renamed and stuff

particle-track-and-trace/src/advection/AdvectionKernel.h

@@ -0,0 +1,31 @@
+#ifndef ADVECTIONKERNEL_H
+#define ADVECTIONKERNEL_H
+
+#include <tuple>
+
+#include "Vel.h"
+
+/*
+ * Implement this class for every integration method.
+ */
+class AdvectionKernel {
+public:
+    /**
+     * This function must take a time, latitude and longitude of a particle and must output
+     * a new latitude and longitude after being advected once for AdvectionKernel::DT time as defined above.
+     * @param time Time since the beginning of the data
+     * @param latitude Latitude of particle
+     * @param longitude Longitude of particle
+     * @return A pair of latitude and longitude of particle.
+     */
+    virtual std::pair<double, double> advect(int time, double latitude, double longitude, int dt) const = 0;
+
+    // Taken from Parcels https://github.com/OceanParcels/parcels/blob/daa4b062ed8ae0b2be3d87367d6b45599d6f95db/parcels/tools/converters.py#L155
+    const static double metreToDegrees(double metre) {
+        return metre / 1000. / 1.852 / 60.;
+    }
+
+    virtual ~AdvectionKernel() = default; // Apparently I need this, idk why
+};
+
+#endif //ADVECTIONKERNEL_H

particle-track-and-trace/src/advection/EulerAdvectionKernel.cpp

@@ -0,0 +1,13 @@
+
+#include "EulerAdvectionKernel.h"
+#include "interpolate.h"
+
+using namespace std;
+
+EulerAdvectionKernel::EulerAdvectionKernel(std::shared_ptr<UVGrid> grid) : grid(grid) {}
+
+std::pair<double, double> EulerAdvectionKernel::advect(int time, double latitude, double longitude, int dt) const {
+  auto [u, v] = bilinearinterpolate(*grid, time, latitude, longitude);
+
+  return {latitude + metreToDegrees(v * dt), longitude + metreToDegrees(u * dt)};
+}

particle-track-and-trace/src/advection/EulerAdvectionKernel.h

@@ -0,0 +1,25 @@
+#ifndef EULERADVECTIONKERNEL_H
+#define EULERADVECTIONKERNEL_H
+
+#include "AdvectionKernel.h"
+#include "UVGrid.h"
+
+/**
+ * Implementation of AdvectionKernel.
+ * The basic equation is:
+ * new_latitude = latitude + v*DT
+ * new_longitude = longitude + u*DT
+ *
+ * Uses bilinear interpolation as implemented in interpolate.h
+ */
+class EulerAdvectionKernel: public AdvectionKernel {
+private:
+    std::shared_ptr<UVGrid> grid;
+public:
+    explicit EulerAdvectionKernel(std::shared_ptr<UVGrid> grid);
+    std::pair<double, double> advect(int time, double latitude, double longitude, int dt) const override;
+
+};
+
+
+#endif //EULERADVECTIONKERNEL_H

particle-track-and-trace/src/advection/RK4AdvectionKernel.cpp

@@ -0,0 +1,35 @@
+#include "RK4AdvectionKernel.h"
+#include "interpolate.h"
+
+using namespace std;
+
+RK4AdvectionKernel::RK4AdvectionKernel(std::shared_ptr<UVGrid> grid): grid(grid) { }
+
+std::pair<double, double> RK4AdvectionKernel::advect(int time, double latitude, double longitude, int dt) const {
+    auto [u1, v1] = bilinearinterpolate(*grid, time, latitude, longitude);
+//    lon1, lat1 = (particle.lon + u1*.5*particle.dt, particle.lat + v1*.5*particle.dt);
+    double lon1 = longitude + metreToDegrees(u1 * 0.5*dt);
+    double lat1 = latitude + metreToDegrees(v1 * 0.5*dt);
+
+//    (u2, v2) = fieldset.UV[time + .5 * particle.dt, particle.depth, lat1, lon1, particle]
+    auto [u2, v2] = bilinearinterpolate(*grid, time + 0.5 * dt, lat1, lon1);
+
+//    lon2, lat2 = (particle.lon + u2*.5*particle.dt, particle.lat + v2*.5*particle.dt)
+    double lon2 = longitude + metreToDegrees(u2 * 0.5 * dt);
+    double lat2 = latitude + metreToDegrees(v2 * 0.5 * dt);
+
+//    (u3, v3) = fieldset.UV[time + .5 * particle.dt, particle.depth, lat2, lon2, particle]
+    auto [u3, v3] = bilinearinterpolate(*grid, time + 0.5 * dt, lat2, lon2);
+
+//    lon3, lat3 = (particle.lon + u3*particle.dt, particle.lat + v3*particle.dt)
+    double lon3 = longitude + metreToDegrees(u3 * dt);
+    double lat3 = latitude + metreToDegrees(v3 * dt);
+
+//    (u4, v4) = fieldset.UV[time + particle.dt, particle.depth, lat3, lon3, particle]
+    auto [u4, v4] = bilinearinterpolate(*grid, time + dt, lat3, lon3);
+
+    double lonFinal = longitude + metreToDegrees((u1 + 2 * u2 + 2 * u3 + u4) / 6.0 * dt);
+    double latFinal = latitude + metreToDegrees((v1 + 2 * v2 + 2 * v3 + v4) / 6.0 * dt);
+
+    return {latFinal, lonFinal};
+}

particle-track-and-trace/src/advection/RK4AdvectionKernel.h

@@ -0,0 +1,22 @@
+#ifndef RK4ADVECTIONKERNEL_H
+#define RK4ADVECTIONKERNEL_H
+
+#include "AdvectionKernel.h"
+#include "UVGrid.h"
+
+/**
+ * Implementation of Advection kernel using RK4 integration
+ * See https://en.wikipedia.org/wiki/Runge%E2%80%93Kutta_methods for more details.
+ * Uses bilinear interpolation as implemented in interpolate.h
+ */
+class RK4AdvectionKernel: public AdvectionKernel {
+private:
+    std::shared_ptr<UVGrid> grid;
+public:
+    explicit RK4AdvectionKernel(std::shared_ptr<UVGrid> grid);
+    std::pair<double, double> advect(int time, double latitude, double longitude, int dt) const override;
+
+};
+
+
+#endif //RK4ADVECTIONKERNEL_H

particle-track-and-trace/src/advection/UVGrid.cpp

@@ -0,0 +1,66 @@
+#include <ranges>
+
+#include "UVGrid.h"
+#include "readdata.h"
+
+#define sizeError2 "The sizes of the hydrodynamic data files are different"
+#define sizeError "The sizes of the hydrodynamicU or -V files does not correspond with the sizes of the grid file"
+
+using namespace std;
+
+UVGrid::UVGrid() {
+  auto us = readHydrodynamicU();
+  auto vs = readHydrodynamicV();
+  if (us.size() != vs.size()) {
+    throw domain_error(sizeError2);
+  }
+
+  tie(times, lats, lons) = readGrid();
+
+  timeSize = times.size();
+  latSize = lats.size();
+  lonSize = lons.size();
+
+  size_t gridSize = timeSize * latSize * lonSize;
+  if (gridSize != us.size()) {
+    throw domain_error(sizeError);
+  }
+
+  uvData.reserve(gridSize);
+
+  for (auto vel: views::zip(us, vs)) {
+    uvData.push_back(Vel(vel));
+  }
+}
+
+const Vel &UVGrid::operator[](size_t timeIndex, size_t latIndex, size_t lonIndex) const {
+  if (timeIndex < 0 or timeIndex >= timeSize
+      or latIndex < 0 or latIndex >= latSize
+      or lonIndex < 0 or lonIndex >= lonSize) {
+    throw std::out_of_range("Index out of bounds");
+  }
+  size_t index = timeIndex * (latSize * lonSize) + latIndex * lonSize + lonIndex;
+  return uvData[index];
+}
+
+double UVGrid::lonStep() const {
+  return lons[1] - lons[0];
+}
+
+double UVGrid::latStep() const {
+  return lats[1] - lats[0];
+}
+
+int UVGrid::timeStep() const {
+  return times[1] - times[0];
+}
+
+void UVGrid::streamSlice(ostream &os, size_t t) {
+  for (int x = 0; x < latSize; x++) {
+    for (int y = 0; y < lonSize; y++) {
+      auto vel = (*this)[t, x, y];
+      os << vel << " ";
+    }
+    os << endl;
+  }
+}

particle-track-and-trace/src/advection/UVGrid.h

@@ -0,0 +1,65 @@
+#ifndef UVGRID_H
+#define UVGRID_H
+
+#include <vector>
+#include "Vel.h"
+
+class UVGrid {
+private:
+    /**
+     * 1D data vector of all the us and vs
+     */
+    std::vector<Vel> uvData;
+public:
+    UVGrid();
+
+    /**
+     * The matrix has shape (timeSize, latSize, lonSize)
+     */
+    size_t timeSize;
+    size_t latSize;
+    size_t lonSize;
+
+    /**
+     * Assuming grid is a regular grid, gives the longitudinal spacing of grid.
+     * @return longitudinal spacing
+     */
+    double lonStep() const;
+
+    /**
+     * Assuming grid is a regular grid, gives the latitudinal spacing of grid.
+     * @return latitudinal spacing
+     */
+    double latStep() const;
+
+    /**
+     * Assuming grid is a regular grid, gives the time spacing of grid.
+     * @return time spacing
+     */
+    int timeStep() const;
+
+    /**
+     * times, lats, lons are vector of length timeSize, latSize, lonSize respectively.
+     * The maintain the following invariant:
+     * grid[timeIndex,latIndex,lonIndex] gives the u,v at the point with latitude at lats[latIndex],
+     * with longitude at lons[lonIndex], and with time at times[timeIndex].
+     */
+    std::vector<int> times;
+    std::vector<double> lats;
+    std::vector<double> lons;
+
+    /**
+     * The 3D index into the data. The array is sized by [8761][67][116]
+     * @return Velocity at that index
+     */
+    const Vel& operator[](size_t timeIndex, size_t latIndex, size_t lonIndex) const;
+
+    /**
+     * Streams a slice at timeIndex t of the matrix to the outstream given by os
+     * @param os outstream
+     * @param t index with which to slice matrix
+     */
+    void streamSlice(std::ostream &os, size_t t);
+};
+
+#endif //UVGRID_H

particle-track-and-trace/src/advection/Vel.cpp

@@ -0,0 +1,40 @@
+#include "Vel.h"
+#include <stdexcept>
+#include <iomanip>
+
+using namespace std;
+
+Vel::Vel(double u, double v) : u(u), v(v) {}
+
+Vel::Vel(const std::pair<double, double>& p) : u(p.first), v(p.second) {}
+
+Vel& Vel::operator=(const std::pair<double, double>& p) {
+    u = p.first;
+    v = p.second;
+    return *this;
+}
+
+Vel Vel::operator+(const Vel& other) const {
+    return Vel(u + other.u, v + other.v);
+}
+
+Vel& Vel::operator+=(const Vel& other) {
+    u += other.u;
+    v += other.v;
+    return *this;
+}
+
+template<typename Scalar>
+Vel Vel::operator/(Scalar scalar) const {
+    if (scalar == 0) throw std::runtime_error("Division by zero");
+    return Vel(u / scalar, v / scalar);
+}
+
+std::ostream& operator<<(ostream& os, const Vel& vel) {
+    os << "(";
+    os << fixed << setprecision(2) << setw(5) << vel.u;
+    os << ", ";
+    os << fixed << setprecision(2) << setw(5) << vel.v;
+    os << ")";
+    return os;
+}

particle-track-and-trace/src/advection/Vel.h

@@ -0,0 +1,44 @@
+#ifndef VEL_H
+#define VEL_H
+
+#include <utility>
+#include <stdexcept>
+#include <iostream>
+#include <format>
+
+class Vel {
+public:
+    double u; // Eastward Current Velocity in the Water Column
+    double v; // Northward Current Velocity in the Water Column
+
+    Vel(double u, double v);
+    Vel(const std::pair<double, double>& p);  // Conversion constructor
+    Vel& operator=(const std::pair<double, double>& p);
+
+    // Operator + to add two Vel objects
+    Vel operator+(const Vel& other) const;
+
+    // Operator += to add another Vel object to this object
+    Vel& operator+=(const Vel& other);
+
+    // Operator * to multiply Vel by a scalar, defined as a member template
+    template<typename Scalar>
+    Vel operator*(Scalar scalar) const {
+        return Vel(u * scalar, v * scalar);
+    }
+
+    // Operator / to divide Vel by a scalar, defined as a member template
+    template<typename Scalar>
+    Vel operator/(Scalar scalar) const;
+
+    // Friend declaration for the stream insertion operator
+    friend std::ostream& operator<<(std::ostream& os, const Vel& vel);
+};
+
+// Non-member function for scalar multiplication on the left
+template<typename Scalar>
+Vel operator*(Scalar scalar, const Vel& p) {
+    return Vel(p.u * scalar, p.v * scalar);
+}
+
+#endif //VEL_H

particle-track-and-trace/src/advection/interpolate.cpp

@@ -0,0 +1,47 @@
+#include "interpolate.h"
+
+using namespace std;
+
+Vel bilinearinterpolate(const UVGrid &uvGrid, int time, double lat, double lon) {
+    double latStep = uvGrid.latStep();
+    double lonStep = uvGrid.lonStep();
+    int timeStep = uvGrid.timeStep();
+
+    int latIndex = (lat - uvGrid.lats[0]) / latStep;
+    int lonIndex = (lon - uvGrid.lons[0]) / lonStep;
+    int timeIndex = (time - uvGrid.times[0]) / timeStep;
+
+    double timeRatio = (static_cast<double>(time) - uvGrid.times[timeIndex]) / timeStep;
+    double latRatio = (lat - uvGrid.lats[latIndex]) / latStep;
+    double lonRatio = (lon - uvGrid.lons[lonIndex]) / lonStep;
+
+    Vel point = {0, 0};
+    for (int timeOffset = 0; timeOffset <= 1; timeOffset++) {
+        for (int latOffset = 0; latOffset <= 1; latOffset++) {
+            for (int lonOffset = 0; lonOffset <= 1; lonOffset++) {
+                auto vertex = uvGrid[
+                        timeIndex + 1 < uvGrid.timeSize ? timeIndex + timeOffset : timeIndex,
+                                latIndex + 1 < uvGrid.latSize ? latIndex + latOffset : latIndex,
+                                lonIndex + 1 < uvGrid.lonSize ? lonIndex + lonOffset : lonIndex
+                ];
+
+                double timeRation = (1 - timeOffset) * (1 - timeRatio) + timeOffset * timeRatio;
+                double latRation = (1 - latOffset) * (1 - latRatio) + latOffset * latRatio;
+                double lonRation = (1 - lonOffset) * (1 - lonRatio) + lonOffset * lonRatio;
+                point += timeRation * latRation * lonRation * vertex;
+            }
+        }
+    }
+
+    return point;
+}
+
+vector<Vel> bilinearinterpolation(const UVGrid &uvGrid, vector<tuple<int, double, double>> points) {
+    vector<Vel> result;
+    result.reserve(points.size());
+    for (auto [time, lat, lon]: points) {
+        result.push_back(bilinearinterpolate(uvGrid, time, lat, lon));
+    }
+
+    return result;
+}

particle-track-and-trace/src/advection/interpolate.h

@@ -0,0 +1,28 @@
+#ifndef INTERPOLATE_H
+#define INTERPOLATE_H
+
+#include <vector>
+
+#include "UVGrid.h"
+
+/**
+ * Bilinearly interpolate the point (time, lat, lon) to produce the interpolated velocity.
+ * Since it is in 3D, this means that it interpolates against 8 points (excluding edges).
+ * As described in https://numerical.recipes/book.html Chapter 3.6
+ * @param uvGrid velocity grid
+ * @param time time of point
+ * @param lat latitude of point
+ * @param lon longitude of point
+ * @return interpolated velocity
+ */
+Vel bilinearinterpolate(const UVGrid &uvGrid, int time, double lat, double lon);
+
+/**
+ * Helper function for bilnearly interpolating a vector of points
+ * @param uvGrid velocity grid
+ * @param points vector of points
+ * @return interpolated velocities
+ */
+std::vector<Vel> bilinearinterpolation(const UVGrid &uvGrid, std::vector<std::tuple<int, double, double>> points);
+
+#endif //INTERPOLATE_H

particle-track-and-trace/src/advection/readdata.cpp

@@ -0,0 +1,50 @@
+#include <stdexcept>
+
+#include <netcdf>
+
+#include "readdata.h"
+
+using namespace std;
+using namespace netCDF;
+
+template <typename T>
+vector<T> getVarVector(const NcVar &var) {
+    int length = 1;
+    for (NcDim dim : var.getDims()) {
+        length *= dim.getSize();
+    }
+
+    vector<T> vec(length);
+
+    var.getVar(vec.data());
+
+    return vec;
+}
+
+vector<double> readHydrodynamicU() {
+    // Vs and Us flipped cause the files are named incorrectly
+    netCDF::NcFile data("../../../../data/hydrodynamic_V.h5", netCDF::NcFile::read);
+
+    multimap< string, NcVar > vars = data.getVars();
+
+    return getVarVector<double>(vars.find("vo")->second);
+}
+
+vector<double> readHydrodynamicV() {
+    // Vs and Us flipped cause the files are named incorrectly
+    netCDF::NcFile data("../../../../data/hydrodynamic_U.h5", netCDF::NcFile::read);
+
+    multimap< string, NcVar > vars = data.getVars();
+
+    return getVarVector<double>(vars.find("uo")->second);
+}
+
+tuple<vector<int>, vector<double>, vector<double>> readGrid() {
+    netCDF::NcFile data("../../../../data/grid.h5", netCDF::NcFile::read);
+    multimap< string, NcVar > vars = data.getVars();
+    vector<int> time = getVarVector<int>(vars.find("times")->second);
+    vector<double> longitude = getVarVector<double>(vars.find("longitude")->second);
+    vector<double> latitude = getVarVector<double>(vars.find("latitude")->second);
+
+    return {time, latitude, longitude};
+}

particle-track-and-trace/src/advection/readdata.h

@@ -0,0 +1,22 @@
+#ifndef READDATA_H
+#define READDATA_H
+
+/**
+ * reads the file hydrodynamic_U.h5
+ * @return the data vector of us
+ */
+std::vector<double> readHydrodynamicU();
+
+/**
+ * reads the file hydrodynamic_V.h5
+ * @return the data vector of vs
+ */
+std::vector<double> readHydrodynamicV();
+
+/**
+ * Reads the file grid.h5
+ * @return a tuple of (times, latitude, longitude)
+ */
+std::tuple<std::vector<int>, std::vector<double>, std::vector<double>> readGrid();
+
+#endif //READDATA_H