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/* Ergo, version 3.8, a program for linear scaling electronic structure
* calculations.
* Copyright (C) 2019 Elias Rudberg, Emanuel H. Rubensson, Pawel Salek,
* and Anastasia Kruchinina.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
* Primary academic reference:
* Ergo: An open-source program for linear-scaling electronic structure
* calculations,
* Elias Rudberg, Emanuel H. Rubensson, Pawel Salek, and Anastasia
* Kruchinina,
* SoftwareX 7, 107 (2018),
* <http://dx.doi.org/10.1016/j.softx.2018.03.005>
*
* For further information about Ergo, see <http://www.ergoscf.org>.
*/
/** @file matrix_utilities.h
@brief Utilities related to the hierarchical matrix library (HML),
including functions for setting up permutations of basis functions
to increase data locality in the hierarchical matrix data
structure.
*/
#ifndef MATRIX_UTILITIES_HEADER
#define MATRIX_UTILITIES_HEADER
#include "matrix_typedefs.h"
#include "basisinfo.h"
#if 0
/** prepare_matrix_permutation creates a perm object as required by
further matrix manipulation routines. */
Perm* prepare_matrix_permutation(const BasisInfoStruct& basisInfo,
int sparse_block_size,
int factor1, int factor2, int factor3);
#else
mat::SizesAndBlocks prepareMatrixSizesAndBlocks(int n_basis_functions,
int sparse_block_size,
int factor1,
int factor2,
int factor3);
void getMatrixPermutation(const BasisInfoStruct& basisInfo,
int sparse_block_size,
int factor1,
int factor2,
int factor3,
std::vector<int> & permutation);
void getMatrixPermutation(const BasisInfoStruct& basisInfo,
int sparse_block_size,
int factor1,
int factor2,
int factor3,
std::vector<int> & permutation,
std::vector<int> & inversePermutation);
void getMatrixPermutationOnlyFactor2(const std::vector<ergo_real> & xcoords,
const std::vector<ergo_real> & ycoords,
const std::vector<ergo_real> & zcoords,
int sparse_block_size_lowest,
int first_factor, // this factor may be different from 2, all other factors are always 2.
std::vector<int> & permutation,
std::vector<int> & inversePermutation);
void getMatrixPermutationOnlyFactor2(const BasisInfoStruct& basisInfo,
int sparse_block_size_lowest,
int first_factor, // this factor may be different from 2, all other factors are always 2.
std::vector<int> & permutation,
std::vector<int> & inversePermutation);
#endif
void fill_matrix_with_random_numbers(int n, symmMatrix & M);
void add_random_diag_perturbation(int n,
symmMatrix & M,
ergo_real eps);
bool check_if_matrix_contains_strange_elements(const symmMatrix & M,
std::vector<int> const & inversePermutationHML);
void output_matrix(int n, const ergo_real* matrix, const char* matrixName);
template<class Tmatrix>
ergo_real compute_maxabs_sparse(const Tmatrix & M)
{
return M.maxAbsValue();
}
template<typename RandomAccessIterator>
struct matrix_utilities_CompareClass {
RandomAccessIterator first;
explicit matrix_utilities_CompareClass(RandomAccessIterator firstel)
: first(firstel){}
bool operator() (int i,int j) { return (*(first + i) < *(first + j));}
};
template<typename Tmatrix>
void get_all_nonzeros( Tmatrix const & A,
std::vector<int> const & inversePermutation,
std::vector<int> & rowind,
std::vector<int> & colind,
std::vector<ergo_real> & values) {
rowind.resize(0);
colind.resize(0);
values.resize(0);
size_t nvalues = 0;
size_t nvalues_tmp = A.nvalues();
std::vector<int> rowind_tmp; rowind_tmp.reserve(nvalues_tmp);
std::vector<int> colind_tmp; colind_tmp.reserve(nvalues_tmp);
std::vector<ergo_real> values_tmp; values_tmp.reserve(nvalues_tmp);
A.get_all_values(rowind_tmp,
colind_tmp,
values_tmp,
inversePermutation,
inversePermutation);
// Count the number of nonzeros
for(size_t i = 0; i < nvalues_tmp; i++) {
nvalues += ( values_tmp[i] != 0 );
}
rowind.reserve(nvalues);
colind.reserve(nvalues);
values.reserve(nvalues);
// Extract all nonzeros
for(size_t i = 0; i < nvalues_tmp; i++) {
if ( values_tmp[i] != 0 ) {
rowind.push_back( rowind_tmp[i] );
colind.push_back( colind_tmp[i] );
values.push_back( values_tmp[i] );
}
}
} // end get_all_nonzeros(...)
template<typename Tmatrix>
void write_matrix_in_matrix_market_format( Tmatrix const & A,
std::vector<int> const & inversePermutation,
std::string filename,
std::string identifier,
std::string method_and_basis)
{
// Get all matrix elements
size_t nvalues = 0;
std::vector<int> rowind;
std::vector<int> colind;
std::vector<ergo_real> values;
get_all_nonzeros( A, inversePermutation, rowind, colind, values);
nvalues = values.size();
// Now we have all matrix elements
// Open file stream
std::string mtx_filename = filename + ".mtx";
std::ofstream os(mtx_filename.c_str());
time_t rawtime;
struct tm * timeinfo;
time ( &rawtime );
timeinfo = localtime ( &rawtime );
std::string matrix_market_matrix_type = "general";
bool matrixIsSymmetric = (A.obj_type_id() == "MatrixSymmetric");
if (matrixIsSymmetric)
matrix_market_matrix_type = "symmetric";
os << "%%MatrixMarket matrix coordinate real " << matrix_market_matrix_type << std::endl
<< "%===============================================================================" << std::endl
<< "% Generated by the Ergo quantum chemistry program version " << VERSION << " (www.ergoscf.org)" << std::endl
<< "% Date : " << asctime (timeinfo) // newline added by asctime
<< "% ID-string : " << identifier << std::endl
<< "% Method : " << method_and_basis << std::endl
<< "%" << std::endl
<< "% MatrixMarket file format:" << std::endl
<< "% +-----------------" << std::endl
<< "% | % comments" << std::endl
<< "% | nrows ncols nentries" << std::endl
<< "% | i_1 j_1 A(i_1,j_1)" << std::endl
<< "% | i_2 j_2 A(i_2,j_2)" << std::endl
<< "% | ..." << std::endl
<< "% | i_nentries j_nentries A(i_nentries,j_nentries) " << std::endl
<< "% +----------------" << std::endl
<< "% Note that indices are 1-based, i.e. A(1,1) is the first element." << std::endl
<< "%" << std::endl
<< "%===============================================================================" << std::endl;
os << A.get_nrows() << " " << A.get_ncols() << " " << nvalues << std::endl;
if (matrixIsSymmetric)
for(size_t i = 0; i < nvalues; i++) {
// Output lower triangle
if ( rowind[i] < colind[i] )
os << colind[i]+1 << " " << rowind[i]+1 << " " << std::setprecision(10) << (double)values[i] << std::endl;
else
os << rowind[i]+1 << " " << colind[i]+1 << " " << std::setprecision(10) << (double)values[i] << std::endl;
}
else
for(size_t i = 0; i < nvalues; i++) {
os << rowind[i]+1 << " " << colind[i]+1 << " " << std::setprecision(10) << (double)values[i] << std::endl;
}
os.close();
} // end write_matrix_in_matrix_market_format(...)
#endif
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