def step5(cfg, cfg2, cfg5):
"""
This function creates the adjoint neutron source and writes the
PARTISN input file for adjoint neutron transport.
Parameters
----------
cfg : dictionary
User input from 'general' section of config.yml file
cfg2 : dictionary
User input for step 2 from the config.yml file
cfg5 : dictionary
User input for step 3 from the config.yml file
"""
# Get user-input from config file
num_n_groups = cfg['n_groups']
num_p_groups = cfg['p_groups']
n_geom = cfg2['n_geom_file']
decay_times = str(cfg2['decay_times']).split(' ')
meshflux = cfg5['meshflux']
# Base of geometry file name
basename = n_geom.split("/")[-1].split(".")[0]
# The total number of photon and neutron energy groups
total_num_groups = num_n_groups + num_p_groups
# Read given flux file and tag to a mesh
if meshflux:
# Adjoint flux file is an hdf5 mesh file
fw_n_err = meshflux
m = Mesh(structured=True, mesh=fw_n_err, mats=None)
else:
raise RuntimeError("No neutron flux file given")
# Size of flux tag is equal to the total number of energy groups
m.ERROR_TAG = NativeMeshTag(num_n_groups, name="ERROR_TAG")
fw_n_err = m.ERROR_TAG[:]
# Load geometry and get material assignments
load(n_geom)
ml = MaterialLibrary(n_geom)
mat_names = list(ml.keys())
cell_mats = cell_material_assignments(n_geom)
# Load T matrix
if not os.path.exists('step2_T.npy'):
raise RuntimeError("T matrix from step 2 (step2_T.npy) not found")
T = np.load('step2_T.npy')
# Loop over mesh voxels and calculate the error in the photon source by multiplying neutron flux and T matrix
dg = discretize_geom(m)
for t, dt in enumerate(decay_times):
temp = np.zeros(shape=(len(m), num_p_groups))
for i in range(len(m)):
for row in np.atleast_1d(dg[dg["idx"] == i]):
cell = row[1]
if not cell_mats[cell] in mat_names:
continue
vol_frac = row[2]
mat = mat_names.index(cell_mats[cell])
for h in range(num_p_groups):
for g in range(num_n_groups):
temp[i, h] += (fw_n_err[i, g]**2) * T[mat, t, g,
h] * vol_frac
print("err ", temp[i, h])
# Tag the mesh with the squared error in the photon source values
tag_name = "sq_err_q_src_{0}".format(dt)
m.err_q_src = NativeMeshTag(num_p_groups, name=tag_name)
m.err_q_src[:] = temp
# Save adjoint neutron source mesh file tagged with values for all decay times
m.save("sq_err_q_src.h5m")
