def test_material2():
# load the material library
output_lib = MaterialLibrary()
output_lib.from_hdf5(filename, '/materials')
# create the material for the test
Nitrogen = Material({70140000: 0.99636, 70150000: 0.00364})
for material in output_lib.iteritems():
if material[1].metadata['original_name'] == 'Nitrogen':
assert_almost_equal(material[1].comp, Nitrogen.comp, places=4)
def test_setitem_str():
mat = Material(nucvec)
assert_equal(mat.mass, 9.0)
assert_equal(mat[922350], 1.0)
mat['U235'] = 2.0
assert_equal(mat.mass, 10.0)
assert_equal(mat[922350], 2.0)
mat = Material(leu)
assert_equal(mat.mass, 1.0)
assert_equal(mat[922350], 0.04)
assert_equal(mat[922380], 0.96)
assert_raises(KeyError, lambda: mat[922340])
mat['U234'] = 17.0
assert_equal(mat.mass, 18.0)
assert_equal(mat[922340], 17.0)
assert_equal(mat[922350], 0.04)
assert_equal(mat[922380], 0.96)
def test_natural_elements():
water = Material()
water.from_atom_frac({10000000: 2.0, 80000000: 1.0})
expected_comp = {
10000000: 0.11189838783149784,
80000000: 0.8881016121685023
}
for key in expected_comp:
assert_almost_equal(water.comp[key], expected_comp[key])
def test_getitem_sequence():
mat = Material(nucvec)
mat1 = mat[922380, 922350]
assert_equal(mat1.mass, 2.0)
assert_equal(set(mat1.keys()), set([922380, 922350]))
mat1 = mat[922380, 'H2', 'h1']
assert_equal(mat1.mass, 2.0)
assert_equal(set(mat1.keys()), set([922380, 10010]))
def __init__(self, mass_msol, composition):
self.mass_g = mass_msol * msun_to_cgs
self.material = Material(self._normalize_composition(composition))
self._pad_material()
atomic_masses = self.get_masses()
self.n_per_g = [
1 / atomic_masses[item]
for item in self.get_all_children_nuc_name()
]
def transmute(self,
x,
t=None,
phi=None,
tol=None,
log=None,
*args,
**kwargs):
"""Transmutes a material into its daughters.
Parameters
----------
x : Material or similar
Input material for transmutation.
t : float
Transmutations time [sec].
phi : float or array of floats
Neutron flux vector [n/cm^2/sec]. Currently this must either be
a scalar or match the group structure of EAF.
tol : float
Tolerance level for chain truncation.
log : file-like or None
The log file object should be written. A None imples the log is
not desired.
Returns
-------
y : Material
The output material post-transmutation.
"""
if not isinstance(x, Material):
x = Material(x)
if t is not None:
self.t = t
if phi is not None:
self.phi = phi
if log is not None:
self.log = log
if tol is not None:
self.tol = tol
x_atoms = x.to_atom_frac()
y_atoms = {}
for nuc, adens in x_atoms.items():
# Find output for root of unit density and scale all output by
# actual nuclide density and add to final output.
partial = self._transmute_partial(nuc)
for part_nuc, part_adens in partial.items():
y_atoms[part_nuc] = part_adens * adens + y_atoms.get(
part_nuc, 0.0)
mw_x = x.molecular_mass()
y = from_atom_frac(y_atoms, atoms_per_molecule=x.atoms_per_molecule)
# even though it doesn't look likt it, the following line is actually
# mass_y = MW_y * mass_x / MW_x
y.mass *= x.mass / mw_x
return y
def test_metadatatag():
mats = {
0: Material({
'H1': 1.0,
'K39': 1.0
}, density=42.0),
1: Material({
'H1': 0.1,
'O16': 1.0
}, density=43.0),
2: Material({'He4': 42.0}, density=44.0),
3: Material({'Tm171': 171.0}, density=45.0),
}
m = gen_mesh(mats=mats)
m.doc = MetadataTag(m, 'doc', doc="extra documentaion")
m.doc[:] = ['write', 'awesome', 'code', 'now']
# Getting tags
assert_equal(m.doc[0], 'write')
assert_equal(m.doc[::2], ['write', 'code'])
mask = np.array([True, False, True, True], dtype=bool)
assert_equal(m.doc[mask], ['write', 'code', 'now'])
assert_equal(m.doc[1, 0, 1, 3], ['awesome', 'write', 'awesome', 'now'])
# setting tags
m.doc[0] = 65.0
assert_equal(m.doc[0], 65.0)
m.doc[::2] = 18.0
m.doc[1::2] = [36.0, 54.0]
assert_array_equal(m.doc[:], np.array([18.0, 36.0, 18.0, 54.0]))
mask = np.array([True, False, True, True], dtype=bool)
m.doc[mask] = 9.0
mask = np.array([True, True, False, False], dtype=bool)
m.doc[mask] = (19.0, 29.0)
assert_array_equal(m.doc[:], np.array([19.0, 29.0, 9.0, 9.0]))
m.doc[[2]] = 28.0
m.doc[3, 1] = 6.0, 4128.0
assert_array_equal(m.doc[1:], np.array([4128.0, 28.0, 6.0]))
# deleting tag
del m.doc[:]
def test_nativetag():
mats = {
0: Material({
'H1': 1.0,
'K39': 1.0
}, density=42.0),
1: Material({
'H1': 0.1,
'O16': 1.0
}, density=43.0),
2: Material({'He4': 42.0}, density=44.0),
3: Material({'Tm171': 171.0}, density=45.0),
}
m = gen_mesh(mats=mats)
m.f = NativeMeshTag(mesh=m, name='f')
m.f[:] = [1.0, 2.0, 3.0, 4.0]
# Getting tags
assert_equal(m.f[0], 1.0)
assert_array_equal(m.f[::2], [1.0, 3.0])
mask = np.array([True, False, True, True], dtype=bool)
assert_array_equal(m.f[mask], [1.0, 3.0, 4.0])
assert_array_equal(m.f[1, 0, 1, 3], [2.0, 1.0, 2.0, 4.0])
# setting tags
m.f[0] = 65.0
assert_equal(m.f[0], 65.0)
m.f[::2] = 18.0
m.f[1::2] = [36.0, 54.0]
assert_array_equal(m.f[:], np.array([18.0, 36.0, 18.0, 54.0]))
mask = np.array([True, False, True, True], dtype=bool)
m.f[mask] = 9.0
mask = np.array([True, True, False, False], dtype=bool)
m.f[mask] = (19.0, 29.0)
assert_array_equal(m.f[:], np.array([19.0, 29.0, 9.0, 9.0]))
m.f[[2]] = 28.0
m.f[3, 1] = 6.0, 4128.0
assert_array_equal(m.f[1:], np.array([4128.0, 28.0, 6.0]))
# deleting tag
del m.f[:]
def test_del_nativetag():
mats = {
0: Material({
'H1': 1.0,
'K39': 1.0
}, density=42.0),
1: Material({
'H1': 0.1,
'O16': 1.0
}, density=43.0),
2: Material({'He4': 42.0}, density=44.0),
3: Material({'Tm171': 171.0}, density=45.0),
}
m = gen_mesh(mats=mats)
m.f = NativeMeshTag(mesh=m, name='f')
m.f[:] = [1.0, 2.0, 3.0, 4.0]
m.g = NativeMeshTag(mesh=m, name='g')
m.g[:] = [1.0, 2.0, 3.0, 4.0]
assert_raises(ValueError, m.delete_tag, -12)
import sys
# make a new reference to the tag that will not
# be deleted
tag_ref = m.f
# deleting tag by tag name
m.delete_tag('f')
# ensure that there are only 2 references to this tag
# 1. is the tag_ref created above
# 2. is the one that automatically is the temporary
# reference created as the argument to getrefcount
assert_equal(2, sys.getrefcount(tag_ref))
assert_raises(RuntimeError, m.mesh.tag_get_handle, 'f')
# deleting tag by tag handle
tag_ref = m.g
m.delete_tag(m.g)
assert_equal(2, sys.getrefcount(tag_ref))
assert_raises(RuntimeError, m.mesh.tag_get_handle, 'g')
def test_write_tape4():
mat = Material({"U235": 0.95, 80160000: 0.05})
tape4 = StringIO()
origen22.write_tape4(mat, tape4)
tape4.seek(0)
observed = tape4.read()
expected = ("1 80160 5.0000000000E-02 0 0 0 0 0 0\n"
"2 922350 9.5000000000E-01 0 0 0 0 0 0\n"
"0 0 0 0\n")
assert_equal(observed, expected)
def test_act_2(self):
mat = Material(nucvec)
mat1 = mat.sub_act()
assert_equal(mat1.comp[922350], 1.0 / 6.0)
assert_equal(mat1.comp[922380], 1.0 / 6.0)
assert_equal(mat1.comp[942390], 1.0 / 6.0)
assert_equal(mat1.comp[942410], 1.0 / 6.0)
assert_equal(mat1.comp[952420], 1.0 / 6.0)
assert_equal(mat1.comp[962440], 1.0 / 6.0)
assert_equal(mat1.mass, 6.0)
def test_mat4():
mat = Material({
922350000: 0.05,
922380000: 0.95
},
15,
metadata={'units': 'kg'})
assert_equal(mat.comp, {922350000: 0.05, 922380000: 0.95})
assert_equal(mat.mass, 15.0)
assert_equal(mat.metadata['units'], 'kg')
def test_mesh_to_geom():
if not HAVE_PYMOAB:
raise SkipTest
expected_geom = os.path.join(thisdir, "files_test_alara", "alara_geom.txt")
expected_matlib = os.path.join(thisdir, "files_test_alara",
"alara_matlib.txt")
geom = os.path.join(os.getcwd(), "alara_geom")
matlib = os.path.join(os.getcwd(), "alara_matlib")
mats = {
0: Material({'H1': 1.0, 'K39': 1.0}, density=1.1),
1: Material({'H1': 0.1, 'O16': 1.0}, density=1.2),
2: Material({'He4': 42.0}, density=1.3),
3: Material({'Tm171': 171.0}, density=1.4),
}
m = Mesh(structured_coords=[[-1, 0, 1], [-1, 0, 1], [0, 1]], structured=True,
mats=mats)
mesh_to_geom(m, geom, matlib)
with open(expected_geom) as f:
written = f.readlines()
with open(geom) as f:
expected = f.readlines()
assert_equal(written, expected)
if os.path.isfile(geom):
os.remove(geom)
with open(expected_matlib) as f:
written = f.readlines()
with open(matlib) as f:
expected = f.readlines()
assert_equal(written, expected)
if os.path.isfile(matlib):
os.remove(matlib)
def test_dump_json():
leu = {"U238": 0.96, "U235": 0.04}
exp = jsoncpp.Value({
"mass": 1.0,
"comp": leu,
"density": -1.0,
"metadata": {},
"atoms_per_molecule": -1.0
})
obs = Material(leu).dump_json()
assert_equal(exp, obs)
def test_matlib_hdf5():
filename = "matlib.h5"
if filename in os.listdir("."):
os.remove(filename)
water = Material()
water.from_atom_frac({10000000: 2.0, 80000000: 1.0})
water.metadata["name"] = "Aqua sera."
lib = {"leu": Material(leu), "nucvec": nucvec, "aqua": water}
wmatlib = MaterialLibrary(lib)
wmatlib.write_hdf5(filename, "/mats1")
rmatlib = MaterialLibrary()
rmatlib.from_hdf5(filename, "/mats1")
os.remove(filename)
# Round trip!
rmatlib.write_hdf5(filename, "/mats1")
wmatlib = MaterialLibrary(filename, "/mats1")
assert_equal(set(wmatlib), set(rmatlib))
for key in rmatlib:
assert_mat_almost_equal(wmatlib[key], rmatlib[key])
os.remove(filename)
def AtomicDensityToMassDensity(heu_atom):
print "\n\n",heu_atom
print "========heu_atom molecular mass ",heu_atom.molecular_mass()
heu=Material()
heu.from_atom_frac(heu_atom)
print "\n\n",heu
print "ERROR: heu molecular mass is not correct heu.molecular_mass() = ", heu.molecular_mass()
heu.metadata=heu_atom.metadata
heu.metadata['density_g_per_cc']=heu.mass
heu.normalize()
return heu
def test_sub_range(self):
mat = Material(nucvec)
mat1 = mat.sub_range(920000, 930000)
assert_equal(mat1.mass, 2.0)
for nuc in mat1:
assert_true(920000 <= nuc < 930000)
mat1 = mat.sub_range(upper="U238")
assert_equal(mat1.mass, 4.0)
for nuc in mat1:
assert_true(nuc < 922380)
def test_matlib_query():
water = Material()
water.from_atom_frac({10000000: 2.0, 80000000: 1.0})
water.metadata["name"] = "Aqua sera."
mat_nucvec = Material(nucvec)
mat_nucvec.metadata["name"] = "nucvec"
lib = {"nucvec": nucvec, "aqua": water}
matlib = MaterialLibrary(lib)
matlib_aqua = matlib["aqua"]
assert_mat_almost_equal(water, matlib_aqua)
matlib_nucvec = matlib["nucvec"]
assert_mat_almost_equal(mat_nucvec, matlib_nucvec)
mat_leu = Material(leu)
mat_leu.metadata["name"] = "leu"
matlib["leu"] = mat_leu
matlib_leu = matlib["leu"]
assert_mat_almost_equal(mat_leu, matlib_leu)
def test_iter():
mats = {
0: Material({
'H1': 1.0,
'K39': 1.0
}, density=42.0),
1: Material({
'H1': 0.1,
'O16': 1.0
}, density=43.0),
2: Material({'He4': 42.0}, density=44.0),
3: Material({'Tm171': 171.0}, density=45.0),
}
m = gen_mesh(mats=mats)
j = 0
idx_tag = m.mesh.getTagHandle('idx')
for i, mat, ve in m:
assert_equal(j, i)
assert_is(mats[i], mat)
assert_equal(j, idx_tag[ve])
j += 1
def test_with_external_data():
mat = Material(nucvec, density=7.8)
mat = mat.expand_elements()
assert_equal(id("He3") in mat.comp, False)
assert_equal(id("Co58") in mat.comp, False)
assert_equal(id("Ni58") in mat.comp, False)
assert_equal(id("H1") in mat.comp, True)
assert_equal(id("Fe56") in mat.comp, True)
assert_equal(id("Mn55") in mat.comp, True)
def test_with_external_data():
mat = Material(nucvec, density=7.8)
mat = mat.expand_elements()
assert_equal(id('He3') in mat.comp, False)
assert_equal(id('Co58') in mat.comp, False)
assert_equal(id('Ni58') in mat.comp, False)
assert_equal(id('H1') in mat.comp, True)
assert_equal(id('Fe56') in mat.comp, True)
assert_equal(id('Mn55') in mat.comp, True)
def test_iter():
mats = {
0: Material({
'H1': 1.0,
'K39': 1.0
}, density=42.0),
1: Material({
'H1': 0.1,
'O16': 1.0
}, density=43.0),
2: Material({'He4': 42.0}, density=44.0),
3: Material({'Tm171': 171.0}, density=45.0),
}
m = gen_mesh(mats=mats)
j = 0
idx_tag = m.mesh.tag_get_handle('idx')
for i, mat, ve in m:
assert_equal(j, i)
assert_is(mats[i], mat)
assert_equal(j, m.mesh.tag_get_data(idx_tag, ve, flat=True)[0])
j += 1
def test_against_nuc_data():
nuc_data = pyne_conf.NUC_DATA_PATH
if not os.path.isfile(nuc_data):
raise RuntimeError(
"Tests require nuc_data.h5. Please run nuc_data_make.")
obs_matslib = MaterialLibrary(nuc_data,
datapath="/material_library/materials",
nucpath="/material_library/nucid")
gasoline = Material({
"H": 0.157000,
"C": 0.843000,
},
density=0.721,
metadata={
"name": "Gasoline"
}).expand_elements()
pubr3 = Material(
{
"Br": 0.500617,
"Pu-238": 0.000250,
"Pu-239": 0.466923,
"Pu-240": 0.029963,
"Pu-241": 0.001998,
"Pu-242": 0.000250
},
density=6.75,
metadata={
"name": "Plutonium Bromide"
}).expand_elements()
obs_gasoline = obs_matslib["Gasoline"]
assert_equal(set(obs_gasoline.comp.items()), set(gasoline.comp.items()))
assert_equal(obs_gasoline.density, gasoline.density)
assert_equal(obs_gasoline.metadata["name"], gasoline.metadata["name"])
obs_pubr3 = obs_matslib["Plutonium Bromide"]
assert_equal(set(obs_pubr3.comp.items()), set(pubr3.comp.items()))
assert_equal(obs_pubr3.density, pubr3.density)
assert_equal(obs_pubr3.metadata["name"], pubr3.metadata["name"])
def test_mesh_to_geom():
if not HAVE_PYTAPS:
raise SkipTest
mats = {
0: Material({'H1': 1.0, 'K39': 1.0}, density=42.0),
1: Material({'H1': 0.1, 'O16': 1.0}, density=43.0),
2: Material({'He4': 42.0}, density=44.0),
3: Material({'Tm171': 171.0}, density=45.0),
4: Material({'C12': 1.0}, density=47.0),
5: Material({'1002': 1.0}, density=5.0),
}
m = Mesh(structured_coords=[[0, 1, 2, 3], [0, 1, 2], [0, 1]], mats=mats,
structured=True)
geom = mcnp.mesh_to_geom(m)
exp_geom = (
"Generated from PyNE Mesh\n"
"1 1 42.0 1 -2 5 -6 8 -9\n"
"2 2 43.0 1 -2 6 -7 8 -9\n"
"3 3 44.0 2 -3 5 -6 8 -9\n"
"4 4 45.0 2 -3 6 -7 8 -9\n"
"5 5 47.0 3 -4 5 -6 8 -9\n"
"6 6 5.0 3 -4 6 -7 8 -9\n"
"7 0 -1:4:-5:7:-8:9\n"
"\n"
"1 px 0.0\n"
"2 px 1.0\n"
"3 px 2.0\n"
"4 px 3.0\n"
"5 py 0.0\n"
"6 py 1.0\n"
"7 py 2.0\n"
"8 pz 0.0\n"
"9 pz 1.0\n"
"\n"
"C density = 42.0\n"
"m1\n"
" 1001 -5.0000e-01\n"
" 19039 -5.0000e-01\n"
"C density = 43.0\n"
"m2\n"
" 1001 -9.0909e-02\n"
" 8016 -9.0909e-01\n"
"C density = 44.0\n"
"m3\n"
" 2004 -1.0000e+00\n"
"C density = 45.0\n"
"m4\n"
" 69171 -1.0000e+00\n"
"C density = 47.0\n"
"m5\n"
" 6012 -1.0000e+00\n"
"C density = 5.0\n"
"m6\n"
" 1002 -1.0000e+00\n")
assert_equal(geom, exp_geom)
def test_matproptag():
mats = {
0: Material({
'H1': 1.0,
'K39': 1.0
}, density=42.0),
1: Material({
'H1': 0.1,
'O16': 1.0
}, density=43.0),
2: Material({'He4': 42.0}, density=44.0),
3: Material({'Tm171': 171.0}, density=45.0),
}
m = gen_mesh(mats=mats)
# Getting tags
assert_equal(m.density[0], 42.0)
assert_array_equal(m.density[::2], np.array([42.0, 44.0]))
mask = np.array([True, False, True, True], dtype=bool)
assert_array_equal(m.density[mask], np.array([42.0, 44.0, 45.0]))
assert_array_equal(m.density[1, 0, 1, 3],
np.array([43.0, 42.0, 43.0, 45.0]))
# setting tags
m.density[0] = 65.0
assert_equal(m.density[0], 65.0)
m.density[::2] = 18.0
m.density[1::2] = [36.0, 54.0]
assert_array_equal(m.density[:], np.array([18.0, 36.0, 18.0, 54.0]))
mask = np.array([True, False, True, True], dtype=bool)
m.density[mask] = 9.0
mask = np.array([True, True, False, False], dtype=bool)
m.density[mask] = (19.0, 29.0)
assert_array_equal(m.density[:], np.array([19.0, 29.0, 9.0, 9.0]))
m.density[[2]] = 28.0
m.density[3, 1] = 6.0, 4128.0
assert_array_equal(m.density[1:], np.array([4128.0, 28.0, 6.0]))
def test_expand_elements1():
natmat = Material({
'C': 1.0,
902320000: 0.5,
'PU': 4.0,
'U': 3.0
},
metadata={'y': 1.0})
expmat = natmat.expand_elements()
assert_true(60120000 in expmat.comp)
assert_false(60000000 in expmat.comp)
assert_true(natmat.metadata == expmat.metadata)
assert_false(natmat.metadata is expmat.metadata)
def test_default_uranium_cascade():
casc = enr.default_uranium_cascade()
assert_equal(casc.alpha, 1.05)
assert_equal(casc.Mstar, 236.5)
assert_equal(casc.j, 922350)
assert_equal(casc.k, 922380)
assert_equal(casc.N, 30.0)
assert_equal(casc.M, 10.0)
assert_equal(casc.x_feed_j, 0.0072)
assert_equal(casc.x_prod_j, 0.05)
assert_equal(casc.x_tail_j, 0.0025)
assert_equal(casc.mat_feed, Material({922340: 5.5e-05, 922350: 0.0072,
922380: 0.992745}, 1.0, 1.0))
def test_map_str_material():
m = MapStrMaterial()
m['leu'] = Material(leu)
m['heu'] = Material({'U238': 0.01, 'U235': 0.99}, 42.0)
assert_equal(len(m), 2)
assert_equal(m['leu'].mass, 1.0)
assert_equal(m['leu']['U235'], 0.04)
assert_equal(m['heu'].mass, 42.0)
assert_equal(m['heu']['U238'], 0.42)
m = MapStrMaterial({
'leu': Material(leu),
'heu': Material({
'U238': 0.01,
'U235': 0.99
}, 42.0)
})
assert_equal(len(m), 2)
assert_equal(m['leu'].mass, 1.0)
assert_equal(m['leu']['U235'], 0.04)
assert_equal(m['heu'].mass, 42.0)
assert_equal(m['heu']['U238'], 0.42)
n = MapStrMaterial(m, False)
assert_equal(len(n), 2)
assert_equal(n['leu'].mass, 1.0)
assert_equal(n['leu']['U235'], 0.04)
assert_equal(n['heu'].mass, 42.0)
assert_equal(n['heu']['U238'], 0.42)
# points to the same underlying map
n['other'] = Material({'PU239': 15.0})
assert_equal(m['other'].mass, 15.0)
assert_equal(m['other']['PU239'], 15.0)
assert_equal(n['leu'].mass, 1.0)
assert_equal(n['leu']['U235'], 0.04)
assert_equal(n['heu'].mass, 42.0)
assert_equal(n['heu']['U238'], 0.42)
def test_with_internal_data():
orig = pyne_conf.NUC_DATA_PATH
pyne_conf.NUC_DATA_PATH = b'thisisanonsensedatapath'
mat = Material(nucvec, density=7.8)
mat = mat.expand_elements()
assert_equal(id('He3') in mat.comp, False)
assert_equal(id('Co58') in mat.comp, False)
assert_equal(id('Ni58') in mat.comp, False)
assert_equal(id('H1') in mat.comp, True)
assert_equal(id('Fe56') in mat.comp, True)
assert_equal(id('Mn55') in mat.comp, True)
def test_write_mcnp():
if 'mcnp_mass_fracs.txt' in os.listdir('.'):
os.remove('mcnp_mass_fracs.txt')
leu = Material(nucvec={
'U235': 0.04,
'U238': 0.96
},
metadata={
'mat_number':
2,
'table_ids': {
'92235': '15c',
'92238': '25c'
},
'mat_name':
'LEU',
'source':
'Some URL',
'comments':
('this is a long comment that will definitly '
'go over the 80 character limit, for science'),
'name':
'leu'
},
density=19.1)
leu.write_mcnp('mcnp_mass_fracs.txt')
leu.write_mcnp('mcnp_mass_fracs.txt', frac_type='atom')
with open('mcnp_mass_fracs.txt') as f:
written = f.read()
expected = (
'C name: leu\n'
'C density = 19.1\n'
'C source: Some URL\n'
'C comments: this is a long comment that will definitly go over the 80 character\n'
'C limit, for science\n'
'm2\n'
' 92235.15c -4.0000E-02\n'
' 92238.25c -9.6000E-01\n'
'C name: leu\n'
'C density = 19.1\n'
'C source: Some URL\n'
'C comments: this is a long comment that will definitly go over the 80 character\n'
'C limit, for science\n'
'm2\n'
' 92235.15c 4.0491E-02\n'
' 92238.25c 9.5951E-01\n')
assert_equal(written, expected)
os.remove('mcnp_mass_fracs.txt')
