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Merge pull request #392 from parikshitbajpai/joss-review-6805
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Typos found during JOSS review
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@Yurlungur
Yurlungur authored Jul 22, 2024
2 parents 9aeae78 + c91f19c commit 8412436
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46 changes: 23 additions & 23 deletions doc/sphinx/src/building.rst
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Expand Up @@ -41,17 +41,17 @@ provided below.
A CMake configuration option is provided that allows developers to
select a specific mode (``SINGULARITY_FORCE_SUBMODULE_MODE``), however
this is intended for internal development only. The intended workflow is
to let ``singularity-eos`` decide that appropriate mode, which it
to let ``singularity-eos`` decide the appropriate mode, which it
decides based on inspecting the project directory that the source
resides in.

Dependencies
------------

``singularity-eos`` has a number of required and optional depdencies.
``singularity-eos`` has a number of required and optional depdencies.

====================================== =============================== ===========================================
Package Name Distribution Comment
Package Name Distribution Comment
====================================== =============================== ===========================================
`ports-of-call`_ submodule / external Required
`mpark_variant`_ submodule / external Required
Expand All @@ -61,10 +61,10 @@ Dependencies
`kokkos`_ submodule / external Optional; enables GPU offloading.
`Eigen`_ submodule / external Optional; used for linear algebra on the CPU when doing mixed-cell closures.
`kokkos-kernels`_ submodule / external Optional; used for linear algebra on the GPU when doing mixed-cell closures.
`pybind11`_ external / fetchable [*]_ Optional
`pybind11`_ external / fetchable [*]_ Optional
====================================== =============================== ===========================================

.. [*] availible as a git submodule for in-tree builds
.. [*] available as a git submodule for in-tree builds
.. [*] located outside the build tree and discoverable by CMake
.. [*] CMake can download and configure this source in-tree
Expand Down Expand Up @@ -99,7 +99,7 @@ sections detailing those build modes.
The main CMake options to configure building are in the following table:

====================================== ======= ===========================================
Option Default Comment
Option Default Comment
====================================== ======= ===========================================
``SINGULARITY_USE_SPINER`` ON Enables EOS objects that use ``spiner``.
``SINGULARITY_USE_FORTRAN`` ON Enable Fortran API for equation of state.
Expand Down Expand Up @@ -143,7 +143,7 @@ These options are listed in the following table, along with their
preconditions:

============================================== ================================================================================= ===========================================
Option Precondition Comment
Option Precondition Comment
============================================== ================================================================================= ===========================================
``SINGULARITY_USE_SPINER_WITH_HDF5`` ``SINGULARITY_USE_SPINER=ON`` Requests that ``spiner`` be configured for ``HDF5`` support.
``SINGULARITY_USE_CUDA`` ``SINGULARITY_USE_KOKKOS=ON`` Target nvidia GPUs for ``Kokkos`` offloading.
Expand Down Expand Up @@ -180,7 +180,7 @@ presets, see the `cmake documentation on
presets <https://cmake.org/cmake/help/latest/manual/cmake-presets.7.html>`__

.. warning::
CMake presets are only available if ``singularity-eos`` is the
CMake presets are only available if ``singularity-eos`` is the
top-level project.

Predefined presets
Expand Down Expand Up @@ -286,8 +286,8 @@ source should be placed below the top-level of a host project
# An example directory layout when using singularity-eos in submodule mode
my_project
|_CMakeLists.txt
|_README.md
|_src
|_README.md
|_src
|_include
|_tpl/singularity-eos
Expand All @@ -312,7 +312,7 @@ code, along with the interfaces of the internal dependencies

.. code:: c++

// in source of my_project
// in source of my_project

#include<singularity-eos/eos/eos.hpp>
// from the internal ports-of-call submodule
Expand Down Expand Up @@ -348,7 +348,7 @@ expected to be discoverable by CMake. This can be done several ways
invocation to be aware of these installs

*standalone* mode is the mode used to install ``singularity-eos`` to a
system as a common library. If, for example, you use Spack to to install
system as a common library. If, for example, you use Spack to install
packages, ``singularity-eos`` will be built and installed in
*standalone* mode.

Expand All @@ -368,7 +368,7 @@ overview of how to use Spack to develop and deploy ``singularigy-eos``,
but for more in-depth information, please refer to the `official Spack
documentation <spack.readthedocs.io>`__.

Preperation
Preparation
^^^^^^^^^^^

First, we need to clone the Spack repository. You can place this
Expand All @@ -386,7 +386,7 @@ To start using Spack, we use the provided activation script

.. code:: bash
# equivalent scripts for tcsh, fish are located here as well
# equivalent scripts for tcsh, fish are located here as well
$> source ~/spack/share/spack/setup-env.sh
You will always need to *activate* spack for each new shell. You may
Expand Down Expand Up @@ -494,7 +494,7 @@ You may also manually edit the ``packages.yaml`` file to switch the
``buildable`` flag for the troublesome package, but you will need to be
a least familiar with YAML schema.

First install with spack
First install with Spack
^^^^^^^^^^^^^^^^^^^^^^^^

Let's walk through a simple Spack workflow for installing. First, we
Expand Down Expand Up @@ -522,7 +522,7 @@ library for multigrid methods.
develop [git] https://github.com/hypre-space/hypre.git on branch master
2.28.0 https://github.com/hypre-space/hypre/archive/v2.28.0.tar.gz
# ... more versions listed
# ... more versions listed
Variants:
Name [Default] When Allowed values Description
Expand All @@ -532,7 +532,7 @@ library for multigrid methods.
gfx1030, gfx90c,
gfx90a, gfx1101,
gfx908, gfx1010,
# ... lots of amd targets listed
# ... lots of amd targets listed
build_system [autotools] -- autotools Build systems supported by the package
caliper [off] -- on, off Enable Caliper support
complex [off] -- on, off Use complex values
Expand Down Expand Up @@ -663,13 +663,13 @@ Installing ``singularity-eos`` using Spack
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
. warning::
The spack build is currently experimental.
The spack build is currently experimental.
Please report problems you havee as github issues.
The spackage is available in the main `Spack`_
repositories, and we provide a spackage for ``singularity-eos`` witin the
the singularity-eos source repository. The distributed spackage may be
more up-to-date than the one in the main `Spack`_ repository. If you
the singularity-eos source repository. The distributed spackage may be
more up-to-date than the one in the main `Spack`_ repository. If you
have spack installed, simply call
.. _Spack: https://spack.io/
Expand Down Expand Up @@ -724,13 +724,13 @@ supports a number of relevant variants:
| tests [off] | on, off | Build tests |
+-----------------------------+-----------------+-----------------------------+
Developing ``singularigy-eos`` using Spack
Developing ``singularity-eos`` using Spack
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Spack is a powerful tool that can help develop ``singularigy-eos`` for a
Spack is a powerful tool that can help develop ``singularity-eos`` for a
variety of platforms and hardware.
1. Install the dependencies ``singularigy-eos`` needs using Spack
1. Install the dependencies ``singularity-eos`` needs using Spack
.. code:: bash
Expand Down
16 changes: 8 additions & 8 deletions doc/sphinx/src/contributing.rst
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Expand Up @@ -6,7 +6,7 @@ Contributing
=============

If you have any trouble with the project, or are interested in
participating, please contact us by creating an issue on the github
participating, please contact us by creating an issue on the GitHub
repository, or submit a pull request!

Pull request protocol
Expand Down Expand Up @@ -37,7 +37,7 @@ useful output. For example:
Several sets of tests are triggered on a pull request: a static format
check, a docs buld, and unit tests of analytic models and the stellar
collapse model. These are run through github's CPU infrastructure. We
collapse model. These are run through GitHub's CPU infrastructure. We
have a second set of tests run on a wider set of architectures that
also access the Sesame library, which we are not able to make public.

Expand Down Expand Up @@ -127,7 +127,7 @@ Interwoven Dependencies
``singularity-eos`` depends on several other open-source, Los Alamos
maintained, projects. In particular, ``spiner`` and
``ports-of-call``. If you have issues with these projects, ideally
submit issues on the relevant github pages. However, if you can't
submit issues on the relevant GitHub pages. However, if you can't
figure out where an issue belongs, no big deal. Submit where you can
and we'll engage with you to figure out how to proceed.

Expand Down Expand Up @@ -217,7 +217,7 @@ wrapped with ``#ifdef SINGULARITY_USE_EOSPAC``. This might look something like
#endif
>{};

Note the placement of commas and angle brackets. This example excludes
Note the placement of commas and angle brackets. This example excludes

Step 3: Create tests for your EOS
`````````````````````````````````
Expand All @@ -229,7 +229,7 @@ same. In general, we recommend you copy the general structure of one of the
existing EOS-specific unit tests.

After creating your tests, you will need to include the ``.cpp`` for your new
test in the ``CMakeLists.txt`` file,
test in the ``CMakeLists.txt`` file,

.. code-block:: cmake
Expand Down Expand Up @@ -402,7 +402,7 @@ Some notes on style and code architecture
but many of the coding habits advocated for by Holzmann produce
long-lived, easy to understand, easy to parse, and easy to maintain code.
And we take many of the rules to heart. Here are a few that are most
relevant to ``singularity-eos``. They have been adapted slightly to
relevant to ``singularity-eos``. They have been adapted slightly to
our context.

#. Avoid complex flow constructs such as gotos.
Expand Down Expand Up @@ -458,7 +458,7 @@ style. Here we briefly discuss a few things one should be aware of.
``PORTABLE_FORCEINLINE_FUNCTION``. These macros are imported from
the `ports-of-call`_ library and resolve to the appropriate
decorations for a given device-side backend such as cuda so the code
compiles correctly. Code that doesn't need to run on device,
compiles correctly. Code that doesn't need to run on device,
such as EOS class constructors, does not need these decorations.

* **Relocatable device code:** It is common in C++ to split code
Expand Down Expand Up @@ -714,7 +714,7 @@ Main``. Typically the branch for this merge request should be called
full test suite passes for this PR.

After that pull request is merged, go to the ``releases`` tab on the
right sidebar on github, and draft a new release. Set the tag to
right sidebar on GitHub, and draft a new release. Set the tag to
``v[release number]``, fill the comment with the changes in the
changelog since the last release, and make the release.

Expand Down
8 changes: 4 additions & 4 deletions doc/sphinx/src/getting-started.rst
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Expand Up @@ -12,15 +12,15 @@ At it's most basic, you can download and compile ``singularity-eos`` with:
mkdir bin
cd bin
cmake -DSINGULARITY_FORCE_SUBMODULE_MODE=ON -DSINGULARITY_USE_FORTRAN=OFF ..
make -j
make -j
make install # optional: install into directory defined via CMAKE_INSTALL_PREFIX
This will downloady singularity-eos with no optional dependencies and
This will download ``singularity-eos`` with no optional dependencies and
compile the capabilities available in that form. For more details, see
:ref:`our build page <building>`.

If the library is in your include and lib paths (or you built it
in-tree), you can include the eos part of the library with
in-tree), you can include the ``eos`` part of the library with

.. code-block:: cpp
Expand Down Expand Up @@ -78,7 +78,7 @@ And that's it!
Going Deeper
--------------

* You can find code examples in the ``examples`` source directory.
* You can find code examples in the ``example`` source directory.
* To learn more about the design philosophy, look :ref:`here <philosophy>`.
* To learn about how to build, look at :ref:`our build document <building>`.
* To learn more about the equation of state API, look :ref:`here <using-eos>`.
Expand Down
14 changes: 7 additions & 7 deletions doc/sphinx/src/using-closures.rst
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Expand Up @@ -3,7 +3,7 @@
Mixed Cell Closures
====================

In the single-material Euler equations, the mass and energy are typically
In the single-material Euler equations, mass and energy are typically
evolved and the EOS is called to provide a pressure for the momentum equations.
When transitioning to a multi-material approach, a single velocity is typically
used and the Euler equations are solved with respect to the bulk fluid motion.
Expand All @@ -20,7 +20,7 @@ to compute thermodynamic quantities in that cell for each material.
Governing Equations and Assumptions
------------------------------------

In a general sense then the mixed
In a general sense the mixed
material closure rule takes the form

.. math::
Expand Down Expand Up @@ -75,7 +75,7 @@ Similarly the energy can be summed in a similar way so that

.. math::
u = \rho \epsilon = \sum_{i = 0}^{N - 1} \rho_i \epsilon_i
u = \rho \epsilon = \sum_{i = 0}^{N - 1} \rho_i \epsilon_i
= \sum_{i = 0}^{N - 1} u_i
where :math:`u` is the total internal energy density (internal energy per unit
Expand Down Expand Up @@ -156,7 +156,7 @@ closure state.
fractions by the material bulk moduli to reflect the relative
compressibilities.

Pressure-Temperature Equilibirum
Pressure-Temperature Equilibrium
--------------------------------

At present, ``singularity-eos`` focuses on several methods for finding a PTE
Expand All @@ -169,12 +169,12 @@ In essence, the PTE equations can be posed as two residual equations:

.. math::
f_\mathrm{tot} - \sum\limits_{i=0}^{N-1} f_i =
f_\mathrm{tot} - \sum\limits_{i=0}^{N-1} f_i =
\sum\limits_{i=0}^{N-1} f_i^*(x_i^*, y_i^*) - f_i(x_i, y_i)
.. math::
u_\mathrm{tot} - \sum\limits_{i=0}^{N-1} u_i =
u_\mathrm{tot} - \sum\limits_{i=0}^{N-1} u_i =
\sum\limits_{i=0}^{N-1} u_i^*(x_i^*, y_i^*) - u_i(x_i, y_i)
where the superscript :math:`^*` denotes the variables at the PTE state,
Expand Down Expand Up @@ -267,7 +267,7 @@ derivatives must be transformed to volume fraction derivatives via

.. math::
\left(\frac{\partial Q}{\partial f_i}\right)_X
\left(\frac{\partial Q}{\partial f_i}\right)_X
= - \frac{\rho_i^2}{\rho}\left(\frac{\partial Q}{\partial \rho_i}\right)_X,
were :math:`Q` and :math:`X` are arbitrary thermodynamic variables. At this
Expand Down
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