Netcdf output

CMakeLists.txt

@@ -330,6 +330,7 @@ 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 +343,7 @@ target_link_libraries(ngen
         NGen::forcing
         NGen::core_mediator
         NGen::logging
+        NGen::output
 )
 
 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`
+ - requirments.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 +46,20 @@ 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
+        */
+
+        virtual std::vector<std::string>&& get_output_variable_names() 
+        { 
+            std::vector<std::string> output_variables;
+
+
+            return std::move(output_variables);
+        }
+
         /***
          * @brief Run one simulation timestep for this model associated with the domain
          * 
@@ -80,6 +94,13 @@ 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;
     };

include/core/Layer.hpp

@@ -13,6 +13,22 @@
 
 namespace ngen
 {
+
+    /**
+     * @brief an enumeration of the types of layer classes
+     */
+
+    enum LayerClass
+    {
+        kLayer = 1,
+        kSurfaceLayer = 2,
+        kDomainLayer = 3,
+        kCatchmentLayer = 4,
+        kNexusLayer = 5,
+        kRoutingLayer = 6,
+        kOverlayLayer = 7
+    };
+
 
     class Layer
     {    
@@ -64,6 +80,24 @@ namespace ngen
 
         virtual ~Layer() {}
 
+        /**
+        * @brief Get a class id for this layer object
+        * 
+        * @return int
+        */
+        virtual int class_id() { return LayerClass::kLayer; }
+
+        /**
+         * @brief Get a list of output variables names for this layer
+         * 
+         * @return vector of output variable names
+        */
+
+        virtual std::vector<std::string>&& get_output_variable_names() 
+        { 
+            return std::move(std::vector<std::string>());
+        }
+
         /***
          * @brief Return the next timestep that will be processed by this layer in epoch time units
         */

include/core/Partition_Parser.hpp

@@ -25,24 +25,24 @@
 class Partitions_Parser {
 
     public:
-        //Constructor that takes an input json file path and points to the root of the tree in json file
+        //Constructor that takes an input json file path and points to the root of the config_ptree in json file
         Partitions_Parser(const std::string &file_path) {
             boost::property_tree::ptree loaded_tree;
             boost::property_tree::json_parser::read_json(file_path, loaded_tree);
             std::cout << "file read success" << std::endl;
-            this->tree = loaded_tree;
+            this->config_ptree = loaded_tree;
             std::cout << "file_path: " << file_path << std::endl;
         };
 
-        Partitions_Parser(const boost::property_tree::ptree tree){
-            this->tree = tree;
+        Partitions_Parser(const boost::property_tree::ptree config_ptree){
+            this->config_ptree = config_ptree;
         }
 
         virtual ~Partitions_Parser(){};
 
         //The function that parses the json file and build a unordered set and vector of structs for each line in the json list
         void parse_partition_file() {
-            std::cout << "\nroot_tree: " << tree.size() << std::endl;
+            std::cout << "\nroot_tree: " << config_ptree.size() << std::endl;
 
             //Declare two partition_data type structs
             PartitionData part_data;
@@ -55,7 +55,7 @@ class Partitions_Parser {
             PartitionData::Tuple tmp_tuple;
             std::vector<PartitionData::Tuple> remote_conn_vec;
             int part_counter = 0;
-            for(auto &partition: tree.get_child("partitions"))  {
+            for(auto &partition: config_ptree.get_child("partitions"))  {
                 //Get partition id
                 std::string part_id = (partition.second).get<std::string>("id");
 
@@ -85,7 +85,7 @@ class Partitions_Parser {
 
                 if( part.at("remote-connections").get_type() == geojson::PropertyType::List ) 
                 {
-                    //It is valid to have no remote connections, but the backend property tree parser
+                    //It is valid to have no remote connections, but the backend property config_ptree parser
                     //can't represent empty lists/objects, so it turns into an empty string (which is iterable)
                     //so we check to ensure the remote connections are a list type (not string) before we attempt
                     //to process the remote-connections.  If they are empty, this step gets skipped entirely.
@@ -179,7 +179,7 @@ class Partitions_Parser {
         std::vector<std::tuple<int, std::string, std::string> > remote_connections;
         std::tuple<int, std::string, std::string> remote_tuple;
 
-        boost::property_tree::ptree tree;
+        boost::property_tree::ptree config_ptree;
 };
 
 #endif // NGEN_MPI_ACTIVE

include/core/SurfaceLayer.hpp

@@ -30,6 +30,13 @@ namespace ngen
         */
         void update_models() override;
 
+        /**
+        * @brief Get a class id for this layer object
+        * 
+        * @return int
+        */
+        int class_id() { return LayerClass::kSurfaceLayer; }
+
         private:
 
         std::vector<std::string> nexus_ids;