CRYLSQ : Structure factor least-squares refinement

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`CRYLSQ` : Structure factor least-squares refinement

disper	dispersion factor
scale	scale factor
extinc	extinction parameters
maxhkl	reflection limits
xabs	absolute-structure parameter
select	select subset of atoms from the bdf
dptype	change atomic displacement parameter type
group	group or identical molecule refinement
atomgr ^[a]	atoms per group
restr ^[b]	establish conditions for positional parameters
constr ^[b]	constrain one parameter to be a function of otherparameters
noref ^[b]	shut off refinement of specified parameters
block	matrix blocking line
^[a]Must be preceded by a group line ^[b]Order specific lines. restr lines precede constr which precede noref lines.

CRYLSQ	Option	Code	Arg		Def
	number of refine cycles	`cy`	`n`		`1`
	refinement coefficient	`fr`		F
		`f2`		$F^{2}$
		`in`		intensity
		`fh`		F(heavy atom)
	derivative matrices	`bd`		block-diagonal
		`fm`		full-matrix
		`bl`		specified in block lines
	reflection weight	`ws`		$1/\sigma ^{2}$
		`wu`		unit weights
		`ww`	`n`	bdf wt with id=190 `n`	`0`
	scale factor(s)	`us`		refine together
		`ss`		refine separately
	dispersion	`ad`		apply but do not refine
		`rd`		apply and refine
	extinction	`ax`		apply but do not refine
		`rx`		apply and refine
	abs-struct. param	`aa`		apply but do not refine
		`ra`		apply and refine
	thermal displacement type	`mx`		mixed iso and aniso (as in bdf)
		`is`		isotropic
		`an`		anisotropic
		`ov`		overall
	population	`pp`		yes
	dataset number	`ds`	`n`	data set number	bdf or `1`
	reflection skip	`sk`	`n`	use every `n` $^{th}$ reflection
	fixed atoms used	`ap`		apply values from prior run
		`ep`		apply & store on output bdf
	type hkl as rcode2 ^[a]	`tl`	`q`	only if Y < `q` $\sigma$ Y
	use in matrix	`mr`	`q`	only if w $\Delta$ Y < `q`
	rcode2 use in matrix	`ml`		only if $Y_{{\rm cal}}$ > $Y_{{\rm obs}}$
	shift damping factor	`fu`	`q`	for `bd`	`0.8`
				for `fm`	`1.0`
	non positive-def. U	`tr`		make pos. def. and continue
		`tw`		tell user and continue
		`tt`		terminate calculation
	termination criterion	`tc`		stop if no convergence of R
	list reflections	`l1`		last cycle	no
		`l2`		every cycle
	list poor reflections	`lr`	`q`	if w $\Delta$ Y > `q`
	atom lines to `pch`file	`p1`		last cycle	no
		`p2`		every cycle	no
	list correl. matrix	`m1`	`q`	if > q after the last cycle
	list deriv. matrices	`m3`		after last cycle only
		`m4`		after every cycle
	save correl. matrix	`ms`		output to file `cmx`
	old atomic parameters	`ao`		output old params to the bdf
^[a]Applies for the current run only and does not affect the bdf.

disper	1	atom-type name
	2	real part of dispersion scattering factor
	3	imaginary part of dispersion scattering factor
	4-6	as in 1-3, or use separate disper lines

scale	1	$F_{{\rm rel}}$ scale factor
	2	scale group number	`1`
	3, 4	as in 1, 2, or use separate scale lines

extinc	1	extinction correction method
		Zachariasen	`zach`
		Becker-Coppens, type I	`typ1`
		Becker-Coppens, type II	`typ2`
		Becker-Coppens, type I and II	`gen`
	2	extinction type
		isotropic	`is`
		anisotropic (not implemented)	`an`
	3	mosaic distribution
		Gaussian distribution	`gaus`
		Lorentzian distribution	`lore`
	4	isotropic extinction parameter( `zach`or `typ1`)		(g)	`0`
	5	isotropic extinction parameter( `typ2`or `gen`)		( $\rho$ )	`0`
	6	mean value of T in mm		Xray	`0.3`
				neutron	`1.5`

maxhkl	1-3	max \|h\|, \|k\|, \|l\| applied in refinement process	`999`
	4	min value of sin $\theta$ / $\lambda$ applied	`0`
	5	max value of sin $\theta$ / $\lambda$ applied	`10`

xabs 1 Flack absolute structure parameter 0.5

select	1-	atom label or atom label string ^[a]
^[a]An atom label string is two atom labels separated by a slash '/'. The first label identifies the first atom , and the second label the last atom in a sequence of atoms.

dptype	1	atom type symbol
	2	thermal displacement type
		overall U	`ov`
		isotropic U	`is`
		anisotropic $U_{ij}$	`an`
	3-4	as in 1, 2, or use separate dptype lines

group	1	group refinement number of molecule			`0`
	2-4	x, y, z fractional coordinate of centre of gravity, if fixed
	5	Euler angle refinement signal		not fixed
		Euler angles invariant	`0`
		symmetry element is parallel or perp. to a-axis	`1`
		symmetry element is parallel or perp. to b-axis	`2`
		symmetry element is parallel or perp. to c-axis	`3`
	6	signal for the refinement of isotropic U
		group isotropic U	`+1`
		invariant U	`0`
		individual isotropic U	`-1`
	7	signal for population parameter refinement		no constraints
		group population	`+1`
		invariant population	`0`
		individual population	`-1`

atomgr	1	atom label string ^[a]
^[a]An atom label string is two atom labels separated by a slash '/'. The first label identifies the first atom , and the second label the last atom in a sequence of atoms.

restr ^[a]	1	restraint class
		bond length	`bond`	(n=2 atoms)
		bond angle	`angle`	(n=3 atoms)
		dihedral angle	`dihed`	(n=4 atoms)
	2	atom labels of the n restrained atoms ^[b]
	n+2	ideal values of bond length, angle or dihedral angle
	n+3	standard deviation of ideal value
^[a] restr is an order specific line and cannot be preceded by constr or noref lines. ^[b]These atom labels may each be followed by an optional field indicating a symmetry operation to be applied to the coordinates of the atom. This field has the form (n_mmm), where n is the symop number from `STARTX` , and mmm is the translation based on the number 555. The parentheses are mandatory.

constr ^[a]	1	contraints equation ^[b] (see `CRYLSQ` )
^[a] constr is an order specific line and cannot be preceded by noref lines. ^[b]Embedded blanks are allowed. The order of the constraints is not arbitrary - reference atoms must occur higher in the atom list than subject atoms. Furthermore, for parameters belonging to the same atom, the reference parameters must occur earlier in the parameter list than the subject parameters. The parameters may be any of the following: SKF, UOV, EXT, DSP, X, Y, Z, U, U11, U22, U33, U12, U13, U23, POP, APP, and NEU.

noref	1	invariant parameter string ^[a]
^[a]No embedded blanks are allowed. See the constr line for the list of parameters and for special atom names.

block ^[a]	1	matrix block ( same format as noref )
^[a] Any block lines must cover all selected parameters. When no parameter symbol is given, a new block is started.

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