization. 5 IMAGE Columns 33-34 IMAGE GRAPHIC REPRESENTATION OF THE POWDER PATTERN. BLANK NO GRAPHIC OUTPUT INTEGER GRAPHIC OUTPUT OF INTENSITIES IN STEPS OF 1/(2*INTEGER) OF THETA Example: 2 means listing in steps of 1/(2*2) degrees theta, while blank means no listing. 5 SYMLP Columns 35-36 SYMLP EXPERIMENTAL TECHNIQUE DS DEBYE-SCHERRER BLANK POWDER-DIFFRACTOMETER & MONOCHROMATOR NE NEUTRON DIFFRACTION GN GUINIER-DE WOLFF CAMERA GH GUINIER-HAEGG CAMERA THE FORMULAE FOR THE LORENTZ - POLARISATION FACTORS ARE GIVEN AT THE END OF THIS DESCRIPTION. 1 NO LP-FACTOR CORRECTION APPLIED Example: GN represents the diffraction technique, where: BLANK means Debye-Scherrer or diffractometer data. NE means NEutron powder diffractometer. GN means GuiNier camera. GH means Guinier-Hagg camera. 1 means no Lorentz polarization correction. (Lorentz polarization factors given later). 5 IANO Columns 38 IANO CORRECTION FOR ANOMALOUS DISPERSION (X RAYS ONLY) BLANK CORRECTION IS MADE N NO CORRECTION IS MADE. Example: N means no correction for anomalous dispersion. blank means dispersion correction. For ionized atoms (not recommended) no dispersion correction will be made, and no correction will be made for neutron, synchrotron (yet) nor other diffractometer data. 5 notes It is recommended to compute all structures with neutral atoms. If form factors for ionized atoms are used the programme will not make dispersion corrections. No dispersion correction will be made for neutron diffraction. If no CONDIT card is given, copper radiation and Debye-Scherrer technique is assumed, correction for anomalous dispersion will be made and a complete powder pattern will be calculated. 5 lorentz Lorentz polarization factors (SYMLP) Debye-Scherrer technique L = 1.0/(sin(theta)**2*cos(theta)) P = (1.0+ cos(2*theta)**2)/2. Guinier technique L = 1.0/(sin(theta)**2*cos(theta)*cos(2*theta-beta)) P = (1.0+ cos(2*theta)**2*cos(2*alpha)**2)/(1+cos(2*alpha)**2) alpha = diffraction angle of monochromator. beta = angle between the normal to the specimen and the direction of the incident beam. Note: alpha and beta depend on the geometry of the Guinier camera and the d-spacing of the reflecting planes of the monochromator crystal. For Guinier cameras other than Guinier-de Wolff or Guinier-Hagg, or for monochromator crystals other than quartz, changes in the programme have to be made. 4 CEll Lattice constants (Required) example: CELL 4.5678, 5.6789 16.7890, 90 122.3, 90 Free format (separated by spaces, tabs or commas) 'CELL', A, B*, C*, Alpha*, Beta*, Gamma* Note: Items (*) which may be left blank, must use a comma to indicated that the item is blank unless they are at the end of the line. See help items below for the situations in which items may be left out. A, B, and C are lattice parameters in angstroms. Alpha, Beta, Gamma are the lattice angles in degrees. 5 Cubic Omit B,C,ALPHA,BETA,GAMMA 5 Hexagonal Omit B,ALPHA,BETA, and set GAMMA=120. 5 Rhombohedra Rhombohedral cells should be calculated on Hexagonal axes. If Rhombohedral axes are required, the structure must be described in the Triclinic system. 5 Tetragonal Omit B,ALPHA,BETA,GAMMA 5 Orthorhombic Omit ALPHA,BETA,GAMMA 5 Monoclinic Omit ALPHA,GAMMA 4 SPcgr Space group (Required unless LAtice and SYmtry are used.) Free format example: SPCGRP P M N A example: SPCGRP P 21/C The list of permitted symbols is given below, sorted by the lattice symmetry. No other symbols are permitted. Do NOT include the * preceding some of the symbols. The * indicates centrosymmetric space groups which have been described with several settings. The programme generates only the setting with the centre of symmetry at the origin of the unit cell. Note that instead of using the SPCGRP symbol, you may use the explicit space group operators. For non-standard settings, LATICE and SYMTRY lines must be used. 5 rules Hermann Mauguin symbol for the space group adjust to the left of the field. Rules for coding: * Symmetry operators are separated by a slash or by a blank. * The bar operation is coded as minus *-*. * Screw axes are given by two integers that are not separated by a blank. EXAMPLES: P B C N P 21/C P -3 5 warning For all other symbols the programme may generate wrong equipoints without error messages. Please check the listing after running the programme. For non standard space group settings SYMTRY- AND LATICE- cards must be used. 5 notes For centro-symmetric groups, the programme assumes the setting with the centre at the origin. For R-space groups, the hexagonal setting is assumed R-space groups with rhombohedral axes must be simulated using LATICE and SYMTRY lines corresponding to a triclinic description. Do NOT include the * preceding some of the symbols. The * indicates centrosymmetric space groups which have been described with several settings. The programme generates only the setting with the centre of symmetry at the origin of the unit cell. Note that instead of using the SPCGRP symbol, you may use the explicit space group operators (SYMTRY command). 5 TRICLINIC P 1 P -1 5 MONOCLINIC P 2 P 21 C 2 P M P C C M C C P 2/M P 21/M C 2/M P 2/C P 21/C C 2/C The equivalent positions generated from these symbols correspond to the monoclinic setting with the b-axis unique (alpha=gamma=90) 5 ORTHORHOMBIC P 2 2 2 P 2 2 21 P 21 21 2 P 21 21 21 C 2 2 21 C 2 2 2 F 2 2 2 I 2 2 2 I 21 21 21 P M M 2 P M C 21 P C C 2 P M A 2 P C A 21 P N C 2 P M N 21 P B A 2 P N A 21 P N N 2 C M M 2 C M C 21 C C C 2 A M M 2 A B M 2 A M A 2 A B A 2 F M M 2 F D D 2 I M M 2 I B A 2 I M A 2 P M M M *P N N N P C C M *P B A N P M M A P N N A P M N A P C C A P B A M P C C N P B C M P N N M *P M M N P B C N P B C A P N M A C M C M C M C A C M M M C C C M C M M A *C C C A F M M M *F D D D I M M M I B A M I B C A I M M A Do NOT include the * preceding some of the symbols. 5 TETRAGONAL P 4 P 41 P 42 P 43 I 4 I 41 P -4 I -4 P 4/M P 42/M *P 4/N *P 42/N I 4/M *I 41/A P 4 2 2 P 4 21 2 P 41 2 2 P 41 21 2 P 42 2 2 P 42 21 2 P 43 2 2 P 43 21 2 I 4 2 2 I 41 2 2 P 4 M M P 4 B M P 42 C M P 42 N M P 4 C C P 4 N C P 42 M C P 42 B C I 4 M M I 4 C M I 41 M D I 41 C D P -4 2 M P -4 2 C P -4 21 M P -4 21 C I -4 M 2 P -4 C 2 P -4 B 2 P -4 N 2 P -4 M 2 I -4 C 2 P -4 2 M I -4 2 D P 4/M M M P 4/M C C *P 4/N B M *P 4/N N C P 4/M B M P 4/M N C *P 4/N M M *P 4/N C C P 42/M M C P 42/M C M *P 42/N B C *P 42/N N M P 42/M B C P 42/M N M *P 42/N M C *P 42/N C M I 4/M M M I 4/M C M *I 41/A M D *I 41/A C D Do NOT include the * preceding some of the symbols. 5 TRIGONAL P 3 P 31 P 32 R 3 P -3 R -3 P 3 1 2 P 3 2 1 P 31 1 2 P 31 2 1 P 32 1 2 P 32 2 1 R 3 2 P 3 M 1 P 3 1 M P 3 C 1 P 3 1 C R 3 M R 3 C P -3 1 M P -3 1 C P -3 M 1 P -3 C 1 R -3 M R -3 C Note: All R-space groups refer to the hexagonal setting. 5 RHOMBOHEDRAL Rhombohedral cells should be calculated on Hexagonal axes. If Rhombohedral axes are required, the structure must be described in the Triclinic system. 5 HEXAGONAL P 6 P 61 P 65 P 62 P 64 P 63 P -6 P 6/M P 63/M P 6 2 2 P 61 2 2 P 65 2 2 P 62 2 2 P 64 2 2 P 63 2 2 P 6 M M P 6 C C P 63 C M P 63 M C P -6 M 2 P -6 C 2 P -6 2 M P -6 2 C P 6/M M M P 6/M C C P 63/M C M P 63/M M C 5 CUBIC P 2 3 F 2 3 I 2 3 P 21 3 I 21 3 P M 3 *P N 3 F M 3 *F D 3 I M 3 P A 3 I A 3 P 4 3 2 P 42 3 2 F 4 3 2 F 41 3 2 I 4 3 2 P 43 3 2 P 41 3 2 I 41 3 2 P -4 3 M F -4 3 M I -4 3 M P -4 3 N F -4 3 C I -4 3 D P M 3 M *P N 3 N P M 3 N *P N 3 M F M 3 M F M 3 C *F D 3 M *F D 3 C I M 3 M I A 3 D Do NOT include the * preceding some of the symbols. 4 ATom Atom identifier and coordinates (Required) Free format 'ATOM ' ELEMT, IDE*, X, Y, Z, BTEMP*, FOCCU* Note: Items (*) which may be left blank, must use a comma to indicated that the item is blank unless they are at the end of the line. See help items below for the situations in which items may be left out. example: ATOM CA 3 0.3333 0.6667-0.512 0.5 1.0 example: ATOM CA 3 1/3,2/3,0.512 1/2 1 example: ATOM CA2+ 4 1/3,2/3,0.512 1/2 1 5 ELEMT Symbol of element and ionisation state. Only listed symbols listed an be given. Examples: CA symbol for calcium(neutral) CA2+ symbol for calcium(ionized) Do NOT include the asterisk preceding an atom symbol. This asterisk indicates atom identifiers that are allowed for both X-ray and neutron diffraction. All other symbols are allowed for X-ray diffraction only. Atom symbols followed by a point have a special meaning (see below). In case of X-ray diffraction, use neutral atoms unless you know exactly what you want to calculate. 6 Symbols *AC *C *DY *HE LU3+ NP4+ *PU SI. TM3+ AC3+ C. DY3+ *HF *MG NP6+ PU3+ SI4+ *U *AG *CA .... HF4+ MG2+ .... PU4+ SM U3+ AG1+ CA2+ *ER *HG *MN *O PU6+ SM3+ U4+ AG2+ *CD ER3+ HG1+ MN2+ O1- .... *SN U6+ *AL CD2+ *EU HG2+ MN3+ O2-. RA SN2+ .... AL3+ *CE EU2+ *HO MN4+ *OS RA2+ SN4+ *V AM CE3+ EU3+ HO3+ *MO OS4+ *RB *SR V2+ *AR CE4+ .... .... MO3+ .... RB1+ SR2+ V3+ *AS CF *F I MO5+ *P *RE .... V5+ AT *CL F1- I1- MO6+ PA *RH *TA .... *AU CL1- *FE *IN .... *PB RH3+ TA5+ *W AU1+ CM FE2+ IN3+ *N PB2+ RH4+ *TB W6+ AU3+ *CO FE3+ *IR *NA PB4+ RN TB3+ .... .... CO2+ FR IR3+ NA1+ *PD *RU *TC *XE *B CO3+ .... IR4+ *NB PD2+ RU3+ *TE .... *BA *CR *GA .... NB3+ PD4+ RU4+ *TH *Y BA2+ CR2+ GA3+ *K NB5+ PM .... TH4+ Y3+ *BE CR3+ *GD K1+ *ND PM3+ *S *TI *YB BE2+ *CS GD3+ KR ND3+ PO *SB TI2+ YB2+ *BI CS1+ *GE .... *NE *PR SB3+ TI3+ YB3+ BI3+ *CU GE4+ *LA *NI PR3+ SB5+ TI4+ .... BI5+ CU1+ .... LA3+ NI2+ PR4+ *SC *TL *ZN BK CU2+ *H *LI NI3+ *PT SC3+ TL1+ *ZN2+ *BR .... H. LI1+ *NP PT2+ *SE TL3+ *ZR BR1- D. H1- *LU NP3+ PT4+ *SI *TM ZR4+ 6 Special Symbols with special meaning (indicated by a point '.'): H. hydrogen HF scattering factor C. carbon HF scattering factor SI. silicon HF scattering factor D. deuterium HF scattering factor O2-. taken from Acta Cryst. Vol.19, P.486(1965) 5 IDE Sequence number or atom label. (May be left blank.) 5 XYZ X, Y, or Z coordinate. Only coordinates between -1.and+1. are allowed. Fractions may be given as integers separated by a slash example: ATOM H 1/3 2/3 0.512 is equivalent to ATOM H .33333 .666667 0.512 5 BTEMP Debye-Waller factor If left blank no temperature factor correction will be made. 5 FOCCOU Occupation factor This factor is usually 1 (=full occupancy of the site) but it may be smaller in disordered structures. If left blank full occupancy will be assumed. 4 LAtice Optional FORMAT(3A2,2X,A1,2X,A1) 'LATICE ' ISYMCE, SYMBR example: LATICE A P ISYMCE CENTER OF SYMMETRY AT ORIGIN C YES (CENTRIC) A NO (ACENTRIC) SYMBR BRAVAIS LATTICE INDICATOR P PRIMITIVE A A CENTERED I BODY CENTERED B B CENTERED R RHOMBOHEDRAL C C CENTERED F FACE CENTERED BLANK PRIMITIVE * For Trigonal P-space groups, use P with the hexagonal setting. * For R-space groups, use R with an hexagonal cell (the programme assumes the standard obverse setting) or use P with a rhombohedral cell and give a, b, c and all angles on the cell card. * If no SPCGRP nor LATICE line is given, a primitive acentric cell is assumed. 4 SYmtry Optional (but requited if SYMTRY lines are given). free format example: SYMTRY X, 1/2-Y, 1/2+Z Equivalent positions line is in free format with x,y,z separated by commas. For centrosymmetric cells (ISYMCE=C in LATICE), give only one of the two centro-symmetrically related positions. For I-, R-, F-, A-, B- and C- cells (SYMBR=I,R,F,A,B OR C in LATICE), give only one of the positions related by centering. If no SYMTRY command is given, X,Y,Z is automatically assumed, however if SYMTRY commands are given then the X,Y,Z position must be included. You may use the Bilbao Space Group Generator to obtain these space group generators (see http://www.cryst.ehu.es/cryst/get_gen.html). 4 ENd Required END (This must be the last line for each structure set). 4 FInish Required (but a bit redundant, since only do 1 material.) Note: This command must come after the last end command. It initiates execution of the programme. 4 example TITLE CeB6 CONDIT 1.55 NE CELL 4.1396 SPCGRP p m -3 m atom CE 1 0 0 0 0 ATOM B, , 0.1993, 1/2, 1/2, , 0.94 END FINISH 2 Outputfiles Output file names will be of the form .struct (Structure information, based on Lazy-Pulverix) .spur (Spurion information) .log (Log file, in case program fails) .debug (Temporary debugging info) Optional output file names will be of the form .bufout (Optional output Q buffer from this program) ! .lpiout (Optional output Lazy-Pulverix input file) .icp (Optional ICP dry run, contains spect angles) _bw.ps (Optional B&W postscript file, lattice plot) _cl.ps (Optional color postscript file, lattice plot) _scbw.ps (Optional B&W postscript file, scan plot) _sccl.ps (Optional color postscript file, scan plot) ! This section describes the output files created by SPURION ! and hopefully describes what good thay are! ! !3 spurion_out ! ! spurion.out (always created) ! !3 structinfo_out ! ! structinfo.out (always created) ! !3 outbuffer ! ! sample.obuf optionally created by Write command, with your choice of ! file name. ! !3 fort_2 ! ! fort.2 is created by mistake, since no open statement. ! (needs correcting.) ! !3 core ! ! Program needs more debugging. ! !3 temporary ! ! There are some temporary files that are created and automatically deleted. ! ! 2 Warnings Terse warnings appear on the second line of the main menu and also appear in red on both the "lattice" page and the "scan" page. Currently there are 4 separate kinds of warnings, nearly all of which are due to logical inconsistencies in the values in the q-buffer in memory, either as it was read in originally or subsequently modified. 1. The scattering q is out of the scattering plane or the scattering triangle can not be closed or there is some problem with with calculating k_f. 2. There is no item in the q-buffer which is stepped in the scan. Normally, either q, the energy or the temperature is stepped. 3. The number of steps in the scan is either zero or larger than the array sizes in the program. 4. Miscellaneous other warnings, involving nonsensical lattice angles and lattice parameters, or data files producing read errors.