sc::MBPT2_R12 Class Reference

The MBPT2_R12 class implements several linear R12 second-order perturbation theory methods. More...

#include <mbptr12.h>

Inheritance diagram for sc::MBPT2_R12:

Collaboration diagram for sc::MBPT2_R12:

Public Member Functions
	MBPT2_R12 (StateIn &)
	MBPT2_R12 (const Ref< KeyVal > &)
	The KeyVal constructor. More...
void	save_data_state (StateOut &)
	Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them. More...
Ref< GaussianBasisSet >	aux_basis () const
Ref< GaussianBasisSet >	vir_basis () const
bool	gbc () const
bool	ebc () const
LinearR12::ABSMethod	abs_method () const
LinearR12::StandardApproximation	stdapprox () const
bool	spinadapted () const
R12IntEvalInfo::StoreMethod	r12ints_method () const
const std::string &	r12ints_file () const
double	corr_energy ()
double	r12_corr_energy ()
RefSymmSCMatrix	density ()
	Returns the SO density.
void	obsolete ()
	Marks all results as being out of date. More...
int	gradient_implemented () const
int	value_implemented () const
	Information about the availability of values, gradients, and hessians.
void	print (std::ostream &o=ExEnv::out0()) const
	Print information about the object.
Public Member Functions inherited from sc::MBPT2
	MBPT2 (StateIn &)
	MBPT2 (const Ref< KeyVal > &)
	The KeyVal constructor. More...
Ref< SCF >	ref ()
double	ref_energy ()
double	corr_energy ()
RefSCVector	ref_energy_gradient ()
RefSCVector	corr_energy_gradient ()
int	nelectron ()
	Returns the number of electrons.
int	nfzcore () const
int	nfzvirt () const
int	spin_polarized ()
	Return 1 if the alpha density is not equal to the beta density.
void	symmetry_changed ()
	Call this if you have changed the molecular symmetry of the molecule contained by this MolecularEnergy.
Public Member Functions inherited from sc::Wavefunction
	Wavefunction (StateIn &)
	Wavefunction (const Ref< KeyVal > &)
	The KeyVal constructor. More...
void	save_data_state (StateOut &)
	Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them. More...
double	density (const SCVector3 &)
double	density_gradient (const SCVector3 &, double *)
double	natural_orbital (const SCVector3 &r, int iorb)
double	natural_orbital_density (const SCVector3 &r, int orb, double *orbval=0)
double	orbital (const SCVector3 &r, int iorb, const RefSCMatrix &orbs)
double	orbital_density (const SCVector3 &r, int iorb, const RefSCMatrix &orbs, double *orbval=0)
double	charge ()
	Returns the charge.
virtual RefSymmSCMatrix	ao_density ()
	Returns the AO density.
virtual RefSCMatrix	natural_orbitals ()
	Returns the natural orbitals.
virtual RefDiagSCMatrix	natural_density ()
	Returns the natural density (a diagonal matrix).
virtual RefSymmSCMatrix	alpha_density ()
	Return alpha electron densities in the SO basis.
virtual RefSymmSCMatrix	beta_density ()
	Return beta electron densities in the SO basis.
virtual RefSymmSCMatrix	alpha_ao_density ()
	Return alpha electron densities in the AO basis.
virtual RefSymmSCMatrix	beta_ao_density ()
	Return beta electron densities in the AO basis.
virtual RefSCMatrix	nao (double *atom_charges=0)
	returns the ao to nao transformation matrix
virtual RefSymmSCMatrix	overlap ()
	Returns the SO overlap matrix.
virtual RefSymmSCMatrix	core_hamiltonian ()
	Returns the SO core Hamiltonian.
virtual double	nuclear_repulsion_energy ()
	Returns the nuclear repulsion energy. More...
void	nuclear_repulsion_energy_gradient (double *g)
	Computes the nuclear repulsion gradient. More...
virtual void	nuclear_repulsion_energy_gradient (double **g)
	Computes the nuclear repulsion gradient. More...
RefSCDimension	ao_dimension ()
	Atomic orbital dimension.
RefSCDimension	so_dimension ()
	Symmetry adapted orbital dimension.
RefSCDimension	oso_dimension ()
	Orthogonalized symmetry adapted orbital dimension.
Ref< SCMatrixKit >	basis_matrixkit ()
	Matrix kit for AO, SO, orthogonalized SO, and MO dimensioned matrices.
Ref< Molecule >	molecule () const
	Returns the Molecule.
Ref< GaussianBasisSet >	basis () const
	Returns the basis set.
Ref< GaussianBasisSet >	atom_basis () const
	Returns the basis set describing the nuclear charge distributions.
const double *	atom_basis_coef () const
	Returns the coefficients of the nuclear charge distribution basis functions.
Ref< Integral >	integral ()
	Returns the integral evaluator.
void	symmetry_changed ()
	Call this if you have changed the molecular symmetry of the molecule contained by this MolecularEnergy.
RefSCMatrix	so_to_orthog_so ()
	Returns a matrix which does the default transform from SO's to orthogonal SO's. More...
RefSCMatrix	so_to_orthog_so_inverse ()
	Returns the inverse of the transformation returned by so_to_orthog_so.
OverlapOrthog::OrthogMethod	orthog_method () const
	Returns the orthogonalization method.
void	set_orthog_method (const OverlapOrthog::OrthogMethod &)
	(Re)Sets the orthogonalization method and makes this obsolete
double	lindep_tol () const
	Returns the tolerance for linear dependencies.
void	set_lindep_tol (double)
	Re(Sets) the tolerance for linear dependencies.
void	obsolete ()
	Marks all results as being out of date. More...
void	print (std::ostream &=ExEnv::out0()) const
	Print information about the object.
Public Member Functions inherited from sc::MolecularEnergy
	MolecularEnergy (const MolecularEnergy &)
	MolecularEnergy (const Ref< KeyVal > &)
	The KeyVal constructor. More...
	MolecularEnergy (StateIn &)
void	set_checkpoint ()
	Set up checkpointing.
void	set_checkpoint_file (const char *)
void	set_checkpoint_freq (int freq)
bool	if_to_checkpoint () const
	Check if need to checkpoint.
const char *	checkpoint_file () const
int	checkpoint_freq () const
MolecularEnergy &	operator= (const MolecularEnergy &)
virtual double	energy ()
	A wrapper around value();.
virtual RefSCDimension	moldim () const
void	guess_hessian (RefSymmSCMatrix &)
	Compute a quick, approximate hessian.
RefSymmSCMatrix	inverse_hessian (RefSymmSCMatrix &)
RefSymmSCMatrix	hessian ()
	If a molecule hessian object is given, it will be used to provide a hessian.
int	hessian_implemented () const
void	set_x (const RefSCVector &)
	Set and retrieve the coordinate values.
RefSCVector	get_cartesian_x ()
	Return the cartesian coordinates.
RefSCVector	get_cartesian_gradient ()
	Return the cartesian gradient.
RefSymmSCMatrix	get_cartesian_hessian ()
	Return the cartesian hessian.
Ref< MolecularCoor >	molecularcoor ()
Ref< NonlinearTransform >	change_coordinates ()
	An optimizer can call change coordinates periodically to give the function an opportunity to change its coordinate system. More...
void	print_natom_3 (const RefSCVector &, const char *t=0, std::ostream &o=ExEnv::out0()) const
	Nicely print n x 3 data that are stored in a vector.
void	print_natom_3 (double **, const char *t=0, std::ostream &o=ExEnv::out0()) const
void	print_natom_3 (double *, const char *t=0, std::ostream &o=ExEnv::out0()) const
Public Member Functions inherited from sc::Function
virtual RefSCVector	gradient ()
int	gradient_needed () const
int	do_gradient (int)
virtual void	set_desired_gradient_accuracy (double)
virtual double	actual_gradient_accuracy () const
virtual double	desired_gradient_accuracy () const
AccResultRefSCVector &	gradient_result ()
int	hessian_needed () const
int	do_hessian (int)
virtual void	set_desired_hessian_accuracy (double)
virtual double	actual_hessian_accuracy () const
virtual double	desired_hessian_accuracy () const
AccResultRefSymmSCMatrix &	hessian_result ()
RefSCVector	get_x () const
const RefSCVector &	get_x_no_copy () const
	Function ()
	Function (StateIn &)
	Function (const Function &)
	Function (const Ref< KeyVal > &, double funcacc=DBL_EPSILON, double gradacc=DBL_EPSILON, double hessacc=DBL_EPSILON)
	The keyval constructor reads the following keywords: More...
virtual	~Function ()
Function &	operator= (const Function &)
Ref< SCMatrixKit >	matrixkit () const
	Return the SCMatrixKit used to construct vectors and matrices.
RefSCDimension	dimension () const
	Return the SCDimension of the problem.
virtual double	value ()
	Return the value of the function.
int	value_needed () const
	Returns nonzero if the current value is not up-to-date.
int	do_value (int)
	If passed a nonzero number, compute the value the next time compute() is called. More...
AccResultdouble &	value_result ()
virtual void	set_desired_value_accuracy (double)
	Set the accuracy to which the value is to be computed.
virtual double	actual_value_accuracy () const
	Return the accuracy with which the value has been computed.
virtual double	desired_value_accuracy () const
	Return the accuracy with which the value is to be computed.
Public Member Functions inherited from sc::SavableState
SavableState &	operator= (const SavableState &)
void	save_state (StateOut &)
	Save the state of the object as specified by the StateOut object. More...
void	save_object_state (StateOut &)
	This can be used for saving state when the exact type of the object is known for both the save and the restore. More...
virtual void	save_vbase_state (StateOut &)
	Save the virtual bases for the object. More...
Public Member Functions inherited from sc::DescribedClass
	DescribedClass (const DescribedClass &)
DescribedClass &	operator= (const DescribedClass &)
ClassDesc *	class_desc () const throw ()
	This returns the unique pointer to the ClassDesc corresponding to the given type_info object. More...
const char *	class_name () const
	Return the name of the object's exact type.
int	class_version () const
	Return the version of the class.
Public Member Functions inherited from sc::RefCount
int	lock_ptr () const
	Lock this object.
int	unlock_ptr () const
	Unlock this object.
void	use_locks (bool inVal)
	start and stop using locks on this object
refcount_t	nreference () const
	Return the reference count.
refcount_t	reference ()
	Increment the reference count and return the new count.
refcount_t	dereference ()
	Decrement the reference count and return the new count.
int	managed () const
void	unmanage ()
	Turn off the reference counting mechanism for this object. More...
int	managed () const
	Return 1 if the object is managed. Otherwise return 0.
Public Member Functions inherited from sc::Identity
Identifier	identifier ()
	Return the Identifier for this argument. More...

Protected Member Functions
void	compute ()
	Recompute at least the results that have compute true and are not already computed. More...
Protected Member Functions inherited from sc::MBPT2
void	init_variables ()
void	eigen (RefDiagSCMatrix &vals, RefSCMatrix &vecs, RefDiagSCMatrix &occs)
void	compute_hsos_v1 ()
distsize_t	compute_v2_memory (int ni, int nfuncmax, int nbfme, int nshell, int ndocc, int nsocc, int nvir, int nproc)
void	compute_hsos_v2 ()
void	compute_hsos_v2_lb ()
int	compute_cs_batchsize (size_t mem_static, int nocc_act)
distsize_t	compute_cs_dynamic_memory (int ni, int nocc_act)
int	make_cs_gmat (RefSymmSCMatrix &Gmat, double *DPmat)
int	make_cs_gmat_new (RefSymmSCMatrix &Gmat, const RefSymmSCMatrix &DPmat)
void	form_max_dens (double *DPmat, signed char *maxp)
int	init_cs_gmat ()
void	done_cs_gmat ()
int	make_g_d_nor (RefSymmSCMatrix &Gmat, double *DPmat, const double *mgdbuff)
void	cs_cphf (double **scf_vector, double *Laj, double *eigval, RefSCMatrix &P2aj)
void	s2pdm_contrib (const double *intderbuf, double *PHF, double *P2AO, double **hf_ginter, double **ginter)
void	hcore_cs_grad (double *PHF, double *PMP2, double **hf_ginter, double **ginter)
void	overlap_cs_grad (double *WHF, double *WMP2, double **hf_ginter, double **ginter)
void	compute_cs_grad ()
Protected Member Functions inherited from sc::Wavefunction
double	min_orthog_res ()
double	max_orthog_res ()
void	copy_orthog_info (const Ref< Wavefunction > &)
Protected Member Functions inherited from sc::MolecularEnergy
void	failure (const char *)
virtual void	set_energy (double)
	This is just a wrapper around set_value().
virtual void	set_gradient (RefSCVector &)
	These are passed gradients and hessian in cartesian coordinates. More...
virtual void	set_hessian (RefSymmSCMatrix &)
void	x_to_molecule ()
void	molecule_to_x ()
Protected Member Functions inherited from sc::Function
virtual void	set_value (double)
virtual void	set_matrixkit (const Ref< SCMatrixKit > &)
	Set the SCMatrixKit that should be used to construct the requisite vectors and matrices.
virtual void	set_dimension (const RefSCDimension &)
virtual void	set_actual_value_accuracy (double)
virtual void	set_actual_gradient_accuracy (double)
virtual void	set_actual_hessian_accuracy (double)
RefSCVector &	get_x_reference ()
	Get read/write access to the coordinates for modification.
void	do_change_coordinates (const Ref< NonlinearTransform > &)
	Change the coordinate system and apply the given transform to intermediates matrices and vectors.
Protected Member Functions inherited from sc::SavableState
	SavableState (const SavableState &)
	SavableState (StateIn &)
	Each derived class StateIn CTOR handles the restore corresponding to calling save_object_state, save_vbase_state, and save_data_state listed above. More...
Protected Member Functions inherited from sc::RefCount
	RefCount (const RefCount &)
RefCount &	operator= (const RefCount &)

Additional Inherited Members
Static Public Member Functions inherited from sc::SavableState
static void	save_state (SavableState *s, StateOut &)
static SavableState *	restore_state (StateIn &si)
	Restores objects saved with save_state. More...
static SavableState *	key_restore_state (StateIn &si, const char *keyword)
	Like restore_state, but keyword is used to override values while restoring.
static SavableState *	dir_restore_state (StateIn &si, const char *objectname, const char *keyword=0)
Protected Attributes inherited from sc::MBPT2
Ref< SCF >	reference_
Ref< MemoryGrp >	mem
int	nfzc
int	nfzv
size_t	mem_alloc
double	cphf_epsilon_
int	eliminate_in_gmat_
const double *	intbuf_
Ref< TwoBodyInt >	tbint_
Ref< TwoBodyInt > *	tbints_
Ref< TwoBodyDerivInt > *	tbintder_
int	nbasis
int	noso
Ref< MessageGrp >	msg_
int	nvir
int	nocc
int	nsocc
Ref< ThreadGrp >	thr_
int	dynamic_
double	print_percent_
int	max_norb_
int *	symorb_irrep_
int *	symorb_num_
char *	method_
char *	algorithm_
int	do_d1_
int	do_d2_
int	nfuncmax
double	hf_energy_
RefSCVector	hf_gradient_
double	restart_ecorr_
int	restart_orbital_v1_
int	restart_orbital_memgrp_
Protected Attributes inherited from sc::Wavefunction
int	debug_
Protected Attributes inherited from sc::MolecularEnergy
Ref< PointGroup >	initial_pg_
int	print_molecule_when_changed_
Protected Attributes inherited from sc::Function
Ref< SCMatrixKit >	matrixkit_
	Used to construct new matrices.
RefSCVector	x_
	The variables.
RefSCDimension	dim_
	The dimension of x_.
AccResultdouble	value_
	The value of the function at x_.
AccResultRefSCVector	gradient_
	The gradient at x_.
AccResultRefSymmSCMatrix	hessian_
	The hessian at x_.

Detailed Description

The MBPT2_R12 class implements several linear R12 second-order perturbation theory methods.

Constructor & Destructor Documentation

MBPT2_R12()

sc::MBPT2_R12::MBPT2_R12

(

const Ref< KeyVal > &

)

The KeyVal constructor.

gbc

This boolean specifies whether Generalized Brillouin Condition (GBC) is assumed to hold. The default is "true". This keyword is only valid if stdapprox=A'. The effect of setting this keyword to true is rather small – hence it is not recommended to use this keyword.

ebc

This boolean specifies whether Extended Brillouin Condition (EBC) is assumed to hold. The default is "true". This keyword is only valid if stdapprox=A'. The effect of setting this keyword to true is rather small – hence it is not recommended to use this keyword.

stdapprox

This gives a string that must take on one of the values below. The default is A'.

A

Use second order Møller-Plesset perturbation theory with linear R12 terms in standard approximation A (MP2-R12/A). Only energies can be computed with the MP2-R12/A method.

A'

Use second order Møller-Plesset perturbation theory with linear R12 terms in standard approximation A' (MP2-R12/A'). This will cause MP2-R12/A energies to be computed also. Only energies can be computed with the MP2-R12/A' method.

B

Use second order Møller-Plesset perturbation theory with linear R12 terms in standard approximation B. This method is not implemented yet.

spinadapted

This boolean specifies whether to compute spin-adapted or spin-orbital pair energies. Default is to compute spin-adapted energies.

aux_basis

This specifies the auxiliary basis to be used for the resolution of the identity. Default is to use the same basis as for the orbital expansion.

vir_basis

This specifies the basis to be used for the virtual orbitals. Default is to use the same basis as for the orbital expansion.

include_mp1

This specifies whether to compute MP1 correction to the MP2 and MP2-R12 energies. This option only has effect if vir_basis is not the same as basis. MP1 correction is a perturbative estimate of the difference between the HF energy computed in vir_basis and basis. Usually, it is a very poor estimate – therefore this keyword should be avoided by non-experts. Default is false.

abs_method

This string specifies whether the old ABS method, introduced by Klopper and Samson, or the new ABS variant, CABS, introduced by Valeev, should be used. Valid values are "ABS" (Klopper and Samson), "ABS+", "CABS", and "CABS+", where the "+" labels a method where the union of OBS and ABS is used to construct the RI basis. The default is "ABS". The default in 2.3.0 and later will be "CABS+".

lindep_tol

The tolerance used to detect linearly dependent basis functions in the RI basis set. The precise meaning depends on the orthogonalization method. The default value is 1e-8.

r12ints

This specifies how to store transformed MO integrals. Valid values are:

mem-posix

Store integrals in memory for single-pass situations and in a binary file on task 0's node using POSIX I/O for multipass situations. posix is usually less efficient than mpi for distributed parallel multipass runs since the I/O is performed by one task only. However, this method is guaranteed to work in all types of environments, hence mem-posix is the default.

posix

Store integrals in a binary file on task 0's node using POSIX I/O. This method is different from mem-posix in that it forces the integrals out to disk even if they could be stored in memory. posix should only be used for benchmarking and testing purposes.

mem-mpi

Store integrals in memory for single-pass situations and in a binary file using MPI-I/O for multipass situations. This method assumes the availability of MPI-I/O. mem-mpi is the preferred choice in distributed environments which have MPI-I/O available.

mpi

Store integrals in a binary file using MPI-I/O. This method is different from mem-mpi in that it forces the integrals out to disk even if they could be stored in memory. mpi should only be used for benchmarking and testing purposes.

mem

Store integrals in memory. Can only be used with single-pass transformations for MP2-R12/A and MP2-R12/A' methods. This method should only be used for testing purposes.

If r12ints is not specified, then mem-posix method will be used. If user wishes to use MPI-I/O, pending its availability, for higher parallel efficiency, r12ints should be explicitly set to mem-mpi.

r12ints_file

This specifies the prefix for the transformed MO integrals file if r12ints is set to posix, mpi, mem-posix or mem-mpi is used. Default is "./<i>inputbasename</i>.r12ints", where inputbasename is the name of the input file without ".in". If MPI-I/O is used then it is user's responsibility to ensure that the file resides on a file system that supports MPI-I/O.

twopdm_grid_aa

This optional keyword specifies a TwoBodyGrid object which to use for coordinates at which to compute alpha-alpha part of 2-PDM.

twopdm_grid_ab

This optional keyword specifies a TwoBodyGrid object which to use for coordinates at which to compute alpha-beta part of 2-PDM.

Member Function Documentation

compute()

void sc::MBPT2_R12::compute ( )

protectedvirtual

Recompute at least the results that have compute true and are not already computed.

This should only be called by Result's members.

Reimplemented from sc::MBPT2.

obsolete()

void sc::MBPT2_R12::obsolete ( )

virtual

Marks all results as being out of date.

Any subsequent access to results will cause Compute::compute() to be called.

Reimplemented from sc::MBPT2.

save_data_state()

void sc::MBPT2_R12::save_data_state ( StateOut &  )

virtual

Save the base classes (with save_data_state) and the members in the same order that the StateIn CTOR initializes them.

This must be implemented by the derived class if the class has data.

Reimplemented from sc::MBPT2.

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

• mbptr12.h