/// <summary>
/// Constructor for the autotroph processor: initialises necessary classes
/// </summary>
public AutotrophProcessor()
{
_PhytoplanktonConversionRatio = EcologicalParameters.Parameters["AutotrophProcessor.ConvertNPPtoAutotroph.PhytoplanktonConversionRatio"];
// Initialise the utility functions
Utilities = new UtilityFunctions();
}
/// <summary>
/// Constructor for dispersal: assigns all parameter values
/// </summary>
public AdvectiveDispersal(string globalModelTimeStepUnit, Boolean DrawRandomly)
{
InitialiseParatemersAdvectiveDispersal();
// Initialise the utility functions
UtilityFunctions Utilities = new UtilityFunctions();
// Calculate the scalar to convert from the time step units used by this implementation of dispersal to the global model time step units
_DeltaT = Utilities.ConvertTimeUnits(globalModelTimeStepUnit, _TimeUnitImplementation);
// Initialise the advective dispersal temporal scaling to adjust between time steps appropriately
_AdvectionTimeStepsPerModelTimeStep = Utilities.ConvertTimeUnits(globalModelTimeStepUnit, "day") * 24 / _AdvectiveModelTimeStepLengthHours;
// Convert velocity from m/s to km/month. Note that if the _TimeUnitImplementation changes, this will also have to change.
VelocityUnitConversion = 60 * 60 * 24 * Utilities.ConvertTimeUnits(globalModelTimeStepUnit, "day") * _DeltaT / 1000;
// Set the seed for the random number generator
RandomNumberGenerator = new NonStaticSimpleRNG();
if (DrawRandomly)
{
RandomNumberGenerator.SetSeedFromSystemTime();
}
else
{
RandomNumberGenerator.SetSeed(14141);
}
}
/// <summary>
/// Constructor for starvation mortality: assigns all parameter values
///
/// </summary>
public StarvationMortality(string globalModelTimeStepUnit)
{
InitialiseParametersStarvationMortality();
// Initialise the utility functions
UtilityFunctions Utilities = new UtilityFunctions();
// Calculate the scalar to convert from the time step units used by this implementation of mortality to the global model time step units
_DeltaT = Utilities.ConvertTimeUnits(globalModelTimeStepUnit, _TimeUnitImplementation);
}
/// <summary>
/// Constructor for metabolism: assigns all parameter values
/// </summary>
public MetabolismEndotherm(string globalModelTimeStepUnit)
{
// Initialise ecological parameters for metabolism
InitialiseMetabolismParameters();
// Initialise the utility functions
Utilities = new UtilityFunctions();
// Calculate the scalar to convert from the time step units used by this implementation of metabolism to the global model time step units
_DeltaT = Utilities.ConvertTimeUnits(globalModelTimeStepUnit, _TimeUnitImplementation);
}
/// <summary>
/// Constructor for metabolism: assigns all parameter values
/// </summary>
public MetabolismHeterotroph(string globalModelTimeStepUnit)
{
// Initialise ecological parameters for metabolism
InitialiseMetabolismParameters();
// Initialise the utility functions
Utilities = new UtilityFunctions();
// Calculate the scalar to convert from the time step units used by this implementation of metabolism to the global model time step units
_DeltaT = Utilities.ConvertTimeUnits(globalModelTimeStepUnit, _TimeUnitImplementation);
// Set the constant to convert temperature in degrees Celsius to Kelvin
_TemperatureUnitsConvert = 273.0;
}
/// <summary>
/// Constructor for dispersal: assigns all parameter values
/// </summary>
public DiffusiveDispersal(string globalModelTimeStepUnit, Boolean DrawRandomly)
{
InitialiseParametersDiffusiveDispersal();
// Initialise the utility functions
UtilityFunctions Utilities = new UtilityFunctions();
// Calculate the scalar to convert from the time step units used by this implementation of dispersal to the global model time step units
_DeltaT = Utilities.ConvertTimeUnits(globalModelTimeStepUnit, _TimeUnitImplementation);
// Set the seed for the random number generator
RandomNumberGenerator = new NonStaticSimpleRNG();
if (DrawRandomly)
{
RandomNumberGenerator.SetSeedFromSystemTime();
}
else
{
RandomNumberGenerator.SetSeed(14141);
}
}
/// <summary>
/// Assigns all parameter values for repsonsive dispersal
/// </summary>
public ResponsiveDispersal(string globalModelTimeStepUnit, Boolean DrawRandomly)
{
InitialiseParametersResponsiveDispersal();
// Initialise the utility functions
UtilityFunctions Utilities = new UtilityFunctions();
// Calculate the scalar to convert from the time step units used by this implementation of dispersal to the global model time step units
_DeltaT = Utilities.ConvertTimeUnits(globalModelTimeStepUnit, _TimeUnitImplementation);
// Set the seed for the random number generator
RandomNumberGenerator = new NonStaticSimpleRNG();
if (DrawRandomly)
{
RandomNumberGenerator.SetSeedFromSystemTime();
}
else
{
RandomNumberGenerator.SetSeed(14141);
}
}
/// <summary>
/// Constructor for reproduction: assigns all parameter values
/// <param name="globalModelTimeStepUnit">The time step of the global model</param>
/// <param name="drawRandomly">Indicates whether to draw values randomly</param>
/// </summary>
public ReproductionBasic(string globalModelTimeStepUnit, Boolean drawRandomly)
{
// Initialise ecological parameters for reproduction
InitialiseReproductionParameters();
// Initialise the utility class
UtilityFunctions Utilities = new UtilityFunctions();
// Calculate the scalar to convert from the time step units used by this implementation of herbivory to the global model time step units
_DeltaT = Utilities.ConvertTimeUnits(globalModelTimeStepUnit, _TimeUnitImplementation);
// Instantiate the random number generator
RandomNumberGenerator = new NonStaticSimpleRNG();
// Set the seed for the random number generator
if (drawRandomly)
{
RandomNumberGenerator.SetSeedFromSystemTime();
}
else
{
RandomNumberGenerator.SetSeed(4000);
}
}
/// <summary>
/// Constructor for reproduction: assigns all parameter values
/// <param name="globalModelTimeStepUnit">The time step of the global model</param>
/// <param name="drawRandomly">Indicates whether to draw values randomly</param>
/// </summary>
public ReproductionBasic(string globalModelTimeStepUnit, Boolean drawRandomly)
{
// Initialise ecological parameters for reproduction
InitialiseReproductionParameters();
// Initialise the utility class
UtilityFunctions Utilities = new UtilityFunctions();
// Calculate the scalar to convert from the time step units used by this implementation of herbivory to the global model time step units
_DeltaT = Utilities.ConvertTimeUnits(globalModelTimeStepUnit, _TimeUnitImplementation);
// Instantiate the random number generator
RandomNumberGenerator = new NonStaticSimpleRNG();
// Set the seed for the random number generator
if (drawRandomly)
{
RandomNumberGenerator.SetSeedFromSystemTime();
}
else
{
RandomNumberGenerator.SetSeed(4000);
}
}
/// <summary>
/// Overloaded constructor for model grid to construct the grid for specific locations
/// </summary>
/// <param name="minLat">Minimum grid latitude (degrees)</param>
/// <param name="minLon">Minimum grid longitude (degrees, currently -180 to 180)</param>
/// <param name="maxLat">Maximum grid latitude (degrees)</param>
/// <param name="maxLon">Maximum grid longitude (degrees, currently -180 to 180)</param>
/// <param name="latCellSize">Latitudinal size of grid cells</param>
/// <param name="lonCellSize">Longitudinal size of grid cells</param>
/// <param name="cellList">List of indices of active cells in the model grid</param>
/// <param name="enviroStack">List of environmental data layers</param>
/// <param name="cohortFunctionalGroups">The functional group definitions for cohorts in the model</param>
/// <param name="stockFunctionalGroups">The functional group definitions for stocks in the model</param>
/// <param name="globalDiagnostics">Global diagnostic variables</param>
/// <param name="tracking">Whether process tracking is enabled</param>
/// <param name="specificLocations">Whether the model is to be run for specific locations</param>
/// <param name="runInParallel">Whether model grid cells will be run in parallel</param>
public ModelGrid(float minLat, float minLon, float maxLat, float maxLon, float latCellSize, float lonCellSize, List<uint[]> cellList,
SortedList<string, EnviroData> enviroStack, FunctionalGroupDefinitions cohortFunctionalGroups,
FunctionalGroupDefinitions stockFunctionalGroups, SortedList<string, double> globalDiagnostics, Boolean tracking,
Boolean specificLocations, Boolean runInParallel)
{
// Add one to the counter of the number of grids. If there is more than one model grid, exit the program with a debug crash.
NumGrids = NumGrids + 1;
//Debug.Assert(NumGrids < 2, "You have initialised more than one grid on which to apply models. At present, this is not supported");
// Initialise the utility functions
Utilities = new UtilityFunctions();
// CURRENTLY DEFINING MODEL CELLS BY BOTTOM LEFT CORNER
_MinLatitude = minLat;
_MinLongitude = minLon;
_MaxLatitude = maxLat;
_MaxLongitude = maxLon;
_LatCellSize = latCellSize;
_LonCellSize = lonCellSize;
_GridCellRarefaction = 1;
// Check to see if the number of grid cells is an integer
Debug.Assert((((_MaxLatitude - _MinLatitude) % _LatCellSize) == 0), "Error: number of grid cells is non-integer: check cell size");
_NumLatCells = (UInt32)((_MaxLatitude - _MinLatitude) / _LatCellSize);
_NumLonCells = (UInt32)((_MaxLongitude - _MinLongitude) / _LonCellSize);
_Lats = new float[_NumLatCells];
_Lons = new float[_NumLonCells];
// Set up latitude and longitude vectors - lower left
for (int ii = 0; ii < _NumLatCells; ii++)
{
_Lats[ii] = _MinLatitude + ii * _LatCellSize;
}
for (int jj = 0; jj < _NumLonCells; jj++)
{
_Lons[jj] = _MinLongitude + jj * _LonCellSize;
}
// Set up a grid of grid cells
InternalGrid = new GridCell[_NumLatCells, _NumLonCells];
// Instantiate the arrays of lists of cohorts to disperse
DeltaFunctionalGroupDispersalArray = new List<uint>[_NumLatCells, _NumLonCells];
DeltaCohortNumberDispersalArray = new List<uint>[_NumLatCells, _NumLonCells];
// Instantiate the array of lists of grid cells to disperse those cohorts to
DeltaCellToDisperseToArray = new List<uint[]>[_NumLatCells, _NumLonCells];
// Instantiate the arrays of cell entry and exit directions
DeltaCellExitDirection = new List<uint>[_NumLatCells, _NumLonCells];
DeltaCellEntryDirection = new List<uint>[_NumLatCells, _NumLonCells];
// An array of lists of cells to which organisms in each cell can disperse to; includes all cells which contribute to the
// perimeter list, plus diagonal cells if they are in the same realm
CellsForDispersal = new List<uint[]>[_NumLatCells, _NumLonCells];
// An array of lists of directions corresponding to cells which organisms can disperse to
CellsForDispersalDirection = new List<uint>[_NumLatCells, _NumLonCells];
Console.WriteLine("Initialising grid cell environment:");
int Count = 0;
int NCells = cellList.Count;
if (!runInParallel)
{
// Loop over cells to set up the model grid
for (int ii = 0; ii < cellList.Count; ii++)
{
// Create the grid cell at the specified position
InternalGrid[cellList[ii][0], cellList[ii][1]] = new GridCell(_Lats[cellList[ii][0]], cellList[ii][0],
_Lons[cellList[ii][1]], cellList[ii][1], latCellSize, lonCellSize, enviroStack, _GlobalMissingValue,
cohortFunctionalGroups, stockFunctionalGroups, globalDiagnostics, tracking, specificLocations);
if (!specificLocations)
{
CellsForDispersal[cellList[ii][0], cellList[ii][1]] = new List<uint[]>();
CellsForDispersalDirection[cellList[ii][0], cellList[ii][1]] = new List<uint>();
Count++;
Console.Write("\rInitialised {0} of {1}", Count, NCells);
}
else
{
Console.Write("\rRow {0} of {1}", ii + 1, NumLatCells / GridCellRarefaction);
Console.WriteLine("");
Console.WriteLine("");
}
}
}
else
{
// Run a parallel loop over rows
Parallel.For(0, NCells, ii =>
{
// Create the grid cell at the specified position
InternalGrid[cellList[ii][0], cellList[ii][1]] = new GridCell(_Lats[cellList[ii][0]], cellList[ii][0],
_Lons[cellList[ii][1]], cellList[ii][1], latCellSize, lonCellSize, enviroStack, _GlobalMissingValue,
cohortFunctionalGroups, stockFunctionalGroups, globalDiagnostics, tracking, specificLocations);
if (!specificLocations)
{
CellsForDispersal[cellList[ii][0], cellList[ii][1]] = new List<uint[]>();
CellsForDispersalDirection[cellList[ii][0], cellList[ii][1]] = new List<uint>();
}
Count++;
Console.Write("\rInitialised {0} of {1}", Count, NCells);
}
);
}
if (!specificLocations)
{
InterpolateMissingValues();
// Fill in the array of dispersable perimeter lengths for each grid cell
CalculatePerimeterLengthsAndCellsDispersableTo();
CellHeightsKm = new double[_Lats.Length];
CellWidthsKm = new double[_Lats.Length];
// Calculate the lengths of widths of grid cells in each latitudinal strip
// Assume that we are at the midpoint of each cell when calculating lengths
for (int ii = 0; ii < _Lats.Length; ii++)
{
CellHeightsKm[ii] = Utilities.CalculateLengthOfDegreeLatitude(_Lats[ii] + _LatCellSize / 2) * _LatCellSize;
CellWidthsKm[ii] = Utilities.CalculateLengthOfDegreeLongitude(_Lats[ii] + _LatCellSize / 2) * _LonCellSize;
}
}
Console.WriteLine("\n");
}
/// <summary>
/// Initializes the ecosystem model
/// </summary>
/// <param name="initialisation">An instance of the model initialisation class</param>
/// <param name="scenarioParameters">The parameters for the scenarios to run</param>
/// <param name="scenarioIndex">The index of the scenario being run</param>
/// <param name="outputFilesSuffix">The suffix to be applied to all outputs from this model run</param>
/// <param name="globalModelTimeStepUnit">The time step unit used in the model</param>
/// <param name="simulation">The index of the simulation being run</param>
public MadingleyModel(MadingleyModelInitialisation initialisation, ScenarioParameterInitialisation scenarioParameters, int scenarioIndex,
string outputFilesSuffix, string globalModelTimeStepUnit, int simulation)
{
// Assign the properties for this model run
AssignModelRunProperties(initialisation, scenarioParameters, scenarioIndex, outputFilesSuffix);
// Set up list of global diagnostics
SetUpGlobalDiagnosticsList();
// Set up the model grid
SetUpModelGrid(initialisation, scenarioParameters, scenarioIndex, simulation);
// Set up model outputs
SetUpOutputs(initialisation, simulation, scenarioIndex);
// Make the initial outputs
InitialOutputs(outputFilesSuffix, initialisation, CurrentMonth);
// Instance the array of process trackers
ProcessTrackers = new ProcessTracker[_CellList.Count];
// Temporary variables
Boolean varExists;
// Set up process trackers for each grid cell
for (int i = 0; i < _CellList.Count; i++)
{
ProcessTrackers[i] = new ProcessTracker(NumTimeSteps,
EcosystemModelGrid.Lats, EcosystemModelGrid.Lons,
_CellList,
initialisation.ProcessTrackingOutputs,
initialisation.TrackProcesses,
CohortFunctionalGroupDefinitions,
EcosystemModelGrid.GlobalMissingValue,
outputFilesSuffix,
initialisation.OutputPath, initialisation.ModelMassBins,
SpecificLocations, i, initialisation,
EcosystemModelGrid.GetEnviroLayer("Realm", 0, _CellList[i][0], _CellList[i][1], out varExists) == 2.0,
EcosystemModelGrid.LatCellSize,
EcosystemModelGrid.LonCellSize);
}
// Set up a cross cell process tracker
TrackCrossCellProcesses = new CrossCellProcessTracker(initialisation.TrackCrossCellProcesses, "DispersalData", initialisation.OutputPath, outputFilesSuffix);
//Set up a global process tracker
if (SpecificLocations) initialisation.TrackGlobalProcesses = false;
TrackGlobalProcesses = new GlobalProcessTracker(NumTimeSteps,
EcosystemModelGrid.Lats, EcosystemModelGrid.Lons,
_CellList,
initialisation.ProcessTrackingOutputs,
initialisation.TrackGlobalProcesses,
CohortFunctionalGroupDefinitions,
StockFunctionalGroupDefinitions,
EcosystemModelGrid.GlobalMissingValue,
outputFilesSuffix,
initialisation.OutputPath, initialisation.ModelMassBins,
SpecificLocations, initialisation,
EcosystemModelGrid.LatCellSize,
EcosystemModelGrid.LonCellSize);
//Set-up the instance of OutputModelState
WriteModelState = new OutputModelState(initialisation, outputFilesSuffix, simulation);
if (SpecificLocations) initialisation.RunRealm = "";
// Record the initial cohorts in the process trackers
RecordInitialCohorts();
// Initialise the class for cross-grid-cell ecology
MadingleyEcologyCrossGridCell = new EcologyCrossGridCell();
// Initialise the time step timer
TimeStepTimer = new StopWatch();
EcologyTimer = new StopWatch();
OutputTimer = new StopWatch();
// Set the global model time step unit
_GlobalModelTimeStepUnit = globalModelTimeStepUnit;
// Initialise the utility functions
Utilities = new UtilityFunctions();
// Initialise the climate change impacts class
ClimateChangeSimulator = new ClimateChange();
// Initialise the harvesting impacts class
HarvestingSimulator = new Harvesting(EcosystemModelGrid.Lats, EcosystemModelGrid.Lons, (float)EcosystemModelGrid.LatCellSize);
}
/// <summary>
/// Constructor for a grid cell; creates cell and reads in environmental data
/// </summary>
/// <param name="latitude">The latitude of the grid cell</param>
/// <param name="latIndex">The latitudinal index of the grid cell</param>
/// <param name="longitude">The longitude of the grid cell</param>
/// <param name="lonIndex">The longitudinal index of the grid cell</param>
/// <param name="latCellSize">The latitudinal dimension of the grid cell</param>
/// <param name="lonCellSize">The longitudinal dimension of the grid cell</param>
/// <param name="dataLayers">A list of environmental data variables in the model</param>
/// <param name="missingValue">The missing value to be applied to all data in the grid cell</param>
/// <param name="cohortFunctionalGroups">The definitions for cohort functional groups in the model</param>
/// <param name="stockFunctionalGroups">The definitions for stock functional groups in the model</param>
/// <param name="globalDiagnostics">A list of global diagnostic variables for the model grid</param>
/// <param name="tracking">Whether process-tracking is enabled</param>
/// <param name="specificLocations">Whether the model is being run for specific locations</param>
public GridCell(float latitude, uint latIndex, float longitude, uint lonIndex, float latCellSize, float lonCellSize,
SortedList<string, EnviroData> dataLayers, double missingValue, FunctionalGroupDefinitions cohortFunctionalGroups,
FunctionalGroupDefinitions stockFunctionalGroups, SortedList<string, double> globalDiagnostics,Boolean tracking,
bool specificLocations)
{
// Boolean to track when environmental data are missing
Boolean EnviroMissingValue;
// Initialise the utility functions
Utilities = new UtilityFunctions();
// Temporary vector for holding initial values of grid cell properties
double[] tempVector;
// Initialise deltas sorted list
_Deltas = new Dictionary<string, Dictionary<string, double>>();
// Initialize delta abundance sorted list with appropriate processes
Dictionary<string, double> DeltaAbundance = new Dictionary<string, double>();
DeltaAbundance.Add("mortality", 0.0);
// Add delta abundance sorted list to deltas sorted list
_Deltas.Add("abundance", DeltaAbundance);
// Initialize delta biomass sorted list with appropriate processes
Dictionary<string, double> DeltaBiomass = new Dictionary<string, double>();
DeltaBiomass.Add("metabolism", 0.0);
DeltaBiomass.Add("predation", 0.0);
DeltaBiomass.Add("herbivory", 0.0);
DeltaBiomass.Add("reproduction", 0.0);
// Add delta biomass sorted list to deltas sorted list
_Deltas.Add("biomass", DeltaBiomass);
// Initialize delta reproductive biomass vector with appropriate processes
Dictionary<string, double> DeltaReproductiveBiomass = new Dictionary<string, double>();
DeltaReproductiveBiomass.Add("reproduction", 0.0);
// Add delta reproduction sorted list to deltas sorted list
_Deltas.Add("reproductivebiomass", DeltaReproductiveBiomass);
// Initialize organic pool delta vector with appropriate processes
Dictionary<string, double> DeltaOrganicPool = new Dictionary<string, double>();
DeltaOrganicPool.Add("herbivory", 0.0);
DeltaOrganicPool.Add("predation", 0.0);
DeltaOrganicPool.Add("mortality", 0.0);
// Add delta organic pool sorted list to deltas sorted list
_Deltas.Add("organicpool", DeltaOrganicPool);
// Initialize respiratory CO2 pool delta vector with appropriate processes
Dictionary<string, double> DeltaRespiratoryCO2Pool = new Dictionary<string, double>();
DeltaRespiratoryCO2Pool.Add("metabolism", 0.0);
// Add delta respiratory CO2 pool to deltas sorted list
_Deltas.Add("respiratoryCO2pool", DeltaRespiratoryCO2Pool);
// Set the grid cell values of latitude, longitude and missing value as specified
_Latitude = latitude;
_Longitude = longitude;
// Initialise list of environmental data layer values
_CellEnvironment = new SortedList<string, double[]>();
//Add the latitude and longitude
tempVector = new double[1];
tempVector[0] = latitude;
_CellEnvironment.Add("Latitude", tempVector);
tempVector = new double[1];
tempVector[0] = longitude;
_CellEnvironment.Add("Longitude", tempVector);
// Add an organic matter pool to the cell environment to track organic biomass not held by animals or plants with an initial value of 0
tempVector = new double[1];
tempVector[0] = 0.0;
_CellEnvironment.Add("Organic Pool", tempVector);
// Add a repsiratory CO2 pool to the cell environment with an initial value of 0
tempVector = new double[1];
tempVector[0] = 0.0;
_CellEnvironment.Add("Respiratory CO2 Pool", tempVector);
// Add the grid cell area (in km2) to the cell environment with an initial value of 0
tempVector = new double[1];
// Calculate the area of this grid cell
tempVector[0] = Utilities.CalculateGridCellArea(latitude, lonCellSize, latCellSize);
// Add it to the cell environment
_CellEnvironment.Add("Cell Area", tempVector);
//Add the latitude and longitude indices
tempVector = new double[1];
tempVector[0] = latIndex;
_CellEnvironment.Add("LatIndex", tempVector);
tempVector = new double[1];
tempVector[0] = lonIndex;
_CellEnvironment.Add("LonIndex", tempVector);
// Add the missing value of data in the grid cell to the cell environment
tempVector = new double[1];
tempVector[0] = missingValue;
_CellEnvironment.Add("Missing Value", tempVector);
// Loop through environmental data layers and extract values for this grid cell
// Also standardise missing values
// Loop over variables in the list of environmental data
foreach (string LayerName in dataLayers.Keys)
{
// Initiliase the temporary vector of values to be equal to the number of time intervals in the environmental variable
tempVector = new double[dataLayers[LayerName].NumTimes];
// Loop over the time intervals in the environmental variable
for (int hh = 0; hh < dataLayers[LayerName].NumTimes; hh++)
{
// Add the value of the environmental variable at this time interval to the temporary vector
tempVector[hh] = dataLayers[LayerName].GetValue(_Latitude, _Longitude, (uint)hh, out EnviroMissingValue,latCellSize,lonCellSize);
// If the environmental variable is a missing value, then change the value to equal the standard missing value for this cell
if (EnviroMissingValue)
tempVector[hh] = missingValue;
}
// Add the values of the environmental variables to the cell environment, with the name of the variable as the key
_CellEnvironment.Add(LayerName, tempVector);
}
if (_CellEnvironment.ContainsKey("LandSeaMask"))
{
if (_CellEnvironment["LandSeaMask"][0].CompareTo(0.0) == 0)
{
if (ContainsData(_CellEnvironment["OceanTemp"], _CellEnvironment["Missing Value"][0]))
{
//This is a marine cell
tempVector = new double[1];
tempVector[0] = 2.0;
_CellEnvironment.Add("Realm", tempVector);
_CellEnvironment.Add("NPP", _CellEnvironment["OceanNPP"]);
_CellEnvironment.Add("DiurnalTemperatureRange", _CellEnvironment["OceanDTR"]);
if (_CellEnvironment.ContainsKey("Temperature"))
{
if(_CellEnvironment.ContainsKey("SST"))
{
_CellEnvironment["Temperature"] = _CellEnvironment["SST"];
}
else
{
}
}
else
{
_CellEnvironment.Add("Temperature", _CellEnvironment["SST"]);
}
}
else
{
//This is a freshwater cell and in this model formulation is characterised as belonging to the terrestrial realm
tempVector = new double[1];
tempVector[0] = 2.0;
_CellEnvironment.Add("Realm", tempVector);
_CellEnvironment.Add("NPP", _CellEnvironment["LandNPP"]);
_CellEnvironment.Add("DiurnalTemperatureRange", _CellEnvironment["LandDTR"]);
}
}
else
{
//This is a land cell
tempVector = new double[1];
tempVector[0] = 1.0;
_CellEnvironment.Add("Realm", tempVector);
_CellEnvironment.Add("NPP", _CellEnvironment["LandNPP"]);
_CellEnvironment.Add("DiurnalTemperatureRange", _CellEnvironment["LandDTR"]);
}
}
else
{
Debug.Fail("No land sea mask defined - a mask is required to initialise appropriate ecology");
}
//Calculate and add the standard deviation of monthly temperature as a measure of seasonality
//Also calculate and add the annual mean temperature for this cell
tempVector = new double[12];
double[] sdtemp = new double[12];
double[] meantemp = new double[12];
tempVector = _CellEnvironment["Temperature"];
double Average = tempVector.Average();
meantemp[0] = Average;
double SumOfSquaresDifferences = tempVector.Select(val => (val - Average) * (val - Average)).Sum();
sdtemp[0] = Math.Sqrt(SumOfSquaresDifferences / tempVector.Length);
_CellEnvironment.Add("SDTemperature", sdtemp);
_CellEnvironment.Add("AnnualTemperature", meantemp);
//Remove unrequired cell environment layers
if (_CellEnvironment.ContainsKey("LandNPP")) _CellEnvironment.Remove("LandNPP");
if (_CellEnvironment.ContainsKey("LandDTR")) _CellEnvironment.Remove("LandDTR");
if (_CellEnvironment.ContainsKey("OceanNPP")) _CellEnvironment.Remove("OceanNPP");
if (_CellEnvironment.ContainsKey("OceanDTR")) _CellEnvironment.Remove("OceanDTR");
if (_CellEnvironment.ContainsKey("SST")) _CellEnvironment.Remove("SST");
// CREATE NPP SEASONALITY LAYER
_CellEnvironment.Add("Seasonality", CalculateNPPSeasonality(_CellEnvironment["NPP"], _CellEnvironment["Missing Value"][0]));
// Calculate other climate variables from temperature and precipitation
// Declare an instance of the climate variables calculator
ClimateVariablesCalculator CVC = new ClimateVariablesCalculator();
// Calculate the fraction of the year that experiences frost
double[] NDF = new double[1];
NDF[0] = CVC.GetNDF(_CellEnvironment["FrostDays"], _CellEnvironment["Temperature"],_CellEnvironment["Missing Value"][0]);
_CellEnvironment.Add("Fraction Year Frost", NDF);
double[] frostMonthly = new double[12];
frostMonthly[0] = Math.Min(_CellEnvironment["FrostDays"][0] / 31.0, 1.0);
frostMonthly[1] = Math.Min(_CellEnvironment["FrostDays"][1] / 28.0, 1.0);
frostMonthly[2] = Math.Min(_CellEnvironment["FrostDays"][2] / 31.0, 1.0);
frostMonthly[3] = Math.Min(_CellEnvironment["FrostDays"][3] / 30.0, 1.0);
frostMonthly[4] = Math.Min(_CellEnvironment["FrostDays"][4] / 31.0, 1.0);
frostMonthly[5] = Math.Min(_CellEnvironment["FrostDays"][5] / 30.0, 1.0);
frostMonthly[6] = Math.Min(_CellEnvironment["FrostDays"][6] / 31.0, 1.0);
frostMonthly[7] = Math.Min(_CellEnvironment["FrostDays"][7] / 31.0, 1.0);
frostMonthly[8] = Math.Min(_CellEnvironment["FrostDays"][8] / 30.0, 1.0);
frostMonthly[9] = Math.Min(_CellEnvironment["FrostDays"][9] / 31.0, 1.0);
frostMonthly[10] = Math.Min(_CellEnvironment["FrostDays"][10] / 30.0, 1.0);
frostMonthly[11] = Math.Min(_CellEnvironment["FrostDays"][11] / 31.0, 1.0);
_CellEnvironment.Add("Fraction Month Frost", frostMonthly);
_CellEnvironment.Remove("FrostDays");
// Calculate AET and the fractional length of the fire season
Tuple<double[], double, double> TempTuple = new Tuple<double[], double, double>(new double[12], new double(), new double());
TempTuple = CVC.MonthlyActualEvapotranspirationSoilMoisture(_CellEnvironment["AWC"][0], _CellEnvironment["Precipitation"], _CellEnvironment["Temperature"]);
_CellEnvironment.Add("AET", TempTuple.Item1);
_CellEnvironment.Add("Fraction Year Fire", new double[1] { TempTuple.Item3 / 360 });
// Designate a breeding season for this grid cell, where a month is considered to be part of the breeding season if its NPP is at
// least 80% of the maximum NPP throughout the whole year
double[] BreedingSeason = new double[12];
for (int i = 0; i < 12; i++)
{
if ((_CellEnvironment["Seasonality"][i] / _CellEnvironment["Seasonality"].Max()) > 0.5)
{
BreedingSeason[i] = 1.0;
}
else
{
BreedingSeason[i] = 0.0;
}
}
_CellEnvironment.Add("Breeding Season", BreedingSeason);
// Initialise the grid cell cohort and stock handlers
_GridCellCohorts = new GridCellCohortHandler(cohortFunctionalGroups.GetNumberOfFunctionalGroups());
_GridCellStocks = new GridCellStockHandler(stockFunctionalGroups.GetNumberOfFunctionalGroups());
}
/// <summary>
/// Constructor for human appropriation of autotroph matter
/// </summary>
public HumanAutotrophMatterAppropriation()
{
_Utilities = new UtilityFunctions();
}
/// <summary>
/// Constructor for herbivory: assigns all parameter values
/// </summary>
/// <param name="cellArea">The area (in square km) of the grid cell</param>
/// <param name="globalModelTimeStepUnit">The time step unit used in the model</param>
public RevisedHerbivory(double cellArea, string globalModelTimeStepUnit)
{
InitialiseParametersHerbivory();
// Initialise the utility functions
Utilities = new UtilityFunctions();
// Calculate the scalar to convert from the time step units used by this implementation of herbivory to the global model time step units
_DeltaT = Utilities.ConvertTimeUnits(globalModelTimeStepUnit, _TimeUnitImplementation);
// Store the specified cell area in this instance of this herbivory implementation
_CellArea = cellArea;
_CellAreaHectares = cellArea * 100;
}
/// <summary>
/// Constructor for model grid: assigns grid properties and initialises the grid cells
/// </summary>
/// <param name="minLat">Minimum grid latitude (degrees)</param>
/// <param name="minLon">Minimum grid longitude (degrees, currently -180 to 180)</param>
/// <param name="maxLat">Maximum grid latitude (degrees)</param>
/// <param name="maxLon">Maximum grid longitude (degrees, currently -180 to 180)</param>
/// <param name="latCellSize">Latitudinal resolution of grid cell</param>
/// <param name="lonCellSize">Longitudinal resolution of grid cell</param>
/// <param name="cellRarefaction">The rarefaction to be applied to active grid cells in the model</param>
/// <param name="enviroStack">Environmental data layers</param>
/// <param name="cohortFunctionalGroups">The functional group definitions for cohorts in the model</param>
/// <param name="stockFunctionalGroups">The functional group definitions for stocks in the model</param>
/// <param name="globalDiagnostics">Global daignostic variables</param>
/// <param name="tracking">Whether process-tracking is enabled</param>
/// <param name="DrawRandomly">Whether the model is set to use a random draw</param>
/// <param name="specificLocations">Whether the model is to be run for specific locations</param>
public ModelGrid(float minLat, float minLon,float maxLat,float maxLon,float latCellSize,float lonCellSize,
SortedList<string,EnviroData> enviroStack, FunctionalGroupDefinitions cohortFunctionalGroups, FunctionalGroupDefinitions
stockFunctionalGroups, SortedList<string, double> globalDiagnostics, Boolean tracking, Boolean DrawRandomly,
Boolean specificLocations, string globalModelTimeStepUnit)
{
// Add one to the counter of the number of grids. If there is more than one model grid, exit the program with a debug crash.
NumGrids = NumGrids + 1;
//Debug.Assert(NumGrids < 2, "You have initialised more than one grid on which to apply models. At present, this is not supported");
// Initialise the utility functions
Utilities = new UtilityFunctions();
// Seed the random number generator
// Set the seed for the random number generator
RandomNumberGenerator = new NonStaticSimpleRNG();
if (DrawRandomly)
{
RandomNumberGenerator.SetSeedFromSystemTime();
}
else
{
RandomNumberGenerator.SetSeed(4315);
}
// CURRENTLY DEFINING MODEL CELLS BY BOTTOM LEFT CORNER
_MinLatitude = minLat;
_MinLongitude = minLon;
_MaxLatitude = maxLat;
_MaxLongitude = maxLon;
_LatCellSize = latCellSize;
_LonCellSize = lonCellSize;
// Check to see if the number of grid cells is an integer
Debug.Assert((((_MaxLatitude - _MinLatitude) % _LatCellSize) == 0), "Error: number of grid cells is non-integer: check cell size");
_NumLatCells = (UInt32)((_MaxLatitude - _MinLatitude) / _LatCellSize);
_NumLonCells = (UInt32)((_MaxLongitude - _MinLongitude) / _LonCellSize);
_Lats = new float[_NumLatCells];
_Lons = new float[_NumLonCells];
// Set up latitude and longitude vectors - lower left
for (int ii = 0; ii < _NumLatCells; ii++)
{
_Lats[ii] = _MinLatitude + ii * _LatCellSize;
}
for (int jj = 0; jj < _NumLonCells; jj++)
{
_Lons[jj] = _MinLongitude + jj * _LonCellSize;
}
// Instantiate a grid of grid cells
InternalGrid = new GridCell[_NumLatCells, _NumLonCells];
// Instantiate the arrays of lists of cohorts to disperse
DeltaFunctionalGroupDispersalArray = new List<uint>[_NumLatCells, _NumLonCells];
DeltaCohortNumberDispersalArray = new List<uint>[_NumLatCells, _NumLonCells];
// Instantiate the array of lists of grid cells to disperse those cohorts to
DeltaCellToDisperseToArray = new List<uint[]>[_NumLatCells, _NumLonCells];
// Instantiate the arrays of cell entry and exit directions
DeltaCellExitDirection = new List<uint>[_NumLatCells, _NumLonCells];
DeltaCellEntryDirection = new List<uint>[_NumLatCells, _NumLonCells];
// An array of lists of cells to which organisms in each cell can disperse to; includes all cells which contribute to the
// perimeter list, plus diagonal cells if they are in the same realm
CellsForDispersal = new List<uint[]>[_NumLatCells, _NumLonCells];
// An array of lists of directions corresponding to cells which organisms can disperse to
CellsForDispersalDirection = new List<uint>[_NumLatCells, _NumLonCells];
Console.WriteLine("Initialising grid cell environment:");
// Loop through to set up model grid
for (int ii = 0; ii < _NumLatCells; ii+=GridCellRarefaction)
{
for (int jj = 0; jj < _NumLonCells; jj+=GridCellRarefaction)
{
InternalGrid[ii, jj] = new GridCell(_Lats[ii],(uint)ii, _Lons[jj],(uint)jj, LatCellSize, LonCellSize, enviroStack,
GlobalMissingValue, cohortFunctionalGroups, stockFunctionalGroups, globalDiagnostics, tracking, specificLocations,globalModelTimeStepUnit);
CellsForDispersal[ii,jj] = new List<uint[]>();
CellsForDispersalDirection[ii, jj] = new List<uint>();
Console.Write("\rRow {0} of {1}", ii+1, NumLatCells/GridCellRarefaction);
}
}
Console.WriteLine("");
Console.WriteLine("");
InterpolateMissingValues(globalModelTimeStepUnit);
// Fill in the array of dispersable perimeter lengths for each grid cell
CalculatePerimeterLengthsAndCellsDispersableTo();
CellHeightsKm = new double[_Lats.Length];
CellWidthsKm = new double[_Lats.Length];
// Calculate the lengths of widths of grid cells in each latitudinal strip
// Assume that we are at the midpoint of each cell when calculating lengths
for (int ii = 0; ii < _Lats.Length; ii++)
{
CellHeightsKm[ii] = Utilities.CalculateLengthOfDegreeLatitude(_Lats[ii] + _LatCellSize / 2) * _LatCellSize;
CellWidthsKm[ii] = Utilities.CalculateLengthOfDegreeLongitude(_Lats[ii] + _LatCellSize / 2) * _LonCellSize;
}
}
/// <summary>
/// Constructor for human appropriation of autotroph matter
/// </summary>
public HumanAutotrophMatterAppropriation()
{
_Utilities = new UtilityFunctions();
}
/// <summary>
/// Constructor for EnviroData
/// </summary>
/// <param name="fileName">Filename (including extension)</param>
/// <param name="dataName">The name of the variable that contains the data within the specified file</param>
/// <param name="dataType">Type of data, nc = NetCDF, ascii = ESRI ASCII)</param>
/// <param name="dataResolution">The temporal resolution of the environmental variable</param>
/// <param name="units">The units of the data</param>
/// <todo>Check whether lat/lon or 0/1 are fixed for all NetCDFs</todo>
/// <todo>CHECK IF DIMENSIONS HAVE TO BE THE SAME FOR ALL VARIABLES IN A NETCDF AND HOW TO EXTRACT DIMENSIONS FOR A SINGLE VARIABLE IF NECESSARY</todo>
/// <todo>Write code to check for equal cell sizes in NetCDFs</todo>
public EnviroData(string fileName, string dataName, string dataType, string dataResolution, string units)
{
// Initialise the utility functions
Utilities = new UtilityFunctions();
// Temporary array to hold environmental data
double[,] tempDoubleArray;
// Temporary vectors to hold dimension data
Single[] tempSingleVector;
Int32[] tempInt32Vector;
Int16[] tempInt16Vector;
// Vectors of possible names of the dimension variables to search in the files for
string[] LonSearchStrings = new string[] { "lon", "Lon", "longitude", "Longitude", "lons", "Lons", "long", "Long", "longs", "Longs", "longitudes", "Longitudes", "x", "X" };
string[] LatSearchStrings = new string[] { "lat", "Lat", "latitude", "Latitude", "lats", "Lats", "latitudes", "Latitudes", "y", "Y" };
string[] MonthSearchStrings = new string[] { "month", "Month", "months", "Months", "Time", "time" };
//Integer counter for iterating through search strings
int kk = 0;
// Intialise the list of arrays to hold the values of the environmental data
_DataArray = new List<double[,]>();
// Construct the string required to access the file using Scientific Dataset
_ReadFileString = "msds:" + dataType + "?file=" + fileName + "&openMode=readOnly";
// Open the data file using Scientific Dataset
DataSet internalData = DataSet.Open(_ReadFileString);
// Store the specified units
_Units = units;
// Switch based on the tempeoral resolution and data type
switch (dataResolution)
{
case "year":
switch (dataType)
{
case "esriasciigrid":
// Extract the number of latidudinal and longitudinal cells in the file
_NumLats = (uint)internalData.Dimensions["x"].Length;
_NumLons = (uint)internalData.Dimensions["y"].Length;
// Set number of time intervals equal to 1
_NumTimes = 1;
// Initialise the vector of time steps with length 1
_Times = new double[1];
// Assign the single value of the time step dimension to be equal to 1
_Times[0] = 1;
// Get the value used for missing data in this environmental variable
_MissingValue = internalData.GetAttr<double>(1, "NODATA_value");
// Get the latitudinal and longitudinal sizes of grid cells
_LatStep = internalData.GetAttr<double>(1, "cellsize");
_LonStep = _LatStep;
// Get longitudinal 'x' and latitudinal 'y' corners of the bottom left of the data grid
_LatMin = internalData.GetAttr<double>(1, "yllcorner");
_LonMin = internalData.GetAttr<double>(1, "xllcorner");
// Create vectors holding the latitudes and longitudes of the bottom-left corners of the grid cells
_Lats = new double[NumLats];
for (int ii = 0; ii < NumLats; ii++)
{
_Lats[NumLats - 1 - ii] = LatMin + ii * _LatStep;
}
_Lons = new double[NumLons];
for (int ii = 0; ii < NumLons; ii++)
{
_Lons[ii] = LonMin + ii * _LonStep;
}
//Fill in the two-dimensional environmental data array
// Note: currently assumes Lats (x), Lons (y) in SDS - this is different to ESRI ASCII
tempDoubleArray = new double[NumLats, NumLons];
tempDoubleArray = internalData.GetData<double[,]>(dataName);
_DataArray.Add(tempDoubleArray);
break;
case "nc":
// Loop over possible names for the latitude dimension until a match in the data file is found
kk = 0;
while ((kk < LatSearchStrings.Length) && (!internalData.Variables.Contains(LatSearchStrings[kk]))) kk++;
// If a match for the latitude dimension has been found then read in the data, otherwise throw an error
if (kk < LatSearchStrings.Length)
{
// Get number of latitudinal cells in the file
_NumLats = (uint)internalData.Dimensions[LatSearchStrings[kk]].Length;
// Read in the values of the latitude dimension from the file
// Check which format the latitude dimension data are in; if unrecognized, then throw an error
if (internalData.Variables[LatSearchStrings[kk]].TypeOfData.Name.ToString().ToLower() == "single")
{
// Read the latitude dimension data to a temporary vector
tempSingleVector = internalData.GetData<Single[]>(LatSearchStrings[kk]);
// Convert the dimension data to double format and add to the vector of dimension values
_Lats = new double[tempSingleVector.Length];
for (int jj = 0; jj < tempSingleVector.Length; jj++)
{
_Lats[jj] = (double)tempSingleVector[jj];
}
}
else if (internalData.Variables[LatSearchStrings[kk]].TypeOfData.Name.ToString().ToLower() == "double")
{
// Read the dimension data directly into the vector of dimension values
_Lats = internalData.GetData<double[]>(LatSearchStrings[kk]);
}
else
{
// Data format unrecognized, so throw an error
Debug.Fail("Unrecognized data format for latitude dimension");
}
}
else
{
// Didn't find a plausible match for latitude dimension data, so throw an error
Debug.Fail("Cannot find any variables that look like latitude dimensions");
}
// Loop over possible names for the latitude dimension until a match in the data file is found
kk = 0;
while ((kk < LonSearchStrings.Length) && (!internalData.Variables.Contains(LonSearchStrings[kk]))) kk++;
// If a match for the longitude dimension has been found then read in the data, otherwise throw an error
if (kk < LonSearchStrings.Length)
{
// Get number of longitudinal cells in the file
_NumLons = (uint)internalData.Dimensions[LonSearchStrings[kk]].Length;
// Read in the values of the longitude dimension from the file
// Check which format the longitude dimension data are in; if unrecognized, then throw an error
if (internalData.Variables[LonSearchStrings[kk]].TypeOfData.Name.ToString().ToLower() == "single")
{
// Read the longitude dimension data to a temporary vector
tempSingleVector = internalData.GetData<Single[]>(LonSearchStrings[kk]);
// Convert the dimension data to double format and add to the vector of dimension values
_Lons = new double[tempSingleVector.Length];
for (int jj = 0; jj < tempSingleVector.Length; jj++)
{
_Lons[jj] = (double)tempSingleVector[jj];
}
}
else if (internalData.Variables[LonSearchStrings[kk]].TypeOfData.Name.ToString().ToLower() == "double")
{
// Read the dimension data directly into the vector of dimension values
_Lons = internalData.GetData<double[]>(LonSearchStrings[kk]);
}
else
{
// Data format unrecognized, so throw an error
Debug.Fail("Unrecognized data format for longitude dimension");
}
}
else
{
// Didn't find a plausible match for longitude dimension data, so throw an error
Debug.Fail("Cannot find any variables that look like longitude dimensions");
}
// Set number of time intervals equal to 1
_NumTimes = 1;
// Initialise the vector of time steps with length 1
_Times = new double[1];
// Assign the single value of the time step dimension to be equal to 1
_Times[0] = 1;
// Get the latitudinal and longitudinal sizes of grid cells
_LatStep = (_Lats[1] - _Lats[0]);
_LonStep = (_Lons[1] - _Lons[0]);
// Convert vectors of latitude and longutiude dimension data from cell-centre references to bottom-left references
//if LatStep is positive then subtract the step to convert to the bottom left corner of the cell,
// else if LatStep is negative, then need to add the step to convert to the bottom left
for (int ii = 0; ii < _Lats.Length; ii++)
{
_Lats[ii] = (_LatStep.CompareTo(0.0) > 0) ? _Lats[ii] - (_LatStep / 2) : _Lats[ii] + (_LatStep / 2);
}
for (int jj = 0; jj < _Lons.Length; jj++)
{
_Lons[jj] = (_LonStep.CompareTo(0.0) > 0) ? _Lons[jj] - (_LonStep / 2) : _Lons[jj] + (_LonStep / 2);
}
// Check whether latitudes and longitudes are inverted in the NetCDF file
bool LatInverted = (_Lats[1] < _Lats[0]);
bool LongInverted = (_Lons[1] < _Lons[0]);
// Run method to read in the environmental data and the dimension data from the NetCDF
EnvironmentListFromNetCDF(internalData, dataName, LatInverted, LongInverted);
// Get longitudinal 'x' and latitudinal 'y' corners of the bottom left of the data grid
_LatMin = _Lats[0];
_LonMin = _Lons[0];
break;
default:
// Data type not recognized, so throw an error
Debug.Fail("Data type not supported");
break;
}
break;
case "month":
switch (dataType)
{
case "esriasciigrid":
// This combination does not work in the model, so throw an error
Debug.Fail("Variables at monthly temporal resolution must be stored as three-dimensional NetCDFs");
break;
case "nc":
// Loop over possible names for the latitude dimension until a match in the data file is found
kk = 0;
while ((kk < LatSearchStrings.Length) && (!internalData.Variables.Contains(LatSearchStrings[kk]))) kk++;
// If a match for the latitude dimension has been found then read in the data, otherwise throw an error
if (kk < LatSearchStrings.Length)
{
// Get number of latitudinal cells in the file
_NumLats = (uint)internalData.Dimensions[LatSearchStrings[kk]].Length;
// Read in the values of the latitude dimension from the file
// Check which format the latitude dimension data are in; if unrecognized, then throw an error
if (internalData.Variables[LatSearchStrings[kk]].TypeOfData.Name.ToString().ToLower() == "single")
{
// Read the latitude dimension data to a temporary vector
tempSingleVector = internalData.GetData<Single[]>(LatSearchStrings[kk]);
// Convert the dimension data to double format and add to the vector of dimension values
_Lats = new double[tempSingleVector.Length];
for (int jj = 0; jj < tempSingleVector.Length; jj++)
{
_Lats[jj] = (double)tempSingleVector[jj];
}
}
else if (internalData.Variables[LatSearchStrings[kk]].TypeOfData.Name.ToString().ToLower() == "double")
{
// Read the dimension data directly into the vector of dimension values
_Lats = internalData.GetData<double[]>(LatSearchStrings[kk]);
}
else
{
// Data format unrecognized, so throw an error
Debug.Fail("Unrecognized data format for latitude dimension");
}
}
else
{
// Didn't find a plausible match for latitude dimension data, so throw an error
Debug.Fail("Cannot find any variables that look like latitude dimensions");
}
// Loop over possible names for the latitude dimension until a match in the data file is found
kk = 0;
while ((kk < LonSearchStrings.Length) && (!internalData.Variables.Contains(LonSearchStrings[kk]))) kk++;
// If a match for the longitude dimension has been found then read in the data, otherwise throw an error
if (kk < LonSearchStrings.Length)
{
// Get number of longitudinal cells in the file
_NumLons = (uint)internalData.Dimensions[LonSearchStrings[kk]].Length;
// Read in the values of the longitude dimension from the file
// Check which format the longitude dimension data are in; if unrecognized, then throw an error
if (internalData.Variables[LonSearchStrings[kk]].TypeOfData.Name.ToString().ToLower() == "single")
{
// Read the longitude dimension data to a temporary vector
tempSingleVector = internalData.GetData<Single[]>(LonSearchStrings[kk]);
// Convert the dimension data to double format and add to the vector of dimension values
_Lons = new double[tempSingleVector.Length];
for (int jj = 0; jj < tempSingleVector.Length; jj++)
{
_Lons[jj] = (double)tempSingleVector[jj];
}
}
else if (internalData.Variables[LonSearchStrings[kk]].TypeOfData.Name.ToString().ToLower() == "double")
{
// Read the dimension data directly into the vector of dimension values
_Lons = internalData.GetData<double[]>(LonSearchStrings[kk]);
}
else
{
// Data format unrecognized, so throw an error
Debug.Fail("Unrecognized data format for longitude dimension");
}
}
else
{
// Didn't find a plausible match for longitude dimension data, so throw an error
Debug.Fail("Cannot find any variables that look like longitude dimensions");
}
// Loop over possible names for the monthly temporal dimension until a match in the data file is found
kk = 0;
while ((kk < MonthSearchStrings.Length) && (!internalData.Variables.Contains(MonthSearchStrings[kk]))) kk++;
// Of a match for the monthly temporal dimension has been found then read in the data, otherwise thrown an error
if (internalData.Variables.Contains(MonthSearchStrings[kk]))
{
// Get the number of months in the temporal dimension
_NumTimes = (uint)internalData.Dimensions[MonthSearchStrings[kk]].Length;
// Check that the number of months is 12
Debug.Assert(_NumTimes == 12, "Number of time intervals in an environmental data file with specified monthly temporal resolution is not equal to 12");
// Read in the values of the temporal dimension from the file
// Check which format the temporal dimension data are in; if unrecognized, then throw an error
if (internalData.Variables[MonthSearchStrings[kk]].TypeOfData.Name.ToString().ToLower() == "single")
{
// Read the temporal dimension data to a temporary vector
tempSingleVector = internalData.GetData<Single[]>(MonthSearchStrings[kk]);
// Convert the dimension data to double format and add to the vector of dimension values
_Times = new double[_NumTimes];
for (int hh = 0; hh < tempSingleVector.Length; hh++)
{
_Times[hh] = (double)tempSingleVector[hh];
}
}
else if (internalData.Variables[MonthSearchStrings[kk]].TypeOfData.Name.ToString().ToLower() == "double")
{
// Read the dimension data directly into the vector of dimension values
_Times = internalData.GetData<double[]>(MonthSearchStrings[kk]);
}
else if (internalData.Variables[MonthSearchStrings[kk]].TypeOfData.Name.ToString().ToLower() == "int32")
{
// Read the temporal dimension data to a temporary vector
tempInt32Vector = internalData.GetData<Int32[]>(MonthSearchStrings[kk]);
// Convert the dimension data to double format and add to the vector of dimension values
_Times = new double[_NumTimes];
for (int hh = 0; hh < tempInt32Vector.Length; hh++)
{
_Times[hh] = (double)tempInt32Vector[hh];
}
}
else if (internalData.Variables[MonthSearchStrings[kk]].TypeOfData.Name.ToString().ToLower() == "int16")
{
// Read the temporal dimension data to a temporary vector
tempInt16Vector = internalData.GetData<Int16[]>(MonthSearchStrings[kk]);
// Convert the dimension data to double format and add to the vector of dimension values
_Times = new double[_NumTimes];
for (int hh = 0; hh < tempInt16Vector.Length; hh++)
{
_Times[hh] = (double)tempInt16Vector[hh];
}
}
else
{
// Data format unrecognized, so throw an error
Debug.Fail("Unrecognized data format for time dimension");
}
}
else
{
// Didn't find a plausible match for temporal dimension data, so throw an error
Debug.Fail("Cannot find any variables that look like a monthly temporal dimension");
}
// Convert the values of the time dimension to equal integers between 1 and 12 (the format currently recognized by the model)
for (int hh = 0; hh < _NumTimes; hh++)
{
if (_Times[hh] != hh + 1) _Times[hh] = hh + 1;
}
// Get the latitudinal and longitudinal sizes of grid cells
_LatStep = (_Lats[1] - _Lats[0]);
_LonStep = (_Lons[1] - _Lons[0]);
// Convert vectors of latitude and longutiude dimension data from cell-centre references to bottom-left references
for (int ii = 0; ii < _Lats.Length; ii++)
{
_Lats[ii] = _Lats[ii] - (_LatStep / 2);
}
for (int jj = 0; jj < _Lons.Length; jj++)
{
_Lons[jj] = _Lons[jj] - (_LonStep / 2);
}
// Check whether latitudes and longitudes are inverted in the NetCDF file
bool LatInverted = (_Lats[1] < _Lats[0]);
bool LongInverted = (_Lons[1] < _Lons[0]);
// Run method to read in the environmental data and the dimension data from the NetCDF
EnvironmentListFromNetCDF3D(internalData, dataName, LatInverted, LongInverted);
// Get longitudinal 'x' and latitudinal 'y' corners of the bottom left of the data grid
_LatMin = _Lats[0];
_LonMin = _Lons[0];
break;
default:
// Data type not recognized, so throw an error
Debug.Fail("Data type not supported");
break;
}
break;
default:
// The model currently only supports variables with temporal resolution 'year' or 'month', so throw an error
Debug.Fail("Temporal resolution not supported");
break;
}
// Check to see whether the environmental variable has longitude values from 0 to 360, instead of -180 to 180 (which the model currently recognizes)
if (_LonMin + (_NumLons * _LonStep) > 180.0)
{
// Convert the longitude values to be -180 to 180, instead of 0 to 360
Utilities.ConvertToM180To180(_Lons);
// Update the minimum longitude value accordingly
_LonMin = _Lons.Min();
}
// Update the variable keeping track of the number of environmental data layers
_NumEnviroLayers = _NumEnviroLayers + 1;
//Close the environmental data file
internalData.Dispose();
}
/// <summary>
/// Overloaded constructor to fetch climate information from the cloud using FetchClimate for specific locations
/// </summary>
/// <param name="dataName">Name of the the climate variable to be fetched</param>
/// <param name="dataResolution">Time resolution requested</param>
/// <param name="latMin">Bottom latitude</param>
/// <param name="lonMin">Leftmost longitude</param>
/// <param name="latMax">Maximum latitude</param>
/// <param name="lonMax">Maximum longitude</param>
/// <param name="cellSize">Size of each grid cell</param>
/// <param name = "cellList">List of cells to be fetched</param>
/// <param name="FetchClimateDataSource">Data source from which to fetch environmental data</param>
public EnviroData(string dataName, string dataResolution, double latMin, double lonMin, double latMax, double lonMax, double cellSize,
List<uint[]> cellList,
EnvironmentalDataSource FetchClimateDataSource)
{
Console.WriteLine("Fetching environmental data for: " + dataName + " with resolution " + dataResolution);
// Initialise the utility functions
Utilities = new UtilityFunctions();
_NumLats = Convert.ToUInt32((latMax - latMin) / cellSize);
_NumLons = Convert.ToUInt32((lonMax - lonMin) / cellSize);
_LatMin = latMin;
_LonMin = lonMin;
_Lats = new double[_NumLats];
_Lons = new double[_NumLons];
for (int ii = 0; ii < _NumLats; ii++)
{
_Lats[ii] = Math.Round(_LatMin + (ii * cellSize), 2);
}
for (int jj = 0; jj < _NumLons; jj++)
{
_Lons[jj] = Math.Round(_LonMin + (jj * cellSize), 2);
}
_LatStep = Math.Round(Lats[1] - _Lats[0], 2);
_LonStep = Math.Round(Lons[1] - Lons[0], 2);
//Declare a dataset to perform the fetch
var ds = DataSet.Open("msds:memory2");
_DataArray = new List<double[,]>();
//Add the required time dimension to the dataset
switch (dataResolution)
{
case "year":
ds.AddClimatologyAxisYearly(yearmin: 1961, yearmax: 1990, yearStep: 30);
break;
case "month":
ds.AddClimatologyAxisMonthly();
break;
default:
break;
}
//Add lat and lon information to the dataset
for (int ii = 0; ii < cellList.Count; ii++)
{
ds.AddAxisCells("longitude", "degrees_east", _Lons[cellList[ii][1]], Lons[cellList[ii][1]] + cellSize, cellSize);
ds.AddAxisCells("latitude", "degrees_north", _Lats[cellList[ii][0]], _Lats[cellList[ii][0]] + cellSize, cellSize);
double[, ,] temp = null;
//Fetch for the required data
switch (dataName.ToLower())
{
case "land_dtr":
ds.Fetch(ClimateParameter.FC_LAND_DIURNAL_TEMPERATURE_RANGE, "landdtr", dataSource: FetchClimateDataSource); //this call will create 2D variable on dimensions records and months and fill it with a FetchClimate
//int NumberOfRecords = ds.Dimensions["RecordNumber"].Length; // get number of records
temp = (double[, ,])ds.Variables["landdtr"].GetData();
_MissingValue = (double)ds.Variables["landdtr"].GetMissingValue();
break;
case "temperature":
ds.Fetch(ClimateParameter.FC_TEMPERATURE, "airt", dataSource: FetchClimateDataSource); //this call will create 2D variable on dimensions records and months and fill it with a FetchClimate
//int NumberOfRecords = ds.Dimensions["RecordNumber"].Length; // get number of records
temp = (double[, ,])ds.Variables["airt"].GetData();
_MissingValue = (double)ds.Variables["airt"].GetMissingValue();
break;
// Commenting out ocean air temperature because it is running too slow when using FetchClimate
case "temperature_ocean":
ds.Fetch(ClimateParameter.FC_OCEAN_AIR_TEMPERATURE, "oceanairt", dataSource: FetchClimateDataSource); //this call will create 2D variable on dimensions records and months and fill it with a FetchClimate
//int NumberOfRecords = ds.Dimensions["RecordNumber"].Length; // get number of records
temp = (double[, ,])ds.Variables["oceanairt"].GetData();
_MissingValue = (double)ds.Variables["oceanairt"].GetMissingValue();
break;
case "precipitation":
ds.Fetch(ClimateParameter.FC_PRECIPITATION, "precip", dataSource: FetchClimateDataSource); //this call will create 2D variable on dimensions records and months and fill it with a FetchClimate
//int NumberOfRecords = ds.Dimensions["RecordNumber"].Length; // get number of records
temp = (double[, ,])ds.Variables["precip"].GetData();
_MissingValue = (double)ds.Variables["precip"].GetMissingValue();
break;
case "frost":
ds.Fetch(ClimateParameter.FC_LAND_FROST_DAY_FREQUENCY, "frost", dataSource: FetchClimateDataSource);
temp = (double[, ,])ds.Variables["frost"].GetData();
_MissingValue = (double)ds.Variables["frost"].GetMissingValue();
break;
default:
Debug.Fail("No Enviro data read in for " + dataName);
break;
}
_NumTimes = (uint)ds.Dimensions["time"].Length;
//Add the fetched data to the Envirodata array
for (int tt = 0; tt < _NumTimes; tt++)
{
double[,] TempArray;
if (_DataArray.Count > tt)
{
TempArray = _DataArray[tt];
}
else
{
TempArray = new double[NumLats, NumLons];
}
// Currently FetchClimate returns longitudes as the last array dimension
TempArray[cellList[ii][0], cellList[ii][1]] = temp[tt, 0, 0];
if (_DataArray.Count > tt)
{
_DataArray.RemoveAt(tt);
_DataArray.Insert(tt, TempArray);
}
else
{
_DataArray.Add(TempArray);
}
}
}
//DataSet Out = ds.Clone("output/" + dataName + ".nc");
//Out.Dispose();
ds.Dispose();
}
/// <summary>
/// Constructor for predation: assigns all parameter values
/// </summary>
/// <param name="cellArea">The area (in square km) of the grid cell</param>
/// <param name="globalModelTimeStepUnit">The time step unit used in the model</param>
public RevisedPredation(double cellArea, string globalModelTimeStepUnit)
{
InitialiseParametersPredation();
// Initialise the utility functions
Utilities = new UtilityFunctions();
// Calculate the scalar to convert from the time step units used by this implementation of predation to the global model time step units
_DeltaT = Utilities.ConvertTimeUnits(globalModelTimeStepUnit, _TimeUnitImplementation);
// Store the specified cell area in this instance of this predation implementation
_CellArea = cellArea;
_CellAreaHectares = cellArea * 100;
HalfNumberOfBins = NumberOfBins / 2;
FeedingPreferenceHalfStandardDeviation = _FeedingPreferenceStandardDeviation * 0.5;
}
/// <summary>
/// Constructor for the plant model
/// </summary>
public RevisedTerrestrialPlantModel()
{
// Initialise parameters
InitialisePlantModelParameters();
// Initialise the utility functions
Utilities = new UtilityFunctions();
}
