WIP: Adding the EcoSIM for ATS PK (#335)

.github/workflows/ats-ci.yml

@@ -36,11 +36,11 @@ jobs:
         else
           echo "ATS_BRANCH=$GITHUB_REF_NAME" >> $GITHUB_ENV
         fi
-    - name: Does Amanzi branch of the same name exist?
+    - name: Set Amanzi branch to the EcoSIM TPLs branch for now.
       id: amanzi_branch
       run: |
-        echo "AMANZI_BRANCH=$(git ls-remote --heads origin ${GITHUB_REF_NAME} | sed 's/.*refs\/heads\///')" >> $GITHUB_ENV
-    - name: If so, checkout Amanzi to get the right TPLs version
+        echo "AMANZI_BRANCH=david/ecosim-tpls" >> $GITHUB_ENV
+    - name: Checkout Amanzi to get the right TPLs version
       id: amanzi_branch_checkout
       uses: actions/checkout@v4
       with:

src/executables/CMakeLists.txt

@@ -42,6 +42,7 @@ include_directories(${ATS_SOURCE_DIR}/src/pks/energy)
 include_directories(${ATS_SOURCE_DIR}/src/pks/flow)
 include_directories(${ATS_SOURCE_DIR}/src/pks/deform)
 include_directories(${ATS_SOURCE_DIR}/src/pks/transport)
+include_directories(${ATS_SOURCE_DIR}/src/pks/ecosim)
 include_directories(${ATS_SOURCE_DIR}/src/operators/upwinding)
 include_directories(${ATS_SOURCE_DIR}/src/operators/advection)
 include_directories(${ATS_SOURCE_DIR}/src/operators/deformation)
@@ -63,6 +64,12 @@ include_evaluators_directories(LISTNAME ATS_BGC_REG_INCLUDES)
 include_evaluators_directories(LISTNAME ATS_MPC_REG_INCLUDES)
 include_evaluators_directories(LISTNAME SED_TRANSPORT_REG_INCLUDES)
 
+
+include_evaluators_directories(LISTNAME ATS_ECOSIM_REG_INCLUDES)
+include_evaluators_directories(LISTNAME ATS_ECOSIM_RELATIONS_REG_INCLUDES)
+include_evaluators_directories(LISTNAME ATS_ECOSIM_DATA_REG_INCLUDES)
+
+
 set(ats_src_files
   ats_mesh_factory.cc
   coordinator.cc
@@ -122,6 +129,21 @@ set(ats_link_libs
   ats_transport_relations
   )
 
+if (ENABLE_ECOSIM)
+  list(APPEND ats_link_libs
+    ats_ecosim
+    ats_ecosim_data
+ #   ats_ecosim_relations
+  )
+endif()
+
+#In theory covered by ECOSIM_LIBRARIES:
+#If not place this in an if statement?
+#  ats_ecosim
+#  ats_ecosim_data
+#  ats_ecosim_relations
+
+message(STATUS ">>>> JDM: In ATS ECOSIM_LIBRARIES = ${ECOSIM_LIBRARIES}")
 
 # note, we can be inclusive here, because if they aren't enabled,
 # these won't be defined and will result in empty strings.
@@ -137,7 +159,8 @@ set(tpl_link_libs
   ${HYPRE_LIBRARIES}
   ${HDF5_LIBRARIES}
   ${CLM_LIBRARIES}
-  )
+  ${ECOSIM_LIBRARIES}
+ )
 
 add_amanzi_library(ats_executable
   SOURCE ${ats_src_files}

src/executables/ats_registration_files.hh

@@ -25,3 +25,8 @@
 #ifdef ALQUIMIA_ENABLED
 #include "pks_chemistry_reg.hh"
 #endif
+#ifdef ECOSIM_ENABLED
+#include "ats_ecosim_registration.hh"
+#include "ats_ecosim_relations_registration.hh"
+#include "ats_ecosim_data_registration.hh"
+#endif

src/pks/CMakeLists.txt

@@ -54,3 +54,7 @@ add_subdirectory(deform)
 add_subdirectory(surface_balance)
 add_subdirectory(biogeochemistry)
 add_subdirectory(mpc)
+
+if (ENABLE_ECOSIM)
+  add_subdirectory(ecosim)
+endif()

src/pks/ecosim/BGCEngine.cc

@@ -0,0 +1,119 @@
+/*
+  Basic architecture based on the Alquima interfece adapted for
+  use in the ATSEcoSIM PK
+
+  Copyright 2010-202x held jointly by LANS/LANL, LBNL, and PNNL.
+  Amanzi is released under the three-clause BSD License.
+  The terms of use and "as is" disclaimer for this license are
+  provided in the top-level COPYRIGHT file.
+
+  Authors: Jeffrey Johnson
+           Sergi Molins <smolins@lbl.gov>
+
+  This implements the Alquimia chemistry engine.
+*/
+
+#include <iostream>
+#include <cstring>
+#include <cstdio>
+#include <assert.h>
+#include "BGCEngine.hh"
+#include "errors.hh"
+#include "exceptions.hh"
+
+// Support for manipulating floating point exception handling.
+#ifdef _GNU_SOURCE
+#define AMANZI_USE_FENV
+#include <fenv.h>
+#endif
+
+namespace Amanzi {
+namespace EcoSIM {
+
+BGCEngine::BGCEngine(const std::string& engineName,
+                                 const std::string& inputFile) :
+  bgc_engine_name_(engineName),
+  bgc_engine_inputfile_(inputFile)
+{
+  Errors::Message msg;
+
+  CreateBGCInterface(bgc_engine_name_.c_str(),
+                    &bgc_);
+
+}
+
+BGCEngine::~BGCEngine()
+{
+  bgc_.Shutdown();
+
+  //Did I forget to implement this?
+  //FreeBGCProperties(&props);
+  //FreeBGCState(&state);
+  //FreeBGCAuxiliaryData(&aux_data);
+  //FreeAlquimiaEngineStatus(&chem_status_);
+}
+
+const BGCSizes&
+BGCEngine::Sizes() const
+{
+  return sizes_;
+}
+
+void BGCEngine::InitState(BGCProperties& properties,
+                                BGCState& state,
+                                BGCAuxiliaryData& aux_data,
+                                int ncells_per_col_,
+                                int num_components,
+                                int num_columns)
+{
+  AllocateBGCProperties(&sizes_, &properties, ncells_per_col_, num_columns);
+  AllocateBGCState(&sizes_, &state, ncells_per_col_, num_components, num_columns);
+}
+
+void BGCEngine::FreeState(BGCProperties& properties,
+                                BGCState& state,
+                                BGCAuxiliaryData& aux_data)
+{
+  FreeBGCProperties(&properties);
+  FreeBGCState(&state);
+}
+
+void BGCEngine::DataTest() {
+
+  bgc_.DataTest();
+}
+
+bool BGCEngine::Setup(BGCProperties& properties,
+                              BGCState& state,
+                              BGCSizes& sizes_,
+                              int num_iterations,
+                              int num_columns,
+                              int ncells_per_col_)
+{
+  bgc_.Setup(&properties,
+                &state,
+                &sizes_,
+                num_iterations,
+                num_columns,
+                ncells_per_col_);
+
+}
+
+bool BGCEngine::Advance(const double delta_time,
+                              BGCProperties& properties,
+                              BGCState& state,
+                              BGCSizes& sizes_,
+                              int num_iterations,
+                              int num_columns)
+{
+  bgc_.Advance(delta_time,
+                &properties,
+                &state,
+                &sizes_,
+                num_iterations,
+                num_columns);
+
+}
+
+} // namespace
+} // namespace

src/pks/ecosim/BGCEngine.hh

@@ -0,0 +1,107 @@
+/*
+  ATS-EcoSIM, Code Adapted for use from Alquimia
+
+  Copyright 2010-202x held jointly by LANS/LANL, LBNL, and PNNL.
+  Amanzi is released under the three-clause BSD License.
+  The terms of use and "as is" disclaimer for this license are
+  provided in the top-level COPYRIGHT file.
+
+  Author: Jeffrey Johnson
+
+  This is a point of contact for the chemistry engine exposed by Alquimia
+  to the rest of Amanzi--it provides the ability to enforce geochemical
+  conditions and to integrate reactions given a chemical configuration.
+*/
+
+#ifndef BGC_ENGINE_HH_
+#define BGC_ENGINE_HH_
+
+#include <string>
+#include <vector>
+#include <map>
+
+#include "BGC_memory.hh"
+#include "BGC_containers.hh"
+
+#include "VerboseObject.hh"
+
+namespace Amanzi {
+namespace EcoSIM {
+
+class BGCEngine {
+ public:
+
+  // Constructs a chemistry engine using the given engine (backend) name and input file.
+  BGCEngine(const std::string& engineName, const std::string& inputFile);
+
+  // Destructor.
+  ~BGCEngine();
+
+  // Returns the name of the backend that does the chemistry.
+  const std::string& Name() const;
+
+  // Returns true if the chemistry engine is thread-safe, false if not.
+  bool IsThreadSafe() const;
+
+  // Returns a reference to a "sizes" object that can be queried to find the sizes of the various
+  // arrays representing the geochemical state within the engine.
+  const BGCSizes& Sizes() const;
+
+  // Initializes the data structures that hold the chemical state information.
+  void InitState(BGCProperties& properties,
+                 BGCState& state,
+                 BGCAuxiliaryData& aux_data,
+                 int ncells_per_col_,
+                 int num_components,
+                 int num_columns);
+
+  // Frees the data structures that hold the chemical state information.
+  void FreeState(BGCProperties& properties,
+                 BGCState& state,
+                 BGCAuxiliaryData& aux_data);
+
+  void DataTest();
+
+  bool Setup(BGCProperties& properties,
+               BGCState& state,
+               BGCSizes& sizes,
+               int num_iterations,
+               int num_columns,
+               int ncells_per_col_);
+
+  bool Advance(const double delta_time,
+               BGCProperties& properties,
+               BGCState& state,
+               BGCSizes& sizes,
+               int num_iterations,
+               int num_columns);
+
+  void CopyBGCState(const BGCState* const source,
+                         BGCState* destination);
+  void CopyBGCProperties(const BGCProperties* const source,
+                              BGCProperties* destination);
+
+ private:
+
+  // bgc data structures.
+  bool bgc_initialized_;
+  void* engine_state_;
+  BGCSizes sizes_;
+  BGCInterface bgc_;
+
+  Teuchos::RCP<VerboseObject> vo_;
+  // Back-end engine name and input file.
+  std::string bgc_engine_name_;
+  std::string bgc_engine_inputfile_;
+
+  // forbidden.
+  BGCEngine();
+  BGCEngine(const BGCEngine&);
+  BGCEngine& operator=(const BGCEngine&);
+
+};
+
+} // namespace
+} // namespace
+
+#endif