From 1ab2230af24d197df6ba41d2f9b72e6d23ac3670 Mon Sep 17 00:00:00 2001 From: Alice Harpole Date: Thu, 21 Feb 2019 16:11:50 -0500 Subject: [PATCH] paper formatting --- paper/paper.md | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index b1f6cb33e..658093c58 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -2,7 +2,7 @@ title: 'pyro: a framework for hydrodynamics explorations and prototyping' tags: -- python +- Python - hydrodynamics - astrophysics - physics @@ -36,41 +36,41 @@ bibliography: paper.bib # Summary -pyro is a python-based simulation framework designed for ease of +`pyro` is a Python-based simulation framework designed for ease of implementation and exploration of hydrodynamics methods. It is built in a object-oriented fashion, allowing for the reuse of the core components and fast prototyping of new methods. -The original goal of pyro was to learn hydrodynamics methods through -example, and it still serves this goal. At Stony Brook, pyro is used +The original goal of `pyro` was to learn hydrodynamics methods through +example, and it still serves this goal. At Stony Brook, `pyro` is used with new undergraduate researchers in our group to introduce them to the ideas of computational hydrodynamics. But the current framework -has evolved to the point where pyro is used for prototyping +has evolved to the point where `pyro` is used for prototyping hydrodynamics solvers before implementing them into science codes. An example of this is the 4th-order compressible solver built on the ideas of spectral deferred corrections (the `compressible_sdc` solver). This implementation was used as the model for the development of higher-order schemes in the Castro hydrodynamics code [@castro]. The low Mach number atmospheric solver (`lm_atm`) is based -on the Maestro code [@maestro] and the pyro implementation will be +on the Maestro code [@maestro] and the `pyro` implementation will be used to prototype new low Mach number algorithms before porting them to science codes. -In the time since the first pyro paper [@pyroI], the code has +In the time since the first `pyro` paper [@pyroI], the code has undergone considerable development, gained a large number of solvers, adopted unit testing through pytest and documentation through sphinx, -and a number of new contributors. pyro's functionality can now +and a number of new contributors. `pyro`'s functionality can now be accessed directly through a `Pyro()` class, in addition to the original commandline script interface. This new interface in particular allows for easy use within Jupyter notebooks. We also now use HDF5 -for output instead of python's `pickle()` function. Previously, we used Fortran +for output instead of Python's `pickle()` function. Previously, we used Fortran to speed up some performance-critical portions of the code. These routines -could be called by the main python code by first compiling them using `f2py`. -In the new version, we have replaced these Fortran routines by python functions -that are compiled at runtime by `numba`. Consequently, pyro is now written -entirely in python. +could be called by the main Python code by first compiling them using `f2py`. +In the new version, we have replaced these Fortran routines by Python functions +that are compiled at runtime by `numba`. Consequently, `pyro` is now written +entirely in Python. -The current pyro solvers are: +The current `pyro` solvers are: - linear advection (including a second-order unsplit CTU scheme, a method-of-lines piecewise linear solver$^\star$, a 4th-order @@ -93,7 +93,7 @@ The current pyro solvers are: - shallow water equations solver$^\star$ -(solvers since the first pyro paper are marked with a $^\star$). Also +(solvers since the first `pyro` paper are marked with a $^\star$). Also, new is support for Lagrangian tracer particles, which can be added to any solver that has a velocity field.