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Required to support OPTIMIZED evaluation in Python-defined PairQuantity calculators.

update once we have the BNL-compatible license.

The following stanzas crash

ni=loadStructure('Ni.stru')
ni.occupancy = 1
createStructureAdapter(ni)

from diffpy.srreal.structureadapter import Atom
aa = Atom()
aa.occupancy = numpy.int64(1)

Design function for evaluating favg, favg**2, favg(Q) from StructureAdapter and ScatteringFactorTable. Useful for PDF conversion and for evaluation of content fractions from PDF scale ratios.

Also replace its call in srfit.

• require sufficient version of libdiffpy library
• convert libdiffpy_version_info to named tuple as in pyobjcryst
• split version.py into a Python only part that does not import srreal_ext. Use for __version__ data in diffpy.srreal

This stanza gives much different PDF values although they should not depend on r-sampling. Find out what is going wrong with qmax cutoff and/or rstep interpolation.

pc = PDFCalculator(qmax=11, rstep=0.01)
ni = loadStructure('nickel.cif')
r0, g0 = pc(ni, rstep=0.01, qmax=11)
r1, g1 = pc(ni, rstep=numpy.pi / 11, qmax=11)

Write draft function that recovers a json-like configuration of calculator objects.

• Move imports of Python modules that somehow tweak the wrapped classes to the end of srreal_ext.cpp.
• Check that unpickled instances in a fresh Python session have all the tweaks loaded.

I was trying the parallel PDF calculator from the parallelPDF.py included in example directory. The parallelizing was successful but the result from parallel calculator seems to be the different from single-pass one.

I only edited the plotting part of parallelPDF.py as following so it shows the legend:

....
plot(r0, g0, label='single')
plot(r1, g1, label='parallel')
plot(r0, gd - 3, label='diff')
plt.legend()
show()

and the result obtained is:

package info:

diffpy-cmi                2.0.2                         0    diffpy
diffpy.pdffit2            1.1                      py27_0    diffpy
diffpy.srfit              1.2                      py27_0    diffpy
diffpy.srreal             1.1.3                    py27_0    diffpy
diffpy.structure          1.3.4                    py27_0    diffpy
diffpy.utils              1.2.1                    py27_0    diffpy

Any thought? Thanks :)

Hi @pavoljuhas @sbillinge @st3107,
When I generate PDF using diffpy.srreal.pdfcalculator.PDFCalculator with parameters as following:
rmin = 1.5
rmax = 30
rstep = np.pi / 23.0
qmin = 0.5
qmax = 23
qdamp = 0.04
qbroad = 0.01
adp = 0.008
Then for any structure loaded from CIF, the PDFs generated for this structure are identical for any qmax>23. I have included an example code for your convenience. If you change qmax for some number larger than 23 and use the same cif file, then you will find the output g's are the same.

from diffpy.structure import Structure, loadStructure
from diffpy.srreal.pdfcalculator import PDFCalculator
s = loadStructure(cif_dir)
s.Uisoequiv = 0.008
cfg = {'qmax': 23, 'qmin': 0.5, 'rmin': 1.5, 'rmax': 30, 'rstep': np.pi / 23.0, 'qdamp': 0.04, 'qbroad': 0.01}
pc = PDFCalculator(**cfg)
r, g = pc(s)

Thank you,
Ling

diffpy.srreal master is the default while dependency libdiffpy has develop as the default branch... and it's incompatible.

getEquivalentAtoms() raises

TypeError: No to_python (by-value) converter found for C++ type: boost::shared_ptr<diffpy::srreal::AtomicStructureAdapter>

• write tests