From 8e0aef7717fad51ed216b6d86b2914fcac1932a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fran=C3=A7ois=20Coppens?= <francois.coppens@uvsq.fr>
Date: Sat, 27 Feb 2021 12:25:55 +0100
Subject: [PATCH] Restructuring complete. Updated makefile.

---
 .gitignore                      |   5 +-
 Makefile                        | 107 ++++++++++++----------
 build.sh                        |  36 --------
 tests/cMaponiA3_test_3x3_3.cpp  |  53 +++++++++++
 tests/fMaponiA3_test_3x3_3.f90  |  59 +++++++++++++
 tests/fMaponiA3_test_4x4_2.f90  | 151 ++++++++++++++++++++++++++++++++
 tests/{test.cpp => test_h5.cpp} |   0
 7 files changed, 323 insertions(+), 88 deletions(-)
 delete mode 100755 build.sh
 create mode 100644 tests/cMaponiA3_test_3x3_3.cpp
 create mode 100644 tests/fMaponiA3_test_3x3_3.f90
 create mode 100644 tests/fMaponiA3_test_4x4_2.f90
 rename tests/{test.cpp => test_h5.cpp} (100%)

diff --git a/.gitignore b/.gitignore
index 970fc12..ef95009 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,10 +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 271570a..147c26e 100644
--- a/Makefile
+++ b/Makefile
@@ -1,49 +1,36 @@
-SRC_DIR := src
-INC_DIR := include
-OBJ_DIR := build
-BIN_DIR := bin
-
-## 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)
+
+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++
 
-## Deps & objs for C++ cMaponiA3_test_3x3_3
-OBJS = $(OBJ_DIR)/SM_MaponiA3.o
-cMaponiA3_test_3x3_3OBJ = cMaponiA3_test_3x3_3.o
-fMaponiA3_test_3x3_3OBJ = SM_MaponiA3_mod.o fMaponiA3_test_3x3_3.o
-fMaponiA3_test_4x4_2OBJ = Helpers_mod.o SM_MaponiA3_mod.o fMaponiA3_test_4x4_2.o
-QMCChem_dataset_testOBJ = Helpers_mod.o SM_MaponiA3_mod.o QMCChem_dataset_test.o
-
-
-## Default build target: build everything
-all: cMaponiA3_test_3x3_3 fMaponiA3_test_3x3_3 fMaponiA3_test_4x4_2 QMCChem_dataset_test tests/test
-
-
-## Compile recipes for C++
-$(OBJ_DIR)/%.o: $(SRC_DIR)/%.cpp | $(OBJ_DIR)
-	$(CXX) $(ARCH) $(CXXFLAGS) $(INCLUDE) -c -o $@ $<
-
-## Compile recepies for Fortran
-$(OBJ_DIR)/%.o: $(SRC_DIR)/%.f90 | $(OBJ_DIR)
-	$(FC) $(ARCH) $(FFLAGS) -c -o $@ $<
-
-## Explicit recipe to trigger rebuild and relinking when headerfile is changed
-$(OBJ_DIR)/SM_MaponiA3.o: $(SRC_DIR)/SM_MaponiA3.cpp $(INC_DIR)/Helpers.hpp| $(OBJ_DIR)
-	$(CXX) $(ARCH) $(CXXFLAGS) $(INCLUDE) -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 -vrf $(OBJ_DIR)
 
@@ -52,22 +39,46 @@ distclean: clean
 	Slater* Updates.dat
 
 
-## Linking the C++ example program
-$(BIN_DIR)/cMaponiA3_test_3x3_3: $(OBJ_DIR)/$(cMaponiA3_test_3x3_3OBJ) $(OBJS) | $(BIN_DIR)
-	$(CXX) $(ARCH) $(CXXFLAGS) $(INCLUDE) -o $@ $^
-
-## Linking Fortran example program calling the C++ function
-$(BIN_DIR)/fMaponiA3_test_3x3_3: $(OBJ_DIR)/$(fMaponiA3_test_3x3_3OBJ) $(OBJS) | $(BIN_DIR)
-	$(FC) $(ARCH) $(FFLAGS) $(FLIBS) -o $@ $^
-
-$(BIN_DIR)/fMaponiA3_test_4x4_2: $(OBJ_DIR)/$(fMaponiA3_test_4x4_2OBJ) $(OBJS) | $(BIN_DIR)
-	$(FC) $(ARCH) $(FFLAGS) $(FLIBS) -o $@ $^
-
-$(BIN_DIR)/QMCChem_dataset_test: $(OBJ_DIR)/$(QMCChem_dataset_testOBJ) $(OBJS) | $(BIN_DIR)
-	$(FC) $(ARCH) $(FFLAGS) $(FLIBS) -o $@ $^
-
-$(BIN_DIR)/test: $(SRC_DIR)/test.cpp $(OBJS) | $(BIN_DIR)
-	$(H5CXX) $(H5CXXFLAGS) $(INCLUDE) -o $@ $^
-
+#### COMPILING
 $(BIN_DIR) $(OBJ_DIR):
 	mkdir -p $@
+
+### IMPLICIT BUILD RULES
+## C++ objects
+$(OBJ_DIR)/%.o: $(TST_DIR)/%.cpp $(INC_DIR)/* | $(OBJ_DIR)
+	$(CXX) $(CXXFLAGS) $(ARCH) $(INCLUDE) -c -o $@ $<
+
+## HDF5/C++ objects
+$(OBJ_DIR)/%_h5.o: $(TST_DIR)/%_h5.cpp $(INC_DIR)/* | $(OBJ_DIR)
+	$(H5CXX) $(H5CXXFLAGS) $(INCLUDE) -c -o $@ $<
+
+## Fortran modules
+$(OBJ_DIR)/%_mod.o: $(SRC_DIR)/%_mod.f90 | $(OBJ_DIR)
+	$(FC) $(FFLAGS) $(ARCH) -module $(OBJ_DIR)/ -c -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/build.sh b/build.sh
deleted file mode 100755
index f4c7e12..0000000
--- a/build.sh
+++ /dev/null
@@ -1,36 +0,0 @@
-
-
-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
diff --git a/tests/cMaponiA3_test_3x3_3.cpp b/tests/cMaponiA3_test_3x3_3.cpp
new file mode 100644
index 0000000..525d15d
--- /dev/null
+++ b/tests/cMaponiA3_test_3x3_3.cpp
@@ -0,0 +1,53 @@
+// 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;
+}
diff --git a/tests/fMaponiA3_test_3x3_3.f90 b/tests/fMaponiA3_test_3x3_3.f90
new file mode 100644
index 0000000..bbc921c
--- /dev/null
+++ b/tests/fMaponiA3_test_3x3_3.f90
@@ -0,0 +1,59 @@
+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
diff --git a/tests/fMaponiA3_test_4x4_2.f90 b/tests/fMaponiA3_test_4x4_2.f90
new file mode 100644
index 0000000..863b87b
--- /dev/null
+++ b/tests/fMaponiA3_test_4x4_2.f90
@@ -0,0 +1,151 @@
+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
diff --git a/tests/test.cpp b/tests/test_h5.cpp
similarity index 100%
rename from tests/test.cpp
rename to tests/test_h5.cpp