SIMPEL : Symbolic-addition phasing

invar structure invariant options
start selection of starting phases options
phase defining starting phase
print print options of different stages
symbad symbolic addition procedure options
setfom define figure of merit parameters
psets specify phase sets to be output

SIMPEL 1 number of generators eligible for starting set 25% of total
  2 number of generators eligible for divergence 50% of total
  3 number of generators eligible for phasing 100% of total
  4 minimum |E| value of input generators from bdf .inv
  5 data set number of |E|'s 1
  6 number of phase sets output on output archive bdf 4

start 1 control invariants used in con/divergence process      
    use triplets only in starting process trip    
    use quartets only in starting process quar    
    use triplets and quartets in starting process all    
  2 probability term used in convergence process      
    use (1) described in Step 1 1    
    use (2) described in Step 1 2    
  3 threshold ALTHR to accept one invariant     10 \(^{th} \) -largest \( \alpha \)
  4 factor used to reduce [alpha] using \( \sigma ][alpha;\)     1
  5 number of symbols to be assigned in convergence process   if no phase lines entered 4
        otherwise 0

invar 1 invariant types to be used in symbolic addition      
    use triplets only trip    
    use quartets only quar    
    use triplets and quartets all    
  2 minimum A of triplets used     from bdf inv
  3 minimum B of quartets used     from bdf inv
  4 maximum triplets allowed per generator     100
  5 maximum quartets allowed per generator     100
  6 low crossvector sum limit for quartets     25% of max XV-sum (up to max of 2.5)
  7 high cross vector sum limit for quartets     75% of max XV-sum (to min of 4.0)
  8 \(\psi \) phase correction applied to negative quartets in degrees   if no fragment \( \psi \) 180
        otherwise 0

print [a] 1- print invariant statistics and sums invar    
    print converge order of generators converg    
    print extension of starting set into converge set extend    
    print extension of starting set into diverge set diverg    
    print symbolic addition extension process symbad    
    print application of accepted symbols to all |E|'s correl    
    print figure-of-merit details fomtest    
    print phase sets output to bdf bdfout    

[a] Entering no options implies that all print options are invoked.

symbad 1 probability factor used in symbolic addition      
    use sum of weighted \(\alpha \) 's (see Step 3.) wa    
    use sum of \(\alpha \) 's and invariant count an    
  2 acceptance procedure if multiple symbols generated      
    accept most probable indication mult    
    reject all but single symbol indication sing    
  3 no. of generators added in blocks to the symbolic process     100
  4 acceptance threshold of weight for wa option     0.3

setfom 1 number of top phase sets applied in FOM tests [a] 16
  2 optimum value for QFOM 0.75
  3 weight of QFOM in CFOM and AMOS 1
  4 optimum value of RFOM 1
  5 weight of RFOM in CFOM and AMOS 1
  6 optimum value of RFAC FOM 0.25
  7 weight of RFAC in CFOM and AMOS 1
  8 optimum value of PSI0 FOM 0.75
  9 weight of PSI0 in CFOM and AMOS 1
  10 optimum value of NEGQ FOM 60
  11 weight of NEGQ in CFOM and AMOS 1

[a] Phase sets are presorted based on the max correlation with the symbolic phases.

phase 1-3 hkl indices      
  4 input phase (in degrees)   assign as new symbolic phase  
  5 Phase status option Code    
    assign as origin defining phase odr    
    assign as enantiomorph phase edr    
    assign as symbolic phase [a] sym    
    assign as numeric phase \(^{1} \) set    
    remove phase from phasing process nul    

[a] The default is sym if field 4 is void; set is default if field 4 is numeric.

psets 1- phase set numbers to be output to output archive bdf [a] none

[a] These numbers are selected from a previous run using identical parameters.


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