abstract.cc

大型并行量子化学软件；支持密度泛函（DFT）。可以进行各种量子化学计算。支持CHARMM并行计算。非常具有应用价值。

//    ioff += i;
    }
  convert(v);
  delete[] v;
}

void
SymmSCMatrix::convert(double**a) const
{
  int i;
  int j;
  int nr;
  nr = n();
  for (i=0; i<nr; i++) {
      for (j=0; j<=i; j++) {
          a[i][j] = get_element(i,j);
        }
    }
}

void
SymmSCMatrix::scale(double a)
{
  Ref<SCElementOp> op = new SCElementScale(a);
  this->element_op(op);
}

void
SymmSCMatrix::scale_diagonal(double a)
{
  Ref<SCElementOp> op = new SCElementScaleDiagonal(a);
  this->element_op(op);
}

void
SymmSCMatrix::shift_diagonal(double a)
{
  Ref<SCElementOp> op = new SCElementShiftDiagonal(a);
  this->element_op(op);
}

void
SymmSCMatrix::unit()
{
  this->assign(0.0);
  this->shift_diagonal(1.0);
}

void
SymmSCMatrix::assign_s(SymmSCMatrix*a)
{
  this->assign(0.0);
  this->accumulate(a);
}

void
SymmSCMatrix::print(ostream&o) const
{
  vprint(0, o, 10);
}

void
SymmSCMatrix::print(const char *t, ostream&o, int i) const
{
  vprint(t, o, i);
}

void
SymmSCMatrix::vprint(const char* title, ostream& out, int i) const
{
  RefSCMatrix m = kit()->matrix(dim(),dim());
  m->assign(0.0);
  m->accumulate(this);
  m->print(title, out, i);
}

SymmSCMatrix*
SymmSCMatrix::clone()
{
  return kit()->symmmatrix(dim());
}

SymmSCMatrix*
SymmSCMatrix::copy()
{
  SymmSCMatrix* result = clone();
  result->assign(this);
  return result;
}

void
SymmSCMatrix::accumulate_symmetric_product(SCMatrix *a)
{
  RefSCMatrix at = a->copy();
  at->transpose_this();
  RefSCMatrix m = kit()->matrix(a->rowdim(),a->rowdim());
  m->assign(0.0);
  m->accumulate_product(a, at.pointer());
  scale(2.0);
  accumulate_symmetric_sum(m.pointer());
  scale(0.5);
}

void
SymmSCMatrix::accumulate_transform(SCMatrix *a, SymmSCMatrix *b,
                                   SCMatrix::Transform t)
{
  RefSCMatrix brect = kit()->matrix(b->dim(),b->dim());
  brect->assign(0.0);
  brect->accumulate(b);

  RefSCMatrix res;

  if (t == SCMatrix::TransposeTransform) {
      RefSCMatrix at = a->copy();
      at->transpose_this();

      RefSCMatrix tmp = at->clone();
      tmp->assign(0.0);

      tmp->accumulate_product(at.pointer(), brect.pointer());
      brect = 0;
      at = 0;

      res = kit()->matrix(dim(),dim());
      res->assign(0.0);
      res->accumulate_product(tmp.pointer(), a);
    }
  else {
      RefSCMatrix tmp = a->clone();
      tmp->assign(0.0);

      tmp->accumulate_product(a,brect);
      brect = 0;

      RefSCMatrix at = a->copy();
      at->transpose_this();

      res = kit()->matrix(dim(),dim());
      res->assign(0.0);
      res->accumulate_product(tmp.pointer(), at.pointer());
      at = 0;
    }

  scale(2.0);
  accumulate_symmetric_sum(res.pointer());
  scale(0.5);
}

void
SymmSCMatrix::accumulate_transform(SCMatrix *a, DiagSCMatrix *b,
                                   SCMatrix::Transform t)
{
  RefSCMatrix m = kit()->matrix(a->rowdim(),a->rowdim());
  RefSCMatrix brect = kit()->matrix(b->dim(),b->dim());
  brect->assign(0.0);
  brect->accumulate(b);

  RefSCMatrix tmp = a->clone();
  tmp->assign(0.0);

  RefSCMatrix res;
  
  if (t == SCMatrix::TransposeTransform) {
      RefSCMatrix at = a->copy();
      at->transpose_this();

      tmp->accumulate_product(at.pointer(), brect.pointer());
      brect = 0;
      at = 0;

      res = kit()->matrix(dim(),dim());
      res->assign(0.0);
      res->accumulate_product(tmp.pointer(), a);
    }
  else {
      tmp->accumulate_product(a, brect.pointer());
      brect = 0;

      RefSCMatrix at = a->copy();
      at->transpose_this();

      res = kit()->matrix(dim(),dim());
      res->assign(0.0);
      res->accumulate_product(tmp.pointer(), at.pointer());
      at = 0;
    }

  tmp = 0;

  scale(2.0);
  accumulate_symmetric_sum(res.pointer());
  scale(0.5);
}

void
SymmSCMatrix::accumulate_transform(SymmSCMatrix *a, SymmSCMatrix *b)
{
  RefSCMatrix m = kit()->matrix(a->dim(),a->dim());
  m->assign(0.0);
  m->accumulate(a);
  accumulate_transform(m.pointer(),b);
}

void
SymmSCMatrix::accumulate_symmetric_outer_product(SCVector *v)
{
  RefSCMatrix m = kit()->matrix(dim(),dim());
  m->assign(0.0);
  m->accumulate_outer_product(v,v);

  scale(2.0);
  accumulate_symmetric_sum(m.pointer());
  scale(0.5);
}

double
SymmSCMatrix::scalar_product(SCVector *v)
{
  RefSCVector v2 = kit()->vector(dim());
  v2->assign(0.0);
  v2->accumulate_product(this,v);
  return v2->scalar_product(v);
}

Ref<MessageGrp>
SymmSCMatrix::messagegrp() const
{
  return kit_->messagegrp();
}

/////////////////////////////////////////////////////////////////////////
// DiagSCMatrix member functions

static ClassDesc DiagSCMatrix_cd(
  typeid(DiagSCMatrix),"DiagSCMatrix",1,"public DescribedClass",
  0, 0, 0);

DiagSCMatrix::DiagSCMatrix(const RefSCDimension&a, SCMatrixKit *kit):
  d(a),
  kit_(kit)
{
}

void
DiagSCMatrix::save(StateOut&s)
{
  int nr = n();
  s.put(nr);
  for (int i=0; i<nr; i++) {
      s.put(get_element(i));
    }
}

void
DiagSCMatrix::restore(StateIn& s)
{
  int nrt, nr = n();
  s.get(nrt);
  if (nrt != nr) {
      ExEnv::errn() << "DiagSCMatrix::restore(): bad dimension" << endl;
      abort();
    }
  for (int i=0; i<nr; i++) {
      double tmp;
      s.get(tmp);
      set_element(i, tmp);
    }
}

double
DiagSCMatrix::maxabs() const
{
  Ref<SCElementMaxAbs> op = new SCElementMaxAbs();
  Ref<SCElementOp> abop = op.pointer();
  ((DiagSCMatrix*)this)->element_op(abop);
  return op->result();
}

void
DiagSCMatrix::randomize()
{
  Ref<SCElementOp> op = new SCElementRandomize();
  this->element_op(op);
}

void
DiagSCMatrix::assign_val(double a)
{
  Ref<SCElementOp> op = new SCElementAssign(a);
  this->element_op(op);
}

void
DiagSCMatrix::assign_p(const double*a)
{
  int i;
  int nr = n();
  for (i=0; i<nr; i++) {
      set_element(i,a[i]);
    }
}

void
DiagSCMatrix::convert(DiagSCMatrix*a)
{
  assign(0.0);
  convert_accumulate(a);
}

void
DiagSCMatrix::convert_accumulate(DiagSCMatrix*a)
{
  Ref<SCElementOp> op = new SCElementAccumulateDiagSCMatrix(a);
  element_op(op);
}

void
DiagSCMatrix::convert(double*a) const
{
  int i;
  int nr = n();
  for (i=0; i<nr; i++) {
      a[i] = get_element(i);
    }
}

void
DiagSCMatrix::scale(double a)
{
  Ref<SCElementOp> op = new SCElementScale(a);
  this->element_op(op);
}

void
DiagSCMatrix::assign_d(DiagSCMatrix*a)
{
  this->assign(0.0);
  this->accumulate(a);
}

void
DiagSCMatrix::print(ostream&o) const
{
  vprint(0, o, 10);
}

void
DiagSCMatrix::print(const char *t, ostream&o, int i) const
{
  vprint(t, o, i);
}

void
DiagSCMatrix::vprint(const char* title, ostream& out, int i) const
{
  RefSCMatrix m = kit()->matrix(dim(),dim());
  m->assign(0.0);
  m->accumulate(this);
  m->print(title, out, i);
}

DiagSCMatrix*
DiagSCMatrix::clone()
{
  return kit()->diagmatrix(dim());
}

DiagSCMatrix*
DiagSCMatrix::copy()
{
  DiagSCMatrix* result = clone();
  result->assign(this);
  return result;
}

Ref<MessageGrp>
DiagSCMatrix::messagegrp() const
{
  return kit_->messagegrp();
}

/////////////////////////////////////////////////////////////////////////
// These member are used by the abstract SCVector classes.
/////////////////////////////////////////////////////////////////////////

static ClassDesc SCVector_cd(
  typeid(SCVector),"SCVector",1,"public DescribedClass",
  0, 0, 0);

SCVector::SCVector(const RefSCDimension&a, SCMatrixKit *kit):
  d(a),
  kit_(kit)
{
}

SCVector::~SCVector()
{
}

void
SCVector::save(StateOut&s)
{
  int nr = n();
  s.put(nr);
  for (int i=0; i<nr; i++) {
      s.put(get_element(i));
    }
}

void
SCVector::restore(StateIn& s)
{
  int nrt, nr = n();
  s.get(nrt);
  if (nrt != nr) {
      ExEnv::errn() << "SCVector::restore(): bad dimension" << endl;
      abort();
    }
  for (int i=0; i<nr; i++) {
      double tmp;
      s.get(tmp);
      set_element(i, tmp);
    }
}

double
SCVector::maxabs() const
{
  Ref<SCElementMaxAbs> op = new SCElementMaxAbs();
  Ref<SCElementOp> abop = op.pointer();
  ((SCVector*)this)->element_op(abop);
  return op->result();
}

void
SCVector::randomize()
{
  Ref<SCElementOp> op = new SCElementRandomize();
  this->element_op(op);
}

void
SCVector::assign_val(double a)
{
  Ref<SCElementOp> op = new SCElementAssign(a);
  this->element_op(op);
}

void
SCVector::assign_p(const double*a)
{
  int i;
  int nr = n();
  for (i=0; i<nr; i++) {
      set_element(i,a[i]);
    }
}

void
SCVector::convert(SCVector*a)
{
  assign(0.0);
  convert_accumulate(a);
}

void
SCVector::convert_accumulate(SCVector*a)
{
  Ref<SCElementOp> op = new SCElementAccumulateSCVector(a);
  element_op(op);
}

void
SCVector::convert(double*a) const
{
  int i;
  int nr = n();
  for (i=0; i<nr; i++) {
      a[i] = get_element(i);
    }
}

void
SCVector::scale(double a)
{
  Ref<SCElementOp> op = new SCElementScale(a);
  this->element_op(op);
}

void
SCVector::assign_v(SCVector*a)
{
  this->assign(0.0);
  this->accumulate(a);
}

void
SCVector::print(ostream&o) const
{
  vprint(0, o, 10);
}

void
SCVector::print(const char *t, ostream&o, int i) const
{
  vprint(t, o, i);
}

void
SCVector::normalize()
{
  double norm = sqrt(scalar_product(this));
  if (norm > 1.e-20) norm = 1.0/norm;
  else {
      ExEnv::errn() << indent
           << "SCVector::normalize: tried to normalize tiny vector\n";
      abort();
    }
  scale(norm);
}

SCVector*
SCVector::clone()
{
  return kit()->vector(dim());
}

SCVector*
SCVector::copy()
{
  SCVector* result = clone();
  result->assign(this);
  return result;
}

void
SCVector::accumulate_product_sv(SymmSCMatrix *m, SCVector *v)
{
  RefSCMatrix mrect = kit()->matrix(m->dim(),m->dim());
  mrect->assign(0.0);
  mrect->accumulate(m);
  accumulate_product(mrect.pointer(), v);
}

Ref<MessageGrp>
SCVector::messagegrp() const
{
  return kit_->messagegrp();
}

/////////////////////////////////////////////////////////////////////////////

// Local Variables:
// mode: c++
// c-file-style: "CLJ"
// End: