read_alara_phtn Module¶

Module includes methods which find the lines in a ‘phtn_src’ file from ALARA that match a specified isotope and cooling time, and tags the photon source information to a mesh.

r2s.io.read_alara_phtn.get_cooling_step_name(coolingstep, fr)¶

Method determines the user-specified cooling step name in a phtn_src file

If coolingstep is a number, we search for the corresponding line in the file stream ‘fr’, and determine the corresponding cooling step string.

Parameters :	coolingstep : int or string number for cooling step index or string for cooling step name fr : readable file stream
Returns :	... : tuple A 2 value tuple: (the cooling step string name, the number of photon energy bins used in the phtn_src file)

Notes

If coolingstep is not an integer, the calling function must catch a ValueError.

r2s.io.read_alara_phtn.main()¶

Method defines an option parser and handles command-line usage of this module.

Notes

Requires command line arguments to be passed - otherwise prints help information.

r2s.io.read_alara_phtn.read_to_h5m(inputfile, meshobj, isotope='TOTAL', coolingstep=0, retag=False, totals=False)¶

Read in a phtn_src file and tag the contents to a mesh.

Method reads in a phtn_src file line by line, looking for a specific isotope at a specific cooling step, and repeats for each voxel. Method tags the mesh with the photon source information, and then saves the mesh.

Parameters :

inputfile : string Path to an ALARA-style ‘phtn_src’ file meshobj : ScdMesh object Structured mesh object to tag, isotope : string Isotope to read data for from ‘phtn_src’ file coolingstep : int or string String cooling step name, or number for index (0’th is ‘shutdown’) retag : boolean Whether to retag existing tags in mesh totals : boolean Whether to tag the total photon source strength for each voxel

r2s.io.read_alara_phtn.tag_phtn_src_totals(mesh, voxels, numergbins=-1, retag=False)¶

Method tags the total photon source strength for each voxel.

Method calculate the total photon source strength, and if retagging is enabled or the tag does not exist, tags the mesh.

Parameters :	mesh : iMesh.Mesh object Mesh from which to get/create/delete tags voxels : list of iMesh.Entity handles List of voxel entity handles (iBase.Type.Region) numergbins : int (optional) Number of energy group tags to read retag : boolean Whether to overwrite existing ‘phtn_src_total’ tag. (Default: False)

read_meshtal Module¶

r2s.io.read_meshtal.find_first_line(meshtal, tally_line)¶

Searchs for the “Energy X Y Z” line, to determine the first line of data

Parameters :	meshtal : string File path to meshtal file. tally_line : int Line number in file where tally begins
Returns :	m : int Line number of first data line for the tally in meshtal

r2s.io.read_meshtal.find_mesh_bounds(meshtal, tally_line)¶

Parse the header of the meshtal to get the x, y, z, and energy boundaries

Parameters :	meshtal : string File path to meshtal file. tally_line : int Line number in file where tally begins
Returns :	... : tuple of 4 ints Tuple of the divisions in x, y, z and energy

r2s.io.read_meshtal.find_meshtal_type(meshtal, tally_line)¶

Searchs the meshtal header to determine if it is a neutron or photon meshtally

Parameters :	meshtal : string File path to meshtal file. tally_line : int Line number in file where tally begins
Returns :	meshtal_type : {‘n’, ‘p’} Tally type; either neutron (‘n’) or photon (‘p) is supported.

r2s.io.read_meshtal.find_tallies(meshtal)¶

Searches the meshtal file to determine the number of tallies present and returns the tallies and lines where they are listed.

Parameters :	meshtal : string File path to meshtal file.
Returns :	tally_numbers : list of strings List of tally numbers (as strings) tally_lines : list of integers List of the line numbers where tallies begin

r2s.io.read_meshtal.main(arguments=None)¶

r2s.io.read_meshtal.read_meshtal(filename, tally_line, norm=1.0, **kw)¶

Read an MCNP meshtal file and return a tagged structured mesh for it

The optional normalization factor will be multiplied into each flux value. This can be used to rescale a tally if a tally multiplier was not used in the original MCNP problem.

Parameters :	filename : string File path to meshtal file. tally_line : int Line number in file where tally begins norm : float, optional Normalization factor to multiply into each flux value. Keyword arguments: : smesh: An existing scdmesh on which to tag the fluxes. A ScdMeshError is raised if this mesh has incompatible ijk dims
Returns :	sm : ScdMesh object Opened structured mesh from filename, with meshtally data tagged

r2s.io.read_meshtal.tag_fluxes(meshtal, meshtal_type, m, spatial_points, e_bins, sm, norm)¶

Tags the fluxes from a meshtally to a structured mesh.

Parameters :

meshtal : string File path to meshtal file. meshtal_type : {‘n’, ‘p’} Tally type; either neutron (‘n’) or photon (‘p) is supported. m : int Line number of first data line for the tally in meshtal spatial_points : int Number of meshtally points (aka voxels) e_bins : int Number of energy bins in the meshtally sm : scdmesh.ScdMesh Structured mesh to tag fluxes to norm : float, optional Normalization factor to multiply into each flux value.

Returns :

N/A :

write_alara_fluxin Module¶

write_alara_fluxin.py is used to create a fluxin file for ALARA. Fluxes are taken from a MOAB mesh, with tag names of the form ‘n_group_###’ where ### is a 3 digit number with leading zeros as needed (e.g. 001).

r2s.io.write_alara_fluxin.find_num_e_groups(sm)¶

Return the number of energy groups used for neutron flux tags on a mesh

Parameters :	sm - Scdmesh.scmesh object : Structured mesh object containing tags of the form ‘n_group_###’.
Returns :	num_e_groups - int : Number of energy groups

r2s.io.write_alara_fluxin.get_flux_tag_handles(mesh)¶

Method identifies all tags containing flux information from a DAGMC meshtally

Parameters :	mesh : iMesh.Mesh object MOAB mesh file object containing tags of the form “TALLY_TAG_lowE-highE”
Returns :	fluxtaghandles : list of iMesh.Tag objects List of tag handles, sorted by tag name, from lowest energy to high

r2s.io.write_alara_fluxin.main()¶

r2s.io.write_alara_fluxin.print_fluxes(mesh, num_e_groups, backward_bool, fluxin_name, tags=None)¶

Method writes tag values to ALARA fluxin format for the flux at each energy for each voxel

Parameters :

mesh : iMesh.Mesh object MOAB mesh file object containing tags of the form TALLY_TAG_lowE-highE num_e_groups : integer Number of energy groups in tally backward_bool : boolean If true, output data is in order from high energy to low energy. Note that this should be true when working with the FENDL libraries. fluxin_name : string Filename for output ALARA fluxin file tags : list of iMesh.Tag objects List of tag handles, sorted by tag name, from lowest energy to high

r2s.io.write_alara_fluxin.write_alara_fluxin(filename, mesh, backwards=False)¶

Load a MOAB mesh and create an alara_fluxin file from tags

Parameters :	filename - string : Output filename for the fluxin file. mesh - ScdMesh or iMesh.Mesh object : MOAB mesh with tags to create fluxin file from. backwards - boolean : If true, prints fluxes from high energy to low energy. Note that this should be true when working with the FENDL libraries.

write_alara_geom Module¶

r2s.io.write_alara_geom.create_mixture_definitions(mesh)¶

Return a list of unique materials tagged onto the mesh.

unique_mixtures is a dictionary mapping mixture tuples (created through _create_mixture_tuple) to lists. The first element in the list is a unique integer ID for the mixtures; the rest of the elements are the hex handles that participate in that mixture.

mat_tags is a list of the material tags from the input mesh. This list is ordered in the same order as the mixture tuples.

Parameters :	mesh : ScdMesh object or iMesh.Mesh object Mesh object to read materials data from
Returns :	... : tuple A tuple of the list of mixtures and tag handles list; i.e. (unique_mixtures, mat_tags)

Notes

It is assumed that the mesh has the ‘matVOID’ tag.

r2s.io.write_alara_geom.main()¶

r2s.io.write_alara_geom.write_alara_geom(filename, mesh, namedict={})¶

Given a mesh with mmgrid tags, write an ALARA geometry file

Parameters :	filename : string Path/filename of mesh file to write ALARA geometry to mesh : ScdMesh object or iMesh.Mesh object Mesh object containing materials tags namedict : dictionary (optional) Dictionary of names for material compositions

r2s.io.write_alara_geom.write_mat_loading(mesh, mat_tags, mixtures, output_file)¶

Write the mat_loading information to the ALARA geometry output

Parameters :	mesh : ScdMesh object or iMesh.Mesh object Mesh object to read materials data from mat_tags : ... ... mixtures : ... ... output_file : file object Opened file for writing contents of ALARA geometry

r2s.io.write_alara_geom.write_mixtures(mixtures, mat_tags, name_dict, output_file)¶

Write the mixture lines to the ALARA geometry output

Parameters :	mixtures : ??? ... mat_tags : list of iMesh.Tag entities ... name_dict : dictionary (optional?) Dictionary of names for material compositions output_file : file object Opened file for writing contents of ALARA geometry

r2s.io.write_alara_geom.write_zones(mesh, output_file)¶

Write the volume and zone lines to the ALARA geometry output

Parameters :	mesh : ScdMesh object or iMesh.Mesh object Mesh object to read materials data from output_file : file object Opened file for writing contents of ALARA geometry

write_gammas Module¶

r2s.io.write_gammas.calc_sm_volumes_list(sm)¶

Create a 1D list of the voxel volumes for a XYZ structured mesh

Parameters :	sm : ScdMesh object A structured mesh object from which to calculate volumes.
Returns :	vols : list of floats A 1D list of voxel volumes in order ‘xyz’

Notes

Voxel ordering follows meshtal file convention which is::

-for x for y iterate z -for x iterate y -iterate x

r2s.io.write_gammas.calc_total_source_strength(mesh, voxels, tag_srcsum=False, **kwargs)¶

r2s.io.write_gammas.gen_gammas_file_from_h5m(sm, outfile='gammas', sampling='v', do_bias=False, cumulative=False, cust_ergbins=False, resample=False, uni_resamp_all=False, **kwargs)¶

Generate gammas file using information from tags on a MOAB Scd mesh.

Method reads tags with photon source strengths from a structured mesh object and generates the gammas file for the modified source.F90 routine source_gamma.F90.

Parameters :

sm : ScdMesh Structured mesh object to generate ‘gammas’ from. outfile : string, optional Output file name for the ‘gammas’ file sampling : {‘v’, ‘u’}, optional Format the file file for voxel sampling (‘v’) or uniform sampling (‘u’) do_bias : boolean, optional Attempt to tag bias values for voxels cumulative : boolean, optional Use the cumulative format for listing energy PDFs of each voxel cust_ergbins : boolean, optional Attempt to use custom energy bins found on ‘sm’ resample : boolean, optional If true, ‘r’ flag is added to gammas, and resampling of particles starting in void regions of voxels is enabled. uni_resamp_all : boolean, optional If true, ‘a’ flag is added to gammas, and particles starting in void regions of voxels, during uniform sampling, are resampled over the entire problem, rather than resampling just the voxel. This has the potential to result in an unfair game. keyword arguments : Currently valid: {‘title’, ‘isotope’, ‘coolingstep’} These are passed to header creation code.

Notes

Requires that the structured mesh has photon source strength tags of the form ‘phtn_src_group_###’.

Will read photon energy bin boundary values if the root set has the tag ‘PHTN_ERG’ (a list of floats).

r2s.io.write_gammas.main()¶

Method defines an option parser and handles command-line usage of this module.

Notes

Requires command line arguments to be passed - otherwise prints help information.