diff --git a/data/bmi/fortran/noah-owp-modular-init-agg-1.namelist.input b/data/bmi/fortran/noah-owp-modular-init-agg-1.namelist.input new file mode 100644 index 0000000000..860f848fd8 --- /dev/null +++ b/data/bmi/fortran/noah-owp-modular-init-agg-1.namelist.input @@ -0,0 +1,68 @@ +&timing ! and output + dt = 1800.0 ! timestep [seconds] + startdate = "199801010630" ! UTC time start of simulation (YYYYMMDDhhmm) + enddate = "199901010630" ! UTC time end of simulation (YYYYMMDDhhmm) + forcing_filename = "data/config/bmi/sugar_creek/noah-mp-modular.dat" ! change filename to match your forcing data + output_filename = "data/config/bmi/sugar_creek/output.nc" +/ + +¶meters + parameter_dir = "extern/noah-owp-modular/noah-owp-modular/parameters/" + general_table = "GENPARM.TBL" ! general param tables and misc params + soil_table = "SOILPARM.TBL" ! soil param table + noahowp_table = "MPTABLE.TBL" ! noah-mp related param tables + soil_class_name = "STAS" ! soil class data source - "STAS" or "STAS-RUC" + veg_class_name = "MODIFIED_IGBP_MODIS_NOAH" ! vegetation class data source - "MODIFIED_IGBP_MODIS_NOAH" or "USGS" +/ + +&location ! for point runs, needs to be modified for gridded + lat = 40.01 ! latitude [degrees] + lon = -88.37 ! longitude [degrees] + terrain_slope = 0.0 ! terrain slope [degrees] + azimuth = 0.0 ! terrain azimuth or aspect [degrees clockwise from north] +/ + +&forcing + ZREF = 10.0 ! measurment height for wind speed + rain_snow_thresh = 1.0 ! rain-snow temperature threshold (degrees Celcius) +/ + +&model_options + precip_phase_option = 2 + snow_albedo_option = 2 ! 1 = BATS, 2 = CLASS + dynamic_veg_option = 1 + runoff_option = 8 + drainage_option = 8 + frozen_soil_option = 1 + dynamic_vic_option = 1 + radiative_transfer_option = 3 + sfc_drag_coeff_option = 1 + canopy_stom_resist_option = 1 + crop_model_option = 0 + snowsoil_temp_time_option = 3 + soil_temp_boundary_option = 2 + supercooled_water_option = 1 + stomatal_resistance_option = 1 + evap_srfc_resistance_option = 1 + subsurface_option = 1 +/ + +&structure + isltyp = 1 ! soil texture class + nsoil = 4 ! number of soil levels + nsnow = 3 ! number of snow levels + nveg = 20 ! number of vegetation types + vegtyp = 1 ! vegetation type modis + croptype = 0 ! crop type (0 = no crops) + sfctyp = 1 ! land surface type, 1:soil, 2:lake + soilcolor = 4 ! soil color code +/ + +&initial_values + dzsnso = 0.0, 0.0, 0.0, 0.1, 0.3, 0.6, 1.0 ! level thickness [m] + sice = 0.0, 0.0, 0.0, 0.0 ! initial soil ice profile [vol] + sh2o = 0.3, 0.3, 0.3, 0.3 ! initial soil liquid profile [vol] + zwt = -2.0 ! initial water table depth below surface [m] +/ + + diff --git a/data/catchment_data_multilayer.geojson b/data/catchment_data_multilayer.geojson new file mode 100644 index 0000000000..aa79fc9eab --- /dev/null +++ b/data/catchment_data_multilayer.geojson @@ -0,0 +1,11 @@ +{ +"type": "FeatureCollection", +"name": "catchment_data", +"crs": {"type": "name", "properties": {"name": "urn:ogc:def:crs:OGC:1.3:CRS84"}}, +"features": [ +{ "type": "Feature", "properties": { "layer": 20, "agg": 0, "areasqkm": 55.356841159445864, "id": "agg-1" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -80.715617203572421, 35.162592318783524 ], [ -80.715461282861213, 35.163159749477792 ], [ -80.715345548657382, 35.164061070133094 ], [ -80.714744503892121, 35.165247080610385 ], [ -80.714185954379701, 35.166247633685273 ], [ -80.714122357235766, 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23:00:00,4.099999904632568,396.70001220703125,0.0,100260.0,0.012600000016391277,290.8000183105469,1.399999976158142,0.699999988079071,4.172046359010436e-07 diff --git a/include/core/HY_Features.hpp b/include/core/HY_Features.hpp index 0f4d5b2c00..335a7489a8 100644 --- a/include/core/HY_Features.hpp +++ b/include/core/HY_Features.hpp @@ -2,6 +2,7 @@ #define HY_FEATURES_H #include +#include #include #include @@ -59,24 +60,14 @@ namespace hy_features { /** * @brief Construct a new HY_Features object from a Network and a set of formulations. * - * Constructs the HY_Catchment objects for each catchment feature in the network, and attaches tha formaulation + * Constructs the HY_Catchment objects for each catchment connecting them with the provided link_key attaches the formulation * associated with the catchment found in the Formulation_Manager. Also constucts each nexus as a HY_PointHydroNexus. * - * @param network - * @param formulations - */ - HY_Features( network::Network network, std::shared_ptr formulations); - - /** - * @brief Construct a new HY_Features object From a GeoJSON feature collection and a set of formulations. - * - * Constructs the network::Network index from the GeoJSON feature collection and link_key and then - * \copydetails HY_Features::HY_Features(network::Network,std::shared_ptr) - * * @param catchments - * @param link_key + * @param link_key * @param formulations */ + HY_Features( geojson::GeoJSON catchments, std::string* link_key, std::shared_ptr formulations); /** @@ -116,6 +107,21 @@ namespace hy_features { */ inline auto catchments(){return network.filter("cat");} + /** + * @brief An iterator of only the catchment feature ids from only the specified layer + * + * @return auto + */ + inline auto catchments(long lyr) { + return network.filter("cat",lyr); + } + + /** + * @brief Return a set of layers that contain a catchment + */ + + inline const auto& layers() { return hf_layers; } + /** * @brief An iterator of only the nexus feature ids * @@ -180,6 +186,8 @@ namespace hy_features { private: + void init(); + /** * @brief Internal mapping of catchment id -> HY_Catchment pointer. * @@ -204,6 +212,13 @@ namespace hy_features { */ std::shared_ptr formulations; + /** + * @brief The set of layers that contain at least one catchment + */ + std::set hf_layers; + + geojson::GeoJSON fabric; + }; } diff --git a/include/core/HY_Features_MPI.hpp b/include/core/HY_Features_MPI.hpp index cd92e5584a..ec26abbda5 100644 --- a/include/core/HY_Features_MPI.hpp +++ b/include/core/HY_Features_MPI.hpp @@ -4,6 +4,7 @@ #ifdef NGEN_MPI_ACTIVE #include +#include #include #include @@ -32,6 +33,16 @@ namespace hy_features { inline bool is_remote_sender_nexus(const std::string& id) { return _nexuses.find(id) != _nexuses.end() && _nexuses[id]->is_remote_sender(); } + + inline auto catchments(long lyr) { + return network.filter("cat",lyr); + } + + /** + * @brief Return a set of layers that contain a catchment + */ + + inline const auto& layers() { return hf_layers; } inline std::vector> destination_nexuses(const std::string& id) { std::vector> downstream; @@ -77,6 +88,7 @@ namespace hy_features { std::unordered_map> _nexuses; network::Network network; std::shared_ptr formulations; + std::set hf_layers; int mpi_rank; int mpi_num_procs; diff --git a/include/core/Layer.hpp b/include/core/Layer.hpp new file mode 100644 index 0000000000..e25fa66884 --- /dev/null +++ b/include/core/Layer.hpp @@ -0,0 +1,147 @@ +#ifndef __NGEN_LAYER__ +#define __NGEN_LAYER__ + +#include "LayerData.hpp" +#include "Simulation_Time.hpp" + +#ifdef NGEN_MPI_ACTIVE +#include "HY_Features_MPI.hpp" +#else +#include "HY_Features.hpp" +#endif + +namespace ngen +{ + + class Layer + { + public: + + #ifdef NGEN_MPI_ACTIVE + using feature_type = hy_features::HY_Features_MPI; + #else + using feature_type = hy_features::HY_Features; + #endif + + Layer( + const LayerDescription& desc, + const std::vector& p_u, + const Simulation_Time& s_t, + feature_type& f, + geojson::GeoJSON cd, + long idx) : + description(desc), + processing_units(p_u), + simulation_time(s_t), + features(f), + catchment_data(cd), + output_time_index(idx) + { + + } + + virtual ~Layer() {} + + /*** + * @brief Return the next timestep that will be processed by this layer in epoch time units + */ + time_t next_timestep_epoch_time() { return simulation_time.next_timestep_epoch_time(); } + + + /*** + * @brief Return the last timestep that was processed by this layer in epoch time units + */ + time_t current_timestep_epoch_time() { return simulation_time.get_current_epoch_time(); } + + + /*** + * @brief Return the numeric id of this layer + */ + int get_id() const { return this->description.id; } + + /*** + * @brief Return the name of this layer + */ + const std::string& get_name() const { return this->description.name; } + + /*** + * @brief Return this time_step interval used for this layer + */ + const double get_time_step() const { return this->description.time_step; } + + /*** + * @brief Return the units for the time_step value of this layer + */ + const std::string& get_time_step_units() const { return this->description.time_step_units; } + + /*** + * @brief Run one simulation timestep for each model in this layer + */ + virtual void update_models() + { + auto idx = simulation_time.next_timestep_index(); + auto step = simulation_time.get_output_interval_seconds(); + + //std::cout<<"Output Time Index: "<(r); + double response = r_c->get_response(output_time_index, simulation_time.get_output_interval_seconds()); + std::string output = std::to_string(output_time_index)+","+current_timestamp+","+ + r_c->get_output_line_for_timestep(output_time_index)+"\n"; + r_c->write_output(output); + //TODO put this somewhere else. For now, just trying to ensure we get m^3/s into nexus output + double area; + try{ + area = catchment_data->get_feature(id)->get_property("areasqkm").as_real_number(); + } + catch(std::invalid_argument &e) + { + area = catchment_data->get_feature(id)->get_property("area_sqkm").as_real_number(); + } + double response_m_s = response * (area * 1000000); + //TODO put this somewhere else as well, for now, an implicit assumption is that a module's get_response returns + //m/timestep + //since we are operating on a 1 hour (3600s) dt, we need to scale the output appropriately + //so no response is m^2/hr...m^2/hr * 1hr/3600s = m^3/hr + double response_m_h = response_m_s / 3600.0; + //update the nexus with this flow + for(auto& nexus : features.destination_nexuses(id)) { + //TODO in a DENDRITIC network, only one destination nexus per catchment + //If there is more than one, some form of catchment partitioning will be required. + //for now, only contribute to the first one in the list + nexus->add_upstream_flow(response_m_h, id, output_time_index); + /*std::cerr << "Add water to nexus ID = " << nexus->get_id() << " from catchment ID = " << id << " value = " + << response << ", ID = " << id << ", time-index = " << output_time_index << std::endl; */ + break; + } + + } //done catchments + + ++output_time_index; + if ( output_time_index < simulation_time.get_total_output_times() ) + { + simulation_time.advance_timestep(); + } + } + + + protected: + + const LayerDescription description; + const std::vector processing_units; + Simulation_Time simulation_time; + feature_type& features; + const geojson::GeoJSON catchment_data; + long output_time_index; + + }; +} + +#endif \ No newline at end of file diff --git a/include/core/LayerData.hpp b/include/core/LayerData.hpp new file mode 100644 index 0000000000..9820402ba5 --- /dev/null +++ b/include/core/LayerData.hpp @@ -0,0 +1,76 @@ +#ifndef __NGEN_LAYER_DATA__ +#define __NGEN_LAYER_DATA__ + +#include +#include +#include + +namespace ngen +{ + /** + * @brief A simple structure to hold meta data related to a computational layer + * + * This structure is used to hold information about a layers time_step, include value and units + * as well as the numeric id that is used to store and retrieve the layer + */ + + struct LayerDescription + { + std::string name; //> The name of the computational layer + std::string time_step_units; //> The time units that time_step is expressed in + int id; //> The layer id which determines the order that this layer will be processed in + double time_step; //> The time step that will be used for models in this layer + }; + + /** + * @brief A class to hold and manage layer metadata for the system + * + * Layer can be accessed by interger id the default valid range is -20 .. 80 + */ + + class LayerDataStorage + { + public: + + LayerDataStorage() {} + + ~LayerDataStorage() {} + + /** + * @brief return the layer object at this numeric id + */ + + const LayerDescription& get_layer(int id) const + { + return stored_layers.at(id); + } + + /** + * @brief store a new layer description in the indicated id slot + */ + + void put_layer(const LayerDescription& desc, int id) + { + stored_layers[id] = desc; + keys.push_back(id); + } + + /*** + * @brief check to see if a layer has been associated with an id number + */ + + bool exists(int id) + { + return stored_layers.find(id) != stored_layers.end(); + } + + std::vector& get_keys() { return keys; } + + private: + + std::unordered_map stored_layers; //< Map object that is used to store layer data objects + std::vector keys; //< A list of the currently valid map keys + }; +} + +#endif \ No newline at end of file diff --git a/include/core/Partition_Parser.hpp b/include/core/Partition_Parser.hpp index 541147d97c..9c0e740bfb 100644 --- a/include/core/Partition_Parser.hpp +++ b/include/core/Partition_Parser.hpp @@ -93,29 +93,37 @@ class Partitions_Parser { } part_data.nexus_ids = nexus_ids; nexus_ids.clear(); - if( part.at("remote-connections").get_type() == geojson::PropertyType::List ) { + + if( part.at("remote-connections").get_type() == geojson::PropertyType::List ) + { //It is valid to have no remote connections, but the backend property tree parser - //can't represent empty lists/objects, so it turns into an ampty string (which is iterable) + //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. //Get remote-connections and set the corresponding part_data struct member + for (auto &remote_conn : part.at("remote-connections").as_list()) { - remote_mpi_rank = remote_conn.at("mpi-rank").as_natural_number(); - remote_nex_id = remote_conn.at("nex-id").as_string(); - remote_cat_id = remote_conn.at("cat-id").as_string(); - direction = remote_conn.at("cat-direction").as_string(); - tmp_tuple = std::make_tuple(remote_mpi_rank, remote_nex_id, remote_cat_id, direction); - remote_conn_vec.push_back(tmp_tuple); + if ( remote_conn.get_type() != geojson::PropertyType::String ) + { + remote_mpi_rank = remote_conn.at("mpi-rank").as_natural_number(); + remote_nex_id = remote_conn.at("nex-id").as_string(); + remote_cat_id = remote_conn.at("cat-id").as_string(); + direction = remote_conn.at("cat-direction").as_string(); + tmp_tuple = std::make_tuple(remote_mpi_rank, remote_nex_id, remote_cat_id, direction); + remote_conn_vec.push_back(tmp_tuple); + } } } + part_data.remote_connections = remote_conn_vec; remote_conn_vec.clear(); //Push part_data struct the vector partition_ranks.push_back(part_data); - part_counter++; + part_counter++; + } }; @@ -158,7 +166,7 @@ class Partitions_Parser { */ return part_data; - }; + } //This example function shows how to get a specific member of the struct int get_mpi_rank(int part_id) @@ -170,7 +178,7 @@ class Partitions_Parser { std::cout << "mpi_world_rank: " << mpi_world_rank << std::endl; return mpi_world_rank; - }; + } // partition_ranks is a vector of struct: PartitionData std::vector partition_ranks; diff --git a/include/core/SurfaceLayer.hpp b/include/core/SurfaceLayer.hpp new file mode 100644 index 0000000000..30bea7a98d --- /dev/null +++ b/include/core/SurfaceLayer.hpp @@ -0,0 +1,40 @@ +#ifndef __NGEN_SURFACE_LAYER__ +#define __NGEN_SURFACE_LAYER__ + +#include "Layer.hpp" + +namespace ngen +{ + class SurfaceLayer : public Layer + { + public: + + SurfaceLayer( + const LayerDescription& desc, + const std::vector& p_u, + const Simulation_Time& s_t, + feature_type& f, + geojson::GeoJSON cd, + long idx, + const std::vector& n_u, + std::unordered_map& output_files) : + Layer(desc,p_u,s_t,f,cd,idx), + nexus_ids(n_u), + nexus_outfiles(output_files) + { + + } + + /*** + * @brief Run one simulation timestep for each model in this layer + */ + void update_models() override; + + private: + + std::vector nexus_ids; + std::unordered_map& nexus_outfiles; + }; +} + +#endif \ No newline at end of file diff --git a/include/core/catchment/HY_Catchment.hpp b/include/core/catchment/HY_Catchment.hpp index d31660dba9..5b0329ec32 100644 --- a/include/core/catchment/HY_Catchment.hpp +++ b/include/core/catchment/HY_Catchment.hpp @@ -21,7 +21,7 @@ class HY_Catchment : public HY_HydroFeature public: HY_Catchment(); - HY_Catchment(std::string id, Nexuses inflows, Nexuses outflows, std::shared_ptr realization): + HY_Catchment(std::string id, Nexuses inflows, Nexuses outflows, std::shared_ptr realization, long lyr = 0): id(std::move(id)), inflows(std::move(inflows)), outflows(std::move(outflows)), @@ -30,10 +30,40 @@ class HY_Catchment : public HY_HydroFeature conjoint_catchment({}), upper_catchment({}), lower_catchment({}), - realization(realization){} + realization(realization), + layer(lyr){} virtual ~HY_Catchment(); const Nexuses& get_outflow_nexuses(){ return outflows; } std::shared_ptr realization; + + /*! \brief get the hydrofabric layer of this catchment + * + * The hydrofabric is divided into multiple layers which are intended to be processed in decreasing numeric order. + * The current defined layers are: + * 80 -- Atmospheric Models (high) + * 60 -- Atmospeheric Models (low) + * 40 -- Canopy Models + * 20 -- Snow melt models + * 0 -- Surface water processes + * -20 -- Ground Water (Shallow) + * -40 -- Ground Water (Deep) + */ + long get_layer() { return layer; } + + /*! \brief set the layer of this catchment + * + * This function changes the layer of a catchment. It should only be used if the type of model being used in the catchment changes. + */ + void set_layer(long lyr) { layer = lyr; } + + const long ATMOSPHERIC_LAYER_HIGH = 80; //!< This is the catchment layer for high air atmospheric models + const long ATMOSPHERIC_Layer_LOW = 60; //!< This is the catchment layer for low air atmospheric models + const long CANOPY_LAYER = 40; //!< This is the catchment layer for canopy layer models + const long SNOW_LAYER = 20; //!< This is the catchment layer for surface snow models + const long SURFACE_LAYER = 0; //!< This is the catchment layer for surface water models + const long GROUND_WATER_SHALLOW_LAYER = -20; //!< This is the catchment layer for shallow groundwater models + const long GROUND_WATER_DEEP_LAYER = -40; //!< This is the catchment layer for deep groundwater models + protected: private: @@ -47,6 +77,8 @@ class HY_Catchment : public HY_HydroFeature Catchment upper_catchment; Catchment lower_catchment; + long layer; + }; #endif // HY_CATCHMENT_H diff --git a/include/core/network.hpp b/include/core/network.hpp index d14726efb8..9949813f4d 100644 --- a/include/core/network.hpp +++ b/include/core/network.hpp @@ -18,6 +18,9 @@ #include namespace network { + + const static int DEFAULT_LAYER_ID = 0; + /** * @brief Selector for using different traversal orders for linear return */ @@ -206,12 +209,53 @@ namespace network { | boost::adaptors::transformed([this](int const& i) { return get_id(i); }) | boost::adaptors::filtered([type](std::string const& s) { if(type == "nex"){ - return s.substr(0,3) == type || s.substr(0,3) == "tnx"; + return s.substr(0,3) == type || s.substr(0,3) == "tnx" || s.substr(0,4) == "tnex"; + } + if(type == "cat"){ + return s.substr(0,3) == type || s.substr(0,3) == "agg"; } return s.substr(0,3) == type; }); } + + /** + * @brief Provides a boost transform_iterator, filtered by @p type , to the topologically ordered graph vertex string id's + * + * This function is useful when only interested in a single type of feature. + * It returns the a topologically ordered set of feature ids. For example, to print all catchments + * in the network: + * @code {.cpp} + * for( auto catchment : network.filter('cat') ){ + * std::cout << catchment; + * } + * @endcode + * + * @param type The type of feature to filter for, i.e. 'cat', 'nex' + * @param target_layer The layer that filtered results should be in + * @param order What order to return results in + * @return auto + */ + auto filter(std::string type, int target_layer, SortOrder order = SortOrder::Topological) + { + //todo need to worry about valivdating input??? + //if type isn't found as a prefix, this iterator range should be empty, + //which is a reasonable semantic + return get_sorted_index(order) | boost::adaptors::reversed + | boost::adaptors::transformed([this](int const& i) { return get_id(i); }) + | boost::adaptors::filtered([this,type,target_layer](std::string const& s) { + if(type == "nex"){ + return (s.substr(0,3) == type || s.substr(0,3) == "tnx" || s.substr(0,4) == "tnex") && + (this->layer_map.find(s) != this->layer_map.end() && this->layer_map[s] == target_layer); + } + if(type == "cat"){ + return (s.substr(0,3) == type || s.substr(0,3) == "agg") && + (this->layer_map.find(s) != this->layer_map.end() && this->layer_map[s] == target_layer); + } + return (s.substr(0,3) == type) && + (this->layer_map.find(s) != this->layer_map.end() && (this->layer_map[s] == target_layer)); + }); + } /** * @brief Get the string id of a given graph vertex_descriptor @p idx * @@ -316,6 +360,12 @@ namespace network { * */ std::unordered_map descriptor_map; + + /** + * @brief Mapping of identifier to hydrofabric layer + * + */ + std::unordered_map layer_map; /** * @brief Get an index of the graph in a particular order. diff --git a/include/geojson/features/FeatureBase.hpp b/include/geojson/features/FeatureBase.hpp index 7df0c8a423..c888d5983a 100644 --- a/include/geojson/features/FeatureBase.hpp +++ b/include/geojson/features/FeatureBase.hpp @@ -384,7 +384,11 @@ namespace geojson { return bounding_box; } - PropertyMap get_properties() const { + const PropertyMap& get_properties() const { + return properties; + } + + PropertyMap& get_properties() { return properties; } diff --git a/include/realizations/catchment/Formulation_Manager.hpp b/include/realizations/catchment/Formulation_Manager.hpp index 1ad5d8c4d7..5133d323cf 100644 --- a/include/realizations/catchment/Formulation_Manager.hpp +++ b/include/realizations/catchment/Formulation_Manager.hpp @@ -16,8 +16,9 @@ #include "features/Features.hpp" #include #include "Formulation_Constructors.hpp" -#include "Simulation_Time.h" +#include "Simulation_Time.hpp" #include "routing/Routing_Params.h" +#include "LayerData.hpp" namespace realization { @@ -129,6 +130,62 @@ namespace realization { */ this->Simulation_Time_Object = std::make_shared(simulation_time_config); + /** + * Read the layer descriptions + */ + + // try to get the json node + auto layers_json_array = tree.get_child_optional("layers"); + + // check to see if the node existed + if (!layers_json_array) { + // layer description struct + ngen::LayerDescription layer_desc; + + // extract and store layer data from the json + layer_desc.name = "surface layer"; + layer_desc.id = 0; + layer_desc.time_step = 3600; + layer_desc.time_step_units = "s"; + + // add the layer to storage + layer_storage.put_layer(layer_desc, layer_desc.id); + } + else + { + for (std::pair layer_config : *layers_json_array) + { + // layer description struct + ngen::LayerDescription layer_desc; + + // extract and store layer data from the json + layer_desc.name = layer_config.second.get("name"); + layer_desc.id = layer_config.second.get("id"); + layer_desc.time_step = layer_config.second.get("time_step"); + boost::optional layer_units = layer_config.second.get_optional("time_step_units"); + if (*layer_units == "") layer_units = "s"; + layer_desc.time_step_units = *layer_units; + + // check to see if this layer was allready defined + if (layer_storage.exists(layer_desc.id) ) + { + std::string message = "A layer with id = "; + message += std::to_string(layer_desc.id); + message += " was defined more than once"; + + std::runtime_error r_error(message); + + throw r_error; + } + + // add the layer to storage + layer_storage.put_layer(layer_desc, layer_desc.id); + + // debuggin print to see parsed data + std::cout << layer_desc.name << ", " << layer_desc.id << ", " << layer_desc.time_step << ", " << layer_desc.time_step_units << "\n"; + } + } + /** * Read routing configurations from configuration file */ @@ -302,6 +359,12 @@ namespace realization { return "./"; } + /** + * @brief return the layer storage used for formulations + * @return a reference to the LayerStorageObject + */ + ngen::LayerDataStorage& get_layer_metadata() { return layer_storage; } + protected: std::shared_ptr construct_formulation_from_tree( @@ -685,6 +748,8 @@ namespace realization { std::shared_ptr routing_config; bool using_routing = false; + + ngen::LayerDataStorage layer_storage; }; } #endif // NGEN_FORMULATION_MANAGER_H diff --git a/include/simulation_time/Simulation_Time.h b/include/simulation_time/Simulation_Time.hpp similarity index 69% rename from include/simulation_time/Simulation_Time.h rename to include/simulation_time/Simulation_Time.hpp index 02832f7b4c..947ef89dd4 100644 --- a/include/simulation_time/Simulation_Time.h +++ b/include/simulation_time/Simulation_Time.hpp @@ -3,6 +3,8 @@ #include #include +#include +#include /** * @brief simulation_time_params providing configuration information for simulation time period. @@ -66,6 +68,12 @@ class Simulation_Time total_output_times = simulation_total_time_seconds / output_interval_seconds + 1; } + Simulation_Time(const Simulation_Time& t, int interval) : Simulation_Time(t) + { + output_interval_seconds = interval; + total_output_times = simulation_total_time_seconds / output_interval_seconds + 1; + } + /** * @brief Accessor to the total number of time steps * @return total_output_times @@ -84,12 +92,23 @@ class Simulation_Time return output_interval_seconds; } + /** + * @brief Accessor to the the current simulation time + * @return current_date_time_epoch + */ + + time_t get_current_epoch_time() + { + return current_date_time_epoch; + } + /** * @brief Accessor to the current timestamp string * @return current_timestamp */ std::string get_timestamp(int current_output_time_index) { + // "get" method mutates state! current_date_time_epoch = start_date_time_epoch + current_output_time_index * output_interval_seconds; struct tm *temp_gmtime_struct; @@ -107,6 +126,42 @@ class Simulation_Time return current_timestamp; } + inline int next_timestep_index(int epoch_time_seconds) + { + return int(epoch_time_seconds - start_date_time_epoch) / output_interval_seconds; + } + + inline int next_timestep_index() + { + return next_timestep_index(current_date_time_epoch); + } + + inline time_t next_timestep_epoch_time(int epoch_time_seconds){ + return start_date_time_epoch + ( next_timestep_index(epoch_time_seconds) * output_interval_seconds ); + } + + inline time_t next_timestep_epoch_time(){ + return next_timestep_epoch_time(current_date_time_epoch); + } + + inline int diff(const Simulation_Time& other){ + return start_date_time_epoch - other.start_date_time_epoch; + } + + /** + * @brief move this simulation time object to represent the next time step as the current time + */ + + inline void advance_timestep(){ + current_date_time_epoch += output_interval_seconds; + + if (current_date_time_epoch > end_date_time_epoch) + { + throw std::runtime_error("Simulation time objects current time exceeded the end_date_time_epoch value for that object"); + } + } + + private: int total_output_times; diff --git a/src/NGen.cpp b/src/NGen.cpp index e19cc2d90b..382bba42bb 100644 --- a/src/NGen.cpp +++ b/src/NGen.cpp @@ -17,6 +17,7 @@ #include #include +#include #ifdef WRITE_PID_FILE_FOR_GDB_SERVER #include @@ -51,6 +52,9 @@ int mpi_rank; int mpi_num_procs; #endif +#include +#include + std::unordered_map nexus_outfiles; int main(int argc, char *argv[]) { @@ -306,11 +310,11 @@ int main(int argc, char *argv[]) { #endif //NGEN_ROUTING_ACTIVE std::string link_key = "toid"; - #ifdef NGEN_MPI_ACTIVE nexus_collection->link_features_from_property(nullptr, &link_key); + #ifdef NGEN_MPI_ACTIVE hy_features::HY_Features_MPI features = hy_features::HY_Features_MPI(local_data, nexus_collection, manager, mpi_rank, mpi_num_procs); #else - hy_features::HY_Features features = hy_features::HY_Features(catchment_collection, &link_key, manager); + hy_features::HY_Features features = hy_features::HY_Features(nexus_collection, manager); #endif //validate dendritic connections @@ -333,74 +337,105 @@ int main(int argc, char *argv[]) { std::cout<<"Running Models"<get_layer_metadata(); + + // get the keys for the existing layers + std::vector& keys = layer_meta_data.get_keys(); + + // get the converted time steps for layers + double min_time_step; + double max_time_step; + std::vector time_steps; + for(int i = 0; i < keys.size(); ++i) + { + auto& m_data = layer_meta_data.get_layer(keys[i]); + double c_value = UnitsHelper::get_converted_value(m_data.time_step_units,m_data.time_step,"s"); + time_steps.push_back(c_value); + } + + std::vector output_time_index; + output_time_index.resize(keys.size()); + std::fill(output_time_index.begin(), output_time_index.end(),0); + + // now create the layer objects + + // first make sure that the layer are listed in decreasing order + boost::range::sort(keys, std::greater()); + + std::vector > layers; + layers.resize(keys.size()); + + for(long i = 0; i < keys.size(); ++i) + { + auto& desc = layer_meta_data.get_layer(keys[i]); + std::vector cat_ids; + + // make a new simulation time object with a different output interval + Simulation_Time sim_time(*manager->Simulation_Time_Object, time_steps[i]); + + for ( std::string id : features.catchments(keys[i]) ) { cat_ids.push_back(id); } + if (keys[i] != 0 ) + { + layers[i] = std::make_shared(desc, cat_ids, sim_time, features, catchment_collection, 0); + } + else + { + layers[i] = std::make_shared(desc, cat_ids, sim_time, features, catchment_collection, 0, nexus_subset_ids, nexus_outfiles); + } + + } + //Now loop some time, iterate catchments, do stuff for total number of output times - for(int output_time_index = 0; output_time_index < manager->Simulation_Time_Object->get_total_output_times(); output_time_index++) { - //std::cout<<"Output Time Index: "<Simulation_Time_Object->get_timestamp(output_time_index); - for(const auto& id : features.catchments()) { - //std::cout<<"Running cat "<(r); - double response = r_c->get_response(output_time_index, 3600.0); - std::string output = std::to_string(output_time_index)+","+current_timestamp+","+ - r_c->get_output_line_for_timestep(output_time_index)+"\n"; - r_c->write_output(output); - //TODO put this somewhere else. For now, just trying to ensure we get m^3/s into nexus output - try{ - response *= (catchment_collection->get_feature(id)->get_property("areasqkm").as_real_number() * 1000000); - }catch(std::invalid_argument &e) + auto num_times = manager->Simulation_Time_Object->get_total_output_times(); + for( int count = 0; count < num_times; count++) + { + // The Inner loop will advance all layers unless doing so will break one of two constraints + // 1) A layer may not proceed ahead of the master simulation object's current time + // 2) A layer may not proceed ahead of any layer that is computed before it + // The do while loop ensures that all layers are tested at least once while allowing + // layers with small time steps to be updated more than once + // If a layer with a large time step is after a layer with a small time step the + // layer with the large time step will wait for multiple timesteps from the preceeding + // layer. + + // this is the time that layers are trying to reach (or get as close as possible) + auto next_time = manager->Simulation_Time_Object->next_timestep_epoch_time(); + + // this is the time that the layer above the current layer is at + auto prev_layer_time = next_time; + + // this is the time that the least advanced layer is at + auto layer_min_next_time = next_time; + do + { + for ( auto& layer : layers ) { - response *= (catchment_collection->get_feature(id)->get_property("area_sqkm").as_real_number() * 1000000); - } - //TODO put this somewhere else as well, for now, an implicit assumption is that a modules get_response returns - //m/timestep - //since we are operating on a 1 hour (3600s) dt, we need to scale the output appropriately - //so no response is m^2/hr...m^2/hr * 1hr/3600s = m^3/hr - response /= 3600.0; - //update the nexus with this flow - for(auto& nexus : features.destination_nexuses(id)) { - //TODO in a dendritic network, only one destination nexus per catchment - //If there is more than one, some form of catchment partitioning will be required. - //for now, only contribute to the first one in the list - nexus->add_upstream_flow(response, id, output_time_index); - break; - } - } //done catchments - //At this point, could make an internal routing pass, extracting flows from nexuses and routing - //across the flowpath to the next nexus. - //Once everything is updated for this timestep, dump the nexus output - for(const auto& id : features.nexuses()) { - #ifdef NGEN_MPI_ACTIVE - if (!features.is_remote_sender_nexus(id)) { //Ensures only one side of the dual sided remote nexus actually doing this... - #endif - - //Get the correct "requesting" id for downstream_flow - const auto& nexus = features.nexus_at(id); - const auto& cat_ids = nexus->get_receiving_catchments(); - std::string cat_id; - if( cat_ids.size() > 0 ) { - //Assumes dendritic, e.g. only a single downstream...it will consume 100% of the available flow - cat_id = cat_ids[0]; + auto layer_next_time = layer->next_timestep_epoch_time(); + + // only advance if you would not pass the master next time and the previous layer next time + if ( layer_next_time <= next_time && layer_next_time <= prev_layer_time) + { + layer->update_models(); + prev_layer_time = layer_next_time; } - else { - //This is a terminal node, SHOULDN'T be remote, so ID shouldn't matter too much - cat_id = "terminal"; + else + { + layer_min_next_time = prev_layer_time = layer->current_timestep_epoch_time(); } - double contribution_at_t = features.nexus_at(id)->get_downstream_flow(cat_id, output_time_index, 100.0); - if(nexus_outfiles[id].is_open()) { - nexus_outfiles[id] << output_time_index << ", " << current_timestamp << ", " << contribution_at_t << std::endl; + + if ( layer_min_next_time > layer_next_time) + { + layer_min_next_time = layer_next_time; } - #ifdef NGEN_MPI_ACTIVE - } - #endif - //std::cout<<"\tNexus "<Simulation_Time_Object->advance_timestep(); + } - //Note: Use below if developing in-memory transfer of nexus flows to routing - //If using below, then another single time vector would be needed to hold the timestamp - //nexus_flows[id].push_back(contribution_at_t); - } //done nexuses } //done time std::cout<<"Finished "<Simulation_Time_Object->get_total_output_times()<<" timesteps."< formulations) - :HY_Features(network::Network(fabric), formulations) +HY_Features::HY_Features(geojson::GeoJSON linked_hydro_fabric, std::shared_ptr formulations) + :network(linked_hydro_fabric), formulations(formulations), fabric(linked_hydro_fabric) { - /* If you nest the constuctor calls like this, then the network, while valid in the next constructor, - is empty once the collection is fully instansiated... - HY_Features(network::Network(fabric)); - */ + init(); } -HY_Features::HY_Features(network::Network network, std::shared_ptr formulations) - :network(network), formulations(formulations) +HY_Features::HY_Features( geojson::GeoJSON catchments, std::string* link_key, std::shared_ptr formulations) + : network(catchments, link_key), formulations(formulations), fabric(catchments) { - std::string feat_id; - std::string feat_type; - std::vector origins, destinations; - - for(const auto& feat_idx : network){ - feat_id = network.get_id(feat_idx);//feature->get_id(); - feat_type = feat_id.substr(0, 3); - - destinations = network.get_destination_ids(feat_id); - if(feat_type == "cat") - { - //Find and prepare formulation - auto formulation = formulations->get_formulation(feat_id); - formulation->set_output_stream(formulations->get_output_root() + feat_id + ".csv"); - // TODO: add command line or config option to have this be omitted - //FIXME why isn't default param working here??? get_output_header_line() fails. - formulation->write_output("Time Step,""Time,"+formulation->get_output_header_line(",")+"\n"); - //Find upstream nexus ids - origins = network.get_origination_ids(feat_id); - //Create the HY_Catchment with the formulation realization - std::shared_ptr c = std::make_shared( - HY_Catchment(feat_id, origins, destinations, formulation) - ); - - _catchments.emplace(feat_id, c); - } - else if(feat_type == "nex" || feat_type == "tnx") - { - _nexuses.emplace(feat_id, std::make_unique( - HY_PointHydroNexus(feat_id, destinations) )); - } - else - { - std::cerr<<"HY_Features::HY_Features unknown feature identifier type "< formulations): - HY_Features(network::Network(catchments, link_key), formulations){ +void HY_Features::init() +{ + std::string feat_id; + std::string feat_type; + std::vector origins, destinations; + + for(const auto& feat_idx : network) + { + feat_id = network.get_id(feat_idx);//feature->get_id(); + feat_type = feat_id.substr(0, 3); + + destinations = network.get_destination_ids(feat_id); + if(feat_type == "cat" || feat_type == "agg") + { + //Find and prepare formulation + auto formulation = formulations->get_formulation(feat_id); + formulation->set_output_stream(formulations->get_output_root() + feat_id + ".csv"); // MERGE bd63e5b + // TODO: add command line or config option to have this be omitted + //FIXME why isn't default param working here??? get_output_header_line() fails. + formulation->write_output("Time Step,""Time,"+formulation->get_output_header_line(",")+"\n"); + //Find upstream nexus ids + origins = network.get_origination_ids(feat_id); + + // get the catchment layer from the hydro fabric + const auto& cat_json_node = fabric->get_feature(feat_id); + long lyr = cat_json_node->has_key("layer") ? cat_json_node->get_property("layer").as_natural_number() : 0; + + // add this layer to the set of layers if needed + if (hf_layers.find(lyr) == hf_layers.end() ) + { + hf_layers.insert(lyr); + } + + //Create the HY_Catchment with the formulation realization + std::shared_ptr c = std::make_shared( + HY_Catchment(feat_id, origins, destinations, formulation, lyr) + ); + _catchments.emplace(feat_id, c); + } + else if(feat_type == "nex" || feat_type == "tnx") + { + _nexuses.emplace(feat_id, std::make_unique( + HY_PointHydroNexus(feat_id, destinations) )); + } + else + { + std::cerr<<"HY_Features::HY_Features unknown feature identifier type "<get_formulation(feat_id); @@ -42,9 +42,20 @@ HY_Features_MPI::HY_Features_MPI( PartitionData partition_data, geojson::GeoJSON // TODO: add command line or config option to have this be omitted //FIXME why isn't default param working here??? get_output_header_line() fails. formulation->write_output("Time Step,""Time,"+formulation->get_output_header_line(",")+"\n"); + + // get the catchment layer from the hydro fabric + const auto& cat_json_node = linked_hydro_fabric->get_feature(feat_id); + long lyr = cat_json_node->has_key("layer") ? cat_json_node->get_property("layer").as_natural_number() : 0; + + // add this layer to the set of layers if needed + if (hf_layers.find(lyr) == hf_layers.end() ) + { + hf_layers.insert(lyr); + } + //Create the HY_Catchment with the formulation realization std::shared_ptr c = std::make_shared( - HY_Catchment(feat_id, origins, destinations, formulation) + HY_Catchment(feat_id, origins, destinations, formulation, lyr) ); _catchments.emplace(feat_id, c); diff --git a/src/core/SurfaceLayer.cpp b/src/core/SurfaceLayer.cpp new file mode 100644 index 0000000000..3eec688fa8 --- /dev/null +++ b/src/core/SurfaceLayer.cpp @@ -0,0 +1,53 @@ +#include "SurfaceLayer.hpp" + +/*** + * @breif Run one simulation timestep for each model in this layer, then gather catchment output +*/ + +void ngen::SurfaceLayer::update_models() +{ + long current_time_index = output_time_index; + + Layer::update_models(); + + //At this point, could make an internal routing pass, extracting flows from nexuses and routing + //across the flowpath to the next nexus. + //Once everything is updated for this timestep, dump the nexus output + for(const auto& id : features.nexuses()) + { + std::string current_timestamp = simulation_time.get_timestamp(current_time_index); + + #ifdef NGEN_MPI_ACTIVE + if (!features.is_remote_sender_nexus(id)) { //Ensures only one side of the dual sided remote nexus actually doing this... + #endif + + //Get the correct "requesting" id for downstream_flow + const auto& nexus = features.nexus_at(id); + const auto& cat_ids = nexus->get_receiving_catchments(); + std::string cat_id; + if( cat_ids.size() > 0 ) { + //Assumes dendridic, e.g. only a single downstream...it will consume 100% of the available flow + cat_id = cat_ids[0]; + } + else { + //This is a terminal node, SHOULDN'T be remote, so ID shouldn't matter too much + cat_id = "terminal"; + } + + //std::cerr << "Requesting water from nexus, id = " << id << " at time = " <get_id(); + if( this->descriptor_map.find( feature_id ) == this->descriptor_map.end() ) { //Haven't visited this feature yet, add it to graph @@ -43,6 +44,20 @@ Network::Network( geojson::GeoJSON fabric ){ else{ v1 = this->descriptor_map[ feature_id]; } + + if ( this->layer_map.find(feature_id) == this->layer_map.end() ) + { + if ( feature->has_property("layer") ) + { + const auto& prop = feature->get_property("layer"); + this->layer_map.emplace( feature_id, prop.as_natural_number() ); + } + else + { + this->layer_map.emplace( feature_id, DEFAULT_LAYER_ID); + } + } + //Add the downstream features/edges for( auto& downstream: feature->destination_features() ) { diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index 9729b0304b..b050239c1c 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -174,6 +174,22 @@ ngen_add_test( # NGEN_WITH_MPI ) +########################## MultiLayer Tests +ngen_add_test( + test_multilayer + OBJECTS + core/multilayer/MultiLayerParserTest.cpp + LIBRARIES + NGen::core + NGen::geojson + NGen::realizations_catchment + NGen::core_mediator + NGen::forcing + REQUIRES + NGEN_WITH_NETCDF +) + + ########################## BMI C++ Tests ngen_add_test( test_bmi_cpp @@ -375,6 +391,7 @@ ngen_add_test( core/mediator/UnitsHelper_Tests.cpp realizations/Formulation_Manager_Test.cpp core/nexus/NexusTests.cpp + core/multilayer/MultiLayerParserTest.cpp utils/Partition_Test.cpp utils/mdarray_Test.cpp utils/mdframe_Test.cpp diff --git a/test/core/multilayer/MultiLayerParserTest.cpp b/test/core/multilayer/MultiLayerParserTest.cpp new file mode 100644 index 0000000000..1ce12aae5a --- /dev/null +++ b/test/core/multilayer/MultiLayerParserTest.cpp @@ -0,0 +1,61 @@ + +#include "gtest/gtest.h" +#include + +class MultiLayerParserTest : public ::testing::Test { + protected: + + MultiLayerParserTest() : + nexus_data_path("./data/nexus_data.geojson"), + catchment_data_path("./data/catchment_data_multilayer.geojson"), + realization_config_path("./data/example_multilayer_realization_config.json") + { + + } + + ~MultiLayerParserTest() override { + + } + + void SetUp() override { + nexus_collection = geojson::read(nexus_data_path.c_str()); + std::cout << "Building Catchment collection" << std::endl; + + catchment_collection = geojson::read(catchment_data_path.c_str()); + + // add the catchments to the nexus collection + for(auto& feature: *catchment_collection) + { + nexus_collection->add_feature(feature); + } + } + + void TearDown() override { + + } + + geojson::GeoJSON nexus_collection; + geojson::GeoJSON catchment_collection; + std::shared_ptr manager; + + std::string nexus_data_path; + std::string catchment_data_path; + std::string realization_config_path; + + +}; + +TEST_F(MultiLayerParserTest, TestInit0) +{ + manager = std::make_shared(realization_config_path.c_str()); + + ASSERT_TRUE(true); +} + +TEST_F(MultiLayerParserTest, TestRead0) +{ + manager = std::make_shared(realization_config_path.c_str()); + manager->read(catchment_collection, utils::getStdOut()); + + ASSERT_TRUE(true); +} \ No newline at end of file diff --git a/test/simulation_time/Simulation_Time_Test.cpp b/test/simulation_time/Simulation_Time_Test.cpp index 6e2951356b..aab9efc77b 100644 --- a/test/simulation_time/Simulation_Time_Test.cpp +++ b/test/simulation_time/Simulation_Time_Test.cpp @@ -1,5 +1,5 @@ #include "gtest/gtest.h" -#include "Simulation_Time.h" +#include "Simulation_Time.hpp" #include #include #include @@ -70,4 +70,55 @@ TEST_F(SimulationTimeTest, TestSimulationTime) } +TEST_F(SimulationTimeTest, TestSimTimeNextIndex) +{ + simulation_time_params other_stp("2015-12-14 21:00:00", "2015-12-30 23:00:00", 3600); + + int next_index; + + // for 2.5h in the future + next_index = Simulation_Time_Object1->next_timestep_index(other_stp.start_t + (3600 * 2.5)); + + EXPECT_EQ(2, next_index); + + // for 2.0h in the future + next_index = Simulation_Time_Object1->next_timestep_index(other_stp.start_t + (3600 * 2.00)); + + EXPECT_EQ(2, next_index); + +} + +TEST_F(SimulationTimeTest, TestSimTimeNextEpochTime) +{ + simulation_time_params other_stp("2015-12-14 21:00:00", "2015-12-30 23:00:00", 3600); + + int next_time; + + // for 2.5h in the future + next_time = Simulation_Time_Object1->next_timestep_epoch_time(other_stp.start_t + (3600 * 2.5)); + + EXPECT_EQ(other_stp.start_t + (3600 * 2.0), next_time); + + // for 2.0h in the future + next_time = Simulation_Time_Object1->next_timestep_epoch_time(other_stp.start_t + (3600 * 2.00)); + + EXPECT_EQ(other_stp.start_t + (3600 * 2.0), next_time); + +} + +TEST_F(SimulationTimeTest, TestSimTimeDiff) +{ + simulation_time_params other_stp("2015-12-14 23:00:00", "2015-12-30 23:00:00", 3600); + Simulation_Time other_st(other_stp); + int diff; + + diff = other_st.diff(*Simulation_Time_Object1); + + EXPECT_EQ(7200, diff); + + diff = Simulation_Time_Object1->diff(other_st); + + EXPECT_EQ(-7200, diff); + +}