=========================================
Extensible periodic table of the elements
This package provides a periodic table of the elements with
support for mass, density and xray/neutron scattering information.
Neutron scattering calculations use values collected by the
Atomic Institute of the Austrian Universities as they appear in the neutron
data booklet, with support for some energy dependent scattering
in rare earth elements given by Lynn and Seeger (1990). X-ray scattering
calculations use a combination of empirical and theoretical values from
the LBL Center for X-ray Optics.
Tabulated values differ from those given in other sources such as the
International Tables for Crystallography, Volume C, and so computed
cross sections may give different results from other packages.
Neutron activation calculations are based on Shleien (1998), with
isotopes important to health physics. They do not perform a full
activation analysis, but instead give a gross estimate of the amount
of activation expected for a sample in the beam.
Install using::
pip install periodictable
There are several web interfaces to this package:
NIST Center for Neutron Research (NCNR) <https://www.ncnr.nist.gov/resources/activation>_Forschungs-Neutronenquelle Heinz Maier-Leibnitz (FRM II) <https://webapps.frm2.tum.de/intranet/activation/>_SLD Calulator <https://sld-calculator.appspot.com/>_
Documentation is available online <https://periodictable.readthedocs.io>_.
Source links:
|CI| |RTD| |DOI|
.. |CI| image:: https://github.com/pkienzle/periodictable/workflows/Test/badge.svg
:alt: Build status
:target: https://github.com/pkienzle/periodictable/actions
.. |DOI| image:: https://zenodo.org/badge/1146700.svg
:alt: DOI tag
:target: https://zenodo.org/badge/latestdoi/1146700
.. |RTD| image:: https://readthedocs.org/projects/periodictable/badge/?version=latest
:alt: Documentation status
:target: https://periodictable.readthedocs.io/en/latest/?badge=latest
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.
-
Incoherent scattering calculations for energy-dependent rare earth elements
is underestimated. The calculation requires bound incoherent scattering
length (b_i) but only the bound coherent scattering length (b_c) is
included.
Change history
1.7.0 2023-07-??
Modified:
- Move to IAEA AME2020 for isotope mass
- Move to IUPAC CIAAW 2021 for atomic weight and isotopic abundance
- Li-6:Li-7 mass ratio changed from 12.2 to 19.6 (delta = 2.7%)
- Isotope percentage changed by 0.1 to 0.5 for B, Zn, Ge, Se, Mo, Er, Yb, Pt, Hg
- Atomic weight changed by 0.04% for Zn, 0.02% for S and 0.01% for Li, Ge, Se, Mo
- Neutron b_c changed for Zn-70 from 6.9 to 6.0 (fixes a typo in the original table)
- Fix typos in uncertainties in the neutron table (Zr-90, Te-124, Ba-138, Sm-147)
1.6.1 2022-05-18
Modified:
- 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 2021-04-21
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
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 2020-11-04
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 contrast-matched 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 2019-11-19
Modified:
- 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 2019-09-09
Modified:
- 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 2017-05-11
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 2014-02-04
Modified:
- default density is now the isotopic density rather than the natural density
1.4.0 2013-12-20
1.3.10 2013-10-25
Modified:
- fix activation calculation to ignore fast neutrons in thermal environment
- add emission spectra for remaining elements above neon
1.3.9 2013-04-23
Modified:
- Update requirements to pyparsing<2.0.0 (we don't support python 3 yet)
1.3.8 2013-04-08
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 2013-03-05
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 2013-02-26
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 X-ray 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 2010-12-05
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 2010-04-28
New:
- support pickle: id(H) == id(loads(dumps(H)))
- support ions, with magnetic form factors and x-ray 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 2009-01-20
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