/// <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>
/// 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>
/// Initializes the ecosystem model
/// </summary>
/// <param name="initialisation">An instance of the model initialisation class</param>
/// <param name="scenarioParameters">The parameters for the scenarios to run</param>
/// <param name="scenarioIndex">The index of the scenario being run</param>
/// <param name="outputFilesSuffix">The suffix to be applied to all outputs from this model run</param>
/// <param name="globalModelTimeStepUnit">The time step unit used in the model</param>
/// <param name="simulation">The index of the simulation being run</param>
public MadingleyModel(MadingleyModelInitialisation initialisation, ScenarioParameterInitialisation scenarioParameters, int scenarioIndex,
string outputFilesSuffix, string globalModelTimeStepUnit, int simulation)
{
// Assign the properties for this model run
AssignModelRunProperties(initialisation, scenarioParameters, scenarioIndex, outputFilesSuffix);
// Set up list of global diagnostics
SetUpGlobalDiagnosticsList();
// Set up the model grid
SetUpModelGrid(initialisation, scenarioParameters, scenarioIndex, simulation);
// Set up model outputs
SetUpOutputs(initialisation, simulation, scenarioIndex);
// Make the initial outputs
InitialOutputs(outputFilesSuffix, initialisation, CurrentMonth);
// Instance the array of process trackers
ProcessTrackers = new ProcessTracker[_CellList.Count];
// Temporary variables
Boolean varExists;
// Set up process trackers for each grid cell
for (int i = 0; i < _CellList.Count; i++)
{
ProcessTrackers[i] = new ProcessTracker(NumTimeSteps,
EcosystemModelGrid.Lats, EcosystemModelGrid.Lons,
_CellList,
initialisation.ProcessTrackingOutputs,
initialisation.TrackProcesses,
CohortFunctionalGroupDefinitions,
EcosystemModelGrid.GlobalMissingValue,
outputFilesSuffix,
initialisation.OutputPath, initialisation.ModelMassBins,
SpecificLocations, i, initialisation,
EcosystemModelGrid.GetEnviroLayer("Realm", 0, _CellList[i][0], _CellList[i][1], out varExists) == 2.0,
EcosystemModelGrid.LatCellSize,
EcosystemModelGrid.LonCellSize);
}
// Set up a cross cell process tracker
TrackCrossCellProcesses = new CrossCellProcessTracker(initialisation.TrackCrossCellProcesses, "DispersalData", initialisation.OutputPath, outputFilesSuffix);
//Set up a global process tracker
if (SpecificLocations) initialisation.TrackGlobalProcesses = false;
TrackGlobalProcesses = new GlobalProcessTracker(NumTimeSteps,
EcosystemModelGrid.Lats, EcosystemModelGrid.Lons,
_CellList,
initialisation.ProcessTrackingOutputs,
initialisation.TrackGlobalProcesses,
CohortFunctionalGroupDefinitions,
StockFunctionalGroupDefinitions,
EcosystemModelGrid.GlobalMissingValue,
outputFilesSuffix,
initialisation.OutputPath, initialisation.ModelMassBins,
SpecificLocations, initialisation,
EcosystemModelGrid.LatCellSize,
EcosystemModelGrid.LonCellSize);
//Set-up the instance of OutputModelState
WriteModelState = new OutputModelState(initialisation, outputFilesSuffix, simulation);
if (SpecificLocations) initialisation.RunRealm = "";
// Record the initial cohorts in the process trackers
RecordInitialCohorts();
// Initialise the class for cross-grid-cell ecology
MadingleyEcologyCrossGridCell = new EcologyCrossGridCell();
// Initialise the time step timer
TimeStepTimer = new StopWatch();
EcologyTimer = new StopWatch();
OutputTimer = new StopWatch();
// Set the global model time step unit
_GlobalModelTimeStepUnit = globalModelTimeStepUnit;
// Initialise the utility functions
Utilities = new UtilityFunctions();
// Initialise the climate change impacts class
ClimateChangeSimulator = new ClimateChange();
// Initialise the harvesting impacts class
HarvestingSimulator = new Harvesting(EcosystemModelGrid.Lats, EcosystemModelGrid.Lons, (float)EcosystemModelGrid.LatCellSize);
}
/// <summary>
/// Generates the console outputs for the current time step
/// </summary>
/// <param name="currentTimeStep">The current time step</param>
/// <param name="timeStepTimer">The timer for the current time step</param>
private void TimeStepConsoleOutputs(uint currentTimeStep, StopWatch timeStepTimer)
{
}
/// <summary>
/// Runs the specified number of simulations for each of the specified scenarios
/// </summary>
/// <param name="simulationInitialisationFilename">Filename of the file from which to read initialisation information</param>
/// <param name="scenarios">Contains scenario information for this set of simulations</param>
/// <param name="outputPath">The path to which outputs should be written</param>
public void RunAllSimulations(string simulationInitialisationFilename, string definitionsFilename, string outputsFilename, ScenarioParameterInitialisation scenarios, string outputPath)
{
// Declare an instance of the class for initializing the Madingley model
MadingleyModelInitialisation InitialiseMadingley = new MadingleyModelInitialisation(simulationInitialisationFilename, definitionsFilename, outputsFilename, outputPath);
// Specify the output path in this instance
InitialiseMadingley.OutputPath = outputPath;
// List to hold the names of the scenarios to run
List<string> ScenarioNames = new List<string>();
// String variable to hold the index suffix to apply to output files for a given simulation
string OutputFilesSuffix;
// Loop over scenario names and add the name of the scenario to the list of scenarion names
foreach (var scenario in scenarios.scenarioParameters)
{
ScenarioNames.Add(scenario.Item1);
}
// Check whether there is only one simulation to run
if (scenarios.scenarioNumber == 1 && scenarios.scenarioParameters.ElementAt(scenarios.scenarioNumber-1).Item2==1)
{
// For a single simulation
// Set-up the suffix for the output files
OutputFilesSuffix = "_";
// Loop over the parameters for this scenario
for (int i = 0; i < ScenarioNames.Count; i++)
{
// Add the parameter information to the suffix for this simulation
OutputFilesSuffix += ScenarioNames[0] + "_";
}
// Add a zero index to the end of the suffix
OutputFilesSuffix += "0";
//Run the simulation
RunSimulation(scenarios, 0, InitialiseMadingley, OutputFilesSuffix, 0);
Console.ReadKey();
}
else
{
if (InitialiseMadingley.RunSimulationsInParallel)
{
// Loop over specified scenarios iteratively
for (int ScenarioIndex = 0; ScenarioIndex < scenarios.scenarioNumber; ScenarioIndex++)
{
//Create an array of new MadingleyModel instances for simulations under this scenario combination
MadingleyModel[] MadingleyEcosystemModels = new MadingleyModel
[scenarios.scenarioParameters.ElementAt(ScenarioIndex).Item2];
for (int simulation = 0; simulation < scenarios.scenarioParameters.ElementAt(ScenarioIndex).Item2; simulation++)
{
// Set up the suffix for the output files
OutputFilesSuffix = "_";
// Add the scenario label to the suffix for the output files
OutputFilesSuffix += ScenarioNames[ScenarioIndex] + "_";
// Add the simulation index number to the suffix
OutputFilesSuffix += simulation.ToString();
// Initialize the instance of MadingleyModel
MadingleyEcosystemModels[simulation] = new MadingleyModel(InitialiseMadingley, scenarios, ScenarioIndex, OutputFilesSuffix,
InitialiseMadingley.GlobalModelTimeStepUnit, simulation);
}
// Loop over the specified number of simulations for each scenario
//for (int simulation = 0; simulation< scenarios.scenarioSimulationsNumber[ScenarioIndex]; simulation++)
Parallel.For(0, scenarios.scenarioParameters.ElementAt(ScenarioIndex).Item2, simulation =>
{
// Declare and start a timer
StopWatch s = new StopWatch();
s.Start();
// Run the simulation
MadingleyEcosystemModels[simulation].RunMadingley(InitialiseMadingley);
// Stop the timer and write out the time taken to run this simulation
s.Stop();
Console.WriteLine("Model run finished");
Console.WriteLine("Total elapsed time was {0} seconds", s.GetElapsedTimeSecs());
});
}
}
else
{
//Run simulations sequentially
// Loop over specified scenarios
for (int ScenarioIndex = 0; ScenarioIndex < scenarios.scenarioNumber; ScenarioIndex++)
{
// Loop over the specified number of simulations for each scenario
for (int simulation = 0; simulation < scenarios.scenarioParameters.ElementAt(ScenarioIndex).Item2; simulation++)
{
// Set up the suffix for the output files
OutputFilesSuffix = "_";
// Add the scenario label to the suffix for the output files
OutputFilesSuffix += ScenarioNames[ScenarioIndex] + "_";
// Add the simulation index number to the suffix
OutputFilesSuffix += simulation.ToString();
// Run the current simulation
RunSimulation(scenarios, ScenarioIndex, InitialiseMadingley, OutputFilesSuffix, simulation);
}
}
}
}
}
/// <summary>
/// Runs a single simulation of the Madingley model
/// </summary>
/// <param name="scenarios">Parameter information and simulation number for all scenarios to be run</param>
/// <param name="scenarioIndex">The index of the scenario to be run in this simulation</param>
/// <param name="initialiseMadingley">Model initialization information for all simulations</param>
/// <param name="outputFileSuffix">Suffix to be applied to the names of files written out by this simulation</param>
/// <param name="simulation">The index of the simulation being run</param>
public void RunSimulation(ScenarioParameterInitialisation scenarios, int scenarioIndex, MadingleyModelInitialisation initialiseMadingley,
string outputFileSuffix, int simulation)
{
// Declare an instance of the class that runs a Madingley model simulation
MadingleyModel MadingleyEcosystemModel;
// Declare and start a timer
StopWatch s = new StopWatch();
s.Start();
StopWatch t = new StopWatch();
t.Start();
// Initialize the instance of MadingleyModel
MadingleyEcosystemModel = new MadingleyModel(initialiseMadingley, scenarios, scenarioIndex, outputFileSuffix,
initialiseMadingley.GlobalModelTimeStepUnit,simulation);
t.Stop();
// Run the simulation
MadingleyEcosystemModel.RunMadingley(initialiseMadingley);
// Stop the timer and write out the time taken to run this simulation
s.Stop();
Console.WriteLine("Model run finished");
Console.WriteLine("Total elapsed time was {0} seconds", s.GetElapsedTimeSecs());
Console.WriteLine("Model setup time was {0} seconds", t.GetElapsedTimeSecs());
Console.WriteLine("Model run time was {0} seconds", s.GetElapsedTimeSecs() - t.GetElapsedTimeSecs());
}
/// <summary>
/// Generates the console outputs for the current time step
/// </summary>
/// <param name="currentTimeStep">The current model time step</param>
/// <param name="currentMonth">The current month in the model run</param>
/// <param name="timeStepTimer">The timer for the current time step</param>
private void TimeStepConsoleOutputs(uint currentTimeStep, uint currentMonth, StopWatch timeStepTimer)
{
// Console outputs for all levels of detail
Console.ForegroundColor = ConsoleColor.Red;
Console.WriteLine("Completed time step " + (currentTimeStep + 1) + "(Month: " + (currentMonth + 1) + ")\n");
Console.ForegroundColor = ConsoleColor.White;
Console.WriteLine("Elapsed time in seconds this time step: " + timeStepTimer.GetElapsedTimeSecs() + "\n");
Console.ForegroundColor = ConsoleColor.Green;
Console.WriteLine("Living biomass = " + String.Format("{0:E}", TotalLivingBiomass / 1000) + " kg");
Console.WriteLine("Total abundance = " + String.Format("{0:E}", TotalAbundance) + " inds / km^2");
// Console outputs for medium or high detail levels
if ((ModelOutputDetail == OutputDetailLevel.Medium) || (ModelOutputDetail == OutputDetailLevel.High))
{
Console.WriteLine("Total number of cohorts = " + TotalNumberOfCohorts);
Console.WriteLine("Total number of stocks = " + TotalNumberOfStocks);
Console.WriteLine("Number of cohorts extinct = " + NumberOfCohortsExtinct);
Console.WriteLine("Number of cohorts produced = " + NumberOfCohortsProduced);
Console.WriteLine("Number of cohorts combined = " + NumberOfCohortsCombined);
// Console ouputs for high detail level
if (ModelOutputDetail == OutputDetailLevel.High)
{
Console.WriteLine("Total biomass (all) = " + String.Format("{0:E}", TotalBiomass / 1000) + " kg");
Console.WriteLine("Respiratory pool biomass = " + String.Format("{0:E}", RespiratoryPoolOut / 1000) + " kg");
Console.WriteLine("Organic pool biomass = " + String.Format("{0:E}", OrganicPoolOut / 1000) + " kg");
}
}
// Blank line at end of console time step outputs
Console.WriteLine(" ");
Console.ForegroundColor = ConsoleColor.White;
}
/// <summary>
/// Generates the outputs for the current time step
/// </summary>
/// <param name="ecosystemModelGrid">The model grid</param>
/// <param name="currentTimeStep">The current model time step</param>
/// <param name="currentMonth">The current month in the model run</param>
/// <param name="timeStepTimer">The timer for the current time step</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="cellIndices">List of indices of active cells in the model grid</param>
/// <param name="globalDiagnosticVariables">The global diagnostic variables for the model run</param>
/// <param name="initialisation">The Madingley Model initialisation</param>
public void TimeStepOutputs(ModelGrid ecosystemModelGrid, uint currentTimeStep, uint currentMonth, StopWatch timeStepTimer,
FunctionalGroupDefinitions cohortFunctionalGroupDefinitions, FunctionalGroupDefinitions stockFunctionalGroupDefinitions,
List<uint[]> cellIndices, SortedList<string, double> globalDiagnosticVariables, MadingleyModelInitialisation initialisation)
{
// Calculate the output variables for this time step
CalculateOutputs(cohortFunctionalGroupDefinitions, stockFunctionalGroupDefinitions, ecosystemModelGrid, cellIndices,
globalDiagnosticVariables, initialisation);
// Generate the time step console outputs
TimeStepConsoleOutputs(currentTimeStep, currentMonth, timeStepTimer);
// Generate the time step file outputs
TimeStepFileOutputs(ecosystemModelGrid, currentTimeStep);
}
