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 \(\sigma \) 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 \(\psi \) applied to negative quartets (in degrees)   if no fragment \( \psi \) 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 α * generator) gwa    
    test for maximum reflections phased in oneiteration gen    
    test for maximum invariants involved in oneiteration inv    
    test for maximum sum of(weighted \(\alpha \) ) 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  

[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 \(\alpha \) \(^{2} \) thresholdto extension eligibility     auto
  6 reduction fraction of \(\alpha \) \(^{2} \) threshold per cycle     0.7
  7 refinement cutoff as fraction of average \(\alpha \) \(^{2} \) shift     0.02
  8 fix odr phase for nrefinement iterations     30
  9 fix edr phase for nrefinement iterations     10
  10 fix perm phase for nrefinement iterations     5
  11 fix set phase for nrefinement iterations     5
  12 disable null phase for nrefinementiterations     30

partsf 1 control application of fragment \( \psi \) estimate      
    include \(\psi \) estimated fromfragment data qpsi    
    exclude \(\psi \) 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 xof \(F_{{\rm cal}}\) phases acceptedif \(F_{{\rm cal}}\) > x* \(F_{{\rm rel}}\)     0.5
  6 \(F_{{\rm rel}}\) 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

[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  

[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

[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:  

[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.


Banner

 Overview
 News
+Example Graphics
 History
-Documentation
   -Xtal Users Manual
      +Preface
      +Primer
      -Program controls
          System
           ABSORB
           ADDATM
           ADDPAT
           ADDREF
           ATABLE
           BAYEST
           BONDAT
           BONDLA
           BUNYIP
           CBAZA
           CHARGE
           CIFIO
           CIFENT
           CONTRS
           CREDUC
           CRILSQ
           CRISP
           CRYLSQ
           DIFDAT
           DYNAMO
           EXPAND
           FC
           FOURR
           GENEV
           GENSIN
         + GENTAN  <-
           GIP
           LATCON
           LISTFC
           LSABS
           LSLS
           LSQPL
           LSRES
           MAPLST
           MAPXCH
           MODEL
           MODHKL
           NEWCEL
           NEWMAN
           ORTEP
           OUTSRC
           PARTN
           PATSEE
           PEKPIK
           PIG
           PLOTX
           POWGEN
           PREABS
           PREPUB
           PREVUE
           REFCAL
           REFM90
           REGFE
           REGWT
           RFOURR
           RIGBOD
           RMAP
           RSCAN
           SCATOM
           SHAPE
           SHELIN
           SIMPEL
           SLANT
           SORTRF
           STARTX
           SURFIN
           VUBDF
           XTINCT
      +Reference Manual
      +Archive
       Symmetry
    FAQ
   +Developer Info
   +Retired Program Info
 Download
+Extra Software
 Support
 Contributors
 Citations
 Year 2000
 Disclaimer

Home Feedback
Copyright © 2005 Xtal System, University of Western Australia.
Prev   Next