Netcdf output

CMakeLists.txt

@@ -198,6 +198,7 @@ if(NGEN_WITH_NETCDF)
     endif()
 
     add_compile_definitions(NETCDF_ACTIVE)
+    add_compile_definitions(NGEN_WITH_NETCDF)
 endif()
 
 if(NGEN_WITH_EXTERN_SLOTH)
@@ -330,6 +331,7 @@ add_subdirectory("src/forcing")
 add_subdirectory("src/utilities/mdarray")
 add_subdirectory("src/utilities/mdframe")
 add_subdirectory("src/utilities/logging")
+add_subdirectory("src/output")
 
 target_link_libraries(ngen
     PUBLIC
@@ -342,6 +344,7 @@ target_link_libraries(ngen
         NGen::forcing
         NGen::core_mediator
         NGen::logging
+        NGen::output
 )
 
 if(NGEN_WITH_SQLITE)
@@ -354,6 +357,11 @@ if(NGEN_WITH_ROUTING)
     target_link_libraries(ngen PUBLIC NGen::routing)
 endif()
 
+if(NGEN_WITH_NETCDF)
+    add_subdirectory("src/utilities/netcdf")
+    target_link_libraries(ngen PUBLIC NGen::netcdf_utils)
+endif()
+
 add_executable(partitionGenerator src/partitionGenerator.cpp)
 target_include_directories(partitionGenerator PUBLIC "${PROJECT_BINARY_DIR}/include")
 if(NGEN_WITH_SQLITE)

data/example_ncout_realization_config.json

@@ -0,0 +1,165 @@
+{
+    "global": {
+      "formulations": [
+        {
+          "name": "bmi_c++",
+          "params": {
+            "model_type_name": "test_bmi_cpp",
+            "library_file": "./extern/test_bmi_cpp/cmake_build/libtestbmicppmodel.so",
+            "init_config": "./data/bmi/c/test/test_bmi_c_config.ini",
+            "main_output_variable": "OUTPUT_VAR_2",
+            "variables_names_map" : {
+              "INPUT_VAR_2": "TMP_2maboveground",
+              "INPUT_VAR_1": "precip_rate"
+            },
+            "create_function": "bmi_model_create",
+            "destroy_function": "bmi_model_destroy",
+            "uses_forcing_file": false
+          }
+        }
+      ],
+      "forcing": {
+          "file_pattern": ".*{{id}}.*.csv",
+          "path": "./data/forcing/"
+      }
+    },
+    "time": {
+        "start_time": "2015-12-01 00:00:00",
+        "end_time": "2015-12-30 23:00:00",
+        "output_interval": 3600
+    },
+    "outputs" : {
+      "nc_file1" : {
+        "name" : "netcdf_output_1.nc",
+        "type" : "NetCDF4",
+        "dimensions" : {
+          "X" : {
+            "size" : 1000
+          },
+          "Y" : {
+            "size" : 500
+          },
+          "Z" : {
+            "size" : 100
+          }
+        },
+        "variables" : {
+          "inflitration_excess" : {
+            "type" : "float",
+            "dimensions" : "X, Y"
+          },
+           "soil_moisture_content" : {
+            "type" : "float",
+            "dimensions" : "X, Y"
+          }
+        }
+      },
+      "nc_file2" : {
+        "name" : "netcdf_output_2.nc",
+        "type" : "NetCDF4",
+        "dimensions" : {
+          "D1" : {
+            "size" : 10
+          },
+          "D2" : {
+            "size" : 100
+          },
+          "D3" : {
+            "size" : 1000
+          },
+          "D4" : {
+            "size" : 10000
+          }
+        },
+        "variables" : {
+          "var1" : {
+            "type" : "float",
+            "dimensions" : "D1"
+          },
+          "var2" : {
+            "type" : "int",
+            "dimensions" : "D2"
+          },
+          "var3" : {
+            "type" : "char",
+            "dimensions" : "D3"
+          },
+          "var4" : {
+            "type" : "int64",
+            "dimensions" : "D4"
+          }      
+        }
+      }
+    },
+    "catchments": {
+        "cat-27": {
+          "formulations": [
+            {
+              "name": "bmi_c++",
+              "params": {
+                "model_type_name": "test_bmi_cpp",
+                "library_file": "./extern/test_bmi_cpp/cmake_build/libtestbmicppmodel.so",
+                "init_config": "./data/bmi/c/test/test_bmi_c_config.ini",
+                "main_output_variable": "OUTPUT_VAR_2",
+                "variables_names_map" : {
+                  "INPUT_VAR_2": "TMP_2maboveground",
+                  "INPUT_VAR_1": "precip_rate"
+                },
+                "create_function": "bmi_model_create",
+                "destroy_function": "bmi_model_destroy",
+                "uses_forcing_file": false
+              }
+            }
+          ],
+          "forcing": {
+              "path": "./data/forcing/cat-27_2015-12-01 00_00_00_2015-12-30 23_00_00.csv"
+          }
+        },
+        "cat-52": {
+          "formulations": [
+            {
+              "name": "bmi_c++",
+              "params": {
+                "model_type_name": "test_bmi_cpp",
+                "library_file": "./extern/test_bmi_cpp/cmake_build/libtestbmicppmodel.so",
+                "init_config": "./data/bmi/c/test/test_bmi_c_config.ini",
+                "main_output_variable": "OUTPUT_VAR_2",
+                "variables_names_map" : {
+                  "INPUT_VAR_2": "TMP_2maboveground",
+                  "INPUT_VAR_1": "precip_rate"
+                },
+                "create_function": "bmi_model_create",
+                "destroy_function": "bmi_model_destroy",
+                "uses_forcing_file": false
+              }
+            }
+          ],
+          "forcing": {
+              "path": "./data/forcing/cat-52_2015-12-01 00_00_00_2015-12-30 23_00_00.csv"
+          }
+        },
+        "cat-67": {
+          "formulations": [
+            {
+              "name": "bmi_c++",
+              "params": {
+                "model_type_name": "test_bmi_cpp",
+                "library_file": "./extern/test_bmi_cpp/cmake_build/libtestbmicppmodel.so",
+                "init_config": "./data/bmi/c/test/test_bmi_c_config.ini",
+                "main_output_variable": "OUTPUT_VAR_2",
+                "variables_names_map" : {
+                  "INPUT_VAR_2": "TMP_2maboveground",
+                  "INPUT_VAR_1": "precip_rate"
+                },
+                "create_function": "bmi_model_create",
+                "destroy_function": "bmi_model_destroy",
+                "uses_forcing_file": false
+              }
+            }
+          ],
+          "forcing": {
+              "path": "./data/forcing/cat-67_2015-12-01 00_00_00_2015-12-30 23_00_00.csv"
+          }
+        }
+    }
+}

extern/test_bmi_py/README.md

@@ -5,6 +5,7 @@
  - run_bmi_unit_test.py: This is a file that runs each BMI unit test to make sure that the BMI is complete and functioning as expected.
  - config.yml: This is a configuration file that the BMI reads to set inital_time (initial value of current_model_time) and time_step_seconds (time_step_size).
  - environment.yml: Environment file with the required Python libraries needed to run the model with BMI. Create the environment with this command: `conda env create -f environment.yml`, then activate it with `conda activate bmi_test`
+ - requirements.txt: This file is used to install needed packages into system or venv directories using the command 'pip install -r requirements.txt'
 
 # About
 This is an implementation of a Python-based model that fulfills the Python language BMI interface and can be used in the Framework. It is intended to serve as a control for testing purposes, freeing the framework from dependency on any real-world model in order to test BMI related functionality.
@@ -28,4 +29,4 @@ model time, input_1, input_2, output_1, output_2, output_3
 457200.00, 3.57, 1.31, 228.50, 167.46, 0.00  
 918000.00, 5.18, 1.77, 662.80, 453.24, 0.00  
 1839600.00, 3.68, 3.75, 943.04, 1919.17, 0.00  
-3682800.00, 8.62, 1.63, 4412.11, 1668.66, 0.00  
+3682800.00, 8.62, 1.63, 4412.11, 1668.66, 0.00  

include/core/DomainLayer.hpp

@@ -46,6 +46,12 @@ namespace ngen
             formulation->write_output("Time Step,""Time,"+formulation->get_output_header_line(",")+"\n");
         }
 
+        /**
+         * @brief Get a list of output variables names for this layer
+         * 
+         * @return vector of output variable names
+        */
+
         /***
          * @brief Run one simulation timestep for this model associated with the domain
          * 
@@ -56,7 +62,7 @@ namespace ngen
          * Any required connection to other components, e.g. providing inputs to a catchment feature,
          * is not yet implemented in this class.
         */
-        void update_models() override{
+        void update_models(std::shared_ptr<data_output::OutputWriter> writer) override{
             std::string current_timestamp = simulation_time.get_timestamp(output_time_index);
             try{
                 formulation->get_response(output_time_index, simulation_time.get_output_interval_seconds());
@@ -80,6 +86,13 @@ namespace ngen
 
         }
 
+        /**
+        * @brief Get a class id for this layer object
+        * 
+        * @return int
+        */
+        int class_id() { return LayerClass::kDomainLayer; }
+
         private:
         std::shared_ptr<realization::Catchment_Formulation> formulation;
     };