diff --git a/.gitignore b/.gitignore
index c4bd975..ef95009 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,11 +1,7 @@
 *.o
 *.mod
 .vscode
-cMaponiA3_test*
-fMaponiA3_test*
-QMCChem_dataset_test
 Slater*
 Updates*
-tests/test
 datasets/datasets.*
-
+bin/
diff --git a/Makefile b/Makefile
index 127e584..147c26e 100644
--- a/Makefile
+++ b/Makefile
@@ -1,68 +1,84 @@
-# ARCH = -xCORE-AVX2
-
-## Used compilers
+## Compilers
+ARCH = -xCORE-AVX2
 H5CXX = h5c++
 CXX = icpc
 FC = ifort
 
-## Compiler flags & common obs & libs
+## Compiler flags
 H5CXXFLAGS = -O0 -g
 CXXFLAGS = -O0 -g -traceback
 FFLAGS = -O0 -g -traceback
+
+INCLUDE = -I $(INC_DIR)/
+DEPS_CXX = $(OBJ_DIR)/SM_MaponiA3.o
+DEPS_F = $(DEPS_CXX) $(OBJ_DIR)/SM_MaponiA3_mod.o $(OBJ_DIR)/Helpers_mod.o
 FLIBS = -lstdc++
-OBJS = SM_MaponiA3.o
 
-## Deps & objs for C++ cMaponiA3_test_3x3_3
-cMaponiA3_test_3x3_3OBJ = cMaponiA3_test_3x3_3.o
-fMaponiA3_test_3x3_3OBJ = SM_MaponiA3_mod.o fMaponiA3_test_3x3_3.o
-fMaponiA3_test_4x4_2OBJ = Helpers_mod.o SM_MaponiA3_mod.o fMaponiA3_test_4x4_2.o
-QMCChem_dataset_testOBJ = Helpers_mod.o SM_MaponiA3_mod.o QMCChem_dataset_test.o
-
-
-## Default build target: build everything
-all: cMaponiA3_test_3x3_3 fMaponiA3_test_3x3_3 fMaponiA3_test_4x4_2 QMCChem_dataset_test tests/test
-
-
-## Compile recipes for C++
-%.o: %.cpp
-	$(CXX) $(ARCH) $(CXXFLAGS) -c -o $@ $<
-
-## Compile recepies for Fortran
-%.o: %.f90
-	$(FC) $(ARCH) $(FFLAGS) -c -o $@ $<
-
-## Explicit recipe to trigger rebuild and relinking when headerfile is changed
-SM_MaponiA3.o: SM_MaponiA3.cpp Helpers.hpp
-	$(CXX) $(ARCH) $(CXXFLAGS) -fPIC -c -o $@ $<
+SRC_DIR := src
+TST_DIR := tests
+INC_DIR := include
+OBJ_DIR := build
+BIN_DIR := bin
 
+EXEC := $(BIN_DIR)/cMaponiA3_test_3x3_3 \
+		$(BIN_DIR)/test_h5 \
+		$(BIN_DIR)/fMaponiA3_test_3x3_3 \
+		$(BIN_DIR)/fMaponiA3_test_4x4_2 \
+		$(BIN_DIR)/QMCChem_dataset_test
 
 ## Build tagets
 .PHONY: all clean distclean
 
+all: $(EXEC)
+
 clean:
-	@rm -vf *.o *.mod
+	@rm -vrf $(OBJ_DIR)
 
 distclean: clean
-	@rm -vf cMaponiA3_test_3x3_3 \
-	fMaponiA3_test_3x3_3 fMaponiA3_test_4x4_2 \
-	QMCChem_dataset_test \
-	Slater* Updates.dat \
-	tests/test
+	@rm -vrf $(BIN_DIR) \
+	Slater* Updates.dat
 
 
-## Linking the C++ example program
-cMaponiA3_test_3x3_3: $(cMaponiA3_test_3x3_3OBJ) $(OBJS)
-	$(CXX) $(ARCH) $(CXXFLAGS) -o $@ $^
+#### COMPILING
+$(BIN_DIR) $(OBJ_DIR):
+	mkdir -p $@
 
-## Linking Fortran example program calling the C++ function
-fMaponiA3_test_3x3_3: $(fMaponiA3_test_3x3_3OBJ) $(OBJS)
-	$(FC) $(ARCH) $(FFLAGS) $(FLIBS) -o $@ $^
+### IMPLICIT BUILD RULES
+## C++ objects
+$(OBJ_DIR)/%.o: $(TST_DIR)/%.cpp $(INC_DIR)/* | $(OBJ_DIR)
+	$(CXX) $(CXXFLAGS) $(ARCH) $(INCLUDE) -c -o $@ $<
 
-fMaponiA3_test_4x4_2: $(fMaponiA3_test_4x4_2OBJ) $(OBJS)
-	$(FC) $(ARCH) $(FFLAGS) $(FLIBS) -o $@ $^
+## HDF5/C++ objects
+$(OBJ_DIR)/%_h5.o: $(TST_DIR)/%_h5.cpp $(INC_DIR)/* | $(OBJ_DIR)
+	$(H5CXX) $(H5CXXFLAGS) $(INCLUDE) -c -o $@ $<
 
-QMCChem_dataset_test: $(QMCChem_dataset_testOBJ) $(OBJS)
-	$(FC) $(ARCH) $(FFLAGS) $(FLIBS) -o $@ $^
+## Fortran modules
+$(OBJ_DIR)/%_mod.o: $(SRC_DIR)/%_mod.f90 | $(OBJ_DIR)
+	$(FC) $(FFLAGS) $(ARCH) -module $(OBJ_DIR)/ -c -o $@ $<
 
-tests/test: tests/test.cpp SM_MaponiA3.o
-	$(H5CXX) $(ARCH) $(H5CXXFLAGS) -o $@ $^
+## Fortran objects
+$(OBJ_DIR)/%.o: $(TST_DIR)/%.f90 | $(OBJ_DIR)
+	$(FC) $(FFLAGS) $(ARCH) -I $(OBJ_DIR)/ -c -o $@ $<
+
+### EXPLICIT BUILD RULES
+## special compiler flag -fPIC otherwise h5c++ builds fail
+$(OBJ_DIR)/SM_MaponiA3.o: $(SRC_DIR)/SM_MaponiA3.cpp $(INC_DIR)/* | $(OBJ_DIR)
+	$(CXX) $(CXXFLAGS) -fPIC $(ARCH) $(INCLUDE) -c -o $@ $<
+
+
+
+#### LINKING
+$(BIN_DIR)/cMaponiA3_test_3x3_3: $(OBJ_DIR)/cMaponiA3_test_3x3_3.o $(DEPS_CXX) | $(BIN_DIR)
+	$(CXX) -o $@ $^
+
+$(BIN_DIR)/test_h5: $(OBJ_DIR)/test_h5.o $(DEPS_CXX) | $(BIN_DIR)
+	$(H5CXX) -o $@ $^
+
+$(BIN_DIR)/fMaponiA3_test_3x3_3: $(DEPS_F) $(OBJ_DIR)/fMaponiA3_test_3x3_3.o  | $(BIN_DIR)
+	$(FC) $(FLIBS) -o $@ $^
+
+$(BIN_DIR)/fMaponiA3_test_4x4_2: $(DEPS_F) $(OBJ_DIR)/fMaponiA3_test_4x4_2.o  | $(BIN_DIR)
+	$(FC) $(FLIBS) -o $@ $^
+
+$(BIN_DIR)/QMCChem_dataset_test: $(DEPS_F) $(OBJ_DIR)/QMCChem_dataset_test.o  | $(BIN_DIR)
+	$(FC) $(FLIBS) -o $@ $^
diff --git a/Helpers.hpp b/include/Helpers.hpp
similarity index 100%
rename from Helpers.hpp
rename to include/Helpers.hpp
diff --git a/SM_MaponiA3.hpp b/include/SM_MaponiA3.hpp
similarity index 100%
rename from SM_MaponiA3.hpp
rename to include/SM_MaponiA3.hpp
diff --git a/mwe/compile.sh b/mwe/compile.sh
deleted file mode 100755
index 72b5010..0000000
--- a/mwe/compile.sh
+++ /dev/null
@@ -1 +0,0 @@
-icpc -c worker.cpp && ifort -c main.f90 && ifort -lstdc++ worker.o main.o -o test
diff --git a/mwe/main.cpp b/mwe/main.cpp
deleted file mode 100644
index cdf7867..0000000
--- a/mwe/main.cpp
+++ /dev/null
@@ -1,23 +0,0 @@
-#include <iostream>
-
-
-int main()
-{
-
-    typedef int (*to2D)[3]; //pint2 is a pointer to an array of 2 ints
-    int linArray[9] = {0,1,2,3,4,5,6,7,8};
-    
-    to2D dArray = (to2D)linArray;
-    
-    std::cout << dArray[0][0] << std::endl;
-    std::cout << dArray[0][1] << std::endl;
-    std::cout << dArray[0][2] << std::endl;
-    std::cout << dArray[1][0] << std::endl;
-    std::cout << dArray[1][1] << std::endl;
-    std::cout << dArray[1][2] << std::endl;
-    std::cout << dArray[2][0] << std::endl;
-    std::cout << dArray[2][1] << std::endl;
-    std::cout << dArray[2][2] << std::endl;
-
-    return 0;
-}
diff --git a/mwe/main.f90 b/mwe/main.f90
deleted file mode 100644
index 4d9a8e1..0000000
--- a/mwe/main.f90
+++ /dev/null
@@ -1,12 +0,0 @@
-program test
-  use iso_c_binding
-  implicit none
-
-  interface
-    subroutine hello() bind(C, name="worker")
-    end subroutine
-  end interface
-
-  call hello()
-
-end program test
diff --git a/mwe/worker.cpp b/mwe/worker.cpp
deleted file mode 100644
index 1b678b8..0000000
--- a/mwe/worker.cpp
+++ /dev/null
@@ -1,7 +0,0 @@
-#include "worker.h"
-
-void worker()
-{
-  std::cout << "Hello, World!" << std::endl;
-}
-
diff --git a/mwe/worker.h b/mwe/worker.h
deleted file mode 100644
index 70ff209..0000000
--- a/mwe/worker.h
+++ /dev/null
@@ -1,6 +0,0 @@
-#include <iostream>
-
-extern "C"
-{
-  void worker();
-}
diff --git a/QMCChem_dataset_test.m b/octave-tests/QMCChem_dataset_test.m
similarity index 100%
rename from QMCChem_dataset_test.m
rename to octave-tests/QMCChem_dataset_test.m
diff --git a/Octave-tests/SM-Coppens-1.m b/octave-tests/SM-Coppens-1.m
similarity index 100%
rename from Octave-tests/SM-Coppens-1.m
rename to octave-tests/SM-Coppens-1.m
diff --git a/Octave-tests/SMMaponiA3.m b/octave-tests/SMMaponiA3.m
similarity index 100%
rename from Octave-tests/SMMaponiA3.m
rename to octave-tests/SMMaponiA3.m
diff --git a/Octave-tests/SMMaponiA4.m b/octave-tests/SMMaponiA4.m
similarity index 100%
rename from Octave-tests/SMMaponiA4.m
rename to octave-tests/SMMaponiA4.m
diff --git a/Helpers_mod.f90 b/src/Helpers_mod.f90
similarity index 100%
rename from Helpers_mod.f90
rename to src/Helpers_mod.f90
diff --git a/SM_MaponiA3.cpp b/src/SM_MaponiA3.cpp
similarity index 100%
rename from SM_MaponiA3.cpp
rename to src/SM_MaponiA3.cpp
diff --git a/SM_MaponiA3_mod.f90 b/src/SM_MaponiA3_mod.f90
similarity index 100%
rename from SM_MaponiA3_mod.f90
rename to src/SM_MaponiA3_mod.f90
diff --git a/det.irp.f b/src/det.irp.f
similarity index 100%
rename from det.irp.f
rename to src/det.irp.f
diff --git a/QMCChem_dataset_test.f90 b/tests/QMCChem_dataset_test.f90
similarity index 100%
rename from QMCChem_dataset_test.f90
rename to tests/QMCChem_dataset_test.f90
diff --git a/cMaponiA3_test_3x3_3.cpp b/tests/cMaponiA3_test_3x3_3.cpp
similarity index 100%
rename from cMaponiA3_test_3x3_3.cpp
rename to tests/cMaponiA3_test_3x3_3.cpp
diff --git a/fMaponiA3_test_3x3_3.f90 b/tests/fMaponiA3_test_3x3_3.f90
similarity index 100%
rename from fMaponiA3_test_3x3_3.f90
rename to tests/fMaponiA3_test_3x3_3.f90
diff --git a/fMaponiA3_test_4x4_2.f90 b/tests/fMaponiA3_test_4x4_2.f90
similarity index 100%
rename from fMaponiA3_test_4x4_2.f90
rename to tests/fMaponiA3_test_4x4_2.f90
diff --git a/tests/test.cpp b/tests/test_h5.cpp
similarity index 95%
rename from tests/test.cpp
rename to tests/test_h5.cpp
index 01ae2b5..ef96b0e 100644
--- a/tests/test.cpp
+++ b/tests/test_h5.cpp
@@ -3,13 +3,13 @@
 #include "hdf5/serial/hdf5.h"
 #include "H5Cpp.h"
 
-#include "../SM_MaponiA3.hpp"
-#include "../Helpers.hpp"
+#include "SM_MaponiA3.hpp"
+#include "Helpers.hpp"
 
 using namespace H5;
-#define DEBUG 1
+//#define DEBUG 0
 
-const H5std_string FILE_NAME( "datasets.small.hdf5" );
+const H5std_string FILE_NAME( "datasets.hdf5" );
 
 void read_int(H5File file, std::string key, unsigned int * data) {
   DataSet ds = file.openDataSet(key);
diff --git a/tests/convert-to-h5.py b/tools/convert-to-h5.py
similarity index 97%
rename from tests/convert-to-h5.py
rename to tools/convert-to-h5.py
index 72a1173..e3dcaf9 100644
--- a/tests/convert-to-h5.py
+++ b/tools/convert-to-h5.py
@@ -7,7 +7,7 @@ def rl(rf):
 
 
 with h5py.File('datasets.hdf5', 'w') as f:
-    with open('datasets.short.dat', 'r') as rf:
+    with open('datasets.dat', 'r') as rf:
         while(1):
             line = rl(rf)
             if not line or not line.startswith('#START_PACKET'):