Remove element Z=0 (neutron) from table. Refs #45

doc/sphinx/guide/using.rst

@@ -56,15 +56,12 @@ Import all elements:
     >>> print(periodictable.H.mass)
     1.008
 
-Deuterium and tritium are special isotopes named D and T
-some neutron information is available as 'n':
+Deuterium and tritium are special isotopes named D and T:
 
 .. doctest::
 
     >>> print("D mass %s"%D.mass)
     D mass 2.01410177784
-    >>> print("neutron mass %s"%n.mass)
-    neutron mass 1.0086649159
 
 Process all the elements:
 
@@ -73,7 +70,6 @@ Process all the elements:
     >>> import periodictable
     >>> for el in periodictable.elements: # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
     ...     print("%s %s"%(el.symbol,el.name))
-    n neutron
     H hydrogen
     He helium
        ...
@@ -86,7 +82,6 @@ Another example for processing all elements:
     >>> from periodictable import elements
     >>> for el in elements: # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
     ...     print("%s %s"%(el.symbol,el.number))
-    n 0
     H 1
     He 2
        ...

periodictable/core.py

@@ -188,8 +188,7 @@ class PeriodicTable(object):
         56-Fe
 
 
-    Deuterium and tritium are defined as 'D' and 'T'.  Some
-    neutron properties are available in ``elements[0]``.
+    Deuterium and tritium are defined as 'D' and 'T'.
 
     To show all the elements in the table, use the iterator:
 
@@ -198,7 +197,6 @@ class PeriodicTable(object):
         >>> from periodictable import *
         >>> for el in elements:  # lists the element symbols
         ...     print("%s %s"%(el.symbol, el.name))  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
-        n neutron
         H hydrogen
         He helium
         ...
@@ -606,7 +604,7 @@ def _make_isotope_ion(table, Z, n, c):
 element_base = {
     # number: name symbol common_ions uncommon_ions
     # ion info comes from Wikipedia: list of oxidation states of the elements.
-    0: ['Neutron',     'n',  [],         []],
+    # 0: ['Neutron',     'n',  [],         []],
     1: ['Hydrogen',    'H',  [-1, 1],    []],
     2: ['Helium',      'He', [],         [1, 2]],  # +1,+2  http://periodic.lanl.gov/2.shtml
     3: ['Lithium',     'Li', [1],        []],

periodictable/covalent_radius.py

@@ -75,7 +75,8 @@ def init(table, reload=False):
         return
     table.properties.append('covalent_radius')
 
-    table[0].covalent_radius = 0.20
+    # neutron covalent radius of 0.20 A ? Not sure where that value came from
+    # table[0].covalent_radius = 0.20
     Element.covalent_radius_units = 'angstrom'
     Element.covalent_radius = None
     Element.covalent_radius_uncertainty = None

periodictable/crystal_structure.py

@@ -42,7 +42,6 @@
 
 
 crystal_structures = [\
-    None, #X
     {'symmetry': 'diatom', 'd': 0.74}, #H
     {'symmetry': 'atom'}, #He
     {'symmetry': 'BCC', 'a': 3.49}, #Li
@@ -155,5 +154,5 @@ def init(table, reload=False):
         return
     table.properties.append('crystal_structure')
 
-    for Z, struct in enumerate(crystal_structures):
-        table[Z].crystal_structure = struct
+    for k, struct in enumerate(crystal_structures):
+        table[k+1].crystal_structure = struct

periodictable/density.py

@@ -170,8 +170,7 @@ def init(table, reload=False):
             el.density_caveat = ""
 
 element_densities = dict(
-    # TODO: stop pretending that a bare neutron is element zero.
-    n=None,
+    # n=None,  # No longer using element 0 for a bare neutron
     H=(0.0708, "T=-252.87"),
     He=(0.122, "T=-268.93"),
     Li=0.534,

periodictable/mass.py

@@ -119,13 +119,13 @@ def init(table, reload=False):
         #iso._abundance, iso._abundance_unc = parse_uncertainty(p)
         iso._abundance, iso._abundance_unc = 0, 0
 
-    # A single neutron is an isotope of element 0
-    from .constants import neutron_mass, neutron_mass_unc
-    el = table[0]
-    el._mass, el._mass_unc = neutron_mass, neutron_mass_unc
-    iso = el.add_isotope(1)
-    iso._mass, iso._mass_unc = neutron_mass, neutron_mass_unc
-    iso._abundance, iso._abundance_unc = 100, 0
+    # # A single neutron is an isotope of element 0
+    # from .constants import neutron_mass, neutron_mass_unc
+    # el = table[0]
+    # el._mass, el._mass_unc = neutron_mass, neutron_mass_unc
+    # iso = el.add_isotope(1)
+    # iso._mass, iso._mass_unc = neutron_mass, neutron_mass_unc
+    # iso._abundance, iso._abundance_unc = 100, 0
 
     # Parse element mass table where each line looks like:
     #    z  El  element mass(unc)|[low,high]|- note note ...

periodictable/mass_2001.py

@@ -81,13 +81,13 @@ def init(table, reload=False):
         iso._mass, iso._mass_unc = parse_uncertainty(m)
         iso._abundance,iso._abundance_unc = parse_uncertainty(p) if p else (0,0)
 
-    # A single neutron is an isotope of element 0
-    from .constants import neutron_mass
-    el = table[0]
-    el._mass = neutron_mass
-    iso = el.add_isotope(1)
-    iso._mass = neutron_mass
-    iso._abundance = 100
+    # # A single neutron is an isotope of element 0
+    # from .constants import neutron_mass
+    # el = table[0]
+    # el._mass = neutron_mass
+    # iso = el.add_isotope(1)
+    # iso._mass = neutron_mass
+    # iso._abundance = 100
 
 # z-El-n,iso_mass(unc),abundance%(unc),element_mass(unc)
 massdata = """\

periodictable/nsf.py

@@ -567,6 +567,9 @@ def init(table, reload=False):
         symbol = parts[1]
         isotope_number = int(parts[2]) if len(parts) == 3 else 0
 
+        if Z == 0: # Skip row 0-n-1
+            continue
+
         # Fetch element from the table and check that the symbol matches
         element = table[Z]
         assert element.symbol == symbol, \
@@ -576,13 +579,6 @@ def init(table, reload=False):
         # it can calculate sld.
         nsf._number_density = element.number_density # N/cm^3 = N/cm^3
 
-
-        # For new elements, clear out 'neutron' attribute for isotopes
-        # This protects against isotope using the element data when
-        # they don't have any specific neutron data.
-        #if isotope_number == 0 or not hasattr(element,'neutron'):
-        #    for iso in element: iso.neutron = None
-
         if isotope_number == 0:
             # Bulk values using laboratory abundances of isotopes
             element.neutron = nsf
@@ -1876,8 +1872,6 @@ def coherent_comparison_table(table=None, tol=None):
 
         >>> coherent_comparison_table (tol=0.5) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
         Comparison of (4 pi |b_c|^2/100) and coherent
-                 n   172.03    43.01 300.0%
-               1-n   172.03    43.01 300.0%
                 Sc    18.40    19.00  -3.2%
              45-Sc    18.40    19.00  -3.2%
              65-Cu    13.08    14.10  -7.2%
@@ -1908,8 +1902,6 @@ def total_comparison_table(table=None, tol=None):
 
         >>> total_comparison_table (tol=0.1)
         Comparison of total cross section to (coherent + incoherent)
-                 n    43.01     ----
-               1-n    43.01     ----
              84-Kr     6.60     ----
             149-Sm   200.00   200.50  -0.2%
                 Eu     9.20     9.07   1.4%

test/test_core.py

@@ -22,8 +22,8 @@ def test():
 
     # Check that "for el in elements" works and for iso in el works
     els = tuple(el for el in elements)
-    assert els[0].number == 0
-    assert els[1].number == 1
+    assert els[0].number == 1
+    assert els[1].number == 2
     isotopes = tuple(iso for iso in O)
     assert isotopes[0].isotope == 12  # 12 is the first oxygen isotope listed
 

test/test_mass.py

@@ -15,8 +15,6 @@ def test():
     assert abs(periodictable.Pb[206].abundance - Pb_206_abundance) < 1e-14
     assert abs(periodictable.Pb[209].abundance - Pb_209_abundance) < 1e-14
     assert periodictable.Pb.mass == Pb_mass
-    from periodictable.constants import neutron_mass
-    assert periodictable.n.mass == neutron_mass
 
     # Check abundance totals to 0% or 100%
     for el in periodictable.elements: