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Code Issues Projects Releases Packages Wiki Activity Actions 5

Merge branch 'develop' into batchwise_pr

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Lorenzo Chierici 2024-03-20 09:04:35 +01:00 • committed by GitHub
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8
.github/workflows/ci.yml vendored
View file

@ -93,10 +93,10 @@ jobs:
RDMAV_FORK_SAFE: 1
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
@ -128,7 +128,7 @@ jobs:
$GITHUB_WORKSPACE/tools/ci/gha-install.sh
- name: cache-xs
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: |
~/nndc_hdf5
@ -156,7 +156,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Coveralls Finished
uses: coverallsapp/github-action@master
uses: coverallsapp/github-action@v2
with:
github-token: ${{ secrets.github_token }}
parallel-finished: true

8
.github/workflows/dockerhub-publish-dagmc-libmesh.yml vendored
View file

@ -10,20 +10,20 @@ jobs:
steps:
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
-
name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
id: docker_build
uses: docker/build-push-action@v4
uses: docker/build-push-action@v5
with:
push: true
tags: openmc/openmc:latest-dagmc-libmesh

8
.github/workflows/dockerhub-publish-dagmc.yml vendored
View file

@ -10,20 +10,20 @@ jobs:
steps:
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
-
name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
id: docker_build
uses: docker/build-push-action@v4
uses: docker/build-push-action@v5
with:
push: true
tags: openmc/openmc:latest-dagmc

8
.github/workflows/dockerhub-publish-dev.yml vendored
View file

@ -10,20 +10,20 @@ jobs:
steps:
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
-
name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
id: docker_build
uses: docker/build-push-action@v4
uses: docker/build-push-action@v5
with:
push: true
tags: openmc/openmc:develop

8
.github/workflows/dockerhub-publish-develop-dagmc-libmesh.yml vendored
View file

@ -10,20 +10,20 @@ jobs:
steps:
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
-
name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
id: docker_build
uses: docker/build-push-action@v4
uses: docker/build-push-action@v5
with:
push: true
tags: openmc/openmc:develop-dagmc-libmesh

8
.github/workflows/dockerhub-publish-develop-dagmc.yml vendored
View file

@ -10,20 +10,20 @@ jobs:
steps:
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
-
name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
id: docker_build
uses: docker/build-push-action@v4
uses: docker/build-push-action@v5
with:
push: true
tags: openmc/openmc:develop-dagmc

8
.github/workflows/dockerhub-publish-develop-libmesh.yml vendored
View file

@ -10,20 +10,20 @@ jobs:
steps:
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
-
name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
id: docker_build
uses: docker/build-push-action@v4
uses: docker/build-push-action@v5
with:
push: true
tags: openmc/openmc:develop-libmesh

8
.github/workflows/dockerhub-publish-libmesh.yml vendored
View file

@ -10,20 +10,20 @@ jobs:
steps:
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
-
name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
id: docker_build
uses: docker/build-push-action@v4
uses: docker/build-push-action@v5
with:
push: true
tags: openmc/openmc:latest-libmesh

10
.github/workflows/dockerhub-publish-release-dagmc-libmesh.yml vendored
View file

@ -8,25 +8,25 @@ jobs:
main:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Set env
run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
-
name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
id: docker_build
uses: docker/build-push-action@v4
uses: docker/build-push-action@v5
with:
push: true
tags: openmc/openmc:${{ env.RELEASE_VERSION }}-dagmc-libmesh

10
.github/workflows/dockerhub-publish-release-dagmc.yml vendored
View file

@ -8,25 +8,25 @@ jobs:
main:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Set env
run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
-
name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
id: docker_build
uses: docker/build-push-action@v4
uses: docker/build-push-action@v5
with:
push: true
tags: openmc/openmc:${{ env.RELEASE_VERSION }}-dagmc

10
.github/workflows/dockerhub-publish-release-libmesh.yml vendored
View file

@ -8,25 +8,25 @@ jobs:
main:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Set env
run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
-
name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
id: docker_build
uses: docker/build-push-action@v4
uses: docker/build-push-action@v5
with:
push: true
tags: openmc/openmc:${{ env.RELEASE_VERSION }}-libmesh

10
.github/workflows/dockerhub-publish-release.yml vendored
View file

@ -8,25 +8,25 @@ jobs:
main:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Set env
run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
-
name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
id: docker_build
uses: docker/build-push-action@v4
uses: docker/build-push-action@v5
with:
push: true
tags: openmc/openmc:${{ env.RELEASE_VERSION }}

8
.github/workflows/dockerhub-publish.yml vendored
View file

@ -10,20 +10,20 @@ jobs:
steps:
-
name: Set up QEMU
uses: docker/setup-qemu-action@v2
uses: docker/setup-qemu-action@v3
-
name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
uses: docker/setup-buildx-action@v3
-
name: Login to DockerHub
uses: docker/login-action@v2
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push
id: docker_build
uses: docker/build-push-action@v4
uses: docker/build-push-action@v5
with:
push: true
tags: openmc/openmc:latest

2
.github/workflows/format-check.yml vendored
View file

@ -13,7 +13,7 @@ jobs:
cpp-linter:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- uses: cpp-linter/cpp-linter-action@v2
id: linter
env:

10
CMakeLists.txt
View file

@ -193,12 +193,10 @@ endif()
if(NOT MSVC)
if(OPENMC_USE_OPENMP)
find_package(OpenMP)
if(OPENMP_FOUND)
# In CMake 3.9+, can use the OpenMP::OpenMP_CXX imported target
list(APPEND cxxflags ${OpenMP_CXX_FLAGS})
list(APPEND ldflags ${OpenMP_CXX_FLAGS})
endif()
find_package(OpenMP REQUIRED)
# In CMake 3.9+, can use the OpenMP::OpenMP_CXX imported target
list(APPEND cxxflags ${OpenMP_CXX_FLAGS})
list(APPEND ldflags ${OpenMP_CXX_FLAGS})
endif()
set(CMAKE_POSITION_INDEPENDENT_CODE ON)

7
docs/source/io_formats/settings.rst
View file

@ -276,6 +276,13 @@ then, OpenMC will only use up to the :math:`P_1` data.
.. note:: This element is not used in the continuous-energy
:ref:`energy_mode`.
---------------------------
``<max_splits>`` Element
---------------------------
The ``<max_splits>`` element indicates the number of times a particle can split during a history.
*Default*: 1000
--------------------------------------
``<max_write_lost_particles>`` Element

1
docs/source/pythonapi/base.rst
View file

@ -35,6 +35,7 @@ Simulation Settings
:nosignatures:
:template: myfunction.rst
openmc.read_source_file
openmc.write_source_file
openmc.wwinp_to_wws

1
include/openmc/capi.h
View file

@ -106,6 +106,7 @@ int openmc_mesh_filter_set_translation(int32_t index, double translation[3]);
int openmc_mesh_get_id(int32_t index, int32_t* id);
int openmc_mesh_set_id(int32_t index, int32_t id);
int openmc_mesh_get_n_elements(int32_t index, size_t* n);
int openmc_mesh_get_volumes(int32_t index, double* volumes);
int openmc_mesh_material_volumes(int32_t index, int n_sample, int bin,
int result_size, void* result, int* hits, uint64_t* seed);
int openmc_meshsurface_filter_get_mesh(int32_t index, int32_t* index_mesh);

2
openmc/cell.py
View file

@ -722,7 +722,7 @@ class Cell(IDManagerMixin):
Dictionary mapping surface IDs to :class:`openmc.Surface` instances
materials : dict
Dictionary mapping material ID strings to :class:`openmc.Material`
instances (defined in :math:`openmc.Geometry.from_xml`)
instances (defined in :meth:`openmc.Geometry.from_xml`)
get_universe : function
Function returning universe (defined in
:meth:`openmc.Geometry.from_xml`)

87
openmc/data/data.py
View file

@ -179,6 +179,93 @@ ATOMIC_SYMBOL = {0: 'n', 1: 'H', 2: 'He', 3: 'Li', 4: 'Be', 5: 'B', 6: 'C',
118: 'Og'}
ATOMIC_NUMBER = {value: key for key, value in ATOMIC_SYMBOL.items()}
DADZ = {
'(n,2nd)': (-3, -1),
'(n,2n)': (-1, 0),
'(n,3n)': (-2, 0),
'(n,na)': (-4, -2),
'(n,n3a)': (-12, -6),
'(n,2na)': (-5, -2),
'(n,3na)': (-6, -2),
'(n,np)': (-1, -1),
'(n,n2a)': (-8, -4),
'(n,2n2a)': (-9, -4),
'(n,nd)': (-2, -1),
'(n,nt)': (-3, -1),
'(n,n3He)': (-3, -2),
'(n,nd2a)': (-10, -5),
'(n,nt2a)': (-11, -5),
'(n,4n)': (-3, 0),
'(n,2np)': (-2, -1),
'(n,3np)': (-3, -1),
'(n,n2p)': (-2, -2),
'(n,npa)': (-5, -3),
'(n,gamma)': (1, 0),
'(n,p)': (0, -1),
'(n,d)': (-1, -1),
'(n,t)': (-2, -1),
'(n,3He)': (-2, -2),
'(n,a)': (-3, -2),
'(n,2a)': (-7, -4),
'(n,3a)': (-11, -6),
'(n,2p)': (-1, -2),
'(n,pa)': (-4, -3),
'(n,t2a)': (-10, -5),
'(n,d2a)': (-9, -5),
'(n,pd)': (-2, -2),
'(n,pt)': (-3, -2),
'(n,da)': (-5, -3),
'(n,5n)': (-4, 0),
'(n,6n)': (-5, 0),
'(n,2nt)': (-4, -1),
'(n,ta)': (-6, -3),
'(n,4np)': (-4, -1),
'(n,3nd)': (-4, -1),
'(n,nda)': (-6, -3),
'(n,2npa)': (-6, -3),
'(n,7n)': (-6, 0),
'(n,8n)': (-7, 0),
'(n,5np)': (-5, -1),
'(n,6np)': (-6, -1),
'(n,7np)': (-7, -1),
'(n,4na)': (-7, -2),
'(n,5na)': (-8, -2),
'(n,6na)': (-9, -2),
'(n,7na)': (-10, -2),
'(n,4nd)': (-5, -1),
'(n,5nd)': (-6, -1),
'(n,6nd)': (-7, -1),
'(n,3nt)': (-5, -1),
'(n,4nt)': (-6, -1),
'(n,5nt)': (-7, -1),
'(n,6nt)': (-8, -1),
'(n,2n3He)': (-4, -2),
'(n,3n3He)': (-5, -2),
'(n,4n3He)': (-6, -2),
'(n,3n2p)': (-4, -2),
'(n,3n2a)': (-10, -4),
'(n,3npa)': (-7, -3),
'(n,dt)': (-4, -2),
'(n,npd)': (-3, -2),
'(n,npt)': (-4, -2),
'(n,ndt)': (-5, -2),
'(n,np3He)': (-4, -3),
'(n,nd3He)': (-5, -3),
'(n,nt3He)': (-6, -3),
'(n,nta)': (-7, -3),
'(n,2n2p)': (-3, -2),
'(n,p3He)': (-4, -3),
'(n,d3He)': (-5, -3),
'(n,3Hea)': (-6, -4),
'(n,4n2p)': (-5, -2),
'(n,4n2a)': (-11, -4),
'(n,4npa)': (-8, -3),
'(n,3p)': (-2, -3),
'(n,n3p)': (-3, -3),
'(n,3n2pa)': (-8, -4),
'(n,5n2p)': (-6, -2),
}
# Values here are from the Committee on Data for Science and Technology
# (CODATA) 2018 recommendation (https://physics.nist.gov/cuu/Constants/).

80
openmc/deplete/abc.py
View file

@ -3,6 +3,7 @@
This module contains Abstract Base Classes for implementing operator, integrator, depletion system solver, and operator helper classes
"""
from __future__ import annotations
from abc import ABC, abstractmethod
from collections import namedtuple, defaultdict
from collections.abc import Iterable, Callable
@ -13,17 +14,20 @@ from contextlib import contextmanager
import os
from pathlib import Path
import time
from typing import Optional, Union, Sequence
from warnings import warn
from numpy import nonzero, empty, asarray
import numpy as np
from uncertainties import ufloat
from openmc.checkvalue import check_value, check_type, check_greater_than, PathLike
from openmc.mpi import comm
from openmc import Material
from .stepresult import StepResult
from .chain import Chain
from .results import Results
from .pool import deplete
from .reaction_rates import ReactionRates
from .transfer_rates import TransferRates
from openmc import Material, Cell
from .reactivity_control import (
@ -181,7 +185,7 @@ class TransportOperator(ABC):
pass
@abstractmethod
def write_bos_data(self, step):
def write_bos_data(self, step: int):
"""Document beginning of step data for a given step
Called at the beginning of a depletion step and at
@ -220,7 +224,7 @@ class ReactionRateHelper(ABC):
def __init__(self, n_nucs, n_react):
self._nuclides = None
self._results_cache = empty((n_nucs, n_react))
self._results_cache = np.empty((n_nucs, n_react))
@abstractmethod
def generate_tallies(self, materials, scores):
@ -237,7 +241,12 @@ class ReactionRateHelper(ABC):
self._nuclides = nuclides
@abstractmethod
def get_material_rates(self, mat_id, nuc_index, react_index):
def get_material_rates(
self,
mat_id: int,
nuc_index: Sequence[str],
react_index: Sequence[str]
):
"""Return 2D array of [nuclide, reaction] reaction rates
Parameters
@ -250,7 +259,7 @@ class ReactionRateHelper(ABC):
Ordering of reactions
"""
def divide_by_atoms(self, number):
def divide_by_atoms(self, number: Sequence[float]):
"""Normalize reaction rates by number of atoms
Acts on the current material examined by :meth:`get_material_rates`
@ -267,7 +276,7 @@ class ReactionRateHelper(ABC):
normalized by the number of nuclides
"""
mask = nonzero(number)
mask = np.nonzero(number)
results = self._results_cache
for col in range(results.shape[1]):
results[mask, col] /= number[mask]
@ -299,7 +308,7 @@ class NormalizationHelper(ABC):
"""Reset state for normalization"""
@abstractmethod
def prepare(self, chain_nucs, rate_index):
def prepare(self, chain_nucs: Sequence[str], rate_index: dict):
"""Perform work needed to obtain energy produced
This method is called prior to calculating the reaction rates
@ -338,7 +347,7 @@ class NormalizationHelper(ABC):
self._nuclides = nuclides
@abstractmethod
def factor(self, source_rate):
def factor(self, source_rate: float):
"""Return normalization factor
Parameters
@ -441,7 +450,7 @@ class FissionYieldHelper(ABC):
in parallel mode.
"""
def update_tally_nuclides(self, nuclides):
def update_tally_nuclides(self, nuclides: Sequence[str]) -> list:
"""Return nuclides with non-zero densities and yield data
Parameters
@ -567,8 +576,16 @@ class Integrator(ABC):
"""
def __init__(self, operator, timesteps, power=None, power_density=None,
source_rates=None, timestep_units='s', solver="cram48"):
def __init__(
self,
operator: TransportOperator,
timesteps: Sequence[float],
power: Optional[Union[float, Sequence[float]]] = None,
power_density: Optional[Union[float, Sequence[float]]] = None,
source_rates: Optional[Sequence[float]] = None,
timestep_units: str = 's',
solver: str = "cram48"
):
# Check number of stages previously used
if operator.prev_res is not None:
res = operator.prev_res[-1]
@ -640,8 +657,8 @@ class Integrator(ABC):
else:
raise ValueError("Invalid timestep unit '{}'".format(unit))
self.timesteps = asarray(seconds)
self.source_rates = asarray(source_rates)
self.timesteps = np.asarray(seconds)
self.source_rates = np.asarray(source_rates)
self.transfer_rates = None
self._reactivity_control = None
@ -705,7 +722,14 @@ class Integrator(ABC):
return time.time() - start, results
@abstractmethod
def __call__(self, n, rates, dt, source_rate, i):
def __call__(
self,
n: Sequence[np.ndarray],
rates: ReactionRates,
dt: float,
source_rate: float,
i: int
):
"""Perform the integration across one time step
Parameters
@ -758,7 +782,7 @@ class Integrator(ABC):
self.operator.write_bos_data(step_index + self._i_res)
return x, res
def _get_bos_data_from_restart(self, step_index, source_rate, bos_conc):
def _get_bos_data_from_restart(self, source_rate, bos_conc):
"""Get beginning of step concentrations, reaction rates from restart"""
res = self.operator.prev_res[-1]
# Depletion methods expect list of arrays
@ -860,8 +884,14 @@ class Integrator(ABC):
self.operator.finalize()
def add_transfer_rate(self, material, components, transfer_rate,
transfer_rate_units='1/s', destination_material=None):
def add_transfer_rate(
self,
material: Union[str, int, Material],
components: Sequence[str],
transfer_rate: float,
transfer_rate_units: str = '1/s',
destination_material: Optional[Union[str, int, Material]] = None
):
"""Add transfer rates to depletable material.
Parameters
@ -1001,9 +1031,17 @@ class SIIntegrator(Integrator):
"""
def __init__(self, operator, timesteps, power=None, power_density=None,
source_rates=None, timestep_units='s', n_steps=10,
solver="cram48"):
def __init__(
self,
operator: TransportOperator,
timesteps: Sequence[float],
power: Optional[Union[float, Sequence[float]]] = None,
power_density: Optional[Union[float, Sequence[float]]] = None,
source_rates: Optional[Sequence[float]] = None,
timestep_units: str = 's',
n_steps: int = 10,
solver: str = "cram48"
):
check_type("n_steps", n_steps, Integral)
check_greater_than("n_steps", n_steps, 0)
super().__init__(
@ -1050,7 +1088,7 @@ class SIIntegrator(Integrator):
if self.operator.prev_res is None:
n, res = self._get_bos_data_from_operator(i, p, n)
else:
n, res = self._get_bos_data_from_restart(i, p, n)
n, res = self._get_bos_data_from_restart(p, n)
else:
# Pull rates, k from previous iteration w/o
# re-running transport

188
openmc/deplete/chain.py
View file

@ -7,115 +7,109 @@ loaded from an .xml file and all the nuclides are linked together.
from io import StringIO
from itertools import chain
import math
import os
import re
from collections import defaultdict, namedtuple
from collections.abc import Mapping, Iterable
from numbers import Real, Integral
from warnings import warn
from openmc.checkvalue import check_type, check_greater_than
from openmc.data import gnds_name, zam, DataLibrary
from openmc.exceptions import DataError
from .nuclide import FissionYieldDistribution
import lxml.etree as ET
import scipy.sparse as sp
from openmc.checkvalue import check_type, check_greater_than
from openmc.data import gnds_name, zam
from .nuclide import FissionYieldDistribution, Nuclide
import openmc.data
from openmc._xml import clean_indentation
from .nuclide import Nuclide, DecayTuple, ReactionTuple
# tuple of (possible MT values, (dA, dZ), secondaries) where dA is the change in
# the mass number and dZ is the change in the atomic number
ReactionInfo = namedtuple('ReactionInfo', ('mts', 'dadz', 'secondaries'))
# tuple of (possible MT values, secondaries)
ReactionInfo = namedtuple('ReactionInfo', ('mts', 'secondaries'))
REACTIONS = {
'(n,2nd)': ReactionInfo({11}, (-3, -1), ('H2',)),
'(n,2n)': ReactionInfo(set(chain([16], range(875, 892))), (-1, 0), ()),
'(n,3n)': ReactionInfo({17}, (-2, 0), ()),
'(n,na)': ReactionInfo({22}, (-4, -2), ('He4',)),
'(n,n3a)': ReactionInfo({23}, (-12, -6), ('He4', 'He4', 'He4')),
'(n,2na)': ReactionInfo({24}, (-5, -2), ('He4',)),
'(n,3na)': ReactionInfo({25}, (-6, -2), ('He4',)),
'(n,np)': ReactionInfo({28}, (-1, -1), ('H1',)),
'(n,n2a)': ReactionInfo({29}, (-8, -4), ('He4', 'He4')),
'(n,2n2a)': ReactionInfo({30}, (-9, -4), ('He4', 'He4')),
'(n,nd)': ReactionInfo({32}, (-2, -1), ('H2',)),
'(n,nt)': ReactionInfo({33}, (-3, -1), ('H3',)),
'(n,n3He)': ReactionInfo({34}, (-3, -2), ('He3',)),
'(n,nd2a)': ReactionInfo({35}, (-10, -5), ('H2', 'He4', 'He4')),
'(n,nt2a)': ReactionInfo({36}, (-11, -5), ('H3', 'He4', 'He4')),
'(n,4n)': ReactionInfo({37}, (-3, 0), ()),
'(n,2np)': ReactionInfo({41}, (-2, -1), ('H1',)),
'(n,3np)': ReactionInfo({42}, (-3, -1), ('H1',)),
'(n,n2p)': ReactionInfo({44}, (-2, -2), ('H1', 'H1')),
'(n,npa)': ReactionInfo({45}, (-5, -3), ('H1', 'He4')),
'(n,gamma)': ReactionInfo({102}, (1, 0), ()),
'(n,p)': ReactionInfo(set(chain([103], range(600, 650))), (0, -1), ('H1',)),
'(n,d)': ReactionInfo(set(chain([104], range(650, 700))), (-1, -1), ('H2',)),
'(n,t)': ReactionInfo(set(chain([105], range(700, 750))), (-2, -1), ('H3',)),
'(n,3He)': ReactionInfo(set(chain([106], range(750, 800))), (-2, -2), ('He3',)),
'(n,a)': ReactionInfo(set(chain([107], range(800, 850))), (-3, -2), ('He4',)),
'(n,2a)': ReactionInfo({108}, (-7, -4), ('He4', 'He4')),
'(n,3a)': ReactionInfo({109}, (-11, -6), ('He4', 'He4', 'He4')),
'(n,2p)': ReactionInfo({111}, (-1, -2), ('H1', 'H1')),
'(n,pa)': ReactionInfo({112}, (-4, -3), ('H1', 'He4')),
'(n,t2a)': ReactionInfo({113}, (-10, -5), ('H3', 'He4', 'He4')),
'(n,d2a)': ReactionInfo({114}, (-9, -5), ('H2', 'He4', 'He4')),
'(n,pd)': ReactionInfo({115}, (-2, -2), ('H1', 'H2')),
'(n,pt)': ReactionInfo({116}, (-3, -2), ('H1', 'H3')),
'(n,da)': ReactionInfo({117}, (-5, -3), ('H2', 'He4')),
'(n,5n)': ReactionInfo({152}, (-4, 0), ()),
'(n,6n)': ReactionInfo({153}, (-5, 0), ()),
'(n,2nt)': ReactionInfo({154}, (-4, -1), ('H3',)),
'(n,ta)': ReactionInfo({155}, (-6, -3), ('H3', 'He4')),
'(n,4np)': ReactionInfo({156}, (-4, -1), ('H1',)),
'(n,3nd)': ReactionInfo({157}, (-4, -1), ('H2',)),
'(n,nda)': ReactionInfo({158}, (-6, -3), ('H2', 'He4')),
'(n,2npa)': ReactionInfo({159}, (-6, -3), ('H1', 'He4')),
'(n,7n)': ReactionInfo({160}, (-6, 0), ()),
'(n,8n)': ReactionInfo({161}, (-7, 0), ()),
'(n,5np)': ReactionInfo({162}, (-5, -1), ('H1',)),
'(n,6np)': ReactionInfo({163}, (-6, -1), ('H1',)),
'(n,7np)': ReactionInfo({164}, (-7, -1), ('H1',)),
'(n,4na)': ReactionInfo({165}, (-7, -2), ('He4',)),
'(n,5na)': ReactionInfo({166}, (-8, -2), ('He4',)),
'(n,6na)': ReactionInfo({167}, (-9, -2), ('He4',)),
'(n,7na)': ReactionInfo({168}, (-10, -2), ('He4',)),
'(n,4nd)': ReactionInfo({169}, (-5, -1), ('H2',)),
'(n,5nd)': ReactionInfo({170}, (-6, -1), ('H2',)),
'(n,6nd)': ReactionInfo({171}, (-7, -1), ('H2',)),
'(n,3nt)': ReactionInfo({172}, (-5, -1), ('H3',)),
'(n,4nt)': ReactionInfo({173}, (-6, -1), ('H3',)),
'(n,5nt)': ReactionInfo({174}, (-7, -1), ('H3',)),
'(n,6nt)': ReactionInfo({175}, (-8, -1), ('H3',)),
'(n,2n3He)': ReactionInfo({176}, (-4, -2), ('He3',)),
'(n,3n3He)': ReactionInfo({177}, (-5, -2), ('He3',)),
'(n,4n3He)': ReactionInfo({178}, (-6, -2), ('He3',)),
'(n,3n2p)': ReactionInfo({179}, (-4, -2), ('H1', 'H1')),
'(n,3n2a)': ReactionInfo({180}, (-10, -4), ('He4', 'He4')),
'(n,3npa)': ReactionInfo({181}, (-7, -3), ('H1', 'He4')),
'(n,dt)': ReactionInfo({182}, (-4, -2), ('H2', 'H3')),
'(n,npd)': ReactionInfo({183}, (-3, -2), ('H1', 'H2')),
'(n,npt)': ReactionInfo({184}, (-4, -2), ('H1', 'H3')),
'(n,ndt)': ReactionInfo({185}, (-5, -2), ('H2', 'H3')),
'(n,np3He)': ReactionInfo({186}, (-4, -3), ('H1', 'He3')),
'(n,nd3He)': ReactionInfo({187}, (-5, -3), ('H2', 'He3')),
'(n,nt3He)': ReactionInfo({188}, (-6, -3), ('H3', 'He3')),
'(n,nta)': ReactionInfo({189}, (-7, -3), ('H3', 'He4')),
'(n,2n2p)': ReactionInfo({190}, (-3, -2), ('H1', 'H1')),
'(n,p3He)': ReactionInfo({191}, (-4, -3), ('H1', 'He3')),
'(n,d3He)': ReactionInfo({192}, (-5, -3), ('H2', 'He3')),
'(n,3Hea)': ReactionInfo({193}, (-6, -4), ('He3', 'He4')),
'(n,4n2p)': ReactionInfo({194}, (-5, -2), ('H1', 'H1')),
'(n,4n2a)': ReactionInfo({195}, (-11, -4), ('He4', 'He4')),
'(n,4npa)': ReactionInfo({196}, (-8, -3), ('H1', 'He4')),
'(n,3p)': ReactionInfo({197}, (-2, -3), ('H1', 'H1', 'H1')),
'(n,n3p)': ReactionInfo({198}, (-3, -3), ('H1', 'H1', 'H1')),
'(n,3n2pa)': ReactionInfo({199}, (-8, -4), ('H1', 'H1', 'He4')),
'(n,5n2p)': ReactionInfo({200}, (-6, -2), ('H1', 'H1')),
'(n,2nd)': ReactionInfo({11}, ('H2',)),
'(n,2n)': ReactionInfo(set(chain([16], range(875, 892))), ()),
'(n,3n)': ReactionInfo({17}, ()),
'(n,na)': ReactionInfo({22}, ('He4',)),
'(n,n3a)': ReactionInfo({23}, ('He4', 'He4', 'He4')),
'(n,2na)': ReactionInfo({24}, ('He4',)),
'(n,3na)': ReactionInfo({25}, ('He4',)),
'(n,np)': ReactionInfo({28}, ('H1',)),
'(n,n2a)': ReactionInfo({29}, ('He4', 'He4')),
'(n,2n2a)': ReactionInfo({30}, ('He4', 'He4')),
'(n,nd)': ReactionInfo({32}, ('H2',)),
'(n,nt)': ReactionInfo({33}, ('H3',)),
'(n,n3He)': ReactionInfo({34}, ('He3',)),
'(n,nd2a)': ReactionInfo({35}, ('H2', 'He4', 'He4')),
'(n,nt2a)': ReactionInfo({36}, ('H3', 'He4', 'He4')),
'(n,4n)': ReactionInfo({37}, ()),
'(n,2np)': ReactionInfo({41}, ('H1',)),
'(n,3np)': ReactionInfo({42}, ('H1',)),
'(n,n2p)': ReactionInfo({44}, ('H1', 'H1')),
'(n,npa)': ReactionInfo({45}, ('H1', 'He4')),
'(n,gamma)': ReactionInfo({102}, ()),
'(n,p)': ReactionInfo(set(chain([103], range(600, 650))), ('H1',)),
'(n,d)': ReactionInfo(set(chain([104], range(650, 700))), ('H2',)),
'(n,t)': ReactionInfo(set(chain([105], range(700, 750))), ('H3',)),
'(n,3He)': ReactionInfo(set(chain([106], range(750, 800))), ('He3',)),
'(n,a)': ReactionInfo(set(chain([107], range(800, 850))), ('He4',)),
'(n,2a)': ReactionInfo({108}, ('He4', 'He4')),
'(n,3a)': ReactionInfo({109}, ('He4', 'He4', 'He4')),
'(n,2p)': ReactionInfo({111}, ('H1', 'H1')),
'(n,pa)': ReactionInfo({112}, ('H1', 'He4')),
'(n,t2a)': ReactionInfo({113}, ('H3', 'He4', 'He4')),
'(n,d2a)': ReactionInfo({114}, ('H2', 'He4', 'He4')),
'(n,pd)': ReactionInfo({115}, ('H1', 'H2')),
'(n,pt)': ReactionInfo({116}, ('H1', 'H3')),
'(n,da)': ReactionInfo({117}, ('H2', 'He4')),
'(n,5n)': ReactionInfo({152}, ()),
'(n,6n)': ReactionInfo({153}, ()),
'(n,2nt)': ReactionInfo({154}, ('H3',)),
'(n,ta)': ReactionInfo({155}, ('H3', 'He4')),
'(n,4np)': ReactionInfo({156}, ('H1',)),
'(n,3nd)': ReactionInfo({157}, ('H2',)),
'(n,nda)': ReactionInfo({158}, ('H2', 'He4')),
'(n,2npa)': ReactionInfo({159}, ('H1', 'He4')),
'(n,7n)': ReactionInfo({160}, ()),
'(n,8n)': ReactionInfo({161}, ()),
'(n,5np)': ReactionInfo({162}, ('H1',)),
'(n,6np)': ReactionInfo({163}, ('H1',)),
'(n,7np)': ReactionInfo({164}, ('H1',)),
'(n,4na)': ReactionInfo({165}, ('He4',)),
'(n,5na)': ReactionInfo({166}, ('He4',)),
'(n,6na)': ReactionInfo({167}, ('He4',)),
'(n,7na)': ReactionInfo({168}, ('He4',)),
'(n,4nd)': ReactionInfo({169}, ('H2',)),
'(n,5nd)': ReactionInfo({170}, ('H2',)),
'(n,6nd)': ReactionInfo({171}, ('H2',)),
'(n,3nt)': ReactionInfo({172}, ('H3',)),
'(n,4nt)': ReactionInfo({173}, ('H3',)),
'(n,5nt)': ReactionInfo({174}, ('H3',)),
'(n,6nt)': ReactionInfo({175}, ('H3',)),
'(n,2n3He)': ReactionInfo({176}, ('He3',)),
'(n,3n3He)': ReactionInfo({177}, ('He3',)),
'(n,4n3He)': ReactionInfo({178}, ('He3',)),
'(n,3n2p)': ReactionInfo({179}, ('H1', 'H1')),
'(n,3n2a)': ReactionInfo({180}, ('He4', 'He4')),
'(n,3npa)': ReactionInfo({181}, ('H1', 'He4')),
'(n,dt)': ReactionInfo({182}, ('H2', 'H3')),
'(n,npd)': ReactionInfo({183}, ('H1', 'H2')),
'(n,npt)': ReactionInfo({184}, ('H1', 'H3')),
'(n,ndt)': ReactionInfo({185}, ('H2', 'H3')),
'(n,np3He)': ReactionInfo({186}, ('H1', 'He3')),
'(n,nd3He)': ReactionInfo({187}, ('H2', 'He3')),
'(n,nt3He)': ReactionInfo({188}, ('H3', 'He3')),
'(n,nta)': ReactionInfo({189}, ('H3', 'He4')),
'(n,2n2p)': ReactionInfo({190}, ('H1', 'H1')),
'(n,p3He)': ReactionInfo({191}, ('H1', 'He3')),
'(n,d3He)': ReactionInfo({192}, ('H2', 'He3')),
'(n,3Hea)': ReactionInfo({193}, ('He3', 'He4')),
'(n,4n2p)': ReactionInfo({194}, ('H1', 'H1')),
'(n,4n2a)': ReactionInfo({195}, ('He4', 'He4')),
'(n,4npa)': ReactionInfo({196}, ('H1', 'He4')),
'(n,3p)': ReactionInfo({197}, ('H1', 'H1', 'H1')),
'(n,n3p)': ReactionInfo({198}, ('H1', 'H1', 'H1')),
'(n,3n2pa)': ReactionInfo({199}, ('H1', 'H1', 'He4')),
'(n,5n2p)': ReactionInfo({200}, ('H1', 'H1')),
}
__all__ = ["Chain", "REACTIONS"]
@ -418,9 +412,9 @@ class Chain:
if parent in reactions:
reactions_available = set(reactions[parent].keys())
for name in transmutation_reactions:
mts, changes, _ = REACTIONS[name]
mts = REACTIONS[name].mts
delta_A, delta_Z = openmc.data.DADZ[name]
if mts & reactions_available:
delta_A, delta_Z = changes
A = data.nuclide['mass_number'] + delta_A
Z = data.nuclide['atomic_number'] + delta_Z
daughter = '{}{}'.format(openmc.data.ATOMIC_SYMBOL[Z], A)

28
openmc/filter_expansion.py
View file

@ -53,6 +53,34 @@ class ExpansionFilter(Filter):
order = int(elem.find('order').text)
return cls(order, filter_id=filter_id)
def merge(self, other):
"""Merge this filter with another.
This overrides the behavior of the parent Filter class, since its
merging technique is to take the union of the set of bins of each
filter. That technique does not apply to expansion filters, since the
argument should be the maximum filter order rather than the list of all
bins.
Parameters
----------
other : openmc.Filter
Filter to merge with
Returns
-------
merged_filter : openmc.Filter
Filter resulting from the merge
"""
if not self.can_merge(other):
msg = f'Unable to merge "{type(self)}" with "{type(other)}"'
raise ValueError(msg)
# Create a new filter with these bins and a new auto-generated ID
return type(self)(max(self.order, other.order))
class LegendreFilter(ExpansionFilter):
r"""Score Legendre expansion moments up to specified order.

28
openmc/lib/mesh.py
View file

@ -39,6 +39,9 @@ _dll.openmc_mesh_set_id.errcheck = _error_handler
_dll.openmc_mesh_get_n_elements.argtypes = [c_int32, POINTER(c_size_t)]
_dll.openmc_mesh_get_n_elements.restype = c_int
_dll.openmc_mesh_get_n_elements.errcheck = _error_handler
_dll.openmc_mesh_get_volumes.argtypes = [c_int32, POINTER(c_double)]
_dll.openmc_mesh_get_volumes.restype = c_int
_dll.openmc_mesh_get_volumes.errcheck = _error_handler
_dll.openmc_mesh_material_volumes.argtypes = [
c_int32, c_int, c_int, c_int, POINTER(_MaterialVolume),
POINTER(c_int), POINTER(c_uint64)]
@ -149,11 +152,18 @@ class Mesh(_FortranObjectWithID):
_dll.openmc_mesh_set_id(self._index, mesh_id)
@property
def n_elements(self):
def n_elements(self) -> int:
n = c_size_t()
_dll.openmc_mesh_get_n_elements(self._index, n)
return n.value
@property
def volumes(self) -> np.ndarray:
volumes = np.empty((self.n_elements,))
_dll.openmc_mesh_get_volumes(
self._index, volumes.ctypes.data_as(POINTER(c_double)))
return volumes
def material_volumes(
self,
n_samples: int = 10_000,
@ -276,6 +286,10 @@ class RegularMesh(Mesh):
are given, it is assumed that the mesh is an x-y mesh.
width : numpy.ndarray
The width of mesh cells in each direction.
n_elements : int
Total number of mesh elements.
volumes : numpy.ndarray
Volume of each mesh element in [cm^3]
"""
mesh_type = 'regular'
@ -358,6 +372,10 @@ class RectilinearMesh(Mesh):
The upper-right corner of the structrued mesh.
width : numpy.ndarray
The width of mesh cells in each direction.
n_elements : int
Total number of mesh elements.
volumes : numpy.ndarray
Volume of each mesh element in [cm^3]
"""
mesh_type = 'rectilinear'
@ -457,6 +475,10 @@ class CylindricalMesh(Mesh):
The upper-right corner of the structrued mesh.
width : numpy.ndarray
The width of mesh cells in each direction.
n_elements : int
Total number of mesh elements.
volumes : numpy.ndarray
Volume of each mesh element in [cm^3]
"""
mesh_type = 'cylindrical'
@ -555,6 +577,10 @@ class SphericalMesh(Mesh):
The upper-right corner of the structrued mesh.
width : numpy.ndarray
The width of mesh cells in each direction.
n_elements : int
Total number of mesh elements.
volumes : numpy.ndarray
Volume of each mesh element in [cm^3]
"""
mesh_type = 'spherical'

2
openmc/material.py
View file

@ -571,7 +571,7 @@ class Material(IDManagerMixin):
for component, params in components.items():
cv.check_type('component', component, str)
if isinstance(params, float):
if isinstance(params, Real):
params = {'percent': params}
else:

14
openmc/model/model.py
View file

@ -449,7 +449,7 @@ class Model:
# Create directory if required
d = Path(directory)
if not d.is_dir():
d.mkdir(parents=True)
d.mkdir(parents=True, exist_ok=True)
self.settings.export_to_xml(d)
self.geometry.export_to_xml(d, remove_surfs=remove_surfs)
@ -488,13 +488,16 @@ class Model:
# if the provided path doesn't end with the XML extension, assume the
# input path is meant to be a directory. If the directory does not
# exist, create it and place a 'model.xml' file there.
if not str(xml_path).endswith('.xml') and not xml_path.exists():
os.mkdir(xml_path)
if not str(xml_path).endswith('.xml'):
if not xml_path.exists():
xml_path.mkdir(parents=True, exist_ok=True)
elif not xml_path.is_dir():
raise FileExistsError(f"File exists and is not a directory: '{xml_path}'")
xml_path /= 'model.xml'
# if this is an XML file location and the file's parent directory does
# not exist, create it before continuing
elif not xml_path.parent.exists():
os.mkdir(xml_path.parent)
xml_path.parent.mkdir(parents=True, exist_ok=True)
if remove_surfs:
warnings.warn("remove_surfs kwarg will be deprecated soon, please "
@ -709,9 +712,10 @@ class Model:
self.export_to_model_xml(**export_kwargs)
else:
self.export_to_xml(**export_kwargs)
path_input = export_kwargs.get("path", None)
openmc.run(particles, threads, geometry_debug, restart_file,
tracks, output, Path('.'), openmc_exec, mpi_args,
event_based)
event_based, path_input)
# Get output directory and return the last statepoint written
if self.settings.output and 'path' in self.settings.output:

24
openmc/model/surface_composite.py
View file

@ -617,7 +617,7 @@ class RectangularParallelepiped(CompositeSurface):
class XConeOneSided(CompositeSurface):
"""One-sided cone parallel the x-axis
A one-sided cone is composed of a normal cone surface and an "ambiguity"
A one-sided cone is composed of a normal cone surface and a "disambiguation"
surface that eliminates the ambiguity as to which region of space is
included. This class acts as a proper surface, meaning that unary `+` and
`-` operators applied to it will produce a half-space. The negative side is
@ -634,7 +634,9 @@ class XConeOneSided(CompositeSurface):
z0 : float, optional
z-coordinate of the apex. Defaults to 0.
r2 : float, optional
Parameter related to the aperature. Defaults to 1.
Parameter related to the aperture [:math:`\\rm cm^2`].
It can be interpreted as the increase in the radius squared per cm along
the cone's axis of revolution.
up : bool
Whether to select the side of the cone that extends to infinity in the
positive direction of the coordinate axis (the positive half-space of
@ -647,7 +649,7 @@ class XConeOneSided(CompositeSurface):
cone : openmc.XCone
Regular two-sided cone
plane : openmc.XPlane
Ambiguity surface
Disambiguation surface
up : bool
Whether to select the side of the cone that extends to infinity in the
positive direction of the coordinate axis (the positive half-space of
@ -675,7 +677,7 @@ class XConeOneSided(CompositeSurface):
class YConeOneSided(CompositeSurface):
"""One-sided cone parallel the y-axis
A one-sided cone is composed of a normal cone surface and an "ambiguity"
A one-sided cone is composed of a normal cone surface and a "disambiguation"
surface that eliminates the ambiguity as to which region of space is
included. This class acts as a proper surface, meaning that unary `+` and
`-` operators applied to it will produce a half-space. The negative side is
@ -692,7 +694,9 @@ class YConeOneSided(CompositeSurface):
z0 : float, optional
z-coordinate of the apex. Defaults to 0.
r2 : float, optional
Parameter related to the aperature. Defaults to 1.
Parameter related to the aperture [:math:`\\rm cm^2`].
It can be interpreted as the increase in the radius squared per cm along
the cone's axis of revolution.
up : bool
Whether to select the side of the cone that extends to infinity in the
positive direction of the coordinate axis (the positive half-space of
@ -705,7 +709,7 @@ class YConeOneSided(CompositeSurface):
cone : openmc.YCone
Regular two-sided cone
plane : openmc.YPlane
Ambiguity surface
Disambiguation surface
up : bool
Whether to select the side of the cone that extends to infinity in the
positive direction of the coordinate axis (the positive half-space of
@ -727,7 +731,7 @@ class YConeOneSided(CompositeSurface):
class ZConeOneSided(CompositeSurface):
"""One-sided cone parallel the z-axis
A one-sided cone is composed of a normal cone surface and an "ambiguity"
A one-sided cone is composed of a normal cone surface and a "disambiguation"
surface that eliminates the ambiguity as to which region of space is
included. This class acts as a proper surface, meaning that unary `+` and
`-` operators applied to it will produce a half-space. The negative side is
@ -744,7 +748,9 @@ class ZConeOneSided(CompositeSurface):
z0 : float, optional
z-coordinate of the apex. Defaults to 0.
r2 : float, optional
Parameter related to the aperature. Defaults to 1.
Parameter related to the aperture [:math:`\\rm cm^2`].
It can be interpreted as the increase in the radius squared per cm along
the cone's axis of revolution.
up : bool
Whether to select the side of the cone that extends to infinity in the
positive direction of the coordinate axis (the positive half-space of
@ -757,7 +763,7 @@ class ZConeOneSided(CompositeSurface):
cone : openmc.ZCone
Regular two-sided cone
plane : openmc.ZPlane
Ambiguity surface
Disambiguation surface
up : bool
Whether to select the side of the cone that extends to infinity in the
positive direction of the coordinate axis (the positive half-space of

23
openmc/plotter.py
View file

@ -58,6 +58,11 @@ ELEMENT_NAMES = list(openmc.data.ELEMENT_SYMBOL.values())[1:]
def _get_legend_label(this, type):
"""Gets a label for the element or nuclide or material and reaction plotted"""
if isinstance(this, str):
if type in openmc.data.DADZ:
z, a, m = openmc.data.zam(this)
da, dz = openmc.data.DADZ[type]
gnds_name = openmc.data.gnds_name(z + dz, a + da, m)
return f'{this} {type} {gnds_name}'
return f'{this} {type}'
elif this.name == '':
return f'Material {this.id} {type}'
@ -100,7 +105,7 @@ def _get_title(reactions):
def plot_xs(reactions, divisor_types=None, temperature=294., axis=None,
sab_name=None, ce_cross_sections=None, mg_cross_sections=None,
enrichment=None, plot_CE=True, orders=None, divisor_orders=None,
**kwargs):
energy_axis_units="eV", **kwargs):
"""Creates a figure of continuous-energy cross sections for this item.
Parameters
@ -143,6 +148,10 @@ def plot_xs(reactions, divisor_types=None, temperature=294., axis=None,
**kwargs :
All keyword arguments are passed to
:func:`matplotlib.pyplot.figure`.
energy_axis_units : {'eV', 'keV', 'MeV'}
Units used on the plot energy axis
.. versionadded:: 0.14.1
Returns
-------
@ -156,6 +165,9 @@ def plot_xs(reactions, divisor_types=None, temperature=294., axis=None,
import matplotlib.pyplot as plt
cv.check_type("plot_CE", plot_CE, bool)
cv.check_value("energy_axis_units", energy_axis_units, {"eV", "keV", "MeV"})
axis_scaling_factor = {"eV": 1.0, "keV": 1e-3, "MeV": 1e-6}
# Generate the plot
if axis is None:
@ -212,6 +224,8 @@ def plot_xs(reactions, divisor_types=None, temperature=294., axis=None,
if divisor_types[line] != 'unity':
types[line] += ' / ' + divisor_types[line]
E *= axis_scaling_factor[energy_axis_units]
# Plot the data
for i in range(len(data)):
data[i, :] = np.nan_to_num(data[i, :])
@ -227,9 +241,12 @@ def plot_xs(reactions, divisor_types=None, temperature=294., axis=None,
ax.set_xscale('log')
ax.set_yscale('log')
ax.set_xlabel('Energy [eV]')
ax.set_xlabel(f"Energy [{energy_axis_units}]")
if plot_CE:
ax.set_xlim(_MIN_E, _MAX_E)
ax.set_xlim(
_MIN_E * axis_scaling_factor[energy_axis_units],
_MAX_E * axis_scaling_factor[energy_axis_units],
)
else:
ax.set_xlim(E[-1], E[0])

34
openmc/source.py
View file

@ -885,3 +885,37 @@ def write_source_file(
with h5py.File(filename, **kwargs) as fh:
fh.attrs['filetype'] = np.string_("source")
fh.create_dataset('source_bank', data=arr, dtype=source_dtype)
def read_source_file(filename: PathLike) -> typing.List[SourceParticle]:
"""Read a source file and return a list of source particles.
.. versionadded:: 0.14.1
Parameters
----------
filename : str or path-like
Path to source file to read
Returns
-------
list of SourceParticle
Source particles read from file
See Also
--------
openmc.SourceParticle
"""
with h5py.File(filename, 'r') as fh:
filetype = fh.attrs['filetype']
arr = fh['source_bank'][...]
if filetype != b'source':
raise ValueError(f'File {filename} is not a source file')
source_particles = []
for *params, particle in arr:
source_particles.append(SourceParticle(*params, ParticleType(particle)))
return source_particles

3
openmc/stats/univariate.py
View file

@ -280,6 +280,9 @@ class Discrete(Univariate):
Discrete distribution with low-importance points removed
"""
cv.check_less_than("tolerance", tolerance, 1.0, equality=True)
cv.check_greater_than("tolerance", tolerance, 0.0, equality=True)
# Determine (reversed) sorted order of probabilities
intensity = self.p * self.x
index_sort = np.argsort(intensity)[::-1]

35
openmc/surface.py
View file

@ -1748,6 +1748,11 @@ class Sphere(QuadricMixin, Surface):
class Cone(QuadricMixin, Surface):
"""A conical surface parallel to the x-, y-, or z-axis.
.. Note::
This creates a double cone, which is two one-sided cones that meet at their apex.
For a one-sided cone see :class:`~openmc.model.XConeOneSided`,
:class:`~openmc.model.YConeOneSided`, and :class:`~openmc.model.ZConeOneSided`.
Parameters
----------
x0 : float, optional
@ -1757,7 +1762,9 @@ class Cone(QuadricMixin, Surface):
z0 : float, optional
z-coordinate of the apex in [cm]. Defaults to 0.
r2 : float, optional
Parameter related to the aperature. Defaults to 1.
Parameter related to the aperture [:math:`\\rm cm^2`].
It can be interpreted as the increase in the radius squared per cm along
the cone's axis of revolution.
dx : float, optional
x-component of the vector representing the axis of the cone.
Defaults to 0.
@ -1791,7 +1798,7 @@ class Cone(QuadricMixin, Surface):
z0 : float
z-coordinate of the apex in [cm]
r2 : float
Parameter related to the aperature
Parameter related to the aperature [cm^2]
dx : float
x-component of the vector representing the axis of the cone.
dy : float
@ -1900,6 +1907,10 @@ class XCone(QuadricMixin, Surface):
"""A cone parallel to the x-axis of the form :math:`(y - y_0)^2 + (z - z_0)^2 =
r^2 (x - x_0)^2`.
.. Note::
This creates a double cone, which is two one-sided cones that meet at their apex.
For a one-sided cone see :class:`~openmc.model.XConeOneSided`.
Parameters
----------
x0 : float, optional
@ -1909,7 +1920,9 @@ class XCone(QuadricMixin, Surface):
z0 : float, optional
z-coordinate of the apex in [cm]. Defaults to 0.
r2 : float, optional
Parameter related to the aperature. Defaults to 1.
Parameter related to the aperture [:math:`\\rm cm^2`].
It can be interpreted as the increase in the radius squared per cm along
the cone's axis of revolution.
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}, optional
Boundary condition that defines the behavior for particles hitting the
surface. Defaults to transmissive boundary condition where particles
@ -1995,6 +2008,10 @@ class YCone(QuadricMixin, Surface):
"""A cone parallel to the y-axis of the form :math:`(x - x_0)^2 + (z - z_0)^2 =
r^2 (y - y_0)^2`.
.. Note::
This creates a double cone, which is two one-sided cones that meet at their apex.
For a one-sided cone see :class:`~openmc.model.YConeOneSided`.
Parameters
----------
x0 : float, optional
@ -2004,7 +2021,9 @@ class YCone(QuadricMixin, Surface):
z0 : float, optional
z-coordinate of the apex in [cm]. Defaults to 0.
r2 : float, optional
Parameter related to the aperature. Defaults to 1.
Parameter related to the aperture [:math:`\\rm cm^2`].
It can be interpreted as the increase in the radius squared per cm along
the cone's axis of revolution.
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}, optional
Boundary condition that defines the behavior for particles hitting the
surface. Defaults to transmissive boundary condition where particles
@ -2090,6 +2109,10 @@ class ZCone(QuadricMixin, Surface):
"""A cone parallel to the z-axis of the form :math:`(x - x_0)^2 + (y - y_0)^2 =
r^2 (z - z_0)^2`.
.. Note::
This creates a double cone, which is two one-sided cones that meet at their apex.
For a one-sided cone see :class:`~openmc.model.ZConeOneSided`.
Parameters
----------
x0 : float, optional
@ -2099,7 +2122,9 @@ class ZCone(QuadricMixin, Surface):
z0 : float, optional
z-coordinate of the apex in [cm]. Defaults to 0.
r2 : float, optional
Parameter related to the aperature. Defaults to 1.
Parameter related to the aperature [cm^2].
This is the square of the radius of the cone 1 cm from.
This can also be treated as the square of the slope of the cone relative to its axis.
boundary_type : {'transmission, 'vacuum', 'reflective', 'white'}, optional
Boundary condition that defines the behavior for particles hitting the
surface. Defaults to transmissive boundary condition where particles

3
src/cell.cpp
View file

@ -1272,6 +1272,9 @@ struct ParentCellStack {
//! compute an instance for the provided distribcell index
int32_t compute_instance(int32_t distribcell_index) const
{
if (distribcell_index == C_NONE)
return 0;
int32_t instance = 0;
for (const auto& parent_cell : this->parent_cells_) {
auto& cell = model::cells[parent_cell.cell_index];

11
src/mesh.cpp
View file

@ -1881,6 +1881,17 @@ extern "C" int openmc_mesh_get_n_elements(int32_t index, size_t* n)
return 0;
}
//! Get the volume of each element in the mesh
extern "C" int openmc_mesh_get_volumes(int32_t index, double* volumes)
{
if (int err = check_mesh(index))
return err;
for (int i = 0; i < model::meshes[index]->n_bins(); ++i) {
volumes[i] = model::meshes[index]->volume(i);
}
return 0;
}
extern "C" int openmc_mesh_material_volumes(int32_t index, int n_sample,
int bin, int result_size, void* result, int* hits, uint64_t* seed)
{

5
tests/unit_tests/test_deplete_chain.py
View file

@ -5,6 +5,7 @@ from itertools import product
from math import log
import os
from pathlib import Path
import warnings
import numpy as np
from openmc.mpi import comm
@ -438,9 +439,9 @@ def test_validate(simple_chain):
simple_chain["C"].yield_data = {0.0253: {"A": 1.4, "B": 0.6}}
assert simple_chain.validate(strict=True, tolerance=0.0)
with pytest.warns(None) as record:
with warnings.catch_warnings():
warnings.simplefilter("error")
assert simple_chain.validate(strict=False, quiet=False, tolerance=0.0)
assert len(record) == 0
# Mess up "earlier" nuclide's reactions
decay_mode = simple_chain["A"].decay_modes.pop()

5
tests/unit_tests/test_deplete_nuclide.py
View file

@ -1,6 +1,7 @@
"""Tests for the openmc.deplete.Nuclide class."""
import copy
import warnings
import lxml.etree as ET
import numpy as np
@ -277,9 +278,9 @@ def test_validate():
}
# nuclide is good and should have no warnings raise
with pytest.warns(None) as record:
with warnings.catch_warnings():
warnings.simplefilter("error")
assert nuc.validate(strict=True, quiet=False, tolerance=0.0)
assert len(record) == 0
# invalidate decay modes
decay = nuc.decay_modes.pop()

14
tests/unit_tests/test_lib.py
View file

@ -566,6 +566,8 @@ def test_regular_mesh(lib_init):
assert mesh.upper_right == pytest.approx(ur)
assert mesh.width == pytest.approx(width)
np.testing.assert_allclose(mesh.volumes, 1.0)
meshes = openmc.lib.meshes
assert isinstance(meshes, Mapping)
assert len(meshes) == 1
@ -644,6 +646,8 @@ def test_rectilinear_mesh(lib_init):
for k, diff_z in enumerate(np.diff(z_grid)):
assert np.all(mesh.width[i, j, k, :] == (10, 10, 10))
np.testing.assert_allclose(mesh.volumes, 1000.0)
with pytest.raises(exc.AllocationError):
mesh2 = openmc.lib.RectilinearMesh(mesh.id)
@ -688,6 +692,9 @@ def test_cylindrical_mesh(lib_init):
for k, _ in enumerate(np.diff(z_grid)):
assert np.allclose(mesh.width[i, j, k, :], (5, deg2rad(10), 10))
np.testing.assert_allclose(mesh.volumes[::2], 10/360 * pi * 5**2 * 10)
np.testing.assert_allclose(mesh.volumes[1::2], 10/360 * pi * (10**2 - 5**2) * 10)
with pytest.raises(exc.AllocationError):
mesh2 = openmc.lib.CylindricalMesh(mesh.id)
@ -734,6 +741,13 @@ def test_spherical_mesh(lib_init):
for k, _ in enumerate(np.diff(phi_grid)):
assert np.allclose(mesh.width[i, j, k, :], (5, deg2rad(10), deg2rad(10)))
dtheta = lambda d1, d2: np.cos(deg2rad(d1)) - np.cos(deg2rad(d2))
f = 1/3 * deg2rad(10.)
np.testing.assert_allclose(mesh.volumes[::4], f * 5**3 * dtheta(0., 10.))
np.testing.assert_allclose(mesh.volumes[1::4], f * (10**3 - 5**3) * dtheta(0., 10.))
np.testing.assert_allclose(mesh.volumes[2::4], f * 5**3 * dtheta(10., 20.))
np.testing.assert_allclose(mesh.volumes[3::4], f * (10**3 - 5**3) * dtheta(10., 20.))
with pytest.raises(exc.AllocationError):
mesh2 = openmc.lib.SphericalMesh(mesh.id)

6
tests/unit_tests/test_model.py
View file

@ -585,3 +585,9 @@ def test_single_xml_exec(run_in_tmpdir):
with pytest.raises(RuntimeError, match='input_dir'):
openmc.run(path_input='input_dir/pincell.xml')
# Make sure path can be specified with run
pincell_model.run(path='my_model.xml')
os.mkdir('subdir')
pincell_model.run(path='subdir')

11
tests/unit_tests/test_plotter.py
View file

@ -77,10 +77,19 @@ def test_plot_xs(this):
from matplotlib.figure import Figure
assert isinstance(openmc.plot_xs({this: ['total', 'elastic']}), Figure)
def test_plot_xs_mat(test_mat):
from matplotlib.figure import Figure
assert isinstance(openmc.plot_xs({test_mat: ['total']}), Figure)
@pytest.mark.parametrize("units", ["eV", "keV", "MeV"])
def test_plot_xs_energy_axis(units):
plot = openmc.plot_xs({'Be9': ['(n,2n)']}, energy_axis_units=units)
axis_text = plot.get_axes()[0].get_xaxis().get_label().get_text()
assert axis_text == f'Energy [{units}]'
def test_plot_axes_labels():
# just nuclides
axis_label = openmc.plotter._get_yaxis_label(
@ -156,4 +165,4 @@ def test_get_title():
mat1.set_density('g/cm3', 1)
mat1.name = 'my_mat'
title = openmc.plotter._get_title(reactions={mat1: [205]})
assert title == 'Cross Section Plot For my_mat'
assert title == 'Cross Section Plot For my_mat'

24
tests/unit_tests/test_source_file.py
View file

@ -45,6 +45,30 @@ def test_source_file(run_in_tmpdir):
assert np.all(arr['particle'] == 0)
# Ensure sites read in are consistent
sites = openmc.read_source_file('test_source.h5')
assert filetype == b'source'
xs = np.array([site.r[0] for site in sites])
ys = np.array([site.r[1] for site in sites])
zs = np.array([site.r[2] for site in sites])
assert np.all((xs > 0.0) & (xs < 1.0))
assert np.all(ys == np.arange(1000))
assert np.all(zs == 0.0)
u = np.array([s.u for s in sites])
assert np.all(u[..., 0] == 0.0)
assert np.all(u[..., 1] == 0.0)
assert np.all(u[..., 2] == 1.0)
E = np.array([s.E for s in sites])
assert np.all(E == n - np.arange(n))
wgt = np.array([s.wgt for s in sites])
assert np.all(wgt == 1.0)
dgs = np.array([s.delayed_group for s in sites])
assert np.all(dgs == 0)
p_types = np.array([s.particle for s in sites])
assert np.all(p_types == 0)
def test_wrong_source_attributes(run_in_tmpdir):
# Create a source file with animal attributes
source_dtype = np.dtype([

6
tests/unit_tests/test_stats.py
View file

@ -89,6 +89,12 @@ def test_clip_discrete():
d_same = d.clip(1e-6, inplace=True)
assert d_same is d
with pytest.raises(ValueError):
d.clip(-1.)
with pytest.raises(ValueError):
d.clip(5)
def test_uniform():
a, b = 10.0, 20.0