Merge pull request #58 from kyleniemeyer/patch-1

makes minor JOSS paper edits

Author: ruohai0925

JOSS_paper/paper.md

@@ -89,19 +89,19 @@ The IAMReX code has undergone considerable development since 2023 and gained a f
 
 # Scholarly effort
 
-IAMReX's scholarly effort lies in its transformation from a standard incompressible flow solver into a unified, high-performance, multi-physics framework for complex interfacial and particulate flows. This is achieved through several key contributions. First, IAMReX introduces a modular architecture that supports distinct and advanced physics modules within a single platform. This includes a sharp-interface model for immiscible two-phase flows using an advanced level set method, complete with conservative advection and mass-preserving reinitialization schemes. Simultaneously, it offers a robust framework for particle-resolved fluid-structure interaction (FSI) by implementing a Diffused Immersed Boundary Method (DIBM). Second, a significant effort was dedicated to developing a comprehensive system for particle-resolved simulations. This system features a DIBM implementation for handling the motion of 6-DOF rigid bodies without requiring mesh conformity. It is further enhanced with a particle-particle collision model using spatial hashing for efficient detection and a repulsive potential model for resolution. Last but not least, IAMReX leverages the GPU acceleration capabilities to ensure efficiency for particle-resolved simulations. All major particle operations, including fluid-solid coupling, force spreading, and collision detection, are designed to be GPU-compatible. A key optimization for memory efficiency involves constraining the Lagrangian markers used for the fluid-particle interface to exist only on the finest grid level.
+IAMReX's scholarly effort lies in its transformation from a standard incompressible flow solver into a unified, high-performance, multi-physics framework for complex interfacial and particulate flows. This is achieved through several key contributions. First, IAMReX introduces a modular architecture that supports distinct and advanced physics modules within a single platform. This includes a sharp-interface model for immiscible two-phase flows using an advanced level set method, complete with conservative advection and mass-preserving reinitialization schemes. Simultaneously, it offers a robust framework for particle-resolved fluid-structure interaction (FSI) by implementing a diffused immersed boundary method (DIBM). Second, a significant effort was dedicated to developing a comprehensive system for particle-resolved simulations. This system features a DIBM implementation for handling the motion of 6-DOF rigid bodies without requiring mesh conformity. It is further enhanced with a particle-particle collision model using spatial hashing for efficient detection and a repulsive potential model for resolution. Last but not least, IAMReX leverages the GPU acceleration capabilities to ensure efficiency for particle-resolved simulations. All major particle operations, including fluid-solid coupling, force spreading, and collision detection, are designed to be GPU-compatible. A key optimization for memory efficiency involves constraining the Lagrangian markers used for the fluid-particle interface to exist only on the finest grid level.
 
 # Relation to previous work
 
-IAMReX is built upon the foundations established in three of our previous publications. The implementation of the level set method is adapted from Zeng et al. [@zeng2022parallel], with a key distinction: IAMReX employs a semi-staggered grid rather than a collocated grid, which strengthens the pressure-velocity coupling during the solution process. Furthermore, the Diffused Immersed Boundary Method is derived from Li et al. [@li2024open]; while the original work was limited to CPU-based parallelism and a basic particle collision model, IAMReX has been tested on GPUs for select cases and is designed to accommodate more advanced collision models. Finally, our approach to optimizing computational efficiency through the Adaptive Mesh Refinement (AMR) technique, particularly the selection of simulation parameters, was informed by the guidance provided in Liu et al. [@liu2025investigate].
+IAMReX is built upon the foundations established in three of our previous publications. The implementation of the level set method is adapted from @zeng2022parallel, with a key distinction: IAMReX employs a semi-staggered grid rather than a collocated grid, which strengthens the pressure-velocity coupling during the solution process. Furthermore, the Diffused Immersed Boundary Method is derived from @li2024open; while the original work was limited to CPU-based parallelism and a basic particle collision model, IAMReX has been tested on GPUs for select cases and is designed to accommodate more advanced collision models. Finally, our approach to optimizing computational efficiency through the adaptive mesh refinement (AMR) technique, particularly the selection of simulation parameters, was informed by the guidance provided by @liu2025investigate.
 
 # Statement of need
 
 IAMReX is suitable for modeling multiphase flow problems and fluid-structure interaction problems. Its level set-based interface capturing technique can be beneficial for researchers studying phenomena such as wind over waves, breaking waves, and simulating the formation and disappearance of bubbles and droplets. Additionally, the immersed boundary method along with the collision models can parallelly resolve large-scale particles and capture their motions. Researchers working on studies of biological particle aggregation, sandstorms, wind erosion of ground surfaces, and seawater erosion of riverbeds are also among the target audience for this software.
 
 # State of the field
 
-We made great efforts to simulate more complex multiphase flows at higher resolution using IAMReX. One effort is to combine the AMR technique with the multidirect forcing immersed boundary method to resolve particles only on the finest-level grid. It significantly reduces the grid requirements for particle-resolved simulations compared with commonly used uniform grid solvers [Incompact3d](https://github.com/xcompact3d/Incompact3d), [CaNS](https://github.com/CaNS-World/CaNS), and [CP3d](https://github.com/GongZheng-Justin/CP3d). Additionally, we utilized a subcycling technique to alleviate the time step constraint on coarser levels. It minimizes the total number of time steps needed for time advancement compared with the non-subcycling technique used in other AMR-related packages, such as [IBAMR](https://github.com/IBAMR/IBAMR.git), [Basilisk](http://basilisk.fr/), and [incflo](https://github.com/AMReX-Fluids/incflo.git).
+We made great efforts to simulate more complex multiphase flows at higher resolution using IAMReX. One effort is to combine the AMR technique with the multidirect forcing immersed boundary method to resolve particles only on the finest-level grid. It significantly reduces the grid requirements for particle-resolved simulations compared with commonly used uniform grid solvers like [Incompact3d](https://github.com/xcompact3d/Incompact3d), [CaNS](https://github.com/CaNS-World/CaNS), and [CP3d](https://github.com/GongZheng-Justin/CP3d). Additionally, we utilized a subcycling technique to alleviate the time step constraint on coarser levels. It minimizes the total number of time steps needed for time advancement compared with the non-subcycling technique used in other AMR-related packages, such as [IBAMR](https://github.com/IBAMR/IBAMR.git), [Basilisk](http://basilisk.fr/), and [incflo](https://github.com/AMReX-Fluids/incflo.git).
 
 # Acknowledgements