Materials

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materials

Materials¶

Materials are the primary container for radionuclides. They map nuclides to mass weights, though they contain methods for converting to/from atom fractions as well. In many ways they take inspiration from numpy arrays and python dictionaries. Materials have two main attributes which define them.

  1. comp: a normalized composition mapping from nuclides (zzaaam-ints) to mass-weights (floats).
  2. mass: the mass of the material.

By keeping the mass and the composition separate, operations that only affect one attribute may be performed independent of the other. Additionally, most of the functionality is implemented in a C++ class by the same name, so this interface is very fast and light-weight. Materials may be initialized in a number of different ways. For example, initializing from dictionaries of compositions are shown below.

In [1]:
from pyne.material import Material

leu = Material({'U238': 0.96, 'U235': 0.04}, 42)
leu
-c:1: QAWarning: pyne.nucname is not yet QA compliant.
-c:1: QAWarning: pyne.data is not yet QA compliant.
-c:1: QAWarning: pyne.material is not yet QA compliant.
Out[1]:
pyne.material.Material({922350000: 0.04, 922380000: 0.96}, 42.0, -1.0, -1.0, {})
In [2]:
nucvec = {10010:  1.0, 80160:  1.0, 691690: 1.0, 922350: 1.0,
          922380: 1.0, 942390: 1.0, 942410: 1.0, 952420: 1.0,
          962440: 1.0}
mat = Material(nucvec)
print mat
Material:
mass = 9.0
density = -1.0
atoms per molecule = -1.0
-------------------------
H1     0.111111111111
O16    0.111111111111
Tm169  0.111111111111
U235   0.111111111111
U238   0.111111111111
Pu239  0.111111111111
Pu241  0.111111111111
Am242  0.111111111111
Cm244  0.111111111111

Normalization¶

Materials may also be initialized from plain text or HDF5 files (see Material.from_text and Material.from_hdf5). Once you have a Material instance, you can always obtain the unnormalized mass vector through Material.mult_by_mass. Normalization routines to normalize the mass Material.normalize or the composition Material.norm_comp are also available.

In [3]:
leu.mult_by_mass()
Out[3]:
{922350000: 1.68, 922380000: 40.32}
In [4]:
mat.normalize()
mat.mult_by_mass()
Out[4]:
{10010000: 0.1111111111111111, 80160000: 0.1111111111111111, 691690000: 0.1111111111111111, 922350000: 0.1111111111111111, 922380000: 0.1111111111111111, 942390000: 0.1111111111111111, 942410000: 0.1111111111111111, 952420000: 0.1111111111111111, 962440000: 0.1111111111111111}
In [5]:
mat.mass
Out[5]:
1.0

Material Arithmetic¶

Furthermore, various arithmetic operations between Materials and numeric types are also defined. Adding two Materials together will return a new Material whose values are the weighted union of the two original. Multiplying a Material by 2, however, will simply double the mass.

In [6]:
other_mat = mat * 2
other_mat
Out[6]:
pyne.material.Material({10010000: 0.11111111111111108, 80160000: 0.11111111111111108, 691690000: 0.11111111111111108, 922350000: 0.11111111111111108, 922380000: 0.11111111111111108, 942390000: 0.11111111111111108, 942410000: 0.11111111111111108, 952420000: 0.11111111111111108, 962440000: 0.11111111111111108}, 2.0, -1.0, -1.0, {})
In [7]:
other_mat.mass
Out[7]:
2.0
In [8]:
weird_mat = leu + mat * 18
print weird_mat
Material:
mass = 60.0
density = -1.0
atoms per molecule = -1.0
-------------------------
H1     0.0333333333333
O16    0.0333333333333
Tm169  0.0333333333333
U235   0.0613333333333
U238   0.705333333333
Pu239  0.0333333333333
Pu241  0.0333333333333
Am242  0.0333333333333
Cm244  0.0333333333333

Raw Member Access¶

You may also change the attributes of a material directly without generating a new material instance.

In [9]:
other_mat.mass = 10
other_mat.comp = {10020: 3, 922350: 15.0}
print other_mat
Material:
mass = 10.0
density = -1.0
atoms per molecule = -1.0
-------------------------
H2     3.0
U235   15.0

Of course when you do this you have to be careful because the composition and mass may now be out of sync. This may always be fixed with normalization.

In [10]:
other_mat.norm_comp()
print other_mat
Material:
mass = 10.0
density = -1.0
atoms per molecule = -1.0
-------------------------
H2     0.166666666667
U235   0.833333333333

Indexing & Slicing¶

Additionally (and very powerfully!), you may index into either the material or the composition to get, set, or remove sub-materials. Generally speaking, the composition you may only index into by integer-key and only to retrieve the normalized value. Indexing into the material allows the full range of operations and returns the unnormalized mass weight. Moreover, indexing into the material may be performed with integer-keys, string-keys, slices, or sequences of nuclides.

In [11]:
leu.comp[922350000]
Out[11]:
0.04
In [12]:
leu['U235']
Out[12]:
1.68
In [13]:
weird_mat['U':'Am']
Out[13]:
pyne.material.Material({922350000: 0.07359999999999998, 922380000: 0.8464, 942390000: 0.03999999999999998, 942410000: 0.03999999999999998}, 50.0, -1.0, -1.0, {})
In [14]:
other_mat[:920000000] = 42.0
print other_mat
Material:
mass = 84.0
density = -1.0
atoms per molecule = -1.0
-------------------------
H2     0.5
U235   0.5
In [15]:
del mat[962440, 'TM169', 'Zr90', 80160]
mat[:]
Out[15]:
pyne.material.Material({10010000: 0.16666666666666663, 922350000: 0.16666666666666663, 922380000: 0.16666666666666663, 942390000: 0.16666666666666663, 942410000: 0.16666666666666663, 952420000: 0.16666666666666663}, 0.666666666667, -1.0, -1.0, {})

Other methods also exist for obtaining commonly used sub-materials, such as gathering the Uranium or Plutonium vector.

Molecular Mass & Atom Fractions¶

You may also calculate the molecular mass of a material via the Material.molecular_mass method. This uses the pyne.data.atomic_mass function to look up the atomic mass values of the constituent nuclides.

In [16]:
leu.molecular_mass()
Out[16]:
237.92903775287186

Note that by default, materials are assumed to have one atom per molecule. This is a poor assumption for more complex materials. For example, take water. Without specifying the number of atoms per molecule, the molecular mass calculation will be off by a factor of 3. This can be remedied by passing the correct number to the method. If there is no other valid number of molecules stored on the material, this will set the appropriate attribute on the class.

In [17]:
h2o = Material({10010000: 0.11191487328808077, 80160000: 0.8880851267119192})
h2o.molecular_mass()
Out[17]:
6.003521561343334
In [18]:
h2o.molecular_mass(3.0)
h2o.atoms_per_molecule
Out[18]:
3.0

It is often also useful to be able to convert the current mass-weighted material to an atom fraction mapping. This can be easily done via the :meth:Material.to_atom_frac method. Continuing with the water example, if the number of atoms per molecule is properly set then the atom fraction return is normalized to this amount. Alternatively, if the atoms per molecule are set to its default state on the class, then a truly fractional number of atoms is returned.

In [19]:
h2o.to_atom_frac()
Out[19]:
{10010000: 2.0, 80160000: 1.0}
In [20]:
h2o.atoms_per_molecule = -1.0
h2o.to_atom_frac()
Out[20]:
{10010000: 0.6666666666666666, 80160000: 0.3333333333333333}

Additionally, you may wish to convert the an existing set of atom fractions to a new material stream. This can be done with the :meth:Material.from_atom_frac method, which will clear out the current contents of the material's composition and replace it with the mass-weighted values. Note that when you initialize a material from atom fractions, the sum of all of the atom fractions will be stored as the atoms per molecule on this class. Additionally, if a mass is not already set on the material, the molecular mass will be used.

In [21]:
h2o_atoms = {10010: 2.0, 'O16': 1.0}
h2o = Material()
h2o.from_atom_frac(h2o_atoms)

print h2o.comp
print h2o.atoms_per_molecule
print h2o.mass
print h2o.molecular_mass()
{10010: 0.1111425112195276, 80160000: 0.8888574887804724}
3.0
17.9949146196
17.9949146196

Moreover, other materials may also be used to specify a new material from atom fractions. This is a typical case for reactors where the fuel vector is convolved inside of another chemical form. Below is an example of obtaining the Uranium-Oxide material from Oxygen and low-enriched uranium.

In [22]:
uox = Material()
uox.from_atom_frac({leu: 1.0, 'O16': 2.0})
print uox
Material:
mass = 269.918866992
density = -1.0
atoms per molecule = 3.0
------------------------
O16    0.118516462356
U235   0.0352593415057
U238   0.846224196138

NOTE: Materials may be used as keys in a dictionary because they are hashable.

User-defined Metadata¶

Materials also have an attrs attribute which allows users to store arbitrary custom information about the material. This can include things like units, comments, provenance information, or anything else the user desires. This is implemented as an in-memory JSON object attached to the C++ class. Therefore, what may be stored in the attrs is subject to the same restrictions as JSON itself. The top-level of the attrs should be a dictionary, though this is not explicitly enforced.

In [23]:
leu = Material({922350: 0.05, 922380: 0.95}, 15, attrs={'units': 'kg'})
leu
Out[23]:
pyne.material.Material({922350000: 0.05, 922380000: 0.95}, 15.0, -1.0, -1.0, {})
In [24]:
print leu
Material:
mass = 15.0
density = -1.0
atoms per molecule = -1.0
-------------------------
U235   0.05
U238   0.95
In [25]:
leu.metadata
Out[25]:
{}
In [26]:
m = leu.metadata
m['comments'] = ['Anthony made this material.']
leu.metadata['comments'].append('And then Katy made it better!')
m['id'] = 42
leu.metadata
Out[26]:
{"comments":["Anthony made this material.","And then Katy made it better!"],"id":42}
In [27]:
leu.metadata = {'units': 'solar mass'}
leu.metadata
Out[27]:
{"units":"solar mass"}
In [28]:
m
Out[28]:
{"units":"solar mass"}
In [29]:
leu.metadata['units'] = 'not solar masses'
leu.metadata['units']
Out[29]:
u'not solar masses'

As you can see from the above, the attrs interface provides a view into the underlying JSON object. This can be manipulated directly or by renaming it to another variable. Additionally, attrs can be replaced with a new object of the appropriate type. Doing so invalidates any previous views into this container.