Package: periodictable
This package provides a periodic table of the elements with
support for mass, density and xray/neutron scattering information.Masses, densities and natural abundances come from the
NIST Physics Laboratory, but do not represent a critical
evaluation by NIST scientists.Neutron scattering calculations use values collected by the
Atomic Institute of the Austrian Universities.  These values
do corresponding to those from other packages, though there
are some differences depending to the tables used.  Bound
coherent neutron scattering for gold in particular is significantly
different from older value: 7.63(6) as measured in 1974
compared to 7.90(7) as measured in 1990.X-ray scattering calculations use a combination of empirical and
theoretical values from the LBL Center for X-ray Optics.  These
values differ from those given in other sources such as the
International Tables for Crystallography, Volume C, and so may
give different results from other packages.Install using:pip install periodictableThere are several web interfaces to this package:NIST Center for Neutron Research (NCNR)Forschungs-Neutronenquelle Heinz Maier-Leibnitz (FRM II)SLD CalulatorDocumentation isavailable online.Source links:https://github.com/pkienzle/periodictablehttps://github.com/scattering/activationKnown issuesIncoherent scattering computed for contrast matched mixture in D2O_sld(),
differs from the value that would be computed for a compound with the same
isotope proportions and density computed in neutron_sld(). This may change
in a future release.The mass and composition tables are out of date. This package uses tables
from 1997 but IUPAC produced new tables in 2009.Incoherent scattering calculations for energy-dependent rare earth elements
is underestimated. The calculation requires bound incoherent scattering
lengths (b_i) and the bound coherent lengths (b_c), but only b_c is
included.Change history1.6.1 2022-05-18Modified:Calculate decay time correctly in the presence of significant long-lived
activation.Calculate b mode activation correctly for Eu[151] => Gd[152]1.6.0 2021-04-21New:Add energy dependence for rare earths (Lynn and Seeger, 1990).Modified:Use complex b_c when computing the coherent cross section, leading to
correct values of sigma_c and sigma_i for materials with large absorption.
With this change the tabulated values for B[10] are now shown to be
self-consistent within a few percent.Breaking changes:Neutron scattering factors are returned with one value for each wavelength
even for energy independent elements. Previous versions returned a scalar
if the returned value was identical for each wavelength.1.5.3 2020-11-04Breaking changes:Fix calculation of contrast match points for biomolecules. The old
formula used the density of H2O for the D2O sld calculation.Modify biomolecule support to use H[1] rather than T for labile hydrogen.
This will result in less error when the labile formula is used in lieu
of the natural formula or the contrast-matched formula, and make it more
obvious from glancing at the formula that labile hydrogen is present.Modifyfasta.Moleculeattributes, droppingHmassandHsld.Hnaturalhas been moved tonatural_formula. The formula with labile hydrogen is
stored inlabile_formula, as well asformulaas before.New:Addreplace()method to formula to allow isotope substitution.Addnsf.D2O_match()andnsf.D2O_sld()functions.Modified:Neutron wavelength now defaults to 1.798 A when wavelength and energy are
both None inneutron_sld()andneutron_scattering()rather than
throwing an assertion error.tablecan be passed to neutron sld calculators as the source of isotope
information when parsing the chemical formula.Switch unit test framework from nose to pytest.Update docs.1.5.2 2019-11-19Modified:Carbon density changed from 2.1 to 2.2 to match CXRO, CRC and RSC. The NIST
X-ray attenuation tables use 2.26; the Handbook of Mineralogy has 2.09-2.23.
The Neutron Data Booklet gave the value as 1.9-2.3, and 2.1 was chosen
from this range.  The remaining density will continue to use values from the
Neutron Data Booklet, which cites CRC as the primary source.Updated references.1.5.1 2019-09-09Modified:fasta uses natural abundance of H for biomolecule when computing the
D2O contrast match rather than the biomolecule with pure H[1].remove half-life units from column header in activation table since
each row gives its own units.1.5.0 2017-05-11New:mixture by mass and volume, e.g., 5 g NaCl // 50 mL H2O@1multilayer materials, e.g., 5 um Si // 3 nm Cr // 8 nm Auadd support for bio molecules with labile hydrogensupdate list of possible oxidation states to include rare statesModified:fixed computation of incoherent cross section so it is consistent with
coherent cross section and total cross section1.4.1 2014-02-04Modified:default density is now the isotopic density rather than the natural density1.4.0 2013-12-20support python 3.31.3.10 2013-10-25Modified:fix activation calculation to ignore fast neutrons in thermal environmentadd emission spectra for remaining elements above neon1.3.9 2013-04-23Modified:Update requirements to pyparsing<2.0.0 (we don’t support python 3 yet)1.3.8 2013-04-08New:formula parser supports density spec and mix by weight/mix by volumeModified:py2exe/py2app wrapping now includes missing activation.datskipping bad 1.3.7 build which didn’t include all changes1.3.6 2013-03-05New:add activation decay time to neutron activation calculatorModified:Change neutron scattering calculations for incoherent cross section
to be the linear combination of the incoherent cross sections of the
individual atoms rather than total cross section minus the coherent
cross section.  Penetration depth of the unscattered beam still uses
the total cross section plus the absorption cross section.1.3.5 2013-02-26New:formulas now report charge and mass_fractionformula parser accepts ions as Yy{#+} or Yy[#]{#+} for isotopessupport neutron activation calculationssupport xray refraction index and mirror reflectivityModified:update X-ray scattering tables for Zradjust ion mass for number of electronsions now display as Yy{#+} rather than Yy^{#+}fix formula.natural_densityfix formula.hill so C,H come firstfix element.interatomic_distanceformula(value=…) -> formula(compound=…)1.3  2010-12-05New:mix_by_weight and mix_by_volume formula constructorsuse natural density to set density for isotope specific formulasadd neutron_scattering function which returns xs, sld and penetration depthModified:need wavelength= or energy= for xray/neutron sldimproved docs and testing1.2  2010-04-28New:support pickle: id(H) == id(loads(dumps(H)))support ions, with magnetic form factors and x-ray f0 scattering factorsupport py2exe wrappersallow density to be calculated from structure (bcc, fcc, hcp, cubic, diamond)estimate molecular volumesupport private tables with some values replaced by applicationModified:rename package periodictablerename table to periodictable.elementsneutron sld returns real and imaginary coherent and incoherent
instead of coherent, absorption and incoherentbug fix: sld for H[2] was wrong when queried before sld for H.remove CrysFML ionic radius definitions1.1  2009-01-20Modified:Restructure package, separating tests into different directoryWhen defining table extensions, you should now do:from elements.core import periodic_table, Element, Isotoperather than:from elements import periodic_table
from elements.elements import Element, Isotope