def test_from_atom_frac_func():
h2o = {10010: 2.0, 80160: 1.0}
mat = from_atom_frac(h2o)
assert_equal(mat.atoms_per_mol, 3.0)
assert_equal(mat.comp[10010], 0.11191487328808077)
assert_equal(mat.comp[80160], 0.8880851267119192)
assert_equal(mat.mass, 18.01056468403)
assert_equal(mat.molecular_weight(), 18.01056468403)
h2 = Material({10010: 1.0}, atoms_per_mol=2.0)
h2o = {'O16': 1.0, h2: 1.0}
mat = from_atom_frac(h2o)
assert_equal(mat.atoms_per_mol, 3.0)
assert_equal(mat.comp[10010], 0.11191487328808077)
assert_equal(mat.comp[80160], 0.8880851267119192)
assert_equal(mat.molecular_weight(), 18.01056468403)
ihm = from_atom_frac({922350: 0.5, 922380: 0.5})
uox = {ihm: 1.0, 'O16': 2.0}
mat = from_atom_frac(uox)
assert_equal(mat.atoms_per_mol, 3.0)
assert_almost_equal(mat.comp[80160], 0.11912625316479536, 16)
assert_almost_equal(mat.comp[922350], 0.43763757948940346, 15)
assert_almost_equal(mat.comp[922380], 0.44323616734580107, 15)
assert_almost_equal(mat.molecular_weight() / 268.53718965614, 1.0, 15)
def test_from_atom_frac_func():
h2o = {10010: 2.0, 80160: 1.0}
mat = from_atom_frac(h2o)
assert_equal(mat.atoms_per_mol, 3.0)
assert_equal(mat.comp[10010], 0.11191487328808077)
assert_equal(mat.comp[80160], 0.8880851267119192)
assert_equal(mat.mass, 18.01056468403)
assert_equal(mat.molecular_weight(), 18.01056468403)
h2 = Material({10010: 1.0}, atoms_per_mol=2.0)
h2o = {'O16': 1.0, h2: 1.0}
mat = from_atom_frac(h2o)
assert_equal(mat.atoms_per_mol, 3.0)
assert_equal(mat.comp[10010], 0.11191487328808077)
assert_equal(mat.comp[80160], 0.8880851267119192)
assert_equal(mat.molecular_weight(), 18.01056468403)
ihm = from_atom_frac({922350: 0.5, 922380: 0.5})
uox = {ihm: 1.0, 'O16': 2.0}
mat = from_atom_frac(uox)
assert_equal(mat.atoms_per_mol, 3.0)
assert_almost_equal(mat.comp[80160], 0.11912625316479536, 16)
assert_almost_equal(mat.comp[922350], 0.43763757948940346, 15)
assert_almost_equal(mat.comp[922380], 0.44323616734580107, 15)
assert_almost_equal(mat.molecular_weight()/268.53718965614, 1.0, 15)
def test_from_atom_frac_func():
h2o = {10010000: 2.0, 80160000: 1.0}
mat = from_atom_frac(h2o)
assert_equal(mat.atoms_per_molecule, 3.0)
assert_equal(mat.comp[10010000], 0.11191487328808077)
assert_equal(mat.comp[80160000], 0.8880851267119192)
assert_equal(mat.mass, 18.01056468403)
assert_equal(mat.molecular_mass(), 18.01056468403)
h2 = Material({10010000: 1.0}, atoms_per_molecule=2.0)
h2o = {'O16': 1.0, h2: 1.0}
mat = from_atom_frac(h2o)
assert_equal(mat.atoms_per_molecule, 3.0)
assert_equal(mat.comp[10010000], 0.11191487328808077)
assert_equal(mat.comp[80160000], 0.8880851267119192)
assert_equal(mat.molecular_mass(), 18.01056468403)
ihm = from_atom_frac({922350000: 0.5, 922380000: 0.5})
uox = {ihm: 1.0, 'O16': 2.0}
mat = from_atom_frac(uox)
assert_equal(mat.atoms_per_molecule, 3.0)
assert_almost_equal(mat.comp[80160000], 0.11912625367051276, 16)
assert_almost_equal(mat.comp[922350000], 0.43763757904405304, 15)
assert_almost_equal(mat.comp[922380000], 0.44323616728543414, 15)
assert_almost_equal(mat.molecular_mass()/268.53718851614, 1.0, 15)
def test_from_atom_frac_func():
h2o = {10010000: 2.0, 80160000: 1.0}
mat = from_atom_frac(h2o)
assert_equal(mat.atoms_per_molecule, 3.0)
assert_equal(mat.comp[10010000], 0.11191487328808077)
assert_equal(mat.comp[80160000], 0.8880851267119192)
assert_equal(mat.mass, 18.01056468403)
assert_equal(mat.molecular_mass(), 18.01056468403)
h2 = Material({10010000: 1.0}, atoms_per_molecule=2.0)
h2o = {'O16': 1.0, h2: 1.0}
mat = from_atom_frac(h2o)
assert_equal(mat.atoms_per_molecule, 3.0)
assert_equal(mat.comp[10010000], 0.11191487328808077)
assert_equal(mat.comp[80160000], 0.8880851267119192)
assert_equal(mat.molecular_mass(), 18.01056468403)
ihm = from_atom_frac({922350000: 0.5, 922380000: 0.5})
uox = {ihm: 1.0, 'O16': 2.0}
mat = from_atom_frac(uox)
assert_equal(mat.atoms_per_molecule, 3.0)
assert_almost_equal(mat.comp[80160000], 0.11912625367051276, 16)
assert_almost_equal(mat.comp[922350000], 0.43763757904405304, 15)
assert_almost_equal(mat.comp[922380000], 0.44323616728543414, 15)
assert_almost_equal(mat.molecular_mass() / 268.53718851614, 1.0, 15)
def execute_origen(xs_tape9, time, nuclide, phi, origen, decay_tape9):
xs_tape9 = xs_tape9
if not os.path.isabs(xs_tape9):
xs_tape9 = os.path.join(LIBS_DIR, xs_tape9)
parsed_xs_tape9 = parse_tape9(xs_tape9)
parsed_decay_tape9 = parse_tape9(decay_tape9)
merged_tape9 = merge_tape9([parsed_decay_tape9, parsed_xs_tape9])
# Can set outfile to change directory, but the file name needs to be
# TAPE9.INP.
write_tape9(merged_tape9)
decay_nlb, xsfpy_nlb = nlbs(parsed_xs_tape9)
# Can set outfile, but the file name should be called TAPE5.INP.
write_tape5_irradiation("IRF", time/(60*60*24), phi,
xsfpy_nlb=xsfpy_nlb, cut_off=0, out_table_num=[4, 5],
out_table_nes=[True, False, False])
M = from_atom_frac({nuclide: 1}, mass=1, atoms_per_molecule=1)
write_tape4(M)
# Make pyne use naive atomic mass numbers to match ORIGEN
for i in pyne.data.atomic_mass_map:
pyne.data.atomic_mass_map[i] = float(pyne.nucname.anum(i))
origen_time, data = time_func(run_origen, origen)
logger.info("ORIGEN runtime: %s", origen_time)
return origen_time, data
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 like it, the following line is actually
# mass_y = MW_y * mass_x / MW_x
y.mass *= x.mass / mw_x
return y
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 num_density_to_mesh(lines, time, m):
"""num_density_to_mesh(lines, time, m)
This function reads ALARA output containing number density information and
creates material objects which are then added to a supplied PyNE Mesh object.
The volumes within ALARA are assummed to appear in the same order as the
idx on the Mesh object.
Parameters
----------
lines : list or str
ALARA output from ALARA run with 'number_density' in the 'output' block
of the input file. Lines can either be a filename or the equivalent to
calling readlines() on an ALARA output file. If reading in ALARA output
from stdout, call split('\n') before passing it in as the lines parameter.
time : str
The decay time for which number densities are requested (e.g. '1 h',
'shutdown', etc.)
m : PyNE Mesh
Mesh object for which mats will be applied to.
"""
if isinstance(lines, basestring):
with open(lines) as f:
lines = f.readlines()
elif not isinstance(lines, collections.Sequence):
raise TypeError("Lines argument not a file or sequence.")
# Advance file to number density portion.
header = 'Number Density [atoms/cm3]'
line = ""
while line.rstrip() != header:
line = lines.pop(0)
# Get decay time index from next line (the column the decay time answers
# appear in.
line_strs = lines.pop(0).replace('\t', ' ')
time_index = [s.strip() for s in line_strs.split(' ')
if s.strip()].index(time)
# Create a dict of mats for the mesh.
mats = {}
count = 0
# Read through file until enough material objects are create to fill mesh.
while count != len(m):
# Pop lines to the start of the next material.
while (lines.pop(0) + " ")[0] != '=':
pass
# Create a new material object and add to mats dict.
line = lines.pop(0)
nucvec = {}
density = 0.0
# Read lines until '=' delimiter at the end of a material.
while line[0] != '=':
nuc = line.split()[0]
n = float(line.split()[time_index])
if n != 0.0:
nucvec[nuc] = n
density += n * anum(nuc) / N_A
line = lines.pop(0)
mat = from_atom_frac(nucvec, density=density, mass=0)
mats[count] = mat
count += 1
m.mats = mats
def test_number_density():
ethanol = from_atom_frac({'C':2, 'H':6, 'O':1}, density=0.78900)
obs = ethanol.number_density()
exp = 9.2825E22
assert_almost_equal(obs / exp, 1.0, 4)
def test_mass_density():
ethanol = from_atom_frac({'C':2, 'H':6, 'O':1})
atom_density_ethanol = 9.282542841E22 # atom density not molecule density
mass_density = ethanol.mass_density(atom_density_ethanol)
expected_mass_density = 0.78900
assert_almost_equal(mass_density, expected_mass_density, 4)
def num_density_to_mesh(lines, time, m):
"""num_density_to_mesh(lines, time, m)
This function reads ALARA output containing number density information and
creates material objects which are then added to a supplied PyNE Mesh object.
The volumes within ALARA are assummed to appear in the same order as the
idx on the Mesh object.
Parameters
----------
lines : list or str
ALARA output from ALARA run with 'number_density' in the 'output' block
of the input file. Lines can either be a filename or the equivalent to
calling readlines() on an ALARA output file. If reading in ALARA output
from stdout, call split('\n') before passing it in as the lines parameter.
time : str
The decay time for which number densities are requested (e.g. '1 h',
'shutdown', etc.)
m : PyNE Mesh
Mesh object for which mats will be applied to.
"""
if isinstance(lines, basestring):
with open(lines) as f:
lines = f.readlines()
elif not isinstance(lines, collections.Sequence):
raise TypeError("Lines argument not a file or sequence.")
# Advance file to number density portion.
header = 'Number Density [atoms/cm3]'
line = ""
while line.rstrip() != header:
line = lines.pop(0)
# Get decay time index from next line (the column the decay time answers
# appear in.
line_strs = lines.pop(0).replace('\t', ' ')
time_index = [s.strip() for s in line_strs.split(' ')
if s.strip()].index(time)
# Create a dict of mats for the mesh.
mats = {}
count = 0
# Read through file until enough material objects are create to fill mesh.
while count != len(m):
# Pop lines to the start of the next material.
while (lines.pop(0) + " " )[0] != '=':
pass
# Create a new material object and add to mats dict.
line = lines.pop(0)
nucvec = {}
density = 0.0
# Read lines until '=' delimiter at the end of a material.
while line[0] != '=':
nuc = line.split()[0]
n = float(line.split()[time_index])
if n != 0.0:
nucvec[nuc] = n
density += n * anum(nuc)/N_A
line = lines.pop(0)
mat = from_atom_frac(nucvec, density=density, mass=0)
mats[count] = mat
count += 1
m.mats = mats
def _ensure_mats(self, rc):
"Ensure we have a fuel material, clad material, and cooling material."
if 'fuel_material'in rc:
rc.fuel_material = ensure_mat(rc.fuel_material)
elif 'fuel_chemical_form' in rc and 'initial_heavy_metal' in rc:
ihm_mat = Material(rc.initial_heavy_metal)
atom_frac = {nucname.id(k): v for k, v in
rc.fuel_chemical_form.items() if k != "IHM"}
atom_frac[ihm_mat] = rc.fuel_chemical_form.get("IHM", 0.0)
rc.fuel_material = from_atom_frac(atom_frac)
else:
raise ValueError("Please specify a fuel.")
if 'clad_material' in rc:
rc.clad_material = ensure_mat(rc.clad_material)
else:
rc.clad_material = Material({
# Natural Zirconium
400900: 0.98135 * 0.5145,
400910: 0.98135 * 0.1122,
400920: 0.98135 * 0.1715,
400940: 0.98135 * 0.1738,
400960: 0.98135 * 0.0280,
# The plastic is all melted and the natural Chromium too..
240500: 0.00100 * 0.04345,
240520: 0.00100 * 0.83789,
240530: 0.00100 * 0.09501,
240540: 0.00100 * 0.02365,
# Natural Iron
260540: 0.00135 * 0.05845,
260560: 0.00135 * 0.91754,
260570: 0.00135 * 0.02119,
260580: 0.00135 * 0.00282,
# Natural Nickel
280580: 0.00055 * 0.68077,
280600: 0.00055 * 0.26223,
280610: 0.00055 * 0.01140,
280620: 0.00055 * 0.03634,
280640: 0.00055 * 0.00926,
# Natural Tin
501120: 0.01450 * 0.0097,
501140: 0.01450 * 0.0065,
501150: 0.01450 * 0.0034,
501160: 0.01450 * 0.1454,
501170: 0.01450 * 0.0768,
501180: 0.01450 * 0.2422,
501190: 0.01450 * 0.0858,
501200: 0.01450 * 0.3259,
501220: 0.01450 * 0.0463,
501240: 0.01450 * 0.0579,
# We Need Oxygen!
80160: 0.00125,
})
if 'cool_material' in rc:
rc.cool_material = ensure_mat(rc.cool_material)
else:
MW = (2 * 1.0) + (1 * 16.0) + (0.199 * 550 * 10.0**-6 * 10.0) + \
(0.801 * 550 * 10.0**-6 * 11.0)
rc.cool_material = Material({
10010: (2 * 1.0) / MW,
80160: (1 * 16.0) / MW,
50100: (0.199 * 550 * 10.0**-6 * 10.0) / MW,
50110: (0.801 * 550 * 10.0**-6 * 11.0) / MW,
})
def test_number_density():
ethanol = from_atom_frac({'C': 2, 'H': 6, 'O': 1}, density=0.78900)
obs = ethanol.number_density()
exp = 9.2825E22
assert_almost_equal(obs / exp, 1.0, 4)
def test_mass_density():
ethanol = from_atom_frac({'C': 2, 'H': 6, 'O': 1})
atom_density_ethanol = 9.282542841E22 # atom density not molecule density
mass_density = ethanol.mass_density(atom_density_ethanol)
expected_mass_density = 0.78900
assert_almost_equal(mass_density, expected_mass_density, 4)
def __init__(self):
## Define the system: materials, surfaces, regions, cells.
self.sys = definition.SystemDefinition(verbose=False)
## Materials.
# Must provide a name as a keyword argument for material cards. See the
# documentation for :py:mod:`pyne.material` for more information.
uo2 = material.from_atom_frac({'U235': 0.05, 'U238': 0.95, 'O16' : 2.00})
self.uo2 = cards.Material(uo2, name='UO2')
h2o = material.from_atom_frac({'H1' : 2.0, 'O16': 1.0}, attrs={'name': 'H2O'})
self.h2o = cards.Material(h2o)
## Surfaces.
# There are two surfaces: one for the pin and one for the unit cell
# boundary.
radius = 0.40
# This creates an axis-aligned and axis-centered cylinder along the z
# axis, with radius 0.40 cm.
self.pin = cards.AxisCylinder('pin', 'Z', radius)
# The Parallelepiped is a macrobody. The surface is reflecting,
# creating an infinte geometry. The surface is infinite in the z
# direction.
pitch = 1.2
self.cellbound = cards.Parallelepiped('bound',
-pitch / 2, pitch / 2, -pitch / 2, pitch / 2, 0, 0,
reflecting=True)
## Cells.
# We combine the materials and surfaces above into cells. We use MCNP
# cells in order to specify particle importances and volumes directly
# on the cell card. We could alternatively use the
# :py:class:`Importance` and :py:class:`Volume` cards.
# fuel cell.
# The fuel is the region of space inside the pin, pin.neg.
self.fuelregion = self.pin.neg
# The neutron importance is 1, and the user-provided volume is 1 cm^3.
self.fuel = cards.CellMCNP('fuel', self.fuelregion, self.uo2,
11.0, 'g/cm^3',
importance=('neutron', 1),
volume=1)
# coolant cell.
# The region is between the pin and the unit cell boundary.
self.coolantregion = self.pin.pos | self.cellbound.neg
self.coolant = cards.CellMCNP('coolant', self.coolantregion, self.h2o,
1.0, 'g/cm^3',
importance=('neutron', 1),
volume=1)
# graveyard cell: where particles go to die.
# The region is everything beyond the unit cell boundary.
self.graveyardregion = self.cellbound.pos
# This is a void cell, meaning it does not have a material.
self.graveyard = cards.CellMCNP('graveyard', self.graveyardregion,
importance=('neutron', 0))
# We add the cells to the system. The order we add them is the order
# they are printed in the input file.
self.sys.add_cell(self.fuel)
# We can add multiple cells at once.
self.sys.add_cell(self.coolant, self.graveyard)
## Define the simulation: sources, tallies, misc. Don't clutter the
# command window.
self.sim = definition.MCNPSimulation(self.sys, verbose=False)
# Specify a thermal scattering law for the H2O material. This is a
# unique card per material.
self.sim.add_misc(cards.ScatteringLaw('H2O', {'H1': 'lwtr'}))
# Add a criticality source, use default values. This is a unique card,
# so we do not provide a card name.
self.sim.add_source(cards.Criticality())
# Add points at which to start neutrons; use default point (0, 0, 0).
self.sim.add_source(cards.CriticalityPoints())
# Tally neutron flux in both the fuel and coolant cells.
self.sim.add_tally(cards.CellFlux('flux', 'neutron',
['fuel', 'coolant']))
# The energy grid on which to tally neutrons, applied to all tallies.
self.sim.add_misc(cards.EnergyGrid('egrid0', None,
10**np.arange(-9.9, 1.1, 0.1)))