Add the JOSS paper (#148)

* Add template for the JOSS paper * Add applications * Update * Update * Update * Add references * Add application * Backup * Add related work * Add material models * Add title * Add logo * Add caption for logo * Update * Update * Fix image * Smaller image * Even smaller image * Smaller image * Image * Add numerical analysis reuslts * Backup * Add statement of need * Add paper draft action * Add correct path * Add dependencies * Add Prashant * Test latex commands * Add equation * Add second equaiton * Fix equaiton * Fix equation * Add equations * spell check * Add time schemes * Add image * Add discrete items * Fix equations * Fix equations * Fix equation * Add PD equation * Add discrete state-based equation * spellcheck * Add numerical analsysis section * update summary * Update paper.md * Update paper.bib * use 'x' and not '\bx' * fix latex err * change author orders * fig size * Update paper.md * use ';' for multiple references * fig size * Update * Update paper.md * Update paper.md * Update paper.md * Add code of conduct anf contribution guide lines * Add GSoC as funding * Update * Update branch * Katies comments * More comments * Update paper.md * Add DOI * Remove duplicates * Remove preprint with pulication * Add DOIs * Fix pibtex * Minor grammar fixes * Move sections * Work on the easy fixes * Update the paper with the editor's comment * Update references * Add missing DOI * Add Katie's comment * Fix Cmake to compile again * Fix build Co-authored-by: Prashant K. Jha <pjha.sci@gmail.com>
nonlocalmodels · Sep 27, 2021 · 449091d · 449091d
1 parent dbee419
commit 449091d
Show file tree

Hide file tree

Showing 6 changed files with 418 additions and 2 deletions.
diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
@@ -0,0 +1,19 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          paper-path: docs/paper.md 
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          path: docs/paper.pdf
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -18,8 +18,6 @@ set (VERSION_UPDATE 0)
 
 cmake_minimum_required(VERSION 3.10)
 
-
-
 # Provide the configuration file to get the version
 configure_file (
   "${PROJECT_SOURCE_DIR}/Config.h.in"

diff --git a/assets/logo/logo_joss.png b/assets/logo/logo_joss.png
diff --git a/docs/discrete.pdf b/docs/discrete.pdf
diff --git a/docs/paper.bib b/docs/paper.bib
@@ -0,0 +1,292 @@
+@article{jha2018numerical,
+	author = {Jha, Prashant K and Lipton, Robert},
+	journal = {SIAM Journal on Numerical Analysis},
+	number = {2},
+	pages = {906--941},
+	publisher = {SIAM},
+	title = {Numerical analysis of nonlocal fracture models in Holder space},
+	volume = {56},
+	year = {2018},
+    doi={10.1137/17m1112236}
+}
+
+@article{geuzaine2009gmsh,
+	author = {Geuzaine, Christophe and Remacle, Jean-Fran{\c c}ois},
+	journal = {International journal for numerical methods in engineering},
+	number = {11},
+	pages = {1309--1331},
+	publisher = {Wiley Online Library},
+	title = {Gmsh: A 3-D finite element mesh generator with built-in pre-and post-processing facilities},
+	volume = {79},
+	year = {2009},
+    doi={10.1002/nme.2579}
+}
+
+@article{jha2019numerical,
+	author = {Jha, Prashant K and Lipton, Robert},
+	journal = {Computer Methods in Applied Mechanics and Engineering},
+	pages = {184--225},
+	publisher = {Elsevier},
+	title = {Numerical convergence of finite difference approximations for state based peridynamic fracture models},
+	volume = {351},
+	year = {2019},
+    doi={10.1016/j.cma.2019.03.024}
+}
+
+@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}
+}
+
+@article{lipton2018free,
+	author = {Lipton, Robert and Said, Eyad and Jha, Prashant},
+	journal = {Journal of Elasticity},
+	number = {2},
+	pages = {129--153},
+	publisher = {Springer},
+	title = {Free damage propagation with memory},
+	volume = {133},
+	year = {2018},
+    doi={10.1007/s10659-018-9672-7}
+}
+
+@article{jha2020kinetic,
+	author = {Jha, Prashant K and Lipton, Robert P},
+	journal = {International Journal of Fracture},
+	pages = {1--15},
+	publisher = {Springer},
+	title = {Kinetic relations and local energy balance for LEFM from a nonlocal peridynamic model},
+	year = {2020},
+    doi={10.1007/s10704-020-00480-0}
+}
+
+@article{littlewood2015roadmap,
+	author = {Littlewood, David J},
+	journal = {SAND Report, Sandia National Laboratories, Albuquerque, NM and Livermore, CA},
+	title = {Roadmap for peridynamic software implementation},
+	year = {2015},
+    doi={10.2172/1226115}
+}
+
+@article{parks2008implementing,
+	author = {Parks, Michael L and Lehoucq, Richard B and Plimpton, Steven J and Silling, Stewart A},
+	journal = {Computer Physics Communications},
+	number = {11},
+	pages = {777--783},
+	publisher = {Elsevier},
+	title = {Implementing peridynamics within a molecular dynamics code},
+	volume = {179},
+	year = {2008},
+    doi={10.1016/j.cpc.2008.06.011}
+}
+
+@article{ren20173d,
+	author = {Ren, Bo and Wu, CT and Askari, E},
+	journal = {International Journal of Impact Engineering},
+	pages = {14--25},
+	publisher = {Elsevier},
+	title = {A 3D discontinuous Galerkin finite element method with the bond-based peridynamics model for dynamic brittle failure analysis},
+	volume = {99},
+	year = {2017},
+    doi={10.1016/j.ijimpeng.2016.09.003}
+}
+
+@article{mossaiby2017opencl,
+	author = {Mossaiby, Farshid and Shojaei, A and Zaccariotto, M and Galvanetto, U},
+	journal = {Computers \& Mathematics with Applications},
+	number = {8},
+	pages = {1856--1870},
+	publisher = {Elsevier},
+	title = {OpenCL implementation of a high performance 3D Peridynamic model on graphics accelerators},
+	volume = {74},
+	year = {2017},
+    doi={10.1016/j.camwa.2017.06.045}
+}
+
+@mastersthesis{diehl2012implementierung,
+	author = {Diehl, Patrick},
+	doi = {10.18419/opus-2879},
+	title = {Implementierung eines Peridynamik-Verfahrens auf GPU},
+	year = {2012}
+}
+
+@incollection{diehl2015efficient,
+	author = {Diehl, Patrick and Schweitzer, Marc Alexander},
+	booktitle = {Meshfree Methods for Partial Differential Equations VII},
+	pages = {81--95},
+	publisher = {Springer},
+	title = {Efficient neighbor search for particle methods on GPUs},
+	year = {2015},
+    doi={10.1007/978-3-319-06898-5_5}
+}
+
+@article{silling2007peridynamic,
+	author = {Silling, Stewart A and Epton, M and Weckner, O and Xu, Ji and Askari},
+	journal = {Journal of Elasticity},
+	number = {2},
+	pages = {151--184},
+	publisher = {Springer},
+	title = {Peridynamic states and constitutive modeling},
+	volume = {88},
+	year = {2007},
+    doi={10.1007/s10659-007-9125-1}
+}
+
+@article{lipton2014dynamic,
+	author = {Lipton, Robert},
+	journal = {Journal of Elasticity},
+	number = {1},
+	pages = {21--50},
+	publisher = {Springer},
+	title = {Dynamic brittle fracture as a small horizon limit of peridynamics},
+	volume = {117},
+	year = {2014},
+    doi={10.1007/s10659-013-9463-0}
+}
+
+@article{lipton2016cohesive,
+	author = {Lipton, Robert},
+	journal = {Journal of Elasticity},
+	number = {2},
+	pages = {143--191},
+	publisher = {Springer},
+	title = {Cohesive dynamics and brittle fracture},
+	volume = {124},
+	year = {2016},
+    doi={10.1007/s10659-015-9564-z}
+}
+
+@article{silling2005meshfree,
+	author = {Silling, Stewart A and Askari, Ebrahim},
+	journal = {Computers \& structures},
+	number = {17-18},
+	pages = {1526--1535},
+	publisher = {Elsevier},
+	title = {A meshfree method based on the peridynamic model of solid mechanics},
+	volume = {83},
+	year = {2005},
+    doi={10.1016/j.compstruc.2004.11.026}
+}
+
+@inbook{Lipton2018,
+	abstract = {We introduce a regularized model for free fracture propagation based on nonlocal potentials. We work within the small deformation setting, and the model is developed within a state-based peridynamic formulation. At each instant of the evolution, we identify the softening zone where strains lie above the strength of the material. We show that deformation discontinuities associated with flaws larger than the length scale of nonlocality $\delta$ can become unstable and grow. An explicit inequality is found that shows that the volume of the softening zone goes to zero linearly with the length scale of nonlocal interaction. This scaling is consistent with the notion that a softening zone of width proportional to $\delta$ converges to a sharp fracture set as the length scale of nonlocal interaction goes to zero. Here the softening zone is interpreted as a regularization of the crack network. Inside quiescent regions with no cracks or softening, the nonlocal operator converges to the local elastic operator at a rate proportional to the radius of nonlocal interaction. This model is designed to be calibrated to measured values of critical energy release rate, shear modulus, and bulk modulus of material samples. For this model one is not restricted to Poisson ratios of 1/4 and can choose the potentials so that small strain behavior is specified by the isotropic elasticity tensor for any material with prescribed shear and Lam{\'e} moduli.},
+	address = {Cham},
+	author = {Lipton, Robert and Said, Eyad and Jha, Prashant K.},
+	booktitle = {Handbook of Nonlocal Continuum Mechanics for Materials and Structures},
+	doi = {10.1007/978-3-319-22977-5_33-1},
+	editor = {Voyiadjis, George Z.},
+	isbn = {978-3-319-22977-5},
+	pages = {1--27},
+	publisher = {Springer International Publishing},
+	title = {Dynamic Brittle Fracture from Nonlocal Double-Well Potentials: A State-Based Model},
+	url = {https://doi.org/10.1007/978-3-319-22977-5_33-1},
+	year = {2018}
+}
+
+@article{Kaiser2020,
+	author = {Kaiser, Hartmut and Diehl, Patrick and Lemoine, Adrian S. and Lelbach, Bryce Adelstein and Amini, Parsa and Berge, Agust{\'\i}n and Biddiscombe, John and Brandt, Steven R. and Gupta, Nikunj and Heller, Thomas and Huck, Kevin and Khatami, Zahra and Kheirkhahan, Alireza and Reverdell, Auriane and Shirzad, Shahrzad and Simberg, Mikael and Wagle, Bibek and Wei, Weile and Zhang, Tianyi},
+	doi = {10.21105/joss.02352},
+	journal = {Journal of Open Source Software},
+	number = {53},
+	pages = {2352},
+	publisher = {The Open Journal},
+	title = {HPX - The C++ Standard Library for Parallelism and Concurrency},
+	url = {https://doi.org/10.21105/joss.02352},
+	volume = {5},
+	year = {2020}
+}
+
+@inproceedings{iglberger2012high,
+	author = {Iglberger, Klaus and Hager, Georg and Treibig, Jan and R{\"u}de, Ulrich},
+	booktitle = {2012 International Conference on High Performance Computing \& Simulation (HPCS)},
+	organization = {IEEE},
+	pages = {367--373},
+	title = {High performance smart expression template math libraries},
+	year = {2012},
+    doi={10.1109/hpcsim.2012.6266939}
+}
+
+@book{schroeder2004visualization,
+	author = {Schroeder, Will J and Lorensen, Bill and Martin, Ken},
+	publisher = {Kitware},
+	title = {The visualization toolkit: an object-oriented approach to 3D graphics},
+	year = {2004}
+}
+
+@article{diehl2019review,
+	author = {Diehl, Patrick and Prudhomme, Serge and L{\'e}vesque, Martin},
+	journal = {Journal of Peridynamics and Nonlocal Modeling},
+	number = {1},
+	pages = {14--35},
+	publisher = {Springer},
+	title = {A review of benchmark experiments for the validation of peridynamics models},
+	volume = {1},
+	year = {2019},
+    doi={10.1007/s42102-018-0004-x}
+}
+
+
+@article{diehl2018implementation,
+  title={An asynchronous and task-based implementation of peridynamics utilizing HPX—the C++ standard library for parallelism and concurrency},
+  author={Diehl, Patrick and Jha, Prashant K and Kaiser, Hartmut and Lipton, Robert and L{\'e}vesque, Martin},
+  journal={SN Applied Sciences},
+  volume={2},
+  number={12},
+  pages={1--21},
+  year={2020},
+  publisher={Springer},
+  doi={10.1007/s42452-020-03784-x}
+}
+
+
+
+@article{Diehl2020,
+	author = {Diehl, Patrick},
+	doi = {10.6084/m9.figshare.12320726.v1},
+	month = {5},
+	title = {EMU-nodal discretization},
+	url = {https://figshare.com/articles/figure/EMU-nodal_discretization/12320726},
+	year = {2020}
+}
+
+
+@article{DBLP:journals/corr/abs-2108-02336,
+  author    = {Matthias Birner and
+               Patrick Diehl and
+               Robert Lipton and
+               Marc Alexander Schweitzer},
+  title     = {A Fracture Multiscale Model for Peridynamic enrichment within the
+               Partition of Unity Method: Part {I}},
+  journal   = {CoRR},
+  volume    = {abs/2108.02336},
+  year      = {2021},
+  url       = {https://arxiv.org/abs/2108.02336},
+  eprinttype = {arXiv},
+  eprint    = {2108.02336},
+  timestamp = {Wed, 11 Aug 2021 15:24:08 +0200},
+  biburl    = {https://dblp.org/rec/journals/corr/abs-2108-02336.bib},
+  bibsource = {dblp computer science bibliography, https://dblp.org}
+}
+
+@misc{bhattacharya2021peridynamics,
+      title={Peridynamics for Quasistatic Fracture Modeling}, 
+      author={Debdeep Bhattacharya and Patrick Diehl and Robert P. Lipton},
+      year={2021},
+      eprint={2107.14665},
+      archivePrefix={arXiv},
+      primaryClass={cond-mat.soft}
+}
+
+@article{diehl2021comparative,
+  title={A comparative review of peridynamics and phase-field models for engineering fracture mechanics},
+  author={Diehl, Patrick and Lipton, Robert and Wick, Thomas and Tyagi, Mayank},
+  publisher={engrXiv},
+  doi={10.31224/osf.io/gty2b}
+}