Merge branch 'development' into common_integrators

networks/ignition_simple/actual_network.H

@@ -151,8 +151,8 @@ namespace RHS
 
     template<int rate>
     AMREX_GPU_HOST_DEVICE AMREX_INLINE
-    void postprocess_rate (const rhs_state_t& state, rate_t& rates,
-                           rate_t& rates1, [[maybe_unused]] rate_t& rates2, [[maybe_unused]] rate_t& rates3)
+    void postprocess_rate ([[maybe_unused]] const rhs_state_t& state, [[maybe_unused]] rate_t& rates,
+                           [[maybe_unused]] rate_t& rates1, [[maybe_unused]] rate_t& rates2, [[maybe_unused]] rate_t& rates3)
     {
         using namespace Species;
         using namespace Rates;

sphinx_docs/source/conf.py

@@ -219,6 +219,12 @@ def get_version():
 ]
 
 
+# -- Options for linkcheck
+
+linkcheck_retries = 3
+linkcheck_timeout = 100
+user_agent = "Mozilla/5.0 (X11; Linux x86_64; rv:25.0) Gecko/20100101 Firefox/25.0"
+
 # -- Options for Texinfo output -------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples

sphinx_docs/source/refs.bib

@@ -507,7 +507,6 @@ @article{mott_qss
         year = {2000},
         issn = {0021-9991},
         doi = {https://doi.org/10.1006/jcph.2000.6605},
-        url = {https://www.sciencedirect.com/science/article/pii/S0021999100966051},
         author = {David R. Mott and Elaine S. Oran and Bram {van Leer}},
         abstract = {A quasi-steady-state method is presented that integrates stiff differential equations arising from reaction kinetics. This predictor–corrector method is A-stable for linear equations and second-order accurate. The method is used for all species regardless of the time scales of the individual equations, and it works well for problems typical of hydrocarbon combustion. Start-up costs are low, making the method ideal for use in process-split reacting-flow simulations which require the solution of an initial-value problem in every computational cell for every global time step. The algorithm is described, and error analysis and linear stability analysis are included. The algorithm is also applied to several test problems, and the results are compared to those of the stiff integrator CHEMEQ. The method, which we call α-QSS, is more stable, more accurate, and less costly than CHEMEQ.}
 }

unit_test/burn_cell_primordial_chem/GNUmakefile

@@ -19,12 +19,6 @@ USE_MICROPHYSICS_DEBUG = TRUE
 
 EBASE = main
 
-USE_CXX_REACTIONS ?= TRUE
-
-ifeq ($(USE_CXX_REACTIONS),TRUE)
-  DEFINES += -DCXX_REACTIONS
-endif
-
 # define the location of the Microphysics top directory
 MICROPHYSICS_HOME  := ../..
 

unit_test/test_aprox_rates/main.cpp

@@ -158,12 +158,11 @@ void main_main ()
     ParallelDescriptor::ReduceRealMax(stop_time, IOProc);
 
     std::string name = "test_aprox_rates.";
-    std::string language = ".cxx";
 
     // Write a plotfile
-    WriteSingleLevelPlotfile(name + eos_name + language, state, names, geom, time, 0);
+    WriteSingleLevelPlotfile(name + eos_name, state, names, geom, time, 0);
 
-    write_job_info(name + eos_name + language);
+    write_job_info(name + eos_name);
 
     // Tell the I/O Processor to write out the "run time"
     amrex::Print() << "Run time = " << stop_time << std::endl;

unit_test/test_ase/GNUmakefile

@@ -16,12 +16,6 @@ USE_NSE_NET = TRUE
 EBASE = main
 
 
-USE_CXX_REACTIONS ?= TRUE
-
-ifeq ($(USE_CXX_REACTIONS),TRUE)
-  DEFINES += -DCXX_REACTIONS
-endif
-
 # define the location of the Microphysics top directory
 MICROPHYSICS_HOME  := ../..
 

unit_test/test_conductivity/main.cpp

@@ -157,12 +157,11 @@ void main_main ()
     ParallelDescriptor::ReduceRealMax(stop_time, IOProc);
 
     std::string name = "test_conductivity.";
-    std::string language = ".cxx";
 
     // Write a plotfile
-    WriteSingleLevelPlotfile(name + cond_name + language, state, names, geom, time, 0);
+    WriteSingleLevelPlotfile(name + cond_name, state, names, geom, time, 0);
 
-    write_job_info(name + cond_name + language);
+    write_job_info(name + cond_name);
 
     // Tell the I/O Processor to write out the "run time"
     amrex::Print() << "Run time = " << stop_time << std::endl;

unit_test/test_eos/main.cpp

@@ -149,12 +149,11 @@ void main_main ()
 
 
     std::string name = "test_eos.";
-    std::string language = ".cxx";
 
     // Write a plotfile
-    WriteSingleLevelPlotfile(name + eos_name + language, state, names, geom, time, 0);
+    WriteSingleLevelPlotfile(name + eos_name, state, names, geom, time, 0);
 
-    write_job_info(name + eos_name + language);
+    write_job_info(name + eos_name);
 
     // Tell the I/O Processor to write out the "run time"
     amrex::Print() << "Run time = " << stop_time << std::endl;

unit_test/test_react/main.cpp

@@ -249,12 +249,10 @@ void main_main ()
     std::string name = "test_react.";
     std::string integrator = buildInfoGetModuleVal(int_idx);
 
-    std::string language = ".cxx";
-
     // Write a plotfile
-    WriteSingleLevelPlotfile(prefix + name + integrator + language, state, names, geom, time, 0);
+    WriteSingleLevelPlotfile(prefix + name + integrator, state, names, geom, time, 0);
 
-    write_job_info(prefix + name + integrator + language);
+    write_job_info(prefix + name + integrator);
 
     // output stats on the number of RHS calls
 

unit_test/test_sdc/main.cpp

@@ -241,12 +241,10 @@ void main_main ()
     std::string name = "test_react.";
     std::string integrator = buildInfoGetModuleVal(int_idx);
 
-    std::string language = ".cxx";
-
     // Write a plotfile
-    WriteSingleLevelPlotfile(prefix + name + integrator + language, state, names, geom, time, 0);
+    WriteSingleLevelPlotfile(prefix + name + integrator, state, names, geom, time, 0);
 
-    write_job_info(prefix + name + integrator + language);
+    write_job_info(prefix + name + integrator);
 
     // Tell the I/O Processor to write out the "run time"
     amrex::Print() << "Run time = " << stop_time << std::endl;