Source code for pyne.r2s

from os.path import isfile
from pyne.utils import QA_warn
import numpy as np

from pyne.mesh import Mesh
from pyne.mcnp import Meshtal
from pyne.alara import mesh_to_fluxin, record_to_geom, photon_source_to_hdf5, \
    photon_source_hdf5_to_mesh, responses_output_zone

QA_warn(__name__)


[docs]def resolve_mesh(mesh_reference, tally_num=None, flux_tag="n_flux", output_material=False): """This function creates a method that will consume many mesh-like objects (e.g. mesh, an h5m file, a meshtal file, etc) and returns a robust PyNE mesh object accordingly. Parameters ---------- mesh_reference : Mesh object, unstructured mesh file, Meshtal, meshtal file, or PyNE Meshtal object. The source of the neutron flux information. This can be a PyNE Meshtal object, a pyne Mesh object, or the filename an MCNP meshtal file, or the filename of an unstructured mesh tagged with fluxes. tally_num : int The MCNP FMESH4 tally number of the neutron flux tally within the meshtal file. flux_tag : str, optional The tag name for the neutron flux. output_material : bool, optional If true, output mesh will have materials as determined by dagmc.discretize_geom(). Returns ------- m : PyNE mesh object The PyNE mesh object of the flux data. """ # mesh_reference is Mesh object if isinstance(mesh_reference, Mesh): m = mesh_reference # mesh_reference is unstructured mesh file elif isinstance(mesh_reference, str) and isfile(mesh_reference) \ and mesh_reference.endswith(".h5m"): m = Mesh(structured=False, mesh=mesh_reference) # mesh_reference is Meshtal or meshtal file elif tally_num is not None: # mesh_reference is meshtal file if isinstance(mesh_reference, str) and isfile(mesh_reference): mesh_reference = Meshtal(mesh_reference, {tally_num: (flux_tag, flux_tag + "_err", flux_tag + "_total", flux_tag + "_err_total")}, meshes_have_mats=output_material) m = mesh_reference.tally[tally_num] # mesh_reference is Meshtal object elif isinstance(mesh_reference, Meshtal): m = mesh_reference.tally[tally_num] else: raise ValueError("meshtal argument not a Mesh object, Meshtal" " object, MCNP meshtal file or meshtal.h5m file.") # mesh_references is a Meshtal file but no tally_num provided else: raise ValueError( "Need to provide a tally number when reading a Meshtal file") return m
[docs]def irradiation_setup(flux_mesh, cell_mats, cell_fracs, alara_params, tally_num=4, num_rays=10, grid=False, flux_tag="n_flux", fluxin="alara_fluxin", reverse=False, alara_inp="alara_inp", alara_matlib="alara_matlib", output_mesh="r2s_step1.h5m", output_material=False, decay_times=None, sub_voxel=False, responses=None, wdr_file=None): """This function is used to setup the irradiation inputs after the first R2S transport step. Parameters ---------- flux_mesh : PyNE Meshtal object, Mesh object, or str The source of the neutron flux information. This can be a PyNE Meshtal object, a pyne Mesh object, or the filename an MCNP meshtal file, or the filename of an unstructured mesh tagged with fluxes. cell_mats : dict Maps geometry cell numbers to PyNE Material objects. cell_fracs : record array The output of dagmc.discretize_geom(). alara_params : str The ALARA input blocks specifying everything except the geometry and materials. This can either be passed as string or as a file name. tally_num : int The MCNP FMESH4 tally number of the neutron flux tally within the meshtal file. num_rays : int, optional The number of rays to fire down a mesh row for geometry discretization. This number must be a perfect square if grid=True. grid : bool, optional The if False, geometry discretization will be done with randomly fired rays. If true, a grid of sqrt(num_rays) x sqrt(num_rays) rays is used for each mesh row. flux_tag : str, optional The mesh tag for the neutron flux. fluxin : str, optional The name of the ALARA fluxin file to be created. reverse : bool, optional If True the fluxes in the fluxin file will be printed in the reverse order of how they appear within the flux vector tag. Since MCNP and the Meshtal class order fluxes from low energy to high energy, this option should only be true if the transmutation data being used is ordered from high energy to low energy. alara_inp : str, optional The name of the ALARA input file to be created. alara_matlib : str, optional The name of the alara_matlib file to be created. output_mesh : str, optional A mesh containing all the fluxes and materials used for irradiation setup. output_material : bool, optional If true, output mesh will have materials as determined by dagmc.discretize_geom() decay_times: list List of the decay times. If no decay times given, use '1 s'. sub_voxel : bool, optional If true, sub-voxel r2s work flow will be used. responses : list of str, optional The list of requested responses. wdr_file : str Path to the wdr file. """ m = resolve_mesh(flux_mesh, tally_num, flux_tag, output_material) if output_material: m.cell_fracs_to_mats(cell_fracs, cell_mats) mesh_to_fluxin(m, flux_tag, fluxin, reverse, sub_voxel, cell_fracs, cell_mats) record_to_geom(m, cell_fracs, cell_mats, alara_inp, alara_matlib, sub_voxel=sub_voxel) # write decay times into alara_inp if decay_times is None: decay_times = ['1 s'] decay_str = 'cooling\n' for dc in decay_times: decay_str = ''.join([decay_str, ' ', dc, '\n']) decay_str = ''.join([decay_str, 'end\n']) with open(alara_inp, 'a') as f: f.write(decay_str) if isfile(alara_params): with open(alara_params, 'r') as f: alara_params = f.read() with open(alara_inp, 'a') as f: f.write("\n" + alara_params) # append responses output zone with open(alara_inp, 'a') as f: f.write(responses_output_zone(responses, wdr_file, alara_params)) m.write_hdf5(output_mesh)
[docs]def photon_sampling_setup(mesh, phtn_src, tags): """This function reads in an ALARA photon source file and creates and tags photon source densities onto a Mesh object for the second R2S transport step. Parameters ---------- mesh : PyNE Mesh The object containing the mesh instance to be tagged. phtn_src : str The path of the ALARA phtn_file. tags: dict A dictionary were the keys are tuples with two values. The first is a string denoting an nuclide in any form that is understood by pyne.nucname (e.g. '1001', 'U-235', '242Am') or 'TOTAL' for all nuclides. The second is a string denoting the decay time as it appears in the phtn_src file (e.g. 'shutdown', '1 h' '3 d'). The values of the dictionary are the requested tag names for the combination of nuclide and decay time. These tag names should be the tag names that are read by the sampling subroutine. For example: tags = {('U-235', 'shutdown'): 'tag1', ('TOTAL', '1 h'): 'tag2'} """ photon_source_to_hdf5(phtn_src) h5_file = phtn_src + ".h5" photon_source_hdf5_to_mesh(mesh, h5_file, tags)
[docs]def total_photon_source_intensity(m, tag_name, sub_voxel=False): """This function reads mesh tagged with photon source densities and returns the total photon emission desinty. Parameters ---------- m : PyNE Mesh The mesh-based photon emission density distribution in p/cm3/s. tag_name : str The name of the tag on the mesh with the photon emission density information. sub_voxel: bool, optional If true, sub-voxel r2s work flow will be used. Returns ------- intensity : float The total photon emission density across the entire mesh (p/s). """ sd_tag = m.get_tag(tag_name) intensity = 0.0 if sub_voxel: cell_fracs = m.cell_fracs[:] else: # create a cell_fracs cell_fracs = np.ones(shape=(len(m), 1), dtype=float) max_num_cells = len(cell_fracs[0]) num_e_groups = len(sd_tag[list(m.iter_ve())[0]]) // max_num_cells for idx, _, ve in m: ve_data = sd_tag[ve] for svid in range(max_num_cells): vol = m.elem_volume(ve) * cell_fracs[idx][svid] sv_data = ve_data[num_e_groups*svid:num_e_groups*(svid+1)] intensity += vol * np.sum(sv_data) return intensity