Replaced the old configuration with the standard one for musica fortr…

…an test
NCAR · Jan 9, 2024 · 264396b · 264396b
1 parent d8bc429
commit 264396b
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Showing 8 changed files with 141 additions and 12 deletions.
diff --git a/Dockerfile.fortran b/Dockerfile.fortran
@@ -70,6 +70,6 @@ RUN cd musica/musica-fortran/test \
     && make
 
 RUN cd musica/musica-fortran/test \
-    && cp -r micm_config ./build/micm_config
+    && cp -r configs/chapman ./build/chapman
 
 WORKDIR musica/musica-fortran/test/build
diff --git a/musica-fortran/test/configs/chapman/config.json b/musica-fortran/test/configs/chapman/config.json
@@ -0,0 +1,6 @@
+{
+  "camp-files": [
+    "species.json",
+    "reactions.json"
+  ]
+}
diff --git a/musica-fortran/test/configs/chapman/reactions.json b/musica-fortran/test/configs/chapman/reactions.json
@@ -0,0 +1,97 @@
+{
+    "camp-data": [
+        {
+            "name": "Chapman",
+            "type": "MECHANISM",
+            "reactions": [
+                {
+                    "type": "PHOTOLYSIS",
+                    "reactants": {
+                        "O2": {}
+                    },
+                    "products": {
+                        "O": {
+                            "yield": 2.0
+                        }
+                    },
+                    "MUSICA name": "R1"
+                },
+                {
+                    "type": "ARRHENIUS",
+                    "A": 8.018e-17,
+                    "reactants": {
+                        "O": {},
+                        "O2": {}
+                    },
+                    "products": {
+                        "O3": {}
+                    },
+                    "MUSICA name": "R2"
+                },
+                {
+                    "type": "PHOTOLYSIS",
+                    "reactants": {
+                        "O3": {}
+                    },
+                    "products": {
+                        "O": {},
+                        "O2": {}
+                    },
+                    "MUSICA name": "R3"
+                },
+                {
+                    "type": "ARRHENIUS",
+                    "A": 1.576e-15,
+                    "reactants": {
+                        "O": {},
+                        "O3": {}
+                    },
+                    "products": {
+                        "O2": {
+                            "yield": 2.0
+                        }
+                    },
+                    "MUSICA name": "R4"
+                },
+                {
+                    "type": "PHOTOLYSIS",
+                    "reactants": {
+                        "O3": {}
+                    },
+                    "products": {
+                        "O1D": {},
+                        "O2": {}
+                    },
+                    "MUSICA name": "R5"
+                },
+                {
+                    "type": "ARRHENIUS",
+                    "A": 7.11e-11,
+                    "reactants": {
+                        "O1D": {},
+                        "M": {}
+                    },
+                    "products": {
+                        "O": {},
+                        "M": {}
+                    },
+                    "MUSICA name": "R6"
+                },
+                {
+                    "type": "ARRHENIUS",
+                    "A": 1.2e-10,
+                    "reactants": {
+                        "O1D": {},
+                        "O3": {}
+                    },
+                    "products": {
+                        "O2": {
+                            "yield": 2.0
+                        }
+                    },
+                    "MUSICA name": "R7"
+                }
+            ]
+        }
+    ]
+}
diff --git a/musica-fortran/test/configs/chapman/species.json b/musica-fortran/test/configs/chapman/species.json
@@ -0,0 +1,29 @@
+{
+    "camp-data": [
+        {
+            "name": "M",
+            "type": "CHEM_SPEC",
+            "tracer type": "CONSTANT"
+        },
+        {
+            "name": "O2",
+            "type": "CHEM_SPEC",
+            "tracer type": "CONSTANT"
+        },
+        {
+            "name": "O",
+            "type": "CHEM_SPEC",
+            "absolute tolerance": 1e-12
+        },
+        {
+            "name": "O1D",
+            "type": "CHEM_SPEC",
+            "absolute tolerance": 1e-12
+        },
+        {
+            "name": "O3",
+            "type": "CHEM_SPEC",
+            "absolute tolerance": 1e-12
+        }
+    ]
+}
diff --git a/musica-fortran/test/micm_config/mechanism.json b/musica-fortran/test/micm_config/mechanism.json
diff --git a/musica-fortran/test/micm_config/species.json b/musica-fortran/test/micm_config/species.json
diff --git a/musica-fortran/test/test_musica_api.F90 b/musica-fortran/test/test_musica_api.F90
@@ -7,17 +7,17 @@ program test
     real(c_double) :: temperature      
     real(c_double) :: pressure
     real(c_double) :: time_step
-    real(c_double), dimension(10) :: concentrations
+    real(c_double), dimension(5) :: concentrations
     integer(c_size_t) :: num_concentrations
 
     temperature = 10d0
     pressure = 20d0
     time_step = 1d0
-    concentrations = (/ 1d0, 2d0, 3d0, 4d0, 5d0, 6d0, 7d0, 8d0, 9d0, 10d0 /)
-    num_concentrations = 10
+    concentrations = (/ 0.75, 0.4, 0.8, 0.01, 0.02 /)
+    num_concentrations = 5
 
     write(*,*) "  * [Fortran] Creating MICM"
-    m = micm_t("micm_config")
+    m = micm_t("chapman")
 
     write(*,*) "  * [Fortran] Creating solver"
     write(*,*) "  * [Fortran] Solver creating status indicates ", m%create_solver(), " (1 is success, else failure) "

diff --git a/musica/src/micm/micm.cpp b/musica/src/micm/micm.cpp
@@ -29,7 +29,7 @@ int MICM::create_solver()
         params.reorder_state_ = false;
         solver_ = new VectorRosenbrockSolver{solver_params.system_,
                                             solver_params.processes_,
-                                            params}; 
+                                            params};
     }
     else
     {
@@ -42,15 +42,14 @@ int MICM::create_solver()
 
 void MICM::solve(double temperature, double pressure, double time_step, double*& concentrations, size_t num_concentrations)
 {
-    v_concentrations_.assign(concentrations, concentrations + num_concentrations);
-
-    auto state = solver_->GetState();
+    micm::State state = solver_->GetState();
 
     for(size_t i{}; i < NUM_GRID_CELLS; ++i) {
         state.conditions_[i].temperature_ = temperature;
         state.conditions_[i].pressure_ = pressure;
     }
 
+    v_concentrations_.assign(concentrations, concentrations + num_concentrations);
     state.variables_[0] = v_concentrations_;
 
     auto result = solver_->Solve(time_step, state);
@@ -60,4 +59,4 @@ void MICM::solve(double temperature, double pressure, double time_step, double*&
     {
         concentrations[i] = v_concentrations_[i];
     }
-}
+}