add advecting with different time horizons

10 files changed, 377 insertions, 273 deletions

diff --git a/environment.hpp b/environment.hpp
index fb2eec6..dedf017 100644
--- a/environment.hpp
+++ b/environment.hpp
@@ -63,32 +63,39 @@ public:
     Environment(Parser &value)
     {
         parser = value;
-        timestep = 0;
+        timestep_surface = 0;
+        timestep_subsurface = 0;
 
         std::cout << "[env] building the environment" << std::endl;
 
         read_grid();
-        read_environment(timestep);
+        read_environment(timestep_surface);
 
         std::cout << std::endl;
         std::cout << "[env] initialised 0th environment" << std::endl;
 
     }
 
-    void update()
-    {
-
-        timestep = timestep + 1;
-        read_environment(timestep);
 
-        std::cout << "[env] updated to " << timestep << "th environment" << std::endl;
+    void update_surface()
+    {
+        timestep_surface = timestep_surface + 1;
+        read_environment_surface(timestep_surface);
+        std::cout << "[env] updated surface to " << timestep_surface << "th environment" << std::endl;
+    }
 
+    void update_subsurface()
+    {
+        timestep_subsurface = timestep_subsurface + 1;
+        read_environment_subsurface(timestep_subsurface);
+        std::cout << "[env] updated subsurface to " << timestep_subsurface << "th environment" << std::endl;
     }
 
 private:
 
     Parser parser;
-    int timestep;
+    int timestep_surface;
+    int timestep_subsurface;
 
     // ------------------------------------------------------------------------
     // generic read function for dataset
@@ -271,15 +278,34 @@ private:
 
     }
 
-    // ------------------------------------------------------------------------
-    // read in environment variables
-    // ------------------------------------------------------------------------
-    void read_environment(int timestep)
+    void read_environment_subsurface(int timestep)
     {
+        H5::H5File fp_subsurface = H5::H5File(parser.subsurface_data_file.c_str(),
+                                              H5F_ACC_RDONLY);
 
-        //
-        // we start with surface environment variables
-        //
+        // darcy velocity in x-direction
+        read_variable(fp_subsurface,
+                      DARCY_VELOCITY_X,
+                      parser.subsurface_data_group[timestep],
+                      darcy_velocity_x);
+
+        // darcy velocity in y-direction
+        read_variable(fp_subsurface,
+                      DARCY_VELOCITY_Y,
+                      parser.subsurface_data_group[timestep],
+                      darcy_velocity_y);
+
+        // darcy velocity in z-direction
+        read_variable(fp_subsurface,
+                      DARCY_VELOCITY_Z,
+                      parser.subsurface_data_group[timestep],
+                      darcy_velocity_z);
+
+        fp_subsurface.close();
+    }
+
+    void read_environment_surface(int timestep)
+    {
         H5::H5File fp_surface = H5::H5File(parser.surface_data_file.c_str(),
                                            H5F_ACC_RDONLY);
 
@@ -316,33 +342,23 @@ private:
                       evaporation_flux);
 
         fp_surface.close();
+    }
+
+    // ------------------------------------------------------------------------
+    // read in environment variables
+    // ------------------------------------------------------------------------
+    void read_environment(int timestep)
+    {
 
         //
-        // now we read in subsurface
+        // we start with surface environment variables
         //
-        H5::H5File fp_subsurface = H5::H5File(parser.subsurface_data_file.c_str(),
-                                              H5F_ACC_RDONLY);
-
-        // darcy velocity in x-direction
-        read_variable(fp_subsurface,
-                      DARCY_VELOCITY_X,
-                      parser.subsurface_data_group[timestep],
-                      darcy_velocity_x);
-
-        // darcy velocity in y-direction
-        read_variable(fp_subsurface,
-                      DARCY_VELOCITY_Y,
-                      parser.subsurface_data_group[timestep],
-                      darcy_velocity_y);
-
-        // darcy velocity in z-direction
-        read_variable(fp_subsurface,
-                      DARCY_VELOCITY_Z,
-                      parser.subsurface_data_group[timestep],
-                      darcy_velocity_z);
-
-        fp_subsurface.close();
+        read_environment_surface(timestep);
 
+        //
+        // now we read in subsurface
+        //
+        read_environment_subsurface(timestep);
     }
 
 };
diff --git a/header.hpp b/header.hpp
index 0575269..d4f7e00 100644
--- a/header.hpp
+++ b/header.hpp
@@ -46,6 +46,7 @@
 #define OUTLET_FLAG 3
 #define EVAPORATION_FLAG 4
 
+#define TIME_FUZZ 1.0e-3
 #define WATERDEPTH_DRY 1.0e-8
 #define ZERO_VELOCITY 1.0e-10
 #define DT_MAX 432000.0
diff --git a/input/options.input b/input/options.input
index f48010d..2ec212f 100644
--- a/input/options.input
+++ b/input/options.input
@@ -6,13 +6,14 @@ seed            : 108						// Random seed
 n_iteration     : 1000						// Number of iteration steps
 subgrid_dx      : 5.0						// Subgrid cell size
 
-surfacemesh	: ./input/test/ats_vis_surface_mesh.h5		// Surface mesh file
-surfacedata	: ./input/test/ats_vis_surface_data.h5		// Surface data file
-surfacetime     : ./input/times.txt				// Time levels for surface 
+surfacemesh	: ./example/ats_vis_surface_mesh.h5		// Surface mesh file
+surfacedata	: ./example/ats_vis_surface_data.h5		// Surface data file
+surfacetime     : ./input/times.txt				// Time levels for surface
 surfacegroup	: ./input/groups.txt				// Group names for surface
 
-subsurfacemesh  : ./input/test/ats_vis_mesh.h5			// Subsurface mesh file
-subsurfacedata  : ./input/test/ats_vis_data.h5			// Subsurface data file
+subsurfacemesh  : ./example/ats_vis_mesh.h5			// Subsurface mesh file
+subsurfacedata  : ./example/ats_vis_data.h5			// Subsurface data file
 subsurfacetime  : ./input/subtimes.txt			 	// Time levels for subsurface
 subsurfacegroup : ./input/subgroups.txt				// Group names for subsurface
 
+restartfile : none
\ No newline at end of file
diff --git a/input/subtimes.txt b/input/subtimes.txt
index 45adcab..d4bdb70 100644
--- a/input/subtimes.txt
+++ b/input/subtimes.txt
@@ -1,43 +1,43 @@
 0
-118276
-236550
-354826
-473100
-591376
-709651
-827926
-946201
-1.06447e+06
-1.18276e+06
-1.30103e+06
-1.4193e+06
-1.53757e+06
-1655856
-1.77413e+06
-1.8924e+06
-2.01067e+06
-2.12896e+06
-2.24723e+06
-2.3655e+06
-2.48378e+06
-2.60206e+06
-2.72033e+06
-2.8386e+06
-2.95688e+06
-3.07516e+06
-3.19343e+06
-3.3117e+06
-3.42998e+06
-3.54826e+06
-3.66653e+06
-3.7848e+06
-3.90308e+06
-4.02136e+06
-4.13963e+06
-4.2579e+06
-4.37618e+06
-4.49446e+06
-4.61273e+06
-4.731e+06
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+432001
+864000
+1.296e+06
+1.728e+06
+2.16e+06
+2.592e+06
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+4.32001e+06
+4.75201e+06
+5.184e+06
+5.61599e+06
+6.04801e+06
+6.48001e+06
+6.912e+06
+7.34399e+06
+7.77601e+06
+8.20801e+06
+8.64e+06
+9.07199e+06
+9.50401e+06
+9.93601e+06
+1.0368e+07
+1.08e+07
+1.1232e+07
+1.1664e+07
+1.2096e+07
+1.2528e+07
+1.296e+07
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+1.3824e+07
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+1.5552e+07
+1.5984e+07
+1.6416e+07
+1.6848e+07
+1.728e+07
+1.7712e+07
+1.8144e+07
diff --git a/input/times.txt b/input/times.txt
index 45adcab..dbbe0ca 100644
--- a/input/times.txt
+++ b/input/times.txt
@@ -1,43 +1,108 @@
 0
-118276
-236550
-354826
-473100
-591376
-709651
-827926
-946201
-1.06447e+06
-1.18276e+06
-1.30103e+06
-1.4193e+06
-1.53757e+06
-1655856
-1.77413e+06
-1.8924e+06
-2.01067e+06
-2.12896e+06
-2.24723e+06
-2.3655e+06
-2.48378e+06
-2.60206e+06
-2.72033e+06
-2.8386e+06
-2.95688e+06
-3.07516e+06
-3.19343e+06
-3.3117e+06
-3.42998e+06
-3.54826e+06
-3.66653e+06
-3.7848e+06
-3.90308e+06
-4.02136e+06
-4.13963e+06
-4.2579e+06
-4.37618e+06
-4.49446e+06
-4.61273e+06
-4.731e+06
-4.84928e+06
-4.96756e+06
+172800
+345600
+518400
+691200
+864000
+1.0368e+06
+1.2096e+06
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+1.9008e+06
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+1.07136e+07
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+1.10592e+07
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+1.77984e+07
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+1.84896e+07
diff --git a/main.cpp b/main.cpp
index 45d3cb1..76277cf 100644
--- a/main.cpp
+++ b/main.cpp
@@ -44,8 +44,6 @@ int main(int argc, char* argv[])
     if (flag == "-c") {
         Mesh mesh = Mesh(parser);
         mesh.compile();
-        // mesh.subgrid();
-        // mesh.map();
         mesh.dump();
         std::cout << "[   ] meshing completed, enjoy the subgrid" << std::endl;
         std::cout << std::endl;
@@ -59,11 +57,76 @@ int main(int argc, char* argv[])
 
         ParticleManager pmanager = ParticleManager(parser);
 
-        for (size_t t = 1; t < parser.surface_time.size(); ++t) {
-            pmanager.advect(parser.surface_time[t]);
-            pmanager.environment.update();
+        size_t nstep_surface = parser.surface_time.size();
+        size_t nstep_subsurface = parser.subsurface_time.size();
+
+        size_t step_surface = 1;
+        size_t step_subsurface = 1;
+
+        // bootstrap
+        double t_surface = parser.surface_time[0];
+        double t_subsurface = parser.subsurface_time[0];
+        double t_combined = std::min(t_surface, t_subsurface);
+
+        // we compute the difference between the next time level
+        // and the combined time level to check if we need to
+        // update the environment.  the first step is "free".
+        double dt_surface = 0.0;
+        double dt_subsurface = 0.0;
+
+        bool fin_surface = false;
+        bool fin_subsurface = false;
+
+        // (step_surface < nstep_surface) || (step_subsurface < nstep_subsurface)
+        while (!fin_surface || !fin_subsurface) {
+
+            // advect all particles
+            pmanager.advect(t_combined);
+
+            // check if the surface environment needs to be updated
+            if (!fin_surface && dt_surface <= TIME_FUZZ) {
+
+                step_surface ++;
+                t_surface = parser.surface_time[step_surface]; // get new time step
+                pmanager.environment.update_surface(); // update environment
+                t_combined = std::min(t_surface, t_subsurface);
+
+                if (step_surface == nstep_surface - 1) {
+                    fin_surface = true;
+                }
+
+            }
+
+            // check if the subsurface environment needs to be updated
+            if (!fin_subsurface && dt_subsurface <= TIME_FUZZ) {
+
+                step_subsurface ++;
+                t_subsurface = parser.subsurface_time[step_subsurface];
+                pmanager.environment.update_subsurface();
+                t_combined = std::min(t_surface, t_subsurface);
+
+                if (step_subsurface == nstep_subsurface - 1) {
+                    fin_subsurface = true;
+                }
+
+            }
+
+            dt_surface = std::fabs(t_combined - t_surface);
+            dt_subsurface = std::fabs(t_combined - t_subsurface);
+
+            if (fin_surface) {
+                t_combined = t_subsurface;
+            }
+
+            if (fin_subsurface) {
+                t_combined = t_surface;
+            }
+
         }
 
+        std::cout << "[   ] particle advecting completed, enjoy the results!" << std::endl;
+        std::cout << std::endl;
+
         for (size_t i = 0; i < pmanager.particles.size(); ++i) {
             pmanager.particles[i].dump(i);
         }
diff --git a/parser.hpp b/parser.hpp
index fa4e3ab..f0142a0 100644
--- a/parser.hpp
+++ b/parser.hpp
@@ -72,6 +72,7 @@ public:
     std::string surface_data_file;
     std::string subsurface_mesh_file;
     std::string subsurface_data_file;
+    std::string checkfile;
 
     std::vector<std::string> surface_data_group;
     std::vector<double> surface_time;
@@ -119,6 +120,7 @@ public:
         for (uint i = 0; i < subsurface_data_group.size(); i ++)
             std::cout << subsurface_data_group[i] << " ";
         std::cout << std::endl;
+        std::cout << "[prs] restart file: " << checkfile << std::endl;
         std::cout << std::endl;
 
     }
@@ -151,41 +153,45 @@ public:
                         pline.value >> surface_data_file;
                     } else if (!strcmp("surfacetime", pline.key.c_str())) {
 
-		      std::string timefile;
-		      pline.value >> timefile;
+                        std::string timefile;
+                        pline.value >> timefile;
 
-		      std::ifstream in(timefile);
-		      double time;
+                        std::ifstream in(timefile);
+                        double time;
 
-		      if (in.is_open()) {
-			
-			while (!in.eof()) {
-			  in >> time;
-			  surface_time.push_back(time);
-			}
+                        if (in.is_open()) {
+
+                            while (!in.eof()) {
+                                in >> time;
+                                if (in.good()) {
+                                    surface_time.push_back(time);
+                                }
+                            }
+
+                        } else {
+                            std::cerr << "[err] file " << timefile << " can't be opened" << std::endl;
+                        }
 
-		      } else {
-			std::cerr << "[err] file " << timefile << " can't be opened" << std::endl;
-		      }
-		      
                     } else if (!strcmp("surfacegroup", pline.key.c_str())) {
 
-		      std::string groupfile;
-		      pline.value >> groupfile;
+                        std::string groupfile;
+                        pline.value >> groupfile;
 
-		      std::ifstream in(groupfile);
-		      std::string group;
+                        std::ifstream in(groupfile);
+                        std::string group;
 
-		      if (in.is_open()) {
+                        if (in.is_open()) {
 
-			while (!in.eof()) {
-			  in >> group;
-			  surface_data_group.push_back(group);
-			}
+                            while (!in.eof()) {
+                                in >> group;
+                                if (in.good()) {
+                                    surface_data_group.push_back(group);
+                                }
+                            }
 
-		      } else {
-			std::cerr << "[err] file " << groupfile << " can't be opened" << std::endl;
-		      }
+                        } else {
+                            std::cerr << "[err] file " << groupfile << " can't be opened" << std::endl;
+                        }
 
                     } else if (!strcmp("subsurfacemesh", pline.key.c_str())) {
                         pline.value >> subsurface_mesh_file;
@@ -193,42 +199,46 @@ public:
                         pline.value >> subsurface_data_file;
                     } else if (!strcmp("subsurfacetime", pline.key.c_str())) {
 
-		      std::string timefile;
-		      pline.value >> timefile;
+                        std::string timefile;
+                        pline.value >> timefile;
+
+                        std::ifstream in(timefile);
+                        double time;
 
-		      std::ifstream in(timefile);
-		      double time;
+                        if (in.is_open()) {
 
-		      if (in.is_open()) {
-		      
-			while (!in.eof()) {
-			  in >> time;
-			  subsurface_time.push_back(time);
-			}
+                            while (!in.eof()) {
+                                in >> time;
+                                if (in.good()) {
+                                    subsurface_time.push_back(time);
+                                }
+                            }
+
+                        } else {
+                            std::cerr << "[err] file " << timefile << " can't be opened" << std::endl;
+                        }
 
-		      } else {
-			std::cerr << "[err] file " << timefile << " can't be opened" << std::endl;
-		      }
-		      
                     } else if (!strcmp("subsurfacegroup", pline.key.c_str())) {
 
-		      std::string groupfile;
-		      pline.value >> groupfile;
+                        std::string groupfile;
+                        pline.value >> groupfile;
+
+                        std::ifstream in(groupfile);
+                        std::string group;
 
-		      std::ifstream in(groupfile);
-		      std::string group;
+                        if (in.is_open()) {
 
-		      if (in.is_open()) {
+                            while (!in.eof()) {
+                                in >> group;
+                                if (in.good()) {
+                                    subsurface_data_group.push_back(group);
+                                }
+                            }
 
-			while (!in.eof()) {
-			  in >> group;
-			  subsurface_data_group.push_back(group);
-			}
+                        } else {
+                            std::cerr << "[err] file " << groupfile << " can't be opened" << std::endl;
+                        }
 
-		      } else {
-			std::cerr << "[err] file " << groupfile << " can't be opened" << std::endl;
-		      }
-		      
                     } else if (!strcmp("n_agent", pline.key.c_str())) {
                         pline.value >> n_agent;
                     } else if (!strcmp("fuzz", pline.key.c_str())) {
@@ -239,6 +249,8 @@ public:
                         pline.value >> seed;
                     } else if (!strcmp("n_iteration", pline.key.c_str())) {
                         pline.value >> n_iteration;
+                    } else if (!strcmp("restartfile", pline.key.c_str())) {
+                        pline.value >> checkfile;
                     } else {
                         std::cerr << "[err] unrecognised option key" << std::endl;
                     }
diff --git a/particle.hpp b/particle.hpp
index 0f5026a..5f95ff5 100644
--- a/particle.hpp
+++ b/particle.hpp
@@ -116,41 +116,45 @@ public:
         rng = std::default_random_engine(parser.seed);
         dist = std::uniform_real_distribution<double>(0.0, 1.0);
 
-        for (int i = 0; i < parser.n_agent; ++ i) {
+        if (!strcmp("none", parser.checkfile.c_str())) {
 
-            Particle p;
+            for (int i = 0; i < parser.n_agent; ++ i) {
 
-            p.cell_index = -9999;
-            int ix, iy, iz;
+                Particle p;
 
-            while (p.cell_index == -9999) {
+                p.cell_index = -9999;
+                int ix, iy, iz;
 
-                ix = xdist(rng);
-                iy = ydist(rng);
-                iz = zdist(rng) * 0;
+                while (p.cell_index == -9999) {
 
-                p.cell_index = environment.indices[ix][iy][iz];
+                    ix = xdist(rng);
+                    iy = ydist(rng);
+                    iz = zdist(rng) * 0;
 
-            }
+                    p.cell_index = environment.indices[ix][iy][iz];
 
-            // get the coordinates
-            p.x = environment.xll_corner + 0.5 * dx + ix * dx;
-            p.y = environment.yhl_corner - 0.5 * dx - iy * dx;
-            p.z = environment.elevations[ix][iy][iz];
-            p.t = parser.start_time;
-
-            if (iz > 0) {
-                // if the particle is not in the top layer, it's in the subsurface
-                p.domain.push_back(SUBSURFACE_FLAG);
-            } else {
-                // otherwise, it's at the surface
-                p.domain.push_back(SURFACE_FLAG);
-            }
+                }
 
-            p.coordinates.push_back({ p.x, p.y, p.z });
-            p.time.push_back(p.t);
+                // get the coordinates
+                p.x = environment.xll_corner + 0.5 * dx + ix * dx;
+                p.y = environment.yhl_corner - 0.5 * dx - iy * dx;
+                p.z = environment.elevations[ix][iy][iz];
+                p.t = parser.start_time;
+
+                if (iz > 0) {
+                    // if the particle is not in the top layer, it's in the subsurface
+                    p.domain.push_back(SUBSURFACE_FLAG);
+                } else {
+                    // otherwise, it's at the surface
+                    p.domain.push_back(SURFACE_FLAG);
+                }
 
-            particles.push_back(p);
+                p.coordinates.push_back({ p.x, p.y, p.z });
+                p.time.push_back(p.t);
+
+                particles.push_back(p);
+
+            }
 
         }
 
@@ -369,64 +373,6 @@ public:
 
     }
 
-
-    // // move particle in the subsurface
-    // void advectv()
-    // {
-
-    //     std::cout << "[ptl] advecting particles" << std::endl;
-
-    //     size_t i;
-    //     double dx = parser.subgrid_dx;
-
-    //     #pragma omp parallel
-    //     {
-
-    //         #pragma omp for private(i)
-    //         for (i = 0; i < particles.size(); ++i) {
-
-    //             while (particles[i].time.back() < timehorizon) {
-
-    //                 int flag = particles[i].domain.back();
-
-    //                 double vx, vy, vz, vmag, dt;
-
-    //                 vx = environment.velocity_x[particles[i].cell_index];
-    //                 vy = environment.velocity_y[particles[i].cell_index];
-
-    //                 vmag = std::sqrt(vx * vx + vy * vy);
-
-    //                 dt = CFL * dx / (vmag + 1.0e-10);
-    //                 dt = std::min(dt, DT_MAX);
-    //                 dt = std::min(dt, timehorizon - particles[i].time.back());
-
-    //                 particles[i].advect(vx, vy, 0.0, dt);
-
-    //                 // get the indices
-    //                 int ix, iy, iz;
-    //                 ix = (int) floor((particles[i].x - environment.xll_corner) / dx);
-    //                 iy = (int) floor((environment.yhl_corner - particles[i].y) / dx);
-    //                 iz = 0;
-
-    //                 // update the particle
-    //                 particles[i].time.push_back(particles[i].t);
-    //                 particles[i].cell_index = environment.indices[ix][iy][iz];
-    //                 particles[i].z = environment.elevations[ix][iy][iz];
-    //                 particles[i].coordinates.push_back({particles[i].x,
-    //                                                     particles[i].y,
-    //                                                     particles[i].z});
-    //                 particles[i].domain.push_back(flag);
-
-    //             }
-
-    //         }
-
-    //     }
-
-    // }
-
-
-
 private:
 
     Parser parser;
diff --git a/tools/extract.sh b/tools/extract.sh
index 7222f83..79cd72b 100644
--- a/tools/extract.sh
+++ b/tools/extract.sh
@@ -5,4 +5,4 @@ groupname=$2
 
 ./extract-groups.sh ${filename} ${groupname} > _tmpgroups.txt
 cat _tmpgroups.txt | ./extract-times.sh ${filename} ${groupname} > _tmptimes.txt
-cat _tmptimes.txt | awk '{ print $1 * 360000.0 * 24 }'
+cat _tmptimes.txt | awk '{ print $1 * 365.25 * 3600 * 24 }'
diff --git a/tools/plot-paths-integrated.gp b/tools/plot-paths-integrated.gp
index 8fe4a06..723c693 100644
--- a/tools/plot-paths-integrated.gp
+++ b/tools/plot-paths-integrated.gp
@@ -1,7 +1,7 @@
 #!/usr/bin/env gnuplot
 
 set term png font "hack"
-set output "output/figure.png"
+set output "../output/figure.png"
 
 set border linecolor rgbcolor "white"
 set key textcolor rgbcolor "white"
@@ -20,7 +20,7 @@ set ytics 1
 set size ratio -1
 
 splot \
-	for [i = 100:999] "output/p-000".i.".csv" \
+	for [i = 100:999] "../output/p-000".i.".csv" \
 	u ($3/1000):($4/1000):($5/1000)\
 	with lines\
 	notitle