DIFDAT : Process diffractometer data

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`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 `.tsu`file 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