The Gnu Xtal System User's Manual
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3.27. GENTAN: Tangent phasing

invar	control structure invariant relationships used
select	control starting phase selection process
phi	input specific starting phase
assign	assign starting phase by sequence number
refine	parameters controlling tangent refinement process
partsf	parameters for partial structure factor input
setfom	input figure-of-merit parameters
psets	specify phase sets to be output
dump	print detailed information on the phasing process
archiv	control items output to logical record lrrefl: of bdf

GENTAN	Option	Code	Arg		Def
	min \|E\| applied	emin	e	only \|E\|'s > e phased
	max phases calc.	rmax	m	the m largest \|E\|'s phased	from file `inv`
	max phase sets	pset	s	calculate s permutations	`64`
	max phase sets bdf	pout	k	output k phase sets to the bdf	`4`
	list phase sets	plis	x	list top x phase sets (max 8)	`0`
	phase convergence	pacc		fix phase when converged
		nacc		phase refined every cycle
	bdf starting phases	nbdf		do not use bdf phases to start process
		pbdf		use bdf phases to start
	data set number	dset	n		`1`

invar	1	invariant types to be used in the phasing process
		use triplet and quartet invariants	all
		use triplets only	trip
		use quartets only	quar
	2	minimum A of triplets used			from file `inv`
	3	minimum B of quartets used			from file `inv`
	4	maximum triplets allowed per generator			`100`
	5	maximum quartets allowed per generator			`100`
	6	reduce A and B values by this fraction of A and B			`1`
	7	control eligible quartets according to X-vector sum
		include quartets with XVsums<LO or >HI	parxv
		include all quartets	allxv
		include quartets with X-vectors in the data sphere	insxv
		include only quartets with X-vectors out of sphere	outxv
		use negative quartets actively	active
	8	lower limit for cross-vector sums - LO			25% of max to 2.5
	9	upper limit for cross-vector sums - HI			75% of max to 4.0
	10	invariant applied to negative quartets (in degrees)		if no fragment estimate	`180`
				otherwise	`0`

select	1	method to select starting phases
		permute phases in specified increments(def: centro)	perm
		permute phases using magic integers(def: noncentro)	magic
		assign random values to all but ODR phases	random
	2	number of initial starting phases selected (other than ODR, EDR)		if random	`0`
				if permute ,	`1`
				if magic	`2`
	3	maximum starting phases selected with MAXEXT process		number needed to connect 75% of field 4
	4	maximum generators used in MAXEXT selection process			`100`
	5	types of relationships used in selection processes
		use all invariants except negative quartets	all
		use only triplet relationships	trip
		use only quartet relationships	quar
	6	criteria for MAXEXT selection process
		test for maximum sum of(weighted * generator)	gwa
		test for maximum reflections phased in oneiteration	gen
		test for maximum invariants involved in oneiteration	inv
		test for maximum sum of(weighted )	wal
	7	increment for permuting restricted phases in degrees			`180`
	8	increment for permuting nonrestricted phases in degrees			`90`
	9	starting weight for phases assigned in random mode			`0.25`
	10	integer used to seed random phase generator			`137`

phi	1-3	hkl indices of input phase
	4	phase (in degrees)			restricted value
					or `45`
	5	starting phase status code
		permute starting phase (permutable)	per
		origin defining phase (non-permutable)	odr
		enantiomorph phase (permutable)	edr
		fixed starting phase (non-permutable)	set
		disable phase from refinement process	null
	6	fix input phase for n refinement iterations		for per or set	`5`
				for edr	`10`
				for odr	`30`
	7	permutation increment between phase sets ( edr and per )		for restricted phases	`180`
				otherwise	`90`
	8	phase weight for refinement		if not null then	`1`
				else	`0`

assign [a]	1-	starting phase status codes followed by groups of sequence numbers
Notes: a. Status codes are the same as defined for the phi line. Generator sequence numbers are in order of decreasing \|E\| value as listed by GENSIN. The status code of a series of starting phases precedes their generator sequence numbers (see GENTAN in the Reference Manual). Any number of assign lines may be entered.

refine	1	phase extension and refinement procedure
		estimate new phases during tangent iteration	cascade
		estimate new phases after tangent iteration	block
	2	tangent weighting scheme
		probabilistic weights	w1
		Hull-Irwin statistical weights	w2
		modified Hull-Irwin statistical weights	w3
	3	maximum number of refinement iterations		`30`
	4	minimum weight to phase extension eligibility		`0.15`
	5	initial ² thresholdto extension eligibility		auto
	6	reduction fraction of ²threshold per cycle		`0.7`
	7	refinement cutoff as fraction of average² shift		`0.02`
	8	fix odr phase for `n` refinement iterations		`30`
	9	fix edr phase for `n` refinement iterations		`10`
	10	fix perm phase for `n` refinement iterations		`5`
	11	fix set phase for `n` refinement iterations		`5`
	12	disable null phase for `n` refinementiterations		`30`

partsf	1	control application of fragment estimate
		include estimated fromfragment data	qpsi
		exclude estimated from fragment data	nqpi
	2	control use of starting phases from input archive bdf
		do not use phases from input archive bdf	no
		include FC phases according to 4, 5 and 6 below	fc
		include GENTAN phases according to 3 and 4 below	gt
	3	phase set number of GENTAN phases to be entered		`1`
	4	minimum \|E\| of phases to be entered		`emin`
	5	fraction `x` of F_cal phases acceptedif F_cal > `x`*F_rel		`0.5`
	6	F_rel scale applied before test in field 5		bdf value

setfom	1	control flag for pretest of FOM values
		pretest FOM values after the 6^th tangent iteration	pret
		do not pretest FOM values	nopr
	2	optimum RFOM value for CFOM/AMOS calculation		`1.0`
	3	optimum RFAC value for CFOM/AMOS calculation		`0.25`
	4	optimum PSI0 value for CFOM/AMOS calculation		`1.5`
	5	optimum NEGQ value for CFOM/AMOS calculation		`60`
	6	weight of RFOM value for CFOM/AMOS calculation		`1`
	7	weight of RFAC value for CFOM/AMOS calculation		`1`
	8	weight of PSI0 value for CFOM/AMOS calculation [a]		`2`
	9	weight of NEGQ value for CFOM/AMOS calculation [a]		`2`
	10	automatic termination of multi-solution process		yes
		continue even if FOMs < optimal FOMs	cont
	11	RFOM lower rejection limit for 014 and 024		`0.25`
Notes: a. The PSI0 weight is scaled down if the number of PSI0 triplets is less than 100. The reduction factor is the number of triplets per 100. The NEGQ weight is similarly adjusted according to the number of negative quartets.

psets [a]	1-	specific phase set numbers to be output to the bdf
Notes: a. Used to select specific phase sets, independent of their FOM values, when repeating an identical GENTAN run.

dump	Option	Code	Arg		Def
	generator & selection list	sel		print start set data
	specify phase set limits	pse	m n	phase sets m to n	`1 1`
	generator set limits	gen	t u	generators t to u	all
	print starting phases [a]	sta		starting phase set
	print phase iterations [a]	ite	p q	iterations p to q	`1 99`
	print invariants [a] [b]	inv		print each invariant
	print phase history map [a]	map		print phase est./iteration
	print FOM sums	fom		print sums used in FOM's
	terminate phasing process	hal	t	stop after phase set t	`1`
Notes: a. These print dumps are limited by pset and gen entries. b. CAUTION! This printout can be enormous unless limited.

archiv [a]	1-	bdf ID numbers to be added or deleted from logical record lrrefl:
Notes: a. Normally this line is not entered. The items added to the reflection record are controlled via pout of the GENTAN control line, not this line. Caution: A maximum of 70 items may appear in the archive list and 64 are generated automatically in order to delete existing phase sets and weights. This means that a maximum of 6 user-generated deletes may be entered on this line. Negative identification numbers indicate the items to be deleted (if present) from the bdf.

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