summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--agent.cpp18
-rw-r--r--agent.hpp3
-rw-r--r--header.hpp19
-rw-r--r--input/options.input16
-rw-r--r--main.cpp112
-rw-r--r--makefile4
-rw-r--r--mesh.cpp34
-rw-r--r--mesh.hpp14
-rw-r--r--parser.cpp114
-rw-r--r--parser.hpp55
-rwxr-xr-xtools/merge-results.sh (renamed from merge-results.sh)0
11 files changed, 314 insertions, 75 deletions
diff --git a/agent.cpp b/agent.cpp
index 97d2e69..68f4c8c 100644
--- a/agent.cpp
+++ b/agent.cpp
@@ -29,12 +29,12 @@ void Agent::advance(Mesh* mesh, size_t step)
// GETTERS AND SETTERS
// ------------------------------------------------------------------------
-Agent::Agent()
+void Agent::init(int n_iteration)
{
- time.resize(N_ITERATION);
- domain.resize(N_ITERATION);
- path.resize(N_ITERATION);
- for (size_t i = 0; i < N_ITERATION; i ++)
+ time.resize(n_iteration);
+ domain.resize(n_iteration);
+ path.resize(n_iteration);
+ for (int i = 0; i < n_iteration; i ++)
path[i].resize(DIM);
}
@@ -150,7 +150,7 @@ void Agent::advance_surface(Mesh* mesh, size_t step)
// check if out of the domain: if the agent travelled thrice the
// maximum length of the cell and still can't find a neighboring
// cell, it must be advected out of the domain
- if (distance_norm > 10.0 * location->get_maximum_length())
+ if (distance_norm > 15.0 * location->get_maximum_length())
domain[step] = OUTSIDE_FLAG;
} else {
@@ -224,9 +224,9 @@ void Agent::advance_subsurface(Mesh* mesh, size_t step)
// check if out of the domain: if the agent travelled thrice the
// maximum length of the cell and still can't find a neighboring
// cell, it must be advected out of the domain
- if (distance_norm > 10.0 * location->get_maximum_length()) {
- domain[step] = OUTSIDE_FLAG;
- }
+ // if (distance_norm > 15.0 * location->get_maximum_length()) {
+ // domain[step] = OUTSIDE_FLAG;
+ // }
// check if exfiltrates
int neighbor_index = mesh->get_cell(cell_index, SUBSURFACE_FLAG)->get_coupled_neighbor();
diff --git a/agent.hpp b/agent.hpp
index f99c2ab..6e4a031 100644
--- a/agent.hpp
+++ b/agent.hpp
@@ -12,8 +12,9 @@ class Agent
public:
- Agent();
+ // Agent();
+ void init(int n_iteration);
void set_cell_index(int value);
void set_domain(int value, size_t step);
void set_path(double x, double y, double z, size_t step);
diff --git a/header.hpp b/header.hpp
index cff75d2..71aeef1 100644
--- a/header.hpp
+++ b/header.hpp
@@ -6,22 +6,21 @@
#include <iostream>
#include <vector>
#include <string> // string class
-//#include <omp.h>
#include <algorithm> // min
#include <float.h> // DBL_MAX
#include <math.h> // fabs, sqrt
#include <mpi.h>
+#include <fstream> // ifstream
+#include <sstream> // stringstream
+#include <string.h> // strcmp
#include <H5Cpp.h>
#include <H5File.h>
#define MAXPRINT 5
-#define MAXTIMESTEP 1.0e5
+#define MAXTIMESTEP 1.0e8
#define EPS 1.0e-10
-#define N_AGENT 100
-#define N_ITERATION 2000
-#define SEED 108
#define CFL 0.5
#define DIM 3
@@ -35,19 +34,13 @@
#define INFILTRATE_TRUE 1
#define INFILTRATE_FALSE 2
-#define SURFACE_MESH_FILE "../test/visdump_surface_mesh.h5"
-#define SURFACE_DATA_FILE "../test/visdump_surface_data.h5"
-#define SUBSURFACE_MESH_FILE "../test/visdump_mesh.h5"
-#define SUBSURFACE_DATA_FILE "../test/visdump_data.h5"
-#define SURFACE_DATA_GROUP_NAME_H5 "11841"
-#define SUBSURFACE_DATA_GROUP_NAME_H5 "11841"
+// #define SURFACE_DATA_GROUP_NAME_H5 "11841"
+// #define SUBSURFACE_DATA_GROUP_NAME_H5 "11841"
#define MESH_MIXED_ELEMENTS "/0/Mesh/MixedElements"
#define MESH_NODES "/0/Mesh/Nodes"
#define AREADIV 0.01
-#define FUZZ 0.1
-#define RADIUS 200.0
#define SUBSURFACE_FLAG 1
#define SURFACE_FLAG 2
diff --git a/input/options.input b/input/options.input
new file mode 100644
index 0000000..345e606
--- /dev/null
+++ b/input/options.input
@@ -0,0 +1,16 @@
+// input file for agent provocateur
+
+n_agent : 100 // Number of agents
+fuzz : 0.1 // Fuzzy equivalence constant, used for geometry
+seed : 108 // Random seed
+n_iteration : 2000 // Number of iteration steps
+
+surfacemesh : ./test/visdump_surface_mesh.h5 // Surface mesh file
+surfacedata : ./test/visdump_surface_data.h5 // Surface data file
+surfacetime : 0.0 236.7 473.5 709.3 941.8 // Time levels
+surfacegroup : 0 3746 6484 9372 11841 // Group names for surface
+
+subsurfacemesh : ./test/visdump_mesh.h5 // Subsurface mesh file
+subsurfacedata : ./test/visdump_data.h5 // Subsurface data file
+subsurfacetime : 0.0 236.7 473.5 709.3 941.8 // Time levels
+subsurfacegroup : 0 3746 6484 9372 11841 // Group names for subsurface
diff --git a/main.cpp b/main.cpp
index 1e45aac..cfa59ca 100644
--- a/main.cpp
+++ b/main.cpp
@@ -2,6 +2,7 @@
#include "mesh.hpp"
#include "agent.hpp"
+#include "parser.hpp"
int main(int argc, char* argv[])
{
@@ -13,25 +14,74 @@ int main(int argc, char* argv[])
MPI_Comm_size(MPI_COMM_WORLD, &size);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- Mesh mesh = Mesh();
-
- H5::H5File fp_subsurface = H5::H5File(SUBSURFACE_MESH_FILE, H5F_ACC_RDONLY);
- H5::H5File dp_subsurface = H5::H5File(SUBSURFACE_DATA_FILE, H5F_ACC_RDONLY);
- H5::H5File fp_surface = H5::H5File(SURFACE_MESH_FILE, H5F_ACC_RDONLY);
- H5::H5File dp_surface = H5::H5File(SURFACE_DATA_FILE, H5F_ACC_RDONLY);
+ if (rank == 0) {
+
+ std::cout << std::endl;
+ std::cout << " / /^ agent provocateur" << std::endl;
+ std::cout << " o--o =================" << std::endl;
+ std::cout << std::endl;
+
+ std::cout << "[~>] Read in input data" << std::endl;
+
+ }
- if (rank == 0)
+ Parser parser;
+ parser.read_options("input/options.input");
+
+ if (rank == 0) {
+
+ std::cout << "[~~>] Number of agents: " << parser.n_agent << std::endl;
+ std::cout << "[~~>] Number of iterations: " << parser.n_iteration << std::endl;
+ std::cout << "[~~>] Random seed: " << parser.seed << std::endl;
+ std::cout << "[~~>] Geometric fuzz: " << parser.fuzz << std::endl;
+
+ std::cout << "[~~>] Surface mesh file: " << parser.surface_mesh_file << std::endl;
+ std::cout << "[~~>] Surface data file: " << parser.surface_data_file << std::endl;
+ std::cout << "[~~>] Surface time: ";
+ for (uint i = 0; i < parser.surface_time.size(); i ++)
+ std::cout << parser.surface_time[i] << " ";
+ std::cout <<std::endl;
+ std::cout << "[~~>] Surface group: ";
+ for (uint i = 0; i < parser.surface_data_group.size(); i ++)
+ std::cout << parser.surface_data_group[i] << " ";
+ std::cout <<std::endl;
+
+ std::cout << "[~~>] Subsurface mesh file: " << parser.subsurface_mesh_file << std::endl;
+ std::cout << "[~~>] Subsurface data file: " << parser.subsurface_data_file << std::endl;
+ std::cout << "[~~>] Subsurface time: ";
+ for (uint i = 0; i < parser.subsurface_time.size(); i ++)
+ std::cout << parser.subsurface_time[i] << " ";
+ std::cout <<std::endl;
+ std::cout << "[~~>] Subsurface group: ";
+ for (uint i = 0; i < parser.subsurface_data_group.size(); i ++)
+ std::cout << parser.subsurface_data_group[i] << " ";
+ std::cout << std::endl;
+ std::cout << std::endl;
+
std::cout << "[~>] Building the subsurface mesh" << std::endl;
+
+ }
+ Mesh mesh = Mesh();
+
+ mesh.set_fuzz(parser.fuzz);
+
+ H5::H5File fp_subsurface = H5::H5File(parser.subsurface_mesh_file.c_str(), H5F_ACC_RDONLY);
+ H5::H5File dp_subsurface = H5::H5File(parser.subsurface_data_file.c_str(), H5F_ACC_RDONLY);
+ H5::H5File fp_surface = H5::H5File(parser.surface_mesh_file.c_str(), H5F_ACC_RDONLY);
+ H5::H5File dp_surface = H5::H5File(parser.surface_data_file.c_str(), H5F_ACC_RDONLY);
+
mesh.build_subsurface_mesh(fp_subsurface);
fp_subsurface.close();
if (rank == 0) {
std::cout << "[~~>] Number of cells: " << mesh.get_n_cells(SUBSURFACE_FLAG) << std::endl;
+ std::cout << std::endl;
+
std::cout << "[~>] Building the surface mesh (includes coupling with subsurface and may take a while)" << std::endl;
}
- mesh.build_surface_mesh(fp_surface, dp_surface);
+ mesh.build_surface_mesh(fp_surface, dp_surface, parser.surface_data_group[0]);
fp_surface.close();
if (rank == 0) {
@@ -39,18 +89,18 @@ int main(int argc, char* argv[])
int len_surf = mesh.get_n_cells(SURFACE_FLAG);
std::cout << "[~~>] Number of cells: " << len_surf << std::endl;
+ std::cout << std::endl;
FILE *mesh_fp = fopen("mesh.csv", "w");
fprintf(mesh_fp, "x (m), y (m), z (m), index\n");
Cell *c;
-
for (int n = 0; n < len_surf; n ++) {
- c = mesh.get_cell(n, SURFACE_FLAG);
- fprintf(mesh_fp, "%f, %f, %f, %d\n",
- c->get_coordinate(0),
- c->get_coordinate(1),
- c->get_coordinate(2), n);
+ c = mesh.get_cell(n, SURFACE_FLAG);
+ fprintf(mesh_fp, "%f, %f, %f, %d\n",
+ c->get_coordinate(0),
+ c->get_coordinate(1),
+ c->get_coordinate(2), n);
}
fclose(mesh_fp);
@@ -59,30 +109,36 @@ int main(int argc, char* argv[])
}
- mesh.build_environment(dp_subsurface, SUBSURFACE_FLAG);
+ mesh.build_environment(dp_subsurface, parser.subsurface_data_group[0], SUBSURFACE_FLAG);
dp_subsurface.close();
- mesh.build_environment(dp_surface, SURFACE_FLAG);
- dp_subsurface.close();
+ if (rank == 0) {
+ std::cout << "[~>] Reading the surface environment" << std::endl;
+ std::cout << std::endl;
+ }
+
+ mesh.build_environment(dp_surface, parser.surface_data_group[0], SURFACE_FLAG);
+ dp_surface.close();
// Place agents in the domain and advance N_ITERATION steps
// Bootstrap
- srand(SEED + rank);
+ srand(parser.seed + rank);
int len = mesh.get_n_cells(SUBSURFACE_FLAG);
int index;
- std::cout << "[~>] Releasing " << N_AGENT << " agents" << std::endl;
+ std::cout << "[~>] Releasing " << parser.n_agent << " agents" << std::endl;
- size_t partition = N_AGENT / size;
+ size_t partition = parser.n_agent / size;
size_t low_bound = rank * partition;
size_t high_bound = (rank + 1) * partition;
if (rank == size - 1) // top processor picks up extras
- high_bound = N_AGENT;
+ high_bound = parser.n_agent;
for (size_t i = low_bound; i < high_bound; i ++) {
Agent agent;
+ agent.init(parser.n_iteration);
index = rand()%len;
agent.set_cell_index(index);
@@ -97,16 +153,20 @@ int main(int argc, char* argv[])
mesh.get_cell(index, SUBSURFACE_FLAG)->get_coordinate(1),
mesh.get_cell(index, SUBSURFACE_FLAG)->get_coordinate(2), 1);
- size_t step;
+ int step;
char output_fname[1024];
// move agent
- for (step = 1; step < N_ITERATION; step ++) {
- if (step % (N_ITERATION / 5) == 0 && i % (N_AGENT / 5) == 0) {
- std::cout << "[~~~>] agent[" << i << "] step = " << step << " dt = " << agent.get_timestepsize() << " s" << std::endl;
+ for (step = 1; step < parser.n_iteration; step ++) {
+ if (step % (parser.n_iteration / 5) == 0 && i % (parser.n_agent / 5) == 0) {
+ std::cout << "[~~>] agent[" << i << "] step = " << step << " dt = " << agent.get_timestepsize() << " s" << std::endl;
}
+
agent.advance(&mesh, step);
+
+ // update environment if necessary
+
}
// write out results
@@ -114,7 +174,7 @@ int main(int argc, char* argv[])
FILE *result_fp = fopen(output_fname, "w");
fprintf(result_fp, "time (s), x (m), y (m), z (m), domain\n");
- for (step = 0; step < N_ITERATION; step ++) {
+ for (step = 0; step < parser.n_iteration; step ++) {
fprintf(result_fp, "%f, %f, %f, %f, %d\n",
agent.get_time(step),
agent.get_path(step, 0),
diff --git a/makefile b/makefile
index 4a91e28..ea6e6aa 100644
--- a/makefile
+++ b/makefile
@@ -2,9 +2,9 @@ PRG=agent-provocateur
#CC=g++-11
CC=mpic++
-CXXFLAGS=-Wall -Wextra -pedantic -O0 -fopenmp
+CXXFLAGS=-Wall -Wextra -pedantic -O0
LFLAGS=-I/opt/hdf5/include -L/opt/hdf5/lib
-SRC=cell.cpp mesh.cpp main.cpp agent.cpp
+SRC=parser.cpp cell.cpp mesh.cpp main.cpp agent.cpp
LIB=-lm -lhdf5 -lhdf5_cpp
OBJ=$(SRC:.cpp=.o)
diff --git a/mesh.cpp b/mesh.cpp
index 8112ede..5004a7e 100644
--- a/mesh.cpp
+++ b/mesh.cpp
@@ -7,14 +7,14 @@
// -- PUBLIC METHODS
// ------------------------------------------------------------------------
-void Mesh::build_surface_mesh(H5::H5File fp, H5::H5File ep)
+void Mesh::build_surface_mesh(H5::H5File fp, H5::H5File ep, std::string datasetname)
{
get_mesh_metadata(fp, SURFACE_NCOL);
handle_surface_node_data(fp);
- build_surface_cells(ep);
+ build_surface_cells(ep, datasetname);
}
@@ -29,20 +29,17 @@ void Mesh::build_subsurface_mesh(H5::H5File fp)
}
-void Mesh::build_environment(H5::H5File ep, int flag)
+void Mesh::build_environment(H5::H5File ep, std::string datasetname, int flag)
{
std::string groupname;
- std::string datasetname;
// Read in velocities in x direction
if (flag == SUBSURFACE_FLAG) {
groupname = "darcy_velocity.cell.0";
- datasetname = SUBSURFACE_DATA_GROUP_NAME_H5;
} else if (flag == SURFACE_FLAG) {
groupname = "surface-velocity.cell.0";
- datasetname = SURFACE_DATA_GROUP_NAME_H5;
}
read_velocity(ep, groupname, datasetname, flag, 0);
@@ -51,10 +48,8 @@ void Mesh::build_environment(H5::H5File ep, int flag)
if (flag == SUBSURFACE_FLAG) {
groupname = "darcy_velocity.cell.1";
- datasetname = SUBSURFACE_DATA_GROUP_NAME_H5;
} else if (flag == SURFACE_FLAG) {
groupname = "surface-velocity.cell.1";
- datasetname = SURFACE_DATA_GROUP_NAME_H5;
}
read_velocity(ep, groupname, datasetname, flag, 1);
@@ -63,10 +58,8 @@ void Mesh::build_environment(H5::H5File ep, int flag)
if (flag == SUBSURFACE_FLAG) {
groupname = "darcy_velocity.cell.2";
- datasetname = SUBSURFACE_DATA_GROUP_NAME_H5;
} else if (flag == SURFACE_FLAG) {
groupname = "surface-surface_subsurface_flux.cell.0";
- datasetname = SURFACE_DATA_GROUP_NAME_H5;
}
read_velocity(ep, groupname, datasetname, flag, 2);
@@ -90,7 +83,7 @@ void Mesh::build_environment(H5::H5File ep, int flag)
}
// Read in water depth
- read_water_depth(ep);
+ read_water_depth(ep, datasetname);
}
#if VERBOSE
@@ -164,6 +157,11 @@ double Mesh::get_low_coordinate(int index)
return low_coordinates[index];
}
+void Mesh::set_fuzz(double value)
+{
+ fuzz = value;
+}
+
// ------------------------------------------------------------------------
// -- PRIVATE METHODS
// ------------------------------------------------------------------------
@@ -198,7 +196,7 @@ void Mesh::handle_surface_node_data(H5::H5File fp)
}
-void Mesh::build_surface_cells(H5::H5File ep)
+void Mesh::build_surface_cells(H5::H5File ep, std::string datasetname)
{
std::vector<double> coords1(DIM-1);
@@ -206,7 +204,7 @@ void Mesh::build_surface_cells(H5::H5File ep)
std::vector<double> coords3(DIM-1);
std::vector<double> coords_avg(DIM-1);
- read_elevation(ep);
+ read_elevation(ep, datasetname);
for (int i = 0; i < n_cells_surface; i ++) {
@@ -270,7 +268,7 @@ void Mesh::build_surface_cells(H5::H5File ep)
double xy_distance = sqrt(distance[0]*distance[0] + distance[1]*distance[1]);
- if (xy_distance <= FUZZ) {
+ if (xy_distance <= fuzz) {
dz = std::min(dz, fabs(distance[2]));
coupled_neighbor = k;
if (dz <= 2.0 * subsurface_cells[k].get_characteristic_length())
@@ -479,11 +477,11 @@ void Mesh::read_velocity(H5::H5File fp, std::string groupname, std::string datas
}
-void Mesh::read_water_depth(H5::H5File fp)
+void Mesh::read_water_depth(H5::H5File fp, std::string datasetname)
{
H5::Group group = fp.openGroup("surface-ponded_depth.cell.0");
- H5::DataSet dataset = group.openDataSet(SURFACE_DATA_GROUP_NAME_H5);
+ H5::DataSet dataset = group.openDataSet(datasetname.c_str());
H5::DataType datatype = dataset.getDataType();
H5::DataSpace dataspace = dataset.getSpace();
@@ -512,11 +510,11 @@ void Mesh::read_water_depth(H5::H5File fp)
}
-void Mesh::read_elevation(H5::H5File fp)
+void Mesh::read_elevation(H5::H5File fp, std::string datasetname)
{
H5::Group group = fp.openGroup("surface-elevation.cell.0");
- H5::DataSet dataset = group.openDataSet(SURFACE_DATA_GROUP_NAME_H5);
+ H5::DataSet dataset = group.openDataSet(datasetname.c_str());
H5::DataType datatype = dataset.getDataType();
H5::DataSpace dataspace = dataset.getSpace();
diff --git a/mesh.hpp b/mesh.hpp
index 70f7c34..18e166e 100644
--- a/mesh.hpp
+++ b/mesh.hpp
@@ -13,10 +13,10 @@ public:
Mesh();
- void build_surface_mesh(H5::H5File fp, H5::H5File ep);
+ void build_surface_mesh(H5::H5File fp, H5::H5File ep, std::string datasetname);
void build_subsurface_mesh(H5::H5File fp);
- void build_environment(H5::H5File ep, int flag);
+ void build_environment(H5::H5File ep, std::string datasetname, int flag);
void build_subsurface_environment(H5::H5File ep);
Cell* get_cell(int index, int flag);
@@ -25,6 +25,7 @@ public:
double get_high_coordinate(int index);
void set_low_coordinate(int index, double value);
double get_low_coordinate(int index);
+ void set_fuzz(double value);
int get_n_cells(int flag);
@@ -32,6 +33,8 @@ private:
int n_cells_subsurface;
int n_cells_surface;
+
+ double fuzz;
std::vector<Cell> subsurface_cells;
std::vector<Cell> surface_cells;
@@ -41,18 +44,17 @@ private:
std::vector<std::vector<double>> nodes;
std::vector<std::vector<int>> element_node_indices;
- //std::vector<std::vector<std::vector<hsize_t>>> edge_ids;
void handle_subsurface_node_data(H5::H5File fp);
void build_subsurface_cells();
void handle_surface_node_data(H5::H5File fp);
- void build_surface_cells(H5::H5File fp);
+ void build_surface_cells(H5::H5File fp, std::string datasetname);
void get_mesh_metadata(H5::H5File fp, int ncol);
void read_velocity(H5::H5File fp, std::string groupname, std::string datasetname, int flag, int index);
- void read_water_depth(H5::H5File fp);
- void read_elevation(H5::H5File fp);
+ void read_water_depth(H5::H5File fp, std::string datasetname);
+ void read_elevation(H5::H5File fp, std::string datasetname);
};
diff --git a/parser.cpp b/parser.cpp
new file mode 100644
index 0000000..39527ed
--- /dev/null
+++ b/parser.cpp
@@ -0,0 +1,114 @@
+#include "header.hpp"
+#include "parser.hpp"
+
+void ParserLine::parse()
+{
+
+ key.clear();
+ value.clear();
+
+ if (!line.empty() && line.find("//", 0) != 0) {
+
+ uint splitloc = line.find(":", 0); // find the colon
+ key = line.substr(0, splitloc); // store the key and value strings
+ key.erase(std::remove(key.begin(), key.end(), ' '), key.end()); // remove spaces and tabs
+ key.erase(std::remove(key.begin(), key.end(), '\t'), key.end());
+ std::string val = line.substr(splitloc+1, line.length()-splitloc);
+
+ size_t splitter = val.find("//", 0);
+ std::string strloc;
+ if (splitter != std::string::npos) {
+ strloc = val.substr(0, splitter);
+ } else {
+ strloc = val;
+ }
+
+ value.clear();
+ value.str(strloc);
+
+ }
+
+}
+
+
+void Parser::read_options(std::string fname)
+{
+
+ std::ifstream fInStream(fname);
+ std::string line;
+ ParserLine pline;
+
+ // initialize all read-in values to -999
+ fuzz = -999;
+ n_agent = -999;
+ n_iteration = -999;
+
+ if (fInStream.is_open()) {
+
+ while (std::getline(fInStream, line)) {
+
+ pline.line = line;
+ pline.parse();
+
+ if (!pline.key.empty()) {
+
+ // Match the key and store the value
+ if (!strcmp("surfacemesh", pline.key.c_str())) {
+ pline.value >> surface_mesh_file;
+ }
+ else if (!strcmp("surfacedata", pline.key.c_str())) {
+ pline.value >> surface_data_file;
+ }
+ else if (!strcmp("surfacetime", pline.key.c_str())) {
+ double time;
+ while (pline.value >> time) {
+ surface_time.push_back(time);
+ }
+ }
+ else if (!strcmp("surfacegroup", pline.key.c_str())) {
+ std::string group;
+ while (pline.value >> group) {
+ surface_data_group.push_back(group);
+ }
+ }
+ else if (!strcmp("subsurfacemesh", pline.key.c_str())) {
+ pline.value >> subsurface_mesh_file;
+ }
+ else if (!strcmp("subsurfacedata", pline.key.c_str())) {
+ pline.value >> subsurface_data_file;
+ }
+ else if (!strcmp("subsurfacetime", pline.key.c_str())) {
+ double time;
+ while (pline.value >> time) {
+ subsurface_time.push_back(time);
+ }
+ }
+ else if (!strcmp("subsurfacegroup", pline.key.c_str())) {
+ std::string group;
+ while (pline.value >> group) {
+ subsurface_data_group.push_back(group);
+ }
+ }
+ else if (!strcmp("n_agent", pline.key.c_str())) {
+ pline.value >> n_agent;
+ }
+ else if (!strcmp("fuzz", pline.key.c_str())) {
+ pline.value >> fuzz;
+ }
+ else if (!strcmp("seed", pline.key.c_str())) {
+ pline.value >> seed;
+ }
+ else if (!strcmp("n_iteration", pline.key.c_str())) {
+ pline.value >> n_iteration;
+ }
+ else {
+ std::cerr << "[!!] Unrecognised option key" << std::endl;
+ }
+
+ }
+
+ }
+
+ }
+
+}
diff --git a/parser.hpp b/parser.hpp
new file mode 100644
index 0000000..7ffda0d
--- /dev/null
+++ b/parser.hpp
@@ -0,0 +1,55 @@
+// -*- mode: c++ -*-
+
+//
+// Purpose: Read-in functionality to define parameters at runtime
+// Based on the implementation of Morales-Hernandez /et al./'s SERGHEI
+//
+
+#ifndef PARSER_HPP
+#define PARSER_HPP
+
+#include "header.hpp"
+
+class ParserLine
+{
+
+public:
+
+ std::string line;
+ std::string key;
+ std::stringstream value;
+
+ void parse();
+
+};
+
+class Parser
+{
+
+public:
+
+ std::string surface_mesh_file;
+ std::string surface_data_file;
+ std::string subsurface_mesh_file;
+ std::string subsurface_data_file;
+
+ std::vector<std::string> surface_data_group;
+ std::vector<double> surface_time;
+
+ std::vector<std::string> subsurface_data_group;
+ std::vector<double> subsurface_time;
+
+ int n_agent;
+ int n_iteration;
+ int seed;
+
+ int surface_np;
+ int subsurface_np;
+
+ double fuzz;
+
+ void read_options(std::string fname);
+
+};
+
+#endif
diff --git a/merge-results.sh b/tools/merge-results.sh
index 5459897..5459897 100755
--- a/merge-results.sh
+++ b/tools/merge-results.sh
generated by cgit v1.2.3-13-gbd6f (git 2.30.0) at 2024-04-30 09:23:31 +0000