/// <summary>
/// Record dispersal events in the dispersal tracker
/// </summary>
/// <param name="inboundCohorts">The cohorts arriving in a cell in the current time step</param>
/// <param name="outboundCohorts">The cohorts leaving a cell in the current time step</param>
/// <param name="outboundCohortWeights">The body masses of cohorts leaving the cell in the current time step</param>
/// <param name="timestep">The current model time step</param>
/// <param name="madingleyModelGrid">The model grid</param>
public void RecordDispersalForACell(uint[, ,] inboundCohorts, uint[, ,] outboundCohorts, List<double>[,] outboundCohortWeights, uint timestep, ModelGrid madingleyModelGrid)
{
var count = inboundCohorts.GetLength(0) * inboundCohorts.GetLength(1);
var copy = new Madingley.Common.GridCellDispersal[count];
for (var kk = 0; kk < count; kk++)
{
var ii = (int)kk / inboundCohorts.GetLength(1);
var jj = kk % inboundCohorts.GetLength(1);
var denter =
new Tuple<Madingley.Common.CohortsEnterDirection, int>[]
{
Tuple.Create(Madingley.Common.CohortsEnterDirection.North, (int)inboundCohorts[ii, jj, 0]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.NorthEast, (int)inboundCohorts[ii, jj, 1]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.East, (int)inboundCohorts[ii, jj, 2]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.SouthEast, (int)inboundCohorts[ii, jj, 3]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.South, (int)inboundCohorts[ii, jj, 4]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.SouthWest, (int)inboundCohorts[ii, jj, 5]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.West, (int)inboundCohorts[ii, jj, 6]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.NorthWest, (int)inboundCohorts[ii, jj, 7]),
};
var enter = denter.ToDictionary(l => l.Item1, l => l.Item2);
var dexit =
new Tuple<Madingley.Common.CohortsExitDirection, int>[]
{
Tuple.Create(Madingley.Common.CohortsExitDirection.North, (int)outboundCohorts[ii, jj, 0]),
Tuple.Create(Madingley.Common.CohortsExitDirection.NorthEast, (int)outboundCohorts[ii, jj, 1]),
Tuple.Create(Madingley.Common.CohortsExitDirection.East, (int)outboundCohorts[ii, jj, 2]),
Tuple.Create(Madingley.Common.CohortsExitDirection.SouthEast, (int)outboundCohorts[ii, jj, 3]),
Tuple.Create(Madingley.Common.CohortsExitDirection.South, (int)outboundCohorts[ii, jj, 4]),
Tuple.Create(Madingley.Common.CohortsExitDirection.SouthWest, (int)outboundCohorts[ii, jj, 5]),
Tuple.Create(Madingley.Common.CohortsExitDirection.West, (int)outboundCohorts[ii, jj, 6]),
Tuple.Create(Madingley.Common.CohortsExitDirection.NorthWest, (int)outboundCohorts[ii, jj, 7]),
};
var exit = dexit.ToDictionary(l => l.Item1, l => l.Item2);
var weights = outboundCohortWeights[ii, jj].ToArray();
var cell = madingleyModelGrid.GetGridCell((uint)ii, (uint)jj);
var ccell = Converters.ConvertCellData(cell);
copy[kk] = new Madingley.Common.GridCellDispersal(enter, exit, weights, ccell);
}
this.GridCellDispersals = copy;
}
/// <summary>
/// Run responsive dispersal
/// </summary>
/// <param name="cellIndices">The longitudinal and latitudinal indices of the current grid cell</param>
/// <param name="gridForDispersal">The model grid to run dispersal for</param>
/// <param name="cohortToDisperse">The cohort for which to apply the dispersal process</param>
/// <param name="actingCohortFunctionalGroup">The functional group index of the acting cohort</param>
/// <param name="actingCohortNumber">The position of the acting cohort within the functional group in the array of grid cell cohorts</param>
/// <param name="currentMonth">The current model month</param>
public void RunDispersal(uint[] cellIndices, ModelGrid gridForDispersal, Cohort cohortToDisperse,
int actingCohortFunctionalGroup, int actingCohortNumber, uint currentMonth)
{
// Starvation driven dispersal takes precedence over density driven dispersal (i.e. a cohort can't do both). Also, the delta
// arrays only allow each cohort to perform one type of dispersal each time step
bool CohortDispersed = false;
// Check for starvation-driven dispersal
CohortDispersed = CheckStarvationDispersal(gridForDispersal, cellIndices[0], cellIndices[1], cohortToDisperse, actingCohortFunctionalGroup, actingCohortNumber);
if (!CohortDispersed)
{
// Check for density driven dispersal
CheckDensityDrivenDispersal(gridForDispersal, cellIndices[0], cellIndices[1], cohortToDisperse, actingCohortFunctionalGroup, actingCohortNumber);
}
}
/// <summary>
/// Run dispersal
/// </summary>
public void RunCrossGridCellEcologicalProcess(uint[] cellIndex, ModelGrid gridForDispersal, bool dispersalOnly, FunctionalGroupDefinitions madingleyCohortDefinitions, FunctionalGroupDefinitions madingleyStockDefinitions, uint currentMonth)
{
// Create a temporary handler for grid cell cohorts
GridCellCohortHandler WorkingGridCellCohorts;
// Get the lat and lon indices
uint ii = cellIndex[0];
uint jj = cellIndex[1];
// A boolean to check that the environmental layer exists
bool varExists;
// Check to see if the cell is marine
double CellRealm = gridForDispersal.GetEnviroLayer("Realm", 0, ii, jj, out varExists);
// Go through all of the cohorts in turn and see if they disperse
WorkingGridCellCohorts = gridForDispersal.GetGridCellCohorts(ii, jj);
// Loop through cohorts, and perform dispersal according to cohort type and status
for (int kk = 0; kk < WorkingGridCellCohorts.Count; kk++)
{
// Work through the list of cohorts
for (int ll = 0; ll < WorkingGridCellCohorts[kk].Count; ll++)
{
// Check to see if the cell is marine and the cohort type is planktonic
if (CellRealm == 2.0 &&
((madingleyCohortDefinitions.GetTraitNames("Mobility", WorkingGridCellCohorts[kk][ll].FunctionalGroupIndex) == "planktonic") || (WorkingGridCellCohorts[kk][ll].IndividualBodyMass <= PlanktonThreshold)))
{
// Run advective dispersal
Implementations["basic advective dispersal"].RunDispersal(cellIndex, gridForDispersal, WorkingGridCellCohorts[kk][ll], kk, ll, currentMonth);
}
// Otherwise, if mature do responsive dispersal
else if (WorkingGridCellCohorts[kk][ll].MaturityTimeStep < uint.MaxValue)
{
// Run diffusive dispersal
Implementations["basic responsive dispersal"].RunDispersal(cellIndex, gridForDispersal, WorkingGridCellCohorts[kk][ll], kk, ll, currentMonth);
}
// If the cohort is immature, run diffusive dispersal
else
{
Implementations["basic diffusive dispersal"].RunDispersal(cellIndex, gridForDispersal, WorkingGridCellCohorts[kk][ll], kk, ll, currentMonth);
}
}
}
}
/// <summary>
/// Initializes the ecosystem model
/// </summary>
/// <param name="mmi">An instance of the model initialisation class</param>
public static void Load(Tuple<Madingley.Common.Environment, SortedList<string, EnviroData>> mmi, bool readData)
{
var e = mmi.Item1;
if (e.SpecificLocations == false)
{
var CellList = new List<Tuple<int, int>>();
var NumLatCells = (uint)((e.TopLatitude - e.BottomLatitude) / e.CellSize);
var NumLonCells = (uint)((e.RightmostLongitude - e.LeftmostLongitude) / e.CellSize);
// Loop over all cells in the model
for (int latitudeIndex = 0; latitudeIndex < NumLatCells; latitudeIndex++)
{
for (int longitudeIndex = 0; longitudeIndex < NumLonCells; longitudeIndex++)
{
// Add the vector to the list of all active grid cells
CellList.Add(Tuple.Create(latitudeIndex, longitudeIndex));
}
}
e.FocusCells = CellList;
}
if (readData)
{
var cellList = e.FocusCells.Select(a => new UInt32[] { (uint)a.Item1, (uint)a.Item2 }).ToList();
var EcosystemModelGrid = new ModelGrid((float)e.BottomLatitude, (float)e.LeftmostLongitude, (float)e.TopLatitude, (float)e.RightmostLongitude,
(float)e.CellSize, (float)e.CellSize, cellList, mmi.Item2,
e.SpecificLocations);
Func<Tuple<int, int>, IDictionary<string, double[]>> convertCellEnvironment =
cell =>
{
var env = EcosystemModelGrid.GetCellEnvironment((uint)cell.Item1, (uint)cell.Item2);
return env.ToDictionary(kv => kv.Key, kv => kv.Value.ToArray());
};
e.CellEnvironment = e.FocusCells.Select(convertCellEnvironment).ToList();
}
}
/// <summary>
/// Calculates the mean trophic level of all individual organisms in a grid cell
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The list of cell indices in the current model simulation</param>
/// <param name="cellIndex">The index of the current cell in the list of cells to run</param>
/// <returns>The mean trophic level of individuals in the grid cell</returns>
public double CalculateMeanTrophicLevelCell(ModelGrid ecosystemModelGrid, List <uint[]> cellIndices, int cellIndex)
{
//Get the cohorts for the specified cell
GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
double BiomassWeightedTI = 0.0;
double TotalBiomass = 0.0;
double CohortBiomass = 0.0;
foreach (var CohortList in CellCohorts)
{
foreach (Cohort c in CohortList)
{
CohortBiomass = (c.IndividualBodyMass + c.IndividualReproductivePotentialMass) * c.CohortAbundance;
BiomassWeightedTI += CohortBiomass * c.TrophicIndex;
TotalBiomass += CohortBiomass;
}
}
return(BiomassWeightedTI / TotalBiomass);
}
/// <summary>
/// Return the distribution of biomasses among trophic level bins
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The list of cell indices to be run in the current model simulation</param>
/// <param name="cellIndex">The index of the current cell in the list of cells to be run</param>
/// <returns>The distribution of biomasses among trophic level bins</returns>
public double[] CalculateTrophicDistribution(ModelGrid ecosystemModelGrid, List <uint[]> cellIndices, int cellIndex)
{
//Get the cohorts for the specified cell
GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
double[] TrophicIndexBinMasses = new double[NumberTrophicBins];
int BinIndex;
foreach (var CohortList in CellCohorts)
{
foreach (Cohort c in CohortList)
{
BinIndex = _TrophicIndexBinValues.ToList().IndexOf(_TrophicIndexBinValues.Last(x => x < c.TrophicIndex));
TrophicIndexBinMasses[BinIndex] += (c.IndividualBodyMass + c.IndividualReproductivePotentialMass) * c.CohortAbundance;
}
}
return(TrophicIndexBinMasses);
}
/// <summary>
/// Run diffusive dispersal
/// </summary>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="gridForDispersal">The model grid to run dispersal for</param>
/// <param name="cohortToDisperse">The cohort for which to run the dispersal process for</param>
/// <param name="actingCohortFunctionalGroup">The functional group index of the acting cohort</param>
/// <param name="actingCohortNumber">The position of the cohort within the functional group in the array of grid cell cohorts</param>
/// <param name="currentMonth">The current model month</param>
public void RunDispersal(uint[] cellIndices, ModelGrid gridForDispersal, Cohort cohortToDisperse,
int actingCohortFunctionalGroup, int actingCohortNumber, uint currentMonth)
{
// Calculate dispersal speed for the cohort
double DispersalSpeed = CalculateDispersalSpeed(cohortToDisperse.IndividualBodyMass);
// A double to indicate whether or not the cohort has dispersed, and if it has dispersed, where to
double CohortDispersed = 0;
// Temporary variables to keep track of directions in which cohorts enter/exit cells during the multiple advection steps per time step
uint ExitDirection = new uint();
uint EntryDirection = new uint();
ExitDirection = 9999;
// Get the probability of dispersal
double[] DispersalArray = CalculateDispersalProbability(gridForDispersal, cellIndices[0], cellIndices[1], DispersalSpeed);
// Check to see if it does disperse
CohortDispersed = CheckForDispersal(DispersalArray[0]);
// If it does, check to see where it will end up
if (CohortDispersed > 0)
{
// Check to see if the direction is actually dispersable
uint[] DestinationCell = CellToDisperseTo(gridForDispersal, cellIndices[0], cellIndices[1], DispersalArray, CohortDispersed, DispersalArray[4], DispersalArray[5], ref ExitDirection, ref EntryDirection);
if (DestinationCell[0] < 999999)
{
// Update the delta array of cohorts
gridForDispersal.DeltaFunctionalGroupDispersalArray[cellIndices[0], cellIndices[1]].Add((uint)actingCohortFunctionalGroup);
gridForDispersal.DeltaCohortNumberDispersalArray[cellIndices[0], cellIndices[1]].Add((uint)actingCohortNumber);
// Update the delta array of cells to disperse to
gridForDispersal.DeltaCellToDisperseToArray[cellIndices[0], cellIndices[1]].Add(DestinationCell);
// Update the delta array of exit and entry directions
gridForDispersal.DeltaCellExitDirection[cellIndices[0], cellIndices[1]].Add(ExitDirection);
gridForDispersal.DeltaCellEntryDirection[cellIndices[0], cellIndices[1]].Add(EntryDirection);
}
}
}
/// <summary>
/// Calculates the geometric community weighted mean body mass
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The list of indices of cells to be run in the current model simulation</param>
/// <param name="cellIndex">The index of the current cell within the list of cells to be run</param>
/// <returns>geometric community weighted mean body mass</returns>
public double CalculateGeometricCommunityMeanBodyMass(ModelGrid ecosystemModelGrid, List <uint[]> cellIndices, int cellIndex)
{
//Get the cohorts for the specified cell
GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
double CumulativeAbundance = 0.0;
double CumulativeLogBiomass = 0.0;
//Retrieve the biomass
foreach (var CohortList in CellCohorts)
{
foreach (Cohort c in CohortList)
{
CumulativeLogBiomass += Math.Log(c.IndividualBodyMass + c.IndividualReproductivePotentialMass) * c.CohortAbundance;
CumulativeAbundance += c.CohortAbundance;
}
}
double CWGMBM = Math.Exp(CumulativeLogBiomass / CumulativeAbundance);
return(CWGMBM);
}
/// <summary>
/// Initializes the ecosystem model
/// </summary>
/// <param name="mmi">An instance of the model initialisation class</param>
public static void Load(Tuple <Madingley.Common.Environment, SortedList <string, EnviroData> > mmi)
{
var e = mmi.Item1;
if (e.SpecificLocations == false)
{
var CellList = new List <Tuple <int, int> >();
var NumLatCells = (uint)((e.TopLatitude - e.BottomLatitude) / e.CellSize);
var NumLonCells = (uint)((e.RightmostLongitude - e.LeftmostLongitude) / e.CellSize);
// Loop over all cells in the model
for (int latitudeIndex = 0; latitudeIndex < NumLatCells; latitudeIndex++)
{
for (int longitudeIndex = 0; longitudeIndex < NumLonCells; longitudeIndex++)
{
// Add the vector to the list of all active grid cells
CellList.Add(Tuple.Create(latitudeIndex, longitudeIndex));
}
}
e.FocusCells = CellList;
}
var cellList = e.FocusCells.Select(a => new UInt32[] { (uint)a.Item1, (uint)a.Item2 }).ToList();
var EcosystemModelGrid = new ModelGrid((float)e.BottomLatitude, (float)e.LeftmostLongitude, (float)e.TopLatitude, (float)e.RightmostLongitude,
(float)e.CellSize, (float)e.CellSize, cellList, mmi.Item2,
e.SpecificLocations);
Func <Tuple <int, int>, IDictionary <string, double[]> > convertCellEnvironment =
cell =>
{
var env = EcosystemModelGrid.GetCellEnvironment((uint)cell.Item1, (uint)cell.Item2);
return(env.ToDictionary(kv => kv.Key, kv => kv.Value.ToArray()));
};
e.CellEnvironment = e.FocusCells.Select(convertCellEnvironment).ToList();
}
/// <summary>
/// Calculates the probability of diffusive dispersal given average individual dispersal speed
/// </summary>
/// <param name="madingleyGrid">The model grid</param>
/// <param name="latIndex">The latitude index of the grid cell to check for dispersal</param>
/// <param name="lonIndex">The longitude index of the grid cell to check for dispersal</param>
/// <param name="dispersalSpeed">The average speed at which individuals in this cohort move around their environment, in km per month</param>
/// <returns>A six element array.
/// The first element is the probability of dispersal.
/// The second element is the probability of dispersing in the u (longitudinal) direction
/// The third element is the probability of dispersing in the v (latitudinal) direction
/// The fourth element is the probability of dispersing in the diagonal direction
/// The fifth element is the u velocity modified by the random diffusion component
/// The sixth element is the v velocity modified by the random diffusion component
/// Note that the second, third, and fourth elements are always positive; thus, they do not indicate 'direction' in terms of dispersal.</returns>
private double[] CalculateDispersalProbability(ModelGrid madingleyGrid, uint latIndex, uint lonIndex, double dispersalSpeed)
{
// Check that the u speed and v speed are not greater than the cell length. If they are, then rescale them; this limits the max velocity
// so that cohorts cannot be advected more than one grid cell per time step
double LatCellLength = madingleyGrid.CellHeightsKm[latIndex];
double LonCellLength = madingleyGrid.CellWidthsKm[latIndex];
// Pick a direction at random
double RandomDirection = RandomNumberGenerator.GetUniform() * 2 * Math.PI;
// Calculate the u and v components given the dispersal speed
double uSpeed = dispersalSpeed * Math.Cos(RandomDirection);
double vSpeed = dispersalSpeed * Math.Sin(RandomDirection);
// Calculate the area of the grid cell that is now outside in the diagonal direction
double AreaOutsideBoth = Math.Abs(uSpeed * vSpeed);
// Calculate the area of the grid cell that is now outside in the u direction (not including the diagonal)
double AreaOutsideU = Math.Abs(uSpeed * LatCellLength) - AreaOutsideBoth;
// Calculate the proportion of the grid cell that is outside in the v direction (not including the diagonal
double AreaOutsideV = Math.Abs(vSpeed * LonCellLength) - AreaOutsideBoth;
// Get the cell area, in kilometres squared
double CellArea = madingleyGrid.GetCellEnvironment(latIndex, lonIndex)["Cell Area"][0];
// Convert areas to a probability
double DispersalProbability = (AreaOutsideU + AreaOutsideV + AreaOutsideBoth) / CellArea;
// Check that the whole cell hasn't moved out. This could happen if dispersal speed was high enough
if (DispersalProbability >= 1)
{
Debug.Fail("Dispersal probability in diffusion should always be <= 1");
}
double[] NewArray = { DispersalProbability, AreaOutsideU / CellArea, AreaOutsideV / CellArea, AreaOutsideBoth / CellArea, uSpeed, vSpeed };
return(NewArray);
}
/// <summary>
/// Generates the file outputs for the current time step
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="currentTimeStep">The current model time step</param>
private void TimeStepFileOutputs(ModelGrid ecosystemModelGrid, uint currentTimeStep)
{
Console.WriteLine("Writing global ouputs to file...\n");
// Write out the basic diagnostic variables
DataConverter.ValueToSDS1D(OrganicPoolOut, "Organic matter pool", "Time step",
ecosystemModelGrid.GlobalMissingValue, BasicOutput, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(RespiratoryPoolOut, "Respiratory CO2 pool", "Time step",
ecosystemModelGrid.GlobalMissingValue, BasicOutput, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(TotalNumberOfCohorts, "Number of cohorts in model", "Time step",
ecosystemModelGrid.GlobalMissingValue, BasicOutput, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(TotalNumberOfStocks, "Number of stocks in model", "Time step",
ecosystemModelGrid.GlobalMissingValue, BasicOutput, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(NumberOfCohortsExtinct, "Number of cohorts extinct", "Time step",
ecosystemModelGrid.GlobalMissingValue, BasicOutput, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(NumberOfCohortsProduced, "Number of cohorts produced", "Time step",
ecosystemModelGrid.GlobalMissingValue, BasicOutput, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(NumberOfCohortsCombined, "Number of cohorts combined", "Time step",
ecosystemModelGrid.GlobalMissingValue, BasicOutput, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(TotalLivingBiomass, "Total living biomass", "Time step",
ecosystemModelGrid.GlobalMissingValue, BasicOutput, (int)currentTimeStep + 1);
}
/// <summary>
/// Calculates the abundances and biomasses within mass bins for all functional groups in the cohort indices array
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="cellIndex">The number of the current cell in the list of indices of active cells</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
private void CalculateMassBinOutputs(ModelGrid ecosystemModelGrid, List<uint[]> cellIndices, int cellIndex, Boolean marineCell)
{
string[] Keys;
if (marineCell)
{
// Get the cohort trait combinations to consider
Keys = CohortTraitIndicesMarine.Keys.ToArray();
}
else
{
// Get the cohort trait combinations to consider
Keys = CohortTraitIndices.Keys.ToArray();
}
// Loop over trait combinations
foreach (var TraitValue in Keys)
{
// Declare vectors to hold abundance and biomass in mass bins for this trait combination
double[] WorkingAbundanceInMassBins = new double[MassBinNumber];
double[] WorkingBiomassInMassBins = new double[MassBinNumber];
// Declare arrays to hold abundance and biomass in juvenile vs. adult mass bins for this trait combination
double[,] WorkingAbundanceJuvenileAdultMassBins = new double[MassBinNumber, MassBinNumber];
double[,] WorkingBiomassJuvenileAdultMassBins = new double[MassBinNumber, MassBinNumber];
// Create a temporary local copy of the cohorts in this grid cell
GridCellCohortHandler TempCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0],cellIndices[cellIndex][1]);
if (marineCell)
{
// Loop over functional groups
foreach (int FunctionalGroupIndex in CohortTraitIndicesMarine[TraitValue])
{
// Loop over all cohorts in this functional group
for (int cohort = 0; cohort < TempCohorts[FunctionalGroupIndex].Count; cohort++)
{
// Find the appropriate mass bin for the cohort
int mb = 0;
do
{
mb++;
} while (mb < (MassBins.Length - 1) && TempCohorts[FunctionalGroupIndex][cohort].IndividualBodyMass > MassBins[mb]);
// Add the cohort's abundance to the approriate mass bin. Note that we have to differentiate here for non-obligate zooplankton, because they are only added in if they are
// below the zooplankton mass threshold (or an obligate zooplankton)
if (String.Equals(TraitValue, "Zooplankton (all)"))
{
if (TempCohorts[FunctionalGroupIndex][cohort].IndividualBodyMass < PlanktonSizeThreshold || CohortTraitIndicesMarine["Obligate zooplankton"].Contains(FunctionalGroupIndex))
{
WorkingAbundanceInMassBins[mb - 1] += TempCohorts[FunctionalGroupIndex][cohort].CohortAbundance;
// Add the cohort's biomass to the approriate mass bin
WorkingBiomassInMassBins[mb - 1] += TempCohorts[FunctionalGroupIndex][cohort].CohortAbundance * TempCohorts[FunctionalGroupIndex][cohort].IndividualBodyMass;
// Find the mass bin appropriate for this cohort's juvenile mass
int j = 0;
do
{
j++;
} while (j < (MassBins.Length - 1) && TempCohorts[FunctionalGroupIndex][cohort].JuvenileMass > MassBins[j]);
// Find the mass bin appropriate for this cohort's adult mass
int a = 0;
do
{
a++;
} while (a < (MassBins.Length - 1) && TempCohorts[FunctionalGroupIndex][cohort].AdultMass > MassBins[a]);
// Add the cohort's abundance to this adult vs juvenile mass bins
WorkingAbundanceJuvenileAdultMassBins[a - 1, j - 1] += TempCohorts[FunctionalGroupIndex][cohort].CohortAbundance;
// Add the cohort's biomass to this adult vs juvenile mass bins
WorkingBiomassJuvenileAdultMassBins[a - 1, j - 1] += TempCohorts[FunctionalGroupIndex][cohort].CohortAbundance * TempCohorts[FunctionalGroupIndex][cohort].IndividualBodyMass;
}
}
else
{
WorkingAbundanceInMassBins[mb - 1] += TempCohorts[FunctionalGroupIndex][cohort].CohortAbundance;
// Add the cohort's biomass to the approriate mass bin
WorkingBiomassInMassBins[mb - 1] += TempCohorts[FunctionalGroupIndex][cohort].CohortAbundance * TempCohorts[FunctionalGroupIndex][cohort].IndividualBodyMass;
// Find the mass bin appropriate for this cohort's juvenile mass
int j = 0;
do
{
j++;
} while (j < (MassBins.Length - 1) && TempCohorts[FunctionalGroupIndex][cohort].JuvenileMass > MassBins[j]);
// Find the mass bin appropriate for this cohort's adult mass
int a = 0;
do
{
a++;
} while (a < (MassBins.Length - 1) && TempCohorts[FunctionalGroupIndex][cohort].AdultMass > MassBins[a]);
// Add the cohort's abundance to this adult vs juvenile mass bins
WorkingAbundanceJuvenileAdultMassBins[a - 1, j - 1] += TempCohorts[FunctionalGroupIndex][cohort].CohortAbundance;
// Add the cohort's biomass to this adult vs juvenile mass bins
WorkingBiomassJuvenileAdultMassBins[a - 1, j - 1] += TempCohorts[FunctionalGroupIndex][cohort].CohortAbundance * TempCohorts[FunctionalGroupIndex][cohort].IndividualBodyMass;
}
}
}
//Copy the working vectors and arrays to the sortedlist for the current key value
AbundancesInMassBins[TraitValue] = WorkingAbundanceInMassBins;
BiomassesInMassBins[TraitValue] = WorkingBiomassInMassBins;
AbundancesInJuvenileAdultMassBins[TraitValue] = WorkingAbundanceJuvenileAdultMassBins;
BiomassesInJuvenileAdultMassBins[TraitValue] = WorkingBiomassJuvenileAdultMassBins;
}
else
{
// Loop over functional groups
foreach (int FunctionalGroupIndex in CohortTraitIndices[TraitValue])
{
// Loop over all cohorts in this functional group
for (int cohort = 0; cohort < TempCohorts[FunctionalGroupIndex].Count; cohort++)
{
// Find the appropriate mass bin for the cohort
int mb = 0;
do
{
mb++;
} while (mb < (MassBins.Length - 1) && TempCohorts[FunctionalGroupIndex][cohort].IndividualBodyMass > MassBins[mb]);
// Add the cohort's abundance to the approriate mass bin
WorkingAbundanceInMassBins[mb - 1] += TempCohorts[FunctionalGroupIndex][cohort].CohortAbundance;
// Add the cohort's biomass to the approriate mass bin
WorkingBiomassInMassBins[mb - 1] += TempCohorts[FunctionalGroupIndex][cohort].CohortAbundance * TempCohorts[FunctionalGroupIndex][cohort].IndividualBodyMass;
// Find the mass bin appropriate for this cohort's juvenile mass
int j = 0;
do
{
j++;
} while (j < (MassBins.Length - 1) && TempCohorts[FunctionalGroupIndex][cohort].JuvenileMass > MassBins[j]);
// Find the mass bin appropriate for this cohort's adult mass
int a = 0;
do
{
a++;
} while (a < (MassBins.Length - 1) && TempCohorts[FunctionalGroupIndex][cohort].AdultMass > MassBins[a]);
// Add the cohort's abundance to this adult vs juvenile mass bins
WorkingAbundanceJuvenileAdultMassBins[a - 1, j - 1] += TempCohorts[FunctionalGroupIndex][cohort].CohortAbundance;
// Add the cohort's biomass to this adult vs juvenile mass bins
WorkingBiomassJuvenileAdultMassBins[a - 1, j - 1] += TempCohorts[FunctionalGroupIndex][cohort].CohortAbundance * TempCohorts[FunctionalGroupIndex][cohort].IndividualBodyMass;
}
}
//Copy the working vectors and arrays to the sortedlist for the current key value
AbundancesInMassBins[TraitValue] = WorkingAbundanceInMassBins;
BiomassesInMassBins[TraitValue] = WorkingBiomassInMassBins;
AbundancesInJuvenileAdultMassBins[TraitValue] = WorkingAbundanceJuvenileAdultMassBins;
BiomassesInJuvenileAdultMassBins[TraitValue] = WorkingBiomassJuvenileAdultMassBins;
}
}
// Loop over trait combinations and log abundances and body masses
foreach (var TraitValue in Keys)
{
for (int i = 0; i < MassBins.Length; i++)
{
AbundancesInMassBins[TraitValue][i] = (AbundancesInMassBins[TraitValue][i] > 0) ? Math.Log(AbundancesInMassBins[TraitValue][i]) : ecosystemModelGrid.GlobalMissingValue;
BiomassesInMassBins[TraitValue][i] = (BiomassesInMassBins[TraitValue][i] > 0) ? Math.Log(BiomassesInMassBins[TraitValue][i]) : ecosystemModelGrid.GlobalMissingValue;
for (int j = 0; j < MassBins.Length; j++)
{
AbundancesInJuvenileAdultMassBins[TraitValue][i, j] = (AbundancesInJuvenileAdultMassBins[TraitValue][i, j] > 0) ? Math.Log(AbundancesInJuvenileAdultMassBins[TraitValue][i, j]) : ecosystemModelGrid.GlobalMissingValue;
BiomassesInJuvenileAdultMassBins[TraitValue][i, j] = (BiomassesInJuvenileAdultMassBins[TraitValue][i, j] > 0) ? Math.Log(BiomassesInJuvenileAdultMassBins[TraitValue][i, j]) : ecosystemModelGrid.GlobalMissingValue;
}
}
}
}
/// <summary>
/// Calculate outputs associated with high-level outputs
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="cellIndex">The number of the current cell in the list of active cells</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
private void CalculateHighLevelOutputs(ModelGrid ecosystemModelGrid, List<uint[]> cellIndices, int cellIndex, Boolean marineCell)
{
// Calcalate the outputs arranged by mass bin
CalculateMassBinOutputs(ecosystemModelGrid, cellIndices, cellIndex, marineCell);
// Declare vectors to hold properties of tracked cohorts
TrackedCohortIndividualMasses = new double[TrackedCohorts.Count];
TrackedCohortAbundances = new double[TrackedCohorts.Count];
// Get a temporary local copy of the cohorts in the grid cell
GridCellCohortHandler TempCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
// Loop over functional groups in the grid cell cohorts
for (int j = 0; j < TempCohorts.Count; j++)
{
// Loop over cohorts within this functional group
for (int k = 0; k < TempCohorts[j].Count; k++)
{
// Loop over all cohort IDs
foreach (uint CohortID in TempCohorts[j][k].CohortID)
{
// Check whether the cohort ID corresponds to a tracked cohort
if (TrackedCohorts.Contains(CohortID))
{
// Get the position of the cohort in the list of tracked cohorts
int position = TrackedCohorts.FindIndex(
delegate(uint i)
{
return i == CohortID;
});
// Add the body mass and abundance of the tracked cohort to the appropriate position in the output vector
TrackedCohortIndividualMasses[position] = TempCohorts[j][k].IndividualBodyMass;
TrackedCohortAbundances[position] = TempCohorts[j][k].CohortAbundance;
}
}
}
}
}
/// <summary>
/// Set up all outputs (live, console and file) prior to the model run
/// </summary>
/// <param name="ecosystemModelGrid">The model grid that output data will be derived from</param>
/// <param name="cohortFunctionalGroupDefinitions">The definitions for cohort functional groups</param>
/// <param name="stockFunctionalGroupDefinitions">The definitions for stock functional groups</param>
/// <param name="numTimeSteps">The number of time steps in the model run</param>
/// <param name="outputFilesSuffix">The suffix to be applied to all output files from the current model run</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="cellIndex">The number of the current grid cell in the list of indices of active cells</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
public void SetUpOutputs(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortFunctionalGroupDefinitions,
FunctionalGroupDefinitions stockFunctionalGroupDefinitions, uint numTimeSteps, string outputFilesSuffix, List<uint[]> cellIndices,
int cellIndex, Boolean marineCell)
{
Console.WriteLine("Setting up grid cell outputs...\n");
// Set the suffix for all output files
_OutputSuffix = outputFilesSuffix + "_Cell" + cellIndex;
// Create vector to hold the values of the time dimension
TimeSteps = new float[numTimeSteps + 1];
// Set the first value to be -1 (this will hold initial outputs)
TimeSteps[0] = 0;
// Fill other values from 0 (this will hold outputs during the model run)
for (int i = 1; i < numTimeSteps + 1; i++)
{
TimeSteps[i] = i;
}
// Initialise the trait based outputs
InitialiseTraitBasedOutputs(cohortFunctionalGroupDefinitions, stockFunctionalGroupDefinitions, marineCell);
// Setup low-level outputs
SetUpLowLevelOutputs(numTimeSteps, ecosystemModelGrid);
if ((ModelOutputDetail == OutputDetailLevel.Medium) || (ModelOutputDetail == OutputDetailLevel.High))
{
// Setup medium-level outputs
SetupMediumLevelOutputs(ecosystemModelGrid, marineCell);
if (ModelOutputDetail == OutputDetailLevel.High)
{
// Setup high-level outputs
SetUpHighLevelOutputs(ecosystemModelGrid, cellIndices,cellIndex, cohortFunctionalGroupDefinitions, marineCell);
}
}
}
/// <summary>
/// Write to the output file values of the output variables at the end of the model run
/// </summary>
/// <param name="EcosystemModelGrid">The model grid to get data from</param>
/// <param name="CohortFunctionalGroupDefinitions">Definitions of the cohort functional groups in the model</param>
/// <param name="StockFunctionalGroupDefinitions">Definitions of the stock functional groups in the model</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="cellNumber">The number of the current cell in the list of indices of active cells</param>
/// <param name="GlobalDiagnosticVariables">List of global diagnostic variables</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
/// <param name="month">The current month in the model run</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
public void FinalOutputs(ModelGrid EcosystemModelGrid, FunctionalGroupDefinitions CohortFunctionalGroupDefinitions,
FunctionalGroupDefinitions StockFunctionalGroupDefinitions, List<uint[]> cellIndices, int cellNumber,
SortedList<string, double> GlobalDiagnosticVariables, MadingleyModelInitialisation initialisation, uint month, Boolean marineCell)
{
// Calculate output variables
CalculateOutputs(EcosystemModelGrid, CohortFunctionalGroupDefinitions, StockFunctionalGroupDefinitions, cellIndices,cellNumber, GlobalDiagnosticVariables, initialisation, month, marineCell);
// Dispose of the dataset objects
BasicOutputMemory.Clone("msds:nc?file="+ _OutputPath + "BasicOutputs" + _OutputSuffix + ".nc&openMode=create");
BasicOutputMemory.Dispose();
if (LiveOutputs)
{
DataSetToViewLive.Dispose();
}
if (ModelOutputDetail == OutputDetailLevel.High)
{
// Dispose of the dataset objects for high detail level outputs
MassBinsOutputMemory.Clone("msds:nc?file="+ _OutputPath + "MassBinsOutputs" + _OutputSuffix + ".nc&openMode=create");
MassBinsOutputMemory.Dispose();
TrackedCohortsOutputMemory.Clone("msds:nc?file="+ _OutputPath + "TrackedCohortsOutputs" + _OutputSuffix + ".nc&openMode=create");
TrackedCohortsOutputMemory.Dispose();
}
Metrics.CloseRserve();
}
/// <summary>
/// Generate file outputs for the current time step
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cohortFunctionalGroupDefinitions">The functional group definitions for cohorts in the model</param>
/// <param name="currentTimeStep">The current time step</param>
/// <param name="MarineCell">Whether the current cell is a marine cell</param>
/// <param name="cellIndices">The list of all cells to run the model for</param>
/// <param name="cellIndex">The index of the current cell in the list of all cells to run the model for</param>
private void TimeStepFileOutputs(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortFunctionalGroupDefinitions,
uint currentTimeStep, Boolean MarineCell, List<uint[]> cellIndices, int cellIndex)
{
Console.WriteLine("Writing grid cell ouputs to file...\n");
//Write the low level outputs first
DataConverter.ValueToSDS1D(TotalLivingBiomassDensity, "Total Biomass density", "Time step",
ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(TotalHeterotrophAbundanceDensity, "Heterotroph Abundance density", "Time step",
ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(TotalHeterotrophBiomassDensity, "Heterotroph Biomass density", "Time step",
ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
// File outputs for medium and high detail levels
if ((ModelOutputDetail == OutputDetailLevel.Medium) || (ModelOutputDetail == OutputDetailLevel.High))
{
if (MarineCell)
{
// Loop over all cohort trait value combinations and output abundances, densities and biomasses
foreach (string TraitValue in CohortTraitIndicesMarine.Keys)
{
DataConverter.ValueToSDS1D(TotalDensitiesOut[TraitValue], TraitValue + " density", "Time step", ecosystemModelGrid.GlobalMissingValue, BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass density", "Time step", ecosystemModelGrid.GlobalMissingValue, BasicOutputMemory, (int)currentTimeStep + 1);
}
// Loop over all stock trait value combinations and output biomasses
foreach (string TraitValue in StockTraitIndicesMarine.Keys)
{
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass density", "Time step",
ecosystemModelGrid.GlobalMissingValue, BasicOutputMemory, (int)currentTimeStep + 1);
}
}
else
{
// Loop over all cohort trait value combinations and output abudnances, densities and biomasses
foreach (string TraitValue in CohortTraitIndices.Keys)
{
DataConverter.ValueToSDS1D(TotalDensitiesOut[TraitValue], TraitValue + " density", "Time step", ecosystemModelGrid.GlobalMissingValue, BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass density", "Time step", ecosystemModelGrid.GlobalMissingValue, BasicOutputMemory, (int)currentTimeStep + 1);
}
// Loop over all stock trait value combinations and output biomasses
foreach (string TraitValue in StockTraitIndices.Keys)
{
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass density", "Time step",
ecosystemModelGrid.GlobalMissingValue, BasicOutputMemory, (int)currentTimeStep + 1);
}
}
// If ouputting ecosystem metrics has been specified then add these metrics to the output
if (OutputMetrics)
{
DataConverter.ValueToSDS1D(Metrics.CalculateMeanTrophicLevelCell(ecosystemModelGrid, cellIndices, cellIndex),
"Mean Trophic Level", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalEvennessRao(ecosystemModelGrid,cohortFunctionalGroupDefinitions, cellIndices, cellIndex,"trophic index"),
"Trophic Evenness", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalEvennessRao(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "biomass"),
"Biomass Evenness", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
double[] FunctionalDiversity = Metrics.CalculateFunctionalDiversity(ecosystemModelGrid, cohortFunctionalGroupDefinitions,
cellIndices, cellIndex);
DataConverter.ValueToSDS1D(FunctionalDiversity[0],
"Functional Richness", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(FunctionalDiversity[1],
"Rao Functional Evenness", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "Biomass")[0],
"Biomass Richness", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "Biomass")[1],
"Min Bodymass", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "Biomass")[2],
"Max Bodymass", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "Trophic index")[0],
"Trophic Richness", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "Trophic index")[1],
"Min Trophic Index", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "Trophic index")[2],
"Max Trophic Index", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(Metrics.CalculateArithmeticCommunityMeanBodyMass(ecosystemModelGrid, cellIndices, cellIndex),
"Arithmetic Mean Bodymass", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(Metrics.CalculateGeometricCommunityMeanBodyMass(ecosystemModelGrid, cellIndices, cellIndex),
"Geometric Mean Bodymass", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
}
if (TrackMarineSpecifics && MarineCell)
{
DataConverter.ValueToSDS1D(TotalIncomingNPP, "Incoming NPP", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, (int)currentTimeStep + 1);
}
if (currentTimeStep % 600 == 0 && currentTimeStep > 0)
{
BasicOutputMemory.Clone("msds:nc?file=" + _OutputPath + "BasicOutputs" + _OutputSuffix + ".nc&openMode=create");
Console.WriteLine("Cloning grid cell ouputs to file...\n");
}
// File outputs for high detail level
if (ModelOutputDetail == OutputDetailLevel.High)
{
if (OutputMetrics)
{
DataConverter.VectorToSDS2D(Metrics.CalculateTrophicDistribution(ecosystemModelGrid,cellIndices,cellIndex), "Trophic Index Distribution",
new string[2] { "Time step", "Trophic Index Bins" }, TimeSteps, Metrics.TrophicIndexBinValues, ecosystemModelGrid.GlobalMissingValue, MassBinsOutputMemory, (int)currentTimeStep + 1);
}
// Loop over trait combinations in the mass bin outputs
foreach (var TraitValue in AbundancesInMassBins.Keys)
{
// Write out abundances in each of the mass bins to the relevant two-dimensional output variables
DataConverter.VectorToSDS2D(AbundancesInMassBins[TraitValue], "Log " + TraitValue + " abundance in mass bins",
new string[2] { "Time step", "Mass bin" }, TimeSteps, MassBins, ecosystemModelGrid.GlobalMissingValue, MassBinsOutputMemory, (int)currentTimeStep + 1);
DataConverter.VectorToSDS2D(BiomassesInMassBins[TraitValue], "Log " + TraitValue + " biomass in mass bins",
new string[2] { "Time step", "Mass bin" }, TimeSteps, MassBins, ecosystemModelGrid.GlobalMissingValue, MassBinsOutputMemory, (int)currentTimeStep + 1);
// Write out abundances in combinations of juvenile and adult mass bins to the relevant three-dimensional output variable
DataConverter.Array2DToSDS3D(AbundancesInJuvenileAdultMassBins[TraitValue], "Log " + TraitValue + " abundance in juvenile vs adult bins",
new string[] { "Adult Mass bin", "Juvenile Mass bin", "Time step" },
(int)currentTimeStep + 1,
ecosystemModelGrid.GlobalMissingValue,
MassBinsOutputMemory);
// Write out biomasses in combinations of juvenile and adult mass bins to the relevant three-dimensional output variable
DataConverter.Array2DToSDS3D(BiomassesInJuvenileAdultMassBins[TraitValue], "Log " + TraitValue + " biomass in juvenile vs adult bins",
new string[] { "Adult Mass bin", "Juvenile Mass bin", "Time step" },
(int)currentTimeStep + 1,
ecosystemModelGrid.GlobalMissingValue,
MassBinsOutputMemory);
}
// Loop over tracked cohorts
for (int i = 0; i < TrackedCohorts.Count; i++)
{
// Add the individual body mass and abundance of the tracked cohort to the output dataset
string[] TrackedCohortDimensions = new string[] { "Time step", "Cohort ID" };
DataConverter.ValueToSDS2D(TrackedCohortIndividualMasses[i], "Individual body mass", TrackedCohortDimensions,
ecosystemModelGrid.GlobalMissingValue, TrackedCohortsOutputMemory, (int)currentTimeStep + 1, i);
DataConverter.ValueToSDS2D(TrackedCohortAbundances[i], "Number of individuals", TrackedCohortDimensions,
ecosystemModelGrid.GlobalMissingValue, TrackedCohortsOutputMemory, (int)currentTimeStep + 1, i);
}
if (currentTimeStep % 600 ==0 && currentTimeStep > 0)
{
MassBinsOutputMemory.Clone("msds:nc?file=" + _OutputPath + "MassBinsOutputs" + _OutputSuffix + ".nc&openMode=create");
TrackedCohortsOutputMemory.Clone("msds:nc?file=" + _OutputPath + "TrackedCohortsOutputs" + _OutputSuffix + ".nc&openMode=create");
}
}
}
}
/// <summary>
/// Run advective dispersal
/// </summary>
/// <param name="cellIndex">The longitudinal and latitudinal indices of the focal grid cell</param>
/// <param name="gridForDispersal">The model grid to run dispersal for</param>
/// <param name="cohortToDisperse">The cohort to run dispersal for</param>
/// <param name="actingCohortFunctionalGroup">The functional group index of the acting cohort</param>
/// <param name="actingCohortNumber">The position of the acting cohort wihtin the functional group in the array of grid cell cohorts</param>
/// <param name="currentMonth">The current model month</param>
public void RunDispersal(uint[] cellIndex, ModelGrid gridForDispersal, Cohort cohortToDisperse, int actingCohortFunctionalGroup,
int actingCohortNumber, uint currentMonth)
{
// An array to hold the dispersal information
double[] DispersalArray = new double[6];
// A double to indicate whether or not the cohort has dispersed, and if it has dispersed, where to
double CohortDispersed = 0;
// Temporary variables to keep track of directions in which cohorts enter/exit cells during the multiple advection steps per time step
uint ExitDirection = new uint();
uint EntryDirection = new uint();
ExitDirection = 9999;
// An array to hold the present cohort location for the intermediate steps that occur before the final dispersal this time step
uint[] PresentLocation = { cellIndex[0], cellIndex[1] };
// Get the u speed and the v speed from the cell data
double uAdvectiveSpeed = gridForDispersal.GetEnviroLayer("uVel", currentMonth, PresentLocation[0], PresentLocation[1],
out varExists);
Debug.Assert(uAdvectiveSpeed != -9999);
double vAdvectiveSpeed = gridForDispersal.GetEnviroLayer("vVel", currentMonth, PresentLocation[0], PresentLocation[1],
out varExists);
Debug.Assert(vAdvectiveSpeed != -9999);
uAdvectiveSpeed = RescaleDispersalSpeed(uAdvectiveSpeed);
vAdvectiveSpeed = RescaleDispersalSpeed(vAdvectiveSpeed);
// Loop through a number of times proportional to the rescaled dispersal
for (int mm = 0; mm < _AdvectionTimeStepsPerModelTimeStep; mm++)
{
// Get the probability of dispersal
DispersalArray = CalculateDispersalProbability(gridForDispersal, PresentLocation[0], PresentLocation[1],
currentMonth, uAdvectiveSpeed, vAdvectiveSpeed);
// Check to see if it does disperse
CohortDispersed = CheckForDispersal(DispersalArray[0]);
// If it does, check to see where it will end up
if (CohortDispersed > 0)
{
// Check to see if the direction is actually dispersable
uint[] DestinationCell = CellToDisperseTo(gridForDispersal, PresentLocation[0], PresentLocation[1],
DispersalArray, CohortDispersed, DispersalArray[4], DispersalArray[5], ref ExitDirection,
ref EntryDirection);
// If it is, go ahead and update the cohort location
if (DestinationCell[0] < 999999)
{
PresentLocation = DestinationCell;
// Get the u speed and the v speed from the cell data
uAdvectiveSpeed = gridForDispersal.GetEnviroLayer("uVel", currentMonth, PresentLocation[0],
PresentLocation[1], out varExists);
vAdvectiveSpeed = gridForDispersal.GetEnviroLayer("vVel", currentMonth, PresentLocation[0],
PresentLocation[1], out varExists);
uAdvectiveSpeed = RescaleDispersalSpeed(uAdvectiveSpeed);
vAdvectiveSpeed = RescaleDispersalSpeed(vAdvectiveSpeed);
}
}
}
// Update the dipersal deltas for this cohort, if necessary
if ((cellIndex[0] != PresentLocation[0]) || (cellIndex[1] != PresentLocation[1]))
{
// Update the delta array of cohorts
gridForDispersal.DeltaFunctionalGroupDispersalArray[cellIndex[0], cellIndex[1]].Add((uint)actingCohortFunctionalGroup);
gridForDispersal.DeltaCohortNumberDispersalArray[cellIndex[0], cellIndex[1]].Add((uint)actingCohortNumber);
// Update the delta array of cells to disperse to
gridForDispersal.DeltaCellToDisperseToArray[cellIndex[0], cellIndex[1]].Add(PresentLocation);
// Update the delta array of exit and entry directions
gridForDispersal.DeltaCellExitDirection[cellIndex[0], cellIndex[1]].Add(ExitDirection);
gridForDispersal.DeltaCellEntryDirection[cellIndex[0], cellIndex[1]].Add(EntryDirection);
}
}
public double[] CalculateFunctionalRichness(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortDefinitions,
List <uint[]> cellIndices, int cellIndex, string trait)
{
//Get the cohorts for the specified cell
GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
double MinCurrentTraitValue = double.MaxValue;
double MaxCurrentTraitValue = double.MinValue;
double MinModelTraitValue = 0.0;
double MaxModelTraitValue = 0.0;
switch (trait.ToLower())
{
case "biomass":
foreach (var CohortList in CellCohorts)
{
foreach (var cohort in CohortList)
{
if (cohort.IndividualBodyMass < MinCurrentTraitValue)
{
MinCurrentTraitValue = cohort.IndividualBodyMass;
}
if (cohort.IndividualBodyMass > MaxCurrentTraitValue)
{
MaxCurrentTraitValue = cohort.IndividualBodyMass;
}
}
}
//Define upper and lower limits for body mass
MinModelTraitValue = cohortDefinitions.GetBiologicalPropertyAllFunctionalGroups("minimum mass").Min();
MaxModelTraitValue = cohortDefinitions.GetBiologicalPropertyAllFunctionalGroups("maximum mass").Max();
break;
case "trophic index":
foreach (var CohortList in CellCohorts)
{
foreach (var cohort in CohortList)
{
if (cohort.TrophicIndex < MinCurrentTraitValue)
{
MinCurrentTraitValue = cohort.TrophicIndex;
}
if (cohort.TrophicIndex > MaxCurrentTraitValue)
{
MaxCurrentTraitValue = cohort.TrophicIndex;
}
}
}
//Define upper and lower limits for body mass
MinModelTraitValue = MinTI;
MaxModelTraitValue = MaxTI;
break;
default:
Debug.Fail("Trait not recognised in calculation of ecosystem metrics: " + trait);
break;
}
Debug.Assert((MaxModelTraitValue - MinModelTraitValue) > 0.0, "Division by zero or negative model trait values in calculation of functional richness");
double[] NewArray = { (MaxCurrentTraitValue - MinCurrentTraitValue) / (MaxModelTraitValue - MinModelTraitValue), MinCurrentTraitValue, MaxCurrentTraitValue };
return(NewArray);
}
// Determine to which cell the cohort disperses
/// <summary>
/// Determines the cell to which a cohort disperses
/// </summary>
/// <param name="madingleyGrid">The ecosystem model grid</param>
/// <param name="latIndex">The latitudinal index of the cell being run</param>
/// <param name="lonIndex">The longitudinal index of the cell being run</param>
/// <param name="dispersalArray"></param>
/// <param name="RandomValue"></param>
/// <param name="uSpeedIncDiffusion"></param>
/// <param name="vSpeedIncDiffusion"></param>
/// <param name="exitDirection"></param>
/// <param name="entryDirection"></param>
/// <returns></returns>
protected uint[] CellToDisperseTo(ModelGrid madingleyGrid, uint latIndex, uint lonIndex, double[] dispersalArray,
double RandomValue, double uSpeedIncDiffusion, double vSpeedIncDiffusion, ref uint exitDirection,
ref uint entryDirection)
{
uint[] DestinationCell;
// Check to see in which axis the cohort disperses
// Note that the values in the dispersal array are the proportional area moved outside the grid cell in each direction; we simply compare the random draw to this
// to determine the direction in which the cohort moves probabilistically
// Longitudinally
if (RandomValue <= dispersalArray[1])
{
// Work out whether dispersal is to the cell to the E or the W
if (uSpeedIncDiffusion > 0)
{
DestinationCell = madingleyGrid.CheckDispersalEast(latIndex, lonIndex);
// Record entry and exit directions. Exit direction is only recorded the first time it happens during a (model) timestep, not each advection time step.
if (exitDirection == 9999)
{
exitDirection = 2;
}
entryDirection = 6;
}
else
{
DestinationCell = madingleyGrid.CheckDispersalWest(latIndex, lonIndex);
// Record entry and exit directions. Exit direction is only recorded the first time it happens during a (model) timestep, not each advection time step.
if (exitDirection == 9999)
{
exitDirection = 6;
}
entryDirection = 2;
}
}
else
{
// Latitudinally
if (RandomValue <= (dispersalArray[1] + dispersalArray[2]))
{
// Work out whether dispersal is to the cell to the N or the S
if (vSpeedIncDiffusion > 0)
{
DestinationCell = madingleyGrid.CheckDispersalNorth(latIndex, lonIndex);
// Record entry and exit directions. Exit direction is only recorded the first time it happens during a (model) timestep, not each advection time step.
if (exitDirection == 9999)
{
exitDirection = 0;
}
entryDirection = 4;
}
else
{
DestinationCell = madingleyGrid.CheckDispersalSouth(latIndex, lonIndex);
// Record entry and exit directions. Exit direction is only recorded the first time it happens during a (model) timestep, not each advection time step.
if (exitDirection == 9999)
{
exitDirection = 4;
}
entryDirection = 0;
}
}
else
{
// Diagonally. Note that DispersalArray[0] is equal to dispersalArray[1] + dispersalArray[2] + dispersalArray[3], but it
// is both faster to compare and also avoids any rounding errors.
if (RandomValue <= (dispersalArray[0]))
{
// Work out to which cell dispersal occurs
if (uSpeedIncDiffusion > 0)
{
if (vSpeedIncDiffusion > 0)
{
DestinationCell = madingleyGrid.CheckDispersalNorthEast(latIndex, lonIndex);
// Record entry and exit directions. Exit direction is only recorded the first time it happens during a (model) timestep, not each advection time step.
if (exitDirection == 9999)
{
exitDirection = 1;
}
entryDirection = 5;
}
else
{
DestinationCell = madingleyGrid.CheckDispersalSouthEast(latIndex, lonIndex);
// Record entry and exit directions. Exit direction is only recorded the first time it happens during a (model) timestep, not each advection time step.
if (exitDirection == 9999)
{
exitDirection = 5;
}
entryDirection = 1;
}
}
else
{
if (vSpeedIncDiffusion > 0)
{
DestinationCell = madingleyGrid.CheckDispersalNorthWest(latIndex, lonIndex);
// Record entry and exit directions. Exit direction is only recorded the first time it happens during a (model) timestep, not each advection time step.
if (exitDirection == 9999)
{
exitDirection = 7;
}
entryDirection = 3;
}
else
{
DestinationCell = madingleyGrid.CheckDispersalSouthWest(latIndex, lonIndex);
// Record entry and exit directions. Exit direction is only recorded the first time it happens during a (model) timestep, not each advection time step.
if (exitDirection == 9999)
{
exitDirection = 3;
}
entryDirection = 7;
}
}
}
else
{
// This should never happen. Means that the random number indicates dispersal by being lower than the probability, but
// that in the comparison abive, it is higher than the probability.
Debug.Fail("Error when determining which cell to disperse to");
Console.WriteLine("Error when determining which cell to disperse to");
Console.ReadKey();
DestinationCell = new uint[2] {
9999999, 9999999
};
}
}
}
return(DestinationCell);
}
public void TimeStepOutputs(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortFunctionalGroupDefinitions, FunctionalGroupDefinitions
stockFunctionalGroupDefinitions, List <uint[]> cellIndices, uint currentTimeStep, MadingleyModelInitialisation initialisation)
{
// Calculate the output variables for this time step
CalculateOutputs(ecosystemModelGrid, cohortFunctionalGroupDefinitions, stockFunctionalGroupDefinitions, cellIndices, initialisation, currentTimeStep);
// Write the total biomass of cohorts to the live display
if (LiveOutputs)
{
DataConverter.Array2DToSDS2D(LogBiomassDensityGridCohorts, "Log(Biomass density, g/km^2)", ecosystemModelGrid.Lats,
ecosystemModelGrid.Lons, 0, DataSetToViewLive);
}
Console.WriteLine("Writing grid ouputs to file...\n");
// Add the grid of total biomass in cells to the file dataset
DataConverter.Array2DToSDS3D(LogBiomassDensityGridCohorts, "Biomass density", new string[] { "Latitude", "Longitude", "Time step" },
(int)currentTimeStep + 1, 0, GridOutput);
// Add the grid of total abudance in cells to the file dataset
DataConverter.Array2DToSDS3D(LogAbundanceDensityGridCohorts, "Abundance density", new string[] { "Latitude", "Longitude", "Time step" },
(int)currentTimeStep + 1, 0, GridOutput);
// Temporary outputs to check plant model
DataConverter.Array2DToSDS3D(Realm, "Realm", new string[] { "Latitude", "Longitude", "Time step" },
(int)currentTimeStep + 1, ecosystemModelGrid.GlobalMissingValue, GridOutput);
DataConverter.Array2DToSDS3D(FrostDays, "Fraction year frost", new string[] { "Latitude", "Longitude", "Time step" },
(int)currentTimeStep + 1, ecosystemModelGrid.GlobalMissingValue, GridOutput);
DataConverter.Array2DToSDS3D(FracEvergreen, "Fraction evergreen", new string[] { "Latitude", "Longitude", "Time step" },
(int)currentTimeStep + 1, ecosystemModelGrid.GlobalMissingValue, GridOutput);
DataConverter.Array2DToSDS3D(HANPP, "HANPP", new string[] { "Latitude", "Longitude", "Time step" },
(int)currentTimeStep + 1, ecosystemModelGrid.GlobalMissingValue, GridOutput);
DataConverter.Array2DToSDS3D(Temperature, "Temperature", new string[] { "Latitude", "Longitude", "Time step" },
(int)currentTimeStep + 1, ecosystemModelGrid.GlobalMissingValue, GridOutput);
if ((ModelOutputDetail == OutputDetailLevel.Medium) || (ModelOutputDetail == OutputDetailLevel.High))
{
foreach (var TraitValue in BiomassDensityGrid.Keys)
{
// Add the biomass grids for individual trait combinations to the file dataset
DataConverter.Array2DToSDS3D(BiomassDensityGrid[TraitValue], TraitValue + "biomass density", new string[]
{ "Latitude", "Longitude", "Time step" }, (int)currentTimeStep + 1, ecosystemModelGrid.GlobalMissingValue, GridOutput);
}
foreach (var Key in AbundanceDensityGrid.Keys)
{
DataConverter.Array2DToSDS3D(AbundanceDensityGrid[Key], Key + "abundance density",
new string[] { "Latitude", "Longitude", "Time step" },
(int)currentTimeStep + 1,
ecosystemModelGrid.GlobalMissingValue,
GridOutput);
}
}
// Output ecosystem metrics
if (OutputMetrics)
{
foreach (string Key in MetricsGrid.Keys)
{
DataConverter.Array2DToSDS3D(MetricsGrid[Key], Key,
new string[] { "Latitude", "Longitude", "Time step" },
(int)currentTimeStep + 1,
ecosystemModelGrid.GlobalMissingValue,
GridOutput);
}
}
}
private bool CheckStarvationDispersal(ModelGrid gridForDispersal, uint latIndex, uint lonIndex, Cohort cohortToDisperse, int functionalGroup, int cohortNumber)
{
// A boolean to check whether a cohort has dispersed
bool CohortHasDispersed = false;
// Check for starvation driven dispersal
// What is the present body mass of the cohort?
// Note that at present we are just tracking starvation for adults
double IndividualBodyMass = cohortToDisperse.IndividualBodyMass;
double AdultMass = cohortToDisperse.AdultMass;
// Temporary variables to keep track of directions in which cohorts enter/exit cells during the multiple advection steps per time step
uint ExitDirection = new uint();
uint EntryDirection = new uint();
ExitDirection = 9999;
// Assume a linear relationship between probability of dispersal and body mass loss, up to _StarvationDispersalBodyMassThreshold
// at which point the cohort will try to disperse every time step
if (IndividualBodyMass < AdultMass)
{
double ProportionalPresentMass = IndividualBodyMass / AdultMass;
// If the body mass loss is greater than the starvation dispersal body mass threshold, then the cohort tries to disperse
if (ProportionalPresentMass < _StarvationDispersalBodyMassThreshold)
{
// Cohort tries to disperse
double[] DispersalArray = CalculateDispersalProbability(gridForDispersal, latIndex, lonIndex, CalculateDispersalSpeed(AdultMass));
double CohortDispersed = CheckForDispersal(DispersalArray[0]);
if (CohortDispersed > 0)
{
uint[] DestinationCell = CellToDisperseTo(gridForDispersal, latIndex, lonIndex, DispersalArray, DispersalArray[0], DispersalArray[4], DispersalArray[5], ref ExitDirection, ref EntryDirection);
// Update the delta array of cells to disperse to, if the cohort moves
if (DestinationCell[0] < 999999)
{
// Update the delta array of cohorts
gridForDispersal.DeltaFunctionalGroupDispersalArray[latIndex, lonIndex].Add((uint)functionalGroup);
gridForDispersal.DeltaCohortNumberDispersalArray[latIndex, lonIndex].Add((uint)cohortNumber);
// Update the delta array of cells to disperse to
gridForDispersal.DeltaCellToDisperseToArray[latIndex, lonIndex].Add(DestinationCell);
// Update the delta array of exit and entry directions
gridForDispersal.DeltaCellExitDirection[latIndex, lonIndex].Add(ExitDirection);
gridForDispersal.DeltaCellEntryDirection[latIndex, lonIndex].Add(EntryDirection);
}
}
// Note that regardless of whether or not it succeeds, if a cohort tries to disperse, it is counted as having dispersed for
// the purposes of not then allowing it to disperse based on its density.
CohortHasDispersed = true;
}
// Otherwise, the cohort has a chance of trying to disperse proportional to its mass loss
else
{
// Cohort tries to disperse with a particular probability
// Draw a random number
if (((1.0 - ProportionalPresentMass) / (1.0 - _StarvationDispersalBodyMassThreshold)) > RandomNumberGenerator.GetUniform())
{
// Cohort tries to disperse
double[] DispersalArray = CalculateDispersalProbability(gridForDispersal, latIndex, lonIndex, CalculateDispersalSpeed(AdultMass));
double CohortDispersed = CheckForDispersal(DispersalArray[0]);
if (CohortDispersed > 0)
{
uint[] DestinationCell = CellToDisperseTo(gridForDispersal, latIndex, lonIndex, DispersalArray, DispersalArray[0], DispersalArray[4], DispersalArray[5], ref ExitDirection, ref EntryDirection);
// Update the delta array of cells to disperse to, if the cohort moves
if (DestinationCell[0] < 999999)
{
// Update the delta array of cohorts
gridForDispersal.DeltaFunctionalGroupDispersalArray[latIndex, lonIndex].Add((uint)functionalGroup);
gridForDispersal.DeltaCohortNumberDispersalArray[latIndex, lonIndex].Add((uint)cohortNumber);
// Update the delta array of cells to disperse to
gridForDispersal.DeltaCellToDisperseToArray[latIndex, lonIndex].Add(DestinationCell);
// Update the delta array of exit and entry directions
gridForDispersal.DeltaCellExitDirection[latIndex, lonIndex].Add(ExitDirection);
gridForDispersal.DeltaCellEntryDirection[latIndex, lonIndex].Add(EntryDirection);
}
}
CohortHasDispersed = true;
}
}
}
return(CohortHasDispersed);
}
public InputModelState(string outputPath, string filename, ModelGrid ecosystemModelGrid, List <uint[]> cellList)
{
//Set the input state flag to be true
_InputState = true;
// Construct the string required to access the file using Scientific Dataset
string _ReadFileString = "msds:nc?file=input/ModelStates/" + filename + ".nc&openMode=readOnly";
// Open the data file using Scientific Dataset
DataSet StateDataSet = DataSet.Open(_ReadFileString);
float[] Latitude = StateDataSet.GetData <float[]>("Latitude");
float[] Longitude = StateDataSet.GetData <float[]>("Longitude");
float[] CohortFunctionalGroup = StateDataSet.GetData <float[]>("Cohort Functional Group");
float[] Cohort = StateDataSet.GetData <float[]>("Cohort");
float[] StockFunctionalGroup = StateDataSet.GetData <float[]>("Stock Functional Group");
float[] Stock = StateDataSet.GetData <float[]>("Stock");
// Check that the longitudes and latitudes in the input state match the cell environment
for (int la = 0; la < Latitude.Length; la++)
{
Debug.Assert(ecosystemModelGrid.GetCellEnvironment((uint)la, 0)["Latitude"][0] == Latitude[la],
"Error: input-state grid doesn't match current model grid");
}
for (int lo = 0; lo < Longitude.Length; lo++)
{
Debug.Assert(ecosystemModelGrid.GetCellEnvironment(0, (uint)lo)["Longitude"][0] == Longitude[lo],
"Error: input-state grid doesn't match current model grid");
}
List <double[, , ]> CohortJuvenileMass = new List <double[, , ]>();
List <double[, , ]> CohortAdultMass = new List <double[, , ]>();
List <double[, , ]> CohortIndividualBodyMass = new List <double[, , ]>();
List <double[, , ]> CohortCohortAbundance = new List <double[, , ]>();
List <double[, , ]> CohortLogOptimalPreyBodySizeRatio = new List <double[, , ]>();
List <double[, , ]> CohortBirthTimeStep = new List <double[, , ]>();
List <double[, , ]> CohortProportionTimeActive = new List <double[, , ]>();
List <double[, , ]> CohortTrophicIndex = new List <double[, , ]>();
double[,,,] tempData = new double[Latitude.Length, Longitude.Length,
CohortFunctionalGroup.Length, Cohort.Length];
tempData = StateDataSet.GetData <double[, , , ]>("CohortJuvenileMass");
for (int la = 0; la < Latitude.Length; la++)
{
CohortJuvenileMass.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortJuvenileMass[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData <double[, , , ]>("CohortAdultMass");
for (int la = 0; la < Latitude.Length; la++)
{
CohortAdultMass.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortAdultMass[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData <double[, , , ]>("CohortIndividualBodyMass");
for (int la = 0; la < Latitude.Length; la++)
{
CohortIndividualBodyMass.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortIndividualBodyMass[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData <double[, , , ]>("CohortCohortAbundance");
for (int la = 0; la < Latitude.Length; la++)
{
CohortCohortAbundance.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortCohortAbundance[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData <double[, , , ]>("CohortLogOptimalPreyBodySizeRatio");
for (int la = 0; la < Latitude.Length; la++)
{
CohortLogOptimalPreyBodySizeRatio.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortLogOptimalPreyBodySizeRatio[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData <double[, , , ]>("CohortBirthTimeStep");
for (int la = 0; la < Latitude.Length; la++)
{
CohortBirthTimeStep.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortBirthTimeStep[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData <double[, , , ]>("CohortProportionTimeActive");
for (int la = 0; la < Latitude.Length; la++)
{
CohortProportionTimeActive.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortProportionTimeActive[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
tempData = StateDataSet.GetData <double[, , , ]>("CohortTrophicIndex");
for (int la = 0; la < Latitude.Length; la++)
{
CohortTrophicIndex.Add(new double[Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Cohort.Length; c++)
{
CohortTrophicIndex[(int)cell[0]][cell[1], fg, c] = tempData[
cell[0], cell[1], fg, c];
}
}
}
_GridCellCohorts = new GridCellCohortHandler[Latitude.Length, Longitude.Length];
long temp = 0;
for (int cell = 0; cell < cellList.Count; cell++)
{
_GridCellCohorts[cellList[cell][0], cellList[cell][1]] = new GridCellCohortHandler(CohortFunctionalGroup.Length);
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
_GridCellCohorts[cellList[cell][0], cellList[cell][1]][fg] = new List <Cohort>();
for (int c = 0; c < Cohort.Length; c++)
{
if (CohortCohortAbundance[(int)cellList[cell][0]][cellList[cell][1], fg, c] > 0.0)
{
Cohort TempCohort = new Cohort(
(byte)fg,
CohortJuvenileMass[(int)cellList[cell][0]][cellList[cell][1], fg, c],
CohortAdultMass[(int)cellList[cell][0]][cellList[cell][1], fg, c],
CohortIndividualBodyMass[(int)cellList[cell][0]][cellList[cell][1], fg, c],
CohortCohortAbundance[(int)cellList[cell][0]][cellList[cell][1], fg, c],
Math.Exp(CohortLogOptimalPreyBodySizeRatio[(int)cellList[cell][0]][cellList[cell][1], fg, c]),
Convert.ToUInt16(CohortBirthTimeStep[(int)cellList[cell][0]][cellList[cell][1], fg, c]),
CohortProportionTimeActive[(int)cellList[cell][0]][cellList[cell][1], fg, c], ref temp,
CohortTrophicIndex[(int)cellList[cell][0]][cellList[cell][1], fg, c],
false);
_GridCellCohorts[cellList[cell][0], cellList[cell][1]][fg].Add(TempCohort);
}
}
}
}
CohortJuvenileMass.RemoveRange(0, CohortJuvenileMass.Count);
CohortAdultMass.RemoveRange(0, CohortAdultMass.Count);
CohortIndividualBodyMass.RemoveRange(0, CohortIndividualBodyMass.Count);
CohortCohortAbundance.RemoveRange(0, CohortCohortAbundance.Count);
CohortLogOptimalPreyBodySizeRatio.RemoveRange(0, CohortLogOptimalPreyBodySizeRatio.Count);
CohortBirthTimeStep.RemoveRange(0, CohortBirthTimeStep.Count);
CohortProportionTimeActive.RemoveRange(0, CohortProportionTimeActive.Count);
CohortTrophicIndex.RemoveRange(0, CohortTrophicIndex.Count);
List <double[, , ]> StockIndividualBodyMass = new List <double[, , ]>();
List <double[, , ]> StockTotalBiomass = new List <double[, , ]>();
double[,,,] tempData2 = new double[Latitude.Length, Longitude.Length,
StockFunctionalGroup.Length, Stock.Length];
tempData2 = StateDataSet.GetData <double[, , , ]>("StockIndividualBodyMass");
for (int la = 0; la < Latitude.Length; la++)
{
StockIndividualBodyMass.Add(new double[Longitude.Length, StockFunctionalGroup.Length, Stock.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < StockFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Stock.Length; c++)
{
StockIndividualBodyMass[(int)cell[0]][cell[1], fg, c] = tempData2[
cell[0], cell[1], fg, c];
}
}
}
tempData2 = StateDataSet.GetData <double[, , , ]>("StockTotalBiomass");
for (int la = 0; la < Latitude.Length; la++)
{
StockTotalBiomass.Add(new double[Longitude.Length, StockFunctionalGroup.Length, Stock.Length]);
}
foreach (uint[] cell in cellList)
{
for (int fg = 0; fg < StockFunctionalGroup.Length; fg++)
{
for (int c = 0; c < Stock.Length; c++)
{
StockTotalBiomass[(int)cell[0]][cell[1], fg, c] = tempData2[
cell[0], cell[1], fg, c];
}
}
}
_GridCellStocks = new GridCellStockHandler[Latitude.Length, Longitude.Length];
for (int cell = 0; cell < cellList.Count; cell++)
{
_GridCellStocks[cellList[cell][0], cellList[cell][1]] = new GridCellStockHandler(StockFunctionalGroup.Length);
for (int fg = 0; fg < StockFunctionalGroup.Length; fg++)
{
_GridCellStocks[cellList[cell][0], cellList[cell][1]][fg] = new List <Stock>();
for (int c = 0; c < Stock.Length; c++)
{
if (StockTotalBiomass[(int)cellList[cell][0]][cellList[cell][1], fg, c] > 0.0)
{
Stock TempStock = new Stock(
(byte)fg,
StockIndividualBodyMass[(int)cellList[cell][0]][cellList[cell][1], fg, c],
StockTotalBiomass[(int)cellList[cell][0]][cellList[cell][1], fg, c]);
_GridCellStocks[cellList[cell][0], cellList[cell][1]][fg].Add(TempStock);
}
}
}
}
}
/// <summary>
/// Extract an array of values from a state variable in a model grid and add to a two-dimensional variable in an SDS object
/// </summary>
/// <param name="ecosystemModelGrid">The model grid to extract data from</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="gridVariableName">The name of the state variable in the model grid</param>
/// <param name="traitValue">The trait value of the functional groups to get data for</param>
/// <param name="variableType">The type of the state variable: 'stock' or 'cohort'</param>
/// <param name="outputVariableName">The name of the variable to write to</param>
/// <param name="SDSObject">The SDS object to write to</param>
/// <param name="functionalGroupHandler">The functional group handler corresponding to cohorts or stocks</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
public void Array2DToSDS2D(ModelGrid ecosystemModelGrid, List <uint[]> cellIndices, string gridVariableName, string traitValue,
string variableType, string outputVariableName, DataSet SDSObject, FunctionalGroupDefinitions functionalGroupHandler,
MadingleyModelInitialisation initialisation)
{
// Get the missing value from the model grid
double MissingValue = ecosystemModelGrid.GlobalMissingValue;
// create an array to hold the data to output
double[,] dataToConvert = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
// generate arrays to hold latitudes and longitudes
float[] lats = new float[ecosystemModelGrid.NumLatCells];
float[] lons = new float[ecosystemModelGrid.NumLonCells];
// Populate arrays of latitudes and longitudes, converting from bottom left cell references as used in the model grid
// to cell centre references as required by SDS
for (uint ii = 0; ii < ecosystemModelGrid.NumLatCells; ii++)
{
lats[ii] = ecosystemModelGrid.Lats[ii] + (ecosystemModelGrid.LatCellSize / 2);
}
for (uint jj = 0; jj < ecosystemModelGrid.NumLonCells; jj++)
{
lons[jj] = ecosystemModelGrid.Lons[jj] + (ecosystemModelGrid.LonCellSize / 2);
}
// Get the required data from the model grid
dataToConvert = ecosystemModelGrid.GetStateVariableGrid(gridVariableName, traitValue, functionalGroupHandler.AllFunctionalGroupsIndex, cellIndices,
variableType, initialisation);
// If not already contained in the SDS, add the dimension information (geographic coordinates)
if (SDSObject.Variables.Contains("Latitude"))
{
}
else
{
SDSObject.AddVariable <float>("Latitude", lats, "Lat");
}
if (SDSObject.Variables.Contains("Longitude"))
{
}
else
{
SDSObject.AddVariable <float>("Longitude", lons, "Lon");
}
// If the SDS object already contains the output variable, then add the data. Otherwise, define the variable and then add the data
if (SDSObject.Variables.Contains(outputVariableName))
{
SDSObject.PutData <double[, ]>(outputVariableName, dataToConvert);
// Commit the changes
SDSObject.Commit();
}
else
{
// Set up the dimensions and add the gridded data
string[] dimensions = { "Lat", "Lon" };
var DataGrid = SDSObject.AddVariable <double>(outputVariableName, dataToConvert, dimensions);
// Add appropriate metadata (including missing values)
DataGrid.Metadata["DisplayName"] = outputVariableName;
DataGrid.Metadata["MissingValue"] = (double)MissingValue;
// Commit changes to update data set
SDSObject.Commit();
}
}
/// <summary>
/// Generates the initial file outputs
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cohortFunctionalGroupDefinitions">The functional group definitions for cohorts in the model</param>
/// <param name="MarineCell">Whether the current cell is a marine cell</param>
/// <param name="cellIndices">The list of all cells to run the model for</param>
/// <param name="cellIndex">The index of the current cell in the list of all cells to run the model for</param>
private void InitialFileOutputs(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortFunctionalGroupDefinitions,
Boolean MarineCell, List<uint[]> cellIndices, int cellIndex)
{
Console.WriteLine("Writing initial grid cell outputs to memory...");
//Write the low level outputs first
DataConverter.ValueToSDS1D(TotalLivingBiomassDensity, "Total Biomass density", "Time step",
ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(TotalHeterotrophAbundanceDensity, "Heterotroph Abundance density", "Time step",
ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(TotalHeterotrophBiomassDensity, "Heterotroph Biomass density", "Time step",
ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
// File outputs for medium and high detail levels
if ((ModelOutputDetail == OutputDetailLevel.Medium) || (ModelOutputDetail == OutputDetailLevel.High))
{
if (MarineCell)
{
foreach (string TraitValue in CohortTraitIndicesMarine.Keys)
{
// Write densities, biomasses and abundances in different functional groups to the relevant one-dimensional output variables
DataConverter.ValueToSDS1D(TotalDensitiesOut[TraitValue], TraitValue + " density", "Time step",
ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass density", "Time step",
ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
}
foreach (string TraitValue in StockTraitIndicesMarine.Keys)
{
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass density", "Time step",
ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
}
}
else
{
foreach (string TraitValue in CohortTraitIndices.Keys)
{
// Write densities, biomasses and abundances in different functional groups to the relevant one-dimensional output variables
DataConverter.ValueToSDS1D(TotalDensitiesOut[TraitValue], TraitValue + " density", "Time step",
ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass density", "Time step",
ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
}
foreach (string TraitValue in StockTraitIndices.Keys)
{
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass density", "Time step",
ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
}
}
if (OutputMetrics)
{
DataConverter.ValueToSDS1D(Metrics.CalculateMeanTrophicLevelCell(ecosystemModelGrid,cellIndices,cellIndex),
"Mean Trophic Level", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalEvennessRao(ecosystemModelGrid, cohortFunctionalGroupDefinitions,cellIndices, cellIndex,"trophic index"),
"Trophic Evenness", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalEvennessRao(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "biomass"),
"Biomass Evenness", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
double[] FunctionalDiversity = Metrics.CalculateFunctionalDiversity(ecosystemModelGrid, cohortFunctionalGroupDefinitions,
cellIndices, cellIndex);
DataConverter.ValueToSDS1D(FunctionalDiversity[0],
"Functional Richness", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(FunctionalDiversity[1],
"Rao Functional Evenness", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "Biomass")[0],
"Biomass Richness", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "Biomass")[1],
"Min Bodymass", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "Biomass")[2],
"Max Bodymass", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "Trophic index")[0],
"Trophic Richness", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "Trophic index")[1],
"Min Trophic Index", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, cellIndex, "Trophic index")[2],
"Max Trophic Index", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(Metrics.CalculateArithmeticCommunityMeanBodyMass(ecosystemModelGrid, cellIndices, cellIndex),
"Arithmetic Mean Bodymass", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
DataConverter.ValueToSDS1D(Metrics.CalculateGeometricCommunityMeanBodyMass(ecosystemModelGrid, cellIndices, cellIndex),
"Geometric Mean Bodymass", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
}
if (MarineCell && TrackMarineSpecifics)
{
DataConverter.ValueToSDS1D(TotalIncomingNPP, "Incoming NPP", "Time step", ecosystemModelGrid.GlobalMissingValue,
BasicOutputMemory, 0);
}
// File outputs for high detail level
if (ModelOutputDetail == OutputDetailLevel.High)
{
if (OutputMetrics)
{
DataConverter.VectorToSDS2D(Metrics.CalculateTrophicDistribution(ecosystemModelGrid,cellIndices,cellIndex), "Trophic Index Distribution",
new string[2] { "Time step", "Trophic Index Bins" }, TimeSteps, Metrics.TrophicIndexBinValues, ecosystemModelGrid.GlobalMissingValue, MassBinsOutputMemory, 0);
}
foreach (var TraitValue in AbundancesInMassBins.Keys)
{
DataConverter.VectorToSDS2D(AbundancesInMassBins[TraitValue], "Log " + TraitValue + " abundance in mass bins",
new string[2] { "Time step", "Mass bin" }, TimeSteps, MassBins, ecosystemModelGrid.GlobalMissingValue, MassBinsOutputMemory, 0);
DataConverter.VectorToSDS2D(BiomassesInMassBins[TraitValue], "Log " + TraitValue + " biomass in mass bins",
new string[2] { "Time step", "Mass bin" }, TimeSteps, MassBins, ecosystemModelGrid.GlobalMissingValue, MassBinsOutputMemory, 0);
// Write out abundances in combinations of juvenile and adult mass bins to the relevant three-dimensional output variables
DataConverter.Array2DToSDS3D(AbundancesInJuvenileAdultMassBins[TraitValue],
"Log " + TraitValue + " abundance in juvenile vs adult bins",
new string[] { "Adult Mass bin", "Juvenile Mass bin", "Time step" },
0,
ecosystemModelGrid.GlobalMissingValue,
MassBinsOutputMemory);
DataConverter.Array2DToSDS3D(BiomassesInJuvenileAdultMassBins[TraitValue],
"Log " + TraitValue + " biomass in juvenile vs adult bins",
new string[] { "Adult Mass bin", "Juvenile Mass bin", "Time step" },
0,
ecosystemModelGrid.GlobalMissingValue,
MassBinsOutputMemory);
}
// Write outputs for tracking individual cohorts
// Loop over tracked cohorts
for (int i = 0; i < TrackedCohorts.Count; i++)
{
// Add the individual body mass of the tracked cohort to the output dataset
string[] TrackedCohortDimensions = new string[] { "Time step", "Cohort ID" };
DataConverter.ValueToSDS2D(TrackedCohortIndividualMasses[i], "Individual body mass", TrackedCohortDimensions,
ecosystemModelGrid.GlobalMissingValue, TrackedCohortsOutputMemory, 0, i);
DataConverter.ValueToSDS2D(TrackedCohortAbundances[i], "Number of individuals", TrackedCohortDimensions,
ecosystemModelGrid.GlobalMissingValue, TrackedCohortsOutputMemory, 0, i);
}
}
}
}
/// <summary>
/// Record dispersal events in the dispersal tracker
/// </summary>
/// <param name="inboundCohorts">The cohorts arriving in a cell in the current time step</param>
/// <param name="outboundCohorts">The cohorts leaving a cell in the current time step</param>
/// <param name="outboundCohortWeights">The body masses of cohorts leaving the cell in the current time step</param>
/// <param name="timestep">The current model time step</param>
/// <param name="madingleyModelGrid">The model grid</param>
public void RecordDispersalForACell(uint[, ,] inboundCohorts, uint[, ,] outboundCohorts, List <double>[,] outboundCohortWeights, uint timestep, ModelGrid madingleyModelGrid)
{
_TrackDispersal.RecordDispersal(inboundCohorts, outboundCohorts, outboundCohortWeights, timestep, madingleyModelGrid);
}
private void CalculateOutputs(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortFunctionalGroupDefinitions,
FunctionalGroupDefinitions stockFunctionalGroupDefinitions, List <uint[]> cellIndices, MadingleyModelInitialisation initialisation, uint currentTimestep)
{
// Get grids of the total biomass densities of all stocks and all cohorts in each grid cell
LogBiomassDensityGridCohorts = ecosystemModelGrid.GetStateVariableGridLogDensityPerSqKm("Biomass", "NA", cohortFunctionalGroupDefinitions.
AllFunctionalGroupsIndex, cellIndices, "cohort", initialisation);
LogBiomassDensityGridStocks = ecosystemModelGrid.GetStateVariableGridLogDensityPerSqKm("Biomass", "NA", stockFunctionalGroupDefinitions.
AllFunctionalGroupsIndex, cellIndices, "stock", initialisation);
// Get grids of total abundance densities of all stocks and all cohorts in each grid cell
LogAbundanceDensityGridCohorts = ecosystemModelGrid.GetStateVariableGridLogDensityPerSqKm("Abundance", "NA", cohortFunctionalGroupDefinitions.
AllFunctionalGroupsIndex, cellIndices, "cohort", initialisation);
// Loop over grid cells and add stock and cohort biomass density to get the total of all biomass densities
for (int ii = 0; ii < ecosystemModelGrid.NumLatCells; ii++)
{
for (int jj = 0; jj < ecosystemModelGrid.NumLonCells; jj++)
{
LogBiomassDensityGrid[ii, jj] = Math.Log(Math.Exp(LogBiomassDensityGridCohorts[ii, jj]) + Math.Exp(LogBiomassDensityGridStocks[ii, jj]));
}
}
string[] Keys = CohortTraitIndices.Keys.ToArray();
foreach (string Key in Keys)
{
BiomassDensityGrid[Key] = ecosystemModelGrid.GetStateVariableGridLogDensityPerSqKm("Biomass", "NA", CohortTraitIndices[Key], cellIndices, "cohort", initialisation);
AbundanceDensityGrid[Key] = ecosystemModelGrid.GetStateVariableGridLogDensityPerSqKm("Abundance", "NA", CohortTraitIndices[Key], cellIndices, "cohort", initialisation);
}
Keys = StockTraitIndices.Keys.ToArray();
foreach (string Key in Keys)
{
BiomassDensityGrid[Key] = ecosystemModelGrid.GetStateVariableGridLogDensityPerSqKm("Biomass", "NA", StockTraitIndices[Key], cellIndices, "stock", initialisation);
}
// Temporary outputs to check plant model
Realm = ecosystemModelGrid.GetEnviroGrid("Realm", 0);
FrostDays = ecosystemModelGrid.GetEnviroGrid("Fraction Year Frost", 0);
Temperature = ecosystemModelGrid.GetEnviroGrid("Temperature", Utils.GetCurrentMonth(currentTimestep, initialisation.GlobalModelTimeStepUnit));
for (int i = 0; i < ecosystemModelGrid.NumLatCells; i++)
{
for (int j = 0; j < ecosystemModelGrid.NumLonCells; j++)
{
FracEvergreen[i, j] = BiomassDensityGrid["evergreen"][i, j] / BiomassDensityGrid["autotroph"][i, j];
}
}
HANPP = ecosystemModelGrid.GetEnviroGrid("HANPP", 0);
if (OutputMetrics)
{
//Calculate the values for the ecosystem metrics for each of the grid cells
for (int i = 0; i < cellIndices.Count; i++)
{
uint latIndex = cellIndices[i][0];
uint lonIndex = cellIndices[i][1];
MetricsGrid["Mean Trophic Level"][latIndex, lonIndex] = Metrics.CalculateMeanTrophicLevelCell(ecosystemModelGrid, cellIndices, i);
MetricsGrid["Trophic Evenness"][latIndex, lonIndex] = Metrics.CalculateFunctionalEvennessRao(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, i, "trophic index");
MetricsGrid["Biomass Evenness"][latIndex, lonIndex] = Metrics.CalculateFunctionalEvennessRao(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, i, "biomass");
double[] FunctionalDiversity = Metrics.CalculateFunctionalDiversity(ecosystemModelGrid, cohortFunctionalGroupDefinitions,
cellIndices, i);
// Functional Richness not currently calculated
//MetricsGrid["Functional Richness"][latIndex, lonIndex] = FunctionalDiversity[0];
MetricsGrid["Rao Functional Evenness"][latIndex, lonIndex] = FunctionalDiversity[1];
MetricsGrid["Biomass Richness"][latIndex, lonIndex] = Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, i, "Biomass")[0];
MetricsGrid["Min Bodymass"][latIndex, lonIndex] = Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, i, "Biomass")[1];
MetricsGrid["Max Bodymass"][latIndex, lonIndex] = Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, i, "Biomass")[2];
MetricsGrid["Trophic Richness"][latIndex, lonIndex] = Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, i, "Trophic Index")[0];
MetricsGrid["Min Trophic Index"][latIndex, lonIndex] = Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, i, "Trophic Index")[1];
MetricsGrid["Max Trophic Index"][latIndex, lonIndex] = Metrics.CalculateFunctionalRichness(ecosystemModelGrid, cohortFunctionalGroupDefinitions, cellIndices, i, "Trophic Index")[2];
MetricsGrid["Arithmetic Mean Bodymass"][latIndex, lonIndex] = Metrics.CalculateArithmeticCommunityMeanBodyMass(ecosystemModelGrid, cellIndices, i);
MetricsGrid["Geometric Mean Bodymass"][latIndex, lonIndex] = Metrics.CalculateGeometricCommunityMeanBodyMass(ecosystemModelGrid, cellIndices, i);
}
}
}
public void InitialOutputs(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortFunctionalGroupDefinitions, FunctionalGroupDefinitions
stockFunctionalGroupDefinitions, List <uint[]> cellIndices, MadingleyModelInitialisation initialisation)
{
Console.WriteLine("Writing initial grid outputs...");
// Calculate the output variables
CalculateOutputs(ecosystemModelGrid, cohortFunctionalGroupDefinitions, stockFunctionalGroupDefinitions, cellIndices, initialisation, 0);
// Write the total biomass of cohorts to the live display
if (LiveOutputs)
{
DataConverter.Array2DToSDS2D(LogBiomassDensityGridCohorts, "Log(Biomass density, g/km^2)", ecosystemModelGrid.Lats,
ecosystemModelGrid.Lons, ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive);
}
// Add the grid of total biomass in cells to the file dataset
DataConverter.Array2DToSDS3D(LogBiomassDensityGridCohorts, "Biomass density", new string[] { "Latitude", "Longitude", "Time step" }, 0,
ecosystemModelGrid.GlobalMissingValue, GridOutput);
DataConverter.Array2DToSDS3D(LogAbundanceDensityGridCohorts, "Abundance density", new string[] { "Latitude", "Longitude", "Time step" }, 0,
ecosystemModelGrid.GlobalMissingValue, GridOutput);
// Temporary outputs to check plant model
DataConverter.Array2DToSDS3D(Realm, "Realm", new string[] { "Latitude", "Longitude", "Time step" },
0, ecosystemModelGrid.GlobalMissingValue, GridOutput);
DataConverter.Array2DToSDS3D(HANPP, "HANPP", new string[] { "Latitude", "Longitude", "Time step" },
0, ecosystemModelGrid.GlobalMissingValue, GridOutput);
DataConverter.Array2DToSDS3D(Temperature, "Temperature", new string[] { "Latitude", "Longitude", "Time step" },
0, ecosystemModelGrid.GlobalMissingValue, GridOutput);
// File outputs for medium and high detail levels
if ((ModelOutputDetail == OutputDetailLevel.Medium) || (ModelOutputDetail == OutputDetailLevel.High))
{
// Add the biomass grids for individual trait combinations to the file dataset
foreach (var Key in BiomassDensityGrid.Keys)
{
DataConverter.Array2DToSDS3D(BiomassDensityGrid[Key], Key + "biomass density", new string[]
{ "Latitude", "Longitude", "Time step" }, 0, ecosystemModelGrid.GlobalMissingValue, GridOutput);
}
// Add the abundance density grid
foreach (var Key in AbundanceDensityGrid.Keys)
{
DataConverter.Array2DToSDS3D(AbundanceDensityGrid[Key], Key + "abundance density",
new string[] { "Latitude", "Longitude", "Time step" },
0,
ecosystemModelGrid.GlobalMissingValue,
GridOutput);
}
// Output ecosystem metrics
if (OutputMetrics)
{
foreach (string Key in MetricsGrid.Keys)
{
DataConverter.Array2DToSDS3D(MetricsGrid[Key], Key,
new string[] { "Latitude", "Longitude", "Time step" },
0,
ecosystemModelGrid.GlobalMissingValue,
GridOutput);
}
}
}
}
/// <summary>
/// Calculates functional diversity of cohorts in a grid cell as functional richness and functional diveregence (using the Rao Index)
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cohortDefinitions">The functional group definitions for cohorts in the model</param>
/// <param name="cellIndices">The list of cell indices in the current model simulation</param>
/// <param name="cellIndex">The index of the current cell within the list of cells to run</param>
/// <returns>A pair of values representing the functional richness and functional divergence (functional richness currently disabled!)</returns>
public double[] CalculateFunctionalDiversity(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortDefinitions,
List <uint[]> cellIndices, int cellIndex)
{
//Get the cohorts for the specified cell
GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
//Variable to hold the functional richness value for the current cohorts
double FunctionalRichness;
//Variable to hold the functional divergence value for the current cohorts
double RaoFunctionalDivergence = 0.0;
double[,] Distances = new double[CellCohorts.GetNumberOfCohorts(), CellCohorts.GetNumberOfCohorts()];
List <string> AllTraitNames = cohortDefinitions.GetAllTraitNames().ToList();
AllTraitNames.Remove("realm");
AllTraitNames.Remove("heterotroph/autotroph");
AllTraitNames.Remove("diet");
string[] TraitNames = AllTraitNames.ToArray();
//Define upper and lower limits for body mass
double MinMass = cohortDefinitions.GetBiologicalPropertyAllFunctionalGroups("minimum mass").Min();
double MaxMass = cohortDefinitions.GetBiologicalPropertyAllFunctionalGroups("maximum mass").Max();
//Define upp and lower limits for trophic index
double MaxTI = 40.0;
double MinTI = 1.0;
// Construct an array of functional trait values for each cohort
// Rows are specific cohorts
// Columns are the functional traits (these include different types:
// quantative: current mass, trophic index
// nominal: diet, reproductive strategy, mobility, metabolism
Tuple <double[], string[]>[] CohortFunctionalTraits = new Tuple <double[], string[]> [CellCohorts.GetNumberOfCohorts()];
double[] IndividualBodyMasses = new double[CellCohorts.GetNumberOfCohorts()];
double[] TrophicIndex = new double[CellCohorts.GetNumberOfCohorts()];
string[][] CohortNominalTraitValues = new string[TraitNames.Length][];
for (int i = 0; i < TraitNames.Length; i++)
{
CohortNominalTraitValues[i] = new string[CellCohorts.GetNumberOfCohorts()];
}
// Construct a vector of cohort biomass (in case we want to weight by them)
double[] CohortTotalBiomasses = new double[CellCohorts.GetNumberOfCohorts()];
string[] TraitValues = new string[TraitNames.Length];
double[] QuantitativeTraitValues = new double[2];
int CohortNumberCounter = 0;
for (int fg = 0; fg < CellCohorts.Count; fg++)
{
foreach (Cohort c in CellCohorts[fg])
{
TraitValues = cohortDefinitions.GetTraitValues(TraitNames, fg);
for (int ii = 0; ii < TraitValues.Length; ii++)
{
CohortNominalTraitValues[ii][CohortNumberCounter] = TraitValues[ii];
}
IndividualBodyMasses[CohortNumberCounter] = c.IndividualBodyMass;
TrophicIndex[CohortNumberCounter] = c.TrophicIndex;
QuantitativeTraitValues[0] = c.IndividualBodyMass;
QuantitativeTraitValues[1] = c.TrophicIndex;
CohortFunctionalTraits[CohortNumberCounter] = new Tuple <double[], string[]>(QuantitativeTraitValues, TraitValues);
CohortTotalBiomasses[CohortNumberCounter] = (c.IndividualBodyMass + c.IndividualReproductivePotentialMass) * c.CohortAbundance;
CohortNumberCounter++;
}
}
List <double[, ]> DistanceList = new List <double[, ]>();
DistanceList.Add(CalculateDistanceMatrix(IndividualBodyMasses, MaxMass, MinMass));
DistanceList.Add(CalculateDistanceMatrix(TrophicIndex, MaxTI, MinTI));
foreach (string[] t in CohortNominalTraitValues)
{
DistanceList.Add(CalculateDistanceMatrix(t));
}
Distances = CalculateAggregateDistance(DistanceList);
RaoFunctionalDivergence = RaoEntropy(Distances, CohortTotalBiomasses);
return(new double[] { 0.0, RaoFunctionalDivergence });
}
/// <summary>
/// Apply all updates from the ecological processes to the properties of the acting cohort and to the environment
/// </summary>
public void UpdateAllCrossGridCellEcology(ModelGrid madingleyModelGrid, ref uint dispersalCounter, CrossCellProcessTracker trackCrossCellProcesses, uint currentTimeStep)
{
// Create an array to hold the number of cohorts dispersing in each direction from each grid cell
uint[, ,] InboundCohorts = new uint[madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0), madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1), 8];
// Create an array to hold the number of cohorts dispersing in each direction to each grid cell
uint[, ,] OutboundCohorts = new uint[madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0), madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1), 8];
// Create an list array to hold the weights of cohorts dispersing from grid cell. Dimensions are: num grid cells lon, num grid cells lat, num cohorts dispersing
List <double>[,] OutboundCohortWeights = new List <double> [madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0), madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1)];
for (uint ii = 0; ii < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0); ii++)
{
for (uint jj = 0; jj < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1); jj++)
{
OutboundCohortWeights[ii, jj] = new List <double>();
}
}
// Loop through the delta array that holds the grid cells of the cohorts that are flagged as needing to be moved
for (uint ii = 0; ii < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0); ii++)
{
for (uint jj = 0; jj < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1); jj++)
{
// No cohorts to move if there are none in the delta dispersal array
if (madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj].Count == 0)
{
}
// Otherwise, loop through the cohorts and change the pointers/references to them one-by-one
else
{
for (int kk = 0; kk < madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj].Count; kk++)
{
// Find out which grid cell it is going to
uint[] CellToDisperseTo = madingleyModelGrid.DeltaCellToDisperseToArray[ii, jj].ElementAt(kk);
// Functional group is identified by the first array
uint CohortToDisperseFG = madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj].ElementAt(kk);
// Cohort number is identified by the second array
uint CohortToDisperseNum = madingleyModelGrid.DeltaCohortNumberDispersalArray[ii, jj].ElementAt(kk);
// If track processes is on, add this to the list of inbound and outbound cohorts
if (trackCrossCellProcesses.TrackCrossCellProcesses)
{
WriteOutCrossGridCell(madingleyModelGrid, CellToDisperseTo, InboundCohorts, OutboundCohorts, OutboundCohortWeights, ii, jj,
CohortToDisperseFG, CohortToDisperseNum, madingleyModelGrid.DeltaCellExitDirection[ii, jj].ElementAt(kk),
madingleyModelGrid.DeltaCellEntryDirection[ii, jj].ElementAt(kk));
}
// Simmply add it to the existing cohorts in that FG in the grid cell to disperse to
madingleyModelGrid.AddNewCohortToGridCell(CellToDisperseTo[0], CellToDisperseTo[1], (int)CohortToDisperseFG, madingleyModelGrid.GetGridCellIndividualCohort(ii, jj, (int)CohortToDisperseFG, (int)CohortToDisperseNum));
// Update the dispersal counter
dispersalCounter++;
// So now there is a pointer in the grid cell to which it is going. We have to delete the pointers in the original cell and in the
// delta array, but we need to do this without messing with the list structure; i.e. wait until all cohorts have been moved
}
}
}
}
// Reset the delta arrays and remove the pointers to the cohorts in the original list
for (uint ii = 0; ii < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(0); ii++)
{
for (uint jj = 0; jj < madingleyModelGrid.DeltaFunctionalGroupDispersalArray.GetLength(1); jj++)
{
// No cohorts to move if there are none in the delta dispersal array
if (madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj].Count == 0)
{
}
// Otherwise, loop through the cohorts and change the pointers/references to them one-by-one
else
{
// Delete the cohorts from the original grid cell. Note that this needs to be done carefully to ensure that the correct ones
// are deleted (lists shift about when an internal element is deleted.
madingleyModelGrid.DeleteGridCellIndividualCohorts(ii, jj, madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj], madingleyModelGrid.DeltaCohortNumberDispersalArray[ii, jj]);
// Reset the lists in the delta dispersal arrays
madingleyModelGrid.DeltaFunctionalGroupDispersalArray[ii, jj] = new List <uint>();
madingleyModelGrid.DeltaCohortNumberDispersalArray[ii, jj] = new List <uint>();
// Reset the list in the grid cells to disperse to array
madingleyModelGrid.DeltaCellToDisperseToArray[ii, jj] = new List <uint[]>();
// Reset the lists in the delta dispersal arrays
madingleyModelGrid.DeltaCellExitDirection[ii, jj] = new List <uint>();
madingleyModelGrid.DeltaCellEntryDirection[ii, jj] = new List <uint>();
}
}
}
if (trackCrossCellProcesses.TrackCrossCellProcesses)
{
// If we are tracking dispersal, then write out how many cohorts have moved to a file
trackCrossCellProcesses.RecordDispersalForACell(InboundCohorts, OutboundCohorts, OutboundCohortWeights, currentTimeStep, madingleyModelGrid);
}
}
/// <summary>
/// Sets up the outputs associated with medium and high levels of output detail
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
private void SetupMediumLevelOutputs(ModelGrid ecosystemModelGrid, Boolean marineCell)
{
string[] TimeDimension = { "Time step" };
if (OutputMetrics)
{
DataConverter.AddVariable(BasicOutputMemory, "Mean Trophic Level", "dimensionless", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Trophic Evenness", "dimensionless", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Biomass Evenness", "dimensionless", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Functional Richness", "dimensionless", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Rao Functional Evenness", "dimensionless", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Biomass Richness", "dimensionless", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Trophic Richness", "dimensionless", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Max Bodymass", "g", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Min Bodymass", "g", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Max Trophic Index", "dimensionless", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Min Trophic Index", "dimensionless", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Geometric Mean Bodymass", "g", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Arithmetic Mean Bodymass", "g", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
}
if (marineCell)
{
foreach (string TraitValue in CohortTraitIndicesMarine.Keys)
{
DataConverter.AddVariable(BasicOutputMemory, TraitValue + " density", "Individuals / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, TraitValue + " biomass density", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
}
foreach (string TraitValue in StockTraitIndicesMarine.Keys)
{
DataConverter.AddVariable(BasicOutputMemory, TraitValue + " biomass density", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
}
if (TrackMarineSpecifics)
{
// Add a variable to keep track of the NPP incoming from the VGPM model
DataConverter.AddVariable(BasicOutputMemory, "Incoming NPP", "gC / m^2 / day", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
}
}
else
{
foreach (string TraitValue in CohortTraitIndices.Keys)
{
DataConverter.AddVariable(BasicOutputMemory, TraitValue + " density", "Individuals / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, TraitValue + " biomass density", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
}
foreach (string TraitValue in StockTraitIndices.Keys)
{
DataConverter.AddVariable(BasicOutputMemory, TraitValue + " biomass density", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
}
}
}
public void OutputCurrentModelState(ModelGrid currentModelGrid, FunctionalGroupDefinitions functionalGroupHandler, List <uint[]> cellIndices, uint currentTimestep, int maximumNumberOfCohorts, string filename)
{
float[] Latitude = currentModelGrid.Lats;
float[] Longitude = currentModelGrid.Lons;
float[] CohortFunctionalGroup = new float[functionalGroupHandler.GetNumberOfFunctionalGroups()];
for (int fg = 0; fg < CohortFunctionalGroup.Length; fg++)
{
CohortFunctionalGroup[fg] = fg;
}
int CellCohortNumber = 0;
GridCellCohortHandler CellCohorts;
for (int cellIndex = 0; cellIndex < cellIndices.Count; cellIndex++)
{
CellCohorts = currentModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
for (int i = 0; i < CellCohorts.Count; i++)
{
if (CellCohorts[i].Count > CellCohortNumber)
{
CellCohortNumber = CellCohorts[i].Count;
}
}
}
int MaxNumberCohorts = Math.Max(CellCohortNumber, maximumNumberOfCohorts);
float[] Cohort = new float[MaxNumberCohorts];
for (int c = 0; c < Cohort.Length; c++)
{
Cohort[c] = c;
}
//Define an array for stock functional group - there are only three currently
float[] StockFunctionalGroup = new float[] { 1, 2, 3 };
//Define an array for index of stocks - there is only one currently
float[] Stock = new float[] { 1 };
string Filename = filename + "_" + currentTimestep.ToString() + Simulation.ToString();
StateOutput = SDSCreator.CreateSDS("netCDF", Filename, _OutputPath);
//Define the cohort properties for output
string[] CohortProperties = new string[]
{ "JuvenileMass", "AdultMass", "IndividualBodyMass", "IndividualReproductivePotentialMass", "CohortAbundance",
"BirthTimeStep", "MaturityTimeStep", "LogOptimalPreyBodySizeRatio",
"MaximumAchievedBodyMass", "Merged", "TrophicIndex", "ProportionTimeActive" };
//define the dimensions for cohort outputs
string[] dims = new string[] { "Latitude", "Longitude", "Cohort Functional Group", "Cohort" };
// Add the variables for each cohort property
// Then calculate the state for this property and put the data to this variable
foreach (string v in CohortProperties)
{
DataConverter.AddVariable(StateOutput, "Cohort" + v, 4,
dims, currentModelGrid.GlobalMissingValue, Latitude,
Longitude, CohortFunctionalGroup, Cohort);
StateOutput.PutData <double[, , , ]>("Cohort" + v,
CalculateCurrentCohortState(currentModelGrid, v, Latitude.Length, Longitude.Length, CohortFunctionalGroup.Length, Cohort.Length, cellIndices));
StateOutput.Commit();
}
//Define the stock properties for output
string[] StockProperties = new string[] { "IndividualBodyMass", "TotalBiomass" };
//define the dimensions for cohort outputs
dims = new string[] { "Latitude", "Longitude", "Stock Functional Group", "Stock" };
// Add the variables for each stock property
// Then calculate the state for this property and put the data to this variable
foreach (string v in StockProperties)
{
DataConverter.AddVariable(StateOutput, "Stock" + v, 4,
dims, currentModelGrid.GlobalMissingValue, Latitude,
Longitude, StockFunctionalGroup, Stock);
StateOutput.PutData <double[, , , ]>("Stock" + v,
CalculateCurrentStockState(currentModelGrid, v, Latitude.Length, Longitude.Length, StockFunctionalGroup.Length, Stock.Length, cellIndices));
StateOutput.Commit();
}
//Close this data set
StateOutput.Dispose();
}
/// <summary>
/// Generate the live outputs for the current time step
/// </summary>
/// <param name="numTimeSteps">The number of time steps in the model run</param>
/// <param name="currentTimeStep">The current time step</param>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
private void TimeStepLiveOutputs(uint numTimeSteps, uint currentTimeStep, ModelGrid ecosystemModelGrid, Boolean marineCell)
{
// Output to the live graph view according to the specified level of detail
if (ModelOutputDetail == OutputDetailLevel.Low)
{
// Rescale the y-axis if necessary
if (TotalLivingBiomass > MaximumYValue)
{
MaximumYValue = TotalLivingBiomass * 1.1;
DataSetToViewLive.Metadata["VisualHints"] = "\"Total living biomass\"[Time step]; Style:Polyline; Visible: 0,1," +
numTimeSteps.ToString() + "," + MaximumYValue.ToString() +
"; LogScale:Y; Stroke:#D95F02; Thickness:3; Title:\"Total Biomass" + "\"";
}
// Write out total living biomass
DataConverter.ValueToSDS1D(TotalLivingBiomass, "Total living biomass", "Time step",
ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, (int)currentTimeStep + 1);
}
else
{
//Find the max value in the TotalBiomassDensities
double MaxVal = 0.0;
foreach (var KVPair in TotalBiomassDensitiesOut)
{
if (KVPair.Value > MaxVal) MaxVal = KVPair.Value;
}
// Rescale the y-axis if necessary
if (MaxVal > MaximumYValue)
{
MaximumYValue = MaxVal * 1.1;
DataSetToViewLive.Metadata["VisualHints"] = "\"autotroph biomass\"[Time step]; Style:Polyline; Visible: 0,1,"
+ numTimeSteps.ToString() + ","
+ MaximumYValue.ToString() + "; LogScale:Y; Stroke:#FF008040;Thickness:3;;\"carnivore biomass\"[Time step] ; Style:Polyline; Visible: 0,1,"
+ numTimeSteps.ToString() + ","
+ MaximumYValue.ToString() + "; LogScale:Y; Stroke:#FFFF0000;Thickness:3;;\"herbivore biomass\"[Time step] ; Style:Polyline; Visible: 0,1,"
+ numTimeSteps.ToString() + ","
+ MaximumYValue.ToString() + "; LogScale:Y; Stroke:#FF00FF00;Thickness:3;;\"omnivore biomass\"[Time step] ; Style:Polyline; Visible: 0,1,"
+ numTimeSteps.ToString() + ","
+ MaximumYValue.ToString() + "; LogScale:Y; Stroke:#FF0000FF;Thickness:3; Title:\"Biomass Densities";
}
if (marineCell)
{
foreach (string TraitValue in CohortTraitIndicesMarine.Keys)
{
// Output the total carnivore, herbivore and omnivore abundances
DataConverter.ValueToSDS1D(TotalDensitiesOut[TraitValue], TraitValue + " density", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, (int)currentTimeStep + 1);
}
foreach (string TraitValue in StockTraitIndicesMarine.Keys)
{
// Add in the initial values of stock biomass density
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, (int)currentTimeStep + 1);
}
}
else
{
foreach (string TraitValue in CohortTraitIndices.Keys)
{
// Output the total carnivore, herbivore and omnivore abundances
DataConverter.ValueToSDS1D(TotalDensitiesOut[TraitValue], TraitValue + " density", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, (int)currentTimeStep + 1);
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, (int)currentTimeStep + 1);
}
foreach (string TraitValue in StockTraitIndices.Keys)
{
// Add in the initial values of stock biomass density
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, (int)currentTimeStep + 1);
}
}
}
}
private double[, , ,] CalculateCurrentCohortState(ModelGrid currentModelState, string variableName, int numLats, int numLons, int numFG, int numCohorts, List <uint[]> cellList)
{
//Calculate the cohort state
double[, , ,] State = new double[numLats, numLons, numFG, numCohorts];
GridCellCohortHandler CellCohorts;
for (int cellIndex = 0; cellIndex < cellList.Count; cellIndex++)
{
CellCohorts = currentModelState.GetGridCellCohorts(cellList[cellIndex][0], cellList[cellIndex][1]);
for (int functionalGroupIndex = 0; functionalGroupIndex < CellCohorts.Count; functionalGroupIndex++)
{
for (int cohortIndex = 0; cohortIndex < CellCohorts[functionalGroupIndex].Count; cohortIndex++)
{
switch (variableName)
{
case "JuvenileMass":
State[cellList[cellIndex][0], cellList[cellIndex][1], functionalGroupIndex, cohortIndex] = CellCohorts[functionalGroupIndex][cohortIndex].JuvenileMass;
break;
case "AdultMass":
State[cellList[cellIndex][0], cellList[cellIndex][1], functionalGroupIndex, cohortIndex] = CellCohorts[functionalGroupIndex][cohortIndex].AdultMass;
break;
case "IndividualBodyMass":
State[cellList[cellIndex][0], cellList[cellIndex][1], functionalGroupIndex, cohortIndex] = CellCohorts[functionalGroupIndex][cohortIndex].IndividualBodyMass;
break;
case "CohortAbundance":
State[cellList[cellIndex][0], cellList[cellIndex][1], functionalGroupIndex, cohortIndex] = CellCohorts[functionalGroupIndex][cohortIndex].CohortAbundance;
break;
case "BirthTimeStep":
State[cellList[cellIndex][0], cellList[cellIndex][1], functionalGroupIndex, cohortIndex] = (double)CellCohorts[functionalGroupIndex][cohortIndex].BirthTimeStep;
break;
case "MaturityTimeStep":
State[cellList[cellIndex][0], cellList[cellIndex][1], functionalGroupIndex, cohortIndex] = (double)CellCohorts[functionalGroupIndex][cohortIndex].MaturityTimeStep;
break;
case "LogOptimalPreyBodySizeRatio":
State[cellList[cellIndex][0], cellList[cellIndex][1], functionalGroupIndex, cohortIndex] = CellCohorts[functionalGroupIndex][cohortIndex].LogOptimalPreyBodySizeRatio;
break;
case "MaximumAchievedBodyMass":
State[cellList[cellIndex][0], cellList[cellIndex][1], functionalGroupIndex, cohortIndex] = CellCohorts[functionalGroupIndex][cohortIndex].MaximumAchievedBodyMass;
break;
case "Merged":
State[cellList[cellIndex][0], cellList[cellIndex][1], functionalGroupIndex, cohortIndex] = Convert.ToDouble(CellCohorts[functionalGroupIndex][cohortIndex].Merged);
break;
case "TrophicIndex":
State[cellList[cellIndex][0], cellList[cellIndex][1], functionalGroupIndex, cohortIndex] = CellCohorts[functionalGroupIndex][cohortIndex].TrophicIndex;
break;
case "ProportionTimeActive":
State[cellList[cellIndex][0], cellList[cellIndex][1], functionalGroupIndex, cohortIndex] = CellCohorts[functionalGroupIndex][cohortIndex].ProportionTimeActive;
break;
}
}
}
}
return(State);
}
/// <summary>
/// Write to the output file values of the output variables before the first time step
/// </summary>
/// <param name="ecosystemModelGrid">The model grid to get data from</param>C:\madingley-ecosystem-model\Madingley\Output and tracking\PredationTracker.cs
/// <param name="cohortFunctionalGroupDefinitions">The definitions of cohort functional groups in the model</param>
/// <param name="stockFunctionalGroupDefinitions">The definitions of stock functional groups in the model</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="cellNumber">The number of the current cell in the list of indices of active cells</param>
/// <param name="globalDiagnosticVariables">List of global diagnostic variables</param>
/// <param name="numTimeSteps">The number of time steps in the model run</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
/// <param name="month">The current month in the model run</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
public void InitialOutputs(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortFunctionalGroupDefinitions,
FunctionalGroupDefinitions stockFunctionalGroupDefinitions, List<uint[]> cellIndices, int cellNumber,
SortedList<string, double> globalDiagnosticVariables, uint numTimeSteps, MadingleyModelInitialisation initialisation,
uint month, Boolean marineCell)
{
// Calculate values of the output variables to be used
CalculateOutputs(ecosystemModelGrid, cohortFunctionalGroupDefinitions, stockFunctionalGroupDefinitions, cellIndices, cellNumber, globalDiagnosticVariables, initialisation, month, marineCell);
// Generate the intial live outputs
if (LiveOutputs)
{
InitialLiveOutputs(ecosystemModelGrid, marineCell);
}
// Generate the intial file outputs
InitialFileOutputs(ecosystemModelGrid, cohortFunctionalGroupDefinitions, marineCell,cellIndices,cellNumber);
}
/// <summary>
/// Calculates the probability of advective dispersal given the grid cell
/// </summary>
/// <param name="madingleyGrid">The model grid</param>
/// <param name="latIndex">The latitude index of the grid cell to check for dispersal</param>
/// <param name="lonIndex">The longitude index of the grid cell to check for dispersal</param>
/// <param name="currentMonth">The current model month</param>
/// <returns>A six element array.
/// The first element is the probability of dispersal.
/// The second element is the probability of dispersing in the u (longitudinal) direction
/// The third element is the probability of dispersing in the v (latitudinal) direction
/// The fourth element is the probability of dispersing in the diagonal direction
/// The fifth element is the distance travelled in the u direction (u velocity modified by the random diffusion component)
/// The sixth element is the distance travelled in the v direction (v velocity modified by the random diffusion component)
/// Note that the second, third, and fourth elements are always positive; thus, they do not indicate 'direction' in terms of dispersal.</returns>
private double[] CalculateDispersalProbability(ModelGrid madingleyGrid, uint latIndex, uint lonIndex, uint currentMonth, double rescaleduSpeed, double rescaledvSpeed)
{
// Distance travelled in u (longitudinal) direction
double uDistanceTravelled;
// Distance travelled in v (latitudinal) direction
double vDistanceTravelled;
// U and V components of the diffusive velocity
double[] DiffusiveUandVComponents = new double[2];
// Length in km of a cell boundary latitudinally
double LatCellLength;
// Length in km of a cell boundary longitudinally
double LonCellLength;
// Area of the grid cell that is outside in the diagonal direction after dispersal, in kilometres squared
double AreaOutsideBoth;
// Area of the grid cell that is outside in the u (longitudinal) direction after dispersal, in kilometres squared
double AreaOutsideU;
// Area of the grid cell that is outside in the v (latitudinal) direction after dispersal, in kilometres squared
double AreaOutsideV;
// Cell area, in kilometres squared
double CellArea;
// Probability of dispersal
double DispersalProbability;
// Calculate the diffusive movement speed, with a direction chosen at random
DiffusiveUandVComponents = CalculateDiffusion();
// Calculate the distance travelled in this dispersal (not global) time step. both advective and diffusive speeds need to have been converted to km / advective model time step
uDistanceTravelled = rescaleduSpeed + DiffusiveUandVComponents[0];
vDistanceTravelled = rescaledvSpeed + DiffusiveUandVComponents[1];
// Check that the u distance travelled and v distance travelled are not greater than the cell length
LatCellLength = madingleyGrid.CellHeightsKm[latIndex];
LonCellLength = madingleyGrid.CellWidthsKm[latIndex];
if (Math.Abs(uDistanceTravelled) >= LonCellLength)
{
Debug.Fail("u velocity greater than cell width");
}
if (Math.Abs(vDistanceTravelled) >= LatCellLength)
{
Debug.Fail("v velocity greater than cell width");
}
// We assume that the whole grid cell moves at the given velocity and calculate the area that is then outside the original grid cell location.
// This then becomes the probability of dispersal
// Calculate the area of the grid cell that is now outside in the diagonal direction.
AreaOutsideBoth = Math.Abs(uDistanceTravelled * vDistanceTravelled);
// Calculate the area of the grid cell that is now outside in the u (longitudinal) direction (not including the diagonal)
AreaOutsideU = Math.Abs(uDistanceTravelled * LatCellLength) - AreaOutsideBoth;
// Calculate the proportion of the grid cell that is outside in the v (latitudinal) direction (not including the diagonal)
AreaOutsideV = Math.Abs(vDistanceTravelled * LonCellLength) - AreaOutsideBoth;
// Get the cell area, in kilometres squared
CellArea = madingleyGrid.GetCellEnvironment(latIndex, lonIndex)["Cell Area"][0];
// Convert areas to a probability
DispersalProbability = (AreaOutsideU + AreaOutsideV + AreaOutsideBoth) / CellArea;
// Check that the whole cell hasn't moved out. Could this happen for the fastest currents in a month? Definitely,
// if current speeds were not constrained
if (DispersalProbability >= 1)
{
Debug.Fail("Dispersal probability in advection should always be <= 1");
}
double[] NewArray = { DispersalProbability, AreaOutsideU / CellArea, AreaOutsideV / CellArea, AreaOutsideBoth / CellArea, uDistanceTravelled, vDistanceTravelled };
return(NewArray);
}
/// <summary>
/// Write to the output file values of the output variables during the model time steps
/// </summary>
/// <param name="ecosystemModelGrid">The model grid to get data from</param>
/// <param name="cohortFunctionalGroupDefinitions">The definitions of the cohort functional groups in the model</param>
/// <param name="stockFunctionalGroupDefinitions">The definitions of the stock functional groups in the model</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="cellNumber">The number of the current cell in the list of indices of active cells</param>
/// <param name="globalDiagnosticVariables">List of global diagnostic variables</param>
/// <param name="timeStepTimer">The timer for the current time step</param>
/// <param name="numTimeSteps">The number of time steps in the model run</param>
/// <param name="currentTimestep">The current model time step</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
/// <param name="month">The current month in the model run</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
public void TimeStepOutputs(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortFunctionalGroupDefinitions,
FunctionalGroupDefinitions stockFunctionalGroupDefinitions, List<uint[]> cellIndices, int cellNumber,
SortedList<string, double> globalDiagnosticVariables, StopWatch timeStepTimer, uint numTimeSteps, uint currentTimestep,
MadingleyModelInitialisation initialisation, uint month, Boolean marineCell)
{
// Calculate values of the output variables to be used
CalculateOutputs(ecosystemModelGrid, cohortFunctionalGroupDefinitions, stockFunctionalGroupDefinitions, cellIndices, cellNumber, globalDiagnosticVariables, initialisation, month, marineCell);
// Generate the live outputs for this time step
if (LiveOutputs)
{
TimeStepLiveOutputs(numTimeSteps, currentTimestep, ecosystemModelGrid, marineCell);
}
// Generate the console outputs for the current time step
TimeStepConsoleOutputs(currentTimestep, timeStepTimer);
// Generate the file outputs for the current time step
TimeStepFileOutputs(ecosystemModelGrid, cohortFunctionalGroupDefinitions, currentTimestep, marineCell, cellIndices,cellNumber);
}
/// <summary>
/// Calculate trophic evenness using the Rao Index
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The list of indices of cells to be run in the current simulation</param>
/// <param name="cellIndex">The index of the current cell within the list of cells to be run</param>
/// <returns>Trophic evenness</returns>
public double CalculateFunctionalEvennessRao(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortDefinitions,
List<uint[]> cellIndices, int cellIndex, string trait)
{
//Get the cohorts for the specified cell
GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
double[] EvennessValues = new double[2];
double[,] Distances = new double[CellCohorts.GetNumberOfCohorts(), CellCohorts.GetNumberOfCohorts()];
double[] FunctionalTrait = new double[CellCohorts.GetNumberOfCohorts()];
double MaxModelTraitValue=0;
double MinModelTraitValue=0;
// Construct a vector of cohort biomass (in case we want to weight by them)
double[] CohortTotalBiomasses = new double[CellCohorts.GetNumberOfCohorts()];
int CohortNumberCounter = 0;
switch (trait.ToLower())
{
case "biomass":
for (int fg = 0; fg < CellCohorts.Count; fg++)
{
foreach (Cohort c in CellCohorts[fg])
{
FunctionalTrait[CohortNumberCounter] = c.IndividualBodyMass;
CohortTotalBiomasses[CohortNumberCounter] = (c.IndividualBodyMass + c.IndividualReproductivePotentialMass) * c.CohortAbundance;
CohortNumberCounter++;
}
}
//Define upper and lower limits for body mass
MinModelTraitValue = cohortDefinitions.GetBiologicalPropertyAllFunctionalGroups("minimum mass").Min();
MaxModelTraitValue = cohortDefinitions.GetBiologicalPropertyAllFunctionalGroups("maximum mass").Max();
break;
case "trophic index":
for (int fg = 0; fg < CellCohorts.Count; fg++)
{
foreach (Cohort c in CellCohorts[fg])
{
FunctionalTrait[CohortNumberCounter] = c.IndividualBodyMass;
CohortTotalBiomasses[CohortNumberCounter] = (c.IndividualBodyMass + c.IndividualReproductivePotentialMass) * c.CohortAbundance;
CohortNumberCounter++;
}
}
MinModelTraitValue = MinTI;
MaxModelTraitValue = MaxTI;
break;
}
Distances = CalculateDistanceMatrix(FunctionalTrait, MaxModelTraitValue, MinModelTraitValue);
return RaoEntropy(Distances, CohortTotalBiomasses);
}
/// <summary>
/// Calculate outputs associated with low-level outputs
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The list of indices of active cells in the model grid</param>
/// <param name="cellIndex">The position of the current cell in the list of active cells</param>
/// <param name="globalDiagnosticVariables">The global diagnostic variables for this model run</param>
/// <param name="cohortFunctionalGroupDefinitions">The functional group definitions of cohorts in the model</param>
/// <param name="stockFunctionalGroupDefinitions">The functional group definitions of stocks in the model</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
/// <param name="month">The current month in the model run</param>
/// <param name="MarineCell">Whether the current cell is a marine cell</param>
private void CalculateLowLevelOutputs(ModelGrid ecosystemModelGrid, List<uint[]> cellIndices, int cellIndex,
SortedList<string,double> globalDiagnosticVariables, FunctionalGroupDefinitions cohortFunctionalGroupDefinitions,
FunctionalGroupDefinitions stockFunctionalGroupDefinitions, MadingleyModelInitialisation initialisation, uint month,
Boolean MarineCell)
{
// Reset the total living biomass
TotalLivingBiomass = 0.0;
string[] Keys;
if (MarineCell)
{
// Get the list of cohort trait combinations to consider
Keys = CohortTraitIndicesMarine.Keys.ToArray();
// Get biomass, abundance and densities for each of the trait combinations. Note that the GetStateVariableDensity function deals with the assessment of whether cohorts contain individuals
// of low enough mass to be considered zooplankton in the marine realm
foreach (string TraitValue in Keys)
{
// Biomass density
TotalBiomassDensitiesOut[TraitValue] = ecosystemModelGrid.GetStateVariableDensity("Biomass", TraitValue, CohortTraitIndicesMarine[TraitValue], cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation) / 1000.0;
// Density
TotalDensitiesOut[TraitValue] = ecosystemModelGrid.GetStateVariableDensity("Abundance", TraitValue, CohortTraitIndicesMarine[TraitValue], cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation);
}
}
else
{
// Get the list of cohort trait combinations to consider
Keys = CohortTraitIndices.Keys.ToArray();
// Get biomass, abundance and densities for each of the trait combinations
foreach (string TraitValue in Keys)
{
// Biomass density
TotalBiomassDensitiesOut[TraitValue] = ecosystemModelGrid.GetStateVariableDensity("Biomass", TraitValue, CohortTraitIndices[TraitValue], cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation) / 1000.0;
// Density
TotalDensitiesOut[TraitValue] = ecosystemModelGrid.GetStateVariableDensity("Abundance", TraitValue, CohortTraitIndices[TraitValue], cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation);
}
}
// Add the total biomass of all cohorts to the total living biomass variable
TotalLivingBiomass += ecosystemModelGrid.GetStateVariable("Biomass", "NA", cohortFunctionalGroupDefinitions.AllFunctionalGroupsIndex,
cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation);
TotalLivingBiomassDensity = ecosystemModelGrid.GetStateVariableDensity("Biomass", "NA", cohortFunctionalGroupDefinitions.AllFunctionalGroupsIndex, cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation) / 1000.0;
TotalHeterotrophAbundanceDensity = ecosystemModelGrid.GetStateVariableDensity("Abundance", "NA", cohortFunctionalGroupDefinitions.AllFunctionalGroupsIndex, cellIndices[cellIndex][0], cellIndices[cellIndex][1], "cohort", initialisation);
TotalHeterotrophBiomassDensity = TotalLivingBiomassDensity;
if (MarineCell)
{
// Get the list of stock trait combinations to consider
Keys = StockTraitIndicesMarine.Keys.ToArray();
// Get biomass and biomass density for each of the trait combinations
foreach (string TraitValue in Keys)
{
// Density
TotalBiomassDensitiesOut[TraitValue] = ecosystemModelGrid.GetStateVariableDensity("Biomass", TraitValue, StockTraitIndicesMarine[TraitValue], cellIndices[cellIndex][0], cellIndices[cellIndex][1], "stock", initialisation) / 1000.0;
}
}
else
{
// Get the list of stock trait combinations to consider
Keys = StockTraitIndices.Keys.ToArray();
// Get biomass and biomass density for each of the trait combinations
foreach (string TraitValue in Keys)
{
// Density
TotalBiomassDensitiesOut[TraitValue] = ecosystemModelGrid.GetStateVariableDensity("Biomass", TraitValue, StockTraitIndices[TraitValue], cellIndices[cellIndex][0], cellIndices[cellIndex][1], "stock", initialisation) / 1000.0;
}
}
// Add the total biomass of all stocks to the total living biomass variable
TotalLivingBiomass += ecosystemModelGrid.GetStateVariable("Biomass", "NA", stockFunctionalGroupDefinitions.AllFunctionalGroupsIndex,
cellIndices[cellIndex][0], cellIndices[cellIndex][1], "stock", initialisation);
TotalLivingBiomassDensity += ecosystemModelGrid.GetStateVariableDensity("Biomass", "NA", stockFunctionalGroupDefinitions.AllFunctionalGroupsIndex, cellIndices[cellIndex][0], cellIndices[cellIndex][1], "stock", initialisation) / 1000.0;
if (TrackMarineSpecifics && MarineCell)
{
bool varExists;
TotalIncomingNPP = ecosystemModelGrid.GetEnviroLayer("NPP", month, cellIndices[cellIndex][0], cellIndices[cellIndex][1], out varExists);
}
}
/// <summary>
/// Calculates the geometric community weighted mean body mass
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The list of indices of cells to be run in the current model simulation</param>
/// <param name="cellIndex">The index of the current cell within the list of cells to be run</param>
/// <returns>geometric community weighted mean body mass</returns>
public double CalculateGeometricCommunityMeanBodyMass(ModelGrid ecosystemModelGrid, List<uint[]> cellIndices, int cellIndex)
{
//Get the cohorts for the specified cell
GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
double CumulativeAbundance = 0.0;
double CumulativeLogBiomass = 0.0;
//Retrieve the biomass
foreach (var CohortList in CellCohorts)
{
foreach (Cohort c in CohortList)
{
CumulativeLogBiomass += Math.Log(c.IndividualBodyMass + c.IndividualReproductivePotentialMass) * c.CohortAbundance;
CumulativeAbundance += c.CohortAbundance;
}
}
double CWGMBM = Math.Exp(CumulativeLogBiomass / CumulativeAbundance);
return (CWGMBM);
}
/// <summary>
/// Calculates the variables to output
/// </summary>
/// <param name="ecosystemModelGrid">The model grid to get output data from</param>
/// <param name="cohortFunctionalGroupDefinitions">Definitions of the cohort functional groups in the model</param>
/// <param name="stockFunctionalGroupDefinitions">Definitions of the stock functional groups in the model</param>
/// <param name="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="cellNumber">The number of the current cell in the list of indices of active cells</param>
/// <param name="globalDiagnosticVariables">The sorted list of global diagnostic variables in the model</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
/// <param name="month">The current month in the model run</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
private void CalculateOutputs(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortFunctionalGroupDefinitions,
FunctionalGroupDefinitions stockFunctionalGroupDefinitions, List<uint[]> cellIndices, int cellNumber, SortedList<string, double>
globalDiagnosticVariables, MadingleyModelInitialisation initialisation, uint month, Boolean marineCell)
{
// Calculate low-level outputs
CalculateLowLevelOutputs(ecosystemModelGrid, cellIndices, cellNumber, globalDiagnosticVariables, cohortFunctionalGroupDefinitions,
stockFunctionalGroupDefinitions, initialisation, month, marineCell);
if (ModelOutputDetail == OutputDetailLevel.High)
{
// Calculate high-level outputs
CalculateHighLevelOutputs(ecosystemModelGrid, cellIndices, cellNumber, marineCell);
}
}
/// <summary>
/// Return the distribution of biomasses among trophic level bins
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The list of cell indices to be run in the current model simulation</param>
/// <param name="cellIndex">The index of the current cell in the list of cells to be run</param>
/// <returns>The distribution of biomasses among trophic level bins</returns>
public double[] CalculateTrophicDistribution(ModelGrid ecosystemModelGrid, List<uint[]> cellIndices, int cellIndex)
{
//Get the cohorts for the specified cell
GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
double[] TrophicIndexBinMasses = new double[NumberTrophicBins];
int BinIndex;
foreach (var CohortList in CellCohorts)
{
foreach (Cohort c in CohortList)
{
BinIndex = _TrophicIndexBinValues.ToList().IndexOf(_TrophicIndexBinValues.Last(x => x < c.TrophicIndex));
TrophicIndexBinMasses[BinIndex] += (c.IndividualBodyMass + c.IndividualReproductivePotentialMass) * c.CohortAbundance;
}
}
return TrophicIndexBinMasses;
}
/// <summary>
/// Sets up the model grid within a Madingley model run
/// </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 that this model is to run</param>
public void SetUpModelGrid(MadingleyModelInitialisation initialisation,
ScenarioParameterInitialisation scenarioParameters, int scenarioIndex, int simulation)
{
// If the intialisation file contains a column pointing to another file of specific locations, and if this column is not blank then read the
// file indicated
if (SpecificLocations)
{
// Set up the model grid using these locations
EcosystemModelGrid = new ModelGrid(BottomLatitude, LeftmostLongitude, TopLatitude, RightmostLongitude,
CellSize, CellSize, _CellList, EnviroStack, CohortFunctionalGroupDefinitions, StockFunctionalGroupDefinitions,
GlobalDiagnosticVariables, initialisation.TrackProcesses, SpecificLocations, RunGridCellsInParallel,GlobalModelTimeStepUnit);
}
else
{
_CellList = new List<uint[]>();
//Switched order so we create cell list first then initialise cells using list rather than grid.
uint NumLatCells = (uint)((TopLatitude - BottomLatitude) / CellSize);
uint NumLonCells = (uint)((RightmostLongitude - LeftmostLongitude) / CellSize);
// Loop over all cells in the model
for (uint ii = 0; ii < NumLatCells; ii += 1)
{
for (uint jj = 0; jj < NumLonCells; jj += 1)
{
// Define a vector to hold the pair of latitude and longitude indices for this grid cell
uint[] cellIndices = new uint[2];
// Add the latitude and longitude indices to this vector
cellIndices[0] = ii;
cellIndices[1] = jj;
// Add the vector to the list of all active grid cells
_CellList.Add(cellIndices);
}
}
EcologyTimer = new StopWatch();
EcologyTimer.Start();
// Set up a full model grid (i.e. not for specific locations)
// Set up the model grid using these locations
EcosystemModelGrid = new ModelGrid(BottomLatitude, LeftmostLongitude, TopLatitude, RightmostLongitude,
CellSize, CellSize, _CellList, EnviroStack, CohortFunctionalGroupDefinitions, StockFunctionalGroupDefinitions,
GlobalDiagnosticVariables, initialisation.TrackProcesses, SpecificLocations, RunGridCellsInParallel, GlobalModelTimeStepUnit);
List<int> cellsToRemove = new List<int>();
if (initialisation.RunRealm == "terrestrial")
{
for (int ii = 0; ii < _CellList.Count; ii += 1)
{
if ((EcosystemModelGrid.GetCellEnvironment(_CellList[ii][0], _CellList[ii][1])["Realm"][0] == 2.0) ||
(EcosystemModelGrid.GetCellEnvironment(_CellList[ii][0], _CellList[ii][1])["LandSeaMask"][0] == 0.0))
{
cellsToRemove.Add(ii);
}
}
}
else if (initialisation.RunRealm == "marine")
{
for (int ii = 0; ii < _CellList.Count; ii += 1)
{
if (EcosystemModelGrid.GetCellEnvironment(_CellList[ii][0], _CellList[ii][1])["Realm"][0] == 1.0)
{
cellsToRemove.Add(ii);
}
}
}
for (int ii = (cellsToRemove.Count - 1); ii >= 0; ii--)
{
_CellList.RemoveAt(cellsToRemove[ii]);
}
EcologyTimer.Stop();
Console.WriteLine("Time to initialise cells: {0}", EcologyTimer.GetElapsedTimeSecs());
Console.ForegroundColor = ConsoleColor.Red;
Console.WriteLine("Madingley Model memory usage post grid cell seed: {0}", GC.GetTotalMemory(true) / 1E9, " (G Bytes)\n");
Console.ForegroundColor = ConsoleColor.White;
}
if (initialisation.InputState)
{
InputModelState = new InputModelState(initialisation.ModelStatePath[simulation],
initialisation.ModelStateFilename[simulation],EcosystemModelGrid, _CellList);
}
// When the last simulation for the current scenario
// if ((scenarioParameters.scenarioSimulationsNumber.Count == 1) && (scenarioIndex == scenarioParameters.scenarioSimulationsNumber[scenarioIndex] - 1)) EnviroStack.Clear();
// Seed stocks and cohorts in the grid cells
// If input state from output from a previous simulation
if (initialisation.InputState)
{
// Seed grid cell cohort and stocks
EcosystemModelGrid.SeedGridCellStocksAndCohorts(_CellList, InputModelState, CohortFunctionalGroupDefinitions, StockFunctionalGroupDefinitions);
//remove cohorts that do not contain any biomass
foreach (uint[] CellPair in _CellList)
{
GridCellCohortHandler workingGridCellCohorts = EcosystemModelGrid.GetGridCellCohorts(CellPair[0], CellPair[1]);
for (int kk = 0; kk < CohortFunctionalGroupDefinitions.GetNumberOfFunctionalGroups(); kk++)
{
// Loop through each cohort in the functional group
for (int ll = (workingGridCellCohorts[kk].Count - 1); ll >= 0; ll--)
{
// If cohort abundance is less than the extinction threshold then add to the list for extinction
if (workingGridCellCohorts[kk][ll].CohortAbundance.CompareTo(0) <= 0 || workingGridCellCohorts[kk][ll].IndividualBodyMass.CompareTo(0.0) == 0)
{
// Remove the extinct cohort from the list of cohorts
workingGridCellCohorts[kk].RemoveAt(ll);
}
}
}
}
}
else
{
EcosystemModelGrid.SeedGridCellStocksAndCohorts(_CellList, CohortFunctionalGroupDefinitions, StockFunctionalGroupDefinitions,
GlobalDiagnosticVariables, ref NextCohortID, InitialisationFileStrings["OutputDetail"] == "high", DrawRandomly,
initialisation.DispersalOnly, InitialisationFileStrings["DispersalOnlyType"], RunGridCellsInParallel);
}
Console.ForegroundColor = ConsoleColor.Red;
Console.WriteLine("Madingley Model memory usage pre Collect: {0}", Math.Round(GC.GetTotalMemory(true) / 1E9, 2), " (GBytes)");
Console.ForegroundColor = ConsoleColor.White;
GC.Collect();
Console.ForegroundColor = ConsoleColor.Red;
Console.WriteLine("Madingley Model memory usage post Collect: {0}", Math.Round(GC.GetTotalMemory(true) / 1E9, 5), " (GBytes)\n");
Console.ForegroundColor = ConsoleColor.White;
}
/// <summary>
/// Record dispersal events in the dispersal tracker
/// </summary>
/// <param name="inboundCohorts">The cohorts arriving in a cell in the current time step</param>
/// <param name="outboundCohorts">The cohorts leaving a cell in the current time step</param>
/// <param name="outboundCohortWeights">The body masses of cohorts leaving the cell in the current time step</param>
/// <param name="timestep">The current model time step</param>
/// <param name="madingleyModelGrid">The model grid</param>
public void RecordDispersalForACell(uint[, ,] inboundCohorts, uint[, ,] outboundCohorts, List <double>[,] outboundCohortWeights, uint timestep, ModelGrid madingleyModelGrid)
{
var count = inboundCohorts.GetLength(0) * inboundCohorts.GetLength(1);
var copy = new Madingley.Common.GridCellDispersal[count];
for (var kk = 0; kk < count; kk++)
{
var ii = (int)kk / inboundCohorts.GetLength(1);
var jj = kk % inboundCohorts.GetLength(1);
var denter =
new Tuple <Madingley.Common.CohortsEnterDirection, int>[]
{
Tuple.Create(Madingley.Common.CohortsEnterDirection.North, (int)inboundCohorts[ii, jj, 0]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.NorthEast, (int)inboundCohorts[ii, jj, 1]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.East, (int)inboundCohorts[ii, jj, 2]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.SouthEast, (int)inboundCohorts[ii, jj, 3]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.South, (int)inboundCohorts[ii, jj, 4]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.SouthWest, (int)inboundCohorts[ii, jj, 5]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.West, (int)inboundCohorts[ii, jj, 6]),
Tuple.Create(Madingley.Common.CohortsEnterDirection.NorthWest, (int)inboundCohorts[ii, jj, 7]),
};
var enter = denter.ToDictionary(l => l.Item1, l => l.Item2);
var dexit =
new Tuple <Madingley.Common.CohortsExitDirection, int>[]
{
Tuple.Create(Madingley.Common.CohortsExitDirection.North, (int)outboundCohorts[ii, jj, 0]),
Tuple.Create(Madingley.Common.CohortsExitDirection.NorthEast, (int)outboundCohorts[ii, jj, 1]),
Tuple.Create(Madingley.Common.CohortsExitDirection.East, (int)outboundCohorts[ii, jj, 2]),
Tuple.Create(Madingley.Common.CohortsExitDirection.SouthEast, (int)outboundCohorts[ii, jj, 3]),
Tuple.Create(Madingley.Common.CohortsExitDirection.South, (int)outboundCohorts[ii, jj, 4]),
Tuple.Create(Madingley.Common.CohortsExitDirection.SouthWest, (int)outboundCohorts[ii, jj, 5]),
Tuple.Create(Madingley.Common.CohortsExitDirection.West, (int)outboundCohorts[ii, jj, 6]),
Tuple.Create(Madingley.Common.CohortsExitDirection.NorthWest, (int)outboundCohorts[ii, jj, 7]),
};
var exit = dexit.ToDictionary(l => l.Item1, l => l.Item2);
var weights = outboundCohortWeights[ii, jj].ToArray();
var cell = madingleyModelGrid.GetGridCell((uint)ii, (uint)jj);
var ccell = Converters.ConvertCellData(cell);
copy[kk] = new Madingley.Common.GridCellDispersal(enter, exit, weights, ccell);
}
this.GridCellDispersals = copy;
}
public void SetupOutputs(ModelGrid ecosystemModelGrid, string outputFilesSuffix, uint numTimeSteps,
FunctionalGroupDefinitions cohortFunctionalGroupDefinitions, FunctionalGroupDefinitions
stockFunctionalGroupDefinitions)
{
// Create an SDS object to hold grid outputs
GridOutput = SDSCreator.CreateSDS("netCDF", "GridOutputs" + outputFilesSuffix, _OutputPath);
// Initilalise trait-based outputs
InitialiseTraitBasedOutputs(cohortFunctionalGroupDefinitions, stockFunctionalGroupDefinitions);
// Create vector to hold the values of the time dimension
TimeSteps = new float[numTimeSteps + 1];
// Set the first value to be 0 (this will hold initial outputs)
TimeSteps[0] = 0;
// Fill other values from 0 (this will hold outputs during the model run)
for (int i = 1; i < numTimeSteps + 1; i++)
{
TimeSteps[i] = i;
}
// Declare vectors for geographical dimension data
float[] outLats = new float[ecosystemModelGrid.NumLatCells];
float[] outLons = new float[ecosystemModelGrid.NumLonCells];
// Populate the dimension variable vectors with cell centre latitude and longitudes
for (int i = 0; i < ecosystemModelGrid.NumLatCells; i++)
{
outLats[i] = ecosystemModelGrid.Lats[i] + (ecosystemModelGrid.LatCellSize / 2);
}
for (int jj = 0; jj < ecosystemModelGrid.NumLonCells; jj++)
{
outLons[jj] = ecosystemModelGrid.Lons[jj] + (ecosystemModelGrid.LonCellSize / 2);
}
//GridOutputArray = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells, numTimeSteps];
// Add output variables that are dimensioned geographically and temporally to grid output file
string[] GeographicalDimensions = { "Latitude", "Longitude", "Time step" };
DataConverter.AddVariable(GridOutput, "Biomass density", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Abundance density", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
// Initialise the arrays that will be used for the grid-based outputs
LogBiomassDensityGridCohorts = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
LogBiomassDensityGridStocks = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
LogBiomassDensityGrid = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
LogAbundanceDensityGridCohorts = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
FrostDays = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
FracEvergreen = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
Realm = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
HANPP = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
Temperature = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
// Temporary outputs for checking plant model
DataConverter.AddVariable(GridOutput, "Fraction year frost", 3, GeographicalDimensions, ecosystemModelGrid.GlobalMissingValue, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Fraction evergreen", 3, GeographicalDimensions, ecosystemModelGrid.GlobalMissingValue, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Realm", 3, GeographicalDimensions, ecosystemModelGrid.GlobalMissingValue, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "HANPP", 3, GeographicalDimensions, ecosystemModelGrid.GlobalMissingValue, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Temperature", 3, GeographicalDimensions, ecosystemModelGrid.GlobalMissingValue, outLats, outLons, TimeSteps);
// Set up outputs for medium or high output levels
if ((ModelOutputDetail == OutputDetailLevel.Medium) || (ModelOutputDetail == OutputDetailLevel.High))
{
double[,] temp = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
foreach (string TraitValue in CohortTraitIndices.Keys)
{
BiomassDensityGrid.Add(TraitValue, temp);
DataConverter.AddVariable(GridOutput, TraitValue + "biomass density", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
AbundanceDensityGrid.Add(TraitValue, temp);
DataConverter.AddVariable(GridOutput, TraitValue + "abundance density", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
}
foreach (string TraitValue in StockTraitIndices.Keys)
{
BiomassDensityGrid.Add(TraitValue, temp);
DataConverter.AddVariable(GridOutput, TraitValue + "biomass density", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
}
if (OutputMetrics)
{
double[,] MTL = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Mean Trophic Level", MTL);
double[,] TE = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Trophic Evenness", TE);
double[,] BE = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Biomass Evenness", BE);
double[,] FR = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Functional Richness", FR);
double[,] RFE = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Rao Functional Evenness", RFE);
double[,] BR = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Biomass Richness", BR);
double[,] TR = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Trophic Richness", TR);
double[,] Bmax = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Max Bodymass", Bmax);
double[,] Bmin = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Min Bodymass", Bmin);
double[,] TImax = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Max Trophic Index", TImax);
double[,] TImin = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Min Trophic Index", TImin);
double[,] ArithMean = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Arithmetic Mean Bodymass", ArithMean);
double[,] GeomMean = new double[ecosystemModelGrid.NumLatCells, ecosystemModelGrid.NumLonCells];
MetricsGrid.Add("Geometric Mean Bodymass", GeomMean);
DataConverter.AddVariable(GridOutput, "Mean Trophic Level", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Trophic Evenness", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Biomass Evenness", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Functional Richness", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Rao Functional Evenness", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Biomass Richness", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Trophic Richness", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Max Bodymass", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Min Bodymass", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Max Trophic Index", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Min Trophic Index", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Arithmetic Mean Bodymass", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
DataConverter.AddVariable(GridOutput, "Geometric Mean Bodymass", 3, GeographicalDimensions, 0, outLats, outLons, TimeSteps);
}
}
}
/// <summary>
/// Sets up the outputs associated with the high level of output detail
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The indices of active cells in the model grid</param>
/// <param name="cellNumber">The index of the current cell in the list of active cells</param>
/// <param name="cohortFunctionalGroupDefinitions">The functional group definitions for cohorts in the model</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
private void SetUpHighLevelOutputs(ModelGrid ecosystemModelGrid, List<uint[]> cellIndices, int cellNumber,
FunctionalGroupDefinitions cohortFunctionalGroupDefinitions, Boolean marineCell)
{
// Create an SDS object for outputs by mass bin
// MassBinsOutput = SDSCreator.CreateSDS("netCDF", "MassBins" + _OutputSuffix, _OutputPath);
MassBinsOutputMemory = SDSCreator.CreateSDSInMemory(true);
// Add relevant output variables to the mass bin output file
string[] MassBinDimensions = { "Time step", "Mass bin" };
string[] DoubleMassBinDimensions = new string[] { "Adult Mass bin", "Juvenile Mass bin", "Time step" };
if (OutputMetrics)
{
DataConverter.AddVariable(MassBinsOutputMemory, "Trophic Index Distribution", 2, new string[] {"Time step","Trophic Index Bins"}, ecosystemModelGrid.GlobalMissingValue, TimeSteps, Metrics.TrophicIndexBinValues);
}
if (marineCell)
{
foreach (string TraitValue in CohortTraitIndicesMarine.Keys)
{
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValue + " abundance in mass bins", 2, MassBinDimensions, ecosystemModelGrid.GlobalMissingValue, TimeSteps, MassBins);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValue + " biomass in mass bins", 2, MassBinDimensions, ecosystemModelGrid.GlobalMissingValue, TimeSteps, MassBins);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValue + " abundance in juvenile vs adult bins", 3, DoubleMassBinDimensions, ecosystemModelGrid.GlobalMissingValue, MassBins, MassBins, TimeSteps);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValue + " biomass in juvenile vs adult bins", 3, DoubleMassBinDimensions, ecosystemModelGrid.GlobalMissingValue, MassBins, MassBins, TimeSteps);
}
}
else
{
foreach (string TraitValue in CohortTraitIndices.Keys)
{
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValue + " abundance in mass bins", 2, MassBinDimensions, ecosystemModelGrid.GlobalMissingValue, TimeSteps, MassBins);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValue + " biomass in mass bins", 2, MassBinDimensions, ecosystemModelGrid.GlobalMissingValue, TimeSteps, MassBins);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValue + " abundance in juvenile vs adult bins", 3, DoubleMassBinDimensions, ecosystemModelGrid.GlobalMissingValue, MassBins, MassBins, TimeSteps);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValue + " biomass in juvenile vs adult bins", 3, DoubleMassBinDimensions, ecosystemModelGrid.GlobalMissingValue, MassBins, MassBins, TimeSteps);
}
}
// Create an SDS object in memory for tracked cohorts outputs
// TrackedCohortsOutput = SDSCreator.CreateSDS("netCDF", "TrackedCohorts" + _OutputSuffix, _OutputPath);
TrackedCohortsOutputMemory = SDSCreator.CreateSDSInMemory(true);
// Initialise list to hold tracked cohorts
TrackedCohorts = new List<uint>();
// Identify cohorts to track
GridCellCohortHandler TempCohorts = null;
bool FoundCohorts = false;
// Get a local copy of the cohorts in the grid cell
TempCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellNumber][0], cellIndices[cellNumber][1]);
// Loop over functional groups and check whether any cohorts exist in this grid cell
foreach (var CohortList in TempCohorts)
{
if (CohortList.Count > 0)
{
FoundCohorts = true;
break;
}
}
// If there are some cohorts in the grid cell, then setup the tracked cohorts
if (FoundCohorts)
{
// Initialise stream writer to hold details of tracked cohorts
StreamWriter sw = new StreamWriter(_OutputPath + "TrackedCohortProperties" + _OutputSuffix + ".txt");
sw.WriteLine("Output ID\tCohort ID\tFunctional group index\tNutrition source\tDiet\tRealm\tMobility\tJuvenile mass\tAdult mass");
// Counter for tracked cohorts
int TrackedCohortCounter = 0;
for (int i = 0; i < TempCohorts.Count; i++)
{
if (TempCohorts[i].Count > 0)
{
for (int j = 0; j < TempCohorts[i].Count; j++)
{
// Write out properties of the selected cohort
sw.WriteLine(Convert.ToString(TrackedCohortCounter) + '\t' + Convert.ToString(TempCohorts[i][j].CohortID[0]) + '\t' + i + '\t' +
cohortFunctionalGroupDefinitions.GetTraitNames("Nutrition source", i) + '\t' + cohortFunctionalGroupDefinitions.
GetTraitNames("Diet", i) + '\t' + cohortFunctionalGroupDefinitions.GetTraitNames("Realm", i) + '\t' +
cohortFunctionalGroupDefinitions.GetTraitNames("Mobility", i) + '\t' + TempCohorts[i][j].JuvenileMass + '\t' +
TempCohorts[i][j].AdultMass);
// Add the ID of the cohort to the list of tracked cohorts
TrackedCohorts.Add(TempCohorts[i][j].CohortID[0]);
// Increment the counter of tracked cohorts
TrackedCohortCounter++;
}
}
}
// Generate an array of floating points to index the tracked cohorts in the output file
float[] OutTrackedCohortIDs = new float[TrackedCohortCounter];
for (int i = 0; i < TrackedCohortCounter; i++)
{
OutTrackedCohortIDs[i] = i;
}
// Set up outputs for tracked cohorts
string[] TrackedCohortsDimensions = { "Time step", "Cohort ID" };
// Add output variables for the tracked cohorts output
DataConverter.AddVariable(TrackedCohortsOutputMemory, "Individual body mass", 2, TrackedCohortsDimensions,
ecosystemModelGrid.GlobalMissingValue, TimeSteps, OutTrackedCohortIDs);
DataConverter.AddVariable(TrackedCohortsOutputMemory, "Number of individuals", 2, TrackedCohortsDimensions,
ecosystemModelGrid.GlobalMissingValue, TimeSteps, OutTrackedCohortIDs);
// Dispose of the streamwriter
sw.Dispose();
}
// Get a list of all possible combinations of trait values as a jagged array
string[][] TraitValueSearch;
if (marineCell)
TraitValueSearch = CalculateAllCombinations(CohortTraitValuesMarine[CohortTraits[0]], CohortTraitValuesMarine[CohortTraits[1]]);
else
TraitValueSearch = CalculateAllCombinations(CohortTraitValues[CohortTraits[0]], CohortTraitValues[CohortTraits[1]]);
// Add the functional group indices of these trait combinations to the list of indices of the trait values to consider,
// keyed with a concatenated version of the trait values
string TraitValueJoin = "";
string[] TimeDimension = { "Time step" };
for (int i = 0; i < TraitValueSearch.Count(); i++)
{
TraitValueJoin = "";
foreach (string TraitValue in TraitValueSearch[i])
{
TraitValueJoin += TraitValue + " ";
}
if (marineCell)
{
// Only add indices of marine functional groups
int[] TempIndices = cohortFunctionalGroupDefinitions.GetFunctionalGroupIndex(CohortTraits, TraitValueSearch[i], true);
Boolean[] TempIndices2 = new Boolean[TempIndices.GetLength(0)];
for (int ii = 0; ii < TempIndices.GetLength(0); ii++)
{
if (cohortFunctionalGroupDefinitions.GetTraitNames("Realm", TempIndices[ii]).Equals("Marine", StringComparison.OrdinalIgnoreCase))
{
TempIndices2[ii] = true;
}
}
// Extract only the indices which are marine
int[] TempIndices3 = Enumerable.Range(0, TempIndices2.Length).Where(zz => TempIndices2[zz]).ToArray();
if (TempIndices3.Length > 0)
{
// Extract the values at these indices
for (int ii = 0; ii < TempIndices3.Length; ii++)
{
TempIndices3[ii] = TempIndices[TempIndices3[ii]];
}
// Add in the indices for this functional group and this realm
CohortTraitIndices.Add(TraitValueJoin, TempIndices3);
DataConverter.AddVariable(BasicOutputMemory, TraitValueJoin + " density", "Individuals / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, TraitValueJoin + " biomass density", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValueJoin + " abundance in mass bins", 2, MassBinDimensions, ecosystemModelGrid.GlobalMissingValue, TimeSteps, MassBins);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValueJoin + " biomass in mass bins", 2, MassBinDimensions, ecosystemModelGrid.GlobalMissingValue, TimeSteps, MassBins);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValueJoin + " abundance in juvenile vs adult bins", 3, DoubleMassBinDimensions, ecosystemModelGrid.GlobalMissingValue, MassBins, MassBins, TimeSteps);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValueJoin + " biomass in juvenile vs adult bins", 3, DoubleMassBinDimensions, ecosystemModelGrid.GlobalMissingValue, MassBins, MassBins, TimeSteps);
TotalBiomassDensitiesOut.Add(TraitValueJoin, 0.0);
TotalDensitiesOut.Add(TraitValueJoin, 0.0);
}
}
else
{
// Only add indices of terrestrial functional groups
int[] TempIndices = cohortFunctionalGroupDefinitions.GetFunctionalGroupIndex(CohortTraits, TraitValueSearch[i], true);
Boolean[] TempIndices2 = new Boolean[TempIndices.GetLength(0)];
for (int ii = 0; ii < TempIndices.GetLength(0); ii++)
{
if (cohortFunctionalGroupDefinitions.GetTraitNames("Realm", TempIndices[ii]).Equals("Terrestrial", StringComparison.OrdinalIgnoreCase))
{
TempIndices2[ii] = true;
}
}
// Extract only the indices which are terrestrial
int[] TempIndices3 = Enumerable.Range(0, TempIndices2.Length).Where(zz => TempIndices2[zz]).ToArray();
if (TempIndices3.Length > 0)
{
// Extract the values at these indices
for (int ii = 0; ii < TempIndices3.Length; ii++)
{
TempIndices3[ii] = TempIndices[TempIndices3[ii]];
}
// Add in the indices for this functional group and this realm
CohortTraitIndices.Add(TraitValueJoin, TempIndices3);
DataConverter.AddVariable(BasicOutputMemory, TraitValueJoin + " density", "Individuals / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, TraitValueJoin + " biomass density", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValueJoin + " abundance in mass bins", 2, MassBinDimensions, ecosystemModelGrid.GlobalMissingValue, TimeSteps, MassBins);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValueJoin + " biomass in mass bins", 2, MassBinDimensions, ecosystemModelGrid.GlobalMissingValue, TimeSteps, MassBins);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValueJoin + " abundance in juvenile vs adult bins", 3, DoubleMassBinDimensions, ecosystemModelGrid.GlobalMissingValue, MassBins, MassBins, TimeSteps);
DataConverter.AddVariable(MassBinsOutputMemory, "Log " + TraitValueJoin + " biomass in juvenile vs adult bins", 3, DoubleMassBinDimensions, ecosystemModelGrid.GlobalMissingValue, MassBins, MassBins, TimeSteps);
TotalBiomassDensitiesOut.Add(TraitValueJoin, 0.0);
TotalDensitiesOut.Add(TraitValueJoin, 0.0);
}
}
}
}
/// <summary>
/// Record dispersal events in the dispersal tracker
/// </summary>
/// <param name="inboundCohorts">The cohorts arriving in a grid cell in the current time step</param>
/// <param name="outboundCohorts">The cohorts leaving a ce ll in the current time step</param>
/// <param name="outboundCohortWeights">The body masses of cohorts leaving the cell in the current time step</param>
/// <param name="currentTimeStep">The current model time step</param>
/// <param name="madingleyModelGrid">The model grid</param>
public void RecordDispersal(uint[, ,] inboundCohorts, uint[, ,] outboundCohorts, List <double>[,] outboundCohortWeights, uint currentTimeStep, ModelGrid madingleyModelGrid)
{
// Loop through cells in the grid and write out the necessary data
for (uint ii = 0; ii < outboundCohorts.GetLength(0); ii++)
{
for (uint jj = 0; jj < outboundCohorts.GetLength(1); jj++)
{
double MeanOutboundCohortWeight = new double();
// Calculate the mean weight of outbound cohorts (ignoring abundance)
if (outboundCohortWeights[ii, jj].Count == 0)
{
MeanOutboundCohortWeight = 0.0;
}
else
{
MeanOutboundCohortWeight = outboundCohortWeights[ii, jj].Average();
}
// Calculate the mean weight of all cohorts (ignoring abundance)
List <double> TempList = new List <double>();
GridCellCohortHandler Temp1 = madingleyModelGrid.GetGridCellCohorts(ii, jj);
// Loop through functional groups
for (int kk = 0; kk < Temp1.Count; kk++)
{
// Loop through cohorts
for (int hh = 0; hh < Temp1[kk].Count; hh++)
{
// Add the cohort weight to the list
TempList.Add(Temp1[kk][hh].IndividualBodyMass);
}
}
// Calculate the mean weight
double MeanCohortWeight = new double();
if (TempList.Count == 0)
{
MeanCohortWeight = 0.0;
}
else
{
MeanCohortWeight = TempList.Average();
}
string newline = Convert.ToString(currentTimeStep) + '\t' + Convert.ToString(ii) + '\t' +
Convert.ToString(jj) + '\t' + Convert.ToString(madingleyModelGrid.GetCellLatitude(ii)) + '\t' +
Convert.ToString(madingleyModelGrid.GetCellLongitude(jj)) + '\t' +
Convert.ToString(outboundCohorts[ii, jj, 0]) + '\t' + Convert.ToString(outboundCohorts[ii, jj, 1]) + '\t' +
Convert.ToString(outboundCohorts[ii, jj, 2]) + '\t' + Convert.ToString(outboundCohorts[ii, jj, 3]) + '\t' +
Convert.ToString(outboundCohorts[ii, jj, 4]) + '\t' + Convert.ToString(outboundCohorts[ii, jj, 5]) + '\t' +
Convert.ToString(outboundCohorts[ii, jj, 6]) + '\t' + Convert.ToString(outboundCohorts[ii, jj, 7]) + '\t' +
Convert.ToString(inboundCohorts[ii, jj, 0]) + '\t' + Convert.ToString(inboundCohorts[ii, jj, 1]) + '\t' +
Convert.ToString(inboundCohorts[ii, jj, 2]) + '\t' + Convert.ToString(inboundCohorts[ii, jj, 3]) + '\t' +
Convert.ToString(inboundCohorts[ii, jj, 4]) + '\t' + Convert.ToString(inboundCohorts[ii, jj, 5]) + '\t' +
Convert.ToString(inboundCohorts[ii, jj, 6]) + '\t' + Convert.ToString(inboundCohorts[ii, jj, 7]) + '\t' +
Convert.ToString(String.Format("{0:.000000}", MeanOutboundCohortWeight) + '\t' +
Convert.ToString(String.Format("{0:.000000}", MeanCohortWeight)));
SyncedDispersalWriter.WriteLine(newline);
}
}
}
/// <summary>
/// Sets up the outputs associated with all levels of output detail
/// </summary>
/// <param name="numTimeSteps">The number of time steps in the model run</param>
/// <param name="ecosystemModelGrid">The model grid</param>
private void SetUpLowLevelOutputs(uint numTimeSteps, ModelGrid ecosystemModelGrid)
{
// Create an SDS object to hold total abundance and biomass data
// BasicOutput = SDSCreator.CreateSDS("netCDF", "BasicOutputs" + _OutputSuffix, _OutputPath);
BasicOutputMemory = SDSCreator.CreateSDSInMemory(true);
string[] TimeDimension = { "Time step" };
DataConverter.AddVariable(BasicOutputMemory, "Total Biomass density", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Heterotroph Abundance density", "Individuals / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
DataConverter.AddVariable(BasicOutputMemory, "Heterotroph Biomass density", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
}
/// <summary>
/// Calculates functional diversity of cohorts in a grid cell as functional richness and functional diveregence (using the Rao Index)
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cohortDefinitions">The functional group definitions for cohorts in the model</param>
/// <param name="cellIndices">The list of cell indices in the current model simulation</param>
/// <param name="cellIndex">The index of the current cell within the list of cells to run</param>
/// <returns>A pair of values representing the functional richness and functional divergence (functional richness currently disabled!)</returns>
public double[] CalculateFunctionalDiversity(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortDefinitions,
List<uint[]> cellIndices, int cellIndex)
{
//Get the cohorts for the specified cell
GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
//Variable to hold the functional richness value for the current cohorts
double FunctionalRichness;
//Variable to hold the functional divergence value for the current cohorts
double RaoFunctionalDivergence = 0.0;
double[,] Distances= new double[CellCohorts.GetNumberOfCohorts(), CellCohorts.GetNumberOfCohorts()];
List<string> AllTraitNames = cohortDefinitions.GetAllTraitNames().ToList();
AllTraitNames.Remove("realm");
AllTraitNames.Remove("heterotroph/autotroph");
AllTraitNames.Remove("diet");
string[] TraitNames = AllTraitNames.ToArray();
//Define upper and lower limits for body mass
double MinMass = cohortDefinitions.GetBiologicalPropertyAllFunctionalGroups("minimum mass").Min();
double MaxMass = cohortDefinitions.GetBiologicalPropertyAllFunctionalGroups("maximum mass").Max();
//Define upp and lower limits for trophic index
double MaxTI = 40.0;
double MinTI = 1.0;
// Construct an array of functional trait values for each cohort
// Rows are specific cohorts
// Columns are the functional traits (these include different types:
// quantative: current mass, trophic index
// nominal: diet, reproductive strategy, mobility, metabolism
Tuple<double[], string[]>[] CohortFunctionalTraits = new Tuple<double[], string[]>[CellCohorts.GetNumberOfCohorts()];
double[] IndividualBodyMasses = new double[CellCohorts.GetNumberOfCohorts()];
double[] TrophicIndex = new double[CellCohorts.GetNumberOfCohorts()];
string[][] CohortNominalTraitValues= new string[TraitNames.Length][];
for (int i = 0; i < TraitNames.Length; i++)
{
CohortNominalTraitValues[i] = new string[CellCohorts.GetNumberOfCohorts()];
}
// Construct a vector of cohort biomass (in case we want to weight by them)
double[] CohortTotalBiomasses = new double[CellCohorts.GetNumberOfCohorts()];
string[] TraitValues = new string[TraitNames.Length];
double[] QuantitativeTraitValues= new double[2];
int CohortNumberCounter = 0;
for (int fg = 0; fg < CellCohorts.Count; fg++)
{
foreach (Cohort c in CellCohorts[fg])
{
TraitValues = cohortDefinitions.GetTraitValues(TraitNames, fg);
for (int ii = 0; ii < TraitValues.Length; ii++)
{
CohortNominalTraitValues[ii][CohortNumberCounter] = TraitValues[ii];
}
IndividualBodyMasses[CohortNumberCounter] = c.IndividualBodyMass;
TrophicIndex[CohortNumberCounter] = c.TrophicIndex;
QuantitativeTraitValues[0] = c.IndividualBodyMass;
QuantitativeTraitValues[1] = c.TrophicIndex;
CohortFunctionalTraits[CohortNumberCounter] = new Tuple<double[], string[]>(QuantitativeTraitValues, TraitValues);
CohortTotalBiomasses[CohortNumberCounter] = (c.IndividualBodyMass + c.IndividualReproductivePotentialMass) * c.CohortAbundance;
CohortNumberCounter++;
}
}
List<double[,]> DistanceList = new List<double[,]>();
DistanceList.Add(CalculateDistanceMatrix(IndividualBodyMasses, MaxMass, MinMass));
DistanceList.Add(CalculateDistanceMatrix(TrophicIndex, MaxTI, MinTI));
foreach (string[] t in CohortNominalTraitValues)
{
DistanceList.Add(CalculateDistanceMatrix(t));
}
Distances = CalculateAggregateDistance(DistanceList);
RaoFunctionalDivergence = RaoEntropy(Distances, CohortTotalBiomasses);
return new double[] {0.0,RaoFunctionalDivergence};
}
public void OutputCurrentModelState(ModelGrid currentModelGrid, List <uint[]> cellIndices, uint currentTimestep)
{
GridCellCohortHandler TempCohorts;
GridCellStockHandler TempStocks;
string context;
string organism;
context = Convert.ToString(currentTimestep) + "\t";
using (var StateWriter = File.AppendText(this.FileName))
{
foreach (uint[] cell in cellIndices)
{
context = Convert.ToString(currentTimestep) + "\t" +
Convert.ToString(currentModelGrid.GetCellLatitude(cell[0])) + "\t" +
Convert.ToString(currentModelGrid.GetCellLongitude(cell[1])) + "\t";
TempStocks = currentModelGrid.GetGridCellStocks(cell[0], cell[1]);
TempCohorts = currentModelGrid.GetGridCellCohorts(cell[0], cell[1]);
foreach (List <Stock> ListS in TempStocks)
{
foreach (Stock S in ListS)
{
organism = "-999\tS" + Convert.ToString(S.FunctionalGroupIndex) + "\t" +
"-999\t-999\t" + Convert.ToString(S.IndividualBodyMass) + "\t" +
Convert.ToString(S.TotalBiomass / S.IndividualBodyMass) + "\t" +
"-999\t-999\t-999\t-999\t-999\t-999";
StateWriter.WriteLine(context + organism);
}
}
foreach (List <Cohort> ListC in TempCohorts)
{
foreach (Cohort C in ListC)
{
#if true
var cohortIds = C.CohortID.Select(id => Convert.ToString(id));
organism = String.Join(";", cohortIds) + "\t" +
#else
organism = Convert.ToString(C.CohortID) + "\t" +
#endif
Convert.ToString(C.FunctionalGroupIndex) + "\t" +
Convert.ToString(C.JuvenileMass) + "\t" +
Convert.ToString(C.AdultMass) + "\t" +
Convert.ToString(C.IndividualBodyMass) + "\t" +
Convert.ToString(C.CohortAbundance) + "\t" +
Convert.ToString(C.BirthTimeStep) + "\t" +
Convert.ToString(C.MaturityTimeStep) + "\t" +
Convert.ToString(C.LogOptimalPreyBodySizeRatio) + "\t" +
Convert.ToString(C.MaximumAchievedBodyMass) + "\t" +
Convert.ToString(C.TrophicIndex) + "\t" +
Convert.ToString(C.ProportionTimeActive);
StateWriter.WriteLine(context + organism);
}
}
}
}
}
public double[] CalculateFunctionalRichness(ModelGrid ecosystemModelGrid, FunctionalGroupDefinitions cohortDefinitions,
List<uint[]> cellIndices, int cellIndex, string trait)
{
//Get the cohorts for the specified cell
GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
double MinCurrentTraitValue = double.MaxValue;
double MaxCurrentTraitValue = double.MinValue;
double MinModelTraitValue = 0.0;
double MaxModelTraitValue = 0.0;
switch (trait.ToLower())
{
case "biomass":
foreach (var CohortList in CellCohorts)
{
foreach (var cohort in CohortList)
{
if (cohort.IndividualBodyMass < MinCurrentTraitValue) MinCurrentTraitValue = cohort.IndividualBodyMass;
if (cohort.IndividualBodyMass > MaxCurrentTraitValue) MaxCurrentTraitValue = cohort.IndividualBodyMass;
}
}
//Define upper and lower limits for body mass
MinModelTraitValue = cohortDefinitions.GetBiologicalPropertyAllFunctionalGroups("minimum mass").Min();
MaxModelTraitValue = cohortDefinitions.GetBiologicalPropertyAllFunctionalGroups("maximum mass").Max();
break;
case "trophic index":
foreach (var CohortList in CellCohorts)
{
foreach (var cohort in CohortList)
{
if (cohort.TrophicIndex < MinCurrentTraitValue) MinCurrentTraitValue = cohort.TrophicIndex;
if (cohort.TrophicIndex > MaxCurrentTraitValue) MaxCurrentTraitValue = cohort.TrophicIndex;
}
}
//Define upper and lower limits for body mass
MinModelTraitValue = MinTI;
MaxModelTraitValue = MaxTI;
break;
default:
Debug.Fail("Trait not recognised in calculation of ecosystem metrics: " + trait);
break;
}
Debug.Assert((MaxModelTraitValue - MinModelTraitValue) > 0.0, "Division by zero or negative model trait values in calculation of functional richness");
double[] NewArray = {(MaxCurrentTraitValue-MinCurrentTraitValue)/(MaxModelTraitValue-MinModelTraitValue),MinCurrentTraitValue,MaxCurrentTraitValue};
return NewArray;
}
/// <summary>
/// Set up the file, screen and live outputs prior to the model run
/// </summary>
/// <param name="EcosystemModelGrid">The model grid that output data will be derived from</param>
/// <param name="CohortFunctionalGroupDefinitions">The definitions for cohort functional groups</param>
/// <param name="StockFunctionalGroupDefinitions">The definitions for stock functional groups</param>
/// <param name="NumTimeSteps">The number of time steps in the model run</param>
public void SetUpOutputs(ModelGrid EcosystemModelGrid, FunctionalGroupDefinitions CohortFunctionalGroupDefinitions,
FunctionalGroupDefinitions StockFunctionalGroupDefinitions, uint NumTimeSteps, string FileOutputs)
{
// Get the functional group indices of herbivore, carnivore and omnivore cohorts, and autotroph stocks
string[] Trait = { "Nutrition source" };
string[] Trait2 = { "Heterotroph/Autotroph" };
string[] TraitValue1 = { "Herbivory" };
string[] TraitValue2 = { "Carnivory" };
string[] TraitValue3 = { "Omnivory" };
string[] TraitValue4 = { "Autotroph" };
HerbivoreIndices = CohortFunctionalGroupDefinitions.GetFunctionalGroupIndex(Trait, TraitValue1, false);
CarnivoreIndices = CohortFunctionalGroupDefinitions.GetFunctionalGroupIndex(Trait, TraitValue2, false);
OmnivoreIndices = CohortFunctionalGroupDefinitions.GetFunctionalGroupIndex(Trait, TraitValue3, false);
AutotrophIndices = StockFunctionalGroupDefinitions.GetFunctionalGroupIndex(Trait2, TraitValue4, false);
// Set up vectors to hold dimension data for the output variables
float[] outLats = new float[EcosystemModelGrid.NumLatCells];
float[] outLons = new float[EcosystemModelGrid.NumLonCells];
float[] IdentityMassBins;
// Populate the dimension variable vectors with cell centre latitude and longitudes
for (int ii = 0; ii < EcosystemModelGrid.NumLatCells; ii++)
{
outLats[ii] = EcosystemModelGrid.Lats[ii] + (EcosystemModelGrid.LatCellSize / 2);
}
for (int jj = 0; jj < EcosystemModelGrid.NumLonCells; jj++)
{
outLons[jj] = EcosystemModelGrid.Lons[jj] + (EcosystemModelGrid.LonCellSize / 2);
}
// Create vector to hold the values of the time dimension
OutTimes = new float[NumTimeSteps + 1];
// Set the first value to be -1 (this will hold initial outputs)
OutTimes[0] = -1;
// Fill other values from 0 (this will hold outputs during the model run)
for (int ii = 1; ii < NumTimeSteps + 1; ii++)
{
OutTimes[ii] = ii + 1;
}
// Set up a vector to hold (log) individual body mass bins
OutMassBins = new float[MassBinNumber];
IdentityMassBins = new float[MassBinNumber];
// Get the (log) minimum and maximum possible (log) masses across all functional groups combined, start with default values of
// Infinity and -Infinity
float MaximumMass = -1 / 0F;
float MinimumMass = 1 / 0F;
foreach (int FunctionalGroupIndex in CohortFunctionalGroupDefinitions.AllFunctionalGroupsIndex)
{
MinimumMass = (float)Math.Min(MinimumMass, Math.Log(CohortFunctionalGroupDefinitions.GetBiologicalPropertyOneFunctionalGroup("minimum mass", FunctionalGroupIndex)));
MaximumMass = (float)Math.Max(MaximumMass, Math.Log(CohortFunctionalGroupDefinitions.GetBiologicalPropertyOneFunctionalGroup("maximum mass", FunctionalGroupIndex)));
}
// Get the interval required to span the range between the minimum and maximum values in 100 steps
float MassInterval = (MaximumMass - MinimumMass) / MassBinNumber;
// Fill the vector of output mass bins with (log) body masses spread evenly between the minimum and maximum values
for (int ii = 0; ii < MassBinNumber; ii++)
{
OutMassBins[ii] = MinimumMass + ii * MassInterval;
IdentityMassBins[ii] = Convert.ToSingle(Math.Exp(Convert.ToDouble(OutMassBins[ii])));
}
// Create file for model outputs
DataSetForFileOutput = CreateSDSObject.CreateSDS("netCDF", FileOutputs);
// Add three-dimensional variables to output file, dimensioned by latitude, longtiude and time
string[] dimensions3D = { "Latitude", "Longitude", "Time step" };
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Biomass density", 3, dimensions3D, 0, outLats, outLons, OutTimes);
dimensions3D = new string[] { "Adult Mass bin", "Juvenile Mass bin", "Time step" };
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Log Carnivore abundance in juvenile vs adult bins", 3, dimensions3D,Math.Log(0), OutMassBins, OutMassBins, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Log Herbivore abundance in juvenile vs adult bins", 3, dimensions3D, Math.Log(0), OutMassBins, OutMassBins, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Log Carnivore biomass in juvenile vs adult bins", 3, dimensions3D, Math.Log(0), OutMassBins, OutMassBins, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Log Herbivore biomass in juvenile vs adult bins", 3, dimensions3D, Math.Log(0), OutMassBins, OutMassBins, OutTimes);
// Add two-dimensional variables to output file, dimensioned by mass bins and time
string[] dimensions2D = { "Time step", "Mass bin" };
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Log Carnivore abundance in mass bins", 2, dimensions2D, Math.Log(0), OutTimes, OutMassBins);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Log Herbivore abundance in mass bins", 2, dimensions2D, Math.Log(0), OutTimes, OutMassBins);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Log Carnivore biomass in mass bins", 2, dimensions2D, Math.Log(0), OutTimes, OutMassBins);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Log Herbivore biomass in mass bins", 2, dimensions2D, Math.Log(0), OutTimes, OutMassBins);
// Add one-dimensional variables to the output file, dimensioned by time
string[] dimensions1D = { "Time step" };
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Herbivore density", "Individuals / km^2", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Herbivore abundance", "Individuals", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Herbivore biomass", "Kg / km^2", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Carnivore density", "Individuals / km^2", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Carnivore abundance", "Individuals", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Carnivore biomass", "Kg / km^2", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Omnivore density", "Individuals / km^2", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Omnivore abundance", "Individuals", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Omnivore biomass", "Kg / km^2", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Autotroph biomass", "Kg / km^2", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Organic matter pool", "Kg / km^2", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Respiratory CO2 pool", "Kg / km^2", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Number of cohorts extinct", "", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Number of cohorts produced", "", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Number of cohorts combined", "", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Number of cohorts in model", "", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
ArraySDSConvert.AddVariable(DataSetForFileOutput, "Number of stocks in model", "", 1, dimensions1D, EcosystemModelGrid.GlobalMissingValue, OutTimes);
// Add one-dimensional variables to the output file, dimensioned by mass bin index
// To enable outputs to be visualised against mass instead of index
// Initialise the arrays that will be used for the grid-based outputs
LogBiomassDensityGridCohorts = new double[EcosystemModelGrid.NumLatCells, EcosystemModelGrid.NumLonCells];
LogBiomassDensityGridStocks = new double[EcosystemModelGrid.NumLatCells, EcosystemModelGrid.NumLonCells];
LogBiomassDensityGrid = new double[EcosystemModelGrid.NumLatCells, EcosystemModelGrid.NumLonCells];
}
/// <summary>
/// Calculates the mean trophic level of all individual organisms in a grid cell
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The list of cell indices in the current model simulation</param>
/// <param name="cellIndex">The index of the current cell in the list of cells to run</param>
/// <returns>The mean trophic level of individuals in the grid cell</returns>
public double CalculateMeanTrophicLevelCell(ModelGrid ecosystemModelGrid,List<uint[]> cellIndices, int cellIndex)
{
//Get the cohorts for the specified cell
GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
double BiomassWeightedTI = 0.0;
double TotalBiomass = 0.0;
double CohortBiomass = 0.0;
foreach (var CohortList in CellCohorts)
{
foreach (Cohort c in CohortList)
{
CohortBiomass = (c.IndividualBodyMass + c.IndividualReproductivePotentialMass) * c.CohortAbundance;
BiomassWeightedTI += CohortBiomass * c.TrophicIndex;
TotalBiomass += CohortBiomass;
}
}
return BiomassWeightedTI/TotalBiomass;
}
/// <summary>
/// Calculates the variables to output
/// </summary>
/// <param name="EcosystemModelGrid">The model grid to get output data from</param>
/// <param name="CohortFunctionalGroupDefinitions">Definitions of the cohort functional groups in the model</param>
/// <param name="StockFunctionalGroupDefinitions">Definitions of the stock functional groups in the model</param>
/// <param name="_LatCellIndices">A vector of the latitudinal indices of live cells in the model grid</param>
/// <param name="_LonCellIndices">A vector of the longitudinal indices of live cells in the model grid</param>
/// <param name="GlobalDiagnosticVariables">The sorted list of global diagnostic variables in the model</param>
public void CalculateOutputs(ModelGrid EcosystemModelGrid, FunctionalGroupDefinitions CohortFunctionalGroupDefinitions,
FunctionalGroupDefinitions StockFunctionalGroupDefinitions, uint[] _LatCellIndices, uint[] _LonCellIndices, SortedList<string, double>
GlobalDiagnosticVariables)
{
# region Get biomasses and abundances from model grid
/// <summary>
/// Calculates trophic evenness using the FRO Index of Mouillot et al.
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="cellIndices">The list of indices of cells to be run in the current model simulation</param>
/// <param name="cellIndex">The index of the current cell within the list of cells to be run</param>
/// <returns>Trophic evenness</returns>
/// <remarks>From Mouillot et al (2005) Functional regularity: a neglected aspect of functional diversity, Oecologia</remarks>
public double CalculateTrophicEvennessFRO(ModelGrid ecosystemModelGrid, List<uint[]> cellIndices, int cellIndex)
{
//Get the cohorts for the specified cell
GridCellCohortHandler CellCohorts = ecosystemModelGrid.GetGridCellCohorts(cellIndices[cellIndex][0], cellIndices[cellIndex][1]);
List<double[]> TrophicIndexBiomassDistribution = new List<double[]>();
double[] TIBiomass;
double[] EW;
foreach (var CohortList in CellCohorts)
{
foreach (Cohort c in CohortList)
{
TIBiomass = new double[2];
TIBiomass[0] = c.TrophicIndex;
TIBiomass[1] = (c.IndividualBodyMass + c.IndividualReproductivePotentialMass) * c.CohortAbundance;
TrophicIndexBiomassDistribution.Add(TIBiomass);
}
}
TrophicIndexBiomassDistribution = TrophicIndexBiomassDistribution.OrderBy(x => x[0]).ToList();
//Use the Mouillot Evenness index - Functional Regularity Index or FRO
//From Mouillot et al (2005) Functional regularity: a neglected aspect of functional diversity, Oecologia
EW = new double[TrophicIndexBiomassDistribution.Count];
double TotalEW = 0.0 ;
for (int ii = 0; ii < TrophicIndexBiomassDistribution.Count-1; ii++)
{
EW[ii] = (TrophicIndexBiomassDistribution[ii + 1][0] - TrophicIndexBiomassDistribution[ii][0]) / (TrophicIndexBiomassDistribution[ii + 1][1] + TrophicIndexBiomassDistribution[ii][1]);
TotalEW += EW[ii];
}
double FRO = 0.0;
for (int ii = 0; ii < TrophicIndexBiomassDistribution.Count - 1; ii++)
{
FRO += Math.Min(EW[ii]/TotalEW,1.0/(TrophicIndexBiomassDistribution.Count-1));
}
return FRO;
}
/// <summary>
/// Generates the intial output to the live dataset view
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="marineCell">Whether the current cell is a marine cell</param>
private void InitialLiveOutputs(ModelGrid ecosystemModelGrid, Boolean marineCell)
{
// Create a string holding the name of the x-axis variable
string[] TimeDimension = { "Time step" };
// Add the x-axis to the plots (time step)
DataSetToViewLive.AddAxis("Time step", "Month", TimeSteps);
// Add the relevant output variables depending on the specified level of detail
if (ModelOutputDetail == OutputDetailLevel.Low)
{
// Add the variable for total living biomass
DataConverter.AddVariable(DataSetToViewLive, "Total living biomass", "kg", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
// Add the initial value of total living biomass
DataConverter.ValueToSDS1D(TotalLivingBiomass, "Total living biomass", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, 0);
}
else
{
if (marineCell)
{
foreach (string TraitValue in CohortTraitIndicesMarine.Keys)
{
// Add in the carnivore and herbivore abundance variables
DataConverter.AddVariable(DataSetToViewLive, TraitValue + " density", "Individuals / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
// Add in the initial values of carnivore and herbivore abundance
DataConverter.ValueToSDS1D(TotalDensitiesOut[TraitValue], TraitValue + " density", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, 0);
// Add in the carnivore and herbivore biomass variables
DataConverter.AddVariable(DataSetToViewLive, TraitValue + " biomass", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
// Add in the initial values of carnivore and herbivore abundance
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, 0);
}
foreach (string TraitValue in StockTraitIndicesMarine.Keys)
{
// Add in the stock biomass variables
DataConverter.AddVariable(DataSetToViewLive, TraitValue + " biomass", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
// Add in the initial value
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, 0);
}
}
else
{
foreach (string TraitValue in CohortTraitIndices.Keys)
{
// Add in the carnivore and herbivore abundance variables
DataConverter.AddVariable(DataSetToViewLive, TraitValue + " density", "Individuals / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
// Add in the initial values of carnivore and herbivore abundance
DataConverter.ValueToSDS1D(TotalDensitiesOut[TraitValue], TraitValue + " density", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, 0);
// Add in the carnivore and herbivore biomass variables
DataConverter.AddVariable(DataSetToViewLive, TraitValue + " biomass", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
// Add in the initial values of carnivore and herbivore abundance
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, 0);
}
foreach (string TraitValue in StockTraitIndices.Keys)
{
// Add in the stock biomass variables
DataConverter.AddVariable(DataSetToViewLive, TraitValue + " biomass", "Kg / km^2", 1, TimeDimension, ecosystemModelGrid.GlobalMissingValue, TimeSteps);
// Add in the initial value
DataConverter.ValueToSDS1D(TotalBiomassDensitiesOut[TraitValue], TraitValue + " biomass", "Time step", ecosystemModelGrid.GlobalMissingValue, DataSetToViewLive, 0);
}
}
}
}
