Merge commit 'f3281b817e8e95739db6be8e8c3ac9ac8f75c075'

paper/paper.bib

@@ -1,18 +1,54 @@
-@online{moose,
-  author = {Gaston, Derek R. and Permann, Cody J. and Peterson, John W. and
-                  Slaughter, Andrew E. and Andrš, David and Wang, Yaqi and
-                  Short, Michael P. and Perez, Danielle M. and Tonks, Michael
-                  R. and Ortensi, Javier and Zou, Ling and Martineau, Richard
-                  C.},
-  title = {MOOSE: Multiphysics Object Oriented Simulation
-                  Environment},
-  url = {https://github.com/idaholab/moose}
+@article{moose,
+	series = {Multi-{Physics} {Modelling} of {LWR} {Static} and {Transient} {Behaviour}},
+	title = {Physics-based multiscale coupling for full core nuclear reactor simulation},
+	volume = {84},
+	issn = {0306-4549},
+	url = {http://www.sciencedirect.com/science/article/pii/S030645491400543X},
+	doi = {10.1016/j.anucene.2014.09.060},
+	abstract = {Numerical simulation of nuclear reactors is a key technology in the quest for improvements in efficiency, safety, and reliability of both existing and future reactor designs. Historically, simulation of an entire reactor was accomplished by linking together multiple existing codes that each simulated a subset of the relevant multiphysics phenomena. Recent advances in the MOOSE (Multiphysics Object Oriented Simulation Environment) framework have enabled a new approach: multiple domain-specific applications, all built on the same software framework, are efficiently linked to create a cohesive application. This is accomplished with a flexible coupling capability that allows for a variety of different data exchanges to occur simultaneously on high performance parallel computational hardware. Examples based on the KAIST-3A benchmark core, as well as a simplified Westinghouse AP-1000 configuration, demonstrate the power of this new framework for tackling{\textemdash}in a coupled, multiscale manner{\textemdash}crucial reactor phenomena such as CRUD-induced power shift and fuel shuffle.},
+	urldate = {2017-04-10},
+	journal = {Annals of Nuclear Energy},
+	author = {Gaston, Derek R. and Permann, Cody J. and Peterson, John W. and Slaughter, Andrew E. and Andr{\v s}, David and Wang, Yaqi and Short, Michael P. and Perez, Danielle M. and Tonks, Michael R. and Ortensi, Javier and Zou, Ling and Martineau, Richard C.},
+	month = oct,
+	year = {2015},
+	keywords = {Multiphysics, Full core reactor simulation, Multiphysics coupling},
+	pages = {45--54},
+	file = {ScienceDirect Full Text PDF:/home/huff/Zotero/storage/SGQXWGJV/Gaston et al. - 2015 - Physics-based multiscale coupling for full core nu.pdf:application/pdf;ScienceDirect Snapshot:/home/huff/Zotero/storage/PI8FZ93W/S030645491400543X.html:text/html}
 }
 
 @online{moltres,
-  author = {Alexander Lindsay and Kathryn Huff},
-  title = {Moltres: Open Source Simulation of Molten Salt Reactors},
-  url = {https://github.com/arfc/moltres},
-  doi = {10.5281/zenodo.801822},
-  year = 2016
-}
+  author = {Lindsay, Alexander and Ridley, Gavin, and Rykhlevskii, Andrei, and
+                  Huff, Kathryn},
+  title = {Introduction to Moltres: an Application for Simulation of Molten Salt
+                  Reactors},
+  journaltitle = {Annals of Nuclear Energy},
+  note = {Accepted for publication},
+  year = {2017}
+}
+
+ @TechReport{petsc,
+            author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Jed Brown and Peter Brune
+                      and Kris Buschelman and Lisandro Dalcin and Victor Eijkhout and William~D. Gropp
+                      and Dinesh Kaushik and Matthew~G. Knepley and Dave~A. May
+                      and Lois Curfman McInnes and Karl Rupp and Patrick Sanan and
+                      Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang},
+            title  = {{PETS}c Users Manual},
+            institution = {Argonne National Laboratory},
+            year   = 2017,
+            number = {ANL-95/11 - Revision 3.8},
+            url    = {http://www.mcs.anl.gov/petsc}
+          }
+
+@article{kophazi_development_2009,
+	title = {Development of a {Three}-{Dimensional} {Time}-{Dependent} {Calculation} {Scheme} for {Molten} {Salt} {Reactors} and {Validation} of the {Measurement} {Data} of the {Molten} {Salt} {Reactor} {Experiment}},
+	volume = {163},
+	abstract = {This paper presents the development, validation, and results of a three-dimensional, time- dependent, coupled-neutronics{\textendash}thermal-hydraulic calculational scheme for channel-type molten salt re- actors (MSRs). The reactor physics part is based on diffusion theory, extended by a term representing the flow of the fuel through the core. The calculation of the temperature field is done by modeling all fuel channels, which are coupled to each other by a three-dimensional heat conduction equation. For the purpose of validation, the results of the MSR Experiment (MSRE) natural-circulation experiment and the thermal feedback coefficients of the reactor have been calculated and compared.
+With the aid of a code system developed to implement this scheme, calculations were carried out for the normal operating state of the MSRE and some debris-induced channel-blocking-incident transients. In the case of the MSRE, it is shown that the severity of such an incident strongly depends on the degree of channel blocking and that high-temperature gradients in the moderator can connect thermally the adjacent fuel channels. Results are included for an unblocking transient (i.e., the debris suddenly exits the core, and the fuel flow reverts to the normal operating pattern), and it was demonstrated that during the unblocking large power peaks can be induced.},
+	number = {2},
+	journal = {Nuclear Science and Engineering},
+	author = {K{\'o}ph{\'a}zi, J. and Lathouwers, D. and Kloosterman, J.L.},
+	year = {2009},
+	keywords = {3D, unread, Molten Salt Reactor (MSR), Core, MSR Experiment (MSRE), Reactor Physics},
+	pages = {118--131},
+	file = {K{\'o}ph{\'a}zi et al. - Development of a Three-Dimensional Time-Dependent .pdf:/home/huff/Zotero/storage/ZIJ5Q643/K{\'o}ph{\'a}zi et al. - Development of a Three-Dimensional Time-Dependent .pdf:application/pdf}
+}

paper/paper.md

@@ -20,15 +20,39 @@ bibliography: paper.bib
 
 # Summary
 
-Moltres [@moltres] is a physics application for multiphysics modeling of fluid-fuelled
-molten salt reactors (MSRs). It couples equations for neutron diffusion, thermal
+Moltres is a physics application for multiphysics modeling of fluid-fueled
+molten salt reactors (MSRs) [@moltres]. It couples equations for neutron diffusion, thermal
 hydraulics, and delayed neutron precursor transport. Neutron diffusion and
 precursor transport equations are set-up using an action system that allows the
 user to use an arbitrary number of neutron energy and precursor groups
 respectively with minimal input changes. Moltres sits on top of the
 Multi-physics Object-Oriented Simulation Environment
-[@moose] which gives it the capability to run seamlessly in
-massively parallel environments. To date Moltres has been used to simulate MSRs
-in 2D-axisymmetric and 3D geometric configurations.
+[@moose] and hence uses the finite element method to discretize the governing
+partial differential equations. In general the resulting system of non-linear
+algebraic equations is linearized using the Newton-Raphson method and then
+solved using the Portable, Extensible Toolkit for Scientific Computation
+[@petsc]. Assembly of the Jacobian and residual, and the linear solve are
+parallelized using MPI which allows Moltres to be run in
+massively parallel environments. Runs on the Blue Waters supercomputer at
+Illinois have utilized up to 608 cores.
+
+Moltres and MOOSE allow use of different basis functions for different system
+variables. Because of the purely diffusive nature of the neutron diffusion
+equations, neutron fluxes are typically discretized using continuous
+first-degree Lagrange polynomials and the degrees of freedom are associated with
+mesh nodes. The temperature variable may also be
+discretized with a continuous Lagrange basis, or a discontinuous basis of
+arbitrary degree monomials may be employed depending on the relative balance of
+heat convection to conduction. The purely hyperbolic precursor transport is
+currently discretized using constant monomials, which is equivalent to a first-order
+finite volume discretization. Moltres supports both segregated (through Picard
+iteration) and monolithic
+solutions of the equation system. However, due to the feedback between the
+power spectrum and temperature dependence of macroscopic cross-sections,
+monolithic solves have demonstrated superior robustness with segregated
+techniques often unable to converge to a solution. This result emphasizes the
+importance of a fully coupled multi-physics framework like the one that Moltres and MOOSE
+provide and suggests that iteratively coupling codes devoted to single physics
+[@kophazi_development_2009] may result in limited flexibility.
 
 # References