Merge pull request #6166 from gassmoeller/update_citation_info

Update citation info on website 1

benchmarks/entropy_adiabat/README.md

@@ -6,3 +6,5 @@ contains a technical benchmark for the entropy advection method.
 The model setup is described in `entropy_adiabat.prm` and requires the shared
 libraries in the `plugins/` directory. In particular it requires a material
 model (`plugins/entropy_model.cc/h`) that is formulated using pressure and entropy as independent variables, a different assembler that assembles the entropy equation (`plugins/entropy_advection.cc/h`) and a different way to compute the adiabatic background profile (`plugins/compute_entropy_profile.cc/h`).
+
+The benchmark and its results are described in {cite:t}`dannberg:etal:2022`. Please remember to cite this paper when using the entropy advection method.

doc/make_cite_html.py

@@ -73,7 +73,12 @@
                "fraters_menno_2020_3900603" : "GWB",
                "Fraters2019c" : "GWB",
                "fraters:etal:2019" : "NewtonSolver",
-               "fraters_billen_2021_cpo" : "CPO"
+               "fraters_billen_2021_cpo" : "CPO",
+               "dannberg:etal:2022" : "entropy",
+               "dannberg:grain:size" : "grainsize",
+               "dannberg:etal:2021" : "boukaremelt",
+               "neuharth:etal:2022" : "fastscape",
+               "dannberg:gassmoeller:etal:2024" : "cbfheatflux"
 }
 
 want = []
@@ -106,7 +111,12 @@
         "gassmoller:etal:2020" : "Rene Gassmöller, Juliane Dannberg, Wolfgang Bangerth, Timo Heister, and Robert Myhill. 2020. “On Formulations of Compressible Mantle Convection.” Geophysical Journal International 221 (2) (February 13): 1264–1280. doi:10.1093/gji/ggaa078. http://dx.doi.org/10.1093/gji/ggaa078.",
         "heister:etal:2017" : "Timo Heister, Juliane Dannberg, Rene Gassmöller, and Wolfgang Bangerth. 2017. “High Accuracy Mantle Convection Simulation through Modern Numerical Methods – II: Realistic Models and Problems.” Geophysical Journal International 210 (2) (May 9): 833–851. doi:10.1093/gji/ggx195. http://dx.doi.org/10.1093/gji/ggx195.",
         "rose_freesurface" : "Ian Rose, Bruce Buffett, and Timo Heister. 2017. “Stability and Accuracy of Free Surface Time Integration in Viscous Flows.” Physics of the Earth and Planetary Interiors 262 (January): 90–100. doi:10.1016/j.pepi.2016.11.007. http://dx.doi.org/10.1016/j.pepi.2016.11.007.",
-        "fraters_billen_2021_cpo" : "Fraters, M. R. T. and Billen, M. I. 2021. “On the Implementation and Usability of Crystal Preferred Orientation Evolution in Geodynamic Modeling” Geochemistry, Geophysics, Geosystems 22 (10): e2021GC009846. doi:10.1029/2021GC009846. https://doi.org/10.1029/2021GC009846."
+        "fraters_billen_2021_cpo" : "Fraters, M. R. T. and Billen, M. I. 2021. “On the Implementation and Usability of Crystal Preferred Orientation Evolution in Geodynamic Modeling” Geochemistry, Geophysics, Geosystems 22 (10): e2021GC009846. doi:10.1029/2021GC009846. https://doi.org/10.1029/2021GC009846.",
+        "dannberg:etal:2022" : "Dannberg, J., Gassmöller, R., Li, R., Lithgow-Bertelloni, C. and Stixrude, L. 2022. An entropy method for geodynamic modelling of phase transitions: capturing sharp and broad transitions in a multiphase assemblage. Geophysical Journal International, 231(3), pp.1833-1849. doi:10.1093/gji/ggac293. https://doi.org/10.1093/gji/ggac293.",
+        "dannberg:grain:size" : "Dannberg, J., Eilon, Z., Faul, U., Gassmöller, R., Moulik, P. and Myhill, R. 2017. The importance of grain size to mantle dynamics and seismological observations. Geochemistry, Geophysics, Geosystems, 18(8), pp.3034-3061. doi:10.1002/2017GC006944. https://doi.org/10.1002/2017GC006944.",
+        "dannberg:etal:2021" : "Dannberg, J., Myhill, R., Gassmöller, R. and Cottaar, S., 2021. The morphology, evolution and seismic visibility of partial melt at the core–mantle boundary: implications for ULVZs. Geophysical Journal International, 227(2), pp.1028-1059.",
+        "neuharth:etal:2022" : "Neuharth, D., Brune, S., Wrona, T., Glerum, A., Braun, J. and Yuan, X. 2022. Evolution of rift systems and their fault networks in response to surface processes. Tectonics, 41(3), e2021TC007166. doi:10.1029/2021TC007166. https://doi.org/10.1029/2021TC007166.",
+        "dannberg:gassmoeller:etal:2024" : "Dannberg, J., Gassmöller, R., Thallner, D., LaCombe, F. and Sprain, C. 2024. Changes in core–mantle boundary heat flux patterns throughout the supercontinent cycle. Geophysical Journal International, 237(3), pp.1251-1274. doi:10.1093/gji/ggae075. https://doi.org/10.1093/gji/ggae075."
 }
 
 

doc/manual/citing_aspect.bib

@@ -161,6 +161,21 @@ @article{Dannberg2017
 journal = {Geochemistry,  Geophysics,  Geosystems}
 }
 
+@article{dannberg2021morphology,
+    author = {Dannberg, Juliane and Myhill, Robert and Gassmöller, Rene and Cottaar, Sanne},
+    title = {The morphology, evolution and seismic visibility of partial melt at the core–mantle boundary: implications for ULVZs},
+    journal = {Geophysical Journal International},
+    volume = {227},
+    number = {2},
+    pages = {1028-1059},
+    year = {2021},
+    month = {06},
+    issn = {0956-540X},
+    doi = {10.1093/gji/ggab242},
+    url = {https://doi.org/10.1093/gji/ggab242},
+    eprint = {https://academic.oup.com/gji/article-pdf/227/2/1028/39556563/ggab242.pdf},
+}
+
 @Article{Heister2017,
 author  = {Heister, Timo and Dannberg, Juliane and Gassm{\"{o}}ller, Rene and Bangerth, Wolfgang},
 journal = {Geophysical Journal International},
@@ -309,6 +324,21 @@ @Article{Dannberg2018
 publisher = {National Acad Sciences},
 }
 
+@article{dannberg:etal:2022,
+author = {Dannberg, Juliane and Gassmöller, Rene and Li, Ranpeng and Lithgow-Bertelloni, Carolina and Stixrude, Lars},
+title = {An entropy method for geodynamic modelling of phase transitions: capturing sharp and broad transitions in a multiphase assemblage},
+journal = {Geophysical Journal International},
+volume = {231},
+number = {3},
+pages = {1833-1849},
+year = {2022},
+month = {07},
+issn = {0956-540X},
+doi = {10.1093/gji/ggac293},
+url = {https://doi.org/10.1093/gji/ggac293},
+eprint = {https://academic.oup.com/gji/article-pdf/231/3/1833/46842522/ggac293.pdf},
+}
+
 @article{vanderwiel2024,
 title={Quantifying mantle mixing through configurational Entropy},
 author={van der Wiel, Erik and Thieulot, Cedric and van Hinsbergen, Douwe JJ},

doc/sphinx/references.bib

@@ -11986,6 +11986,21 @@ @article{Liu2019
   journal = {Geophysical Journal International}
 }
 
+@article{dannberg:gassmoeller:etal:2024,
+author = {Dannberg, Juliane and Gassmöller, Rene and Thallner, Daniele and LaCombe, Frederick and Sprain, Courtney},
+title = "{Changes in core-mantle boundary heat flux patterns throughout the supercontinent cycle}",
+journal = {Geophysical Journal International},
+volume = {237},
+number = {3},
+pages = {1251-1274},
+year = {2024},
+month = {02},
+issn = {0956-540X},
+doi = {10.1093/gji/ggae075},
+url = {https://doi.org/10.1093/gji/ggae075},
+eprint = {https://academic.oup.com/gji/article-pdf/237/3/1251/57214885/ggae075.pdf}
+}
+
 @Article{Fraters2019c,
 AUTHOR = {Fraters, M. and Thieulot, C. and van den Berg, A. and Spakman, W.},
 TITLE = {The Geodynamic World Builder: a solution for complex initial conditions in numerical modeling},
@@ -12154,7 +12169,25 @@ @article{dannberg:grain:size
   number={8},
   pages={3034--3061},
   year={2017},
-  publisher={Wiley Online Library}
+  publisher={Wiley Online Library},
+  doi = {https://doi.org/10.1002/2017GC006944},
+  url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1002/2017GC006944},
+  eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1002/2017GC006944}
+}
+
+@article{dannberg:etal:2021,
+    author = {Dannberg, Juliane and Myhill, Robert and Gassmöller, René and Cottaar, Sanne},
+    title = {The morphology, evolution and seismic visibility of partial melt at the core–mantle boundary: implications for ULVZs},
+    journal = {Geophysical Journal International},
+    volume = {227},
+    number = {2},
+    pages = {1028-1059},
+    year = {2021},
+    month = {06},
+    issn = {0956-540X},
+    doi = {10.1093/gji/ggab242},
+    url = {https://doi.org/10.1093/gji/ggab242},
+    eprint = {https://academic.oup.com/gji/article-pdf/227/2/1028/39556563/ggab242.pdf},
 }
 
 @article{simmons:etal:2019,
@@ -12264,7 +12297,7 @@ @article{macdonald_fyfe_1985
 year = {1985}
 }
 
- @article{Dannberg:Sobolev:2015, 
+@article{Dannberg:Sobolev:2015, 
    title={Low-buoyancy thermochemical plumes resolve controversy of classical mantle plume concept}, 
    author={Dannberg, Juliane and Sobolev, Stephan V.}, 
    year={2015},
@@ -12273,7 +12306,23 @@ @article{Dannberg:Sobolev:2015
    number={11}, 
    journal={Nature Communications}, 
    publisher={Nature Publishing Group}, 
-   pages={6960} }
+   pages={6960}
+}
+
+@article{dannberg:etal:2022,
+author = {Dannberg, Juliane and Gassmöller, Rene and Li, Ranpeng and Lithgow-Bertelloni, Carolina and Stixrude, Lars},
+title = {An entropy method for geodynamic modelling of phase transitions: capturing sharp and broad transitions in a multiphase assemblage},
+journal = {Geophysical Journal International},
+volume = {231},
+number = {3},
+pages = {1833-1849},
+year = {2022},
+month = {07},
+issn = {0956-540X},
+doi = {10.1093/gji/ggac293},
+url = {https://doi.org/10.1093/gji/ggac293},
+eprint = {https://academic.oup.com/gji/article-pdf/231/3/1833/46842522/ggac293.pdf},
+}
 
 @article{stixrude:Lithgow:2022,
   title={Thermal expansivity, heat capacity and bulk modulus of the mantle},
@@ -12318,3 +12367,18 @@ @article{spiegelman:etal:2016
   year={2016},
   publisher={Wiley Online Library}
 }
+
+@article{neuharth:etal:2022,
+author = {Neuharth, Derek and Brune, Sascha and Wrona, Thilo and Glerum, Anne and Braun, Jean and Yuan, Xiaoping},
+title = {Evolution of Rift Systems and Their Fault Networks in Response to Surface Processes},
+journal = {Tectonics},
+volume = {41},
+number = {3},
+pages = {e2021TC007166},
+keywords = {rifts, fault network, surface processes, geodynamics},
+doi = {https://doi.org/10.1029/2021TC007166},
+url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2021TC007166},
+eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2021TC007166},
+note = {e2021TC007166 2021TC007166},
+year = {2022}
+}

include/aspect/global.h

@@ -23,6 +23,7 @@
 #define _aspect_global_h
 
 #include <aspect/config.h>
+#include <aspect/citation_info.h>
 
 #include <deal.II/base/mpi.h>
 

include/aspect/postprocess/heat_flux_densities.h

@@ -41,6 +41,12 @@ namespace aspect
     class HeatFluxDensities : public Interface<dim>, public ::aspect::SimulatorAccess<dim>
     {
       public:
+        /**
+         * Initialize the postprocessor.
+         */
+        void
+        initialize() override;
+
         /**
          * Evaluate.
          */

include/aspect/postprocess/heat_flux_map.h

@@ -41,6 +41,13 @@ namespace aspect
        * The consistent Galerkin FEM for computing derived boundary quantities in thermal and or fluids
        * problems. International Journal for Numerical Methods in Fluids, 7(4), 371-394.
        *
+       * The implementation of the method is benchmarked in
+       *
+       * Juliane Dannberg, Rene Gassmöller, Daniele Thallner, Frederick LaCombe, Courtney Sprain (2024).
+       * Changes in core–mantle boundary heat flux patterns throughout the supercontinent cycle,
+       * Geophysical Journal International, Volume 237, Issue 3, June 2024, Pages 1251–1274,
+       * https://doi.org/10.1093/gji/ggae075.
+       *
        * In summary, the method solves the temperature equation again on the boundary faces, with known
        * temperatures and solving for the boundary fluxes that satisfy the equation. Since the
        * equation is only formed on the faces and it can be solved using only diagonal matrices,
@@ -83,6 +90,12 @@ namespace aspect
     class HeatFluxMap : public Interface<dim>, public ::aspect::SimulatorAccess<dim>
     {
       public:
+        /**
+         * Initialize the postprocessor.
+         */
+        void
+        initialize() override;
+
         /**
          * Evaluate the solution for the heat flux.
          */

include/aspect/postprocess/heat_flux_statistics.h

@@ -40,6 +40,12 @@ namespace aspect
     class HeatFluxStatistics : public Interface<dim>, public ::aspect::SimulatorAccess<dim>
     {
       public:
+        /**
+         * Initialize the postprocessor.
+         */
+        void
+        initialize() override;
+
         /**
          * Evaluate the solution for some heat_flux statistics.
          */

include/aspect/postprocess/visualization/heat_flux_map.h

@@ -44,8 +44,17 @@ namespace aspect
           public Interface<dim>
       {
         public:
+          /**
+           * Constructor.
+           */
           HeatFluxMap();
 
+          /**
+           * Initialize the postprocessor.
+           */
+          void
+          initialize() override;
+
           /**
            * Fill the temporary storage variables with the
            * heat flux for the current time step.

source/initial_composition/world_builder.cc

@@ -23,7 +23,6 @@
 #ifdef ASPECT_WITH_WORLD_BUILDER
 #include <aspect/initial_composition/world_builder.h>
 #include <aspect/geometry_model/interface.h>
-#include <aspect/citation_info.h>
 
 #include <world_builder/world.h>
 

source/initial_temperature/world_builder.cc

@@ -25,7 +25,6 @@
 #include <aspect/initial_temperature/world_builder.h>
 #include <aspect/geometry_model/interface.h>
 #include <aspect/gravity_model/interface.h>
-#include <aspect/citation_info.h>
 
 #include <world_builder/world.h>
 

source/material_model/entropy_model.cc

@@ -71,6 +71,8 @@ namespace aspect
     void
     EntropyModel<dim>::initialize()
     {
+      CitationInfo::add("entropy");
+
       AssertThrow (this->get_parameters().formulation_mass_conservation ==
                    Parameters<dim>::Formulation::MassConservation::projected_density_field,
                    ExcMessage("The 'entropy model' material model was only tested with the "

source/material_model/grain_size.cc

@@ -83,6 +83,8 @@ namespace aspect
     void
     GrainSize<dim>::initialize()
     {
+      CitationInfo::add("grainsize");
+
       n_material_data = material_file_names.size();
       for (unsigned i = 0; i < n_material_data; ++i)
         {

source/material_model/melt_boukare.cc

@@ -71,6 +71,8 @@ namespace aspect
     void
     MeltBoukare<dim>::initialize()
     {
+      CitationInfo::add("boukaremelt");
+
       // Compute parameters for the modified Tait equation of state for the different endmembers
       // derived from the isothermal bulk modulus and its two first pressure derivatives.
       // This corresponds to Equation 4 from Holland and Powell, 2011 (https://doi.org/10.1111/j.1525-1314.2010.00923.x).

source/material_model/reaction_model/grain_size_evolution.cc

@@ -85,6 +85,8 @@ namespace aspect
       void
       GrainSizeEvolution<dim>::initialize_phase_function(std::shared_ptr<MaterialUtilities::PhaseFunction<dim>> &phase_function_)
       {
+        CitationInfo::add("grainsize");
+
         phase_function = phase_function_;
         n_phase_transitions = phase_function->n_phases_for_each_composition()[0] - 1;
       }

source/mesh_deformation/fastscape.cc

@@ -191,6 +191,8 @@ namespace aspect
     void
     FastScape<dim>::initialize ()
     {
+      CitationInfo::add("fastscape");
+
       AssertThrow(Plugins::plugin_type_matches<const GeometryModel::Box<dim>>(this->get_geometry_model()),
                   ExcMessage("FastScape can only be run with a box geometry model."));
 

source/particle/manager.cc

@@ -21,7 +21,6 @@
 #include <aspect/particle/manager.h>
 #include <aspect/global.h>
 #include <aspect/utilities.h>
-#include <aspect/citation_info.h>
 #include <aspect/simulator.h>
 #include <aspect/melt.h>
 

source/particle/property/crystal_preferred_orientation.cc

@@ -20,7 +20,6 @@
 
 #include <aspect/particle/property/crystal_preferred_orientation.h>
 #include <aspect/geometry_model/interface.h>
-#include <aspect/citation_info.h>
 #include <aspect/utilities.h>
 
 #include <world_builder/grains.h>

source/particle/property/grain_size.cc

@@ -41,6 +41,8 @@ namespace aspect
       void
       GrainSize<dim>::initialize ()
       {
+        CitationInfo::add("grainsize");
+
         material_inputs  = MaterialModel::MaterialModelInputs<dim>(1, this->n_compositional_fields());
         material_outputs = MaterialModel::MaterialModelOutputs<dim>(1, this->n_compositional_fields());
 

source/postprocess/dynamic_topography.cc

@@ -505,6 +505,8 @@ namespace aspect
     void
     DynamicTopography<dim>::parse_parameters (ParameterHandler &prm)
     {
+      CitationInfo::add("geoid");
+
       prm.enter_subsection("Postprocess");
       {
         prm.enter_subsection("Dynamic topography");

source/postprocess/geoid.cc

@@ -30,8 +30,6 @@
 #include <deal.II/base/quadrature_lib.h>
 #include <deal.II/fe/fe_values.h>
 
-#include <aspect/citation_info.h>
-
 
 namespace aspect
 {

source/postprocess/heat_flux_densities.cc

@@ -33,6 +33,15 @@ namespace aspect
 {
   namespace Postprocess
   {
+    template <int dim>
+    void
+    HeatFluxDensities<dim>::initialize ()
+    {
+      CitationInfo::add("cbfheatflux");
+    }
+
+
+
     template <int dim>
     std::pair<std::string,std::string>
     HeatFluxDensities<dim>::execute (TableHandler &statistics)

source/postprocess/heat_flux_map.cc

@@ -452,6 +452,13 @@ namespace aspect
       }
     }
 
+    template <int dim>
+    void
+    HeatFluxMap<dim>::initialize ()
+    {
+      CitationInfo::add("cbfheatflux");
+    }
+
 
 
     template <int dim>