Tue Mar 16 10:27:08 PDT 2021

16 files changed, 4 insertions, 192 deletions

diff --git a/.DS_Store b/.DS_Store
index fb6f270..cdfeed8 100644
--- a/.DS_Store
+++ b/.DS_Store
diff --git a/.gitignore~ b/.gitignore~
new file mode 100644
index 0000000..2c04e2e
--- /dev/null
+++ b/.gitignore~
@@ -0,0 +1,2 @@
+*~
+.gitignore
diff --git a/README.md b/README.md
index ed77493..3021956 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,5 @@
+-*- mode: markdown -*-
+
 # agent provocateur
 
 /agent provocateur/ is a HydroAgent realisation that uses [Amanzi/ATS
diff --git a/README.md~ b/README.md~
deleted file mode 100644
index ff87fa6..0000000
--- a/README.md~
+++ /dev/null
@@ -1 +0,0 @@
-# agent provocateur
diff --git a/agent b/agent
deleted file mode 100755
index 548e116..0000000
--- a/agent
+++ /dev/null
diff --git a/agent.hpp~ b/agent.hpp~
deleted file mode 100644
index c3ba110..0000000
--- a/agent.hpp~
+++ /dev/null
@@ -1,6 +0,0 @@
-#ifndef AGENT_HPP
-#define AGENT_HPP
-
-
-
-#endif
diff --git a/header.hpp~ b/header.hpp~
deleted file mode 100644
index 79a2fc3..0000000
--- a/header.hpp~
+++ /dev/null
@@ -1,13 +0,0 @@
-// -*- mode: c++; c-default-style: "linux" -*-
-
-#ifndef HEADER_HPP
-
-#include <iostream>
-
-#include <H5Cpp.h>
-#include <H5File.h>
-
-#include "agent.hpp"
-#include "mesh.hpp"
-
-#endif
diff --git a/main.cpp~ b/main.cpp~
deleted file mode 100644
index 0b8d878..0000000
--- a/main.cpp~
+++ /dev/null
@@ -1,15 +0,0 @@
-// -*- mode: c++; c-default-style: "linux" -*-
-
-#include "header.hpp"
-
-#define N_AGENT 100
-#define N_ITERATION 100000
-#define DT_SURFACE 1.0
-#define DT_SUBSURFACE 3600.0
-
-int main(int argc, char *argv[])
-{
-
-  
-  
-}
diff --git a/main.o b/main.o
deleted file mode 100644
index 7053e5e..0000000
--- a/main.o
+++ /dev/null
diff --git a/makefile~ b/makefile~
deleted file mode 100644
index 89a4798..0000000
--- a/makefile~
+++ /dev/null
@@ -1,32 +0,0 @@
-PRG=agent
-
-CC=g++
-CXXFLAGS=-Wall -Wextra -pedantic
-LFLAGS=-I/opt/hdf5/include -L/opt/hdf5/lib
-SRC=mesh.cpp main.cpp
-LIB=-lm -lhdf5 -lhdf5_cpp -I/opt/hdf5/include -L/opt/hdf5/lib
-
-OBJ=$(SRC:.cpp=.o)
-
-all:$(PRG)
-
-$(PRG): $(OBJ)
-	echo "[OK] linking objects"
-	$(CC) $(LFLAGS) $(CXXFLAGS) $(OBJ) -o $@ $(LIB)
-
-%.o: %.c
-	echo "[OK] building objects"
-	$(CC) $(LFLAGS) $(CXXFLAGS) -c $< -o $@
-
-run: $(PRG)
-	./$(PRG)
-
-clean:
-	rm -f $(PRG) $(OBJ)
-
-cleanall:
-	make clean
-	rm -f *.dat; rm -f *.png
-
-.PHONY: all clean cleanall
-
diff --git a/mesh.cpp~ b/mesh.cpp~
deleted file mode 100644
index d8c775d..0000000
--- a/mesh.cpp~
+++ /dev/null
@@ -1,62 +0,0 @@
-// -*- mode: c++; c-default-style: "linux" -*-
-
-#include "header.hpp"
-
-Cell::Cell(double *coordinates)
-{
-  x = coordinates[0];
-  y = coordinates[1];
-  z = coordinates[2];
-}
-
-double Cell::get_x()
-{
-  return Cell::x;
-}
-
-double Cell::get_y()
-{
-  return Cell::y;
-}
-
-double Cell::get_z()
-{
-  return Cell::z;
-}
-
-
-Mesh::Mesh()
-{
-}
-
-int Mesh::build(H5::H5File fp)
-{
-
-  int flag = -1;
-
-  return flag;
-  
-}
-
-int Cell::initialize_neighborhood()
-{
-
-  return 0;
-  
-}
-
-int main(int argc, char *argv[])
-{
-
-  double coordinates[3];
-  coordinates[0] = 1.0;
-  coordinates[1] = 2.0;
-  coordinates[2] = 3.0;
-  
-  Cell cell = Cell(coordinates);
-
-  std::cout << "x: " << cell.get_x() << "; y: " << cell.get_y() << "; z: " << cell.get_z() << std::endl;
-  
-  return 0;
-  
-}
diff --git a/mesh.hpp~ b/mesh.hpp~
deleted file mode 100644
index 141fbd6..0000000
--- a/mesh.hpp~
+++ /dev/null
@@ -1,62 +0,0 @@
-// -*- mode: c++; c-default-style: "linux" -*-
-
-#ifndef MESH_HPP
-#define MESH_HPP
-
-// mesh.hpp
-// ========
-// Mesh topology to get environment variables that inform the
-// HydroAgent (agent.hpp).
-// Reads in a HDF5 mesh file and builds the topology. The HydroAgent
-// stores the cell it was last located in. Then, in the next iteration
-// it searches the neighborhood to locate itself. This makes the search
-// more efficient.
-
-class Cell
-{
-
-public:
-
-  Cell(double* coordinates);
-
-  double get_x();
-  double get_y();
-  double get_z();
-
-  int initialize_neighborhood(void);
-
-protected:
-
-private:
-  
-  int dim; // n_neighbors = 2 * dim - 1
-
-  double x;
-  double y;
-  double z;
-
-  double h;
-  double *v;
-
-  int *neighbors;
-  
-};
-
-class Mesh
-{
-
-public:
-  
-  Mesh();
-
-  int build(H5::H5File fp);
-
-protected:
-  
-private:
-
-  Cell *cells;
-  
-};
-
-#endif
diff --git a/mesh.o b/mesh.o
deleted file mode 100644
index 930767e..0000000
--- a/mesh.o
+++ /dev/null
diff --git a/tools.cpp~ b/tools.cpp~
deleted file mode 100644
index e69de29..0000000
--- a/tools.cpp~
+++ /dev/null
diff --git a/tools.hpp~ b/tools.hpp~
deleted file mode 100644
index 44cc7e6..0000000
--- a/tools.hpp~
+++ /dev/null
@@ -1 +0,0 @@
-// -*- mode: c++; c-default-style: "linux" -*-
diff --git a/tools.o b/tools.o
deleted file mode 100644
index 6a075d5..0000000
--- a/tools.o
+++ /dev/null