read 'habitatTypeExitConditionHours' for configurable consecutive Nea…

…rshore hours to exit (#13)

* use number of consecutive nearshore hours for exit criteria
* read 'habitatTypeExitConditionHours' from config file
* defaults to 2 hours if not found in config file

run6_config/config_map_2013_data_2014.json

@@ -15,5 +15,6 @@
     "flowSpeedFile": "data/mod_flow_condensed.nc",
     "distribWseTempFile": "data/wse.temp.full.nc",
     "threadCount": 96,
-    "blindChannelSimplificationRadius": 15.0
+    "blindChannelSimplificationRadius": 15.0,
+    "habitatTypeExitConditionHours": 6.0
 }

src/fish.cpp

@@ -64,7 +64,8 @@ inline float forkLengthFromMass(float mass) {
 // This is a sustained swim speed
 const float SWIM_SPEED_BODY_LENGTHS_PER_SEC = 2.0f;
 
-const float SECONDS_PER_TIMESTEP = 60.0f*60.0f;
+constexpr  float HOURS_PER_TIMESTEP = 1.0f;
+constexpr  float SECONDS_PER_TIMESTEP = HOURS_PER_TIMESTEP * 60.0f*60.0f;
 
 // Calculate a sustained-movement swim range (in m) from a fork length (in mm)
 inline float swimSpeedFromForkLength(float forkLength) {
@@ -89,6 +90,7 @@ Fish::Fish(
         travel(0),
         status(FishStatus::Alive),
         exitStatus(FishStatus::Alive),
+        numExitHabitatHours(0),
         lastGrowth(0),
         lastPmax(0),
         lastMortality(0),
@@ -351,6 +353,9 @@ float Fish::getFitness(Model &model, MapNode &loc, float cost) {
     return this->getGrowth(model, loc, cost) / this->getMortality(model, loc);
 }
 
+void Fish::incrementExitHabitatHoursByOneTimestep() {
+    this->numExitHabitatHours += HOURS_PER_TIMESTEP;
+}
 
 /*
  * Perform the movement simulation for this fish
@@ -435,7 +440,6 @@ bool Fish::move(Model &model) {
             break;
         }
     }
-    MapNode *oldLocation = this->location;
     this->location = point;
     this->travel = cost;
 
@@ -444,12 +448,16 @@ bool Fish::move(Model &model) {
         this->locationHistory->push_back(this->location->id);
     }
 
-    if (oldLocation->type == HabitatType::Nearshore && this->location->type == HabitatType::Nearshore) {
-        // Exit if at nearshore (TODO verify this behavior)
+    if (this->location->type == HabitatType::Nearshore) {
+        this->incrementExitHabitatHoursByOneTimestep();
+    } else {
+        this->numExitHabitatHours = 0;
+    }
+    if (this->numExitHabitatHours >= model.habitatTypeExitConditionHours) {
         this->exit(model);
         return false;
     }
-    
+
     /* 
     // simplistic approach to exiting fish when they reach 75mm length or less than 30
     if (this->forkLength >= 75 || this->forkLength < 30) {

src/fish.h

@@ -47,6 +47,8 @@ class Fish {
     FishStatus status;
     // status on model exit; only used for keeping track of fish replays
     FishStatus exitStatus;
+    //number of hours currently spent in an exit habitat (Nearshore)
+    float numExitHabitatHours;
     // last timestep's growth (g) and Pmax
     float lastGrowth;
     float lastPmax;
@@ -88,6 +90,9 @@ class Fish {
     * probability of arriving at the location
     */
     void getDestinationProbs(Model &model, std::unordered_map<MapNode *, float> &out);
+    // increment the number of hours in an exit habitat
+    void incrementExitHabitatHoursByOneTimestep();
+
     /*
     * Run this fish's movement update:
     *   Get all reachable nodes and their costs,

src/model.cpp

@@ -18,6 +18,7 @@
 // default mortality constants
 constexpr float MORT_CONST_C = 0.03096;
 constexpr float MORT_CONST_A = -0.42;
+constexpr float DEFAULT_EXIT_CONDITION_HOURS = 2.0;
 
 /*
  * Constructs a model instance from parameters and data filenames.
@@ -46,6 +47,7 @@ Model::Model(
     std::string recSizeDistsFilename,
     // List of map node IDs where new recruits enter the model
     std::vector<unsigned> recPointIds,
+    float habitatTypeExitConditionHours,
     // Path of the file containing map node descriptions (area, habitat type, elevation, among other columns)
     std::string mapLocationFilename,
     // Path of the file containing map edge descriptions (source and target nodes, path lengths, among other columns)
@@ -74,6 +76,7 @@ Model::Model(
     exitedCount(0),
     mortConstA(MORT_CONST_A),
     mortConstC(MORT_CONST_C),
+    habitatTypeExitConditionHours(habitatTypeExitConditionHours),
     nextFishID(0UL),
     maxThreads(maxThreads),
     recruitTagRate(0.5f)
@@ -127,6 +130,7 @@ Model::Model(
     exitedCount(0),
     mortConstA(MORT_CONST_A),
     mortConstC(MORT_CONST_C),
+    habitatTypeExitConditionHours(DEFAULT_EXIT_CONDITION_HOURS),
     nextFishID(0UL),
     maxThreads(maxThreads),
     recruitTagRate(0.5f)
@@ -1083,6 +1087,9 @@ Model *modelFromConfig(std::string configPath) {
             std::string(d["recruitCountsFile"].GetString()),
             std::string(d["recruitSizesFile"].GetString()),
             recPoints,
+            d.HasMember("habitatTypeExitConditionHours")
+                ? d["habitatTypeExitConditionHours"].GetFloat()
+                : DEFAULT_EXIT_CONDITION_HOURS,
             std::string(d["mapNodesFile"].GetString()),
             std::string(d["mapEdgesFile"].GetString()),
             std::string(d["mapGeometryFile"].GetString()),

src/model.h

@@ -88,6 +88,10 @@ class Model {
     // Mortality constants overridden by ABC
     float mortConstA;
     float mortConstC;
+
+    // number of consecutive Nearshore hours to satisfy exit condition
+    float habitatTypeExitConditionHours;
+
     Model(
         int globalTimeIntercept,
         int hydroTimeIntercept,
@@ -96,6 +100,7 @@ class Model {
         std::string recCountFilename,
         std::string recSizeDistsFilename,
         std::vector<unsigned> recPointIds,
+        float habitatTypeExitConditionHours,
         std::string mapLocationFilename,
         std::string mapEdgeFilename,
         std::string mapGeometryFilename,
@@ -171,7 +176,6 @@ class Model {
     unsigned long nextFishID;
     size_t maxThreads;
     float recruitTagRate;
-
 };
 #define __FISH_MODEL_CLS