ATC version 2.0, date: Aug7

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10561 f3b2605a-c512-4ea7-a41b-209d697bcdaa

lib/atc/SparseVector-inl.h

@@ -0,0 +1,228 @@
+// SparseVector-inl.h: provides templated functions for SparseVector in
+// separate header
+
+
+namespace ATC_matrix {
+
+template<class T>
+SparseVector<T> sparse_rand(INDEX n, INDEX fill, int seed=1234)
+{
+  srand(seed);
+  const double rmax_inv = 1.0/double(RAND_MAX);
+  SparseVector<T> r(n);
+  while (r.size()<fill) 
+    r(std::rand()%r.nRows())=double(std::rand()*rmax_inv);
+  return r;
+}
+
+// Multiplies a Matrix by a SparseVector (M*v) and returns a DenseVector.
+template<class T>
+DenseVector<T> operator*(const Matrix<T> &M, const SparseVector<T> &v)
+{
+  DenseVector<T> y(M.nRows());
+  STORE::const_iterator it=v.data_.begin();
+  for (; it!=v.data_.end(); it++) {
+    const INDEX j  = it->first;
+    const T& vj = it->second;
+     for (INDEX i=0; i<M.nRows(); i++) y(i)+=M(i,j)*vj;
+  }
+  return y;
+}
+
+// Multiplies a SparseVector by a Matrix (M'*v) and returns a DenseVector.
+template<class T>
+DenseVector<T> operator*(const SparseVector<T> &v, const Matrix<T> &M)
+{
+  DenseVector<T> y(M.nCols());
+  STORE::const_iterator it=v.data_.begin();
+  for (; it!=v.data_.end(); it++) {
+    const INDEX i  = it->first;
+    const T& vi = it->second;
+     for (INDEX j=0; j<M.nCols(); j++) y(j)+=vi*M(i,j);
+  }
+  return y;
+}
+
+// Computes the dot product between two SparseVectors of equal length.
+template<class T>
+T dot(const SparseVector<T> &a, const SparseVector<T> &b)
+{
+  T v = 0.0;
+  for (STORE::const_iterator ai=a.data_.begin(); ai!=a.data_.end(); ai++) {
+    STORE::const_iterator bi=b.data_.find(ai->first);
+    if (bi == b.data_.end()) continue;
+    v += ai->second * bi->second;
+  } 
+  return v;
+}
+// Computes the product of a SparseMatrix tranpose with a SparseVector (M'*v).
+template<class T>
+SparseVector<T> operator*(const SparseMatrix<T> &M, const SparseVector<T> &v)
+{
+  SparseVector<T> y(M.nRows());
+  for (INDEX i=0; i<M.nRows(); i++) {
+    double yi=0.0;
+    for (INDEX ij=M._ia[i]; ij<M._ia[i+1]; ij++) {
+      const INDEX j = M._ja[ij];
+      STORE::const_iterator it = v._data.find(j);
+      if (it == v._data.end()) continue;
+      yi += M._v[ij] * it->second;
+    }
+    if (yi!=0.0) y(i)+=yi;
+  }
+  return y; 
+}
+
+// computes the product of a SparseMatrix tranpose with a SparseVector (M'*v).
+template<class T>
+SparseVector<T> operator*(const SparseVector<T> &v, const SparseMatrix<T> &M)
+{
+  SparseVector<T> y(M.nCols());
+  for (INDEX i=0; i<M.nRows(); i++) {
+    STORE::const_iterator it = v._data.find(i);
+    if (it == v._data.end()) continue;
+    for (INDEX ij=M._ia[i]; ij<M._ia[i+1]; ij++) 
+      y(M._ja[ij]) += it->second * M._v[ij];
+  }
+  return y;
+}
+
+// General constructor - sets the vector length.
+template<class T>
+SparseVector<T>::SparseVector(INDEX n) : length_(n){}
+
+// Outputs the vector to string
+template<class T>
+std::string SparseVector<T>::to_string() const
+{
+  if (size() > nRows()/2) return Vector<T>::to_string();
+  STORE::const_iterator it=data_.begin();
+  std::string str;
+  using ATC_Utility::to_string;
+  for (; it!=data_.end(); it++)
+    str += to_string(it->first)+": "+to_string(it->second)+'\n';
+  return str;
+}
+
+// Indexes the ith component of the vector or returns zero if not found. 
+template<class T>
+T SparseVector<T>::operator()(INDEX i, INDEX j) const
+{
+  STORE::const_iterator it = data_.find(i);
+  if (it == data_.end()) return 0.0;
+  return it->second;
+}
+
+// Indexes the ith component of the vector or returns zero if not found. 
+template<class T>
+T& SparseVector<T>::operator()(INDEX i, INDEX j)
+{
+  return data_[i]; 
+}
+
+// Indexes the ith component of the vector or returns zero if not found. 
+template<class T> T SparseVector<T>::operator[](INDEX i) const
+{
+  return (*this)(i);
+}
+
+// Indexes the ith component of the vector or returns zero if not found. 
+template<class T> T& SparseVector<T>::operator[](INDEX i)
+{
+  return (*this)[i];
+}
+
+// Returns a pair (index, value) for a nonzero in the vector.
+template<class T> 
+std::pair<INDEX, T> SparseVector<T>::pair(INDEX i) const
+{
+  STORE::const_iterator it=data_.begin() + i;
+  return std::pair<INDEX, T>(it->first, it->second);
+}
+
+//* Adds SparseVector x, scaled by s to this one.  Can be different sparcity.
+template<class T> 
+void SparseVector<T>::add_scaled(SparseVector<T>& x, const T& s)
+{
+  STORE::const_iterator it;
+  for (it=x.data_.begin(); it!=x.data_.end(); it++)  {
+   data_[it->first] += it->second * s;
+  }
+}
+
+// Returns the number of nonzeros in the sparse vector.
+template<class T> inline INDEX SparseVector<T>::size() const
+{ return data_.size(); }
+
+// Returns the number of nonzeros in the sparse vector.
+template<class T> inline INDEX SparseVector<T>::nRows() const
+{ return length_; }
+
+// Copy constructor for sparse vector.
+template<typename T>
+SparseVector<T>::SparseVector(const SparseVector<T> &c)
+{
+  length_ = c.length_;
+  data_ = c.data_;
+}
+
+// operator equal for sparse vector.
+template<class T>
+SparseVector<T>& SparseVector<T>::operator=(const SparseVector<T> &c)
+{
+  length_ = c.length_;
+  data_ = c.data_;
+  return *this;
+}
+
+// Changes the size of the SparseVector
+template<class T>
+void SparseVector<T>::resize(INDEX nRows, INDEX nCols, bool copy)
+{
+  length_ = nRows;
+  STORE::iterator it;
+  for (it=data_.begin(); it!=data_.end(); it++) {
+    if (it->second >= length_) data_.erase(it);
+    else if (!copy) it->second=T(0);
+  }
+}
+// same as resize, but zero rather than copy
+template<class T>
+void SparseVector<T>::reset(INDEX nRows, INDEX nCols, bool zero)
+{
+  resize(nRows, nCols, !zero);
+}
+// sets all elements to zero but preserves sparcity
+template<class T>
+void SparseVector<T>::zero()
+{
+  STORE::iterator it;
+  for (it=data_.begin(); it!=data_.end(); it++) it->second=T(0);
+}
+
+
+template<class T>
+void SparseVector<T>::copy(const T* ptr, INDEX nRows, INDEX nCols)
+{
+
+}
+
+
+template<class T>
+void SparseVector<T>::write_restart(FILE *F) const
+{
+
+}
+
+// writes a stream to a matlab script to recreate this variable 
+template<class T>
+void SparseVector<T>::matlab(ostream &o, const string &s) const
+{
+  o << s << "=sparse(" << nRows() << ",1);\n";
+  o << showbase << scientific;
+  STORE::const_iterator it;
+  for (it=data_.begin(); it!=data_.end(); it++)
+    o << s << "(" << it->first+1 << ") = " << it->second << ";\n";
+}
+
+} // end namespace