SpeciesSet Class Reference

Custom container for set of attributes for a set of species. More...

Collaboration diagram for SpeciesSet:

Public Types
using	Scalar_t = double
using	SpeciesAttrib_t = std::vector< Scalar_t >
using	AttribList_t = std::vector< SpeciesAttrib_t >

Public Member Functions
int	size () const
	return the number of species More...
int	getTotalNum () const
	return the number of species More...
void	setTotalNum (const unsigned n)
	set the number of species More...
int	numAttributes () const
	return the number of attributes in our list More...
int	addSpecies (const std::string &aname)
	When a name species does not exist, add a new species. More...
int	addAttribute (const std::string &aname)
	for a new attribute, allocate the data, !More often used to get the index of a species More...
int	getAttribute (const std::string &aname) const
	When a name species does not exist, return attribute.size() More...
bool	hasAttribute (const std::string &aname) const
	Check for attribute presence This replaces code that gets numAttributes then tries to addAttribute for a particular name and compares the numAttributes and index of the new Attribute. More...
double	operator() (int i, int j) const
double &	operator() (int i, int j)
	assignment operator More...
void	create (unsigned m)
int	findSpecies (const std::string &name) const
	if the input species is not found, add a new species More...
int	findAttribute (const std::string &name) const
	almost all code ignores this and just uses addAttribute for the same purpose. More...
int	findIndex (const std::string &name, const std::vector< std::string > &alist) const
const std::string &	getSpeciesName (int index) const

Public Attributes
unsigned	TotalNum = 0
	The number of species. More...
std::vector< std::string >	speciesName
	Species name list. More...
std::vector< std::string >	attribName
	attribute name list More...
AttribList_t	d_attrib
	List of species attributes. More...

Detailed Description

Custom container for set of attributes for a set of species.

A confusingly equivalent of std::map<std::string, <std::map<std::string, Scalar>> implemented as two sets of key vectors and a single vector of Scalars. It leaks its implementation details i.e. the indexing to the vectors. Reduces readability and increases semantic load. Looks like premature optimization.

Todo:

prove this helps overall performance, if not remove it. Else document it and it's use

Definition at line 33 of file SpeciesSet.h.

Member Typedef Documentation

AttribList_t

using AttribList_t = std::vector<SpeciesAttrib_t>

Definition at line 38 of file SpeciesSet.h.

Scalar_t

using Scalar_t = double

Definition at line 36 of file SpeciesSet.h.

SpeciesAttrib_t

using SpeciesAttrib_t = std::vector<Scalar_t>

Definition at line 37 of file SpeciesSet.h.

Member Function Documentation

addAttribute()

int addAttribute

(

const std::string &

aname

)

for a new attribute, allocate the data, !More often used to get the index of a species

Parameters

aname

a unique name of an attribute

Returns

the index of a new attribute

Definition at line 45 of file SpeciesSet.cpp.

References SpeciesSet::attribName, SpeciesSet::d_attrib, qmcplusplus::n, and SpeciesSet::TotalNum.

Referenced by RadialJastrowBuilder::buildComponent(), qmcplusplus::create_C_pbc_particlesets(), qmcplusplus::createElectronParticleSet(), QMCGaussianParserBase::createElectronSet(), ParticleSet::createSK(), qmcplusplus::doSOECPotentialTest(), qmcplusplus::generateCuspInfo(), ForceChiesaPBCAA::initBreakup(), StressPBC::initBreakup(), CoulombPBCAB::initBreakup(), QMCGaussianParserBase::QMCGaussianParserBase(), ParticleSet::resetGroups(), EnergyDensityEstimator::set_ptcl(), QMCUpdateBase::setDefaults(), qmcplusplus::setSpeciesProperty(), qmcplusplus::setup_He_wavefunction(), qmcplusplus::test_cartesian_ao(), qmcplusplus::TEST_CASE(), qmcplusplus::test_CoulombPBCAA_3p(), qmcplusplus::test_diamond_2x1x1_xml_input(), qmcplusplus::test_dirac_ao(), qmcplusplus::test_hcpBe_rotation(), qmcplusplus::test_He(), qmcplusplus::test_He_mw(), qmcplusplus::test_He_sto3g_xml_input(), qmcplusplus::test_J1_spline(), qmcplusplus::test_LCAO_DiamondC_2x1x1_cplx(), qmcplusplus::test_LCAO_DiamondC_2x1x1_real(), qmcplusplus::test_lcao_spinor(), qmcplusplus::test_lcao_spinor_excited(), qmcplusplus::test_lcao_spinor_ion_derivs(), qmcplusplus::test_LiH_msd(), qmcplusplus::test_LiH_msd_xml_input(), qmcplusplus::test_LiH_msd_xml_input_with_positron(), qmcplusplus::test_Ne(), qmcplusplus::testElecCase(), and qmcplusplus::testTrialWaveFunction_diamondC_2x1x1().

{
  int i = 0;
  while (i < attribName.size())
  {
    if (attribName[i] == aname)
      return i;
    i++;
  }
  attribName.push_back(aname);
  int n = d_attrib.size();
  d_attrib.push_back(SpeciesAttrib_t(TotalNum));
  return n;
}

addSpecies()

int addSpecies

(

const std::string &

aname

)

When a name species does not exist, add a new species.

Parameters

aname

Unique name of the species be added.

Returns

the index of the species

Definition at line 33 of file SpeciesSet.cpp.

References SpeciesSet::create(), SpeciesSet::findSpecies(), SpeciesSet::speciesName, and SpeciesSet::TotalNum.

Referenced by qmcplusplus::create_C_pbc_particlesets(), qmcplusplus::createElectronParticleSet(), QMCGaussianParserBase::createElectronSet(), qmcplusplus::doSOECPotentialTest(), qmcplusplus::get_two_species_particleset(), qmcplusplus::setup_He_wavefunction(), qmcplusplus::test_cartesian_ao(), qmcplusplus::TEST_CASE(), qmcplusplus::test_CoulombPBCAA_3p(), qmcplusplus::test_diamond_2x1x1_xml_input(), qmcplusplus::test_dirac_ao(), qmcplusplus::test_hcpBe_rotation(), qmcplusplus::test_He(), qmcplusplus::test_He_mw(), qmcplusplus::test_He_sto3g_xml_input(), qmcplusplus::test_J1_spline(), qmcplusplus::test_J3_polynomial3D(), qmcplusplus::test_LCAO_DiamondC_2x1x1_cplx(), qmcplusplus::test_LCAO_DiamondC_2x1x1_real(), qmcplusplus::test_lcao_spinor(), qmcplusplus::test_lcao_spinor_excited(), qmcplusplus::test_lcao_spinor_ion_derivs(), qmcplusplus::test_LiH_msd(), qmcplusplus::test_LiH_msd_xml_input(), qmcplusplus::test_LiH_msd_xml_input_with_positron(), qmcplusplus::test_Ne(), qmcplusplus::testElecCase(), and qmcplusplus::testTrialWaveFunction_diamondC_2x1x1().

{
  int i = findSpecies(aname); // check if the name is registered
  if (i == TotalNum)
  // if not found, add a new species
  {
    create(1);
    speciesName[i] = aname;
  }
  return i; // return an index for a species
}

create()

void create

(

unsigned

m

)

Parameters

m	the number of species to be added

Definition at line 20 of file SpeciesSet.cpp.

References SpeciesSet::d_attrib, qmcplusplus::Units::distance::m, SpeciesSet::speciesName, and SpeciesSet::TotalNum.

Referenced by SpeciesSet::addSpecies().

{
  if (m > 0)
  {
    speciesName.insert(speciesName.end(), m, std::string("none"));
    for (auto& d : d_attrib)
    {
      d.insert(d.end(), m, 0);
    }
    TotalNum += m;
  }
}

findAttribute()

int findAttribute ( const std::string &  name ) const

inline

almost all code ignores this and just uses addAttribute for the same purpose.

Definition at line 128 of file SpeciesSet.h.

References SpeciesSet::attribName, and SpeciesSet::findIndex().

Referenced by SpinDensityNew::getSpeciesSize(), and EinsplineSetBuilder::ReadOrbitalInfo_ESHDF().

{ return findIndex(name, attribName); }

findIndex()

int findIndex ( const std::string &  name, const std::vector< std::string > &  alist  ) const

inline

Definition at line 130 of file SpeciesSet.h.

Referenced by SpeciesSet::findAttribute().

  {
    int i = 0;
    while (i < alist.size())
    {
      if (alist[i] == name)
        return i;
      i++;
    }
    return -1;
  }

findSpecies()

int findSpecies ( const std::string &  name ) const

inline

if the input species is not found, add a new species

Parameters

name	a name of species

Returns

an ID for the species with name.

Definition at line 114 of file SpeciesSet.h.

References SpeciesSet::speciesName.

Referenced by BackflowBuilder::addOneBody(), SpeciesSet::addSpecies(), LCAOrbitalBuilder::createBasisSet(), LCAOrbitalBuilder::createBasisSetH5(), RadialJastrowBuilder::createJ1(), LatticeDeviationEstimator::LatticeDeviationEstimator(), SlaterDetBuilder::putDeterminant(), eeI_JastrowBuilder::putkids(), and ECPotentialBuilder::useXmlFormat().

  {
    int i = 0;
    while (i < speciesName.size())
    {
      if (speciesName[i] == name)
        return i;
      i++;
    }
    return i;
  }

getAttribute()

int getAttribute

(

const std::string &

aname

)

const

When a name species does not exist, return attribute.size()

Parameters

aname

Unique name of the species to be looked up.

Returns

the index of the species

Definition at line 60 of file SpeciesSet.cpp.

References SpeciesSet::attribName.

Referenced by StressPBC::evalConsts_AA(), StressPBC::evaluateLR_AA(), OneBodyDensityMatrices::OneBodyDensityMatrices(), and SpeciesKineticEnergy::SpeciesKineticEnergy().

{
  for (int i = 0; i < attribName.size(); i++)
  {
    if (attribName[i] == aname)
      return i;
  }
  return attribName.size();
}

getSpeciesName()

const std::string& getSpeciesName ( int  index ) const

inline

Definition at line 142 of file SpeciesSet.h.

References SpeciesSet::speciesName.

Referenced by XMLParticleParser::checkGrouping().

{ return speciesName[index]; }

getTotalNum()

int getTotalNum ( ) const

inline

return the number of species

Definition at line 55 of file SpeciesSet.h.

References SpeciesSet::TotalNum.

Referenced by BackflowBuilder::addOneBody(), QMCGaussianParserBase::createIonSet(), RadialJastrowBuilder::createJ1(), XMLSaveParticle::createNode(), ParticleSet::createSK(), JeeIOrbitalSoA< FT >::init(), J1OrbitalSoA< FT >::initialize(), L2Potential::L2Potential(), LocalECPotential::LocalECPotential(), NonLocalECPotential::NonLocalECPotential(), ECPotentialBuilder::put(), ParticleSet::resetGroups(), SkAllEstimator::SkAllEstimator(), SkEstimator::SkEstimator(), SkPot::SkPot(), SoaLocalizedBasisSet< COT, ORBT >::SoaLocalizedBasisSet(), and SOECPotential::SOECPotential().

{ return TotalNum; }

hasAttribute()

bool hasAttribute

(

const std::string &

aname

)

const

Check for attribute presence This replaces code that gets numAttributes then tries to addAttribute for a particular name and compares the numAttributes and index of the new Attribute.

Parameters

aname

Unique name of the species to be looked up.

Returns

is an attribute of that name present

Definition at line 70 of file SpeciesSet.cpp.

References SpeciesSet::attribName.

Referenced by OneBodyDensityMatrices::OneBodyDensityMatrices().

{
  return std::find(attribName.begin(), attribName.end(), aname) != attribName.end();
}

numAttributes()

int numAttributes ( ) const

inline

return the number of attributes in our list

Definition at line 59 of file SpeciesSet.h.

References SpeciesSet::d_attrib.

Referenced by ParticleSet::createSK(), DensityMatrices1B::initialize(), and ParticleSet::resetGroups().

{ return d_attrib.size(); }

operator()() [1/2]

double operator() ( int  i, int  j  ) const

inline

Parameters

i	attribute index
j	species index

Returns

the value of i-th attribute for the j-th species

Definition at line 94 of file SpeciesSet.h.

References SpeciesSet::d_attrib.

{ return d_attrib[i][j]; }

operator()() [2/2]

double& operator() ( int  i, int  j  )

inline

assignment operator

Parameters

i	attribute index
j	species index

Returns

the value of i-th attribute for the j-th species

Definition at line 102 of file SpeciesSet.h.

References SpeciesSet::d_attrib.

{ return d_attrib[i][j]; }

setTotalNum()

void setTotalNum ( const unsigned  n )

inline

set the number of species

Definition at line 57 of file SpeciesSet.h.

References qmcplusplus::n, and SpeciesSet::TotalNum.

{ TotalNum = n; }

size()

int size ( void  ) const

inline

return the number of species

Definition at line 53 of file SpeciesSet.h.

References SpeciesSet::TotalNum.

Referenced by SpinDensityNew::accumulate(), OneBodyDensityMatrices::evaluateMatrix(), OneBodyDensityMatrices::generateParticleBasis(), OneBodyDensityMatrices::generateSampleRatios(), SpinDensityNew::getFullDataSize(), SpinDensityNew::getSpeciesSize(), DensityMatrices1B::initialize(), OneBodyDensityMatrices::OneBodyDensityMatrices(), PairCorrEstimator::PairCorrEstimator(), SlaterDetBuilder::putDeterminant(), eeI_JastrowBuilder::putkids(), SpinDensityNew::registerOperatorEstimator(), OneBodyDensityMatrices::registerOperatorEstimator(), SpinDensityNew::report(), SpinDensity::SpinDensity(), and StaticStructureFactor::StaticStructureFactor().

{ return TotalNum; }

Member Data Documentation

attribName

std::vector<std::string> attribName

attribute name list

Definition at line 47 of file SpeciesSet.h.

Referenced by SpeciesSet::addAttribute(), SpeciesSet::findAttribute(), SpeciesSet::getAttribute(), and SpeciesSet::hasAttribute().

d_attrib

AttribList_t d_attrib

List of species attributes.

Definition at line 50 of file SpeciesSet.h.

Referenced by SpeciesSet::addAttribute(), SpeciesSet::create(), SpeciesSet::numAttributes(), and SpeciesSet::operator()().

speciesName

std::vector<std::string> speciesName

Species name list.

Definition at line 44 of file SpeciesSet.h.

Referenced by SpeciesSet::addSpecies(), SpeciesSet::create(), XMLSaveParticle::createNode(), LatticeDeviationEstimator::evaluate(), SpeciesSet::findSpecies(), SpeciesSet::getSpeciesName(), DensityMatrices1B::initialize(), OneBodyDensityMatrices::OneBodyDensityMatrices(), ParticleSet::print(), SlaterDetBuilder::putDeterminant(), SpinDensityNew::registerOperatorEstimator(), OneBodyDensityMatrices::registerOperatorEstimator(), SpinDensityNew::report(), XMLSaveParticle::reset(), ParticleSet::species_from_index(), SpinDensity::SpinDensity(), and StaticStructureFactor::StaticStructureFactor().

TotalNum

unsigned TotalNum = 0

The number of species.

Definition at line 41 of file SpeciesSet.h.

Referenced by SpeciesSet::addAttribute(), SpeciesSet::addSpecies(), SpeciesSet::create(), StressPBC::evalConsts_AA(), StressPBC::evaluateLR_AA(), SpeciesSet::getTotalNum(), SpeciesSet::setTotalNum(), and SpeciesSet::size().

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