Materials

This module contains the Material class, which is used to represent nuclear materials throughout PyNE.

All functionality may be found in the material package:

from pyne.material import Material

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

In [2]: leu = Material({'U238': 0.96, 'U235': 0.04}, 42)

In [3]: leu
Out[3]: pyne.material.Material({922350: 0.04, 922380: 0.96}, 42.0, -1.0, {})

In [4]: 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}

In [5]: mat = Material(nucvec)

In [6]: print mat
Material:
mass = 9.0
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

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 [7]: leu.mult_by_mass()
Out[7]: {922350: 1.68, 922380: 40.32}

In [8]: mat.normalize()

In [9]: mat.mult_by_mass()
Out[9]: {10010: 0.111111111111, 80160: 0.111111111111, 691690: 0.111111111111,
   ...:  922350: 0.111111111111, 922380: 0.111111111111, 942390: 0.111111111111,
   ...:  942410: 0.111111111111, 952420: 0.111111111111, 962440: 0.111111111111}

In [10]: mat.mass
Out[10]: 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 [11]: other_mat = mat * 2

In [12]: other_mat
Out[12]: pyne.material.Material({10010: 0.111111111111, 80160: 0.111111111111, 691690: 0.111111111111,
   ...:                          922350: 0.111111111111, 922380: 0.111111111111, 942390: 0.111111111111,
   ...:                          942410: 0.111111111111, 952420: 0.111111111111, 962440: 0.111111111111},
   ...:                          2.0, {})

In [13]: other_mat.mass
Out[13]: 2.0

In [14]: weird_mat = leu + mat * 18

In [15]: print weird_mat
Material:
mass = 60.0
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 [16]: other_mat.mass = 10

In [18]: other_mat.comp = {'H2': 3, 922350: 15.0}

In [19]: print other_mat
Material:
mass = 10.0
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 [20]: other_mat.norm_comp()

In [21]: print other_mat
Material:
mass = 10.0
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 [22]: leu.comp[922350]
Out[22]: 0.04

In [23]: leu['U235']
Out[23]: 1.68

In [24]: weird_mat['U':'Am']
Out[24]: pyne.material.Material({922350: 0.0736, 922380: 0.8464, 942390: 0.04, 942410: 0.04}, 50.0, -1.0, {})

In [25]: other_mat[:920000] = 42.0

In [26]: print other_mat
Material:
mass = 50.3333333333
atoms per molecule = -1.0
-------------------------
H2     0.834437086093
U235   0.165562913907

In [27]: del mat[962440, 'TM169', 'Zr90', 80160]

In [28]: mat[:]
Out[28]: pyne.material.Material({10010: 0.166666666667, 922350: 0.166666666667, 922380: 0.166666666667,
   ...:                          942390: 0.166666666667, 942410: 0.166666666667, 952420: 0.166666666667},
   ...:                          0.666666666667, -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 [29]: leu.molecular_mass()
Out[29]: 237.9290388038301

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 [30]: h2o = Material({10010: 0.11191487328808077, 80160: 0.8880851267119192})

In [31]: h2o.molecular_mass()
Out[31]: 6.003521561343334

In [32]: h2o.molecular_mass(3.0)
Out[32]: 18.01056468403

In [33]: h2o.atoms_per_molecule
Out[33]: 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 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 [34]: h2o.to_atom_frac()
Out[34]: {10010: 2.0, 80160: 1.0}

In [35]: h2o.atoms_per_molecule = -1.0

In [36]: h2o.to_atom_frac()
Out[36]: {10010: 0.666666666667, 80160: 0.333333333333}

Additionally, you may wish to convert the an existing set of atom fractions to a new material stream. This can be done with the 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 [37]: h2o_atoms = {10010: 2.0, 'O16': 1.0}

In [38]: h2o = Material()

In [39]: h2o.from_atom_frac(h2o_atoms)

In [40]: h2o.comp
Out[40]: {10010: 0.111914873288, 80160: 0.888085126712}

In [41]: h2o.atoms_per_molecule
Out[41]: 3.0

In [42]: h2o.mass
Out[42]: 18.01056468403

In [43]: h2o.molecular_mass()
Out[43]: 18.01056468403

Similarly, you may also be interested in knowing the atom density of a material. This can be done by using the Material.to_atom_dens() method which returns the atom densities in units [atoms/cc]. Below is an example using water.

In [44]: h2o = {10010000: 0.11191487328808077, 80160000: 0.8880851267119192}

In [45]: mat = Material(h2o, density=1.0)

In [46]: mat.to_atom_dens()
Out[46]: {10010000: 6.687343351693846e+22, 80160000: 3.343671675846923e+22}

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 [47]: uox = Material()

In [48]: uox.from_atom_frac({leu: 1.0, 'O16': 2.0})

In [49]: print uox
Material:
mass = 269.918868043
atoms per molecule = 3.0
------------------------
O16    0.118516461895
U235   0.0352593415242
U238   0.846224196581

Note

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

User-defined Metadata

Materials also have an metadata 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 metadata is subject to the same restrictions as JSON itself. The top-level of the metadata should be a dictionary, though this is not explicitly enforced.

In [50]: leu = Material({922350: 0.05, 922380: 0.95}, 15, metadata={'units': 'kg'})

In [51]: print leu
Material:
mass = 15.0
atoms per molecule = -1.0
units = kg
-------------------------
U235   0.05
U238   0.95

In [52]: leu
Out[52]: pyne.material.Material({922350: 0.05, 922380: 0.95}, 15.0, -1.0 {"units":"kg"})

In [53]: leu.metadata
Out[53]: {"units":"kg"}

In [54]: a = leu.metadata

In [55]: a['comments'] = ['Anthony made this material.']

In [56]: leu.metadata['comments'].append('And then Katy made it better!')

In [57]: a['id'] = 42

In [58]: leu.metadata
Out[58]: {"comments":["Anthony made this material.","And then Katy made it better!"],\
          "id":42,"units":"kg"}

In [59]: leu.attr = {'units': 'solar mass'}

In [60]: leu.attr
Out[60]: {'units': 'solar mass'}

In [61]: a
Out[61]: {"comments":["Anthony made this material.","And then Katy made it better!"],\
          "id":42,"units":"kg"}

In [62]: leu.attr['units'] = 'not solar masses'

In [63]: leu.attr['units']
Out[63]: 'not solar masses'

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


Further information on the Material class may be seen in the library reference Materials – pyne.material.