Update paper.md

Author: drobnyjt

paper/paper.md

@@ -48,7 +48,7 @@ For detailed summaries of the history and theory of binary collision approximati
 
 Ion-material interactions have been historically modeled using analytical and semi-empirical formulas, such as Sigmund's sputtering theory [@Sigmund1987], the Bohdansky formula [@Bohdansky1980; @Bohdansky1984], the Yamamura formula [@Yamamura1982; @Yamamura1983; @Yamamura1984], and the Thomas et al. reflection coefficient [@Thomas1992]. However, for any physical situation beyond the regimes of validity of these formulas (e.g., non-normal angles of incidence), or for complex geometry, or for inhomogeneous composition, straightforward empirical formulas cannot be reliably used. Many BCA codes have been developed to provide computationally efficient solutions to these problems, including SRIM [@Ziegler2010], Tridyn [@Möller1988], F-TRIDYN [@Drobny2017], SDTrimSP [@Mutzke2019] and its derivatives, which are based on the original TRIM [@Biersack1980] code. However, each has limitations that prevent widespread adoption across a broad range of applications. In particular, SRIM, which is free-use but closed-source, suffers from relatively poor computational performance and significant anomalies in sputtered atom angular distributions and light ion sputtering yields [@Shulga2019; @Shulga2018; @Hofsass2014; @Wittmaack2004]. Tridyn and F-TRIDYN, which are not open source, are limited to low ion energy, specific screened-coulomb potentials, mono-angular ion beams, atomically flat and atomically rough surfaces respectively, and are single-threaded. SDTrimSP, although significantly more advanced than the preceding codes, is built on the original TRIM source code and is not open-source.
 
-As far as the authors are aware, there is no widely-used open-source BCA code suitable for simulating plasma-material interactions. Iradina is an open source BCA that has been used for ion-material interactions in a semicondcutor context [@HollandMoritz2017; @Johannes2014], but sputtering yields from iradina have not been shown to agree with direct comparisons to other BCA codes for a wide range of ions, targets, energies, or angles, and reflection coefficients or other key quantities of interest have not yet, to our knowledge, been reported. Additionally, those BCA codes that are available, through licensing agreements or as closed-source software, are not well suited to a wide range of physical problems. Particularly, the direct integration of BCA codes to particle or subsurface dynamics codes, such as those performed using F-TRIDYN for ITER divertor simulations [@Lasa2020], requires costly external wrappers to manage simulations and process output files to perform file-based coupling. RustBCA, as part of the Plasma Surface Interactions 2 SciDAC Project suite of codes, has been developed to fill that gap and expand upon the feature set included in currently available BCA codes. Features unique to RustBCA include the ability to handle attractive-repulsive interatomic potentials, use multiple interatomic potentials in one simulation, handle high-energy incident ions and multiple geometry types, use large file input of incident particles to facilitate coupling to other codes via HDF5, output pre-binned distributions without post-processing of text-based particle lists, and use a human- and machine-readable configuration file. RustBCA has been designed with modern programming techniques, robust error-handling, and multi-threading capability. RustBCA is being developed as both a standalone code and as a library code that may be used to add BCA routines to other high-performance codes to avoid file-based code coupling entirely. Additionally, the TRIM family of codes typically relies on the MAGIC algorithm to approximate the scattering integral with 5 fitting coefficients. RustBCA includes not only an implementation of the MAGIC algorithm, but also Mendenhall-Weller, Gauss-Mehler, and Gauss-Legendre quadrature, the three of which are significantly more accurate than the MAGIC algorithm. We hope that giving users direct access to a user-friendly, flexible, high-performance, open-source BCA will encourage and enable heretofore unexplored research in ion-materials interactions.
+As far as the authors are aware, there is no widely-used open-source BCA code suitable for simulating plasma-material interactions. Iradina is an open source BCA that has been used for ion-material interactions in a semicondcutor context [@HollandMoritz2017; @Johannes2014], but sputtering yields from iradina have not been shown to agree with direct comparisons to other BCA codes for a wide range of ions, targets, energies, or angles, and reflection coefficients or other key quantities of interest have not yet, to our knowledge, been reported. Additionally, those BCA codes that are available, through licensing agreements or as closed-source software, are not well suited to a wide range of physical problems. Particularly, the direct integration of BCA codes to particle or subsurface dynamics codes, such as those performed using F-TRIDYN for ITER divertor simulations [@Lasa2020], requires costly external wrappers to manage simulations and process output files to perform file-based coupling. RustBCA, as part of the  [Plasma Surface Interactions 2 SciDAC Project](https://collab.cels.anl.gov/display/PSIscidac2/Plasma+Surface+Interactions+2) suite of codes, has been developed to fill that gap and expand upon the feature set included in currently available BCA codes. Features unique to RustBCA include the ability to handle attractive-repulsive interatomic potentials, use multiple interatomic potentials in one simulation, handle high-energy incident ions and multiple geometry types, use large file input of incident particles to facilitate coupling to other codes via HDF5, output pre-binned distributions without post-processing of text-based particle lists, and use a human- and machine-readable configuration file. RustBCA has been designed with modern programming techniques, robust error-handling, and multi-threading capability. RustBCA is being developed as both a standalone code and as a library code that may be used to add BCA routines to other high-performance codes to avoid file-based code coupling entirely. Additionally, the TRIM family of codes typically relies on the MAGIC algorithm to approximate the scattering integral with 5 fitting coefficients. RustBCA includes not only an implementation of the MAGIC algorithm, but also Mendenhall-Weller, Gauss-Mehler, and Gauss-Legendre quadrature, the three of which are significantly more accurate than the MAGIC algorithm. We hope that giving users direct access to a user-friendly, flexible, high-performance, open-source BCA will encourage and enable heretofore unexplored research in ion-materials interactions.
 
 ![Figure showing sputtering yields of silicon from SRIM, RustBCA, F-TRIDYN, Yamamura's formula for Q=0.33-0.99, and a smooth analytical fit to experimental data by Wittmaack [@Wittmaack2004], for an incident energy of 1 keV and for many different projectiles.](corrected_yields.png)