Example for diffraction pattern processing for individual pattern
						Anchi Cheng 1997

Objective:	diffraction processing preparation, correction curve generation, indexing and intensity integration.

#!/bin/csh -x
#
# General parameter assignments
set pattern = "pattern_name"
set filmno= "0000000001"		(film-identifier)
set cell_ab = "60.0 60.0"	(untilted crystal a, b axis length in angstrum)
set cell_gamma = "120.0"	(untilted crystal gamma angle in degree)
set title =  "any_title"
#
cd ~/any_directory		(set appropriate path)
#
# BACKAUTO	automatic centering, radial background calculation and y-axis
#			intensity variation estimate.
#	
#
setenv IN      $pattern.pat	(original digitized diffraction pattern)
setenv OUT     $pattern.crt	(background corrected diffraction pattern)
setenv FOR008  ${pattern}b.plt	(radial background plot)
backauto << eot
T,F,		! IREF,IPLOT	(refine center coordinates if IREF=.true.)
 0.0   0.0	! CX,CY	(estimated center coordimates relative to center of film)
$filmno
$title for BACKAUTO
 15		! NPNTS
 600  120      ! IRMAX, IRMIN  (radius limits for the radial background plot only)
 750  400      ! IRMAXC,IRMINC  (max and min limits for YCORRECTION)
eot
#
#
mv fort.2 $pattern.bck
mv fort.4 $pattern.ycr
plt2ps  ${pattern}b.plt ${pattern}b.ps
#
#
# AUTOINDEX	automatic indexing and raster size suggestion
setenv IN      $pattern.crt
setenv OUT      $pattern.avr
autoindex << eot
eot
plt2ps PLOTOUT ${pattern}a.ps
#
#
# PICKPROF	spot intensity integration after final lattice refinement and various correction
#
setenv IN $pattern.pat
setenv INPARAM $pattern.crt
setenv RADIAL $pattern.bck
setenv YCORR $pattern.ycr
setenv PLOTOUT ${pattern}p.plt
pickprofa << eot
$cell_ab,$cell_gamma,0.0,1,1,100,F	!A, B,  G. ANGDIS, SHRINK, TILTDIR, KV, LPRINT
F	! LUNBEND (Use distortion table ? T/F)
F,0,400,F,T,0.01,2.0 ! LPROFIT,LPTYPE,LPRANGE,INTERLEAVE,IFLATTEN,PROFMIN,TSIGMA
 1,1
 50,50
 150,150
 300,300
 600,650
 900,1000
 1500,1700
 Look-up table title, starting from 1,x and end at 1500, y.
${filmno}
${title} for PICKPROF
0.0,0.0,45.0,0.0		!  COORDS OF CENTRE, TILT ANGLES
0.0,0.0,0.0,0.0			! LATTICE PARAMETERS
 3.5, 30.0, 3.5		! ROUT, RIN, PRPMAX
 0,0,  0,0		! nxm,nym,  nxmt,nymt
 1.0, 500., 1.6		! Fract,  Absol, Xamine  (reflection exclusion setup)
eot
mv fort.2 Z$pattern.lst
exit



Merging and and refinement of parameter of electron diffraction derived peak intensities

#!/bin/csh -x
# This example is to refine scale and isotropic temperature factor
cp ~/pattern1/pattern1.lst fort.15
cp ~/pattern2/pattern2.lst fort.16
cp ~/pattern3/pattern3.lst fort.17
.....
cp 3D_f.curve fort.7
set cell_abc= "60.0 60.0 100.0"
set cell_gamma = "120.0"
mergediff << eot
0000000001  CHIP28 3D diffraction
F,T,T,F,F,T				!LIST,SORT,NFILE3,NFILE4,IGUIDE,LSUMMARY
T,T,F					!LREF,LCURVES,BCURVES
T,F,F,1,1,1,1,F			!SCFDET,TA_REFMT,DETWIN,MASK(1-4),LMODMSK
13,$cell_abc,150.0,$cell_gamma,3.5	!ISPGRP,CELL PARAMETERS, WIDTH, ANG, RESMAX
F,F,3.5,30.0,10.0,80000.0,10.0,F,3  !LCF etc., not relevant if LCF = F.
0000000001   pattern1
15,5.00,60.0				!NIN,TAXA,TANGL
0.0 T 0.0 0.0 F F F 0.0 0.0	!SCALE,LBISO,TFPAR,TFPERP,SGNXCH,ROT180,REVHK,WIN,RIN
1,1,1,1,0,0,0,0
0000000002   pattern2
16,60.0,-60.0				!NIN,TAXA,TANGL
0.0 T 0.0 0.0 F F F 0.0 0.0	!SCALE,LBISO,TFPAR,TFPERP,SGNXCH,ROT180,REVHK,WIN,RIN
1,1,1,1,0,0,0,0
0000000003   pattern3
17,160.0,55.0				!NIN,TAXA,TANGL
0.0 T 0.0 0.0 F F F 0.0 0.0	!SCALE,LBISO,TFPAR,TFPERP,SGNXCH,ROT180,REVHK,WIN,RIN
      -100			!TERMINATOR (in place of the position of pattern ID)
eot
mv fort.3 dmerge.dat
mv fort.12 summary.txt
rm fort.*
exit