File tree restructured. Written build script build.sh. TODO: convert buld script into Makefile.

.gitignore

@@ -8,4 +8,3 @@ Slater*
 Updates*
 tests/test
 datasets/datasets.*
-

Makefile

@@ -1,6 +1,10 @@
-# ARCH = -xCORE-AVX2
+SRC_DIR := src
+INC_DIR := include
+OBJ_DIR := build
+BIN_DIR := bin
 
 ## Used compilers
+ARCH = -xCORE-AVX2
 H5CXX = h5c++
 CXX = icpc
 FC = ifort
@@ -9,10 +13,11 @@ FC = ifort
 H5CXXFLAGS = -O0 -g
 CXXFLAGS = -O0 -g -traceback
 FFLAGS = -O0 -g -traceback
+INCLUDE = -I$(INC_DIR)
 FLIBS = -lstdc++
-OBJS = SM_MaponiA3.o
 
 ## Deps & objs for C++ cMaponiA3_test_3x3_3
+OBJS = $(OBJ_DIR)/SM_MaponiA3.o
 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
@@ -24,45 +29,45 @@ all: cMaponiA3_test_3x3_3 fMaponiA3_test_3x3_3 fMaponiA3_test_4x4_2 QMCChem_data
 
 
 ## Compile recipes for C++
-%.o: %.cpp
+$(OBJ_DIR)/%.o: $(SRC_DIR)/%.cpp | $(OBJ_DIR)
-	$(CXX) $(ARCH) $(CXXFLAGS) -c -o $@ $<
+	$(CXX) $(ARCH) $(CXXFLAGS) $(INCLUDE) -c -o $@ $<
 
 ## Compile recepies for Fortran
-%.o: %.f90
+$(OBJ_DIR)/%.o: $(SRC_DIR)/%.f90 | $(OBJ_DIR)
 	$(FC) $(ARCH) $(FFLAGS) -c -o $@ $<
 
 ## Explicit recipe to trigger rebuild and relinking when headerfile is changed
-SM_MaponiA3.o: SM_MaponiA3.cpp Helpers.hpp
+$(OBJ_DIR)/SM_MaponiA3.o: $(SRC_DIR)/SM_MaponiA3.cpp $(INC_DIR)/Helpers.hpp| $(OBJ_DIR)
-	$(CXX) $(ARCH) $(CXXFLAGS) -fPIC -c -o $@ $<
+	$(CXX) $(ARCH) $(CXXFLAGS) $(INCLUDE) -fPIC -c -o $@ $<
 
 
 ## Build tagets
 .PHONY: all clean distclean
 
 clean:
-	@rm -vf *.o *.mod
+	@rm -vrf $(OBJ_DIR)
 
 distclean: clean
-	@rm -vf cMaponiA3_test_3x3_3 \
+	@rm -vrf $(BIN_DIR) \
-	fMaponiA3_test_3x3_3 fMaponiA3_test_4x4_2 \
+	Slater* Updates.dat
-	QMCChem_dataset_test \
-	Slater* Updates.dat \
-	tests/test
 
 
 ## Linking the C++ example program
-cMaponiA3_test_3x3_3: $(cMaponiA3_test_3x3_3OBJ) $(OBJS)
+$(BIN_DIR)/cMaponiA3_test_3x3_3: $(OBJ_DIR)/$(cMaponiA3_test_3x3_3OBJ) $(OBJS) | $(BIN_DIR)
-	$(CXX) $(ARCH) $(CXXFLAGS) -o $@ $^
+	$(CXX) $(ARCH) $(CXXFLAGS) $(INCLUDE) -o $@ $^
 
 ## Linking Fortran example program calling the C++ function
-fMaponiA3_test_3x3_3: $(fMaponiA3_test_3x3_3OBJ) $(OBJS)
+$(BIN_DIR)/fMaponiA3_test_3x3_3: $(OBJ_DIR)/$(fMaponiA3_test_3x3_3OBJ) $(OBJS) | $(BIN_DIR)
 	$(FC) $(ARCH) $(FFLAGS) $(FLIBS) -o $@ $^
 
-fMaponiA3_test_4x4_2: $(fMaponiA3_test_4x4_2OBJ) $(OBJS)
+$(BIN_DIR)/fMaponiA3_test_4x4_2: $(OBJ_DIR)/$(fMaponiA3_test_4x4_2OBJ) $(OBJS) | $(BIN_DIR)
 	$(FC) $(ARCH) $(FFLAGS) $(FLIBS) -o $@ $^
 
-QMCChem_dataset_test: $(QMCChem_dataset_testOBJ) $(OBJS)
+$(BIN_DIR)/QMCChem_dataset_test: $(OBJ_DIR)/$(QMCChem_dataset_testOBJ) $(OBJS) | $(BIN_DIR)
 	$(FC) $(ARCH) $(FFLAGS) $(FLIBS) -o $@ $^
 
-tests/test: tests/test.cpp SM_MaponiA3.o
+$(BIN_DIR)/test: $(SRC_DIR)/test.cpp $(OBJS) | $(BIN_DIR)
-	$(H5CXX) $(ARCH) $(H5CXXFLAGS) -o $@ $^
+	$(H5CXX) $(H5CXXFLAGS) $(INCLUDE) -o $@ $^
+
+$(BIN_DIR) $(OBJ_DIR):
+	mkdir -p $@

build.sh

@@ -0,0 +1,36 @@
+
+
+mkdir build/ bin/
+
+## compile tests/test.cpp
+icpc -O0 -fPIC -c src/SM_MaponiA3.cpp -o build/SM_MaponiA3.o -I include/
+
+## compile tests/fMaponiA3_test_3x3_3.f90
+ifort -c src/SM_MaponiA3_mod.f90 -o build/SM_MaponiA3_mod.o -module build
+ifort -c tests/fMaponiA3_test_3x3_3.f90 -o build/fMaponiA3_test_3x3_3.o -I build/
+## link bin/QMCChem_dataset_test
+ifort -o bin/fMaponiA3_test_3x3_3 build/fMaponiA3_test_3x3_3.o build/SM_MaponiA3_mod.o build/SM_MaponiA3.o -lstdc++
+
+## compile tests/fMaponiA3_test_4x4_2.f90
+ifort -c src/SM_MaponiA3_mod.f90 -o build/SM_MaponiA3_mod.o -module build
+ifort -c src/Helpers_mod.f90 -o build/Helpers_mod.o -module build
+ifort -c tests/fMaponiA3_test_4x4_2.f90 -o build/fMaponiA3_test_4x4_2.o -I build/
+## link bin/QMCChem_dataset_test
+ifort -o bin/fMaponiA3_test_4x4_2 build/fMaponiA3_test_4x4_2.o build/SM_MaponiA3_mod.o build/Helpers_mod.o build/SM_MaponiA3.o -lstdc++
+
+## compile tests/QMCChem_dataset_test.f90
+ifort -c src/SM_MaponiA3_mod.f90 -o build/SM_MaponiA3_mod.o -module build
+ifort -c src/Helpers_mod.f90 -o build/Helpers_mod.o -module build
+ifort -c tests/QMCChem_dataset_test.f90 -o build/QMCChem_dataset_test.o -I build/
+## link bin/QMCChem_dataset_test
+ifort -o bin/QMCChem_dataset_test build/QMCChem_dataset_test.o build/SM_MaponiA3_mod.o build/Helpers_mod.o build/SM_MaponiA3.o  -lstdc++
+
+## compile tests/test.cpp
+h5c++ -c tests/test.cpp -o build/test.o -I include/
+## link bin/test
+h5c++ -o bin/test build/test.o build/SM_MaponiA3.o
+
+## compile tests/cMaponiA3_test_3x3_3.cpp
+icpc -c tests/cMaponiA3_test_3x3_3.cpp -o build/cMaponiA3_test_3x3_3.o -I include/
+## link bin/cMaponiA3_test_3x3_3
+icpc -o bin/cMaponiA3_test_3x3_3 build/cMaponiA3_test_3x3_3.o build/SM_MaponiA3.o

cMaponiA3_test_3x3_3.cpp

@@ -1,53 +0,0 @@
-// main.cpp
-#include "SM_MaponiA3.hpp"
-#include "Helpers.hpp"
-
-int main() {
-
-    unsigned int M = 3; // Dimension of the Slater-matrix
-    unsigned int i, j; // Indices for iterators
-
-    // Declare, allocate all vectors and matrices and fill them with zeros
-    unsigned int *Ar_index = new unsigned int[M];
-    double *A = new double[M*M]; // The matrix to be inverted
-    double *A0 = new double[M*M]; // A diagonal matrix with the digonal elements of A
-    double *Ar = new double[M*M]; // The update matrix
-    double *A0_inv = new double[M*M]; // The inverse
-
-    // Fill with zeros
-    for (i = 0; i < M; i++) {
-        for (j = 0; j < M; j++) {
-            A0[i*M+j] = 0;
-            Ar[i*M+j] = 0;
-            A0_inv[i*M+j] = 0;
-        }
-    }
-
-    // Initialize A with M=3 and fill acc. to Eq. (17) from paper
-    A[0] = 1;    A[3] = 1;    A[6] = -1;
-    A[1] = 1;    A[4] = 1;    A[7] = 0;
-    A[2] = -1;   A[5] = 0;    A[8] = -1;
-
-    showMatrix(A, M, "A");
-
-    // Initialize the diagonal matrix A0,
-    // the inverse of A0_inv of diagonal matrix A0_inv
-    // and the update matrix Ar
-    for (i = 0; i < M; i++) {
-        A0[i*M + i] = A[i*M + i];
-        A0_inv[i*M + i] = 1.0/A[i*M + i];
-        Ar_index[i] = i+1; // ! First column needs to start with 1 !
-        for (j = 0; j < M; j++) {
-            Ar[i*M + j] = A[i*M + j] - A0[i*M + j];
-        }
-    }
-
-    // Define pointers dim and n_updates to use in Sherman-Morrison(...) function call
-    MaponiA3(A0_inv, M, M, Ar, Ar_index);
-    showMatrix(A0_inv, M, "A0_inv");
-
-    // Deallocate all vectors and matrices
-    delete [] A, A0, A0_inv, Ar, Ar_index;
-
-    return 0;
-}

fMaponiA3_test_3x3_3.f90

@@ -1,59 +0,0 @@
-program Interface_test
-    use Sherman_Morrison
-    implicit none
-
-    integer i, j !! Iterators
-    integer(c_int) :: Dim, N_updates
-    integer(c_int), dimension(:), allocatable :: Updates_index
-    real(c_double), dimension(:,:), allocatable :: A, S, Updates
-    real(c_double), dimension(:,:), allocatable :: S_inv
-
-    Dim = 3
-    N_updates = 3
-    allocate(Updates_index(Dim), A(Dim,Dim), S(Dim,Dim), Updates(Dim,Dim), S_inv(Dim,Dim))
-
-    !! Initialize A with M=3 and fill acc. to Eq. (17) from paper
-    A(1,1) = 1.0d0
-    A(1,2) = 1.0d0
-    A(1,3) = -1.0d0
-    A(2,1) = 1.0d0
-    A(2,2) = 1.0d0
-    A(2,3) = 0.0d0
-    A(3,1) = -1.0d0
-    A(3,2) = 0.0d0
-    A(3,3) = -1.0d0
-
-    do i=1,Dim
-        do j=1,Dim
-            write(*,"(F3.0,3X)", advance="no") A(i,j)
-        end do
-        write(*,*)
-    end do
-    write(*,*)
-
-    !! Prepare the diagonal matrix S and the update matrix Updates
-    do i=1,Dim
-        Updates_index(i) = i
-        do j=1,Dim
-            if (i == j) then
-                S(i,j) = A(i,j)
-                S_inv(i,j) = 1.0d0 / S(i,j)
-            else
-                S(i,j) = 0.0d0
-                S_inv(i,j) = 0.0d0
-            end if
-            Updates(i,j) = A(i,j) - S(i,j)
-        end do
-    end do
-
-    call MaponiA3(S_inv, Dim, N_updates, Updates, Updates_index)
-
-    do i=1,Dim
-        do j=1,Dim
-            write(*,"(F3.0,3X)", advance="no") S_inv(i,j)
-        end do
-        write(*,*)
-    end do
-
-    deallocate(Updates_index, A, S, Updates, S_inv)
-end program

fMaponiA3_test_4x4_2.f90

@@ -1,151 +0,0 @@
-program Interface_test
-    use Sherman_Morrison
-    use Helpers
-    implicit none
-
-    integer i, j, col !! Iterators
-    integer(c_int) :: Dim, N_updates
-    integer(c_int), dimension(:), allocatable :: Updates_index
-    real(c_double), dimension(:,:), allocatable :: S, A, Updates
-    real(c_double), dimension(:,:), allocatable :: S_inv, S_inv_t, A_inv
-
-    Dim = 4
-    N_updates = 2
-    allocate( S(Dim,Dim), S_inv(Dim,Dim), S_inv_t(Dim,Dim), A(Dim,Dim), A_inv(Dim,Dim), &
-              Updates(Dim,N_updates), Updates_index(N_updates))
-
-    !! Initialize S, S_inv, A and A_inv
-    S(1,1) = 1.0d0
-    S(1,2) = 0.0d0
-    S(1,3) = 1.0d0
-    S(1,4) = -1.0d0
-    S(2,1) = 0.0d0
-    S(2,2) = 1.0d0
-    S(2,3) = 1.0d0
-    S(2,4) = 0.0d0
-    S(3,1) = -1.0d0
-    S(3,2) = 0.0d0
-    S(3,3) = -1.0d0
-    S(3,4) = 0.0d0
-    S(4,1) = 1.0d0
-    S(4,2) = 1.0d0
-    S(4,3) = 1.0d0
-    S(4,4) = 1.0d0
-
-    S_inv(1,1) = 1.0d0
-    S_inv(1,2) = -1.0d0
-    S_inv(1,3) = 1.0d0
-    S_inv(1,4) = 1.0d0
-    S_inv(2,1) = 1.0d0
-    S_inv(2,2) = 0.0d0
-    S_inv(2,3) = 2.0d0
-    S_inv(2,4) = 1.0d0
-    S_inv(3,1) = -1.0d0
-    S_inv(3,2) = 1.0d0
-    S_inv(3,3) = -2.0d0
-    S_inv(3,4) = -1.0d0
-    S_inv(4,1) = -1.0d0
-    S_inv(4,2) = 0.0d0
-    S_inv(4,3) = -1.0d0
-    S_inv(4,4) = 0.0d0
-
-    A(1,1) = 1.0d0
-    A(1,2) = 0.0d0
-    A(1,3) = 1.0d0
-    A(1,4) = -1.0d0
-    A(2,1) = 0.0d0
-    A(2,2) = -1.0d0
-    A(2,3) = 1.0d0
-    A(2,4) = -1.0d0
-    A(3,1) = -1.0d0
-    A(3,2) = 0.0d0
-    A(3,3) = -1.0d0
-    A(3,4) = 0.0d0
-    A(4,1) = 1.0d0
-    A(4,2) = 1.0d0
-    A(4,3) = 1.0d0
-    A(4,4) = 1.0d0
-
-    A_inv(1,1) = 0.0d0
-    A_inv(1,2) = -1.0d0
-    A_inv(1,3) = -2.0d0
-    A_inv(1,4) = -1.0d0
-    A_inv(2,1) = 1.0d0
-    A_inv(2,2) = 0.0d0
-    A_inv(2,3) = 2.0d0
-    A_inv(2,4) = 1.0d0
-    A_inv(3,1) = 0.0d0
-    A_inv(3,2) = 1.0d0
-    A_inv(3,3) = 1.0d0
-    A_inv(3,4) = 1.0d0
-    A_inv(4,1) = -1.0d0
-    A_inv(4,2) = 0.0d0
-    A_inv(4,3) = -1.0d0
-    A_inv(4,4) = 0.0d0
-
-    !! Prepare Updates and Updates_index
-    Updates(1,1) = 0
-    Updates(1,2) = 0
-    Updates(2,1) = -2
-    Updates(2,2) = -1
-    Updates(3,1) = 0
-    Updates(3,2) = 0
-    Updates(4,1) = 0
-    Updates(4,2) = 0
-
-    Updates_index(1) = 2
-    Updates_index(2) = 4
-
-    !! Write current S and S_inv to file for check in Octave
-    open(unit = 2000, file = "Slater_old.dat")
-    open(unit = 3000, file = "Slater_old_inv.dat")
-    do i=1,dim
-        do j=1,dim
-            write(2000,"(E23.15, 1X)", advance="no") S(i,j)
-            write(3000,"(E23.15, 1X)", advance="no") S_inv(i,j)
-        end do
-        write(2000,*)
-        write(3000,*)
-    end do
-    close(2000)
-    close(3000)
-
-    !! Write Updates to file to check
-    open(unit = 2000, file = "Updates.dat")
-    do i=1,dim
-        do j=1,n_updates
-            write(2000,"(E23.15, 1X)", advance="no") Updates(i,j)
-        end do
-        write(2000,*)
-    end do
-    close(2000)
-
-    !! Update S
-    do i=1,N_updates
-        do j=1,Dim
-            col = Updates_index(i)
-            S(j,col) = S(j,col) + Updates(j,i)
-        end do
-    end do
-            
-    !! Update S_inv
-    call Transpose(S_inv, S_inv_t, Dim)
-    call MaponiA3(S_inv_t, Dim, N_updates, Updates, Updates_index)
-    call Transpose(S_inv_t, S_inv, Dim)
-
-    !! Write new S and S_inv to file for check in Octave
-    open(unit = 4000, file = "Slater.dat")
-    open(unit = 5000, file = "Slater_inv.dat")
-    do i=1,dim
-        do j=1,dim
-            write(4000,"(E23.15, 1X)", advance="no") S(i,j)
-            write(5000,"(E23.15, 1X)", advance="no") S_inv(i,j)
-        end do
-        write(4000,*)
-        write(5000,*)
-    end do
-    close(4000)
-    close(5000)
-
-    deallocate(Updates_index, A, A_inv, S, Updates, S_inv)
-end program

mwe/compile.sh

@@ -1 +0,0 @@
-icpc -c worker.cpp && ifort -c main.f90 && ifort -lstdc++ worker.o main.o -o test

mwe/main.cpp

@@ -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;
-}

mwe/main.f90

@@ -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

mwe/worker.cpp

@@ -1,7 +0,0 @@
-#include "worker.h"
-
-void worker()
-{
-  std::cout << "Hello, World!" << std::endl;
-}
-

mwe/worker.h

@@ -1,6 +0,0 @@
-#include <iostream>
-
-extern "C"
-{
-  void worker();
-}

tests/test.cpp

@@ -3,8 +3,8 @@
 #include "hdf5/serial/hdf5.h"
 #include "H5Cpp.h"
 
-#include "../SM_MaponiA3.hpp"
+#include "SM_MaponiA3.hpp"
-#include "../Helpers.hpp"
+#include "Helpers.hpp"
 
 using namespace H5;
 //#define DEBUG 0