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lammps/lib/atc/DenseMatrix.h
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DenseMatrix.h
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#ifndef DENSEMATRIX_H
#define DENSEMATRIX_H
#include "Matrix.h"
#include <iostream>
namespace ATC_matrix {
/**
* @class DenseMatrix
* @brief Class for storing data in a "dense" matrix form
*/
template <typename T>
class DenseMatrix : public Matrix<T>
{
public:
DenseMatrix(INDEX rows=0, INDEX cols=0, bool z=1): _data(NULL){ _create(rows, cols, z); }
DenseMatrix(const DenseMatrix<T>& c) : Matrix<T>(), _data(NULL){ _copy(c); }
DenseMatrix(const SparseMatrix<T>& c): Matrix<T>(), _data(NULL){ c.dense_copy(*this);}
DenseMatrix(const Matrix<T>& c) : Matrix<T>(), _data(NULL){ _copy(c); }
// const SparseMatrix<T> * p = sparse_cast(&c);
// (p) ? p->dense_copy(*this) : _copy(c); }
~DenseMatrix() { _delete();}
void reset (INDEX rows, INDEX cols, bool zero=true);
void reset (const DenseMatrix<T>& c) {_delete(); _copy(c); };
void reset (const SparseMatrix<T> & c) {_delete(); c.dense_copy(*this);};
void reset (const Matrix<T>& c) {_delete(); _copy(c); }
void resize(INDEX rows, INDEX cols, bool copy=false);
void copy (const T * ptr, INDEX rows, INDEX cols);
/** returns transpose(this) * B */
DenseMatrix<T> transMat(const DenseMatrix<T>& B) const;
/** returns by element multiply A_ij = this_ij * B_ij */
DenseMatrix<T> mult_by_element(const DenseMatrix<T>& B) const;
/** returns by element multiply A_ij = this_ij / B_ij */
DenseMatrix<T> div_by_element(const DenseMatrix<T>& B) const;
/** overloaded virtual functions */
//T& operator()(INDEX i, INDEX j) { MICK(i,j) return DATA(i,j); }
T& operator()(INDEX i, INDEX j) { MICK(i,j) return DATA(i,j); }
T operator()(INDEX i, INDEX j) const { MICK(i,j) return DATA(i,j); }
T operator[](INDEX i) const { VICK(i) return _data[i]; }
T& operator[](INDEX i) { VICK(i) return _data[i]; }
INDEX nRows() const { return _nRows; }
INDEX nCols() const { return _nCols; }
T * ptr() const { return _data; }
void write_restart(FILE *f) const;
void from_file(std::string & name);
void set_all_elements_to(const T &v);
DiagonalMatrix<T> diag() const;
DenseMatrix<T>& operator=(const T &v);
DenseMatrix<T>& operator=(const Matrix<T> &c);
DenseMatrix<T>& operator=(const DenseMatrix<T> &c);
DenseMatrix<T>& operator=(const SparseMatrix<T> &c);
//* checks if all values are within the prescribed range
virtual bool check_range(T min, T max) const;
protected:
void _set_equal(const Matrix<T> &r);
void _delete();
void _create(INDEX rows, INDEX cols, bool zero=false);
void _copy(const Matrix<T> &c);
T *_data;
INDEX _nRows, _nCols;
};
//! Computes the cofactor matrix of A.
template<typename T>
DenseMatrix<T> adjugate(const Matrix<T> &A, bool symmetric=false);
//! Returns a the tensor product of two vectors
template<typename T>
DenseMatrix<T> tensor_product(const Vector<T> &a, const Vector<T> &b);
//----------------------------------------------------------------------------
// Returns an identity matrix, defaults to 3x3.
//----------------------------------------------------------------------------
template<typename T>
DenseMatrix<T> eye(INDEX rows=3, INDEX cols=3)
{
const double dij[] = {0.0, 1.0};
DENS_MAT I(rows, cols, false); // do not need to pre-zero
for (INDEX j=0; j<cols; j++)
for (INDEX i=0; i<rows; i++)
I(i,j) = dij[i==j];
return I;
}
//----------------------------------------------------------------------------
// resizes the matrix and optionally zeros it out (default - zero)
//----------------------------------------------------------------------------
template <typename T>
void DenseMatrix<T>::reset(INDEX rows, INDEX cols, bool zero)
{
if (!this->is_size(rows, cols))
{
_delete();
_create(rows, cols);
}
if (zero) this->zero();
}
//----------------------------------------------------------------------------
// resizes the matrix and optionally copies over what still fits
//----------------------------------------------------------------------------
template <typename T>
void DenseMatrix<T>::resize(INDEX rows, INDEX cols, bool copy)
{
if (this->is_size(rows, cols)) return; // if is correct size, done
if (!copy)
{
_delete();
_create(rows, cols);
return;
}
DenseMatrix<T> temp(*this);
_delete();
_create(rows, cols);
int szi = this->nRows();
int szj = this->nCols();
for (INDEX i = 0; i < szi; i++)
for (INDEX j = 0; j < szj; j++)
(*this)(i,j) = temp.in_range(i,j) ? temp(i,j) : T(0);
}
//----------------------------------------------------------------------------
// resizes the matrix and copies data
//----------------------------------------------------------------------------
template <typename T>
void DenseMatrix<T>::copy(const T * ptr, INDEX rows, INDEX cols)
{
resize(rows, cols, false);
memcpy(_data, ptr, this->size()*sizeof(T));
}
//----------------------------------------------------------------------------
// returns transpose(this) * B
//----------------------------------------------------------------------------
template <typename T>
DenseMatrix<T> DenseMatrix<T>::transMat(const DenseMatrix<T>& B) const
{
DenseMatrix C;
MultAB(*this, B, C, true);
return C;
}
//----------------------------------------------------------------------------
// returns this_ij * B_ij
//----------------------------------------------------------------------------
template <typename T>
DenseMatrix<T> DenseMatrix<T>::mult_by_element(const DenseMatrix<T>& B) const
{
DenseMatrix C;
C.reset(_nRows,_nCols);
if (B.nCols() == _nCols) {
int szi = this->nRows();
int szj = this->nCols();
for (INDEX i = 0; i < szi; i++)
for (INDEX j = 0; j < szj; j++)
C(i,j) = (*this)(i,j)*B(i,j);
}
else if (B.nCols() == 1) {
std::cout << "MULTIPLYING\n";
int szi = this->nRows();
int szj = this->nCols();
for (INDEX i = 0; i < szi; i++)
for (INDEX j = 0; j < szj; j++)
C(i,j) = (*this)(i,j)*B(i,0);
}
else {
SSCK(B, *this, "DenseMatrix::mult_by_element");
}
return C;
}
//----------------------------------------------------------------------------
// returns this_ij / B_ij
//----------------------------------------------------------------------------
template <typename T>
DenseMatrix<T> DenseMatrix<T>::div_by_element(const DenseMatrix<T>& B) const
{
DenseMatrix C;
C.reset(_nRows,_nCols);
if (B.nCols() == _nCols) {
int szi = this->nRows();
int szj = this->nCols();
for (INDEX i = 0; i < szi; i++)
for (INDEX j = 0; j < szj; j++)
C(i,j) = (*this)(i,j)/B(i,j);
}
else if (B.nCols() == 1) {
int szi = this->nRows();
int szj = this->nCols();
for (INDEX i = 0; i < szi; i++)
for (INDEX j = 0; j < szj; j++)
C(i,j) = (*this)(i,j)/B(i,0);
}
else {
SSCK(B, *this, "DenseMatrix::div_by_element");
}
return C;
}
//----------------------------------------------------------------------------
// writes the matrix data to a file
//----------------------------------------------------------------------------
template <typename T>
void DenseMatrix<T>::write_restart(FILE *f) const
{
fwrite(&_nRows, sizeof(INDEX),1,f);
fwrite(&_nCols, sizeof(INDEX),1,f);
if (this->size()) fwrite(_data, sizeof(T), this->size(), f);
}
//----------------------------------------------------------------------------
// reads matrix from text file (matrix needs to be sized)
//----------------------------------------------------------------------------
template <typename T>
void DenseMatrix<T>::from_file(std::string & name)
{
GCHK(_nRows == 0,"from_file needs nRows > 0");
GCHK(_nCols == 0,"from_file needs nCols > 0");
std::ifstream in(name.c_str(),std::ifstream::in);
const int lineSize = 256;
char line[lineSize];
if (! in.good()) gerror(name+" is not available");
in.getline(line,lineSize); // header
int szi = this->nRows();
int szj = this->nCols();
for (INDEX i = 0; i < szi; i++)
for (INDEX j = 0; j < szj; j++)
in >> (*this)(i,j);
}
//----------------------------------------------------------------------------
// sets all elements to a value (optimized)
//----------------------------------------------------------------------------
template <typename T>
inline void DenseMatrix<T>::set_all_elements_to(const T &v)
{
int sz = this->size();
for (INDEX i = 0; i < sz; i++) _data[i] = v;
}
//-----------------------------------------------------------------------------
// Return a diagonal matrix containing the diagonal entries of this matrix
//-----------------------------------------------------------------------------
template<typename T>
DiagonalMatrix<T> DenseMatrix<T>::diag() const
{
DiagonalMatrix<T> D(nRows(), true); // initialized to zero
INDEX i;
for (i=0; i<nRows(); i++)
{
D(i,i) = DATA(i,i);
}
return D;
}
//----------------------------------------------------------------------------
// clears allocated memory
//----------------------------------------------------------------------------
template <typename T>
void DenseMatrix<T>::_delete()
{
_nRows = _nCols = 0;
if (_data){
delete [] _data;
_data = NULL;
}
}
//----------------------------------------------------------------------------
// allocates memory for an rows by cols DenseMatrix
//----------------------------------------------------------------------------
template <typename T>
void DenseMatrix<T>::_create(INDEX rows, INDEX cols, bool zero)
{
_nRows=rows;
_nCols=cols;
_data = (this->size() ? new T [_nCols*_nRows] : NULL);
if (zero) this->zero();
}
//----------------------------------------------------------------------------
// creates a deep memory copy from a general matrix
//----------------------------------------------------------------------------
template <typename T>
void DenseMatrix<T>::_copy(const Matrix<T> &c)
{
if (!_data || this->size()!=c.size())
{
_delete();
_create(c.nRows(), c.nCols());
}
else
{
_nRows = c.nRows();
_nCols = c.nCols();
}
memcpy(_data, c.ptr(), c.size()*sizeof(T));
}
//----------------------------------------------------------------------------
// sets all elements to a constant
//----------------------------------------------------------------------------
template <typename T>
DenseMatrix<T>& DenseMatrix<T>::operator=(const T &v)
{
this->set_all_elements_to(v);
return *this;
}
//----------------------------------------------------------------------------
// copys c with a deep copy
//----------------------------------------------------------------------------
template <typename T>
DenseMatrix<T>& DenseMatrix<T>::operator=(const Matrix<T> &c)
{
_copy(c);
return *this;
}
//----------------------------------------------------------------------------
// copys c with a deep copy
//----------------------------------------------------------------------------
template <typename T>
DenseMatrix<T>& DenseMatrix<T>::operator=(const DenseMatrix<T> &c)
{
_copy(c);
return *this;
}
//-----------------------------------------------------------------------------
// copys c with a deep copy, including zeros
//-----------------------------------------------------------------------------
template <typename T>
DenseMatrix<T>& DenseMatrix<T>::operator=(const SparseMatrix<T> &c)
{
_delete();
_create(c.nRows(), c.nCols(), true);
SparseMatrix<T>::compress(c);
for (INDEX i=0; i<c.size(); i++)
{
TRIPLET<T> x = c.triplet(i);
std::cout << "x.i: "<< x.i << "\nx.j: "<< x.j << "\nv.j: "<< x.v << std::endl << std::endl;
(*this)(x.i, x.j) = x.v;
}
return *this;
}
//----------------------------------------------------------------------------
// general matrix assignment (for densely packed matrices)
//----------------------------------------------------------------------------
template<typename T>
void DenseMatrix<T>::_set_equal(const Matrix<T> &r)
{
this->resize(r.nRows(), r.nCols());
const Matrix<T> *pr = &r;
const DenseMatrix<T> *pdd = dynamic_cast<const DenseMatrix<T>*> (pr);
if (pdd) this->reset(*pdd);
else
{
std::cout <<"Error in general dense matrix assignment\n";
exit(1);
}
}
//* Returns the transpose of the cofactor matrix of A.
//* see http://en.wikipedia.org/wiki/Adjugate_matrix
//* symmetric flag only affects cases N>3
template<typename T>
DenseMatrix<T> adjugate(const Matrix<T> &A, bool symmetric)
{
if (!A.is_square()) gerror("adjugate can only be computed for square matrices.");
DenseMatrix<T> C(A.nRows(), A.nRows());
switch (A.nRows()) {
case 1:
gerror("adjugate must be computed for matrixes of size greater than 1");
case 2:
C(0,0) = A(1,1); C(0,1) =-A(0,1);
C(1,0) =-A(1,0); C(1,1) = A(0,0);
break;
case 3: // 3x3 case was tested vs matlab
C(0,0) = A(1,1)*A(2,2)-A(1,2)*A(2,1);
C(1,0) =-A(1,0)*A(2,2)+A(1,2)*A(2,0); // i+j is odd (reverse sign)
C(2,0) = A(1,0)*A(2,1)-A(1,1)*A(2,0);
C(0,1) =-A(0,1)*A(2,2)+A(0,2)*A(2,1); // i+j is odd
C(1,1) = A(0,0)*A(2,2)-A(0,2)*A(2,0);
C(2,1) =-A(0,0)*A(2,1)+A(0,1)*A(2,0); // i+j is odd
C(0,2) = A(0,1)*A(1,2)-A(0,2)*A(1,1);
C(1,2) =-A(0,0)*A(1,2)+A(0,2)*A(1,0); // i+j is odd
C(2,2) = A(0,0)*A(1,1)-A(0,1)*A(1,0);
break;
default:
// this feature is neither tested nor optimal - use at your own risk!!!
DenseMatrix<T> m(A.nRows()-1, A.nRows()-1);
double sign[] = {1.0, -1.0};
for (INDEX j=0; j<A.nCols(); j++) {
for (INDEX i=0; i<A.nRows(); i++) {
for (INDEX mj=0; mj<m.nCols(); mj++) {
for (INDEX mi=0; mi<m.nRows(); mi++) {
m(mi, mj) = A(mi+(mi>=i), mj+(mj>=j)); // skip row i and col j
}
}
if (!symmetric) C(j,i)=det(m)*sign[(i+j)&1];
if (symmetric && i>=j) C(i,j)=C(j,i)=det(m)*sign[(i+j)&1];
}
}
}
return C;
}
// Returns a the tensor product of two vectors
template<typename T>
DenseMatrix<T> tensor_product(const Vector<T> &a, const Vector<T> &b)
{
DenseMatrix<T> ab(a.size(), b.size(),false);
for (INDEX j=0; j<b.size(); j++)
for (INDEX i=0; i<a.size(); i++)
ab(i,j) = a[i]*b[j];
return ab;
}
//* Returns a DenseMatrix with random values (like matlab rand(m,n)
template<typename T>
DenseMatrix<T> rand(INDEX rows, INDEX cols, int seed=1234)
{
srand(seed);
const double rand_max_inv = 1.0 / double(RAND_MAX);
DenseMatrix<T> R(rows, cols, false);
for (INDEX i=0; i<R.size(); i++) R[i]=double(::rand())*rand_max_inv;
return R;
}
//-----------------------------------------------------------------------------
//* returns true if no value is outside of the range
template<typename T>
inline bool DenseMatrix<T>::check_range(T min, T max) const
{
for (INDEX i = 0; i < this->size(); i++)
if ( (_data[i] > max) || (_data[i] < min) ) return false;
return true;
}
} // end namespace
#endif
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