From 6f34f485d380c116e8176da7fa061b2d613e144e Mon Sep 17 00:00:00 2001 From: Pablo Oliveira Date: Tue, 9 Feb 2021 13:40:52 +0100 Subject: [PATCH] C++ redesign of data-structures - Use flat arrays - Use real type for all matrices - Merge _f MaponiA3 files --- Helpers.hpp | 60 ++++++------------ Makefile | 10 +-- SM_MaponiA3.cpp | 49 ++++++++------- SM_MaponiA3.hpp | 3 +- SM_MaponiA3_f.cpp | 144 -------------------------------------------- SM_MaponiA3_f.hpp | 4 -- SM_MaponiA3_mod.f90 | 8 +-- cppmain.cpp | 63 +++++++------------ fmain.f90 | 24 ++++---- 9 files changed, 90 insertions(+), 275 deletions(-) delete mode 100644 SM_MaponiA3_f.cpp delete mode 100644 SM_MaponiA3_f.hpp diff --git a/Helpers.hpp b/Helpers.hpp index 23bf812..176e97c 100644 --- a/Helpers.hpp +++ b/Helpers.hpp @@ -7,8 +7,8 @@ using namespace std; template unsigned int getMaxIndex(T *vector, unsigned int size) { - unsigned int i; - unsigned int max = vector[0]; + unsigned int i; + unsigned int max = vector[0]; unsigned int maxi = 0; for (i = 1; i < size; i++) { if (vector[i] > max) { @@ -16,7 +16,7 @@ unsigned int getMaxIndex(T *vector, unsigned int size) { maxi = i; } } - return maxi; + return maxi; } template @@ -34,12 +34,12 @@ void showVector(T *vector, unsigned int size, string name) { } template -void showMatrix(T **matrix, unsigned int size, string name) { +void showMatrix(T *matrix, unsigned int M, string name) { cout << name << " = " << endl; - for (unsigned int i = 0; i < size; i++) { + for (unsigned int i = 0; i < M; i++) { cout << "[ "; - for (unsigned int j = 0; j < size; j++) { - cout << matrix[i][j] << " "; + for (unsigned int j = 0; j < M; j++) { + cout << matrix[i*M+j] << " "; } cout << " ]" << endl; } @@ -60,31 +60,12 @@ void showMatrixT(T **matrix, unsigned int size, string name) { } template -T **matMul(T **A, T **B, unsigned int size) { - T **C = new T*[size]; - for (unsigned int i = 0; i < size; i++) { - C[i] = new T[size]; - } - for (unsigned int i = 0; i < size; i++) { - for (unsigned int j = 0; j < size; j++) { - for (unsigned int k = 0; k < size; k++) { - C[i][j] += A[i][k] * B[k][j]; - } - } - } - return C; -} - -template -T **matMul2(T **A, T (*B)[], unsigned int size) { - T **C = new T*[size]; - for (unsigned int i = 0; i < size; i++) { - C[i] = new T[size]; - } - for (unsigned int i = 0; i < size; i++) { - for (unsigned int j = 0; j < size; j++) { - for (unsigned int k = 0; k < size; k++) { - C[i][j] += A[i][k] * B[k][j]; +T *matMul(T *A, T *B, unsigned int M) { + T *C = new T[M*M]; + for (unsigned int i = 0; i < M; i++) { + for (unsigned int j = 0; j < M; j++) { + for (unsigned int k = 0; k < M; k++) { + C[i*M+j] += A[i*M+k] * B[k*M+j]; } } } @@ -93,14 +74,11 @@ T **matMul2(T **A, T (*B)[], unsigned int size) { template -T1 **outProd(T1 *vec1, T2 *vec2, unsigned int size) { - T1 **C = new T1*[size]; - for (unsigned int i = 0; i < size; i++) { - C[i] = new T1[size]; - } - for (unsigned int i = 0; i < size; i++) { - for (unsigned int j = 0; j < size; j++) { - C[i][j] = vec1[i+1] * vec2[j]; +T1 *outProd(T1 *vec1, T2 *vec2, unsigned int M) { + T1 *C = new T1[M*M]; + for (unsigned int i = 0; i < M; i++) { + for (unsigned int j = 0; j < M; j++) { + C[i*M+j] = vec1[i+1] * vec2[j]; } } return C; @@ -140,4 +118,4 @@ T matDet(T **A, unsigned int M) { return det; } delete [] temp; -} \ No newline at end of file +} diff --git a/Makefile b/Makefile index 1a51821..e913743 100644 --- a/Makefile +++ b/Makefile @@ -3,9 +3,9 @@ CXX = icpc FC = ifort ## Compiler flags -CXXFLAGS = -O0 -debug full -traceback -FFLAGS = -O0 -debug full -traceback -# ARCH = -xCORE-AVX2 +CXXFLAGS = -O0 #-debug full -traceback +FFLAGS = -O0 #-debug full -traceback +# ARCH = -xCORE-AVX2 ## Deps & objs for the C++ stuff cppDEPS = cppmain.cpp SM_MaponiA3.cpp SM_MaponiA3.hpp Helpers.hpp @@ -13,7 +13,7 @@ cppOBJ = cppmain.o SM_MaponiA3.o ## Deps & objs for the Fortran stuff fDEPS = fmain.f90 SM_MaponiA3_mod.f90 -fOBJ = SM_MaponiA3_f.o SM_MaponiA3_mod.o fmain.o +fOBJ = SM_MaponiA3.o SM_MaponiA3_mod.o fmain.o fLIBS = -lstdc++ ## Compile recipes for C++ stuff @@ -31,7 +31,7 @@ all: cppSherman-Morrison fSherman-Morrison clean: @rm -vf *.o *.mod - + distclean: clean @rm -vf cppSherman-Morrison fSherman-Morrison diff --git a/SM_MaponiA3.cpp b/SM_MaponiA3.cpp index 9fc477c..7b6a11d 100644 --- a/SM_MaponiA3.cpp +++ b/SM_MaponiA3.cpp @@ -1,21 +1,20 @@ -// SM-MaponiA3.cpp +// SM-MaponiA3_f.cpp // Algorithm 3 from P. Maponi, // p. 283, doi:10.1016/j.laa.2006.07.007 #include "SM_MaponiA3.hpp" #include "Helpers.hpp" -void Sherman_Morrison(int **Slater0, double **Slater_inv, unsigned int *Dim, unsigned int *N_updates, int **Updates, unsigned int *Updates_index) { - unsigned int k, l, lbar, i, j, tmp, M = *Dim; +void MaponiA3(double *Slater0, double *Slater_inv, unsigned int M, unsigned int N_updates, double *Updates, unsigned int *Updates_index) { + + unsigned int k, l, lbar, i, j, tmp = M; unsigned int *p = new unsigned int[M+1]; - unsigned int **Id = new unsigned int*[M]; + double *Id = new double[M*M]; double alpha, beta; - double **U, *breakdown = new double[M+1]; - double **Al = new double*[M]; + double *breakdown = new double[M+1]; + double *Al = new double[M*M]; p[0] = 0; for (i = 0; i < M; i++) { p[i+1] = i + 1; - Id[i] = new unsigned int[M]; - Al[i] = new double[M]; } // Declare auxiliary solution matrix ylk @@ -30,11 +29,11 @@ void Sherman_Morrison(int **Slater0, double **Slater_inv, unsigned int *Dim, uns // Initialize identity matrix for (i = 0; i < M; i++) { for (j = 0; j < M; j++) { - if (i != j) Id[i][j] = 0; - else Id[i][j] = 1; + if (i != j) Id[i*M+j] = 0; + else Id[i*M+j] = 1; } } - + // Initialize ylk with zeros for (l = 0; l < M; l++) { for (k = 0; k < M+1; k++) { @@ -47,7 +46,7 @@ void Sherman_Morrison(int **Slater0, double **Slater_inv, unsigned int *Dim, uns // Calculate all the y0k in M^2 multiplications instead of M^3 for (k = 1; k < M+1; k++) { for (i = 1; i < M+1; i++) { - ylk[0][k][i] = Slater_inv[i-1][i-1] * Updates[i-1][k-1]; + ylk[0][k][i] = Slater_inv[(i-1)*M+(i-1)] * Updates[(i-1)*M+(k-1)]; } } @@ -76,19 +75,19 @@ void Sherman_Morrison(int **Slater0, double **Slater_inv, unsigned int *Dim, uns } } - // Construct A-inverse from A0-inverse and the ylk // Keep the memory location of the passed array 'Slater_inv' before 'Slater_inv' // gets reassigned by 'matMul(...)' in the next line, by creating a new // pointer 'copy' that points to whereever 'Slater_inv' points to now. - double **copy = Slater_inv; + double *copy = Slater_inv; + // Construct A-inverse from A0-inverse and the ylk for (l = 0; l < M; l++) { k = l+1; - U = outProd(ylk[l][p[k]], Id[p[k]-1], M); + double * U = outProd(ylk[l][p[k]], (Id + (p[k]-1)*M), M); beta = 1 + ylk[l][p[k]][p[k]]; for (i = 0; i < M; i++) { for (j = 0; j < M; j++) { - Al[i][j] = Id[i][j] - U[i][j] / beta; + Al[i*M+j] = Id[i*M+j] - U[i*M+j] / beta; } } Slater_inv = matMul(Al, Slater_inv, M); @@ -96,16 +95,24 @@ void Sherman_Morrison(int **Slater0, double **Slater_inv, unsigned int *Dim, uns // Assign the new values of 'Slater_inv' to the old values in 'copy[][]' for (i = 0; i < M; i++) { - for (j = 0; j < M; j++) { - copy[i][j] = Slater_inv[i][j]; - } + for (j = 0; j < M; j++) { + copy[i*M+j] = Slater_inv[i*M+j]; + } } for (l = 0; l < M; l++) { for (k = 0; k < M+1; k++) { delete [] ylk[l][k]; } - delete [] ylk[l], Id[l], U[l], Al[l], Slater_inv[l]; + delete [] ylk[l]; } + delete [] Id, Al; delete [] p, breakdown; -} \ No newline at end of file +} + +extern "C" { + void MaponiA3_f(double **linSlater0, double **linSlater_inv, unsigned int *Dim, unsigned int *N_updates, double **linUpdates, unsigned int **Updates_index) + { + MaponiA3(*linSlater0, *linSlater_inv, *Dim, *N_updates, *linUpdates, *Updates_index); + } +} diff --git a/SM_MaponiA3.hpp b/SM_MaponiA3.hpp index 5e330ba..efc67d7 100644 --- a/SM_MaponiA3.hpp +++ b/SM_MaponiA3.hpp @@ -1,2 +1 @@ -// SM-MaponiA3.hpp -void Sherman_Morrison(int **Slater0, double **Slater_inv, unsigned int *Dim, unsigned int *N_updates, int **Updates, unsigned int *Updates_index); +void MaponiA3(double *Slater0, double *Slater_inv, unsigned int M, unsigned int N_updates, double *Updates, unsigned int *Updates_index); diff --git a/SM_MaponiA3_f.cpp b/SM_MaponiA3_f.cpp deleted file mode 100644 index 4ef5ab4..0000000 --- a/SM_MaponiA3_f.cpp +++ /dev/null @@ -1,144 +0,0 @@ -// SM-MaponiA3_f.cpp -// Algorithm 3 from P. Maponi, -// p. 283, doi:10.1016/j.laa.2006.07.007 -#include "SM_MaponiA3_f.hpp" -#include "Helpers.hpp" - -void MaponiA3(int **linSlater0, double **linSlater_inv, unsigned int *Dim, unsigned int *N_updates, int **linUpdates, unsigned int *Updates_index) { - - // Define new 2D arrays and copy the elements of the - // linear passed Fortran arrays. This block needs to - // be replaced with a suitable casting mechanism to - // avoid copying of memory. - int **Slater0 = new int*[*Dim]; - int **Updates = new int*[*Dim]; - double **Slater_inv = new double*[*Dim]; - for (int i = 0; i < *Dim; i++) { - Slater0[i] = new int[*Dim]; - Updates[i] = new int[*Dim]; - Slater_inv[i] = new double[*Dim]; - } - for (unsigned int i = 0; i < *Dim; i++) { - for (unsigned int j = 0; j < *Dim; j++) { - Slater0[i][j] = linSlater0[0][i+*Dim*j]; - Slater_inv[i][j] = linSlater_inv[0][i+*Dim*j]; - Updates[i][j] = linUpdates[0][i+*Dim*j]; - } - } - // Possible casting candidates - // int (*Slater0)[*Dim] = (int(*)[*Dim])linSlater0[0]; - // double (*Slater_inv)[*Dim] = (double(*)[*Dim])linSlater_inv[0]; - // int (*Updates)[*Dim] = (int(*)[*Dim])linUpdates[0]; - //////////////////////////////////////////////////////////////////////// - - unsigned int k, l, lbar, i, j, tmp, M = *Dim; - unsigned int *p = new unsigned int[M+1]; - unsigned int **Id = new unsigned int*[M]; - double alpha, beta; - double **U, *breakdown = new double[M+1]; - double **Al = new double*[M]; - p[0] = 0; - for (i = 0; i < M; i++) { - p[i+1] = i + 1; - Id[i] = new unsigned int[M]; - Al[i] = new double[M]; - } - - // Declare auxiliary solution matrix ylk - double ***ylk = new double**[M]; - for (l = 0; l < M; l++) { - ylk[l] = new double*[M+1]; - for (k = 0; k < M+1; k++) { - ylk[l][k] = new double[M+1]; - } - } - - // Initialize identity matrix - for (i = 0; i < M; i++) { - for (j = 0; j < M; j++) { - if (i != j) Id[i][j] = 0; - else Id[i][j] = 1; - } - } - - // Initialize ylk with zeros - for (l = 0; l < M; l++) { - for (k = 0; k < M+1; k++) { - for (i = 0; i < M+1; i++) { - ylk[l][k][i] = 0; - } - } - } - - // Calculate all the y0k in M^2 multiplications instead of M^3 - for (k = 1; k < M+1; k++) { - for (i = 1; i < M+1; i++) { - ylk[0][k][i] = Slater_inv[i-1][i-1] * Updates[i-1][k-1]; - } - } - - // Calculate all the ylk from the y0k - for (l = 1; l < M; l++) { - for (j = l; j < M+1; j++) { - breakdown[j] = abs( 1 + ylk[l-1][p[j]][p[j]] ); - } - lbar = getMaxIndex(breakdown, M+1); - for (i = 0; i < M; i++) { - breakdown[i] = 0; - } - tmp = p[l]; - p[l] = p[lbar]; - p[lbar] = tmp; - for (k = l+1; k < M+1; k++) { - beta = 1 + ylk[l-1][p[l]][p[l]]; - if (beta == 0) { - cout << "Break-down condition occured. Exiting..." << endl; - exit; - } - for (i = 1; i < M+1; i++) { - alpha = ylk[l-1][p[k]][p[l]] / beta; - ylk[l][p[k]][i] = ylk[l-1][p[k]][i] - alpha * ylk[l-1][p[l]][i]; - } - } - } - - // Keep the memory location of the passed array 'Slater_inv' before 'Slater_inv' - // gets reassigned by 'matMul(...)' in the next line, by creating a new - // pointer 'copy' that points to whereever 'Slater_inv' points to now. - // double **copy = Slater_inv; - - // Construct A-inverse from A0-inverse and the ylk - for (l = 0; l < M; l++) { - k = l+1; - U = outProd(ylk[l][p[k]], Id[p[k]-1], M); - beta = 1 + ylk[l][p[k]][p[k]]; - for (i = 0; i < M; i++) { - for (j = 0; j < M; j++) { - Al[i][j] = Id[i][j] - U[i][j] / beta; - } - } - Slater_inv = matMul(Al, Slater_inv, M); - } - - // Overwrite the old values in 'copy' with the new ones in Slater_inv - // for (i = 0; i < M; i++) { - // for (j = 0; j < M; j++) { - // copy[i][j] = Slater_inv[i][j]; - // } - // } - - // Overwrite the old values in 'linSlater_inv' with the new values in Slater_inv - for (i = 0; i < M; i++) { - for (j = 0; j < M; j++) { - linSlater_inv[0][i+*Dim*j] = Slater_inv[i][j]; - } - } - - for (l = 0; l < M; l++) { - for (k = 0; k < M+1; k++) { - delete [] ylk[l][k]; - } - delete [] ylk[l], Id[l], U[l], Al[l], Slater_inv[l]; - } - delete [] p, breakdown; -} diff --git a/SM_MaponiA3_f.hpp b/SM_MaponiA3_f.hpp deleted file mode 100644 index 1537a65..0000000 --- a/SM_MaponiA3_f.hpp +++ /dev/null @@ -1,4 +0,0 @@ -// SM-MaponiA3_f.hpp -extern "C" { - void MaponiA3(int **linSlater0, double **linSlater_inv, unsigned int *Dim, unsigned int *N_updates, int **linUpdates, unsigned int *Updates_index); -} diff --git a/SM_MaponiA3_mod.f90 b/SM_MaponiA3_mod.f90 index 1708fd0..d0d8a4c 100644 --- a/SM_MaponiA3_mod.f90 +++ b/SM_MaponiA3_mod.f90 @@ -1,11 +1,11 @@ -module Sherman_Morrison +module Sherman_Morrison interface - subroutine MaponiA3(Slater0, Slater_inv, dim, n_updates, Updates, Updates_index) bind(C, name="MaponiA3") + subroutine MaponiA3(Slater0, Slater_inv, dim, n_updates, Updates, Updates_index) bind(C, name="MaponiA3_f") use, intrinsic :: iso_c_binding, only : c_int, c_double integer(c_int), intent(in) :: dim, n_updates integer(c_int), dimension(:), allocatable, intent(in) :: Updates_index - integer(c_int), dimension(:,:), allocatable, intent(in) :: Slater0, Updates + real(c_double), dimension(:,:), allocatable, intent(in) :: Slater0, Updates real(c_double), dimension(:,:), allocatable, intent(in out) :: Slater_inv end subroutine MaponiA3 end interface -end module Sherman_Morrison \ No newline at end of file +end module Sherman_Morrison diff --git a/cppmain.cpp b/cppmain.cpp index 2592370..0f0645e 100644 --- a/cppmain.cpp +++ b/cppmain.cpp @@ -7,73 +7,52 @@ int main() { srand((unsigned) time(0)); - unsigned int randRange = 1; // to get random integers in range [-randRange, randRange] 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]; - int **A = new int*[M]; // The matrix to be inverted - int **A0 = new int*[M]; // A diagonal matrix with the digonal elements of A - int **Ar = new int*[M]; // The update matrix - double **A0_inv = new double*[M]; // Inverse of A0 - for (i = 0; i < M; i++) { - A[i] = new int[M]; - A0[i] = new int[M]; - Ar[i] = new int[M]; - A0_inv[i] = new double[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][j] = 0; - Ar[i][j] = 0; - A0_inv[i][j] = 0; + 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][0] = 1; A[0][1] = 1; A[0][2] = -1; - A[1][0] = 1; A[1][1] = 1; A[1][2] = 0; - A[2][0] = -1; A[2][1] = 0; A[2][2] = -1; - // // Fill A with random numbers from [-randRange,randRange] - // // and check if A and A0 are invertable - // do { - // for (i = 0; i < M; i++) { - // for (j = 0; j < M; j++) { - // A[i][j] = rand()%(2*randRange+1)-randRange; - // } - // } - // for (i = 0; i < M; i++) { - // A0[i][i] = A[i][i]; - // } - // } while (matDet(A, M) == 0 || matDet(A0, M) == 0); + 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][i] = A[i][i]; - A0_inv[i][i] = 1.0/A[i][i]; + A0[i*M+i] = A[i*M+i]; + A0_inv[i*M+i] = 1.0/A[i*M+i]; Ar_index[i] = i; for (j = 0; j < M; j++) { - Ar[i][j] = A[i][j] - A0[i][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 - unsigned int *dim = new unsigned int(M); - unsigned int *n_updates = new unsigned int(M); - Sherman_Morrison(A0, A0_inv, dim, n_updates, Ar, Ar_index); + unsigned int dim = M; + unsigned int n_updates = M; + MaponiA3(A0, A0_inv, dim, n_updates, Ar, Ar_index); showMatrix(A0_inv, M, "A0_inv"); - - // Deallocate all vectors and matrices - for (i = 0; i < M; i++) { - delete [] A[i], A0[i], A0_inv[i], Ar[i]; - } + + // Deallocate all vectors and matrices delete [] A, A0, A0_inv, Ar, Ar_index; - delete dim, n_updates; return 0; -} \ No newline at end of file +} diff --git a/fmain.f90 b/fmain.f90 index 447ee46..5fdc1d0 100644 --- a/fmain.f90 +++ b/fmain.f90 @@ -6,7 +6,7 @@ program Interface_test integer i, j !! Iterators integer(c_int) :: dim, N_updates integer(c_int), dimension(:), allocatable :: Ar_index - integer(c_int), dimension(:,:), allocatable :: A, A0, Ar + real(c_double), dimension(:,:), allocatable :: A, A0, Ar real(c_double), dimension(:,:), allocatable :: A0_inv dim = 3 @@ -14,15 +14,15 @@ program Interface_test allocate(Ar_index(dim), A(dim,dim), A0(dim,dim), Ar(dim,dim), A0_inv(dim,dim)) !! Initialize A with M=3 and fill acc. to Eq. (17) from paper - A(1,1) = 1 - A(1,2) = 1 - A(1,3) = -1 - A(2,1) = 1 - A(2,2) = 1 - A(2,3) = 0 - A(3,1) = -1 - A(3,2) = 0 - A(3,3) = -1 + 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 !! Prepare the diagonal matrix A0 and the update matrix Ar do i=1,dim @@ -32,13 +32,13 @@ program Interface_test A0(i,j) = A(i,j) A0_inv(i,j) = 1.0d0 / A0(i,j) else - A0(i,j) = 0 + A0(i,j) = 0.0d0 A0_inv(i,j) = 0.0d0 end if Ar(i,j) = A(i,j) - A0(i,j) end do end do - + call MaponiA3(A0, A0_inv, dim, n_updates, Ar, Ar_index) do i=1,dim