elemop.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。

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/////////////////////////////////////////////////////////////////////////
// SCElementInvert members

static ClassDesc SCElementInvert_cd(
  typeid(SCElementInvert),"SCElementInvert",1,"public SCElementOp",
  0, 0, create<SCElementInvert>);
SCElementInvert::SCElementInvert(double threshold):
  threshold_(threshold),
  nbelowthreshold_(0),
  deferred_(0)
{}
SCElementInvert::SCElementInvert(StateIn&s):
  SCElementOp(s)
{
  s.get(threshold_);
  s.get(nbelowthreshold_);
  s.get(deferred_);
}
void
SCElementInvert::save_data_state(StateOut&s)
{
  s.put(threshold_);
  s.put(nbelowthreshold_);
  s.put(deferred_);
}
SCElementInvert::~SCElementInvert() {}
void
SCElementInvert::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      double val = i.get();
      if (fabs(val) > threshold_) val = 1.0/val;
      else { val = 0.0; nbelowthreshold_++; }
      i.set(val);
    }
}

int
SCElementInvert::has_side_effects()
{
  return 1;
}
int
SCElementInvert::has_collect()
{
  return 1;
}
void
SCElementInvert::defer_collect(int h)
{
  deferred_=h;
}
void
SCElementInvert::collect(const Ref<MessageGrp>&msg)
{
  if (!deferred_)
    msg->sum(nbelowthreshold_);
}

/////////////////////////////////////////////////////////////////////////
// SCElementSquareRoot members

static ClassDesc SCElementSquareRoot_cd(
  typeid(SCElementSquareRoot),"SCElementSquareRoot",1,"public SCElementOp",
  0, 0, create<SCElementSquareRoot>);
SCElementSquareRoot::SCElementSquareRoot() {}
SCElementSquareRoot::SCElementSquareRoot(double a) {}
SCElementSquareRoot::SCElementSquareRoot(StateIn&s):
  SCElementOp(s)
{
}
void
SCElementSquareRoot::save_data_state(StateOut&s)
{
}
SCElementSquareRoot::~SCElementSquareRoot() {}
void
SCElementSquareRoot::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      double val = i.get();
      if (val > 0.0) i.set(sqrt(i.get()));
      else i.set(0.0);
    }
}

int
SCElementSquareRoot::has_side_effects()
{
  return 1;
}

/////////////////////////////////////////////////////////////////////////
// SCElementMaxAbs members

static ClassDesc SCElementMaxAbs_cd(
  typeid(SCElementMaxAbs),"SCElementMaxAbs",1,"public SCElementOp",
  0, 0, create<SCElementMaxAbs>);

SCElementMaxAbs::SCElementMaxAbs():deferred_(0), r(0.0) {}
SCElementMaxAbs::SCElementMaxAbs(StateIn&s):
  SCElementOp(s)
{
  s.get(r);
  s.get(deferred_);
}
void
SCElementMaxAbs::save_data_state(StateOut&s)
{
  s.put(r);
  s.put(deferred_);
}
SCElementMaxAbs::~SCElementMaxAbs() {}
void
SCElementMaxAbs::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      if (fabs(i.get()) > r) r = fabs(i.get());
    }
}
double
SCElementMaxAbs::result()
{
  return r;
}
int
SCElementMaxAbs::has_collect()
{
  return 1;
}
void
SCElementMaxAbs::defer_collect(int h)
{
  deferred_=h;
}
void
SCElementMaxAbs::collect(const Ref<MessageGrp>&msg)
{
  if (!deferred_)
    msg->max(r);
}

/////////////////////////////////////////////////////////////////////////
// SCElementMin members

static ClassDesc SCElementMinAbs_cd(
  typeid(SCElementMinAbs),"SCElementMinAbs",1,"public SCElementOp",
  0, 0, create<SCElementMinAbs>);
SCElementMinAbs::SCElementMinAbs(double rinit):deferred_(0), r(rinit) {}
SCElementMinAbs::SCElementMinAbs(StateIn&s):
  SCElementOp(s)
{
  s.get(r);
  s.get(deferred_);
}
void
SCElementMinAbs::save_data_state(StateOut&s)
{
  s.put(r);
  s.put(deferred_);
}
SCElementMinAbs::~SCElementMinAbs() {}
void
SCElementMinAbs::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      if (fabs(i.get()) < r) r = fabs(i.get());
    }
}
double
SCElementMinAbs::result()
{
  return r;
}
int
SCElementMinAbs::has_collect()
{
  return 1;
}
void
SCElementMinAbs::defer_collect(int h)
{
  deferred_=h;
}
void
SCElementMinAbs::collect(const Ref<MessageGrp>&msg)
{
  if (!deferred_)
    msg->min(r);
}

/////////////////////////////////////////////////////////////////////////
// SCElementSumAbs members

static ClassDesc SCElementSumAbs_cd(
  typeid(SCElementSumAbs),"SCElementSumAbs",1,"public SCElementOp",
  0, 0, create<SCElementSumAbs>);
SCElementSumAbs::SCElementSumAbs():deferred_(0), r(0.0) {}
SCElementSumAbs::SCElementSumAbs(StateIn&s):
  SCElementOp(s)
{
  s.get(r);
  s.get(deferred_);
}
void
SCElementSumAbs::save_data_state(StateOut&s)
{
  s.put(r);
  s.put(deferred_);
}
SCElementSumAbs::~SCElementSumAbs() {}
void
SCElementSumAbs::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      r += fabs(i.get());
    }
}
double
SCElementSumAbs::result()
{
  return r;
}
int
SCElementSumAbs::has_collect()
{
  return 1;
}
void
SCElementSumAbs::defer_collect(int h)
{
  deferred_=h;
}
void
SCElementSumAbs::collect(const Ref<MessageGrp>&msg)
{
  if (!deferred_)
    msg->sum(r);
}

/////////////////////////////////////////////////////////////////////////
// SCElementAssign members

static ClassDesc SCElementAssign_cd(
  typeid(SCElementAssign),"SCElementAssign",1,"public SCElementOp",
  0, 0, create<SCElementAssign>);
SCElementAssign::SCElementAssign(double a):assign(a) {}
SCElementAssign::SCElementAssign(StateIn&s):
  SCElementOp(s)
{
  s.get(assign);
}
void
SCElementAssign::save_data_state(StateOut&s)
{
  s.put(assign);
}
SCElementAssign::~SCElementAssign() {}
void
SCElementAssign::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      i.set(assign);
    }
}

int
SCElementAssign::has_side_effects()
{
  return 1;
}

/////////////////////////////////////////////////////////////////////////
// SCElementRandomize members

static ClassDesc SCElementRandomize_cd(
  typeid(SCElementRandomize),"SCElementRandomize",1,"public SCElementOp",
  0, 0, create<SCElementRandomize>);
SCElementRandomize::SCElementRandomize() {}
SCElementRandomize::SCElementRandomize(StateIn&s):
  SCElementOp(s)
{
}
void
SCElementRandomize::save_data_state(StateOut&s)
{
}
SCElementRandomize::~SCElementRandomize() {}
void
SCElementRandomize::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
#ifdef HAVE_DRAND48
      i.set(drand48()*(drand48()<0.5?1.0:-1.0));
#else
      int r=rand();
      double dr = (double) r / 32767.0;
      i.set(dr*(dr<0.5?1.0:-1.0));
#endif
    }
}

int
SCElementRandomize::has_side_effects()
{
  return 1;
}

/////////////////////////////////////////////////////////////////////////
// SCElementShiftDiagonal members

static ClassDesc SCElementShiftDiagonal_cd(
  typeid(SCElementShiftDiagonal),"SCElementShiftDiagonal",1,"public SCElementOp",
  0, 0, create<SCElementShiftDiagonal>);
SCElementShiftDiagonal::SCElementShiftDiagonal(double a):shift_diagonal(a) {}
SCElementShiftDiagonal::SCElementShiftDiagonal(StateIn&s):
  SCElementOp(s)
{
  s.get(shift_diagonal);
}
void
SCElementShiftDiagonal::save_data_state(StateOut&s)
{
  s.put(shift_diagonal);
}
SCElementShiftDiagonal::~SCElementShiftDiagonal() {}
void
SCElementShiftDiagonal::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      if (i.i() == i.j()) i.set(shift_diagonal+i.get());
    }
}

int
SCElementShiftDiagonal::has_side_effects()
{
  return 1;
}

/////////////////////////////////////////////////////////////////////////
// SCElementScaleDiagonal members

static ClassDesc SCElementScaleDiagonal_cd(
  typeid(SCElementScaleDiagonal),"SCElementScaleDiagonal",1,"public SCElementOp",
  0, 0, create<SCElementScaleDiagonal>);
SCElementScaleDiagonal::SCElementScaleDiagonal(double a):scale_diagonal(a) {}
SCElementScaleDiagonal::SCElementScaleDiagonal(StateIn&s):
  SCElementOp(s)
{
  s.get(scale_diagonal);
}
void
SCElementScaleDiagonal::save_data_state(StateOut&s)
{
  s.put(scale_diagonal);
}
SCElementScaleDiagonal::~SCElementScaleDiagonal() {}
void
SCElementScaleDiagonal::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      if (i.i() == i.j()) i.set(scale_diagonal*i.get());
    }
}

int
SCElementScaleDiagonal::has_side_effects()
{
  return 1;
}

/////////////////////////////////////////////////////////////////////////
// SCElementDot members

static ClassDesc SCElementDot_cd(
  typeid(SCElementDot),"SCElementDot",1,"public SCElementOp",
  0, 0, create<SCElementDot>);

SCElementDot::SCElementDot(double**a, double**b, int n):
  avects(a),
  bvects(b),
  length(n)
{
}

SCElementDot::SCElementDot(StateIn&s)
{
  ExEnv::errn() << indent << "SCElementDot does not permit StateIn CTOR\n";
  abort();
}

void
SCElementDot::save_data_state(StateOut&s)
{
  ExEnv::errn() << indent << "SCElementDot does not permit save_data_state\n";
  abort();
}

int
SCElementDot::has_side_effects()
{
  return 1;
}

void
SCElementDot::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      double tmp = i.get();
      double* a = avects[i.i()];
      double* b = bvects[i.j()];
      for (int j = length; j; j--, a++, b++) {
          tmp += *a * *b;
        }
      i.accum(tmp);
    }
}

/////////////////////////////////////////////////////////////////////////
// SCElementAccumulateSCMatrix members

static ClassDesc SCElementAccumulateSCMatrix_cd(
  typeid(SCElementAccumulateSCMatrix),"SCElementAccumulateSCMatrix",1,"public SCElementOp",
  0, 0, 0);

SCElementAccumulateSCMatrix::SCElementAccumulateSCMatrix(SCMatrix*a):
  m(a)
{
}

int
SCElementAccumulateSCMatrix::has_side_effects()
{
  return 1;
}

void
SCElementAccumulateSCMatrix::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      i.accum(m->get_element(i.i(), i.j()));
    }
}

/////////////////////////////////////////////////////////////////////////
// SCElementAccumulateSymmSCMatrix members

static ClassDesc SCElementAccumulateSymmSCMatrix_cd(
  typeid(SCElementAccumulateSymmSCMatrix),"SCElementAccumulateSymmSCMatrix",1,"public SCElementOp",
  0, 0, 0);

SCElementAccumulateSymmSCMatrix::SCElementAccumulateSymmSCMatrix(
    SymmSCMatrix*a):
  m(a)
{
}

int
SCElementAccumulateSymmSCMatrix::has_side_effects()
{
  return 1;
}

void
SCElementAccumulateSymmSCMatrix::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      i.accum(m->get_element(i.i(), i.j()));
    }
}

/////////////////////////////////////////////////////////////////////////
// SCElementAccumulateDiagSCMatrix members

static ClassDesc SCElementAccumulateDiagSCMatrix_cd(
  typeid(SCElementAccumulateDiagSCMatrix),"SCElementAccumulateDiagSCMatrix",1,"public SCElementOp",
  0, 0, 0);

SCElementAccumulateDiagSCMatrix::SCElementAccumulateDiagSCMatrix(
    DiagSCMatrix*a):
  m(a)
{
}

int
SCElementAccumulateDiagSCMatrix::has_side_effects()
{
  return 1;
}

void
SCElementAccumulateDiagSCMatrix::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      i.accum(m->get_element(i.i()));
    }
}

/////////////////////////////////////////////////////////////////////////
// SCElementAccumulateSCVector members

static ClassDesc SCElementAccumulateSCVector_cd(
  typeid(SCElementAccumulateSCVector),"SCElementAccumulateSCVector",1,"public SCElementOp",
  0, 0, 0);

SCElementAccumulateSCVector::SCElementAccumulateSCVector(SCVector*a):
  m(a)
{
}

int
SCElementAccumulateSCVector::has_side_effects()
{
  return 1;
}

void
SCElementAccumulateSCVector::process(SCMatrixBlockIter&i)
{
  for (i.reset(); i; ++i) {
      i.accum(m->get_element(i.i()));
    }
}

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

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