spellcheck the codes with codespell (#1175)

sphinx_docs/source/basics.rst

@@ -130,7 +130,7 @@ of the species defined by the network to interpret the state.
 
 We try to maximize code reuse in the Microphysics source, so the
 solvers (ODE integration for the network and Newton-Raphson root
-finding for the EOS) is separated from the specific implmentations of
+finding for the EOS) is separated from the specific implementations of
 the microphysics.
 
 **All quantities are assumed to be in CGS units**, unless otherwise

sphinx_docs/source/data_structures.rst

@@ -70,7 +70,7 @@ the user will only need to fill/use the following information:
    derive the temperature via the EOS.
 
    Upon exit of the integration, the initial internal energy (offset)
-   is subtracted off, and e now represents the specifc nuclear
+   is subtracted off, and e now represents the specific nuclear
    energy release from the reactions.
 
 * ``burn_state.xn[]``: the mass fractions
@@ -107,7 +107,7 @@ to access the different components of the state:
 
    It is assumed that the first ``nspec`` are the species.
 
-* ``net_ienuc`` : the index of the specifc internal energy in the solution vector
+* ``net_ienuc`` : the index of the specific internal energy in the solution vector
 
 Integrators
 ===========

sphinx_docs/source/eos.rst

@@ -252,12 +252,12 @@ compile type (via C++ templating) for ``eos_re_t`` and ``eos_rep_t``.
 
    All of these modes require composition as an input.  Usually this is
    via the set of mass fractions, ``eos_t.xn[]``, but if ``USE_AUX_THERMO``
-   is set to ``TRUE``, then we instead use the auxillary quantities
+   is set to ``TRUE``, then we instead use the auxiliary quantities
    stored in ``eos_t.aux[]``.
 
 .. _aux_eos_comp:
 
-Auxillary Composition
+Auxiliary Composition
 ---------------------
 
 

sphinx_docs/source/integrators.rst

@@ -20,7 +20,7 @@ The equations we integrate to do a nuclear burn are:
    \frac{de}{dt} = f(\rho,X_k,T)
    :label: eq:enuc_integrate
 
-Here, :math:`X_k` is the mass fraction of species :math:`k`, :math:`e` is the specifc
+Here, :math:`X_k` is the mass fraction of species :math:`k`, :math:`e` is the specific
 nuclear energy created through reactions. Also needed are density :math:`\rho`,
 temperature :math:`T`, and the specific heat. The function :math:`f` provides the energy release from reactions and can often be expressed in terms of the 
 instantaneous reaction terms, :math:`\dot{X}_k`. As noted in the previous
@@ -79,7 +79,7 @@ The input is a ``burn_t``.
    corresponding to this input state through the equation of state
    before integrating.
 
-When integrating the system, we often need auxillary information to
+When integrating the system, we often need auxiliary information to
 close the system.  This is kept in the original ``burn_t`` that was
 passed into the integration routines.  For this reason, we often need
 to pass both the specific integrator's type (e.g. ``dvode_t``) and
@@ -93,7 +93,7 @@ The overall flow of the integrator is (using VODE as the example):
    ``dvode_t``.
 
 #. call the ODE integrator, ``dvode()``, passing in the ``dvode_t`` _and_ the
-   ``burn_t`` --- as noted above, the auxillary information that is
+   ``burn_t`` --- as noted above, the auxiliary information that is
    not part of the integration state will be obtained from the
    ``burn_t``.
 
@@ -109,7 +109,7 @@ The overall flow of the integrator is (using VODE as the example):
    Upon exit, ``burn_t burn_state.e`` is the energy *released* during
    the burn, and not the actual internal energy of the state.
 
-   Optionally, by settting ``integrator.subtract_internal_energy=0``
+   Optionally, by setting ``integrator.subtract_internal_energy=0``
    the output will be the total internal energy, including that released
    burning the burn.
 
@@ -386,7 +386,7 @@ For this investigation, it was assumed that a run with a tolerance of :math:`10^
 corresponded to an exact result,
 so it is used as the basis for the rest of the tests.
 From the figure, one can infer that the :math:`10^{-3}` and :math:`10^{-6}` tolerances
-do not yeild the most accurate results
+do not yield the most accurate results
 because their relative error values are fairly large.
 However, the test with a tolerance of :math:`10^{-9}` is accurate
 and not so low that it takes incredible amounts of computer time,

sphinx_docs/source/networks.rst

@@ -105,7 +105,7 @@ powerlaw
 This is a simple single-step reaction rate.
 We will consider only two species, fuel, :math:`f`, and ash, :math:`a`, through
 the reaction: :math:`f + f \rightarrow a + \gamma`. Baryon conservation
-requres that :math:`A_f = A_a/2`, and charge conservation requires that :math:`Z_f
+requires that :math:`A_f = A_a/2`, and charge conservation requires that :math:`Z_f
 = Z_a/2`. We take
 our reaction rate to be a powerlaw in temperature. The standard way
 to write this is in terms of the number densities, in which case we

sphinx_docs/source/nse.rst

@@ -77,7 +77,7 @@ For this reason, when we are using the NSE network, we always take the
 composition quantities in the EOS directly from ``eos_state.aux[]``
 instead of from ``eos_state.xn[]``.  The ``AUX_THERMO`` preprocessor
 variable is enabled in this case, and the equations of state interpret
-this to use the auxillary data for the composition.  This is described in :ref:`aux_eos_comp`.
+this to use the auxiliary data for the composition.  This is described in :ref:`aux_eos_comp`.
 
 
 NSE Table Outputs
@@ -91,7 +91,7 @@ resulting from the full 125 nuclei network.   It also provides a set of 19
 
 These three quantities are stored as ``aux`` data in the network and
 are indexed as ``iye``, ``iabar``, and ``ibea``.  Additionally, when
-coupling to hydrodynamics, we need to advect these auxillary
+coupling to hydrodynamics, we need to advect these auxiliary
 quantities.
 
 For Strang split coupling of hydro and reactions, :math:`DX_k/Dt = 0`,
@@ -105,7 +105,7 @@ and our evolution equations are:
    \frac{D}{Dt} \left (\frac{B}{A} \right ) &= \sum_k \frac{B_k}{A_k} \frac{DX_k}{Dt} = 0
    \end{align*}
 
-Therefore each of these auxillar equations obeys an advection equation
+Therefore each of these auxiliary equations obeys an advection equation
 in the hydro part of the advancement.
 
 
@@ -259,7 +259,7 @@ There are 3 main criteria discussed in the :cite:`Kushnir_2020`.
      (\alpha, \gamma) \isotm{S}{32}
 
   The general approach to this is to start iterations from the heavy to the light nuclei to
-  use them as the starting point of the cycle. Then the algorithmn checks if isotopes involved
+  use them as the starting point of the cycle. Then the algorithm checks if isotopes involved
   in the network can actually form a cycle using the combination reactions above. If such cycle
   is formed, then we check the rates of these reactions to see if they satisfy the condition
   mention previously. If there are no isotope present in the network that would form
@@ -296,7 +296,7 @@ There are 3 main criteria discussed in the :cite:`Kushnir_2020`.
     light-isotope-group. In this case, if the reaction passes the two criteria mentioned above,
     we merge the groups containing those two isotopes if they're not yet in the same group.
 
-  * There is only one isotope involed in reaction, :math:`k`, that is not in the
+  * There is only one isotope involved in reaction, :math:`k`, that is not in the
     light-isotope-group, which is not necessarily isotope :math:`i` that passes the
     first criteria. In this case, we merge the isotope that is not in LIG into LIG.
 
@@ -326,7 +326,7 @@ nse check:
   the dependency on the cell size, ``dx``, which calculates the sound crossing time, ``t_s``.
   Naturally, we require the timescale of the rates to be smaller than ``t_s`` to ensure the
   states have time to achieve equilibrium. However, sometimes this check can be difficult
-  to acheive, so we leave this as an option for the user to explore.
+  to achieve, so we leave this as an option for the user to explore.
 
 * ``nse.nse_molar_independent = 1`` in the input file allows the user to use the nse mass
   fractions for nse check after the first check (the one that ensures we're close enough

sphinx_docs/source/preface.rst

@@ -16,7 +16,7 @@ currently deal with are the equation of state (EOS) and the nuclear
 burning network.
 
 Microphysics is not a stand-alone code. It is intended to be used in
-conjuction with a simulation code. At the moment, the interfaces and
+conjunction with a simulation code. At the moment, the interfaces and
 build stubs are compatible with the AMReX codes. In many cases we
 will provide test modules that demonstrate a minimal working example
 for how to run the modules (leveraging the AMReX build system). The

sphinx_docs/source/rp_intro.rst

@@ -5,7 +5,7 @@ Runtime parameters
 The behavior of the network and EOS are controlled by many runtime
 parameters. These parameters are defined in plain-text files
 ``_parameters`` located in the different directories that hold the
-microphysics code. At compile time, a script in the AMReX bulid
+microphysics code. At compile time, a script in the AMReX build
 system, findparams.py, locates all of the ``_parameters`` files that
 are needed for the given choice of network, integrator, and EOS, and
 assembles all of the runtime parameters into a set of header files

sphinx_docs/source/sdc.rst

@@ -119,7 +119,7 @@ system we are integrating, including the advective terms.
 
    a. Update the density (this may be redundant).
 
-   b. Fill the ``burn_t``'s ``xn[]``, auxillary data, internal energy,
+   b. Fill the ``burn_t``'s ``xn[]``, auxiliary data, internal energy,
       and call the EOS to get the temperature.
 
 #. Call the ``actual_rhs()`` routine to get just the reaction sources

sphinx_docs/source/templated_networks.rst

@@ -322,7 +322,7 @@ The basic flow is:
 #. Compute all of the intermediate rates.
 
    Since these rates are used multiple times, we compute them once and cache them.
-   This is done soley for performance reasons, since computing the rates is expensive.
+   This is done solely for performance reasons, since computing the rates is expensive.
 
 #. Loop over rates
 

sphinx_docs/source/unit_tests.rst

@@ -200,7 +200,7 @@ variables define absolute tolerances of the ordinary differential
 equations and the ``rtol`` variables define the relative tolerances.  The
 second section of the input file collects the inputs that ``main.f90``
 asks for so that the user does not have to input all 5+
-parameters that are required everytime the test is run.  Each input
+parameters that are required every time the test is run.  Each input
 required is defined and initialized on the lines following
 ``&cellparams``.  The use of the parameters is show below:
 
@@ -250,11 +250,11 @@ logarithmic scales, for all species involved in the simulation.  An
 example of this graph is shown below.
 
 .. figure:: react_aprox13_logX.png
-   :alt: An example of a plot output by the burn_cell unit test. This is the logX output cooresponding to the network aprox13.
+   :alt: An example of a plot output by the burn_cell unit test. This is the logX output corresponding to the network aprox13.
    :width: 4.5in
 
    An example of a plot output by the burn_cell unit test. This is the
-   logX output cooresponding to the network aprox13.
+   logX output corresponding to the network aprox13.