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Add tallies section, Python API requirements

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Paul Romano 2017-04-01 14:56:54 -05:00
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14
docs/source/usersguide/basics.rst
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@ -96,13 +96,13 @@ Serpent, with the added bonus that the XML formats feel much more
Python API
----------
OpenMC's Python API defines a set of functions and classes that roughly
correspond to elements in the XML files. For example, the :class:`openmc.Cell`
Python class directly corresponds to the :ref:`cell_element` in XML. Each XML
file itself also has a corresponding class: :class:`openmc.Geometry` for
``geometry.xml``, :class:`openmc.Materials` for ``materials.xml``,
:class:`openmc.Settings` for ``settings.xml``, and so on. To create a model
then, one creates instances of these classes and then uses the
OpenMC's :ref:`Python API <pythonapi>` defines a set of functions and classes
that roughly correspond to elements in the XML files. For example, the
:class:`openmc.Cell` Python class directly corresponds to the
:ref:`cell_element` in XML. Each XML file itself also has a corresponding class:
:class:`openmc.Geometry` for ``geometry.xml``, :class:`openmc.Materials` for
``materials.xml``, :class:`openmc.Settings` for ``settings.xml``, and so on. To
create a model then, one creates instances of these classes and then uses the
``export_to_xml()`` method, e.g. :meth:`Geometry.export_to_xml`. Most scripts
that generate a full model will look something like the following:

61
docs/source/usersguide/install.rst
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@ -373,6 +373,67 @@ if we wanted to run only the plot tests with 4 processors, we run:
If you want to run the full test suite with different build options please
refer to our :ref:`test suite` documentation.
--------------------
Python Prerequisites
--------------------
OpenMC's :ref:`Python API <pythonapi>` works with either Python 2.7 or Python
3.2+. In addition to Python itself, the API relies on a number of third-party
packages. All prerequisites can be installed using `conda
<http://conda.pydata.org/docs/>`_ (recommended), `pip
<https://pip.pypa.io/en/stable/>`_, or through the package manager in most Linux
distributions.
.. admonition:: Required
:class: error
`six <https://pythonhosted.org/six/>`_
The Python API works with both Python 2.7+ and 3.2+. To do so, the six
compatibility library is used.
`NumPy <http://www.numpy.org/>`_
NumPy is used extensively within the Python API for its powerful
N-dimensional array.
`h5py <http://www.h5py.org/>`_
h5py provides Python bindings to the HDF5 library. Since OpenMC outputs
various HDF5 files, h5py is needed to provide access to data within these
files from Python.
.. admonition:: Optional
:class: note
`SciPy <https://www.scipy.org/>`_
SciPy's special functions, sparse matrices, and spatial data structures
are used for several optional features in the API.
`pandas <http://pandas.pydata.org/>`_
Pandas is used to generate tally DataFrames as demonstrated in
:ref:`examples_pandas` example notebook.
`Matplotlib <http://matplotlib.org/>`_
Matplotlib is used to providing plotting functionality in the API like the
:meth:`Universe.plot` method and the :func:`openmc.plot_xs` function.
`uncertainties <https://pythonhosted.org/uncertainties/>`_
Uncertainties are optionally used for decay data in the :ref:`openmc.data
<pythonapi_data>`.
`Cython <http://cython.org/>`_
Cython is used for resonance reconstruction for ENDF data converted to
:class:`openmc.data.IncidentNeutron`.
`vtk <http://www.vtk.org/>`_
The Python VTK bindings are needed to convert voxel and track files to VTK
format.
`silomesh <https://github.com/nhorelik/silomesh>`_
The silomesh package is needed to convert voxel and track files to SILO
format.
`lxml <http://lxml.de/>`_
lxml is used for the :ref:`scripts_validate` script.
---------------------------
Cross Section Configuration
---------------------------

2
docs/source/usersguide/materials.rst
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@ -71,6 +71,8 @@ you would need to add hydrogen and oxygen to a material and then assign the
water.add_s_alpha_beta('c_H_in_H2O')
water.set_density('g/cm3', 1.0)
.. _usersguide_naming:
------------------
Naming Conventions
------------------

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docs/source/usersguide/plots.rst
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@ -4,6 +4,8 @@
Geometry Visualization
======================
.. currentmodule:: openmc
OpenMC is capable of producing two-dimensional slice plots of a geometry as well
as three-dimensional voxel plots using the geometry plotting :ref:`run mode
<usersguide_run_modes>` is a geometry plotting mode. The geometry plotting mode

306
docs/source/usersguide/tallies.rst
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@ -3,3 +3,309 @@
==================
Specifying Tallies
==================
.. currentmodule:: openmc
In order to obtain estimates of physical quantities in your simulation, you need
to create one or more tallies using the :class:`openmc.Tally` class. As
explained in detail in the :ref:`theory manual <methods_tallies>`, tallies
provide estimates of a scoring function times the flux integrated over some
region of phase space, as in:
.. math::
X = \underbrace{\int d\mathbf{r} \int d\mathbf{\Omega} \int
dE}_{\text{filters}} \underbrace{f(\mathbf{r}, \mathbf{\Omega},
E)}_{\text{scores}} \psi (\mathbf{r}, \mathbf{\Omega}, E)
Thus, to specify a tally, we need to specify what regions of phase space should
be included when deciding whether to score an event as well as what the scoring
function (:math:`f` in the above equation) should be used. The regions of phase
space are called *filters* and the scoring functions are simply called *scores*.
-------
Filters
-------
To specify the regions of phase space, one must create a
:class:`openmc.Filter`. Since :class:`openmc.Filter` is an abstract class, you
actually need to instantiate one of its sub-classes (for a full listing, see
:ref:`pythonapi_tallies`). For example, to indicate that events that occur in a
given cell should score to the tally, we would create a
:class:`openmc.CellFilter`::
cell_filter = openmc.CellFilter([fuel.id, moderator.id, reflector.id])
Another commonly used filter is :class:`openmc.EnergyFilter`, which specifies
multiple energy bins over which events should be scored. Thus, if we wanted to
tally events where the incident particle has an energy in the ranges [0 eV, 4
eV] and [4 eV, 1 MeV], we would do the following::
energy_filter = openmc.EnergyFilter([0.0, 4.0, 1.0e6])
Energies are specified in eV and need to be monotonically increasing.
.. caution:: An energy bin between zero and the lowest energy specified is not
included by default as it is in MCNP.
Once you have created a filter, it should be assigned to a :class:`openmc.Tally`
instance through the :attr:`Tally.filters` attribute::
tally.filters.append(cell_filter)
tally.filters.append(energy_filter)
# ..or..
tally.filters = [cell_filter, energy_filter]
.. note:: You are actually not required to assign any filters to a tally. If you
create a tally with no filters, all events will score to the
tally. This can be useful if you want to know, for example, a reaction
rate over your entire model.
.. _usersguide_scores:
------
Scores
------
To specify the scoring functions, a list of strings needs to be given to the
:attr:`Tally.scores` attribute. You can score the flux ('flux'), a reaction rate
('total', 'fission', etc.), or even scattering moments (e.g., 'scatter-P3'). For
example, to tally the elastic scattering rate and the fission neutron
production, you'd assign::
tally.scores = ['elastic', 'nu-fission']
With no further specification, you will get the total elastic scattering rate
and the total fission neutron production. If you want reaction rates for a
particular nuclide or set of nuclides, you can set the :attr:`Tally.nuclides`
attribute to a list of strings indicating which nuclides. The nuclide names
should follow the same :ref:`naming convention <usersguide_naming>` as that used
for material specification. If we wanted the reaction rates only for U235 and
U238, we'd set::
tally.nuclides = ['U235', 'U238']
You can also list 'all' as a nuclide which will give you a separate reaction
rate for every nuclide in the model.
The following tables show all valid scores:
.. table:: **Flux scores: units are particle-cm per source particle.**
+----------------------+---------------------------------------------------+
|Score | Description |
+======================+===================================================+
|flux |Total flux. |
+----------------------+---------------------------------------------------+
|flux-YN |Spherical harmonic expansion of the direction of |
| |motion :math:`\left(\Omega\right)` of the total |
| |flux. This score will tally all of the harmonic |
| |moments of order 0 to N. N must be between 0 and |
| |10. |
+----------------------+---------------------------------------------------+
.. table:: **Reaction scores: units are reactions per source particle.**
+----------------------+---------------------------------------------------+
|Score | Description |
+======================+===================================================+
|absorption |Total absorption rate. This accounts for all |
| |reactions which do not produce secondary neutrons |
| |as well as fission. |
+----------------------+---------------------------------------------------+
|elastic |Elastic scattering reaction rate. |
+----------------------+---------------------------------------------------+
|fission |Total fission reaction rate. |
+----------------------+---------------------------------------------------+
|scatter |Total scattering rate. Can also be identified with |
| |the "scatter-0" response type. |
+----------------------+---------------------------------------------------+
|scatter-N |Tally the N\ :sup:`th` \ scattering moment, where N|
| |is the Legendre expansion order of the change in |
| |particle angle :math:`\left(\mu\right)`. N must be |
| |between 0 and 10. As an example, tallying the 2\ |
| |:sup:`nd` \ scattering moment would be specified as|
| |``<scores>scatter-2</scores>``. |
+----------------------+---------------------------------------------------+
|scatter-PN |Tally all of the scattering moments from order 0 to|
| |N, where N is the Legendre expansion order of the |
| |change in particle angle |
| |:math:`\left(\mu\right)`. That is, "scatter-P1" is |
| |equivalent to requesting tallies of "scatter-0" and|
| |"scatter-1". Like for "scatter-N", N must be |
| |between 0 and 10. As an example, tallying up to the|
| |2\ :sup:`nd` \ scattering moment would be specified|
| |as ``<scores> scatter-P2 </scores>``. |
+----------------------+---------------------------------------------------+
|scatter-YN |"scatter-YN" is similar to "scatter-PN" except an |
| |additional expansion is performed for the incoming |
| |particle direction :math:`\left(\Omega\right)` |
| |using the real spherical harmonics. This is useful|
| |for performing angular flux moment weighting of the|
| |scattering moments. Like "scatter-PN", "scatter-YN"|
| |will tally all of the moments from order 0 to N; N |
| |again must be between 0 and 10. |
+----------------------+---------------------------------------------------+
|total |Total reaction rate. |
+----------------------+---------------------------------------------------+
|total-YN |The total reaction rate expanded via spherical |
| |harmonics about the direction of motion of the |
| |neutron, :math:`\Omega`. This score will tally all |
| |of the harmonic moments of order 0 to N. N must be|
| |between 0 and 10. |
+----------------------+---------------------------------------------------+
|(n,2nd) |(n,2nd) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,2n) |(n,2n) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,3n) |(n,3n) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,na) |(n,n\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,n3a) |(n,n3\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,2na) |(n,2n\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,3na) |(n,3n\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,np) |(n,np) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,n2a) |(n,n2\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,2n2a) |(n,2n2\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,nd) |(n,nd) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,nt) |(n,nt) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,nHe-3) |(n,n\ :sup:`3`\ He) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,nd2a) |(n,nd2\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,nt2a) |(n,nt2\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,4n) |(n,4n) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,2np) |(n,2np) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,3np) |(n,3np) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,n2p) |(n,n2p) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,n*X*) |Level inelastic scattering reaction rate. The *X* |
| |indicates what which inelastic level, e.g., (n,n3) |
| |is third-level inelastic scattering. |
+----------------------+---------------------------------------------------+
|(n,nc) |Continuum level inelastic scattering reaction rate.|
+----------------------+---------------------------------------------------+
|(n,gamma) |Radiative capture reaction rate. |
+----------------------+---------------------------------------------------+
|(n,p) |(n,p) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,d) |(n,d) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,t) |(n,t) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,3He) |(n,\ :sup:`3`\ He) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,a) |(n,\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,2a) |(n,2\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,3a) |(n,3\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,2p) |(n,2p) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,pa) |(n,p\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,t2a) |(n,t2\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,d2a) |(n,d2\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,pd) |(n,pd) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,pt) |(n,pt) reaction rate. |
+----------------------+---------------------------------------------------+
|(n,da) |(n,d\ :math:`\alpha`\ ) reaction rate. |
+----------------------+---------------------------------------------------+
|*Arbitrary integer* |An arbitrary integer is interpreted to mean the |
| |reaction rate for a reaction with a given ENDF MT |
| |number. |
+----------------------+---------------------------------------------------+
.. table:: **Particle production scores: units are particles produced per
source particles.**
+----------------------+---------------------------------------------------+
|Score | Description |
+======================+===================================================+
|delayed-nu-fission |Total production of delayed neutrons due to |
| |fission. |
+----------------------+---------------------------------------------------+
|prompt-nu-fission |Total production of prompt neutrons due to |
| |fission. |
+----------------------+---------------------------------------------------+
|nu-fission |Total production of neutrons due to fission. |
+----------------------+---------------------------------------------------+
|nu-scatter, |These scores are similar in functionality to their |
|nu-scatter-N, |``scatter*`` equivalents except the total |
|nu-scatter-PN, |production of neutrons due to scattering is scored |
|nu-scatter-YN |vice simply the scattering rate. This accounts for |
| |multiplicity from (n,2n), (n,3n), and (n,4n) |
| |reactions. |
+----------------------+---------------------------------------------------+
.. table:: **Miscellaneous scores: units are indicated for each.**
+----------------------+---------------------------------------------------+
|Score | Description |
+======================+===================================================+
|current |Partial currents on the boundaries of each cell in |
| |a mesh. Units are particles per source |
| |particle. Note that this score can only be used if |
| |a mesh filter has been specified. Furthermore, it |
| |may not be used in conjunction with any other |
| |score. |
+----------------------+---------------------------------------------------+
|events |Number of scoring events. Units are events per |
| |source particle. |
+----------------------+---------------------------------------------------+
|inverse-velocity |The flux-weighted inverse velocity where the |
| |velocity is in units of centimeters per second. |
+----------------------+---------------------------------------------------+
|kappa-fission |The recoverable energy production rate due to |
| |fission. The recoverable energy is defined as the |
| |fission product kinetic energy, prompt and delayed |
| |neutron kinetic energies, prompt and delayed |
| |:math:`\gamma`-ray total energies, and the total |
| |energy released by the delayed :math:`\beta` |
| |particles. The neutrino energy does not contribute |
| |to this response. The prompt and delayed |
| |:math:`\gamma`-rays are assumed to deposit their |
| |energy locally. Units are eV per source particle. |
+----------------------+---------------------------------------------------+
|fission-q-prompt |The prompt fission energy production rate. This |
| |energy comes in the form of fission fragment |
| |nuclei, prompt neutrons, and prompt |
| |:math:`\gamma`-rays. This value depends on the |
| |incident energy and it requires that the nuclear |
| |data library contains the optional fission energy |
| |release data. Energy is assumed to be deposited |
| |locally. Units are eV per source particle. |
+----------------------+---------------------------------------------------+
|fission-q-recoverable |The recoverable fission energy production rate. |
| |This energy comes in the form of fission fragment |
| |nuclei, prompt and delayed neutrons, prompt and |
| |delayed :math:`\gamma`-rays, and delayed |
| |:math:`\beta`-rays. This tally differs from the |
| |kappa-fission tally in that it is dependent on |
| |incident neutron energy and it requires that the |
| |nuclear data library contains the optional fission |
| |energy release data. Energy is assumed to be |
| |deposited locally. Units are eV per source |
| |paticle. |
+----------------------+---------------------------------------------------+
|decay-rate |The delayed-nu-fission-weighted decay rate where |
| |the decay rate is in units of inverse seconds. |
+----------------------+---------------------------------------------------+