InitMolecularSystem Class Reference

Inheritance diagram for InitMolecularSystem:

Collaboration diagram for InitMolecularSystem:

Public Member Functions
	InitMolecularSystem (ParticleSetPool &pset, const char *aname="mosystem")
bool	get (std::ostream &os) const override
	write to a std::ostream More...
bool	put (std::istream &is) override
	read from std::istream More...
bool	put (xmlNodePtr cur) override
	read from an xmlNode More...
void	reset () override
	reset member data More...
void	initAtom (ParticleSet *ions, ParticleSet *els)
	initialize els for an atom More...
void	initMolecule (ParticleSet *ions, ParticleSet *els)
	initialize els position for a molecule More...
void	initWithVolume (ParticleSet *ions, ParticleSet *els)
	initialize els for the systems with a mixed boundary More...
Public Member Functions inherited from OhmmsElementBase
	OhmmsElementBase (const char *aname="none")
	constructor with a name More...
virtual	~OhmmsElementBase ()
	destructor More...
const std::string &	getName () const
	return the name More...
void	setName (const std::string &aname)
	set name More...
void	setIOMode (int imode)
	set iomode More...
virtual bool	add (xmlNodePtr parent)
	add a xmlNode to the children list of parent More...
void	put (const std::string &s)
	read from string More...
virtual void	begin_node (std::ostream &os) const
	write the start of a node More...
virtual void	end_node (std::ostream &os) const
	write the end of a node More...

Private Attributes
ParticleSetPool &	ptclPool
	pointer to ParticleSetPool More...

Additional Inherited Members
Public Types inherited from OhmmsElementBase
enum	{ useLIBXML = 0, useLIBXMLPP, usePLAIN }
	enumeration to choose the xml parser More...
Protected Attributes inherited from OhmmsElementBase
int	myIOMode
	the type of IO mode: default is useLIBXML More...
std::string	myName
	the name of the node, corresponds to the xml tag More...

Detailed Description

Definition at line 30 of file InitMolecularSystem.h.

Constructor & Destructor Documentation

InitMolecularSystem()

InitMolecularSystem	(	ParticleSetPool &	pset,
		const char *	aname = "mosystem"
	)

Definition at line 32 of file InitMolecularSystem.cpp.

    : OhmmsElementBase(aname), ptclPool(pset)
{}

Member Function Documentation

get()

bool get ( std::ostream &  ) const

overridevirtual

write to a std::ostream

Implements OhmmsElementBase.

Definition at line 272 of file InitMolecularSystem.cpp.

{ return true; }

initAtom()

void initAtom	(	ParticleSet *	ions,
		ParticleSet *	els
	)

initialize els for an atom

Definition at line 73 of file InitMolecularSystem.cpp.

References ParticleSet::getTotalNum(), qmcplusplus::makeGaussRandom(), ParticleSet::R, and qmcplusplus::sqrt().

Referenced by InitMolecularSystem::initMolecule().

{
  //3N-dimensional Gaussian
  ParticleSet::ParticlePos chi(els->getTotalNum());
  makeGaussRandom(chi);
  RealType q = std::sqrt(static_cast<RealType>(els->getTotalNum())) * 0.5;
  int nel(els->getTotalNum()), items(0);
  while (nel)
  {
    els->R[items] = ions->R[0] + q * chi[items];
    --nel;
    ++items;
  }
}

initMolecule()

void initMolecule	(	ParticleSet *	ions,
		ParticleSet *	els
	)

initialize els position for a molecule

Use the valence of each ionic species on a sphere

Definition at line 95 of file InitMolecularSystem.cpp.

References ParticleSet::addTable(), ParticleSet::applyBC(), qmcplusplus::Cartesian, ParticleSet::first(), DistanceTableAA::getDistances(), ParticleSet::getDistTableAA(), ParticleSet::getLattice(), ParticleSet::getSpeciesSet(), ParticleSet::getTotalNum(), ParticleSet::GroupID, ParticleSet::groups(), InitMolecularSystem::initAtom(), ParticleSet::last(), qmcplusplus::makeSphereRandom(), omptarget::min(), ParticleSet::R, qmcplusplus::SUPERCELL_OPEN, and ParticleSet::update().

Referenced by InitMolecularSystem::put().

{
  if (ions->getTotalNum() == 1)
    return initAtom(ions, els);

  const int d_ii_ID = ions->addTable(*ions);
  ions->update();
  const ParticleSet::ParticleIndex& grID(ions->GroupID);
  SpeciesSet& Species(ions->getSpeciesSet());
  int Centers = ions->getTotalNum();
  std::vector<int> Qtot(Centers), Qcore(Centers), Qval(Centers, 0);
  //use charge as the core electrons first
  int icharge = Species.addAttribute("charge");
  //Assign default core charge
  for (int iat = 0; iat < Centers; iat++)
    Qtot[iat] = static_cast<int>(Species(icharge, grID[iat]));
  //cutoff radius (Bohr) this a random choice
  RealType cutoff = 4.0;
  ParticleSet::ParticlePos chi(els->getTotalNum());
  //makeGaussRandom(chi);
  makeSphereRandom(chi);
  // the upper limit of the electron index with spin up
  const int numUp = els->last(0);
  // the upper limit of the electron index with spin down. Pay attention to the no spin down electron case.
  const int numDown = els->last(els->groups() > 1 ? 1 : 0) - els->first(0);
  // consumer counter of random numbers chi
  int random_number_counter = 0;
  int nup_tot = 0, ndown_tot = numUp;
  std::vector<LoneElectron> loneQ;
  RealType rmin = cutoff;
  ParticleSet::SingleParticlePos cm;

  const auto& dist = ions->getDistTableAA(d_ii_ID).getDistances();
  // Step 1. Distribute even Q[iat] of atomic center iat. If Q[iat] is odd, put Q[iat]-1 and save the lone electron.
  for (size_t iat = 0; iat < Centers; iat++)
  {
    cm += ions->R[iat];
    for (size_t jat = iat + 1; jat < Centers; ++jat)
    {
      rmin = std::min(rmin, dist[jat][iat]);
    }
    //use 40% of the minimum bond
    RealType sep = rmin * 0.4;
    int v2       = Qtot[iat] / 2;
    if (Qtot[iat] > v2 * 2)
    {
      loneQ.push_back(LoneElectron(iat, sep));
    }
    for (int k = 0; k < v2; k++)
    {
      // initialize electron positions in pairs
      if (nup_tot < numUp)
        els->R[nup_tot++] = ions->R[iat] + sep * chi[random_number_counter++];
      if (ndown_tot < numDown)
        els->R[ndown_tot++] = ions->R[iat] + sep * chi[random_number_counter++];
    }
  }

  // Step 2. Distribute the electrons left alone
  // mmorales: changed order of spin assignment to help with spin
  // imbalances in molecules at large distances.
  // Not guaranteed to work, but should help in most cases
  // as long as atoms in molecules are defined sequencially
  std::vector<LoneElectron>::iterator it(loneQ.begin());
  std::vector<LoneElectron>::iterator it_end(loneQ.end());
  while (it != it_end && nup_tot != numUp && ndown_tot != numDown)
  {
    if (nup_tot < numUp)
    {
      els->R[nup_tot++] = ions->R[(*it).ID] + (*it).BondLength * chi[random_number_counter++];
      ++it;
    }
    if (ndown_tot < numDown && it != it_end)
    {
      els->R[ndown_tot++] = ions->R[(*it).ID] + (*it).BondLength * chi[random_number_counter++];
      ++it;
    }
  }

  // Step 3. Handle more than neutral electrons
  //extra electrons around the geometric center
  RealType cnorm = 1.0 / static_cast<RealType>(Centers);
  RealType sep   = rmin * 2;
  cm             = cnorm * cm;
  if (nup_tot < numUp)
    while (nup_tot < numUp)
      els->R[nup_tot++] = cm + sep * chi[random_number_counter++];
  if (ndown_tot < numDown)
    while (ndown_tot < numDown)
      els->R[ndown_tot++] = cm + sep * chi[random_number_counter++];

  // safety check. all the random numbers should have been consumed once and only once.
  if (random_number_counter != chi.size())
    throw std::runtime_error("initMolecule unexpected random number consumption. Please report a bug!");

  //put all the electrons in a unit box
  if (els->getLattice().SuperCellEnum != SUPERCELL_OPEN)
  {
    els->R.setUnit(PosUnit::Cartesian);
    els->applyBC(els->R);
    els->update(false);
  }
}

initWithVolume()

void initWithVolume	(	ParticleSet *	ions,
		ParticleSet *	els
	)

initialize els for the systems with a mixed boundary

Use the bound of the ionic systems and uniform random positions within a reduced box

Definition at line 213 of file InitMolecularSystem.cpp.

References qmcplusplus::abs(), qmcplusplus::app_log(), ParticleSet::applyBC(), qmcplusplus::Cartesian, ParticleSet::getLattice(), ParticleSet::getTotalNum(), qmcplusplus::Lattice, qmcplusplus::lower_bound(), qmcplusplus::makeUniformRandom(), omptarget::min(), OHMMS_DIM, ParticleSet::R, CrystalLattice< T, D >::set(), ParticleAttrib< T, Alloc >::setUnit(), and qmcplusplus::upper_bound().

Referenced by InitMolecularSystem::put().

{
  TinyVector<RealType, OHMMS_DIM> start(1.0);
  TinyVector<RealType, OHMMS_DIM> end(0.0);

  ParticleSet::ParticlePos Ru(ions->getTotalNum());
  Ru.setUnit(PosUnit::Lattice);
  ions->applyBC(ions->R, Ru);

  for (int iat = 0; iat < Ru.size(); iat++)
  {
    start = lower_bound(Ru[iat], start);
    end   = upper_bound(Ru[iat], end);
  }

  TinyVector<RealType, OHMMS_DIM> shift;
  Tensor<RealType, OHMMS_DIM> newbox(ions->getLattice().R);

  RealType buffer = 2.0; //buffer 2 bohr
  for (int idim = 0; idim < OHMMS_DIM; ++idim)
  {
    //if(ions->getLattice().BoxBConds[idim])
    //{
    //  start[idim]=0.0;
    //  end[idim]=1.0;
    //  shift[idim]=0.0;
    //}
    //else
    {
      RealType buffer_r = buffer * ions->getLattice().OneOverLength[idim];
      start[idim]       = std::max((RealType)0.0, (start[idim] - buffer_r));
      end[idim]         = std::min((RealType)1.0, (end[idim] + buffer_r));
      shift[idim]       = start[idim] * ions->getLattice().Length[idim];
      if (std::abs(end[idim] = start[idim]) < buffer)
      { //handle singular case
        start[idim] = std::max(0.0, start[idim] - buffer_r / 2.0);
        end[idim]   = std::min(1.0, end[idim] + buffer_r / 2.0);
      }

      newbox(idim, idim) = (end[idim] - start[idim]) * ions->getLattice().Length[idim];
    }
  }

  ParticleSet::ParticleLayout slattice(ions->getLattice());
  slattice.set(newbox);

  app_log() << "  InitMolecularSystem::initWithVolume " << std::endl;
  app_log() << "  Effective Lattice shifted by  " << shift << std::endl;
  app_log() << newbox << std::endl;

  Ru.resize(els->getTotalNum());
  makeUniformRandom(Ru);
  for (int iat = 0; iat < Ru.size(); ++iat)
    els->R[iat] = slattice.toCart(Ru[iat]) + shift;
  els->R.setUnit(PosUnit::Cartesian);
}

put() [1/2]

bool put ( std::istream &  )

overridevirtual

read from std::istream

Implements OhmmsElementBase.

Definition at line 270 of file InitMolecularSystem.cpp.

Referenced by ParticleSetPool::randomize(), and QMCMain::validateXML().

{ return true; }

put() [2/2]

bool put ( xmlNodePtr  cur )

overridevirtual

read from an xmlNode

Implements OhmmsElementBase.

Definition at line 36 of file InitMolecularSystem.cpp.

References OhmmsAttributeSet::add(), qmcplusplus::app_log(), ERRORMSG, ParticleSetPool::getParticleSet(), InitMolecularSystem::initMolecule(), InitMolecularSystem::initWithVolume(), qmcplusplus::makeUniformRandom(), InitMolecularSystem::ptclPool, OhmmsAttributeSet::put(), and ParticleSet::spins.

{
  std::string target("e"), source("i"), volume("no");
  OhmmsAttributeSet hAttrib;
  hAttrib.add(target, "target");
  hAttrib.add(source, "source");
  hAttrib.add(volume, "use_volume");
  hAttrib.put(cur);
  ParticleSet* els = ptclPool.getParticleSet(target);
  if (els == 0)
  {
    ERRORMSG("No target particle " << target << " exists.")
    return false;
  }
  ParticleSet* ions = ptclPool.getParticleSet(source);
  if (ions == 0)
  {
    ERRORMSG("No source particle " << source << " exists.")
    return false;
  }

  app_log() << "<init source=\"" << source << "\" target=\"" << target << "\">" << std::endl;

  if (volume == "yes")
    initWithVolume(ions, els);
  else
    initMolecule(ions, els);

  makeUniformRandom(els->spins);
  els->spins *= 2 * M_PI;

  app_log() << "</init>" << std::endl;
  app_log().flush();

  return true;
}

reset()

void reset ( )

overridevirtual

reset member data

Implements OhmmsElementBase.

Definition at line 274 of file InitMolecularSystem.cpp.

{}

Member Data Documentation

ptclPool

ParticleSetPool& ptclPool

private

pointer to ParticleSetPool

QMCHamiltonian needs to know which ParticleSet object is used as an input object for the evaluations. Any number of ParticleSet can be used to describe a QMCHamiltonian.

Definition at line 62 of file InitMolecularSystem.h.

Referenced by InitMolecularSystem::put().

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The documentation for this class was generated from the following files:

• /home/pk7/projects/qmc/for_cron_doxygen/qmcpack/src/Particle/InitMolecularSystem.h
• /home/pk7/projects/qmc/for_cron_doxygen/qmcpack/src/Particle/InitMolecularSystem.cpp