CHAPTER 7 THE INDEX AND RAFIN PROGRAMS 7.1 <run <rafin after having set up the input file : The input data are on <rafin.<dat (teletype input can be used, but is cumbersome) Use <teco to make or correct the file. An example of the input file ( comments in parentheses ) :-- 0 1 (second no. 0/1 for <ub not transferred/transferred to <lsd) 0 (always) 0 -4 -2 28.01 13.75 81.59 42.05 (H K L 2Theta Omega Chi Phi) 4 -6 7 50.84 25.37 34.04 18.41 -2 -6 0 41.55 20.53 66.93 59.99 4 0 4 19.74 9.94 -16.92 -5.40 1 -5 -3 35.59 17.70 82.32 1.40 6 0 0 18.47 9.26 -2.32 -46.95 0 .8405 (0/1 do not/do refine lambda; and lambda) 0 0.0 1 0.0 1 0.0 (0/1 for do not/do refine, 2Theta zero, -0/1 for do not/do refine, Om zero, -0/1 for do not/do refine, Chi zero.) Page 7 - 5 INDEX AND RAFIN. 0 15.9158 0 7.1939 0 14.277 0 90 0 98.72 0 90 (ditto for <a, <b, <c, <alpha, <beta and <gamma) 2 0 0 (H K L list for angles to be calculated) 0 2 0 0 0 2 0 0 0 (end of list) -1 (end of input file) Ensure that <lsd is not running if you wish to transfer the matrix and wavelength directly into its parameter section, otherwise it may not be successful. <rafin will never modify the zeroes for you. This is for you to do by <adding them to the values in <zer of <par. Remember that for a well aligned diffractometer, they will never change by very much. Note: the first two reflections should be far away enough in reciprocal space to define a plane. They must be at least 45 deg apart in Phi and only one may have Chi greater than 45 deg. Note also that higher angle (Theta) reflections usually give a better fit. You cannot, obviously, refine lambda and your cell at the same Page 7 - 6 INDEX AND RAFIN. time. 7.3 <acknowledgements The <index program was written by M.S.Lehmann, and J.M.Savariault. The <rafin program was implemented at the <ill by A.Filhol and M.Thomas. It was implemented on the <pdp 11 system by A.Barthelemy. CHAPTER 8 THE HKLGEN AND GENLIS PROGRAMS 8.4 180 i.e. <up-side-down. If measurement is not possible for any of these conditions, the <hkl is declared <blind. Comments like <fr.pr <hichi <blind indicate these on <tty output. To run the program do :-- ><run <hklgen Input to the program is either from the terminal or from a file <hklgen.dat, already created by the user. 8.4.1 input from the terminal. The first question asked under this option is whether a file <hklgen.dat should be created. If subsequent runs are envisaged, this might be a good idea. In this case <teco can be used to make small changes to the input and the program can be quickly re-run. <hklgen then asks for the following parameters :-- Page 8 - 3 <HKLGEN <AND [200,200]. <hklgen is a program which has evolved in the hands of : A.Filhol, S.Mason. A.Barthelemy and J.Allibon. 8.5 genlis the program generates a list of hkl from a list of reflections produced by coll5n or hklgen. the indices can be permuted, and for coll5n lists limits can be applied to theta and sigma(fsq)/fsq. up to 50 different reflections can be excluded from the list. to produce the list do Page 8 - 9 <HKLGEN <AND <GENLIS >run genlis and answer questions. input file is punch-file produced by coll5n or hklgen. if old data is needed, mount the relevant disk on dk3: for the exercise. the program will accept a series of input files, if needed. output file name is chosen by the user. the permutation of hkl is given by a combination of indices. example: h=-h-k k=H l=-l in addition reflections can be rejected using expressions of the kind k-h>n, where n is an integer. this rejection is done before the permutation. repeated tests of sigma limits without stopping the program will produce a series of files with increasing extension numbers (assuming coll5n data is input, and that all input is on a single file). Page 8 - 10 <HKLGEN <AND