Source code for openmc.deplete.operator

"""OpenMC transport operator

This module implements a transport operator for OpenMC so that it can be used by
depletion integrators. The implementation makes use of the Python bindings to
OpenMC's C API so that reading tally results and updating material number
densities is all done in-memory instead of through the filesystem.


import sys
import copy
from collections import OrderedDict
from itertools import chain
import os
import time
import xml.etree.ElementTree as ET
from warnings import warn

import h5py
import numpy as np
from uncertainties import ufloat

import openmc
import openmc.lib
from . import comm
from .abc import TransportOperator, OperatorResult
from .atom_number import AtomNumber
from .reaction_rates import ReactionRates
from .results_list import ResultsList
from .helpers import (
    DirectReactionRateHelper, ChainFissionHelper, ConstantFissionYieldHelper,
    FissionYieldCutoffHelper, AveragedFissionYieldHelper, EnergyScoreHelper)

__all__ = ["Operator", "OperatorResult"]

def _distribute(items):
    """Distribute items across MPI communicator

    items : list
        List of items of distribute

        Items assigned to process that called

    min_size, extra = divmod(len(items), comm.size)
    j = 0
    for i in range(comm.size):
        chunk_size = min_size + int(i < extra)
        if comm.rank == i:
            return items[j:j + chunk_size]
        j += chunk_size

[docs]class Operator(TransportOperator): """OpenMC transport operator for depletion. Instances of this class can be used to perform depletion using OpenMC as the transport operator. Normally, a user needn't call methods of this class directly. Instead, an instance of this class is passed to an integrator class, such as :class:`openmc.deplete.CECMIntegrator`. Parameters ---------- geometry : openmc.Geometry OpenMC geometry object settings : openmc.Settings OpenMC Settings object chain_file : str, optional Path to the depletion chain XML file. Defaults to the file listed under ``depletion_chain`` in :envvar:`OPENMC_CROSS_SECTIONS` environment variable. prev_results : ResultsList, optional Results from a previous depletion calculation. If this argument is specified, the depletion calculation will start from the latest state in the previous results. diff_burnable_mats : bool, optional Whether to differentiate burnable materials with multiple instances. Default: False. energy_mode : {"energy-deposition", "fission-q"} Indicator for computing system energy. ``"energy-deposition"`` will compute with a single energy deposition tally, taking fission energy release data and heating into consideration. ``"fission-q"`` will use the fission Q values from the depletion chain fission_q : dict, optional Dictionary of nuclides and their fission Q values [eV]. If not given, values will be pulled from the ``chain_file``. Only applicable if ``"energy_mode" == "fission-q"`` dilute_initial : float, optional Initial atom density [atoms/cm^3] to add for nuclides that are zero in initial condition to ensure they exist in the decay chain. Only done for nuclides with reaction rates. Defaults to 1.0e3. fission_yield_mode : {"constant", "cutoff", "average"} Key indicating what fission product yield scheme to use. The key determines what fission energy helper is used: * "constant": :class:`~openmc.deplete.helpers.ConstantFissionYieldHelper` * "cutoff": :class:`~openmc.deplete.helpers.FissionYieldCutoffHelper` * "average": :class:`~openmc.deplete.helpers.AveragedFissionYieldHelper` The documentation on these classes describe their methodology and differences. Default: ``"constant"`` fission_yield_opts : dict of str to option, optional Optional arguments to pass to the helper determined by ``fission_yield_mode``. Will be passed directly on to the helper. Passing a value of None will use the defaults for the associated helper. Attributes ---------- geometry : openmc.Geometry OpenMC geometry object settings : openmc.Settings OpenMC settings object dilute_initial : float Initial atom density [atoms/cm^3] to add for nuclides that are zero in initial condition to ensure they exist in the decay chain. Only done for nuclides with reaction rates. output_dir : pathlib.Path Path to output directory to save results. round_number : bool Whether or not to round output to OpenMC to 8 digits. Useful in testing, as OpenMC is incredibly sensitive to exact values. number : openmc.deplete.AtomNumber Total number of atoms in simulation. nuclides_with_data : set of str A set listing all unique nuclides available from cross_sections.xml. chain : openmc.deplete.Chain The depletion chain information necessary to form matrices and tallies. reaction_rates : openmc.deplete.ReactionRates Reaction rates from the last operator step. burnable_mats : list of str All burnable material IDs heavy_metal : float Initial heavy metal inventory [g] local_mats : list of str All burnable material IDs being managed by a single process prev_res : ResultsList or None Results from a previous depletion calculation. ``None`` if no results are to be used. diff_burnable_mats : bool Whether to differentiate burnable materials with multiple instances """ _fission_helpers = { "average": AveragedFissionYieldHelper, "constant": ConstantFissionYieldHelper, "cutoff": FissionYieldCutoffHelper, } def __init__(self, geometry, settings, chain_file=None, prev_results=None, diff_burnable_mats=False, energy_mode="fission-q", fission_q=None, dilute_initial=1.0e3, fission_yield_mode="constant", fission_yield_opts=None): if fission_yield_mode not in self._fission_helpers: raise KeyError( "fission_yield_mode must be one of {}, not {}".format( ", ".join(self._fission_helpers), fission_yield_mode)) if energy_mode == "energy-deposition": if fission_q is not None: warn("Fission Q dictionary not used if energy deposition " "is used") fission_q = None elif energy_mode != "fission-q": raise ValueError( "energy_mode {} not supported. Must be energy-deposition " "or fission-q".format(energy_mode)) super().__init__(chain_file, fission_q, dilute_initial, prev_results) self.round_number = False self.prev_res = None self.settings = settings self.geometry = geometry self.diff_burnable_mats = diff_burnable_mats # Differentiate burnable materials with multiple instances if self.diff_burnable_mats: self._differentiate_burnable_mats() # Clear out OpenMC, create task lists, distribute openmc.reset_auto_ids() self.burnable_mats, volume, nuclides = self._get_burnable_mats() self.local_mats = _distribute(self.burnable_mats) # Generate map from local materials => material index self._mat_index_map = { lm: self.burnable_mats.index(lm) for lm in self.local_mats} if self.prev_res is not None: # Reload volumes into geometry prev_results[-1].transfer_volumes(geometry) # Store previous results in operator # Distribute reaction rates according to those tracked # on this process if comm.size == 1: self.prev_res = prev_results else: self.prev_res = ResultsList() mat_indexes = _distribute(range(len(self.burnable_mats))) for res_obj in prev_results: new_res = res_obj.distribute(self.local_mats, mat_indexes) self.prev_res.append(new_res) # Determine which nuclides have incident neutron data self.nuclides_with_data = self._get_nuclides_with_data() # Select nuclides with data that are also in the chain self._burnable_nucs = [ for nuc in self.chain.nuclides if in self.nuclides_with_data] # Extract number densities from the geometry / previous depletion run self._extract_number(self.local_mats, volume, nuclides, self.prev_res) # Create reaction rates array self.reaction_rates = ReactionRates( self.local_mats, self._burnable_nucs, self.chain.reactions) # Get classes to assist working with tallies self._rate_helper = DirectReactionRateHelper( self.reaction_rates.n_nuc, self.reaction_rates.n_react) if energy_mode == "fission-q": self._energy_helper = ChainFissionHelper() else: score = "heating" if settings.photon_transport else "heating-local" self._energy_helper = EnergyScoreHelper(score) # Select and create fission yield helper fission_helper = self._fission_helpers[fission_yield_mode] fission_yield_opts = ( {} if fission_yield_opts is None else fission_yield_opts) self._yield_helper = fission_helper.from_operator( self, **fission_yield_opts)
[docs] def __call__(self, vec, power): """Runs a simulation. Simulation will abort under the following circumstances: 1) No energy is computed using OpenMC tallies. Parameters ---------- vec : list of numpy.ndarray Total atoms to be used in function. power : float Power of the reactor in [W] Returns ------- openmc.deplete.OperatorResult Eigenvalue and reaction rates resulting from transport operator """ # Prevent OpenMC from complaining about re-creating tallies openmc.reset_auto_ids() # Update status self.number.set_density(vec) # Update material compositions and tally nuclides self._update_materials() nuclides = self._get_tally_nuclides() self._rate_helper.nuclides = nuclides self._energy_helper.nuclides = nuclides self._yield_helper.update_tally_nuclides(nuclides) # Run OpenMC openmc.lib.reset() # Extract results op_result = self._unpack_tallies_and_normalize(power) return copy.deepcopy(op_result)
[docs] @staticmethod def write_bos_data(step): """Write a state-point file with beginning of step data Parameters ---------- step : int Current depletion step including restarts """ openmc.lib.statepoint_write( "openmc_simulation_n{}.h5".format(step), write_source=False)
def _differentiate_burnable_mats(self): """Assign distribmats for each burnable material """ # Count the number of instances for each cell and material self.geometry.determine_paths(instances_only=True) # Extract all burnable materials which have multiple instances distribmats = set( [mat for mat in self.geometry.get_all_materials().values() if mat.depletable and mat.num_instances > 1]) if distribmats: # Assign distribmats to cells for cell in self.geometry.get_all_material_cells().values(): if cell.fill in distribmats and cell.num_instances > 1: cell.fill = [cell.fill.clone() for i in range(cell.num_instances)] def _get_burnable_mats(self): """Determine depletable materials, volumes, and nuclides Returns ------- burnable_mats : list of str List of burnable material IDs volume : OrderedDict of str to float Volume of each material in [cm^3] nuclides : list of str Nuclides in order of how they'll appear in the simulation. """ burnable_mats = set() model_nuclides = set() volume = OrderedDict() self.heavy_metal = 0.0 # Iterate once through the geometry to get dictionaries for mat in self.geometry.get_all_materials().values(): for nuclide in mat.get_nuclides(): model_nuclides.add(nuclide) if mat.depletable: burnable_mats.add(str( if mat.volume is None: raise RuntimeError("Volume not specified for depletable " "material with ID={}.".format( volume[str(] = mat.volume self.heavy_metal += mat.fissionable_mass # Make sure there are burnable materials if not burnable_mats: raise RuntimeError( "No depletable materials were found in the model.") # Sort the sets burnable_mats = sorted(burnable_mats, key=int) model_nuclides = sorted(model_nuclides) # Construct a global nuclide dictionary, burned first nuclides = list(self.chain.nuclide_dict) for nuc in model_nuclides: if nuc not in nuclides: nuclides.append(nuc) return burnable_mats, volume, nuclides def _extract_number(self, local_mats, volume, nuclides, prev_res=None): """Construct AtomNumber using geometry Parameters ---------- local_mats : list of str Material IDs to be managed by this process volume : OrderedDict of str to float Volumes for the above materials in [cm^3] nuclides : list of str Nuclides to be used in the simulation. prev_res : ResultsList, optional Results from a previous depletion calculation """ self.number = AtomNumber(local_mats, nuclides, volume, len(self.chain)) if self.dilute_initial != 0.0: for nuc in self._burnable_nucs: self.number.set_atom_density(np.s_[:], nuc, self.dilute_initial) # Now extract and store the number densities # From the geometry if no previous depletion results if prev_res is None: for mat in self.geometry.get_all_materials().values(): if str( in local_mats: self._set_number_from_mat(mat) # Else from previous depletion results else: for mat in self.geometry.get_all_materials().values(): if str( in local_mats: self._set_number_from_results(mat, prev_res) def _set_number_from_mat(self, mat): """Extracts material and number densities from openmc.Material Parameters ---------- mat : openmc.Material The material to read from """ mat_id = str( for nuclide, density in mat.get_nuclide_atom_densities().values(): number = density * 1.0e24 self.number.set_atom_density(mat_id, nuclide, number) def _set_number_from_results(self, mat, prev_res): """Extracts material nuclides and number densities. If the nuclide concentration's evolution is tracked, the densities come from depletion results. Else, densities are extracted from the geometry in the summary. Parameters ---------- mat : openmc.Material The material to read from prev_res : ResultsList Results from a previous depletion calculation """ mat_id = str( # Get nuclide lists from geometry and depletion results depl_nuc = prev_res[-1].nuc_to_ind geom_nuc_densities = mat.get_nuclide_atom_densities() # Merge lists of nuclides, with the same order for every calculation geom_nuc_densities.update(depl_nuc) for nuclide in geom_nuc_densities.keys(): if nuclide in depl_nuc: concentration = prev_res.get_atoms(mat_id, nuclide)[1][-1] volume = prev_res[-1].volume[mat_id] number = concentration / volume else: density = geom_nuc_densities[nuclide][1] number = density * 1.0e24 self.number.set_atom_density(mat_id, nuclide, number)
[docs] def initial_condition(self): """Performs final setup and returns initial condition. Returns ------- list of numpy.ndarray Total density for initial conditions. """ # Create XML files if comm.rank == 0: self.geometry.export_to_xml() self.settings.export_to_xml() self._generate_materials_xml() # Initialize OpenMC library comm.barrier() openmc.lib.init(intracomm=comm) # Generate tallies in memory materials = [openmc.lib.materials[int(i)] for i in self.burnable_mats] self._rate_helper.generate_tallies(materials, self.chain.reactions) self._energy_helper.prepare( self.chain.nuclides, self.reaction_rates.index_nuc, materials) # Tell fission yield helper what materials this process is # responsible for self._yield_helper.generate_tallies( materials, tuple(sorted(self._mat_index_map.values()))) # Return number density vector return list(self.number.get_mat_slice(np.s_[:]))
[docs] def finalize(self): """Finalize a depletion simulation and release resources.""" openmc.lib.finalize()
def _update_materials(self): """Updates material compositions in OpenMC on all processes.""" for rank in range(comm.size): number_i = comm.bcast(self.number, root=rank) for mat in number_i.materials: nuclides = [] densities = [] for nuc in number_i.nuclides: if nuc in self.nuclides_with_data: val = 1.0e-24 * number_i.get_atom_density(mat, nuc) # If nuclide is zero, do not add to the problem. if val > 0.0: if self.round_number: val_magnitude = np.floor(np.log10(val)) val_scaled = val / 10**val_magnitude val_round = round(val_scaled, 8) val = val_round * 10**val_magnitude nuclides.append(nuc) densities.append(val) else: # Only output warnings if values are significantly # negative. CRAM does not guarantee positive values. if val < -1.0e-21: print("WARNING: nuclide ", nuc, " in material ", mat, " is negative (density = ", val, " at/barn-cm)") number_i[mat, nuc] = 0.0 # Update densities on C API side mat_internal = openmc.lib.materials[int(mat)] mat_internal.set_densities(nuclides, densities) #TODO Update densities on the Python side, otherwise the # summary.h5 file contains densities at the first time step def _generate_materials_xml(self): """Creates materials.xml from self.number. Due to uncertainty with how MPI interacts with OpenMC API, this constructs the XML manually. The long term goal is to do this through direct memory writing. """ materials = openmc.Materials(self.geometry.get_all_materials() .values()) # Sort nuclides according to order in AtomNumber object nuclides = list(self.number.nuclides) for mat in materials: mat._nuclides.sort(key=lambda x: nuclides.index(x[0])) materials.export_to_xml() def _get_tally_nuclides(self): """Determine nuclides that should be tallied for reaction rates. This method returns a list of all nuclides that have neutron data and are listed in the depletion chain. Technically, we should tally nuclides that may not appear in the depletion chain because we still need to get the fission reaction rate for these nuclides in order to normalize power, but that is left as a future exercise. Returns ------- list of str Tally nuclides """ nuc_set = set() # Create the set of all nuclides in the decay chain in materials marked # for burning in which the number density is greater than zero. for nuc in self.number.nuclides: if nuc in self.nuclides_with_data: if np.sum(self.number[:, nuc]) > 0.0: nuc_set.add(nuc) # Communicate which nuclides have nonzeros to rank 0 if comm.rank == 0: for i in range(1, comm.size): nuc_newset = comm.recv(source=i, tag=i) nuc_set |= nuc_newset else: comm.send(nuc_set, dest=0, tag=comm.rank) if comm.rank == 0: # Sort nuclides in the same order as self.number nuc_list = [nuc for nuc in self.number.nuclides if nuc in nuc_set] else: nuc_list = None # Store list of tally nuclides on each process nuc_list = comm.bcast(nuc_list) return [nuc for nuc in nuc_list if nuc in self.chain] def _unpack_tallies_and_normalize(self, power): """Unpack tallies from OpenMC and return an operator result This method uses OpenMC's C API bindings to determine the k-effective value and reaction rates from the simulation. The reaction rates are normalized by the user-specified power, summing the product of the fission reaction rate times the fission Q value for each material. Parameters ---------- power : float Power of the reactor in [W] Returns ------- openmc.deplete.OperatorResult Eigenvalue and reaction rates resulting from transport operator """ rates = self.reaction_rates rates.fill(0.0) # Get k and uncertainty k_combined = ufloat(*openmc.lib.keff()) # Extract tally bins nuclides = self._rate_helper.nuclides # Form fast map nuc_ind = [rates.index_nuc[nuc] for nuc in nuclides] react_ind = [rates.index_rx[react] for react in self.chain.reactions] # Compute fission power # Keep track of energy produced from all reactions in eV per source # particle self._energy_helper.reset() self._yield_helper.unpack() # Store fission yield dictionaries fission_yields = [] # Create arrays to store fission Q values, reaction rates, and nuclide # numbers, zeroed out in material iteration number = np.empty(rates.n_nuc) fission_ind = rates.index_rx["fission"] # Extract results for i, mat in enumerate(self.local_mats): # Get tally index mat_index = self._mat_index_map[mat] # Zero out reaction rates and nuclide numbers number.fill(0.0) # Get new number densities for nuc, i_nuc_results in zip(nuclides, nuc_ind): number[i_nuc_results] = self.number[mat, nuc] tally_rates = self._rate_helper.get_material_rates( mat_index, nuc_ind, react_ind) # Compute fission yields for this material fission_yields.append(self._yield_helper.weighted_yields(i)) # Accumulate energy from fission self._energy_helper.update(tally_rates[:, fission_ind], mat_index) # Divide by total number and store rates[i] = self._rate_helper.divide_by_adens(number) # Reduce energy produced from all processes # J / s / source neutron energy = comm.allreduce( # Guard against divide by zero if energy == 0: if comm.rank == 0: sys.stderr.flush() print(" No energy reported from OpenMC tallies. Do your HDF5 " "files have heating data?\n", file=sys.stderr, flush=True) comm.barrier() comm.Abort(1) # Scale reaction rates to obtain units of reactions/sec rates *= power / energy # Store new fission yields on the chain self.chain.fission_yields = fission_yields return OperatorResult(k_combined, rates) def _get_nuclides_with_data(self): """Loads a cross_sections.xml file to find participating nuclides. This allows for nuclides that are important in the decay chain but not important neutronically, or have no cross section data. """ # Reads cross_sections.xml to create a dictionary containing # participating (burning and not just decaying) nuclides. try: filename = os.environ["OPENMC_CROSS_SECTIONS"] except KeyError: filename = None nuclides = set() try: tree = ET.parse(filename) except Exception: if filename is None: msg = "No cross_sections.xml specified in materials." else: msg = 'Cross section file "{}" is invalid.'.format(filename) raise IOError(msg) root = tree.getroot() for nuclide_node in root.findall('library'): mats = nuclide_node.get('materials') if not mats: continue for name in mats.split(): # Make a burn list of the union of nuclides in cross_sections.xml # and nuclides in depletion chain. if name not in nuclides: nuclides.add(name) return nuclides
[docs] def get_results_info(self): """Returns volume list, material lists, and nuc lists. Returns ------- volume : dict of str float Volumes corresponding to materials in full_burn_dict nuc_list : list of str A list of all nuclide names. Used for sorting the simulation. burn_list : list of int A list of all material IDs to be burned. Used for sorting the simulation. full_burn_list : list List of all burnable material IDs """ nuc_list = self.number.burnable_nuclides burn_list = self.local_mats volume = {} for i, mat in enumerate(burn_list): volume[mat] = self.number.volume[i] # Combine volume dictionaries across processes volume_list = comm.allgather(volume) volume = {k: v for d in volume_list for k, v in d.items()} return volume, nuc_list, burn_list, self.burnable_mats