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Merge branch 'develop' into properties-exim
This commit is contained in:
Paul Romano
commit
c9d84310d3
71 changed files with 4811 additions and 3405 deletions
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@ -19,7 +19,7 @@ Each ``<surface>`` element can have the following attributes or sub-elements:
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:name:
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An optional string name to identify the surface in summary output
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files. This string is limited to 52 characters for formatting purposes.
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files.
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*Default*: ""
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@ -122,7 +122,6 @@ Each ``<cell>`` element can have the following attributes or sub-elements:
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:name:
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An optional string name to identify the cell in summary output files.
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This string is limmited to 52 characters for formatting purposes.
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*Default*: ""
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@ -235,7 +234,7 @@ the following attributes or sub-elements:
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:name:
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An optional string name to identify the lattice in summary output
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files. This string is limited to 52 characters for formatting purposes.
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files.
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*Default*: ""
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@ -301,7 +300,7 @@ the following attributes or sub-elements:
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:name:
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An optional string name to identify the hex_lattice in summary output
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files. This string is limited to 52 characters for formatting purposes.
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files.
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*Default*: ""
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@ -370,3 +369,40 @@ Here is an example of a properly defined 2d hexagonal lattice:
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202
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</universes>
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</hex_lattice>
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.. _dagmc_element:
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----------------------------
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``<dagmc_universe>`` Element
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----------------------------
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Each ``<dagmc_universe>`` element can have the following attributes or sub-elements:
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:id:
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A unique integer used to identify the universe.
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*Default*: None
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:name:
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An optional string name to identify the surface in summary output
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files.
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*Default*: None
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:auto_geom_ids:
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Boolean value indicating whether the existing geometry IDs will be used or appended
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to the existing ID space of natively defined OpenMC geometry entities.
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*Default*: false
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:auto_mat_ids:
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Boolean value indicating whether the existing material IDs will be used or appended
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to the existing ID space of natively defined OpenMC materials.
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*Default*: false
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:filename:
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A required string indicating the file to be loaded representing the DAGMC universe.
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*Default*: None
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@ -31,7 +31,7 @@ Each ``material`` element can have the following attributes or sub-elements:
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:name:
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An optional string name to identify the material in summary output
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files. This string is limited to 52 characters for formatting purposes.
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files.
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*Default*: ""
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@ -88,14 +88,6 @@ you care. This element has the following attributes/sub-elements:
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*Default*: 0.0
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--------------------------------
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``<dagmc>`` Element
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--------------------------------
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When the DAGMC mode is enabled, the OpenMC geometry will be read from the file
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``dagmc.h5m``. If a :ref:`geometry.xml <io_geometry>` file is present with
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``dagmc`` set to ``true``, it will be ignored.
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----------------------------
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``<delayed_photon_scaling>``
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----------------------------
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@ -24,8 +24,6 @@ The current version of the summary file format is 6.0.
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- **n_universes** (*int*) -- Number of unique universes in the
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problem.
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- **n_lattices** (*int*) -- Number of lattices in the problem.
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- **dagmc** (*int*) -- Indicates that a DAGMC geometry was used
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if present.
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**/geometry/cells/cell <uid>/**
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@ -49,6 +47,8 @@ The current version of the summary file format is 6.0.
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- **lattice** (*int*) -- Unique ID of the lattice which fills the
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cell. Only present if fill_type is set to 'lattice'.
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- **region** (*char[]*) -- Region specification for the cell.
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- **geom_type** (*char[]*) -- Type of geometry used to create the cell.
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Either 'csg' or 'dagmc'.
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**/geometry/surfaces/surface <uid>/**
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@ -62,12 +62,27 @@ The current version of the summary file format is 6.0.
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- **boundary_condition** (*char[]*) -- Boundary condition applied to
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the surface. Can be 'transmission', 'vacuum', 'reflective', or
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'periodic'.
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- **geom_type** (*char[]*) -- Type of geometry used to create the cell.
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Either 'csg' or 'dagmc'.
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**/geometry/universes/universe <uid>/**
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:Datasets:
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- **cells** (*int[]*) -- Array of unique IDs of cells that appear in
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the universe.
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- **geom_type** (*char[]*) -- Type of geometry used to create the cell.
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Either 'csg' or 'dagmc'.
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- **filename** (*char[]*) -- Name of the DAGMC file representing this universe.
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Only present for DAGMC Universes.
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:Attributes:
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- **auto_geom_ids** (*int*) -- ``1`` if geometry IDs of the DAGMC
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model will be appended to the ID space of the natively defined
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CSG geometry, ``0`` if the existing DAGMC IDs will be used.
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- **auto_mat_ids** (*int*) -- ``1`` if UWUW material IDs of the DAGMC
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model will be appended to the ID space of the natively defined
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OpenMC materials, ``0`` if the existing UWUW IDs will be used.
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**/geometry/lattices/lattice <uid>/**
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@ -119,8 +134,8 @@ The current version of the summary file format is 6.0.
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:Attributes: - **volume** (*double[]*) -- Volume of this material [cm^3]. Only
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present if ``volume`` supplied
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- **temperature** (*double[]*) -- Temperature of this material [K].
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Only present in ``temperature`` supplied
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- **depletable** (*int[]*) -- ``1`` if the material can be depleted,
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Only present if ``temperature`` is supplied
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- **depletable** (*int*) -- ``1`` if the material can be depleted,
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``0`` otherwise. Always present
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**/nuclides/**
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@ -31,7 +31,7 @@ The ``<tally>`` element accepts the following sub-elements:
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:name:
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An optional string name to identify the tally in summary output
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files. This string is limited to 52 characters for formatting purposes.
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files.
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*Default*: ""
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@ -433,30 +433,64 @@ will handle creating the unverse::
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Using CAD-based Geometry
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--------------------------
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OpenMC relies on the Direct Accelerated Geometry Monte Carlo toolkit (`DAGMC
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<https://svalinn.github.io/DAGMC/>`_) to represent CAD-based geometry in a
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surface mesh format. A DAGMC run can be enabled in OpenMC by setting the
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``dagmc`` property to ``True`` in the model Settings either via the Python
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:class:`openmc.settings` Python class::
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Defining Geometry
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-----------------
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settings = openmc.Settings()
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settings.dagmc = True
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OpenMC relies on the `Direct Accelerated Geometry Monte Carlo`_ (DAGMC)
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to represent CAD-based geometry in a surface mesh format. DAGMC geometries are
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applied as universes in the OpenMC geometry file. A geometry represented
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entirely by a DAGMC geometry will contain only the DAGMC universe. Using a
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:class:`openmc.DAGMCUniverse` looks like the following::
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or in the :ref:`settings.xml <io_settings>` file::
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dag_univ = openmc.DAGMCUniverse(filename='dagmc.h5m')
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geometry = openmc.Geometry(dag_univ)
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geometry.export_to_xml()
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<dagmc>true</dagmc>
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The resulting ``geometry.xml`` file will be:
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With ``dagmc`` set to true, OpenMC will load the DAGMC model (from a local file
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named ``dagmc.h5m``) when initializing a simulation. If a `geometry.xml
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<../io_formats/geometry.html>`_ is present as well, it will be ignored.
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.. code-block:: xml
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**Note:** DAGMC geometries used in OpenMC are currently required to be clean,
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meaning that all surfaces have been `imprinted and merged
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<https://svalinn.github.io/DAGMC/usersguide/trelis_workflow.html>`_
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successfully and that the model is `watertight
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<https://svalinn.github.io/DAGMC/usersguide/tools.html#make-watertight>`_. Future
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implementations of DAGMC geometry will support small volume overlaps and
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un-merged surfaces.
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<?xml version='1.0' encoding='utf-8'?>
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<geometry>
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<dagmc auto_ids="false" filename="dagmc.h5m" id="1" name="" />
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</geometry>
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DAGMC universes can also be used to fill CSG cells or lattice cells in a geometry::
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cell.fill = dagmc_univ
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It is important in these cases to understand the DAGMC model's position
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with respect to the CSG geometry. DAGMC geometries can be plotted with
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OpenMC to verify that the model matches one's expectations.
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**Note:** DAGMC geometries used in OpenMC are currently required to be clean,
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meaning that all surfaces have been `imprinted and merged
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<https://svalinn.github.io/DAGMC/usersguide/trelis_workflow.html>`_
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successfully and that the model is `watertight
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<https://svalinn.github.io/DAGMC/usersguide/tools.html#make-watertight>`_. Future
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implementations of DAGMC geometry will support small volume overlaps and
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un-merged surfaces.
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Cell, Surface, and Material IDs
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-------------------------------
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By default, DAGMC applies cell and surface IDs defined by the CAD engine that
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the model originated in. If these IDs overlap with IDs in the CSG ID space,
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this will result in an error. However, the ``auto_ids`` property of a DAGMC
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universe can be set to set DAGMC cell and surface IDs by appending to the
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existing CSG cell ID space in the OpenMC model.
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Similar options exist for the material IDs of DAGMC models. If DAGMC material
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assignments are based on natively defined OpenMC materials, no further work is
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required. If DAGMC materials are assigned using the `University of Wisconsin
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Unified Workflow`_ (UWUW), however, material IDs in the UWUW material library
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may overlap with those used in the CSG geometry. In this case, overlaps in the
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UWUW and OpenMC material ID space will cause an error. To automatically resolve
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these ID overlaps, ``auto_ids`` can be set to ``True`` to append the UWUW
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material IDs to the OpenMC material ID space.
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.. _Direct Accelerated Geometry Monte Carlo: https://svalinn.github.io/DAGMC/
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.. _University of Wisconsin Unified Workflow: https://svalinn.github.io/DAGMC/usersguide/uw2.html
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-------------------------
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Calculating Atoms Content
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@ -45,6 +45,23 @@ with the :envvar:`OPENMC_CROSS_SECTIONS` environment variable. It is recommended
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to add a line in your ``.profile`` or ``.bash_profile`` setting the
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:envvar:`OPENMC_CROSS_SECTIONS` environment variable.
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RuntimeError: Failed to open HDF5 file with mode 'w': summary.h5
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****************************************************************
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This often occurs when working with the Python API and executing multiple OpenMC
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runs in a script. If an :class:`openmc.StatePoint` is open in the Python interpreter,
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the file handle of the statepoint file as well as the linked `summary.h5` file will
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be unavailable for writing, causing this error to appear. To avoid this situation,
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it is recommended that data be extracted from statepoint files in a context manager:
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.. code-block:: python
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with openmc.StatePoint('statepoint.10.h5') as sp:
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k_eff = sp.k_combined
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or that the :meth:`StatePoint.close` method is called before executing a subsequent
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OpenMC run.
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Geometry Debugging
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******************
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