Merge pull request #58 from pkienzle/fix-use-iupac-abundance

Use IUPAC tables for atomic weight and isotopic abundance

MANIFEST.in

@@ -1,7 +1,9 @@
 include LICENSE.txt
-include doc
-include periodictable/xsf/*
-include periodictable/activation.dat
+graft doc
 prune doc/sphinx/_build
 prune doc/sphinx/build
-exclude build dist *.pyc
+prune */__pycache__
+prune */*/__pycache__
+prune */*/*/__pycache__
+#recursive-exclude __pycache__ *
+#exclude build dist *.pyc __pycache__/*

README.rst

@@ -5,23 +5,21 @@ 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.
 
-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.
+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::
 
@@ -62,17 +60,28 @@ Known issues
   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
+  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
 ----------------
 

doc/sphinx/guide/data_sources.rst

@@ -7,8 +7,11 @@ Data Sources
 Physical constants
     `NIST Physics Laboratory - Constants, units and uncertainty <http://physics.nist.gov/cuu/index.html>`_
 
-Atomic and isotope mass
-    `NIST Physics Laboratory - Atomic weights and isotope composition <http://physics.nist.gov/PhysRefData/Compositions/>`_
+Isotope mass
+    `IAEA Atomic Mass Data Center AME2020 <https://www-nds.iaea.org/amdc/>`_
+
+Atomic weight and isotope abundance
+    `IUPAC commission on isotope abundances and atomic weights <https://www.ciaaw.org>`_
 
 Atomic density
     *ILL Neutron Data Booklet*

doc/sphinx/guide/formula_grammar.rst

@@ -116,15 +116,15 @@ A formula string is translated into a formula using
 * Specific mass can be giving with count follwed by mass units:
 
     >>> print(formula("5g NaCl // 50mL H2O@1"))
-    NaCl(H2O)32.4407
+    NaCl(H2O)32.4395
 
   Density will be required for materials given by volume.  Mass will be
   stored in the *total_mass* attribute of the resulting formula.
 
 * Multilayers can be specified by thickness:
 
     >>> print(formula("1 um Si // 5 nm Cr // 10 nm Au"))
-    Si119.99CrAu1.41722
+    Si119.992CrAu1.41722
 
   Density will be required for each layer. Thickness will be stored in
   the *total_thickness* attribute of the resulting formula. Thickness can
@@ -135,7 +135,7 @@ A formula string is translated into a formula using
   20:80 by volume with D2O:
 
     >>> print(formula("20vol% (10 wt% [email protected] // H2O@1) // D2O@1n"))
-    NaCl(H2O)29.1966(D2O)122.794
+    NaCl(H2O)29.1956(D2O)122.79
 
 * Empty formulas are supported, e.g., for air or vacuum:
 
@@ -257,7 +257,7 @@ Note that this is different from a 2:1 mixture by weight:
 
     >>> mix = mix_by_weight(H2O,2,D2O,1)
     >>> print(f"{mix} {mix.density:.4g}")
-    (H2O)2.2234D2O 1.035
+    (H2O)2.22339D2O 1.035
 
 Except in the simplest of cases, the density of the mixture cannot be
 computed from the densities of the components, and the resulting density
@@ -273,8 +273,8 @@ compute molar mass and neutron/xray scattering length density:
     >>> import periodictable
     >>> SiO2 = periodictable.formula('SiO2')
     >>> hydrated = SiO2 + periodictable.formula('3H2O')
-    >>> print(f"{hydrated} mass {hydrated.mass}")
-    SiO2(H2O)3 mass 114.13014
+    >>> print(f"{hydrated} mass {hydrated.mass:.3f}")
+    SiO2(H2O)3 mass 114.128
     >>> rho,mu,inc = periodictable.neutron_sld('SiO2+3H2O',density=1.5,wavelength=4.75)
     >>> print(f"{hydrated} neutron sld {rho:.3g}")
     SiO2(H2O)3 neutron sld 0.849

doc/sphinx/guide/using.rst

@@ -18,7 +18,7 @@ Access particular elements by name:
 
     >>> from periodictable import hydrogen
     >>> print("H mass %s %s"%(hydrogen.mass, hydrogen.mass_units))
-    H mass 1.00794 u
+    H mass 1.008 u
 
 Access particular elements as symbols:
 
@@ -54,7 +54,7 @@ Import all elements:
     >>> print(periodictable.H)
     H
     >>> print(periodictable.H.mass)
-    1.00794
+    1.008
 
 Deuterium and tritium are special isotopes named D and T
 some neutron information is available as 'n':
@@ -64,7 +64,7 @@ some neutron information is available as 'n':
     >>> print("D mass %s"%D.mass)
     D mass 2.01410177784
     >>> print("neutron mass %s"%n.mass)
-    neutron mass 1.00866491597
+    neutron mass 1.0086649159
 
 Process all the elements:
 

periodictable/constants.py

@@ -15,12 +15,16 @@
 #: electron radius r_e (m)
 electron_radius = 2.8179402894e-15 #(58) m
 
-# From NIST Reference on Constants, Units, and Uncertainty
+# [CODATA] From NIST Reference on Constants, Units, and Uncertainty
 #   http://physics.nist.gov/cuu/index.html
-# neutron mass = 1.008 664 915 97(43) u
-# atomic mass constant m_u = 1.660 538 782(83) x 10-27 kg
+# [AME2020] "The Ame2020 atomic mass evaluation (II)"
+#     by M.Wang, W.J.Huang, F.G.Kondev, G.Audi and S.Naimi
+#     Chinese Physics C45, 030003, March 2021.
 #: neutron mass (u)
-neutron_mass = 1.00866491597 #(43) u
+neutron_mass = 1.00866491590 #(47) u [AME 2020]
+neutron_mass_unc = 0.00000000047
+#neutron_mass = 1.00866491597 #(43) u [CODATA 2010?]
+#neutron_mass = 1.00866491595 #(49) u [CODATA 2018]
 #: atomic mass constant (kg / u)
 atomic_mass_constant = 1.660538782e-27 #(83) kg / u
 #: electron mass (u)

periodictable/core.py

@@ -378,7 +378,7 @@ def list(self, *props, **kw):
 
             >>> from periodictable import elements
             >>> elements.list('symbol', 'mass', 'density',
-            ...     format="%-2s: %6.2f u %5.2f g/cm^3") # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
+            ...     format="%-2s: %6.2f u %6.2f g/cm^3") # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
             H :   1.01 u   0.07 g/cm^3
             He:   4.00 u   0.12 g/cm^3
             Li:   6.94 u   0.53 g/cm^3

periodictable/fasta.py

@@ -478,14 +478,14 @@ def fasta_table():
     rows += [v for k, v in sorted(NUCLEIC_ACID_COMPONENTS.items())]
     rows += [Sequence("beta casein", beta_casein)]
 
-    print("%20s %7s %7s %7s %5s %5s %5s %5s %5s %5s"
+    print("%25s %7s %7s %7s %5s %5s %5s %5s %5s %5s"
           % ("name", "M(H2O)", "M(D2O)", "volume",
              "den", "#el", "xray", "nH2O", "nD2O", "%D2O match"))
     for v in rows:
         protons = sum(num*el.number for el, num in v.natural_formula.atoms.items())
         electrons = protons - v.charge
         Xsld = xray_sld(v.formula, wavelength=elements.Cu.K_alpha)
-        print("%20s %7.1f %7.1f %7.1f %5.2f %5d %5.2f %5.2f %5.2f %5.1f"%(
+        print("%25s %7.1f %7.1f %7.1f %5.2f %5d %5.2f %5.2f %5.2f %5.1f"%(
             v.name, v.mass, v.Dmass, v.cell_volume, v.natural_formula.density,
             electrons, Xsld[0], v.sld, v.Dsld, v.D2Omatch))
 
@@ -499,11 +499,15 @@ def test():
     # name        Hmass   Dmass   vol     den   #el   xray  Hsld  Dsld
     # =========== ======= ======= ======= ===== ===== ===== ===== =====
     # beta casein 23561.9 23880.9 30872.9  1.27 12614 11.55  1.68  2.75
+    # ... updated for new mass table [2023-08]
+    #   same      23562.3 23881.2   same   1.27 same         1.68  2.75
     seq = Sequence("beta casein", beta_casein)
-    assert abs(seq.mass - 23561.9) < 0.1
-    assert abs(seq.Dmass - 23880.9) < 0.1
+    density = seq.mass/avogadro_number/seq.cell_volume*1e24
+    #print(seq.mass, seq.Dmass, density, seq.sld, seq.Dsld)
+    assert abs(seq.mass - 23562.3) < 0.1
+    assert abs(seq.Dmass - 23881.2) < 0.1
     assert abs(seq.cell_volume - 30872.9) < 0.1
-    assert abs(seq.mass/avogadro_number/seq.cell_volume*1e24 - 1.267) < 0.01
+    assert abs(density - 1.267) < 0.01
     assert abs(seq.sld - 1.68) < 0.01
     assert abs(seq.Dsld - 2.75) < 0.01
 
@@ -516,3 +520,4 @@ def test():
 
 if __name__ == "__main__":
     fasta_table()
+    #test()