DIFDAT : Process diffractometer data

transf [a] transform Miller indices of input reflections
attenu [a] attenuator factors
stands [a] [b] specification of standard reflection signals
sthkls [a] [b] alternative method of establishing standard reflections
fetch definition of the order of the quantities in data lines
data diffractometer data lines
genscl [c] [d] generation of intensity scale factors
setscl [c] [d] set intensity scale factors
discon [c] definition of discontinuities in scale factors

[a] Must precede following option lines.

[b] One or the other but not both may be used.

[c] One of these lines must be present if the data is to be scaled. Otherwise, scale factors are calculated but not applied.

[d] If a setscl line is input before a genscl line, the genscl line will be ignored.

DIFDAT Option Code Arg   Def
  input data mode dat   data lines from input  
    bdf   from archive file  
    cad   CAD4 diffr. file cad  
    niv   Nicolet (Vax) [a]file nic  
    nid   Nicolet (DG) [a]file nic  
    sie   Siemens ascii file sie  
    uwa   P3 special binary file dct  
    tsu   Tsukuba diffr. file tsu  
    spe   special diffr. file dif  
    rd5   Rigaku Denki. file rd5  
    shx   SHELX F4 fixed format file .hkl [b]  
    sh3   SHELX F3 fixed format file .hkl [b]  
    rap [b]   Rigaku Rapid .f2plus  
    rfx [b]   alternate Rigaku Rapid .f2plus  
    rf2 [b]   Rigaku Rapid .f2  
    bru [b]   Bruker Smart file [c] raw  
  filename <256 characters file n change shx / rap input data filename  
  Bruker raw file cos   load direction cosines on to bdf  
  Tsukuba .tsufile data [d] smu n monitor count smoothing across 1<n<21 refl'ns 1
  Nicolet scan mode 2th   Nicolet \(  \theta -2\theta \) scan  
    ome   Nicolet \(  \omega \) scan  
  add bdf refln data noadd   do not add hkl from old bdf  
    add   add new hkl to old bdf [e]  
  print reflection data noprint   print no reflections  
    print n print n all
  print raw data raw   print n lines, defined above  
  scale intensities nap   do not apply scale  
  fate of standards include   include on output bdf  
    exclude   exclude from output bdf  
  backg. time each side bgtime p time in seconds 10
  min. scan time [f] mint t time in seconds 10
  observ. threshold [g] obst n rcode=2 if I < n \(\sigma \) I 2
  set intensity if rcode 2 nobth   store as calculated  
    obth m store as m \(\sigma \) I [h]  
  backg. imbalanced baln q warn if(b1-b2) > q \(\sigma \) I 10
  damp stds variation damp r scaledamping factor .5
  instability option inst o m b option, slope, intercept [i]  
  instability calculation nsc   calc. before scaling after
  instability calculation nrw   do not use raw counts  
  \(\sigma \) I options est f use f*I as \(\sigma \) I  
    sig s incr. \(\sigma \) I with sI .02
  output diffract. angles ang   put angles on the bdf no
  output Eulerian angles eul   put angles on the bdf no
  deadtime correction dtm n add n% to deadtime correction  

[a] Outputs input data as data lines to the punch file

[b] data is stored as f2rl and not irel

[c] The Bruker SMART .raw file contains primary and diffracted beam direction cosines, to represent the orientation of the crystal at reflection measurement time (generally anything other than the bisecting position). DIFDAT contains code to convert those direction cosines to an orientation specified in terms of the Crystal Based Azimuthal Psi Angle (lrefl: IDNUM n011), which should permit absorption correction using programs such as LSABS and LSLS (But NOT ABSORB). This requires the orientation matrix UB to be stored in STARTX. The azimuthal angle calculation has not been verified as correct!

[d] adjustments for bugged software. Generally not required.

[e] The add option copies unaltered reflections from the input logical record lrrefl: and adds newly processed reflections to them. The input file must contain at least the quantities h, k, l, I, \(\sigma \) (I), and rcode. All other quantities are discarded.

[f] If an encountered scan time is less than t following the mint option, the reflection is rejected.

[g] Reflections with intensities greater than nσ above background as defined by the obst n option will be classed as observed, rcode=1. All other reflections will be coded as unobserved with an rcode=2.

[h] The obth option allows the user to replace the value of an intensity with an rcode=2 by the quantity n* \(\sigma \) (I), where n is the value specified in the obst n option. The default allows intensities to be stored just as they are calculated. This includes intensities calculated to have negative values.

[i] See the DIFDAT section in the Reference Manual for a description.

attenu [a] 1- attenuator factors (minimum of 1.0)  

[a] The first attenuator factor does not refer to the open attenuator position. The attenuator factors are used as multiplicative factors.

stands 1 character string that identifies standard or observed reflection [a]      
  2 integer assigned to reflection identified by string in field 1      
    for a normal reflection 1    
    for a standard 2    
  3, 4 same as 1 and 2 above      

[a] The observed reflection/standard reflection identifiers may be either a character string or a single decimal digit. (e.g., #ST or 1). A maximum of 11 pairs (1 observed and up to 10 standards) may appear on the stands line. This line may be used as an alternative to the sthkls lines. Note that this line is used only in conjunction with data lines.

sthkls [a] 1-3 hkl indices of first standard reflection  
  4-6 hkl indices of second standard reflection , and so on  

[a] A maximum of 10 standards may be defined. More than one sthkls line may be used. The first blank h field terminates the scan. These lines may be used as an alternative to a stands line. Note that this line is used only in conjunction with data lines.

fetch [a] 1- mnemonics defining the input fields on data lines      
    field to be skipped [b] skp    
    signal reflections as standard or regular observation [c] sig    
    h index h    
    k index k    
    l index l    
    scan time of \(  \theta -2\theta \) scan [d] sct    
    scan counts scc    
    counts for background 1 [e] bg1    
    counts for background 2 bg2    
    attenuator number [f] atn    
    reflection sequence number [g] rfn    
    \(I_{{\rm rel}}\) irl    
    \(\sigma \) \(I_{{\rm rel}}\) sir    
    \(F^{2}_{{\rm rel}}\) fsq    
    \(\sigma \) \(F^{2}_{{\rm rel}}\) sfs    
    \(F_{{\rm rel}}\) fo    
    \(\sigma \) \(F_{{\rm rel}}\) sfo    
    2 \(\theta \) tth    
    \(\omega \) omg    
    \(\chi \) chi    
    \(\phi \) phi    

[a] The values for h , k and l , and at least one and only one of the group scc , irl , fsq and fo are mandatory.

[b] The skp option may be used more than once.

[c] If sig is not specified, the reflections to be treated as standards must be supplied on sthkls lines.

[d] If sct , the scan time, is not present it is presumed equal to the variable bgtime which is supplied on the DIFDAT line.

[e] If bg1 and bg2 are not specified, they default to zero.

[f] If atn is not specified, the default is to assume no attenuator.

[g] If rfn is not available, the current reflection count will be used during processing.

data [a] 1- reflection input quantities  

[a] These quantities are specified in the fetch line as described previously. In practice the use of a setid line or a field line followed by a setid line may be found useful. The intention is that the diffractometer output tape will be processed through local operating system utilities to form a coded file. This file will be edited using a text editor and then fed to the Xtal system in the input stream. (See examples in the Reference Manual.)

genscl [a] 1 number of standard groups scale factors are smoothed 5

[a] This line will be ignored if preceded by a setscl line. It causes the generation of scale factors based on observations of standard reflections. If setscl lines follow, they will replace specified group scale factors.

setscl 1 scale factor to supersede value for specified standard group  
  2 serial number [a]of the last standard reflection of the group of standards for which this scale supersedes  

[a] The serial number refers to the diffractometer serial number, if that has been supplied, otherwise it refers to the sequence number developed as the reflections are being treated on input. Smoothing will take place over the scale factors unless prevented by discon input lines. The serial number given must be that of the LAST standard reflection of the group of standards used to establish the scale. Otherwise, the setscl line will be ignored.

discon [a] 1- serial number of the last standard reflection of the group of standards used to establish the scale factor  

[a] A preliminary run of DIFDAT may have to be made to find discontinuities in the scale factors.

transf [a] 1-9 transformation matrix \(a_{11}\), \(a_{12}\), \(a_{13}\), \(a_{21}\), \(a_{22}\), \(a_{23}\), \(a_{31}\), \(a_{32}\), \(a_{33}\)  

[a] The transformation is: h'k'l' = hkl* a -matrix