scf_utils.cc File Reference

Various utilities used by SCF code. More...

#include <pthread.h>
#include <sstream>
#include "scf_utils.h"
#include "output.h"
#include "integrals_1el.h"
#include "memorymanag.h"
#include "operator_matrix.h"
#include "integrals_1el_kinetic.h"
#include "integrals_1el_potential.h"
#include "utilities.h"
#include "integrals_2el_explicit.h"
#include "basis_func_pair_list.h"
#include "integrals_2el_boxed.h"
#include "integrals_2el_layer.h"
#include "density_description_file.h"
#include "mat_acc_extrapolate.h"
#include "basis_func_pair_list_1el.h"
#include "integral_matrix_wrappers.h"
#include "units.h"
#include "densitymanager.h"
#include "dft_common.h"
#include "xc_matrix.h"
#include "xc_matrix_sparse.h"

Classes
class	Jworker
class	Kworker
class	Vxc_worker

Functions
template<class Tinvestigator , class Tworker >
static void	do_scan_and_report (Tinvestigator investigator, Tworker worker, const char *scanName, int nSteps, ergo_real startThresh, ergo_real stepFactor)
void	do_acc_scan_J (const symmMatrix &D, const IntegralInfo &integralInfo, const BasisInfoStruct &basisInfo, triangMatrix &invCholFactor, bool doInvCholFactorTransformation, const JK::Params &J_K_params, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, int nSteps, ergo_real startThresh, ergo_real stepFactor)
void	do_acc_scan_K (symmMatrix &D, const IntegralInfo &integralInfo, const BasisInfoStruct &basisInfo, triangMatrix &invCholFactor, bool doInvCholFactorTransformation, const JK::ExchWeights &CAM_params, const JK::Params &J_K_params, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, std::vector< int > const &inversePermutationHML, int nSteps, ergo_real startThresh, ergo_real stepFactor)
void	do_acc_scan_Vxc (symmMatrix &D, const IntegralInfo &integralInfo, const BasisInfoStruct &basisInfo, const Molecule &molecule, const Dft::GridParams &gridParams, int noOfElectrons, triangMatrix &invCholFactor, bool doInvCholFactorTransformation, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, std::vector< int > const &inversePermutationHML, int nSteps, ergo_real startThresh, ergo_real stepFactor)
template<typename Tmatrix >
void	output_sparsity_template (int n, const Tmatrix &M, const char *matrixName, const char *matrixTypeName)
void	output_sparsity (int n, const normalMatrix &M, const char *matrixName)
void	output_sparsity_symm (int n, const symmMatrix &M, const char *matrixName)
void	output_sparsity_triang (int n, const triangMatrix &M, const char *matrixName)
static ergo_real	get_trace (int n, const ergo_real *P, const ergo_real *H_core)
static int	add_square_matrices (int n, const ergo_real *A, const ergo_real *B, ergo_real *C)
int	compute_h_core_matrix_simple_dense (const IntegralInfo &integralInfo, const Molecule &molecule, const BasisInfoStruct &basisInfo, symmMatrix &H_core_Matrix_sparse, ergo_real threshold_integrals_1el, int noOfThreadsForV, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML)
int	compute_h_core_matrix_sparse (const IntegralInfo &integralInfo, const Molecule &molecule, const Molecule &extraCharges, ergo_real electric_field_x, ergo_real electric_field_y, ergo_real electric_field_z, const BasisInfoStruct &basisInfo, symmMatrix &H_core_Matrix_sparse, ergo_real threshold_integrals_1el, int noOfThreadsForV, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, int const create_dipole_mtx, std::vector< int > const *const inversePermutationHML, std::string const *const calculation_identifier, std::string const *const method_and_basis_set)
int	get_gradient_for_given_mol_and_dens (const IntegralInfo &integralInfo, const Molecule &molecule, const BasisInfoStruct &basisInfo, const symmMatrix &D, ergo_real threshold_integrals_1el, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, ergo_real *result_gradient_list)
int	save_symmetric_matrix (symmMatrix &A, const BasisInfoStruct &basisInfo, const char *fileName, std::vector< int > const &inversePermutationHML)
	Saves specified symmetic matrix to a file of specified name. More...
int	add_disturbance_to_matrix (int n, symmMatrix &A, ergo_real disturbance, int specificElementCount, const int *elementIndexVector, std::vector< int > const &permutationHML)
int	get_simple_starting_guess_sparse (int n, int noOfElectrons, symmMatrix &densityMatrix)
int	get_diag_matrix_from_file (int n, symmMatrix &M, const char *fileName, std::vector< int > const &permutationHML)
int	write_diag_elements_to_file (int n, const symmMatrix &M, const char *fileName, std::vector< int > const &permutationHML)
int	write_full_matrix (int n, const symmMatrix &M, const char *fileName, std::vector< int > const &inversePermutationHML)
int	write_basis_func_coord_file (const BasisInfoStruct &basisInfo)
int	write_2el_integral_m_file (const BasisInfoStruct &basisInfo, const IntegralInfo &integralInfo)
static int	get_2e_matrix_and_energy_simple_HF_sparse (const BasisInfoStruct &basisInfo, const Molecule &molecule, const IntegralInfo &integralInfo, const JK::ExchWeights &CAM_params, symmMatrix &twoelMatrix_sparse, symmMatrix &densityMatrix_sparse, const JK::Params &J_K_params, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, std::vector< int > const &inversePermutationHML, ergo_real *energy_2el, int get_J_K_matrices, symmMatrix &J_matrix, symmMatrix &K_matrix)
static int	get_2e_matrices_and_energy_simple_HF_sparse_unrestricted (const BasisInfoStruct &basisInfo, const Molecule &molecule, const IntegralInfo &integralInfo, symmMatrix &twoelMatrix_sparse_alpha, symmMatrix &twoelMatrix_sparse_beta, symmMatrix &densityMatrix_sparse_alpha, symmMatrix &densityMatrix_sparse_beta, const JK::Params &J_K_params, const JK::ExchWeights &CAM_params, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, std::vector< int > const &inversePermutationHML, ergo_real *energy_2el)
static int	get_2e_matrix_and_energy_simple_sparse (const BasisInfoStruct &basisInfo, const Molecule &molecule, const IntegralInfo &integralInfo, symmMatrix &twoelMatrix_sparse, symmMatrix &densityMatrix_sparse, const JK::Params &J_K_params, const JK::ExchWeights &CAM_params, const Dft::GridParams &gridParams, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, std::vector< int > const &inversePermutationHML, ergo_real *energy_2el, int do_xc, int noOfElectrons, int get_J_K_Fxc_matrices, symmMatrix &J_matrix, symmMatrix &K_matrix, symmMatrix &Fxc_matrix, SCF_statistics &stats)
	Routine for computing the two-electron part of the Fock/KS matrix, in sparse form. More...
static int	get_2e_matrices_and_energy_simple_sparse_unrestricted (const BasisInfoStruct &basisInfo, const Molecule &molecule, const IntegralInfo &integralInfo, const JK::ExchWeights &CAM_params, symmMatrix &twoelMatrix_sparse_alpha, symmMatrix &twoelMatrix_sparse_beta, symmMatrix &densityMatrix_sparse_alpha, symmMatrix &densityMatrix_sparse_beta, const JK::Params &J_K_params, const Dft::GridParams &gridParams, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, std::vector< int > const &inversePermutationHML, ergo_real *energy_2el, int do_xc, int noOfElectrons)
int	get_2e_matrix_and_energy_sparse (const BasisInfoStruct &basisInfo, const BasisInfoStruct &basisInfoDensFit, const Molecule &molecule, const IntegralInfo &integralInfo, symmMatrix &twoelMatrix_sparse, symmMatrix &densityMatrix_sparse, const JK::Params &J_K_params, const JK::ExchWeights &CAM_params, const Dft::GridParams &gridParams, int do_xc, ergo_real *energy_2el, int noOfElectrons, DensfitData *df_data, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, std::vector< int > const &inversePermutationHML, int get_J_K_Fxc_matrices, symmMatrix &J_matrix, symmMatrix &K_matrix, symmMatrix &Fxc_matrix, SCF_statistics &stats)
	General routine for computing the two-electron part of the Fock/KS matrix. More...
int	get_2e_matrices_and_energy_sparse_unrestricted (const BasisInfoStruct &basisInfo, const BasisInfoStruct &basisInfoDensFit, const Molecule &molecule, const IntegralInfo &integralInfo, const JK::ExchWeights &CAM_params, symmMatrix &twoelMatrix_sparse_alpha, symmMatrix &twoelMatrix_sparse_beta, symmMatrix &densityMatrix_sparse_alpha, symmMatrix &densityMatrix_sparse_beta, const JK::Params &J_K_params, const Dft::GridParams &gridParams, int do_xc, ergo_real *energy_2el, int noOfElectrons, DensfitData *df_data, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, std::vector< int > const &inversePermutationHML)
int	get_2e_matrices_and_energy_restricted_open (const BasisInfoStruct &basisInfo, const BasisInfoStruct &basisInfoDensFit, const Molecule &molecule, const IntegralInfo &integralInfo, const JK::ExchWeights &CAM_params, symmMatrix &twoelMatrix_Fc, symmMatrix &twoelMatrix_Fo, symmMatrix &densityMatrix_sparse_alpha, symmMatrix &densityMatrix_sparse_beta, const JK::Params &J_K_params, const Dft::GridParams &gridParams, int do_xc, ergo_real *energy_2el, int noOfElectrons, DensfitData *df_data, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, std::vector< int > const &inversePermutationHML)
	Computes G_c and G_o. More...
int	compute_FDSminusSDF_sparse (int n, symmMatrix &F_symm, symmMatrix &D_symm, symmMatrix &S_symm, normalMatrix &result, ergo_real sparse_threshold)
int	determine_number_of_electrons_unrestricted (int noOfElectrons, int alpha_beta_diff, int *noOfElectrons_alpha, int *noOfElectrons_beta)
static ergo_real	compute_dipole_moment_onecoord (const symmMatrix &densityMatrix, const BasisInfoStruct &basisInfo, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, const Molecule &molecule, int coordIdx)
void	get_dipole_moment (const symmMatrix &densityMatrix, const BasisInfoStruct &basisInfo, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, const Molecule &molecule)
static void	get_mulliken_charges (const symmMatrix &densityMatrix, const symmMatrix &S_symm, const BasisInfoStruct &basisInfo, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, std::vector< int > const &inversePermutationHML, const Molecule &molecule, std::vector< ergo_real > &resultVector)
void	do_mulliken_atomic_charges (const symmMatrix &densityMatrix, const symmMatrix &S_symm, const BasisInfoStruct &basisInfo, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, std::vector< int > const &inversePermutationHML, const Molecule &molecule)
void	do_mulliken_spin_densities (const symmMatrix &spinDensityMatrix, const symmMatrix &S_symm, const BasisInfoStruct &basisInfo, mat::SizesAndBlocks const &matrix_size_block_info, std::vector< int > const &permutationHML, std::vector< int > const &inversePermutationHML, const Molecule &molecule)
static int	write_gcube_file_header (FILE *f, const char *firstLine, const Molecule &m, double originX, double originY, double originZ, int NX, double incrX, int NY, double incrY, int NZ, double incrZ)
void	do_density_images (const BasisInfoStruct &basisInfo, const Molecule &molecule, const ergo_real *densityMatrixFull_tot, const ergo_real *densityMatrixFull_spin, double output_density_images_boxwidth)
void	get_hf_weight_and_cam_params (int use_dft, ergo_real *exch_param_alpha, ergo_real *exch_param_beta, ergo_real *exch_param_mu)

Detailed Description

Various utilities used by SCF code.

For example, interface routines converting between HML matrix format used in main SCF code and elementwise format used by integral code.

Author

: Elias Rudberg responsible.

Function Documentation

int add_disturbance_to_matrix	(	int	n,
		symmMatrix &	A,
		ergo_real	disturbance,
		int	specificElementCount,
		const int *	elementIndexVector,
		std::vector< int > const &	permutationHML
	)

References mat::MatrixSymmetric< Treal, Tmatrix >::assign_from_sparse(), B, and mat::MatrixBase< Treal, Tmatrix >::clear().

Referenced by SCF_restricted::add_random_disturbance_to_starting_guess(), and SCF_unrestricted::add_random_disturbance_to_starting_guess().

static int add_square_matrices ( int  n, const ergo_real *  A, const ergo_real *  B, ergo_real *  C  )

static

References mat::MatrixSymmetric< Treal, Tmatrix >::assign_from_sparse(), and Jworker::permutationHML.

Referenced by get_2e_matrix_and_energy_sparse().

static ergo_real compute_dipole_moment_onecoord ( const symmMatrix &  densityMatrix, const BasisInfoStruct &  basisInfo, mat::SizesAndBlocks const &  matrix_size_block_info, std::vector< int > const &  permutationHML, const Molecule &  molecule, int  coordIdx  )

static

References Atom::charge, compute_operator_matrix_sparse_symm(), Atom::coords, Molecule::getAtom(), Molecule::getNoOfAtoms(), mat::MatrixBase< Treal, Tmatrix >::resetSizesAndBlocks(), and mat::MatrixSymmetric< Treal, Tmatrix >::trace_ab().

Referenced by get_dipole_moment().

int compute_FDSminusSDF_sparse	(	int	n,
		symmMatrix &	F_symm,
		symmMatrix &	D_symm,
		symmMatrix &	S_symm,
		normalMatrix &	result,
		ergo_real	sparse_threshold
	)

References mat::MatrixBase< Treal, Tmatrix >::clear(), do_output(), mat::MatrixGeneral< Treal, Tmatrix >::eucl_thresh(), mat::SingletonForTimings::instance(), LOG_AREA_DENSFROMF, LOG_AREA_SCF, LOG_CAT_INFO, output_current_memory_usage(), output_sparsity(), Util::TimeMeter::print(), mat::FileWritable::readFromFile(), mat::SingletonForTimings::reset(), mat::FileWritable::writeAndReadAll(), and mat::FileWritable::writeToFile().

Referenced by SCF_restricted::get_FDSminusSDF(), and SCF_unrestricted::get_FDSminusSDF().

int compute_h_core_matrix_simple_dense	(	const IntegralInfo &	integralInfo,
		const Molecule &	molecule,
		const BasisInfoStruct &	basisInfo,
		symmMatrix &	H_core_Matrix_sparse,
		ergo_real	threshold_integrals_1el,
		int	noOfThreadsForV,
		mat::SizesAndBlocks const &	matrix_size_block_info,
		std::vector< int > const &	permutationHML
	)

References A, mat::MatrixSymmetric< Treal, Tmatrix >::assign_from_sparse(), compute_h_core_matrix_full(), do_output(), Molecule::getAtomListPtr(), Molecule::getNoOfAtoms(), LOG_AREA_SCF, LOG_CAT_ERROR, and BasisInfoStruct::noOfBasisFuncs.

Referenced by SCF_general::SCF_general().

int compute_h_core_matrix_sparse	(	const IntegralInfo &	integralInfo,
		const Molecule &	molecule,
		const Molecule &	extraCharges,
		ergo_real	electric_field_x,
		ergo_real	electric_field_y,
		ergo_real	electric_field_z,
		const BasisInfoStruct &	basisInfo,
		symmMatrix &	H_core_Matrix_sparse,
		ergo_real	threshold_integrals_1el,
		int	noOfThreadsForV,
		mat::SizesAndBlocks const &	matrix_size_block_info,
		std::vector< int > const &	permutationHML,
		int const	create_dipole_mtx,
		std::vector< int > const *const	inversePermutationHML,
		std::string const *const	calculation_identifier,
		std::string const *const	method_and_basis_set
	)

References Atom::charge, mat::MatrixBase< Treal, Tmatrix >::clear(), compute_operator_matrix_sparse_symm(), compute_T_sparse(), compute_V_sparse(), Atom::coords, do_output(), Molecule::getAtom(), Molecule::getNoOfAtoms(), LOG_AREA_SCF, LOG_CAT_ERROR, LOG_CAT_INFO, max, BasisInfoStruct::noOfBasisFuncs, Util::TimeMeter::print(), mat::FileWritable::readFromFile(), mat::MatrixBase< Treal, Tmatrix >::resetSizesAndBlocks(), UNIT_one_Angstrom, write_matrix_in_matrix_market_format(), and mat::FileWritable::writeToFile().

Referenced by do_tdhf_dynamics(), and SCF_general::SCF_general().

int determine_number_of_electrons_unrestricted	(	int	noOfElectrons,
		int	alpha_beta_diff,
		int *	noOfElectrons_alpha,
		int *	noOfElectrons_beta
	)

References do_output(), LOG_AREA_SCF, LOG_CAT_ERROR, and LOG_CAT_INFO.

Referenced by SCF_unrestricted::SCF_unrestricted().

void do_acc_scan_J	(	const symmMatrix &	D,
		const IntegralInfo &	integralInfo,
		const BasisInfoStruct &	basisInfo,
		triangMatrix &	invCholFactor,
		bool	doInvCholFactorTransformation,
		const JK::Params &	J_K_params,
		mat::SizesAndBlocks const &	matrix_size_block_info,
		std::vector< int > const &	permutationHML,
		int	nSteps,
		ergo_real	startThresh,
		ergo_real	stepFactor
	)

References do_scan_and_report(), mat::FileWritable::readFromFile(), and mat::FileWritable::writeToFile().

Referenced by SCF_restricted::get_2e_part_and_energy(), and Ergo::registerInputVariables().

void do_acc_scan_K	(	symmMatrix &	D,
		const IntegralInfo &	integralInfo,
		const BasisInfoStruct &	basisInfo,
		triangMatrix &	invCholFactor,
		bool	doInvCholFactorTransformation,
		const JK::ExchWeights &	CAM_params,
		const JK::Params &	J_K_params,
		mat::SizesAndBlocks const &	matrix_size_block_info,
		std::vector< int > const &	permutationHML,
		std::vector< int > const &	inversePermutationHML,
		int	nSteps,
		ergo_real	startThresh,
		ergo_real	stepFactor
	)

References do_scan_and_report(), mat::FileWritable::readFromFile(), and mat::FileWritable::writeToFile().

Referenced by SCF_restricted::get_2e_part_and_energy(), and Ergo::registerInputVariables().

void do_acc_scan_Vxc	(	symmMatrix &	D,
		const IntegralInfo &	integralInfo,
		const BasisInfoStruct &	basisInfo,
		const Molecule &	molecule,
		const Dft::GridParams &	gridParams,
		int	noOfElectrons,
		triangMatrix &	invCholFactor,
		bool	doInvCholFactorTransformation,
		mat::SizesAndBlocks const &	matrix_size_block_info,
		std::vector< int > const &	permutationHML,
		std::vector< int > const &	inversePermutationHML,
		int	nSteps,
		ergo_real	startThresh,
		ergo_real	stepFactor
	)

References do_scan_and_report(), mat::FileWritable::readFromFile(), and mat::FileWritable::writeToFile().

Referenced by SCF_restricted::get_2e_part_and_energy(), and Ergo::registerInputVariables().

void do_density_images	(	const BasisInfoStruct &	basisInfo,
		const Molecule &	molecule,
		const ergo_real *	densityMatrixFull_tot,
		const ergo_real *	densityMatrixFull_spin,
		double	output_density_images_boxwidth
	)

References Atom::coords, do_output(), get_density(), get_no_of_primitives_for_density(), Molecule::getAtom(), Molecule::getNoOfAtoms(), integrate_density_in_box_2(), LOG_AREA_SCF, LOG_CAT_ERROR, LOG_CAT_INFO, Util::TimeMeter::print(), and write_gcube_file_header().

Referenced by SCF_restricted::output_density_images(), and SCF_unrestricted::output_density_images().

void do_mulliken_atomic_charges	(	const symmMatrix &	densityMatrix,
		const symmMatrix &	S_symm,
		const BasisInfoStruct &	basisInfo,
		mat::SizesAndBlocks const &	matrix_size_block_info,
		std::vector< int > const &	permutationHML,
		std::vector< int > const &	inversePermutationHML,
		const Molecule &	molecule
	)

References Atom::charge, do_output(), get_mulliken_charges(), Molecule::getAtom(), Molecule::getNoOfAtoms(), LOG_AREA_SCF, and LOG_CAT_INFO.

Referenced by SCF_restricted::do_mulliken_pop_stuff(), and SCF_unrestricted::do_mulliken_pop_stuff().

void do_mulliken_spin_densities	(	const symmMatrix &	spinDensityMatrix,
		const symmMatrix &	S_symm,
		const BasisInfoStruct &	basisInfo,
		mat::SizesAndBlocks const &	matrix_size_block_info,
		std::vector< int > const &	permutationHML,
		std::vector< int > const &	inversePermutationHML,
		const Molecule &	molecule
	)

References do_output(), get_mulliken_charges(), Molecule::getNoOfAtoms(), LOG_AREA_SCF, and LOG_CAT_INFO.

Referenced by SCF_unrestricted::do_mulliken_pop_stuff().

template<class Tinvestigator , class Tworker >

static void do_scan_and_report ( Tinvestigator  investigator, Tworker  worker, const char *  scanName, int  nSteps, ergo_real  startThresh, ergo_real  stepFactor  )

static

References do_output(), LOG_AREA_SCF, and LOG_CAT_INFO.

Referenced by do_acc_scan_J(), do_acc_scan_K(), and do_acc_scan_Vxc().

int get_2e_matrices_and_energy_restricted_open	(	const BasisInfoStruct &	basisInfo,
		const BasisInfoStruct &	basisInfoDensFit,
		const Molecule &	molecule,
		const IntegralInfo &	integralInfo,
		const JK::ExchWeights &	CAM_params,
		symmMatrix &	twoelMatrix_Fc,
		symmMatrix &	twoelMatrix_Fo,
		symmMatrix &	densityMatrix_sparse_alpha,
		symmMatrix &	densityMatrix_sparse_beta,
		const JK::Params &	J_K_params,
		const Dft::GridParams &	gridParams,
		int	do_xc,
		ergo_real *	energy_2el,
		int	noOfElectrons,
		DensfitData *	df_data,
		mat::SizesAndBlocks const &	matrix_size_block_info,
		std::vector< int > const &	permutationHML,
		std::vector< int > const &	inversePermutationHML
	)

Computes G_c and G_o.

G_c is defined as J_a + J_b + K_a + K_b. G_o is defined as J_a + J_b + K_a.

References JK::ExchWeights::alpha, mat::MatrixSymmetric< Treal, Tmatrix >::assignFromFull(), mat::MatrixBase< Treal, Tmatrix >::clear(), compute_J_by_boxes_sparse(), compute_K_by_boxes_sparse(), JK::ExchWeights::computeRangeSeparatedExchange, dft_get_uxc_mt(), do_output(), mat::MatrixSymmetric< Treal, Tmatrix >::fullMatrix(), LOG_AREA_SCF, LOG_CAT_ERROR, LOG_CAT_INFO, BasisInfoStruct::noOfBasisFuncs, output_current_memory_usage(), mat::MatrixBase< Treal, Tmatrix >::resetSizesAndBlocks(), mat::MatrixSymmetric< Treal, Tmatrix >::trace_ab(), JK::Params::use_densfit_for_J, and JK::Params::use_naive_fockmatrix_construction.

Referenced by SCF_unrestricted::get_2e_part_and_energy().

static int get_2e_matrices_and_energy_simple_HF_sparse_unrestricted ( const BasisInfoStruct &  basisInfo, const Molecule &  molecule, const IntegralInfo &  integralInfo, symmMatrix &  twoelMatrix_sparse_alpha, symmMatrix &  twoelMatrix_sparse_beta, symmMatrix &  densityMatrix_sparse_alpha, symmMatrix &  densityMatrix_sparse_beta, const JK::Params &  J_K_params, const JK::ExchWeights &  CAM_params, mat::SizesAndBlocks const &  matrix_size_block_info, std::vector< int > const &  permutationHML, std::vector< int > const &  inversePermutationHML, ergo_real *  energy_2el  )

static

References mat::MatrixBase< Treal, Tmatrix >::clear(), compute_J_by_boxes_sparse(), compute_K_by_boxes_sparse(), do_output(), LOG_AREA_SCF, LOG_CAT_ERROR, mat::MatrixBase< Treal, Tmatrix >::resetSizesAndBlocks(), and mat::MatrixSymmetric< Treal, Tmatrix >::trace_ab().

Referenced by get_2e_matrices_and_energy_sparse_unrestricted().

static int get_2e_matrices_and_energy_simple_sparse_unrestricted ( const BasisInfoStruct &  basisInfo, const Molecule &  molecule, const IntegralInfo &  integralInfo, const JK::ExchWeights &  CAM_params, symmMatrix &  twoelMatrix_sparse_alpha, symmMatrix &  twoelMatrix_sparse_beta, symmMatrix &  densityMatrix_sparse_alpha, symmMatrix &  densityMatrix_sparse_beta, const JK::Params &  J_K_params, const Dft::GridParams &  gridParams, mat::SizesAndBlocks const &  matrix_size_block_info, std::vector< int > const &  permutationHML, std::vector< int > const &  inversePermutationHML, ergo_real *  energy_2el, int  do_xc, int  noOfElectrons  )

static

References JK::ExchWeights::alpha, mat::MatrixSymmetric< Treal, Tmatrix >::assignFromFull(), mat::MatrixBase< Treal, Tmatrix >::clear(), compute_J_by_boxes_sparse(), compute_K_by_boxes_sparse(), JK::ExchWeights::computeRangeSeparatedExchange, dft_get_uxc_mt(), do_output(), mat::MatrixSymmetric< Treal, Tmatrix >::fullMatrix(), getUXC_seq(), LOG_AREA_SCF, LOG_CAT_ERROR, LOG_CAT_INFO, BasisInfoStruct::noOfBasisFuncs, output_current_memory_usage(), mat::MatrixBase< Treal, Tmatrix >::resetSizesAndBlocks(), and mat::MatrixSymmetric< Treal, Tmatrix >::trace_ab().

Referenced by get_2e_matrices_and_energy_sparse_unrestricted().

int get_2e_matrices_and_energy_sparse_unrestricted	(	const BasisInfoStruct &	basisInfo,
		const BasisInfoStruct &	basisInfoDensFit,
		const Molecule &	molecule,
		const IntegralInfo &	integralInfo,
		const JK::ExchWeights &	CAM_params,
		symmMatrix &	twoelMatrix_sparse_alpha,
		symmMatrix &	twoelMatrix_sparse_beta,
		symmMatrix &	densityMatrix_sparse_alpha,
		symmMatrix &	densityMatrix_sparse_beta,
		const JK::Params &	J_K_params,
		const Dft::GridParams &	gridParams,
		int	do_xc,
		ergo_real *	energy_2el,
		int	noOfElectrons,
		DensfitData *	df_data,
		mat::SizesAndBlocks const &	matrix_size_block_info,
		std::vector< int > const &	permutationHML,
		std::vector< int > const &	inversePermutationHML
	)

References JK::ExchWeights::alpha, mat::MatrixSymmetric< Treal, Tmatrix >::assignFromFull(), compute_JK_single_box(), JK::ExchWeights::computeRangeSeparatedExchange, dft_get_uxc_mt(), do_output(), mat::MatrixSymmetric< Treal, Tmatrix >::fullMatrix(), get_2e_matrices_and_energy_simple_HF_sparse_unrestricted(), get_2e_matrices_and_energy_simple_sparse_unrestricted(), get_trace(), LOG_AREA_SCF, LOG_CAT_ERROR, LOG_CAT_INFO, BasisInfoStruct::noOfBasisFuncs, output_current_memory_usage(), JK::Params::threshold_J, JK::Params::threshold_K, JK::Params::use_densfit_for_J, JK::Params::use_differential_density, JK::Params::use_fmm, and JK::Params::use_naive_fockmatrix_construction.

Referenced by SCF_unrestricted::get_2e_part_and_energy().

static int get_2e_matrix_and_energy_simple_HF_sparse ( const BasisInfoStruct &  basisInfo, const Molecule &  molecule, const IntegralInfo &  integralInfo, const JK::ExchWeights &  CAM_params, symmMatrix &  twoelMatrix_sparse, symmMatrix &  densityMatrix_sparse, const JK::Params &  J_K_params, mat::SizesAndBlocks const &  matrix_size_block_info, std::vector< int > const &  permutationHML, std::vector< int > const &  inversePermutationHML, ergo_real *  energy_2el, int  get_J_K_matrices, symmMatrix &  J_matrix, symmMatrix &  K_matrix  )

static

References compute_J_by_boxes_sparse(), compute_K_by_boxes_sparse(), do_output(), LOG_AREA_SCF, LOG_CAT_ERROR, LOG_CAT_INFO, mat::MatrixBase< Treal, Tmatrix >::resetSizesAndBlocks(), and mat::MatrixSymmetric< Treal, Tmatrix >::trace_ab().

Referenced by get_2e_matrix_and_energy_sparse().

static int get_2e_matrix_and_energy_simple_sparse ( const BasisInfoStruct &  basisInfo, const Molecule &  molecule, const IntegralInfo &  integralInfo, symmMatrix &  twoelMatrix_sparse, symmMatrix &  densityMatrix_sparse, const JK::Params &  J_K_params, const JK::ExchWeights &  CAM_params, const Dft::GridParams &  gridParams, mat::SizesAndBlocks const &  matrix_size_block_info, std::vector< int > const &  permutationHML, std::vector< int > const &  inversePermutationHML, ergo_real *  energy_2el, int  do_xc, int  noOfElectrons, int  get_J_K_Fxc_matrices, symmMatrix &  J_matrix, symmMatrix &  K_matrix, symmMatrix &  Fxc_matrix, SCF_statistics &  stats  )

static

Routine for computing the two-electron part of the Fock/KS matrix, in sparse form.

This routine is only used when FMM is enabled. This routine does not do density fitting, obviously.

References JK::ExchWeights::alpha, mat::MatrixSymmetric< Treal, Tmatrix >::assignFromFull(), compute_J_by_boxes_sparse(), compute_K_by_boxes_sparse(), JK::ExchWeights::computeRangeSeparatedExchange, dft_get_xc_mt(), do_output(), mat::MatrixSymmetric< Treal, Tmatrix >::fullMatrix(), getXC_mt(), LOG_AREA_SCF, LOG_CAT_ERROR, LOG_CAT_INFO, BasisInfoStruct::noOfBasisFuncs, output_current_memory_usage(), mat::MatrixBase< Treal, Tmatrix >::resetSizesAndBlocks(), SCF_statistics::start_timer(), SCF_statistics::stop_timer(), and mat::MatrixSymmetric< Treal, Tmatrix >::trace_ab().

Referenced by get_2e_matrix_and_energy_sparse().

int get_2e_matrix_and_energy_sparse	(	const BasisInfoStruct &	basisInfo,
		const BasisInfoStruct &	basisInfoDensFit,
		const Molecule &	molecule,
		const IntegralInfo &	integralInfo,
		symmMatrix &	twoelMatrix_sparse,
		symmMatrix &	densityMatrix_sparse,
		const JK::Params &	J_K_params,
		const JK::ExchWeights &	CAM_params,
		const Dft::GridParams &	gridParams,
		int	do_xc,
		ergo_real *	energy_2el,
		int	noOfElectrons,
		DensfitData *	df_data,
		mat::SizesAndBlocks const &	matrix_size_block_info,
		std::vector< int > const &	permutationHML,
		std::vector< int > const &	inversePermutationHML,
		int	get_J_K_Fxc_matrices,
		symmMatrix &	J_matrix,
		symmMatrix &	K_matrix,
		symmMatrix &	Fxc_matrix,
		SCF_statistics &	stats
	)

General routine for computing the two-electron part of the Fock/KS matrix.

Both input and output matrices are in sparse form, but full matrix form may be used in intermediate steps. If FMM is not used, or if CAM is used, or if density fitting is used, full matrix format is applied.

Parameters

basisInfo	the used basis set.
basisInfoDensFit	the auxiliary basis set (may be NULL).
molecule	position of atoms (used for eg. XC grid).
integralInfo	- the integral evaluation object.
twoelMatrix_sparse	- the evaluation result.
densityMatrix_sparse	- the density for which 2e matrix is to be evaluated.
J_K_params	the settings of the integral evaluation.
do_xc	whether xc contribution to 2e matrix and energy are to be added. 1 means that the traditional full matrix code should be called, 2 means that the sparse variant is to be used.
energy_2el	2el energy contribution
noOfElectrons	number of electrons...
CAM_params	a structure containing parameters needed when functionals like CAMB3LYP are used.
gridParams	a structure containing parameters for the grid.
df_data	parameters related to density fitting.
matrix_size_block_info	block sizes etc for hierarchic matrix library.
get_J_K_Fxc_matrices	flag saying if matrices should be saved for statistics/testing purposes. If that feature is active, matrices are saved in parameters
J_matrix
K_matrix
Fxc_matrix	.
stats	a structure holding SCF statistics.
permutationHML	- the permutation of basis functions, needed for transformation between the dense and sparse formats.
inversePermutationHML	- the inverse permutation of basis functions, needed for transformation between the dense and sparse formats.

References add_square_matrices(), JK::ExchWeights::alpha, mat::MatrixSymmetric< Treal, Tmatrix >::assignFromFull(), compute_2e_matrix_coulomb(), compute_2e_matrix_exchange(), compute_2e_matrix_list(), compute_2e_matrix_list_difden(), compute_2e_matrix_list_explicit(), JK::ExchWeights::computeRangeSeparatedExchange, dft_get_xc_mt(), do_output(), mat::MatrixSymmetric< Treal, Tmatrix >::fullMatrix(), get_2e_matrix_and_energy_simple_HF_sparse(), get_2e_matrix_and_energy_simple_sparse(), get_trace(), LOG_AREA_SCF, LOG_CAT_ERROR, LOG_CAT_INFO, BasisInfoStruct::noOfBasisFuncs, output_current_memory_usage(), JK::Params::threshold_J, JK::Params::threshold_K, JK::Params::use_densfit_for_J, JK::Params::use_differential_density, JK::Params::use_fmm, and JK::Params::use_naive_fockmatrix_construction.

Referenced by SCF_restricted::get_2e_part_and_energy().

int get_diag_matrix_from_file	(	int	n,
		symmMatrix &	M,
		const char *	fileName,
		std::vector< int > const &	permutationHML
	)

References mat::MatrixSymmetric< Treal, Tmatrix >::assign_from_sparse(), do_output(), LOG_AREA_MAIN, LOG_AREA_SCF, LOG_CAT_ERROR, and LOG_CAT_INFO.

Referenced by SCF_restricted::get_starting_guess_density(), and SCF_unrestricted::get_starting_guess_density().

void get_dipole_moment	(	const symmMatrix &	densityMatrix,
		const BasisInfoStruct &	basisInfo,
		mat::SizesAndBlocks const &	matrix_size_block_info,
		std::vector< int > const &	permutationHML,
		const Molecule &	molecule
	)

References compute_dipole_moment_onecoord(), do_output(), LOG_AREA_SCF, and LOG_CAT_INFO.

Referenced by SCF_restricted::compute_dipole_moment(), and SCF_unrestricted::compute_dipole_moment().

int get_gradient_for_given_mol_and_dens	(	const IntegralInfo &	integralInfo,
		const Molecule &	molecule,
		const BasisInfoStruct &	basisInfo,
		const symmMatrix &	D,
		ergo_real	threshold_integrals_1el,
		mat::SizesAndBlocks const &	matrix_size_block_info,
		std::vector< int > const &	permutationHML,
		ergo_real *	result_gradient_list
	)

References compute_gradient_of_nucl_and_trDV().

Referenced by SCF_restricted::compute_gradient_fixeddens().

void get_hf_weight_and_cam_params	(	int	use_dft,
		ergo_real *	exch_param_alpha,
		ergo_real *	exch_param_beta,
		ergo_real *	exch_param_mu
	)

References fun_get_cam_param(), and fun_get_hf_weight.

Referenced by es_run(), SCF_general::SCF_general(), and ErgoE2Evaluator::transform().

static void get_mulliken_charges ( const symmMatrix &  densityMatrix, const symmMatrix &  S_symm, const BasisInfoStruct &  basisInfo, mat::SizesAndBlocks const &  matrix_size_block_info, std::vector< int > const &  permutationHML, std::vector< int > const &  inversePermutationHML, const Molecule &  molecule, std::vector< ergo_real > &  resultVector  )

static

References BasisInfoStruct::basisFuncList, BasisFuncStruct_::centerCoords, Atom::coords, Jworker::D, distance(), mat::MatrixGeneral< Treal, Tmatrix >::get_all_values(), mat::MatrixGeneral< Treal, Tmatrix >::get_values(), Molecule::getAtom(), Molecule::getNoOfAtoms(), and BasisInfoStruct::noOfBasisFuncs.

Referenced by do_mulliken_atomic_charges(), and do_mulliken_spin_densities().

int get_simple_starting_guess_sparse	(	int	n,
		int	noOfElectrons,
		symmMatrix &	densityMatrix
	)

References mat::MatrixSymmetric< Treal, Tmatrix >::assign_from_sparse(), do_output(), LOG_AREA_SCF, and LOG_CAT_INFO.

Referenced by SCF_restricted::get_starting_guess_density(), and SCF_unrestricted::get_starting_guess_density().

static ergo_real get_trace ( int  n, const ergo_real *  P, const ergo_real *  H_core  )

static

Referenced by pqrs_struct::compare(), do_power_method(), get_2e_matrices_and_energy_sparse_unrestricted(), and get_2e_matrix_and_energy_sparse().

void output_sparsity	(	int	n,
		const normalMatrix &	M,
		const char *	matrixName
	)

References output_sparsity_template().

Referenced by compute_FDSminusSDF_sparse(), SCF_restricted::get_FDSminusSDF(), and SCF_unrestricted::get_FDSminusSDF().

void output_sparsity_symm	(	int	n,
		const symmMatrix &	M,
		const char *	matrixName
	)

References output_sparsity_template().

Referenced by SCF_restricted::get_new_density_matrix(), SCF_restricted::get_starting_guess_density(), SCF_unrestricted::get_starting_guess_density(), SCF_restricted::output_sparsity_S_F_D(), SCF_unrestricted::output_sparsity_S_F_D(), and SCF_general::SCF_general().

template<typename Tmatrix >

void output_sparsity_template	(	int	n,
		const Tmatrix &	M,
		const char *	matrixName,
		const char *	matrixTypeName
	)

References do_output(), LOG_AREA_SCF, and LOG_CAT_INFO.

Referenced by output_sparsity(), output_sparsity_symm(), and output_sparsity_triang().

void output_sparsity_triang	(	int	n,
		const triangMatrix &	M,
		const char *	matrixName
	)

References output_sparsity_template().

Referenced by SCF_general::SCF_general().

int save_symmetric_matrix	(	symmMatrix &	A,
		const BasisInfoStruct &	basisInfo,
		const char *	fileName,
		std::vector< int > const &	inversePermutationHML
	)

Saves specified symmetic matrix to a file of specified name.

Parameters

A	the matrix to save. The matrix must be saved to a backing store already.
basisInfo	the basis set description.
fileName	The file that will contain the matrix. It will be overwritten without further questions.
inversePermutationHML	permutation information needed when using hierarchic matrices.

References ddf_writeShellListAndDensityMatricesToFile(), do_output(), mat::MatrixGeneral< Treal, Tmatrix >::fullMatrix(), LOG_AREA_SCF, LOG_CAT_INFO, BasisInfoStruct::noOfBasisFuncs, mat::FileWritable::readFromFile(), and mat::FileWritable::writeToFile().

Referenced by SCF_restricted::save_final_potential(), and SCF_general::SCF_general().

int write_2el_integral_m_file	(	const BasisInfoStruct &	basisInfo,
		const IntegralInfo &	integralInfo
	)

References do_2e_integral(), and BasisInfoStruct::noOfBasisFuncs.

Referenced by SCF_general::SCF_general().

int write_basis_func_coord_file

(

const BasisInfoStruct &

basisInfo

)

References BasisInfoStruct::basisFuncList, BasisFuncStruct_::centerCoords, and BasisInfoStruct::noOfBasisFuncs.

Referenced by SCF_general::SCF_general().

int write_diag_elements_to_file	(	int	n,
		const symmMatrix &	M,
		const char *	fileName,
		std::vector< int > const &	permutationHML
	)

References do_output(), mat::MatrixSymmetric< Treal, Tmatrix >::get_values(), LOG_AREA_MAIN, LOG_CAT_ERROR, and LOG_CAT_INFO.

Referenced by SCF_restricted::write_diag_dens_to_file(), and SCF_unrestricted::write_diag_dens_to_file().

int write_full_matrix	(	int	n,
		const symmMatrix &	M,
		const char *	fileName,
		std::vector< int > const &	inversePermutationHML
	)

References mat::MatrixSymmetric< Treal, Tmatrix >::fullMatrix().

Referenced by SCF_restricted::save_full_matrices_for_matlab().

static int write_gcube_file_header ( FILE *  f, const char *  firstLine, const Molecule &  m, double  originX, double  originY, double  originZ, int  NX, double  incrX, int  NY, double  incrY, int  NZ, double  incrZ  )

static

References Atom::charge, Atom::coords, Molecule::getAtom(), and Molecule::getNoOfAtoms().

Referenced by do_density_images().