Inheritance diagram for LCAOHDFParser:

Collaboration diagram for LCAOHDFParser:

Public Member Functions
	LCAOHDFParser ()

	LCAOHDFParser (int argc, char **argv)

void	parse (const std::string &fname) override

void	getGeometry (const std::string &fname)

void	getCell (const std::string &fname)

void	getSuperTwist (const std::string &fname)

void	getMO (const std::string &fname)

void	getGaussianCenters (const std::string fname)

Public Member Functions inherited from QMCGaussianParserBase
	QMCGaussianParserBase ()

	QMCGaussianParserBase (int argc, char **argv)

virtual	~QMCGaussianParserBase ()=default

void	setOccupationNumbers ()

void	createGridNode (int argc, char **argv)

void	createSPOSets (xmlNodePtr, xmlNodePtr)

void	createSPOSetsH5 (xmlNodePtr, xmlNodePtr)

void	PrepareSPOSetsFromH5 (xmlNodePtr, xmlNodePtr)

xmlNodePtr	createElectronSet (const std::string &ion_tag)

xmlNodePtr	createIonSet ()

xmlNodePtr	createCell ()

xmlNodePtr	createHamiltonian (const std::string &ion_tag, const std::string &psi_tag)

xmlNodePtr	createBasisSet ()

xmlNodePtr	createBasisSetWithHDF5 ()

xmlNodePtr	createCenter (int iat, int _off)

void	createCenterH5 (int iat, int _off, int numelem)

void	createShell (int n, int ig, int off_, xmlNodePtr abasis)

void	createShellH5 (int n, int ig, int off_, int numelem)

xmlNodePtr	createDeterminantSet ()

xmlNodePtr	createMultiDeterminantSet ()

xmlNodePtr	createDeterminantSetWithHDF5 ()

xmlNodePtr	createMultiDeterminantSetFromH5 ()

xmlNodePtr	createMultiDeterminantSetCIHDF5 ()

xmlNodePtr	PrepareDeterminantSetFromHDF5 ()

xmlNodePtr	createJ3 ()

xmlNodePtr	createJ2 ()

xmlNodePtr	createJ1 ()

xmlNodePtr	parameter (xmlNodePtr Parent, std::string Mypara, std::string a)

int	numberOfExcitationsCSF (std::string &)

virtual void	dumpPBC (const std::string &psi_tag, const std::string &ion_tag)

virtual void	dump (const std::string &psi_tag, const std::string &ion_tag)

void	dumpStdInput (const std::string &psi_tag, const std::string &ion_tag)

void	dumpStdInputProd (const std::string &psi_tag, const std::string &ion_tag)

Public Member Functions inherited from OhmmsAsciiParser
void	skiplines (std::istream &is, int n)

template<class T >
void	getValue (std::istream &is, T &aval)

template<class T1 , class T2 >
void	getValue (std::istream &is, T1 &aval, T2 &bval)

template<class IT >
void	getValues (std::istream &is, IT first, IT last)

int	search (std::istream &is, const std::string &keyword)

int	search (std::istream &is, const std::string &keyword, std::string &the_line)

bool	lookFor (std::istream &is, const std::string &keyword)

bool	lookFor (std::istream &is, const std::string &keyword, std::string &the_line)

Public Attributes
std::streampos	pivot_begin

std::vector< std::string >	tags

std::string	MOtype

int	readtype

int	numAO

int	NFZC

int	NEXT

int	NTOT

int	NAC

Public Attributes inherited from QMCGaussianParserBase
bool	multideterminant

bool	multidetH5

bool	BohrUnit

bool	SpinRestricted

bool	Periodicity

bool	UseHDF5

bool	PBC

bool	production

bool	zeroCI

bool	orderByExcitation

bool	addJastrow

bool	addJastrow3Body

bool	ECP

bool	debug

bool	Structure

bool	DoCusp

bool	FixValence

bool	singledetH5

bool	optDetCoeffs

bool	usingCSF

bool	isSpinor

int	IonChargeIndex

int	ValenceChargeIndex

int	AtomicNumberIndex

int	NumberOfAtoms

int	NumberOfEls

int	target_state

int	SpinMultiplicity

int	NumberOfAlpha

int	NumberOfBeta

int	SizeOfBasisSet

int	numMO

int	readNO

int	readGuess

int	numMO2print

int	ci_size

int	ci_nca

int	ci_ncb

int	ci_nea

int	ci_neb

int	ci_nstates

int	NbKpts

int	nbexcitedstates

double	ci_threshold

std::vector< double >	STwist_Coord

std::string	Title

std::string	basisType

std::string	basisName

std::string	Normalized

std::string	CurrentCenter

std::string	outputFile

std::string	angular_type

std::string	expandYlm

std::string	h5file

std::string	multih5file

std::string	WFS_name

std::string	CodeName

const SimulationCell	simulation_cell

ParticleSet	IonSystem

std::vector< std::string >	GroupName

std::vector< int >	gShell

std::vector< int >	gNumber

std::vector< int >	gBound

std::vector< int >	Occ_alpha

std::vector< int >	Occ_beta

std::vector< value_type >	Qv

std::vector< value_type >	gExp

std::vector< value_type >	gC0

std::vector< value_type >	gC1

std::vector< value_type >	EigVal_alpha

std::vector< value_type >	EigVal_beta

std::vector< value_type >	EigVec

std::unique_ptr< xmlNode, void(*)(xmlNodePtr)>	gridPtr

std::vector< std::string >	CIalpha

std::vector< std::string >	CIbeta

std::vector< std::string >	CSFocc

std::vector< std::vector< std::string > >	CSFalpha

std::vector< std::vector< std::string > >	CSFbeta

std::vector< std::vector< double > >	CSFexpansion

std::vector< double >	CIcoeff

std::vector< double >	X

std::vector< double >	Y

std::vector< double >	Z

std::vector< int >	Image

std::vector< int >	CIexcitLVL

std::vector< std::pair< int, double > >	coeff2csf

Public Attributes inherited from OhmmsAsciiParser
char	dbuffer [bufferSize]

std::vector< std::string >	currentWords

Additional Inherited Members
Public Types inherited from QMCGaussianParserBase
using	value_type = double

using	SingleParticlePos = ParticleSet::SingleParticlePos

Static Public Member Functions inherited from QMCGaussianParserBase
static void	init ()

Static Public Attributes inherited from QMCGaussianParserBase
static std::map< int, std::string >	IonName

static std::vector< std::string >	gShellType

static std::vector< int >	gShellID

static const std::vector< double >	gCoreTable

Static Public Attributes inherited from OhmmsAsciiParser
static const int	bufferSize = 200

Detailed Description

Definition at line 24 of file LCAOHDFParser.h.

Constructor & Destructor Documentation

◆ LCAOHDFParser() [1/2]

LCAOHDFParser ( )

Definition at line 23 of file LCAOHDFParser.cpp.

References QMCGaussianParserBase::angular_type, QMCGaussianParserBase::basisName, QMCGaussianParserBase::BohrUnit, MOtype, NFZC, QMCGaussianParserBase::Normalized, and readtype.

 {
   basisName    = "Gaussian";
   Normalized   = "no";
   BohrUnit     = true;
   MOtype       = "Canonical";
   angular_type = "cartesian";
   readtype     = 0;
   NFZC         = 0;
 }

◆ LCAOHDFParser() [2/2]

LCAOHDFParser	(	int	argc,
		char **	argv
	)

Definition at line 34 of file LCAOHDFParser.cpp.

References QMCGaussianParserBase::angular_type, QMCGaussianParserBase::basisName, QMCGaussianParserBase::BohrUnit, MOtype, NFZC, QMCGaussianParserBase::Normalized, readtype, and QMCGaussianParserBase::SpinRestricted.

                                                   : QMCGaussianParserBase(argc, argv)
 {
   basisName      = "Gaussian";
   Normalized     = "no";
   BohrUnit       = true;
   MOtype         = "Canonical";
   angular_type   = "cartesian";
   SpinRestricted = true;
   readtype       = 0;
   NFZC           = 0;
 }

Member Function Documentation

◆ getCell()

void getCell ( const std::string & fname )

Definition at line 187 of file LCAOHDFParser.cpp.

References hdf_archive::close(), hdf_archive::open(), hdf_archive::push(), hdf_archive::read(), QMCGaussianParserBase::X, QMCGaussianParserBase::Y, and QMCGaussianParserBase::Z.

Referenced by parse().

 {
   X.resize(3);
   Y.resize(3);
   Z.resize(3);
 
   hdf_archive hin;
 
   if (!hin.open(fname.c_str(), H5F_ACC_RDONLY))
   {
     std::cerr << "Could not open H5 file" << std::endl;
     abort();
   }
   hin.push("Cell");
   Matrix<double> LatticeVec(3, 3);
   hin.read(LatticeVec, "LatticeVectors");
   X[0] = LatticeVec[0][0];
   X[1] = LatticeVec[0][1];
   X[2] = LatticeVec[0][2];
   Y[0] = LatticeVec[1][0];
   Y[1] = LatticeVec[1][1];
   Y[2] = LatticeVec[1][2];
   Z[0] = LatticeVec[2][0];
   Z[1] = LatticeVec[2][1];
   Z[2] = LatticeVec[2][2];
   hin.close();
   std::cout << "Lattice parameters in Bohr:" << std::endl;
   std::cout << X[0] << "  " << X[1] << "  " << X[2] << std::endl;
   std::cout << Y[0] << "  " << Y[1] << "  " << Y[2] << std::endl;
   std::cout << Z[0] << "  " << Z[1] << "  " << Z[2] << std::endl;
 }

◆ getGaussianCenters()

void getGaussianCenters ( const std::string fname )

Definition at line 358 of file LCAOHDFParser.cpp.

Referenced by parse().

358 {}

◆ getGeometry()

void getGeometry ( const std::string & fname )

Definition at line 218 of file LCAOHDFParser.cpp.

References QMCGaussianParserBase::AtomicNumberIndex, hdf_archive::close(), ParticleSet::getSpeciesSet(), ParticleSet::GroupID, QMCGaussianParserBase::GroupName, QMCGaussianParserBase::IonChargeIndex, QMCGaussianParserBase::IonName, QMCGaussianParserBase::IonSystem, QMCGaussianParserBase::NumberOfAtoms, hdf_archive::open(), hdf_archive::pop(), hdf_archive::push(), ParticleSet::R, hdf_archive::read(), and tags.

Referenced by parse().

 {
   hdf_archive hin;
 
   if (!hin.open(fname.c_str(), H5F_ACC_RDONLY))
   {
     std::cerr << "Could not open H5 file" << std::endl;
     abort();
   }
   hin.push("atoms");
 
   //atomic numbers
   std::vector<int> atomic_number;
   std::vector<double> q, pos;
   tags.clear();
   //read atomic info
   //MAP: (Atom Number, Species Index)
   std::vector<int> idx(NumberOfAtoms);
   std::map<int, int> AtomIndexmap;
   hin.read(idx, "species_ids");
   for (int i = 0; i < NumberOfAtoms; i++)
   {
     AtomIndexmap.insert(std::pair<int, int>(i, idx[i]));
   }
   for (int i = 0; i < NumberOfAtoms; i++)
   {
     std::string speciesName("species_");
     speciesName = speciesName + std::to_string(AtomIndexmap[i]);
     hin.push(speciesName);
     int zint;
     double z;
     std::string Name;
     hin.read(zint, "atomic_number");
     atomic_number.push_back(zint);
     hin.read(z, "charge");
     q.push_back(z);
     hin.read(Name, "name");
     tags.push_back(Name);
     hin.pop();
   }
 
   Matrix<double> IonPos(NumberOfAtoms, 3);
   hin.read(IonPos, "positions");
 
   SpeciesSet& species(IonSystem.getSpeciesSet());
   for (int i = 0; i < NumberOfAtoms; i++)
   {
     IonSystem.R[i][0]                     = IonPos[i][0];
     IonSystem.R[i][1]                     = IonPos[i][1];
     IonSystem.R[i][2]                     = IonPos[i][2];
     GroupName[i]                          = IonName[atomic_number[i]];
     int speciesID                         = species.addSpecies(GroupName[i]);
     IonSystem.GroupID[i]                  = speciesID;
     species(AtomicNumberIndex, speciesID) = atomic_number[i];
     species(IonChargeIndex, speciesID)    = q[i];
   }
   hin.close();
 }

◆ getMO()

void getMO ( const std::string & fname )

Definition at line 302 of file LCAOHDFParser.cpp.

References Matrix< T, Alloc >::begin(), hdf_archive::close(), copy(), QMCGaussianParserBase::EigVal_alpha, QMCGaussianParserBase::EigVal_beta, QMCGaussianParserBase::EigVec, Matrix< T, Alloc >::end(), qmcplusplus::n, QMCGaussianParserBase::numMO, hdf_archive::open(), hdf_archive::read(), QMCGaussianParserBase::SizeOfBasisSet, and QMCGaussianParserBase::SpinRestricted.

Referenced by parse().

 {
   EigVal_alpha.resize(numMO);
   EigVal_beta.resize(numMO);
   EigVec.resize(2 * SizeOfBasisSet * numMO);
 
   Matrix<double> CartMat(numMO, SizeOfBasisSet);
 
   hdf_archive hin;
 
   if (!hin.open(fname.c_str(), H5F_ACC_RDONLY))
   {
     std::cerr << "Could not open H5 file" << std::endl;
     abort();
   }
 
   std::string setname = "/Super_Twist/eigenset_0";
   hin.read(CartMat, setname);
   setname = "/Super_Twist/eigenval_0";
   hin.read(EigVal_alpha, setname);
   std::copy(CartMat.begin(), CartMat.end(), EigVec.begin());
 
   if (!SpinRestricted)
   {
     setname = "/Super_Twist/eigenset_1";
     hin.read(CartMat, setname);
     setname = "/Super_Twist/eigenval_1";
     hin.read(EigVal_beta, setname);
   }
   std::copy(CartMat.begin(), CartMat.end(), EigVec.begin() + SizeOfBasisSet * numMO);
 
   hin.close();
   int btot = numMO * SizeOfBasisSet;
   int n = btot / 4, b = 0;
   int dn = btot - n * 4;
   std::ostringstream eig;
 
   eig.setf(std::ios::scientific, std::ios::floatfield);
   eig.setf(std::ios::right, std::ios::adjustfield);
   eig.precision(14);
   eig << "\n";
   for (int k = 0; k < n; k++)
   {
     eig << std::setw(22) << EigVec[b] << std::setw(22) << EigVec[b + 1] << std::setw(22) << EigVec[b + 2]
         << std::setw(22) << EigVec[b + 3] << "\n";
     b += 4;
   }
   for (int k = 0; k < dn; k++)
   {
     eig << std::setw(22) << EigVec[b++];
   }
   std::cout << eig.str() << std::endl;
   std::cout << "Finished reading MO." << std::endl;
   hin.close();
 }

◆ getSuperTwist()

void getSuperTwist ( const std::string & fname )

Definition at line 277 of file LCAOHDFParser.cpp.

References hdf_archive::close(), hdf_archive::open(), hdf_archive::pop(), hdf_archive::push(), hdf_archive::read(), and QMCGaussianParserBase::STwist_Coord.

Referenced by parse().

 {
   Matrix<double> MyVec(1, 3);
   hdf_archive hin;
 
   if (!hin.open(fname.c_str(), H5F_ACC_RDONLY))
   {
     std::cerr << "Could not open H5 file" << std::endl;
     abort();
   }
 
   hin.push("Super_Twist");
 
   STwist_Coord.resize(3);
 
   hin.read(MyVec, "Coord");
 
   hin.pop();
   STwist_Coord[0] = MyVec[0][0];
   STwist_Coord[1] = MyVec[0][1];
   STwist_Coord[2] = MyVec[0][2];
 
   hin.close();
 }

◆ parse()

void parse ( const std::string & fname )

overridevirtual

Implements QMCGaussianParserBase.

Definition at line 46 of file LCAOHDFParser.cpp.

 {
   hdf_archive hin;
 
   if (!hin.open(fname.c_str(), H5F_ACC_RDONLY))
   {
     std::cerr << "Could not open H5 file" << std::endl;
     abort();
   }
 
   hin.push("application");
   hin.read(CodeName, "code");
   hin.pop();
   std::cout << "Converting Wavefunction from the " << CodeName << " Code" << std::endl;
 
   hin.push("PBC");
   hin.read(PBC, "PBC");
   hin.pop();
 
   std::cout << "Periodic Boundary Conditions: " << (PBC ? ("yes") : ("no")) << std::endl;
   std::cout.flush();
 
 
   hin.push("parameters");
   hin.read(ECP, "ECP");
   std::cout << "usingECP: " << (ECP ? ("yes") : ("no")) << std::endl;
   std::cout.flush();
 
   std::cout << "Multideterminants: " << (multideterminant ? ("yes") : ("no")) << std::endl;
   std::cout.flush();
 
   hin.read(SpinRestricted, "SpinRestricted");
   hin.read(numAO, "numAO");
   hin.read(numMO, "numMO");
 
 
   std::cout << "NUMBER OF AOs: " << numAO << std::endl;
   SizeOfBasisSet = numAO;
   std::cout << "Size of Basis Set: " << SizeOfBasisSet << std::endl;
   std::cout << "NUMBER OF MOs: " << numMO << std::endl;
 
   bool bohr = true;
   hin.read(bohr, "Unit");
   std::cout << "Unit in Bohr=" << bohr << std::endl;
   BohrUnit = bohr;
 
   hin.read(NumberOfAlpha, "NbAlpha");
   hin.read(NumberOfBeta, "NbBeta");
   hin.read(NumberOfEls, "NbTotElec");
   int ds;
   hin.read(ds, "spin");
   if (CodeName == "PySCF")
     SpinMultiplicity = ds + 1;
   else
     SpinMultiplicity = ds;
 
   std::cout << "Number of alpha electrons: " << NumberOfAlpha << std::endl;
   std::cout << "Number of beta electrons: " << NumberOfBeta << std::endl;
   std::cout << "Number of electrons: " << NumberOfEls << std::endl;
   std::cout << "SPIN MULTIPLICITY: " << SpinMultiplicity << std::endl;
 
   hin.pop();
   hin.push("atoms");
   hin.read(NumberOfAtoms, "number_of_atoms");
   std::cout << "NUMBER OF ATOMS: " << NumberOfAtoms << std::endl;
   hin.pop();
 
   EigVal_alpha.resize(numMO);
   EigVal_beta.resize(numMO);
   Matrix<double> myvec(1, numMO);
 
   hin.push("Super_Twist");
   if (hin.readEntry(myvec, "eigenval_0"))
   {
     // eigenval_0 exists on file
     for (int i = 0; i < numMO; i++)
       EigVal_alpha[i] = myvec[0][i];
 
     //Reading Eigenvals for Spin unRestricted calculation. This section is needed to set the occupation numbers
     if (!SpinRestricted)
     {
       hin.read(myvec, "eigenval_1");
       for (int i = 0; i < numMO; i++)
         EigVal_beta[i] = myvec[0][i];
     }
   }
   else
   {
     app_warning() << "eigenval_0 doesn't exist in h5 file. Treat all values zero." << std::endl;
   }
   hin.close();
 
 
   IonSystem.create({NumberOfAtoms});
   GroupName.resize(NumberOfAtoms);
   if (PBC)
   {
     getCell(fname);
     getSuperTwist(fname);
     if (debug)
     {
       getGaussianCenters(fname);
       getMO(fname);
     }
   }
   getGeometry(fname);
 
   if (multideterminant)
   {
     hdf_archive hin;
 
     if (!hin.open(outputFile.c_str(), H5F_ACC_RDONLY))
     {
       std::cerr << "Could not open H5 file" << std::endl;
       abort();
     }
 
     hin.push("MultiDet");
 
     hin.read(ci_size, "NbDet");
     hin.read(ci_nstates, "nstate");
     hin.read(nbexcitedstates, "nexcitedstate");
     CIcoeff.clear();
     CIalpha.clear();
     CIbeta.clear();
     CIcoeff.resize(ci_size);
     CIalpha.resize(ci_size);
     CIbeta.resize(ci_size);
 
     int ds  = SpinMultiplicity - 1;
     int neb = (NumberOfEls - ds) / 2;
     int nea = NumberOfEls - NumberOfBeta;
     ci_nea  = NumberOfAlpha;
     ci_neb  = NumberOfBeta;
     ci_nca  = nea - ci_nea;
     ci_ncb  = neb - ci_neb;
     std::cout << " Done reading CIs!!" << std::endl;
     hin.close();
   }
 }

Member Data Documentation

◆ MOtype

std::string MOtype

Definition at line 33 of file LCAOHDFParser.h.

Referenced by LCAOHDFParser().

◆ NAC

int NAC

Definition at line 35 of file LCAOHDFParser.h.

◆ NEXT

int NEXT

Definition at line 35 of file LCAOHDFParser.h.

◆ NFZC

int NFZC

Definition at line 35 of file LCAOHDFParser.h.

Referenced by LCAOHDFParser().

◆ NTOT

int NTOT

Definition at line 35 of file LCAOHDFParser.h.

◆ numAO

int numAO

Definition at line 34 of file LCAOHDFParser.h.

Referenced by parse().

◆ pivot_begin

std::streampos pivot_begin

Definition at line 31 of file LCAOHDFParser.h.

◆ readtype

int readtype

Definition at line 34 of file LCAOHDFParser.h.

Referenced by LCAOHDFParser().

◆ tags

std::vector<std::string> tags

Definition at line 32 of file LCAOHDFParser.h.

Referenced by getGeometry().

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

/home/pk7/projects/qmc/for_cron_doxygen/qmcpack/src/QMCTools/LCAOHDFParser.h
/home/pk7/projects/qmc/for_cron_doxygen/qmcpack/src/QMCTools/LCAOHDFParser.cpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ LCAOHDFParser() [1/2]

◆ LCAOHDFParser() [2/2]

Member Function Documentation

◆ getCell()

◆ getGaussianCenters()

◆ getGeometry()

◆ getMO()

◆ getSuperTwist()

◆ parse()

Member Data Documentation

◆ MOtype

◆ NAC

◆ NEXT

◆ NFZC

◆ NTOT

◆ numAO

◆ pivot_begin

◆ readtype

◆ tags