Extensible periodic table of the elements
Project description
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.
Xray scattering calculations use a combination of empirical and theoretical values from the LBL Center for Xray 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 periodictable
There are several web interfaces to this package:
Documentation is available online.
Source links:
Known issues
Incoherent 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The mass and composition tables are out of date.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 energydependent 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 history
1.6.1 20220518
Modified:
Calculate decay time correctly in the presence of significant longlived activation.
Calculate b mode activation correctly for Eu[151] => Gd[152]
1.6.0 20210421
New:
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 selfconsistent 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 20201104
Breaking 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 contrastmatched formula, and make it more obvious from glancing at the formula that labile hydrogen is present.
Modify fasta.Molecule attributes, dropping Hmass and Hsld. Hnatural has been moved to natural_formula. The formula with labile hydrogen is stored in labile_formula, as well as formula as before.
New:
Add replace() method to formula to allow isotope substitution.
Add nsf.D2O_match() and nsf.D2O_sld() functions.
Modified:
Neutron wavelength now defaults to 1.798 A when wavelength and energy are both None in neutron_sld() and neutron_scattering() rather than throwing an assertion error.
table can 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 20191119
Modified:
Carbon density changed from 2.1 to 2.2 to match CXRO, CRC and RSC. The NIST Xray attenuation tables use 2.26; the Handbook of Mineralogy has 2.092.23. The Neutron Data Booklet gave the value as 1.92.3, 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 20190909
Modified:
fasta uses natural abundance of H for biomolecule when computing the D2O contrast match rather than the biomolecule with pure H[1].
remove halflife units from column header in activation table since each row gives its own units.
1.5.0 20170511
New:
mixture by mass and volume, e.g., 5 g NaCl // 50 mL H2O@1
multilayer materials, e.g., 5 um Si // 3 nm Cr // 8 nm Au
add support for bio molecules with labile hydrogens
update list of possible oxidation states to include rare states
Modified:
fixed computation of incoherent cross section so it is consistent with coherent cross section and total cross section
1.4.1 20140204
Modified:
default density is now the isotopic density rather than the natural density
1.4.0 20131220
support python 3.3
1.3.10 20131025
Modified:
fix activation calculation to ignore fast neutrons in thermal environment
add emission spectra for remaining elements above neon
1.3.9 20130423
Modified:
Update requirements to pyparsing<2.0.0 (we don’t support python 3 yet)
1.3.8 20130408
New:
formula parser supports density spec and mix by weight/mix by volume
Modified:
py2exe/py2app wrapping now includes missing activation.dat
skipping bad 1.3.7 build which didn’t include all changes
1.3.6 20130305
New:
add activation decay time to neutron activation calculator
Modified:
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 20130226
New:
formulas now report charge and mass_fraction
formula parser accepts ions as Yy{#+} or Yy[#]{#+} for isotopes
support neutron activation calculations
support xray refraction index and mirror reflectivity
Modified:
update Xray scattering tables for Zr
adjust ion mass for number of electrons
ions now display as Yy{#+} rather than Yy^{#+}
fix formula.natural_density
fix formula.hill so C,H come first
fix element.interatomic_distance
formula(value=…) > formula(compound=…)
1.3 20101205
New:
mix_by_weight and mix_by_volume formula constructors
use natural density to set density for isotope specific formulas
add neutron_scattering function which returns xs, sld and penetration depth
Modified:
need wavelength= or energy= for xray/neutron sld
improved docs and testing
1.2 20100428
New:
support pickle: id(H) == id(loads(dumps(H)))
support ions, with magnetic form factors and xray f0 scattering factor
support py2exe wrappers
allow density to be calculated from structure (bcc, fcc, hcp, cubic, diamond)
estimate molecular volume
support private tables with some values replaced by application
Modified:
rename package periodictable
rename table to periodictable.elements
neutron sld returns real and imaginary coherent and incoherent instead of coherent, absorption and incoherent
bug fix: sld for H[2] was wrong when queried before sld for H.
remove CrysFML ionic radius definitions
1.1 20090120
Modified:
Restructure package, separating tests into different directory
When defining table extensions, you should now do:
from elements.core import periodic_table, Element, Isotope
rather than:
from elements import periodic_table from elements.elements import Element, Isotope
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