JOSS review: final refinement

prashjha · prashjha · commit 61ec5d657d0b · 2025-11-25T20:36:52.000-07:00
diff --git a/docs/joss/paper.bib b/docs/joss/paper.bib
@@ -1,23 +1,33 @@
-@article{jha2025nodal,
-  title={Nodal finite element approximation of peridynamics},
-  author={Jha, Prashant K. and Diehl, Patrick and Lipton, Robert},
-  journal={Computer Methods in Applied Mechanics and Engineering},
-  volume={434},
-  pages={117519},
-  year={2025},
-  publisher={Elsevier}
+@article{jha2021peridynamics,
+  author = {Jha, Prashant K. and Desai, Prathamesh S. and Bhattacharya, Debdeep and Lipton, Robert},
+  title = {Peridynamics-based discrete element method (PeriDEM) model of granular systems involving breakage of arbitrarily shaped particles},
+  journal = {Journal of the Mechanics and Physics of Solids},
+  volume = {151},
+  pages = {104376},
+  year = {2021},
+  issn = {0022-5096},
+  doi = {10.1016/j.jmps.2021.104376},
+  url = {https://doi.org/10.1016/j.jmps.2021.104376},
+  keywords = {Peridynamics, Discrete element method, Particle attrition, Particle interlocking, Particle breakage, Granular media, Fracture}
 }
 
-@article{Jha2021, doi = {10.21105/joss.03020}, url = {https://doi.org/10.21105/joss.03020}, year = {2021}, publisher = {The Open Journal}, volume = {6}, number = {65}, pages = {3020}, author = {Jha, Prashant K. and Diehl, Patrick}, title = {NLMech: Implementation of finite difference/meshfree discretization of nonlocal fracture models}, journal = {Journal of Open Source Software} }
+@article{yade2021,
+  title        = {Yade Documentation (3rd edition)},
+  author       = {Smilauer, Vaclav and Angelidakis, Vasileios and Catalano, Emanuele and Caulk, Robert and Chareyre, Bruno and Ch{\ifmmode\grave{e}\else\`{e}\fi}vremont, William and Dorofeenko, Sergei and Duriez, J{\ifmmode\acute{e}\else\'{e}\fi}r{\ifmmode\hat{o}\else\^{o}\fi}me and Dyck, Nolan and Elias, Jan and Er, Burak and Eulitz, Alexander and Gladky, Anton and Guo, Ning and Jakob, Christian and Kneib, Francois and Kozicki, Janek and Marzougui, Donia and Maurin, Raphael and Modenese, Chiara and Pekmezi, Gerald and Scholt{\ifmmode\grave{e}\else\`{e}\fi}s, Luc and Sibille, Luc and Stransky, Jan and Sweijen, Thomas and Thoeni, Klaus and Yuan, Chao},
+  year         = {2021},
+  journal      = {Zenodo},
+  doi          = {10.5281/zenodo.5705394}
+}
 
-@article{dosta2024comparing,
-  title={Comparing open-source DEM frameworks for simulations of common bulk processes},
-  author={Dosta, Maksym and Andr{\'e}, Damien and Angelidakis, Vasileios and Caulk, Robert A and Celigueta, Miguel Angel and Chareyre, Bruno and Dietiker, J-F and Girardot, J and Govender, Nicolin and Hubert, C and others},
-  journal={Computer Physics Communications},
-  volume={296},
-  pages={109066},
-  year={2024},
-  publisher={Elsevier}
+@article{govender2016blaze,
+  title={Blaze-DEMGPU: Modular high performance DEM framework for the GPU architecture},
+  author={Govender, Nicolin and Wilke, Daniel N and Kok, Schalk},
+  journal={SoftwareX},
+  volume={5},
+  pages={62--66},
+  year={2016},
+  publisher={Elsevier},
+  doi={10.1016/j.softx.2016.04.004}
 }
 
 @article{zhang_2024_deme,
@@ -27,30 +37,33 @@ @article{zhang_2024_deme
 pages = {109196},
 year = {2024},
 issn = {0010-4655},
-doi = {https://doi.org/10.1016/j.cpc.2024.109196},
+doi = {10.1016/j.cpc.2024.109196},
 author = {Ruochun Zhang and Bonaventura Tagliafierro and Colin {Vanden Heuvel} and Shlok Sabarwal and Luning Bakke and Yulong Yue and Xin Wei and Radu Serban and Dan Negruţ},
 keywords = {Discrete Element Method, GPU computing, Physics-based simulation, Scientific package, BSD3 open-source},
 }
 
-@article{chen2023mechanical,
-  title={Mechanical behavior and particle crushing of irregular granular material under high pressure using discrete element method},
-  author={Chen, Qinglin and Li, Zugui and Dai, Zeyu and Wang, Xiaojun and Zhang, Chao and Zhang, Xuepeng},
-  journal={Scientific Reports},
-  volume={13},
-  number={1},
-  pages={7843},
-  year={2023},
-  publisher={Nature Publishing Group UK London}
+@article{THOMPSON2022108171,
+title = {LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
+journal = {Computer Physics Communications},
+volume = {271},
+pages = {108171},
+year = {2022},
+issn = {0010-4655},
+doi = {10.1016/j.cpc.2021.108171},
+url = {https://www.sciencedirect.com/science/article/pii/S0010465521002836},
+author = {Aidan P. Thompson and H. Metin Aktulga and Richard Berger and Dan S. Bolintineanu and W. Michael Brown and Paul S. Crozier and Pieter J. {in 't Veld} and Axel Kohlmeyer and Stan G. Moore and Trung Dac Nguyen and Ray Shan and Mark J. Stevens and Julien Tranchida and Christian Trott and Steven J. Plimpton},
+keywords = {Molecular dynamics, Materials modeling, Parallel algorithms, LAMMPS},
 }
 
-@article{harmon2021modeling,
-  title={Modeling connected granular media: Particle bonding within the level set discrete element method},
-  author={Harmon, John M and Karapiperis, Konstantinos and Li, Liuchi and Moreland, Scott and Andrade, Jos{\'e} E},
-  journal={Computer Methods in Applied Mechanics and Engineering},
-  volume={373},
-  pages={113486},
-  year={2021},
-  publisher={Elsevier}
+@article{dosta2024comparing,
+  title={Comparing open-source DEM frameworks for simulations of common bulk processes},
+  author={Dosta, Maksym and Andr{\'e}, Damien and Angelidakis, Vasileios and Caulk, Robert A and Celigueta, Miguel Angel and Chareyre, Bruno and Dietiker, J-F and Girardot, J and Govender, Nicolin and Hubert, C and others},
+  journal={Computer Physics Communications},
+  volume={296},
+  pages={109066},
+  year={2024},
+  publisher={Elsevier},
+  doi={10.1016/j.cpc.2023.109066}
 }
 
 @article{littlewood2024peridigm,
@@ -61,85 +74,65 @@ @article{littlewood2024peridigm
   number={1},
   pages={118--148},
   year={2024},
-  publisher={Springer}
+  publisher={Springer},
+  doi={10.1007/s42102-023-00100-0}
 }
 
-@article{govender2016blaze,
-  title={Blaze-DEMGPU: Modular high performance DEM framework for the GPU architecture},
-  author={Govender, Nicolin and Wilke, Daniel N and Kok, Schalk},
-  journal={SoftwareX},
-  volume={5},
-  pages={62--66},
-  year={2016},
-  publisher={Elsevier}
-}
 
-@article{yade2021,
-  title        = {Yade Documentation (3rd edition)},
-  author       = {Smilauer, Vaclav and Angelidakis, Vasileios and Catalano, Emanuele and Caulk, Robert and Chareyre, Bruno and Ch{\ifmmode\grave{e}\else\`{e}\fi}vremont, William and Dorofeenko, Sergei and Duriez, J{\ifmmode\acute{e}\else\'{e}\fi}r{\ifmmode\hat{o}\else\^{o}\fi}me and Dyck, Nolan and Elias, Jan and Er, Burak and Eulitz, Alexander and Gladky, Anton and Guo, Ning and Jakob, Christian and Kneib, Francois and Kozicki, Janek and Marzougui, Donia and Maurin, Raphael and Modenese, Chiara and Pekmezi, Gerald and Scholt{\ifmmode\grave{e}\else\`{e}\fi}s, Luc and Sibille, Luc and Stransky, Jan and Sweijen, Thomas and Thoeni, Klaus and Yuan, Chao},
-  year         = {2021},
-  journal      = {Zenodo},
-  doi          = {10.5281/zenodo.5705394}
-}
-
-@article{THOMPSON2022108171,
-title = {LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
-journal = {Computer Physics Communications},
-volume = {271},
-pages = {108171},
-year = {2022},
-issn = {0010-4655},
-doi = {https://doi.org/10.1016/j.cpc.2021.108171},
-url = {https://www.sciencedirect.com/science/article/pii/S0010465521002836},
-author = {Aidan P. Thompson and H. Metin Aktulga and Richard Berger and Dan S. Bolintineanu and W. Michael Brown and Paul S. Crozier and Pieter J. {in 't Veld} and Axel Kohlmeyer and Stan G. Moore and Trung Dac Nguyen and Ray Shan and Mark J. Stevens and Julien Tranchida and Christian Trott and Steven J. Plimpton},
-keywords = {Molecular dynamics, Materials modeling, Parallel algorithms, LAMMPS},
+@article{Jha2021NLMech,
+ doi = {10.21105/joss.03020}, 
+ url = {https://doi.org/10.21105/joss.03020}, 
+ year = {2021}, 
+ publisher = {The Open Journal}, 
+ volume = {6}, 
+ number = {65}, 
+ pages = {3020}, 
+ author = {Jha, Prashant K. and Diehl, Patrick}, 
+ title = {NLMech: Implementation of finite difference/meshfree discretization of nonlocal fracture models}, 
+ journal = {Journal of Open Source Software} 
 }
 
-@article{cundall1979discrete,
-  author = {Cundall, P. A. and Strack, O. D. L.},
-  title = {A discrete numerical model for granular assemblies},
-  journal = {Géotechnique},
-  volume = {29},
-  number = {1},
-  pages = {47-65},
-  year = {1979},
-  doi = {10.1680/geot.1979.29.1.47},
-  url = {https://doi.org/10.1680/geot.1979.29.1.47}
+@article{harmon2021modeling,
+  title={Modeling connected granular media: Particle bonding within the level set discrete element method},
+  author={Harmon, John M and Karapiperis, Konstantinos and Li, Liuchi and Moreland, Scott and Andrade, Jos{\'e} E},
+  journal={Computer Methods in Applied Mechanics and Engineering},
+  volume={373},
+  pages={113486},
+  year={2021},
+  publisher={Elsevier},
+  doi={10.1016/j.cma.2020.113486}
 }
 
-@article{jha2021peridynamics,
-  author = {Jha, Prashant K. and Desai, Prathamesh S. and Bhattacharya, Debdeep and Lipton, Robert},
-  title = {Peridynamics-based discrete element method (PeriDEM) model of granular systems involving breakage of arbitrarily shaped particles},
-  journal = {Journal of the Mechanics and Physics of Solids},
-  volume = {151},
-  pages = {104376},
-  year = {2021},
-  issn = {0022-5096},
-  doi = {10.1016/j.jmps.2021.104376},
-  url = {https://doi.org/10.1016/j.jmps.2021.104376},
-  keywords = {Peridynamics, Discrete element method, Particle attrition, Particle interlocking, Particle breakage, Granular media, Fracture}
+@article{chen2023mechanical,
+  title={Mechanical behavior and particle crushing of irregular granular material under high pressure using discrete element method},
+  author={Chen, Qinglin and Li, Zugui and Dai, Zeyu and Wang, Xiaojun and Zhang, Chao and Zhang, Xuepeng},
+  journal={Scientific Reports},
+  volume={13},
+  number={1},
+  pages={7843},
+  year={2023},
+  publisher={Nature Publishing Group UK London},
+  doi={10.1038/s41598-023-35022-w}
 }
 
-@incollection{silling2016introduction,
-  title={Introduction to peridynamics},
-  author={Silling, Stewart A.},
-  booktitle={Handbook of peridynamic modeling},
-  pages={63--98},
-  year={2016},
-  publisher={Chapman and Hall/CRC}
+@article{huang2021taskflow,
+  title={Taskflow: A lightweight parallel and heterogeneous task graph computing system},
+  author={Huang, Tsung-Wei and Lin, Dian-Lun and Lin, Chun-Xun and Lin, Yibo},
+  journal={IEEE Transactions on Parallel and Distributed Systems},
+  volume={33},
+  number={6},
+  pages={1303--1320},
+  year={2021},
+  publisher={IEEE},
+doi = {10.1109/TPDS.2021.3104255},
+url = {https://doi.org/10.1109/TPDS.2021.3104255}
 }
 
-@article{silling2000reformulation,
-  title = {Reformulation of elasticity theory for discontinuities and long-range forces},
-  journal = {Journal of the Mechanics and Physics of Solids},
-  volume = {48},
-  number = {1},
-  pages = {175-209},
-  year = {2000},
-  issn = {0022-5096},
-  doi = {10.1016/S0022-5096(99)00029-0},
-  url = {https://doi.org/10.1016/S0022-5096(99)00029-0},
-  author = {Silling, S. A.}
+@misc{blanco2014nanoflann,
+  title        = {nanoflann: a {C}++ header-only fork of {FLANN}, a library for Nearest Neighbor ({NN}) with KD-trees},
+  author       = {Blanco, Jose Luis and Rai, Pranjal Kumar},
+  howpublished = {\url{https://github.com/jlblancoc/nanoflann}},
+  year         = {2014}
 }
 
 @article{jha2018numerical,
@@ -190,91 +183,13 @@ @article{Jha2020peri
  abstract = {A simple nonlocal field theory of peridynamic type is applied to model brittle fracture. The kinetic relation for the crack tip velocity given by Linear Elastic Fracture Mechanics (LEFM) is recovered directly from the nonlocal dynamics, this is seen both theoretically and in simulations. An explicit formula for the change of internal energy inside a neighborhood enclosing the crack tip is found for the nonlocal model and applied to LEFM.}
 }
 
-@article{lipton2019complex,
- author = {Lipton, Robert P. and Lehoucq, Richard B. and Jha, Prashant K.},
- journal = {Journal of Peridynamics and Nonlocal Modeling},
- number = {2},
- pages = {122--130},
- publisher = {Springer},
- title = {Complex fracture nucleation and evolution with nonlocal elastodynamics},
- volume = {1},
- year = {2019},
-doi = {10.1007/s42102-019-00010-0},
-url = {https://doi.org/10.1007/s42102-019-00010-0}
-}
-
-@article{jha2021finite,
-  title={Finite element approximation of nonlocal dynamic fracture models},
-  author={Jha, Prashant K. and Lipton, R.},
-  journal={Discrete \& Continuous Dynamical Systems-B},
-  volume={26},
-  number={3},
-  pages={1675},
-  year={2021},
-  publisher={American Institute of Mathematical Sciences},
-doi = {10.3934/dcdsb.2020178},
-url = {https://doi.org/10.3934/dcdsb.2020178}
-}
-
-@article{lipton2014dynamic,
-  title={Dynamic brittle fracture as a small horizon limit of peridynamics},
-  author={Lipton, Robert},
-  journal={Journal of Elasticity},
-  volume={117},
-  pages={21--50},
-  year={2014},
-  publisher={Springer},
-doi = {10.1007/s10659-013-9463-0},
-url = {https://doi.org/10.1007/s10659-013-9463-0}
-}
-
-@article{karypis1997metis,
-  title={METIS: A software package for partitioning unstructured graphs, partitioning meshes, and computing fill-reducing orderings of sparse matrices},
-  author={Karypis, George and Kumar, Vipin},
-  year={1997},
-url = {https://hdl.handle.net/11299/215346}
-}
-
-@article{silling2007peridynamic,
-  title={Peridynamic states and constitutive modeling},
-  author={Silling, Stewart A. and Epton, M. and Weckner, Olaf and Xu, Jifeng and Askari, E.},
-  journal={Journal of elasticity},
-  volume={88},
-  pages={151--184},
-  year={2007},
-  publisher={Springer},
-doi = {10.1007/s10659-007-9125-1},
-url = {https://doi.org/10.1007/s10659-007-9125-1}
-}
-
-@article{desai2019rheometry,
-  title={A rheometry based calibration of a first-order DEM model to generate virtual avatars of metal Additive Manufacturing (AM) powders},
-  author={Desai, Prathamesh S. and Mehta, Akash and Dougherty, Patrick SM and Higgs III, C Fred},
-  journal={Powder technology},
-  volume={342},
-  pages={441--456},
-  year={2019},
+@article{jha2025nodal,
+  title={Nodal finite element approximation of peridynamics},
+  author={Jha, Prashant K. and Diehl, Patrick and Lipton, Robert},
+  journal={Computer Methods in Applied Mechanics and Engineering},
+  volume={434},
+  pages={117519},
+  year={2025},
   publisher={Elsevier},
-doi = {10.1016/j.powtec.2018.09.047},
-url = {https://doi.org/10.1016/j.powtec.2018.09.047}
-}
-
-@article{huang2021taskflow,
-  title={Taskflow: A lightweight parallel and heterogeneous task graph computing system},
-  author={Huang, Tsung-Wei and Lin, Dian-Lun and Lin, Chun-Xun and Lin, Yibo},
-  journal={IEEE Transactions on Parallel and Distributed Systems},
-  volume={33},
-  number={6},
-  pages={1303--1320},
-  year={2021},
-  publisher={IEEE},
-doi = {10.1109/TPDS.2021.3104255},
-url = {https://doi.org/10.1109/TPDS.2021.3104255}
-}
-
-@misc{blanco2014nanoflann,
-  title        = {nanoflann: a {C}++ header-only fork of {FLANN}, a library for Nearest Neighbor ({NN}) with KD-trees},
-  author       = {Blanco, Jose Luis and Rai, Pranjal Kumar},
-  howpublished = {\url{https://github.com/jlblancoc/nanoflann}},
-  year         = {2014}
-}
+  doi={10.1016/j.cma.2024.117519}
+}
diff --git a/docs/joss/paper.md b/docs/joss/paper.md
@@ -29,7 +29,7 @@ Implemented in \texttt{C++}, PeriDEM is designed for extensibility and ease of d
 
 # Statement of Need
 
-Granular materials play a central role in many engineered systems, but modeling their behavior under high loading, deformation, and fragmentation remains an open problem. Popular open-source DEM codes such as YADE [@yade2021], BlazeDEM [@govender2016blaze], Chrono DEM-Engine [@zhang_2024_deme], and LAMMPS [@THOMPSON2022108171] are widely used but typically treat particles as rigid, limiting their accuracy in scenarios involving internal deformation and breakage. A recent review by Dosta et al. [@dosta2024comparing] compares several DEM libraries. Meanwhile, peridynamics-based codes such as Peridigm [@littlewood2024peridigm] and NLMech [@Jha2021] are designed to simulate deformation and fracture within a single structure, with limited support for multi-structure simulations. 
+Granular materials play a central role in many engineered systems, but modeling their behavior under high loading, deformation, and fragmentation remains an open problem. Popular open-source DEM codes such as YADE [@yade2021], BlazeDEM [@govender2016blaze], Chrono DEM-Engine [@zhang_2024_deme], and LAMMPS [@THOMPSON2022108171] are widely used but typically treat particles as rigid, limiting their accuracy in scenarios involving internal deformation and breakage. A recent review by Dosta et al. [@dosta2024comparing] compares several DEM libraries. Meanwhile, peridynamics-based codes such as Peridigm [@littlewood2024peridigm] and NLMech [@Jha2021NLMech] are designed to simulate deformation and fracture within a single structure, with limited support for multi-structure simulations. 
 
 PeriDEM fills this gap by integrating state-based peridynamics for intra-particle deformation with DEM-style contact laws for particle interactions. This hybrid approach enables direct simulation of particle fragmentation, stress redistribution, and dynamic failure propagation—capabilities essential for modeling granular compaction, attrition, and crushing.
 
