def test_matlib_delete():
water = Material()
water.from_atom_frac({10000000: 2.0, 80000000: 1.0})
water.metadata["name"] = "Aqua sera."
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()
lib = {"pubr3": pubr3, "aqua": water}
matlib = MaterialLibrary(lib)
# test delete methods
matlib.remove_material("pubr3")
assert len(matlib) == 1
del matlib["aqua"]
assert len(matlib) == 0
def make_matslib(fname):
"""Make a pyne.material.MaterialLibrary. First makes elements, then
materials from compendium.
Parameters
----------
fname : str
Path to materials compendium.
Returns
-------
matslib : pyne.material.MaterialLibrary
All the materials you could want, in a handy MaterialLibrary instance.
"""
matslib = MaterialLibrary(make_elements())
matsdict = grab_materials_compendium(fname)
matslib.update(matsdict)
return matslib
def test_matlib_hdf5_nuc_data():
matlib = MaterialLibrary()
matlib.from_hdf5(nuc_data, "/materials")
matlib.write_hdf5("matlib_test.h5")
mat_lib_load_test = MaterialLibrary("matlib_test.h5")
os.remove("matlib_test.h5")
for key in matlib:
assert_mat_almost_equal(matlib[key], mat_lib_load_test[key])
def setup():
global MATS, O2HLS
o2benchurl = 'https://github.com/pyne/data/raw/master/' + H5NAME
if not os.path.exists(H5NAME):
sys.stderr.write("\nDownloading " + o2benchurl + ": ")
sys.stderr.flush()
urlretrieve(o2benchurl, H5NAME)
sys.stderr.write("done.\n")
sys.stderr.flush()
MATS = MaterialLibrary(H5NAME)
with open('o2hls.json', 'r') as f:
O2HLS = json.load(f)
O2HLS = {int(nuc): v for nuc, v in O2HLS.items()}
def test_matlib_json():
filename = "matlib.json"
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_json(filename)
rmatlib = MaterialLibrary()
rmatlib.from_json(filename)
assert_equal(set(wmatlib), set(rmatlib))
for key in rmatlib:
assert_mat_almost_equal(wmatlib[key], rmatlib[key])
os.remove(filename)
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)
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"]
# remove empty elements
assert_equal(
{(x, val)
for x, val in set(obs_gasoline.comp.items()) if val > 0},
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"]
# remove empty elements
assert_equal(
{(x, val)
for x, val in set(obs_pubr3.comp.items()) if val > 0},
set(pubr3.comp.items()),
)
assert_equal(obs_pubr3.density, pubr3.density)
assert_equal(obs_pubr3.metadata["name"], pubr3.metadata["name"])
def _get_material_lib(hdf5, data_hdf5path, **kwargs):
"""Read material properties from the loaded dagmc geometry.
"""
# If a set of nuc_names is provided, then collapse elements
if 'nuc_names' in kwargs:
nuc_names = kwargs['nuc_names']
collapse = True
# set of exception nuclides for collapse_elements
mat_except = set(nuc_names.keys())
else:
collapse = False
# collapse isotopes into elements (if required)
mats = MaterialLibrary(hdf5, datapath=data_hdf5path)
mats_collapsed = {}
unique_names = {}
for mat_name in mats:
mat_name = mat_name.decode('utf-8')
fluka_name = mats[mat_name].metadata['fluka_name']
if sys.version_info[0] > 2:
unique_names[mat_name] = str(fluka_name.encode(), 'utf-8')
else:
unique_names[mat_name] = fluka_name.decode('utf-8')
if collapse:
mats_collapsed[fluka_name] = mats[mat_name].collapse_elements(
mat_except)
else:
mats_collapsed[fluka_name] = mats[mat_name]
# convert mass fraction to atom density in units [at/b-cm]
mat_lib = {}
for mat_name in mats_collapsed:
comp = mats_collapsed[mat_name]
atom_dens_dict = comp.to_atom_dens()
comp_list = {}
for nucid, dens in atom_dens_dict.items():
# convert from [at/cc] to [at/b-cm]
comp_list[nucid] = dens * 10.**-24
mat_lib[mat_name] = comp_list
return mat_lib, unique_names
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_hdf5_overwrite():
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 = {"aqua": water}
wmatlib = MaterialLibrary(lib)
wmatlib.write_hdf5(filename, "/mats1")
lib = {"leu": Material(leu)}
umatlib = MaterialLibrary(lib)
# test error raise if path already exists
assert_raises(RuntimeError, umatlib.write_hdf5, filename, "/mats1", False)
# test overwriting
umatlib.write_hdf5(filename, "/mats1", h5_overwrite=True)
rmatlib = MaterialLibrary()
rmatlib.from_hdf5(filename, "/mats1")
# Round trip!
assert_equal(set(umatlib), set(rmatlib))
for key in rmatlib:
assert_mat_almost_equal(umatlib[key], rmatlib[key])
os.remove(filename)
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)
#!/usr/bin/env python3
from pyne.material import Material
from pyne.material_library import MaterialLibrary
mat_lib = MaterialLibrary()
# Create a pyne material for copper
copper = Material({'Cu': 1})
copper = copper.expand_elements()
# Add to material library
mat_lib["copper"] = copper
# Create a pyne material for copper
air = Material({'N': 0.784431, 'O': 0.210748, 'Ar': 0.004821})
air = air.expand_elements()
# Add to material library
mat_lib["air"] = air
#graveyard = Material();
#mat_lib["graveyard"] = graveyard
#vacuum = Material();
#mat_lib["vacuum"] = vacuum
mat_lib.write_hdf5("material_library.h5", "/materials", "/nucid")