Merge branch 'development' into network_docs

zingale · Jan 17, 2025 · 69296c5 · 69296c5
2 parents 2dae3be + 4de2802
commit 69296c5
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diff --git a/Docs/source/data_structures.rst b/Docs/source/data_structures.rst
@@ -43,7 +43,7 @@ network, and they will come in through the ``network_properties.H`` header file.
 There is a lot more information that can be saved here, such as the
 partial derivatives of the thermodynamic state variables with respect
 to each other. To see a complete list, examine the ``eos_type.H``
-file: ``Castro/Microphysics/interfaces/eos_type.H``.
+file.
 
 Networks
 ========
@@ -111,10 +111,30 @@ to access the different components of the state:
 
 * ``neqs`` : the total number of variables we are integrating.
 
-   It is assumed that the first ``nspec`` are the species.
+  It is assumed that the first ``nspec`` are the species.
 
 * ``net_ienuc`` : the index of the specific internal energy in the solution vector
 
+For :ref:`sdc-evolution`, it also defines integer indices for the
+``burn_t y[]`` array:
+
+* ``SFS``:  the first species
+
+* ``SEINT`` the energy
+
+and then a number of components that are not evolved:
+
+* ``SRHO`` density
+
+* ``SMX``, ``SMY``, ``SMZ`` : the momenta
+
+* ``SEDEN`` : the total energy density
+
+* ``SFX`` : the first auxiliary quantity
+
+with the total number of state variables ``SVAR`` and the number of evolved
+variables ``SVAR_EVOLVE``.
+
 Integrators
 ===========
 

diff --git a/Docs/source/nse.rst b/Docs/source/nse.rst
@@ -262,6 +262,11 @@ reaction network.  It solves for the chemical potentials of the proton
 and neutron and from there gets the abundances of each of the nuclei
 under the assumption of NSE, following the procedure outlined in :cite:`Calder_2007`.
 
+.. important::
+
+   Self-consistent NSE does not support the templated C++ networks
+   (like ``aprox13``).  You should use a pynucastro-generated network.
+
 The solve is done using a port of the hybrid Powell method from
 MINPACK (we ported the solver to templated C++).
 

diff --git a/Docs/source/sdc.rst b/Docs/source/sdc.rst
@@ -1,3 +1,5 @@
+.. _sdc-evolution:
+
 *****************************
 Spectral Deferred Corrections
 *****************************

diff --git a/Docs/source/templated_networks.rst b/Docs/source/templated_networks.rst
@@ -384,16 +384,11 @@ Linear Algebra
 
 The VODE integrator needs routines to do LU factorization and back
 substitution.  We build off of the linpack ``dgefa`` and ``dgesl``
-routines, but because we know at compile time which Jacobian terms are
-non-zero, we are able to use ``constexpr`` for-loops to only do the
-calculations on non-zero elements.  This greatly reduces the amount of work
-in the linear algebra.
+routines, using ``constexpr`` for-loops that know the network size
+at compile time.
 
-Note:
-
-* Currently we are still storing a dense Jacobian -- we just skip computation
-  on the elements that are 0.
+.. note::
 
-* These routines do not perform pivoting.  This does not seem to be an
-  issue for the types of matrices we solve with reactions (since they are
-  all of the form :math:`I - \tau J`, where :math:`tau` is the timestep).
+   These routines do not perform pivoting.  This does not seem to be an
+   issue for the types of matrices we solve with reactions (since they are
+   all of the form :math:`I - \tau J`, where :math:`tau` is the timestep).
diff --git a/interfaces/eos.H b/interfaces/eos.H
@@ -394,14 +394,13 @@ void check_inputs (const I input, T& state)
 
 template <typename I, typename T>
 AMREX_GPU_HOST_DEVICE AMREX_INLINE
-void eos (const I input, T& state, bool use_raw_inputs = false)
+void eos (const I input, T& state)
 {
   static_assert(std::is_same_v<I, eos_input_t>, "input must be an eos_input_t");
 
   // Input arguments
 
   bool has_been_reset = false;
-  bool use_composition_routine = true;
 
   // Local variables
 
@@ -411,15 +410,9 @@ void eos (const I input, T& state, bool use_raw_inputs = false)
   }
 #endif
 
-  if (use_raw_inputs) {
-    use_composition_routine = false;
-  }
-
   if constexpr (has_xn<T>::value) {
-      if (use_composition_routine) {
-          // Get abar, zbar, etc.
-          composition(state);
-      }
+      // Get abar, zbar, etc.
+      composition(state);
   }
 
   // Force the inputs to be valid.

diff --git a/networks/Make.package b/networks/Make.package
@@ -7,20 +7,6 @@ include $(MICROPHYSICS_UTIL_PATH)/Make.package
 
 ifeq ($(USE_REACT), TRUE)
 
-  # for backwards compatibility
-  DEFINES += -DNETWORK_HAS_CXX_IMPLEMENTATION
-
-  ifeq ($(INTEGRATOR_DIR), VODE90)
-    override INTEGRATOR_DIR = VODE
-    $(warning VODE90 has been renamed VODE)
-  endif
-
-  ifeq ($(INTEGRATOR_DIR), VODE)
-    ifeq ($(USE_CLEANED_CORRECTOR), TRUE)
-      DEFINES += -DCLEAN_INTEGRATOR_CORRECTION
-    endif
-  endif
-
   VPATH_LOCATIONS += $(MICROPHYSICS_HOME)/networks
 
   CEXE_headers += rhs.H
@@ -98,8 +84,6 @@ AUTO_BUILD_SOURCES += $(NETWORK_OUTPUT_PATH)/network_properties.H
 net_prop_debug: $(NETWORK_OUTPUT_PATH)/network_properties.H
 
 ifneq ($(NETWORK_DIR), general_null)
-  $(NETWORK_OUTPUT_PATH)/network_properties.F90: $(NETWORK_OUTPUT_PATH)/network_properties.H
-
   NAUX := $(shell PYTHONPATH=$(MICROPHYSICS_HOME)/networks/general_null $(MICROPHYSICS_HOME)/networks/get_naux.py --microphysics_path "$(MICROPHYSICS_HOME)" --defines "$(DEFINES)" --net "$(NETWORK_DIR)")
   DEFINES += "-DNAUX_NET=$(NAUX)"
 

diff --git a/unit_test/test_aprox_rates/main.cpp b/unit_test/test_aprox_rates/main.cpp
@@ -102,9 +102,6 @@ void main_main ()
     // for C++
     plot_t vars;
 
-    // for F90
-    Vector<std::string> varnames;
-
     // C++ test
     vars = init_variables();
 

diff --git a/unit_test/test_conductivity/main.cpp b/unit_test/test_conductivity/main.cpp
@@ -102,9 +102,6 @@ void main_main ()
     // for C++
     plot_t vars;
 
-    // for F90
-    Vector<std::string> varnames;
-
     // C++ test
     vars = init_variables();