more work on the JOSS paper

Author: zingale

paper/paper.md

@@ -25,7 +25,9 @@ bibliography: paper.bib
 The AMReX-Astrophysics Microphysics library provides a common set of
 microphysics routines (reaction networks, equations of state, and
 other transport coefficients) for astrophysical simulation codes built
-around the AMReX library.
+around the AMReX library.  Several codes, including Castro, MAESTROeX,
+and Quokka use Microphysics to provide the physics and solvers needed
+to close the hydrodynamics systems that they evolve.  
 
 # History
 
@@ -39,13 +41,41 @@ Microphysis were split off into the AMReX-Astrophysics Microphysics
 library.  Today, the library is completely written in C++ and relies
 on the AMReX data structures.  
 
-# Design
+Several classical Fortran libraries have been converted to header-only C++
+implementations, including the VODE integrator and the hybrid Powell method
+of MINPACK.  
+
 
-Porting many classic solvers from old Fortran to C++
+# Design
 
-header-only library as much as possible
+Microphysics provides several different types of physics: equations of
+state, reaction networks and screening methods, nuclear statistical
+equilibrium solvers and table, conductivities, and opacities, as well
+as the tools needed to work with them, most notably the ODE integrators
+for the networks.
+
+There are two ways to use Microphysics: standalone for simple investigations
+or as part of an (AMReX-based) application code.  In both cases, the core
+requirement is to select a network---this defines the composition that
+is then used by most of the other physics routines.
+
+A key design feature is the separation of the reaction network from
+the integrator.  This allows us to easily experiment with different
+integration methods (such as the RKC integrator) and also support
+different modes of coupling reactions to a simulation code (operator
+splitting and spectral deferred corrections)
+
+We rely on header-only implementations as much as possible, to allow
+for easier compiler inlining.  We also leverage C++17 `if constexpr`
+templating to compile out unnecessary computations for performance.
+For example, our equations of state can compute a lot of thermodynamic
+quantities and derivatives, but for some operations, we only need a
+few of these.  If we pass the general `eos_t` type into the EOS, then
+everything is calculated, but if we pass in to the same interface the
+smaller `eos_re_t` type, then only a few energy terms are computed
+(those that are needed when finding temperature from specific internal
+energy).
 
-C++17
 
 pynucastro integration
 
@@ -54,8 +84,20 @@ pynucastro integration
 
 
 
+
 # Unit tests / examples
 
+Microphysics can be used as a standalone tool through the tests
+in `Microphysics/unit_test/`.  There are 2 types of tests here:
+
+* *comprehensive tests* test performance by setting up a cube of data
+  (with density, temperature, and composition varying in a dimension)
+  and performing an operation on the entire cube (calling the EOS,
+  integrating a network, ...).
+
+* *one-zone tests* simply call one of the physics modules with a
+  single thermodynamic state.  This can be used to explore the physics
+  that is implemented.
 
 # References