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Jonathan Lambrechts authored
bug correction to dgGroupOfInterfaces in 3d + check for not defined boundaries + remove left/right interface on dgGroupOfFaces
Jonathan Lambrechts authoredbug correction to dgGroupOfInterfaces in 3d + check for not defined boundaries + remove left/right interface on dgGroupOfFaces
gmm_inoutput.h 39.33 KiB
// -*- c++ -*- (enables emacs c++ mode)
//===========================================================================
//
// Copyright (C) 2003-2008 Yves Renard
//
// This file is a part of GETFEM++
//
// Getfem++ is free software; you can redistribute it and/or modify it
// under the terms of the GNU Lesser General Public License as published
// by the Free Software Foundation; either version 2.1 of the License, or
// (at your option) any later version.
// This program is distributed in the hope that it will be useful, but
// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
// License for more details.
// You should have received a copy of the GNU Lesser General Public License
// along with this program; if not, write to the Free Software Foundation,
// Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
//
// As a special exception, you may use this file as part of a free software
// library without restriction. Specifically, if other files instantiate
// templates or use macros or inline functions from this file, or you compile
// this file and link it with other files to produce an executable, this
// file does not by itself cause the resulting executable to be covered by
// the GNU General Public License. This exception does not however
// invalidate any other reasons why the executable file might be covered by
// the GNU General Public License.
//
//===========================================================================
/**@file gmm_inoutput.h
@author Yves Renard <Yves.Renard@insa-lyon.fr>
@author Julien Pommier <Julien.Pommier@insa-toulouse.fr>
@date July 8, 2003.
@brief Input/output on sparse matrices
Support Harwell-Boeing and Matrix-Market formats.
*/
#ifndef GMM_INOUTPUT_H
#define GMM_INOUTPUT_H
#include <stdio.h>
#include "gmm_kernel.h"
namespace gmm {
/*************************************************************************/
/* */
/* Functions to read and write Harwell Boeing format. */
/* */
/*************************************************************************/
// Fri Aug 15 16:29:47 EDT 1997
//
// Harwell-Boeing File I/O in C
// V. 1.0
//
// National Institute of Standards and Technology, MD.
// K.A. Remington
// ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// NOTICE
//
// Permission to use, copy, modify, and distribute this software and
// its documentation for any purpose and without fee is hereby granted
// provided that the above copyright notice appear in all copies and
// that both the copyright notice and this permission notice appear in
// supporting documentation.
//
// Neither the Author nor the Institution (National Institute of Standards
// and Technology) make any representations about the suitability of this
// software for any purpose. This software is provided "as is" without // expressed or implied warranty.
// ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
inline void IOHBTerminate(const char *a) { GMM_ASSERT1(false, a);}
inline bool is_complex_double__(std::complex<double>) { return true; }
inline bool is_complex_double__(double) { return false; }
inline int ParseIfmt(const char *fmt, int* perline, int* width) {
if (SECURE_NONCHAR_SSCANF(fmt, " (%dI%d)", perline, width) != 2) {
*perline = 1;
int s = SECURE_NONCHAR_SSCANF(fmt, " (I%d)", width);
GMM_ASSERT1(s == 1, "invalid HB I-format: " << fmt);
}
return *width;
}
inline int ParseRfmt(const char *fmt, int* perline, int* width,
int* prec, int* flag) {
char p;
*perline = *width = *flag = *prec = 0;
#ifdef GMM_SECURE_CRT
if (sscanf_s(fmt, " (%d%c%d.%d)", perline, &p, sizeof(char), width, prec)
< 3 || !strchr("PEDF", p))
#else
if (sscanf(fmt, " (%d%c%d.%d)", perline, &p, width, prec) < 3
|| !strchr("PEDF", p))
#endif
{
*perline = 1;
#ifdef GMM_SECURE_CRT
int s = sscanf_s(fmt, " (%c%d.%d)", &p, sizeof(char), width, prec);
#else
int s = sscanf(fmt, " (%c%d.%d)", &p, width, prec);
#endif
GMM_ASSERT1(s>=2 && strchr("PEDF",p), "invalid HB REAL format: " << fmt);
}
*flag = p;
return *width;
}
/** matrix input/output for Harwell-Boeing format */
struct HarwellBoeing_IO {
int nrows() const { return Nrow; }
int ncols() const { return Ncol; }
int nnz() const { return Nnzero; }
int is_complex() const { return Type[0] == 'C'; }
int is_symmetric() const { return Type[1] == 'S'; }
int is_hermitian() const { return Type[1] == 'H'; }
HarwellBoeing_IO() { clear(); }
HarwellBoeing_IO(const char *filename) { clear(); open(filename); }
~HarwellBoeing_IO() { close(); }
/** open filename and reads header */
void open(const char *filename);
/** read the opened file */
template <typename T, int shift> void read(csc_matrix<T, shift>& A);
template <typename MAT> void read(MAT &M) IS_DEPRECATED;
template <typename T, int shift>
static void write(const char *filename, const csc_matrix<T, shift>& A);
template <typename T, int shift>
static void write(const char *filename, const csc_matrix<T, shift>& A,
const std::vector<T> &rhs);
template <typename T, typename INDI, typename INDJ, int shift>
static void write(const char *filename,
const csc_matrix_ref<T*, INDI*, INDJ*, shift>& A);
template <typename T, typename INDI, typename INDJ, int shift>
static void write(const char *filename,
const csc_matrix_ref<T*, INDI*, INDJ*, shift>& A,
const std::vector<T> &rhs);
/** static method for saving the matrix */
template <typename MAT> static void write(const char *filename,
const MAT& A) IS_DEPRECATED;
private:
FILE *f;
char Title[73], Key[9], Rhstype[4], Type[4];
int Nrow, Ncol, Nnzero, Nrhs;
char Ptrfmt[17], Indfmt[17], Valfmt[21], Rhsfmt[21];
int Ptrcrd, Indcrd, Valcrd, Rhscrd;
int lcount;
void close() { if (f) fclose(f); clear(); }
void clear() {
Nrow = Ncol = Nnzero = Nrhs = 0; f = 0; lcount = 0;
memset(Type, 0, sizeof Type);
memset(Key, 0, sizeof Key);
memset(Title, 0, sizeof Title);
}
char *getline(char *buf) {
if(fgets(buf, BUFSIZ, f) == NULL) return buf; ++lcount;
int s = SECURE_NONCHAR_SSCANF(buf,"%*s");
GMM_ASSERT1(s >= 0, "blank line in HB file at line " << lcount);
return buf;
}
int substrtoi(const char *p, size_type len) {
char s[100]; len = std::min(len, sizeof s - 1);
SECURE_STRNCPY(s, 100, p, len); s[len] = 0; return atoi(s);
}
double substrtod(const char *p, size_type len, int Valflag) {
char s[100]; len = std::min(len, sizeof s - 1);
SECURE_STRNCPY(s, 100, p, len); s[len] = 0;
if ( Valflag != 'F' && !strchr(s,'E')) {
/* insert a char prefix for exp */
int last = strlen(s);
for (int j=last+1;j>=0;j--) {
s[j] = s[j-1];
if ( s[j] == '+' || s[j] == '-' ) {
s[j-1] = Valflag;
break;
}
}
}
return atof(s);
}
template <typename IND_TYPE>
int readHB_data(IND_TYPE colptr[], IND_TYPE rowind[],
double val[]) {
/***********************************************************************/
/* This function opens and reads the specified file, interpreting its */
/* contents as a sparse matrix stored in the Harwell/Boeing standard */
/* format and creating compressed column storage scheme vectors to */
/* hold the index and nonzero value information. */
/* */
/* ---------- */
/* **CAVEAT** */
/* ---------- */
/* Parsing real formats from Fortran is tricky, and this file reader */
/* does not claim to be foolproof. It has been tested for cases */
/* when the real values are printed consistently and evenly spaced on */
/* each line, with Fixed (F), and Exponential (E or D) formats. */
/* */
/* ** If the input file does not adhere to the H/B format, the ** */
/* ** results will be unpredictable. ** */
/* */
/***********************************************************************/
int i,ind,col,offset,count;
int Ptrperline, Ptrwidth, Indperline, Indwidth;
int Valperline, Valwidth, Valprec, Nentries; int Valflag; /* Indicates 'E','D', or 'F' float format */
char line[BUFSIZ];
/* Parse the array input formats from Line 3 of HB file */
ParseIfmt(Ptrfmt,&Ptrperline,&Ptrwidth);
ParseIfmt(Indfmt,&Indperline,&Indwidth);
if ( Type[0] != 'P' ) { /* Skip if pattern only */
ParseRfmt(Valfmt,&Valperline,&Valwidth,&Valprec,&Valflag);
}
cout << "Valwidth = " << Valwidth << endl; getchar();
/* Read column pointer array: */
offset = 0; /* if base 0 storage is declared (via macro def), */
/* then storage entries are offset by 1 */
for (count = 0, i=0;i<Ptrcrd;i++) {
getline(line);
for (col = 0, ind = 0;ind<Ptrperline;ind++) {
if (count > Ncol) break;
colptr[count] = substrtoi(line+col,Ptrwidth)-offset;
count++; col += Ptrwidth;
}
}
/* Read row index array: */
for (count = 0, i=0;i<Indcrd;i++) {
getline(line);
for (col = 0, ind = 0;ind<Indperline;ind++) {
if (count == Nnzero) break;
rowind[count] = substrtoi(line+col,Indwidth)-offset;
count++; col += Indwidth;
}
}
/* Read array of values: */
if ( Type[0] != 'P' ) { /* Skip if pattern only */
if ( Type[0] == 'C' ) Nentries = 2*Nnzero;
else Nentries = Nnzero;
count = 0;
for (i=0;i<Valcrd;i++) {
getline(line);
if (Valflag == 'D') {
// const_cast Due to aCC excentricity
char *p;
while( (p = const_cast<char *>(strchr(line,'D')) )) *p = 'E';
}
for (col = 0, ind = 0;ind<Valperline;ind++) {
if (count == Nentries) break;
val[count] = substrtod(line+col, Valwidth, Valflag);
count++; col += Valwidth;
}
}
}
return 1;
}
};
inline void HarwellBoeing_IO::open(const char *filename) {
int Totcrd,Neltvl,Nrhsix;
char line[BUFSIZ];
close();
SECURE_FOPEN(&f, filename, "r");
GMM_ASSERT1(f, "could not open " << filename);
/* First line: */
#ifdef GMM_SECURE_CRT
sscanf_s(getline(line), "%c%s", Title, 72, Key, 8);
#else
sscanf(getline(line), "%72c%8s", Title, Key);#endif
Key[8] = Title[72] = 0;
/* Second line: */
Totcrd = Ptrcrd = Indcrd = Valcrd = Rhscrd = 0;
SECURE_NONCHAR_SSCANF(getline(line), "%d%d%d%d%d", &Totcrd, &Ptrcrd,
&Indcrd, &Valcrd, &Rhscrd);
/* Third line: */
Nrow = Ncol = Nnzero = Neltvl = 0;
#ifdef GMM_SECURE_CRT
if (sscanf_s(getline(line), "%c%d%d%d%d", Type, 3, &Nrow, &Ncol, &Nnzero,
&Neltvl) < 1)
#else
if (sscanf(getline(line), "%3c%d%d%d%d", Type, &Nrow, &Ncol, &Nnzero,
&Neltvl) < 1)
#endif
IOHBTerminate("Invalid Type info, line 3 of Harwell-Boeing file.\n");
for (size_type i = 0; i < 3; ++i) Type[i] = toupper(Type[i]);
/* Fourth line: */
#ifdef GMM_SECURE_CRT
if ( sscanf_s(getline(line), "%c%c%c%c",Ptrfmt, 16,Indfmt, 16,Valfmt,
20,Rhsfmt, 20) < 3)
#else
if ( sscanf(getline(line), "%16c%16c%20c%20c",Ptrfmt,Indfmt,Valfmt,
Rhsfmt) < 3)
#endif
IOHBTerminate("Invalid format info, line 4 of Harwell-Boeing file.\n");
Ptrfmt[16] = Indfmt[16] = Valfmt[20] = Rhsfmt[20] = 0;
/* (Optional) Fifth line: */
if (Rhscrd != 0 ) {
Nrhs = Nrhsix = 0;
#ifdef GMM_SECURE_CRT
if ( sscanf_s(getline(line), "%c%d%d", Rhstype, 3, &Nrhs, &Nrhsix) != 1)
#else
if ( sscanf(getline(line), "%3c%d%d", Rhstype, &Nrhs, &Nrhsix) != 1)
#endif
IOHBTerminate("Invalid RHS type information, line 5 of"
" Harwell-Boeing file.\n");
}
}
/* only valid for double and complex<double> csc matrices */
template <typename T, int shift> void
HarwellBoeing_IO::read(csc_matrix<T, shift>& A) {
typedef typename csc_matrix<T, shift>::IND_TYPE IND_TYPE;
GMM_ASSERT1(f, "no file opened!");
GMM_ASSERT1(Type[0] != 'P',
"Bad HB matrix format (pattern matrices not supported)");
GMM_ASSERT1(!is_complex_double__(T()) || Type[0] != 'R',
"Bad HB matrix format (file contains a REAL matrix)");
GMM_ASSERT1(is_complex_double__(T()) || Type[0] != 'C',
"Bad HB matrix format (file contains a COMPLEX matrix)");
if (A.pr) { delete[] A.pr; delete[] A.ir; delete[] A.jc; }
A.nc = ncols(); A.nr = nrows();
A.pr = 0;
A.jc = new IND_TYPE[ncols()+1];
A.ir = new IND_TYPE[nnz()];
A.pr = new T[nnz()];
readHB_data(A.jc, A.ir, (double*)A.pr);
for (int i = 0; i <= ncols(); ++i) { A.jc[i] += shift; A.jc[i] -= 1; }
for (int i = 0; i < nnz(); ++i) { A.ir[i] += shift; A.ir[i] -= 1; }
}
template <typename MAT> void
HarwellBoeing_IO::read(MAT &M) {
csc_matrix<typename gmm::linalg_traits<MAT>::value_type> csc; read(csc);
resize(M, mat_nrows(csc), mat_ncols(csc));
copy(csc, M);
}
template <typename IND_TYPE>
inline int writeHB_mat_double(const char* filename, int M, int N, int nz,
const IND_TYPE colptr[],
const IND_TYPE rowind[],
const double val[], int Nrhs,
const double rhs[], const double guess[],
const double exact[], const char* Title,
const char* Key, const char* Type,
const char* Ptrfmt, const char* Indfmt,
const char* Valfmt, const char* Rhsfmt,
const char* Rhstype, int shift) {
/************************************************************************/
/* The writeHB function opens the named file and writes the specified */
/* matrix and optional right-hand-side(s) to that file in */
/* Harwell-Boeing format. */
/* */
/* For a description of the Harwell Boeing standard, see: */
/* Duff, et al., ACM TOMS Vol.15, No.1, March 1989 */
/* */
/************************************************************************/
FILE *out_file;
int i, entry, offset, j, acount, linemod;
int totcrd, ptrcrd, indcrd, valcrd, rhscrd;
int nvalentries, nrhsentries;
int Ptrperline, Ptrwidth, Indperline, Indwidth;
int Rhsperline, Rhswidth, Rhsprec, Rhsflag;
int Valperline, Valwidth, Valprec;
int Valflag; /* Indicates 'E','D', or 'F' float format */
char pformat[16],iformat[16],vformat[19],rformat[19];
if ( Type[0] == 'C' )
{ nvalentries = 2*nz; nrhsentries = 2*M; }
else
{ nvalentries = nz; nrhsentries = M; }
if ( filename != NULL ) {
SECURE_FOPEN(&out_file, filename, "w");
GMM_ASSERT1(out_file != NULL, "Error: Cannot open file: " << filename);
} else out_file = stdout;
if ( Ptrfmt == NULL ) Ptrfmt = "(8I10)";
ParseIfmt(Ptrfmt, &Ptrperline, &Ptrwidth);
SECURE_SPRINTF1(pformat,sizeof(pformat),"%%%dd",Ptrwidth);
ptrcrd = (N+1)/Ptrperline;
if ( (N+1)%Ptrperline != 0) ptrcrd++;
if ( Indfmt == NULL ) Indfmt = Ptrfmt;
ParseIfmt(Indfmt, &Indperline, &Indwidth);
SECURE_SPRINTF1(iformat,sizeof(iformat), "%%%dd",Indwidth);
indcrd = nz/Indperline;
if ( nz%Indperline != 0) indcrd++;
if ( Type[0] != 'P' ) { /* Skip if pattern only */
if ( Valfmt == NULL ) Valfmt = "(4E21.13)";
ParseRfmt(Valfmt, &Valperline, &Valwidth, &Valprec, &Valflag);
if (Valflag == 'D') *strchr(Valfmt,'D') = 'E';
if (Valflag == 'F')
SECURE_SPRINTF2(vformat, sizeof(vformat), "%% %d.%df", Valwidth,
Valprec);
else
SECURE_SPRINTF2(vformat, sizeof(vformat), "%% %d.%dE", Valwidth,
Valprec);
valcrd = nvalentries/Valperline;
if ( nvalentries%Valperline != 0) valcrd++;
} else valcrd = 0;
if ( Nrhs > 0 ) {
if ( Rhsfmt == NULL ) Rhsfmt = Valfmt;
ParseRfmt(Rhsfmt,&Rhsperline,&Rhswidth,&Rhsprec, &Rhsflag);
if (Rhsflag == 'F')
SECURE_SPRINTF2(rformat,sizeof(rformat), "%% %d.%df",Rhswidth,Rhsprec);
else
SECURE_SPRINTF2(rformat,sizeof(rformat), "%% %d.%dE",Rhswidth,Rhsprec);
if (Rhsflag == 'D') *strchr(Rhsfmt,'D') = 'E';
rhscrd = nrhsentries/Rhsperline;
if ( nrhsentries%Rhsperline != 0) rhscrd++;
if ( Rhstype[1] == 'G' ) rhscrd+=rhscrd;
if ( Rhstype[2] == 'X' ) rhscrd+=rhscrd;
rhscrd*=Nrhs;
} else rhscrd = 0;
totcrd = 4+ptrcrd+indcrd+valcrd+rhscrd;
/* Print header information: */
fprintf(out_file,"%-72s%-8s\n%14d%14d%14d%14d%14d\n",Title, Key, totcrd,
ptrcrd, indcrd, valcrd, rhscrd);
fprintf(out_file,"%3s%11s%14d%14d%14d%14d\n",Type," ", M, N, nz, 0);
fprintf(out_file,"%-16s%-16s%-20s", Ptrfmt, Indfmt, Valfmt);
if ( Nrhs != 0 ) {
/* Print Rhsfmt on fourth line and */
/* optional fifth header line for auxillary vector information:*/
fprintf(out_file,"%-20s\n%-14s%d\n",Rhsfmt,Rhstype,Nrhs);
}
else
fprintf(out_file,"\n");
offset = 1 - shift; /* if base 0 storage is declared (via macro def), */
/* then storage entries are offset by 1 */
/* Print column pointers: */
for (i = 0; i < N+1; i++) {
entry = colptr[i]+offset;
fprintf(out_file,pformat,entry);
if ( (i+1)%Ptrperline == 0 ) fprintf(out_file,"\n");
}
if ( (N+1) % Ptrperline != 0 ) fprintf(out_file,"\n");
/* Print row indices: */
for (i=0;i<nz;i++) {
entry = rowind[i]+offset;
fprintf(out_file,iformat,entry);
if ( (i+1)%Indperline == 0 ) fprintf(out_file,"\n");
}
if ( nz % Indperline != 0 ) fprintf(out_file,"\n");
/* Print values: */
if ( Type[0] != 'P' ) { /* Skip if pattern only */
for (i=0;i<nvalentries;i++) {
fprintf(out_file,vformat,val[i]);
if ( (i+1)%Valperline == 0 ) fprintf(out_file,"\n");
}
if ( nvalentries % Valperline != 0 ) fprintf(out_file,"\n");
/* Print right hand sides: */
acount = 1;
linemod=0;
if ( Nrhs > 0 ) {
for (j=0;j<Nrhs;j++) {
for (i=0;i<nrhsentries;i++) { fprintf(out_file,rformat,rhs[i] /* *Rhswidth */);
if ( acount++%Rhsperline == linemod ) fprintf(out_file,"\n");
}
if ( acount%Rhsperline != linemod ) {
fprintf(out_file,"\n");
linemod = (acount-1)%Rhsperline;
}
if ( Rhstype[1] == 'G' ) {
for (i=0;i<nrhsentries;i++) {
fprintf(out_file,rformat,guess[i] /* *Rhswidth */);
if ( acount++%Rhsperline == linemod ) fprintf(out_file,"\n");
}
if ( acount%Rhsperline != linemod ) {
fprintf(out_file,"\n");
linemod = (acount-1)%Rhsperline;
}
}
if ( Rhstype[2] == 'X' ) {
for (i=0;i<nrhsentries;i++) {
fprintf(out_file,rformat,exact[i] /* *Rhswidth */);
if ( acount++%Rhsperline == linemod ) fprintf(out_file,"\n");
}
if ( acount%Rhsperline != linemod ) {
fprintf(out_file,"\n");
linemod = (acount-1)%Rhsperline;
}
}
}
}
}
int s = fclose(out_file);
GMM_ASSERT1(s == 0, "Error closing file in writeHB_mat_double().");
return 1;
}
template <typename T, int shift> void
HarwellBoeing_IO::write(const char *filename,
const csc_matrix<T, shift>& A) {
write(filename, csc_matrix_ref<T*, unsigned*, unsigned *, shift>
(A.pr, A.ir, A.jc, A.nr, A.nc));
}
template <typename T, int shift> void
HarwellBoeing_IO::write(const char *filename,
const csc_matrix<T, shift>& A,
const std::vector<T> &rhs) {
write(filename, csc_matrix_ref<T*, unsigned*, unsigned *, shift>
(A.pr, A.ir, A.jc, A.nr, A.nc), rhs);
}
template <typename T, typename INDI, typename INDJ, int shift> void
HarwellBoeing_IO::write(const char *filename,
const csc_matrix_ref<T*, INDI*, INDJ*, shift>& A) {
const char *t = 0;
if (is_complex_double__(T()))
if (mat_nrows(A) == mat_ncols(A)) t = "CUA"; else t = "CRA";
else
if (mat_nrows(A) == mat_ncols(A)) t = "RUA"; else t = "RRA";
writeHB_mat_double(filename, mat_nrows(A), mat_ncols(A),
A.jc[mat_ncols(A)], A.jc, A.ir,
(const double *)A.pr,
0, 0, 0, 0, "GETFEM++ CSC MATRIX", "CSCMAT",
t, 0, 0, 0, 0, "F", shift);
}
template <typename T, typename INDI, typename INDJ, int shift> void
HarwellBoeing_IO::write(const char *filename,
const csc_matrix_ref<T*, INDI*, INDJ*, shift>& A,
const std::vector<T> &rhs) {
const char *t = 0; if (is_complex_double__(T()))
if (mat_nrows(A) == mat_ncols(A)) t = "CUA"; else t = "CRA";
else
if (mat_nrows(A) == mat_ncols(A)) t = "RUA"; else t = "RRA";
int Nrhs = gmm::vect_size(rhs) / mat_nrows(A);
writeHB_mat_double(filename, mat_nrows(A), mat_ncols(A),
A.jc[mat_ncols(A)], A.jc, A.ir,
(const double *)A.pr,
Nrhs, (const double *)(&rhs[0]), 0, 0,
"GETFEM++ CSC MATRIX", "CSCMAT",
t, 0, 0, 0, 0, "F ", shift);
}
template <typename MAT> void
HarwellBoeing_IO::write(const char *filename, const MAT& A) {
gmm::csc_matrix<typename gmm::linalg_traits<MAT>::value_type>
tmp(gmm::mat_nrows(A), gmm::mat_ncols(A));
gmm::copy(A,tmp);
HarwellBoeing_IO::write(filename, tmp);
}
/** save a "double" or "std::complex<double>" csc matrix into a
HarwellBoeing file
*/
template <typename T, int shift> inline void
Harwell_Boeing_save(const std::string &filename,
const csc_matrix<T, shift>& A)
{ HarwellBoeing_IO::write(filename.c_str(), A); }
/** save a reference on "double" or "std::complex<double>" csc matrix
into a HarwellBoeing file
*/
template <typename T, typename INDI, typename INDJ, int shift> inline void
Harwell_Boeing_save(const std::string &filename,
const csc_matrix_ref<T, INDI, INDJ, shift>& A)
{ HarwellBoeing_IO::write(filename.c_str(), A); }
/** save a "double" or "std::complex<double>" generic matrix
into a HarwellBoeing file making a copy in a csc matrix
*/
template <typename MAT> inline void
Harwell_Boeing_save(const std::string &filename, const MAT& A) {
gmm::csc_matrix<typename gmm::linalg_traits<MAT>::value_type>
tmp(gmm::mat_nrows(A), gmm::mat_ncols(A));
gmm::copy(A, tmp);
HarwellBoeing_IO::write(filename.c_str(), tmp);
}
template <typename MAT, typename VECT> inline void
Harwell_Boeing_save(const std::string &filename, const MAT& A,
const VECT &RHS) {
typedef typename gmm::linalg_traits<MAT>::value_type T;
gmm::csc_matrix<T> tmp(gmm::mat_nrows(A), gmm::mat_ncols(A));
gmm::copy(A, tmp);
std::vector<T> tmprhs(gmm::vect_size(RHS));
gmm::copy(RHS, tmprhs);
HarwellBoeing_IO::write(filename.c_str(), tmp, tmprhs);
}
/** load a "double" or "std::complex<double>" csc matrix from a
HarwellBoeing file
*/
template <typename T, int shift> void
Harwell_Boeing_load(const std::string &filename, csc_matrix<T, shift>& A) {
HarwellBoeing_IO h(filename.c_str()); h.read(A);
}
/** load a "double" or "std::complex<double>" generic matrix from a
HarwellBoeing file */
template <typename MAT> void
Harwell_Boeing_load(const std::string &filename, MAT& A) {
csc_matrix<typename gmm::linalg_traits<MAT>::value_type> csc;
Harwell_Boeing_load(filename, csc);
resize(A, mat_nrows(csc), mat_ncols(csc));
copy(csc, A);
}
/*************************************************************************/
/* */
/* Functions to read and write MatrixMarket format. */
/* */
/*************************************************************************/
/*
* Matrix Market I/O library for ANSI C
*
* See http://math.nist.gov/MatrixMarket for details.
*
*
*/
#define MM_MAX_LINE_LENGTH 1025
#define MatrixMarketBanner "%%MatrixMarket"
#define MM_MAX_TOKEN_LENGTH 64
typedef char MM_typecode[4];
/******************* MM_typecode query functions *************************/
#define mm_is_matrix(typecode) ((typecode)[0]=='M')
#define mm_is_sparse(typecode) ((typecode)[1]=='C')
#define mm_is_coordinate(typecode) ((typecode)[1]=='C')
#define mm_is_dense(typecode) ((typecode)[1]=='A')
#define mm_is_array(typecode) ((typecode)[1]=='A')
#define mm_is_complex(typecode) ((typecode)[2]=='C')
#define mm_is_real(typecode) ((typecode)[2]=='R')
#define mm_is_pattern(typecode) ((typecode)[2]=='P')
#define mm_is_integer(typecode) ((typecode)[2]=='I')
#define mm_is_symmetric(typecode) ((typecode)[3]=='S')
#define mm_is_general(typecode) ((typecode)[3]=='G')
#define mm_is_skew(typecode) ((typecode)[3]=='K')
#define mm_is_hermitian(typecode) ((typecode)[3]=='H')
/******************* MM_typecode modify fucntions ************************/
#define mm_set_matrix(typecode) ((*typecode)[0]='M')
#define mm_set_coordinate(typecode) ((*typecode)[1]='C')
#define mm_set_array(typecode) ((*typecode)[1]='A')
#define mm_set_dense(typecode) mm_set_array(typecode)
#define mm_set_sparse(typecode) mm_set_coordinate(typecode)
#define mm_set_complex(typecode) ((*typecode)[2]='C')
#define mm_set_real(typecode) ((*typecode)[2]='R')
#define mm_set_pattern(typecode) ((*typecode)[2]='P')
#define mm_set_integer(typecode) ((*typecode)[2]='I')
#define mm_set_symmetric(typecode) ((*typecode)[3]='S')
#define mm_set_general(typecode) ((*typecode)[3]='G')
#define mm_set_skew(typecode) ((*typecode)[3]='K')
#define mm_set_hermitian(typecode) ((*typecode)[3]='H')
#define mm_clear_typecode(typecode) ((*typecode)[0]=(*typecode)[1]= \
(*typecode)[2]=' ',(*typecode)[3]='G')
#define mm_initialize_typecode(typecode) mm_clear_typecode(typecode)
/******************* Matrix Market error codes ***************************/
#define MM_COULD_NOT_READ_FILE 11
#define MM_PREMATURE_EOF 12
#define MM_NOT_MTX 13
#define MM_NO_HEADER 14
#define MM_UNSUPPORTED_TYPE 15
#define MM_LINE_TOO_LONG 16
#define MM_COULD_NOT_WRITE_FILE 17
/******************** Matrix Market internal definitions *****************
MM_matrix_typecode: 4-character sequence
object sparse/ data storage
dense type scheme
string position: [0] [1] [2] [3]
Matrix typecode: M(atrix) C(oord) R(eal) G(eneral)
A(array) C(omplex) H(ermitian)
P(attern) S(ymmetric)
I(nteger) K(kew)
***********************************************************************/
#define MM_MTX_STR "matrix"
#define MM_ARRAY_STR "array"
#define MM_DENSE_STR "array"
#define MM_COORDINATE_STR "coordinate"
#define MM_SPARSE_STR "coordinate"
#define MM_COMPLEX_STR "complex"
#define MM_REAL_STR "real"
#define MM_INT_STR "integer"
#define MM_GENERAL_STR "general"
#define MM_SYMM_STR "symmetric"
#define MM_HERM_STR "hermitian"
#define MM_SKEW_STR "skew-symmetric"
#define MM_PATTERN_STR "pattern"
inline char *mm_typecode_to_str(MM_typecode matcode) {
char buffer[MM_MAX_LINE_LENGTH];
const char *types[4] = {0,0,0,0};
/* int error =0; */
/* int i; */
/* check for MTX type */
if (mm_is_matrix(matcode))
types[0] = MM_MTX_STR;
/*
else
error=1;
*/
/* check for CRD or ARR matrix */
if (mm_is_sparse(matcode))
types[1] = MM_SPARSE_STR;
else
if (mm_is_dense(matcode))
types[1] = MM_DENSE_STR;
else
return NULL;
/* check for element data type */
if (mm_is_real(matcode))
types[2] = MM_REAL_STR; else
if (mm_is_complex(matcode))
types[2] = MM_COMPLEX_STR;
else
if (mm_is_pattern(matcode))
types[2] = MM_PATTERN_STR;
else
if (mm_is_integer(matcode))
types[2] = MM_INT_STR;
else
return NULL;
/* check for symmetry type */
if (mm_is_general(matcode))
types[3] = MM_GENERAL_STR;
else if (mm_is_symmetric(matcode))
types[3] = MM_SYMM_STR;
else if (mm_is_hermitian(matcode))
types[3] = MM_HERM_STR;
else if (mm_is_skew(matcode))
types[3] = MM_SKEW_STR;
else
return NULL;
SECURE_SPRINTF4(buffer, sizeof(buffer), "%s %s %s %s", types[0], types[1],
types[2], types[3]);
return SECURE_STRDUP(buffer);
}
inline int mm_read_banner(FILE *f, MM_typecode *matcode) {
char line[MM_MAX_LINE_LENGTH];
char banner[MM_MAX_TOKEN_LENGTH];
char mtx[MM_MAX_TOKEN_LENGTH];
char crd[MM_MAX_TOKEN_LENGTH];
char data_type[MM_MAX_TOKEN_LENGTH];
char storage_scheme[MM_MAX_TOKEN_LENGTH];
char *p;
/* int ret_code; */
mm_clear_typecode(matcode);
if (fgets(line, MM_MAX_LINE_LENGTH, f) == NULL)
return MM_PREMATURE_EOF;
#ifdef GMM_SECURE_CRT
if (sscanf_s(line, "%s %s %s %s %s", banner, sizeof(banner),
mtx, sizeof(mtx), crd, sizeof(crd), data_type,
sizeof(data_type), storage_scheme,
sizeof(storage_scheme)) != 5)
#else
if (sscanf(line, "%s %s %s %s %s", banner, mtx, crd,
data_type, storage_scheme) != 5)
#endif
return MM_PREMATURE_EOF;
for (p=mtx; *p!='\0'; *p=tolower(*p),p++); /* convert to lower case */
for (p=crd; *p!='\0'; *p=tolower(*p),p++);
for (p=data_type; *p!='\0'; *p=tolower(*p),p++);
for (p=storage_scheme; *p!='\0'; *p=tolower(*p),p++);
/* check for banner */
if (strncmp(banner, MatrixMarketBanner, strlen(MatrixMarketBanner)) != 0)
return MM_NO_HEADER;
/* first field should be "mtx" */
if (strcmp(mtx, MM_MTX_STR) != 0)
return MM_UNSUPPORTED_TYPE;
mm_set_matrix(matcode);
/* second field describes whether this is a sparse matrix (in coordinate
storgae) or a dense array */
if (strcmp(crd, MM_SPARSE_STR) == 0)
mm_set_sparse(matcode);
else
if (strcmp(crd, MM_DENSE_STR) == 0)
mm_set_dense(matcode);
else
return MM_UNSUPPORTED_TYPE;
/* third field */
if (strcmp(data_type, MM_REAL_STR) == 0)
mm_set_real(matcode);
else
if (strcmp(data_type, MM_COMPLEX_STR) == 0)
mm_set_complex(matcode);
else
if (strcmp(data_type, MM_PATTERN_STR) == 0)
mm_set_pattern(matcode);
else
if (strcmp(data_type, MM_INT_STR) == 0)
mm_set_integer(matcode);
else
return MM_UNSUPPORTED_TYPE;
/* fourth field */
if (strcmp(storage_scheme, MM_GENERAL_STR) == 0)
mm_set_general(matcode);
else
if (strcmp(storage_scheme, MM_SYMM_STR) == 0)
mm_set_symmetric(matcode);
else
if (strcmp(storage_scheme, MM_HERM_STR) == 0)
mm_set_hermitian(matcode);
else
if (strcmp(storage_scheme, MM_SKEW_STR) == 0)
mm_set_skew(matcode);
else
return MM_UNSUPPORTED_TYPE;
return 0;
}
inline int mm_read_mtx_crd_size(FILE *f, int *M, int *N, int *nz ) {
char line[MM_MAX_LINE_LENGTH];
/* int ret_code;*/
int num_items_read;
/* set return null parameter values, in case we exit with errors */
*M = *N = *nz = 0;
/* now continue scanning until you reach the end-of-comments */
do {
if (fgets(line,MM_MAX_LINE_LENGTH,f) == NULL)
return MM_PREMATURE_EOF;
} while (line[0] == '%');
/* line[] is either blank or has M,N, nz */
if (SECURE_NONCHAR_SSCANF(line, "%d %d %d", M, N, nz) == 3) return 0;
else
do {
num_items_read = SECURE_NONCHAR_FSCANF(f, "%d %d %d", M, N, nz); if (num_items_read == EOF) return MM_PREMATURE_EOF;
}
while (num_items_read != 3);
return 0;
}
inline int mm_read_mtx_crd_data(FILE *f, int, int, int nz, int I[],
int J[], double val[], MM_typecode matcode) {
int i;
if (mm_is_complex(matcode)) {
for (i=0; i<nz; i++)
if (SECURE_NONCHAR_FSCANF(f, "%d %d %lg %lg", &I[i], &J[i],
&val[2*i], &val[2*i+1])
!= 4) return MM_PREMATURE_EOF;
}
else if (mm_is_real(matcode)) {
for (i=0; i<nz; i++) {
if (SECURE_NONCHAR_FSCANF(f, "%d %d %lg\n", &I[i], &J[i], &val[i])
!= 3) return MM_PREMATURE_EOF;
}
}
else if (mm_is_pattern(matcode)) {
for (i=0; i<nz; i++)
if (SECURE_NONCHAR_FSCANF(f, "%d %d", &I[i], &J[i])
!= 2) return MM_PREMATURE_EOF;
}
else return MM_UNSUPPORTED_TYPE;
return 0;
}
inline int mm_write_mtx_crd(const char *fname, int M, int N, int nz,
int I[], int J[], const double val[],
MM_typecode matcode) {
FILE *f;
int i;
if (strcmp(fname, "stdout") == 0)
f = stdout;
else {
SECURE_FOPEN(&f, fname, "w");
if (f == NULL)
return MM_COULD_NOT_WRITE_FILE;
}
/* print banner followed by typecode */
fprintf(f, "%s ", MatrixMarketBanner);
char *str = mm_typecode_to_str(matcode);
fprintf(f, "%s\n", str);
free(str);
/* print matrix sizes and nonzeros */
fprintf(f, "%d %d %d\n", M, N, nz);
/* print values */
if (mm_is_pattern(matcode))
for (i=0; i<nz; i++)
fprintf(f, "%d %d\n", I[i], J[i]);
else
if (mm_is_real(matcode))
for (i=0; i<nz; i++)
fprintf(f, "%d %d %20.16g\n", I[i], J[i], val[i]);
else
if (mm_is_complex(matcode))
for (i=0; i<nz; i++)
fprintf(f, "%d %d %20.16g %20.16g\n", I[i], J[i], val[2*i],
val[2*i+1]); else {
if (f != stdout) fclose(f);
return MM_UNSUPPORTED_TYPE;
}
if (f !=stdout) fclose(f);
return 0;
}
/** matrix input/output for MatrixMarket storage */
class MatrixMarket_IO {
FILE *f;
bool isComplex, isSymmetric, isHermitian;
int row, col, nz;
MM_typecode matcode;
public:
MatrixMarket_IO() : f(0) {}
MatrixMarket_IO(const char *filename) : f(0) { open(filename); }
~MatrixMarket_IO() { if (f) fclose(f); f = 0; }
int nrows() const { return row; }
int ncols() const { return col; }
int nnz() const { return nz; }
int is_complex() const { return isComplex; }
int is_symmetric() const { return isSymmetric; }
int is_hermitian() const { return isHermitian; }
/* open filename and reads header */
void open(const char *filename);
/* read opened file */
template <typename Matrix> void read(Matrix &A);
/* write a matrix */
template <typename T, int shift> static void
write(const char *filename, const csc_matrix<T, shift>& A);
template <typename T, typename INDI, typename INDJ, int shift> static void
write(const char *filename,
const csc_matrix_ref<T*, INDI*, INDJ*, shift>& A);
template <typename MAT> static void
write(const char *filename, const MAT& A);
};
/** load a matrix-market file */
template <typename Matrix> inline void
MatrixMarket_load(const char *filename, Matrix& A) {
MatrixMarket_IO mm; mm.open(filename);
mm.read(A);
}
/** write a matrix-market file */
template <typename T, int shift> void
MatrixMarket_save(const char *filename, const csc_matrix<T, shift>& A) {
MatrixMarket_IO mm; mm.write(filename, A);
}
template <typename T, typename INDI, typename INDJ, int shift> inline void
MatrixMarket_save(const char *filename,
const csc_matrix_ref<T, INDI, INDJ, shift>& A) {
MatrixMarket_IO mm; mm.write(filename, A);
}
inline void MatrixMarket_IO::open(const char *filename) {
if (f) { fclose(f); }
SECURE_FOPEN(&f, filename, "r");
GMM_ASSERT1(f, "Sorry, cannot open file " << filename);
int s1 = mm_read_banner(f, &matcode);
GMM_ASSERT1(s1 == 0, "Sorry, cannnot find the matrix market banner in "
<< filename);
int s2 = mm_is_coordinate(matcode), s3 = mm_is_matrix(matcode);
GMM_ASSERT1(s2 > 0 && s3 > 0, "file is not coordinate storage or is not a matrix");
int s4 = mm_is_pattern(matcode);
GMM_ASSERT1(s4 == 0,
"the file does only contain the pattern of a sparse matrix");
int s5 = mm_is_skew(matcode);
GMM_ASSERT1(s5 == 0, "not currently supporting skew symmetric");
isSymmetric = mm_is_symmetric(matcode) || mm_is_hermitian(matcode);
isHermitian = mm_is_hermitian(matcode);
isComplex = mm_is_complex(matcode);
mm_read_mtx_crd_size(f, &row, &col, &nz);
}
template <typename Matrix> void MatrixMarket_IO::read(Matrix &A) {
typedef typename linalg_traits<Matrix>::value_type T;
GMM_ASSERT1(f, "no file opened!");
GMM_ASSERT1(!is_complex_double__(T()) || isComplex,
"Bad MM matrix format (complex matrix expected)");
GMM_ASSERT1(is_complex_double__(T()) || !isComplex,
"Bad MM matrix format (real matrix expected)");
A = Matrix(row, col);
gmm::clear(A);
std::vector<int> I(nz), J(nz);
std::vector<typename Matrix::value_type> PR(nz);
mm_read_mtx_crd_data(f, row, col, nz, &I[0], &J[0],
(double*)&PR[0], matcode);
for (size_type i = 0; i < size_type(nz); ++i) A(I[i]-1, J[i]-1) = PR[i];
}
template <typename T, int shift> void
MatrixMarket_IO::write(const char *filename, const csc_matrix<T, shift>& A) {
write(filename, csc_matrix_ref<T*,unsigned*,unsigned*,shift>
(A.pr, A.ir, A.jc, A.nr, A.nc));
}
template <typename T, typename INDI, typename INDJ, int shift> void
MatrixMarket_IO::write(const char *filename,
const csc_matrix_ref<T*, INDI*, INDJ*, shift>& A) {
static MM_typecode t1 = {'M', 'C', 'R', 'G'};
static MM_typecode t2 = {'M', 'C', 'C', 'G'};
MM_typecode t;
if (is_complex_double__(T())) std::copy(&(t2[0]), &(t2[0])+4, &(t[0]));
else std::copy(&(t1[0]), &(t1[0])+4, &(t[0]));
size_type nz = A.jc[mat_ncols(A)];
std::vector<int> I(nz), J(nz);
for (size_type j=0; j < mat_ncols(A); ++j) {
for (size_type i = A.jc[j]; i < A.jc[j+1]; ++i) {
I[i] = A.ir[i] + 1 - shift;
J[i] = j + 1;
}
}
mm_write_mtx_crd(filename, mat_nrows(A), mat_ncols(A),
nz, &I[0], &J[0], (const double *)A.pr, t);
}
template <typename MAT> void
MatrixMarket_IO::write(const char *filename, const MAT& A) {
gmm::csc_matrix<typename gmm::linalg_traits<MAT>::value_type>
tmp(gmm::mat_nrows(A), gmm::mat_ncols(A));
gmm::copy(A,tmp);
MatrixMarket_IO::write(filename, tmp);
}
template<typename VEC> static void vecsave(std::string fname, const VEC& V) {
std::ofstream f(fname.c_str()); f.precision(16);
for (size_type i=0; i < gmm::vect_size(V); ++i) f << V[i] << "\n";
}
template<typename VEC> static void vecload(std::string fname,
const VEC& V_) {
VEC &V(const_cast<VEC&>(V_));
std::ifstream f(fname.c_str());
for (size_type i=0; i < gmm::vect_size(V); ++i) f >> V[i];
}
}
#endif // GMM_INOUTPUT_H