Merge remote-tracking branch 'jwpeterson/citations' into devel

Author: jwpeterson

doc/citations/maybe.bib

@@ -2,6 +2,58 @@
 % that they actually use libMesh, and we can't check because they are
 % behind a paywall/not on sci-hub.
 
+% Maybe MOOSE
+% Requested full-text on ResearchGate
+@Article{Gorgogianni_2025,
+  author  = {Anna Gorgogianni and Tanguy Ramanantsoavina and Chlo{\'{e}} Arson},
+  title   = {Error propagation from microstructure changes to apparent stiffness in {2D} biphase matrix-inclusion composites},
+  journal = {European Journal of Mechanics - A/Solids},
+  month   = jul # {--} # aug,
+  year    = 2025,
+  volume  = 112,
+  pages   = {105612 (xx pages)},
+  note    = {\url{https://doi.org/10.1016/j.euromechsol.2025.105612}}
+}
+
+% Maybe MOOSE
+% Article is about NEAMS, not clear if related to MOOSE tools.
+% Requested full-text on ResearchGate
+@Article{Merzari_2025,
+  author  = {Elia Merzari and Igor Bolotnov and Nam Dinh and Emilio Baglietto and Annalisa Manera and Dillon Shaver and Yassin Hassan},
+  title   = {{Building a multiscale framework: An overview of the NEAMS thermal-hydraulics integrated research project}},
+  journal = {Nuclear Engineering and Design},
+  month   = mar,
+  year    = 2025,
+  volume  = 433,
+  pages   = {113807 (xx pages)},
+  note    = {\url{https://doi.org/10.1016/j.nucengdes.2024.113807}}
+}
+
+% Maybe MOOSE
+% They might use MOOSE to compare with their own code's performance.
+@Article{Maqbool_2025,
+  author  = {Shahid Maqbool and Byeong-Joo Lee},
+  title   = {{High performance additive manufacturing phase field simulation: Fortran Do Concurrent vs OpenMP}},
+  journal = {Computational Materials Science},
+  month   = apr,
+  year    = 2025,
+  volume  = 252,
+  pages   = {113788 (xx pages)},
+  note    = {\url{https://doi.org/10.1016/j.commatsci.2025.113788}}
+}
+
+% Maybe MOOSE
+% Requested full-text on ResearchGate
+@InCollection{Lubguban_2025,
+  author    = {Arnold A. Lubguban and Arnold C. Alguno and Roberto M. Malaluan and Gerard G. Dumancas},
+  title     = {{Key factors in computational modeling of RPUF}},
+  pages     = {73--100},
+  year      = 2025,
+  publisher = {Springer Nature Singapore},
+  booktitle = {{Computational Thermo-kinetics of Rigid Polyurethane Foams: Theory and Applications}},
+  note      = {\url{https://doi.org/10.1007/978-981-96-2077-7_3}}
+}
+
 % Maybe MOOSE
 % This is a math paper so it seems unlikely they used MOOSE.
 @Article{Makki_2025,

doc/citations/preprints.bib

@@ -1,5 +1,28 @@
 % Preprints
 
+% MOOSE
+% "Cahn-Hilliard Equation ... was solved using finite element method in MOOSE framework ..."
+@Article{Subedi_2025,
+  author  = {Upadesh Subedi and Nele Moelans and Tomasz Ta{\'{n}}ski and Anil Kunwar},
+  title   = {{Foretelling microstructural interface with multi-generational convolutional-LSTM framework}},
+  journal = {Engineering with Computers},
+  month   = mar,
+  year    = 2025,
+  note    = {\url{https://doi.org/10.1007/s00366-025-02117-z}, SSRN Preprint: \url{https://doi.org/10.2139/ssrn.4486852}}
+}
+
+% MOOSE/NIsoS
+% "The simulations use the transient solver ... provided by MOOSE framework..."
+@Article{YYang_2025,
+  author  = {Yangyiwei Yang and Xiangfeng Li and Junlong Ma and Somnath Bharech and Xiandong Zhou and Xiang-Long Peng and Bai-Xiang Xu},
+  title   = {{High-throughput computational homogenization of porous materials produced by selective laser sintering: A diffuse-interface--based workflow}},
+  journal = {Computational Mechanics},
+  month   = mar,
+  year    = 2025,
+  pages   = {xx (18 pages)},
+  note    = {\url{https://doi.org/10.1007/s00466-025-02610-8}}
+}
+
 % MOOSE
 % "The ... (MOOSE) code framework is specifically equipped to generate training samples and create surrogate models using full-order reactor physics models."
 % Select papers from the PHYSOR 2024 special issue

doc/citations/templates.bib

@@ -66,6 +66,7 @@ @Comment{TechReport_Template
   note        = {\url{}}
 }
 
+% Note: InBook does not display the booktitle so I prefer InCollection
 @Comment{InCollection_Template,
   author    = {},
   title     = {{}},

doc/citations/twentyfive.bib

@@ -1,3 +1,82 @@
+% MOOSE
+@Article{Altahhan_2025,
+  author  = {Muhammad Ramzy Altahhan and Nicholas Herring and Sebastian Schunert and Yousry Azmy},
+  title   = {{Development and integration of a tool for physics-based shape and topology optimization in the MOOSE multiphysics simulation framework}},
+  journal = {Progress in Nuclear Energy},
+  month   = mar,
+  year    = 2025,
+  volume  = 181,
+  pages   = {105619 (16 pages)},
+  note    = {\url{https://doi.org/10.1016/j.pnucene.2025.105619}}
+}
+
+% MOOSE/MASTODON
+% "The numerical simulations are conducted using the open-source finite element application MASTODON..."
+@Article{Veeraraghavan_2025,
+  author  = {Swetha Veeraraghavan and Bhavesh Banjare},
+  title   = {A modified domain reduction method for analysing the {3D} seismic response of long tunnels},
+  journal = {Tunnelling and Underground Space Technology},
+  month   = may,
+  year    = 2025,
+  volume  = 159,
+  pages   = {106461 (xx pages)},
+  note    = {\url{https://doi.org/10.1016/j.tust.2025.106461}}
+}
+
+% MOOSE
+@Article{Simon_2025b,
+  author  = {Pierre-Cl{\'{e}}ment A. Simon and Casey T. Icenhour and Gyanender Singh and Alexander D. Lindsay and Chaitanya Bhave and Lin Yang and Adriaan Riet and Yifeng Che and Paul Humrickhouse and Pattrick Calderoni and Masashi Shimada},
+  title   = {{MOOSE-based Tritium Migration Analysis Program, Version 8 (TMAP8) for advanced open-source tritium transport and fuel cycle modeling}},
+  journal = {Fusion Engineering and Design},
+  month   = may,
+  year    = 2025,
+  volume  = 214,
+  pages   = {114874 (23 pages)},
+  note    = {\url{https://doi.org/10.1016/j.fusengdes.2025.114874}}
+}
+
+% IBAMR/libMesh
+% "The IB/FE LV model is implemented with the open-source IBAMR software ..."
+% "IBAMR is ... leveraging functionality provided by ...  libMesh for finite element discretization management."
+@Article{Gao_2025,
+  author  = {Hao Gao and Debao Guan and Pierre-Fr{\'{e}}d{\'{e}}ric Villard},
+  title   = {Assessing left ventricular pump function using an immersed boundary method combined with finite elements},
+  journal = {International Journal of Fluid Engineering},
+  month   = jun,
+  year    = 2025,
+  volume  = 2,
+  number  = 2,
+  pages   = {024302 (14 pages)},
+  note    = {\url{https://doi.org/10.1063/5.0249784}}
+}
+
+% MOOSE
+% "A tightly coupled multiphysics code system is established using the MOOSE framework ..."
+@Article{Yu_2025,
+  author  = {Y. Yu and H. Park and A. Novak and E. Shemon},
+  title   = {High fidelity multiphysics tightly coupled model for a lead cooled fast reactor concept and application to statistical calculation of hot channel factors},
+  journal = {Nuclear Engineering and Design},
+  month   = apr,
+  year    = 2025,
+  volume  = 435,
+  pages   = {113915 (xx pages)},
+  note    = {\url{https://doi.org/10.1016/j.nucengdes.2025.113915}}
+}
+
+% MOOSE
+% "Here, the tensor mechanics module of the highly parallel code MOOSE was used..."
+@Article{Ellis_2025,
+  author  = {W. M. E. Ellis and L. Reali and A. Davis and H. M. Brooks and I. Katramados and A. J. Thornton and R. A. Akers and S. L. Dudarev},
+  title   = {Mechanical model for a full fusion tokamak enabled by supercomputing},
+  journal = {Nuclear Fusion},
+  month   = feb,
+  year    = 2025,
+  volume  = 65,
+  number  = 3,
+  pages   = {036033 (25 pages)},
+  note    = {\url{https://doi.org/10.1088/1741-4326/adb443}, ArXiv e-print: \url{https://arxiv.org/abs/2409.13554}}
+}
+
 % MOOSE
 % "... JAX-CPFEM features high performance through ... GPU acceleration, achieving a 39x speedup ... compared to MOOSE ..."
 @Article{FHu_2025,

doc/citations/twentyfour.bib

@@ -1,3 +1,14 @@
+% MOOSE/Caribou
+% "Caribou is a MOOSE-based health physics and environmental impact code ..."
+@mastersthesis{Sawatzky_thesis,
+  author = {Kevin Sawatzky},
+  school = {University of Ontario Institute of Technology},
+  title  = {Coupled radiation transport and mobile depletion for health physics and environmental impact applications},
+  note   = {\url{https://ontariotechu.scholaris.ca/handle/10155/1799}},
+  month  = apr,
+  year   = 2024
+}
+
 % MOOSE/SAM
 % "The LOF scenario for the ABTR was first analyzed using the 1-D module of the System Analysis Module (SAM)."
 % author:abulawi bayesian optimized deep ensemble
@@ -1068,18 +1079,6 @@ @Article{DTian_2024
   note    = {\url{https://doi.org/10.1016/j.est.2024.113879}}
 }
 
-% MOOSE
-% "Here, the tensor mechanics module of the highly parallel code MOOSE was used..."
-% author:ellis author:reali author:davis author:brooks mechanical model
-@Misc{Ellis_2024,
-  author       = {W. M. E. Ellis and L. Reali and A. Davis and H. M. Brooks and I. Katramados and A. J. Thornton and R. A. Akers and S. L. Dudarev},
-  title        = {Mechanical model for a full fusion tokamak enabled by supercomputing},
-  month        = sep,
-  year         = 2024,
-  howpublished = {ArXiv e-print},
-  note         = {\url{https://arxiv.org/abs/2409.13554}}
-}
-
 % libMesh/IBAMR
 % "A computational framework for parachute inflation is developed ... within the open-source IBAMR library."
 @Article{YHuang_2024,

doc/citations/twentythree.bib

@@ -1651,18 +1651,6 @@ @Article{DeChant_2023b
   note    = {\url{https://doi.org/10.1016/j.cpc.2023.108837}}
 }
 
-% MOOSE
-% "Cahn-Hilliard Equation ... was solved using finite element method in MOOSE framework ..."
-% author:subedi author:moelans foretelling microstructural interface
-@Misc{Subedi_2023,
-  author       = {Upadesh Subedi and Nele Moelans and Tomasz Ta{\'{n}}ski and Anil Kunwar},
-  title        = {{Foretelling microstructural interface with multi-generational convolutional-LSTM framework}},
-  month        = jul,
-  year         = 2023,
-  howpublished = {SSRN Preprint},
-  note         = {\url{https://doi.org/10.2139/ssrn.4486852}}
-}
-
 % MOOSE/KRAKEN
 % "... we have developed our own multiphysics simulation platform, Kraken, built on top of ... (MOOSE) ..."
 @Article{Wandke_2023b,
@@ -2440,7 +2428,7 @@ @Article{Schunert_2023
 % "3D axisymmetric BISON simulations were performed ..."
 % This has a very similar title to Kobayashi_2022b which came out around the same time, but the author list is different.
 % https://link.springer.com/referenceworkentry/10.1007/978-3-030-72322-4_205-1
-@InBook{Kobayashi_2023,
+@InCollection{Kobayashi_2023,
   author    = {Kazuma Kobayashi and Dinesh Kumar and Matthew Bonney and Souvik Chakraborty and Kyle Paaren and Syed Alam},
   title     = {{Uncertainty quantification and sensitivity analysis for digital twin enabling technology for accident tolerant fuel: Application for BISON fuel performance code}},
   pages     = {1--13},

doc/statistics/cloc_libmesh.py

@@ -301,6 +301,7 @@
     '2024-12-04', 977, 233214, # 9b8e371f
 # 2025
     '2025-01-04', 978, 233494, # 5990e6e3
+    '2025-02-04', 978, 233945, # dd45901d
 ]
 
 # Extract the dates from the data array

doc/statistics/github_traffic_plotclones.csv

@@ -3854,4 +3854,11 @@
 2025-Feb-21,97,67
 2025-Feb-22,50,31
 2025-Feb-23,29,24
-2025-Feb-24,53,26
+2025-Feb-24,118,73
+2025-Feb-25,82,71
+2025-Feb-26,127,75
+2025-Feb-27,60,47
+2025-Feb-28,102,72
+2025-Mar-01,62,47
+2025-Mar-02,50,27
+2025-Mar-03,26,20

doc/statistics/github_traffic_plotviews.csv

@@ -4023,4 +4023,11 @@
 2025-Feb-21,81,26
 2025-Feb-22,59,11
 2025-Feb-23,25,10
-2025-Feb-24,70,18
+2025-Feb-24,146,33
+2025-Feb-25,128,39
+2025-Feb-26,221,53
+2025-Feb-27,120,49
+2025-Feb-28,193,42
+2025-Mar-01,69,22
+2025-Mar-02,49,18
+2025-Mar-03,71,19

doc/statistics/libmesh_citations.py

@@ -44,10 +44,10 @@
 '\'19', 134,
 '\'20', 190,
 '\'21', 215,
-'\'22', 239,
+'\'22', 240,
 '\'23', 237,
-'\'24', 243,
-'\'25', 38,
+'\'24', 249,
+'\'25', 60,
     ]
 
 # Parse command line args