How to run NODIRAX

• Start xdisp, the display program that is part of the denzo package, to view the Laue diffraction image.
• Produce a peak list, using the peak search button of xdisp. Make sure that enough spots were selected: of each important conic at least a small (>3) number of spots should be found by the peak search algorithm. The default number of spots found by xdisp should normally be sufficient.
• Produce a LAUECELL input file name.inp, that looks like:

  
  
           title        This is is a title
           distance     82.0  
           format       FUJI
           beam         1033.4 1244.5
           peaksfile    peaks.file
           mcombine     2
           nrspot       100  500  1000  99999 
           mincon         3    4     6     10 
           qmin         0.25
           ncycle       10
           sigma        0.20  10.0 90.0
           spindle axis Y
           spindle      0.0
           volume       13073.2
           wavelength   0.6  2.0
           resolution   1.0
  
  

  Values for distance, format and beam are required; there are default values for the parameters peaksfile, mcombine, nrspot, mincon, qmin ncycle and sigma. The commands spindle axis, spindle, volume, wavelength and resolution can be given here as well, but will only be used by TRCELL and/or INDXPAT. Other parameters influencing the conic search algorithm that you might want to change, are radius and refine.

• Start LAUECELL (in a separate window).
• Read the input file:

  
  
           @name.inp
  
  

• Start NODIRAX:

  
  
           run nodirax
  
  

  The program will start by reading the peaks file:

  
  
  File opened for reading peaks: peaks.file
  Number of spots read:  1098
  Number of spots rejected with RADIUS criterium:   166
  Number of spots accepted:   932
  
  

  It will calculate a normalized reciprocal lattice vector ( nrlv) for each spot position that lies within the radius criteria, and try to group these vectors in planes. To do so, it starts each of the ncycle cycles by selecting nrspot spots randomly. These spots are indicated on the image by yellow circles (press update/remove predictions twice). The program will form all possible planes containing at least three nrlvs, and tries to extend and combine them:

  
  
  Search for planes: start of cycle    1
  Randomly selected spots are written to file "hklpredictions"
  Total number of triplets found:  1352
  
  Start of combineplane: number of planes:  1352
  End   of combineplane: number of (deleted) planes: (   885)   467
  
  Start of rejectplane: number of planes:   467
  End   of rejectplane: number of planes:   285
  
  Start of combineplane: number of planes:   285
  End   of combineplane: number of (deleted) planes: (    34)   251
  
  Start of rejectplane: number of planes:   251
  End   of rejectplane: number of planes:   126
  
  Start of combineplane: number of planes:   126
  End   of combineplane: number of (deleted) planes: (     1)   125
  
  Start of rejectplane: number of planes:   125
  End   of rejectplane: number of planes:    39
  
  Search for planes: start of cycle    2
  Randomly selected spots are written to file "hklpredictions"
  Total number of triplets found:  1278
  
  Start of combineplane: number of planes:  1278
  End   of combineplane: number of (deleted) planes: (   808)   470
  
  Start of rejectplane: number of planes:   470
  End   of rejectplane: number of planes:   289
  
  Start of combineplane: number of planes:   289
  End   of combineplane: number of (deleted) planes: (    29)   260
  
  Start of rejectplane: number of planes:   260
  End   of rejectplane: number of planes:   133
  
  Start of combineplane: number of planes:   133
  End   of combineplane: number of (deleted) planes: (     0)   133
  
  Start of rejectplane: number of planes:   133
  End   of rejectplane: number of planes:    52
  
  Search for planes: start of cycle    3
  Randomly selected spots are written to file "hklpredictions"
  Total number of triplets found:  1386
  
  Start of combineplane: number of planes:  1386
  End   of combineplane: number of (deleted) planes: (   928)   458
  
  Start of rejectplane: number of planes:   458
  End   of rejectplane: number of planes:   285
  
  Start of combineplane: number of planes:   285
  End   of combineplane: number of (deleted) planes: (    34)   251
  
  Start of rejectplane: number of planes:   251
  End   of rejectplane: number of planes:   111
  
  Start of combineplane: number of planes:   111
  End   of combineplane: number of (deleted) planes: (     0)   111
  
  Start of rejectplane: number of planes:   111
  End   of rejectplane: number of planes:    44
  
  

  After running ncycle cycles, the program will combine all conics having more than mcombine spots in common, and recalculate a least-squares ndlv for each conic, together with a value.

  
  
  Start of combineplane: number of planes:   135
  End   of combineplane: number of (deleted) planes: (    28)   107
  ndlv       1         6.22    56
  ndlv       2        18.20    52
  ndlv       3        22.61    47
  ndlv       4        29.61    43
  ndlv       5        15.83    34
  ndlv       6        20.51    33
  ndlv       7         7.69    29
  ndlv       8         5.82    28
  ndlv       9        16.92    27
  ndlv      10         6.39    26
  ndlv      11         1.15    25
  ndlv      12         1.60    25
  ndlv      13        14.61    24
  ndlv      14         0.50    23
  ndlv      15         1.92    23
  ndlv      16         3.34    23
  ndlv      17        12.58    23
  ndlv      18         5.54    23
  ndlv      19         4.54    23
  ndlv      20        15.57    22
  .......
  ndlv     107         1.94    10
  The first 20 conics are written to file "hklpredictions"