applyPairSelection in calculation

[dragonyanglong]

In fitstructure.py, applyPairSelection is for pdffit server. We need silmar function for CMI to run in calculation.py

def applyPairSelection(self, server, phaseidx):
    """Apply pair selection for calculations of partial PDF.

    server   -- instance of PdfFit engine
    phaseidx -- phase index in PdfFit engine starting from 1
    """
    psf = self.getPairSelectionFlags()
    idx = 0
    for iflag, jflag in zip(psf['firstflags'], psf['secondflags']):
        idx += 1
        server.selectAtomIndex(phaseidx, 'i', idx, iflag)
        server.selectAtomIndex(phaseidx, 'j', idx, jflag)
    return

[dragonyanglong]

lattice=Lattice(a=3.52394, b=3.52394, c=3.52394, alpha=90, beta=90, gamma=90)
Ni 0.000000 0.000000 0.000000 1.0000
Ni 0.000000 0.500000 0.500000 1.0000
O 0.500000 0.000000 0.500000 1.0000
Ni 0.500000 0.500000 0.000000 1.0000

psf in applyPairSelection
{'firstflags': [True, True, False, True], 'fixed_pair_string': u'Ni-O', 'secondflags': [False, False, True, False]}
('iflag', True)
('jflag', False)
('iflag', True)
('jflag', False)
('iflag', False)
('jflag', True)
('iflag', True)
('jflag', False)

[dragonyanglong]

setPairMask( (BasePairQuantity)arg1, (object)i, (object)j, (object)mask [, (object)others=None]) -> None :
Include or exclude specified atom pairs in the calculation.
The pair masking is exclusively based either on site indices
or atom types. This function applies index-based masking and
cancels any type-based masks.

i    -- zero based index of the first site in the pair.
        Can be also an iterable of indices or a string 'all' or 'ALL',
        which select all sites in the structure.
j    -- index of the second site in the pair.  Can be an iterable
        or string 'all', just like argument i
mask -- mask of the atom pair i, j,  True if included, False if excluded.
others -- optional mask applied to all other pairs.  Ignored when None.

No return value.


C++ signature :
    void setPairMask(diffpy::srreal::PairQuantity {lvalue},boost::python::api::object,boost::python::api::object,boost::python::api::object [,boost::python::api::object=None])

Type: instancemethod

[dragonyanglong]

temp solution:
I use setTypeMask.

But compare with PDFgui, the baseline is not correct.

CMI:

PDFgui:

[dragonyanglong]

If all-all:
CMI and PDFFIT are the same: