sc::MBPT2 Class Reference

The MBPT2 class implements several second-order perturbation theory methods. More...

#include <chemistry/qc/mbpt/mbpt.h>

Inheritance diagram for sc::MBPT2:

Public Member Functions
	MBPT2 (StateIn &)
	MBPT2 (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< 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
RefSymmSCMatrix	density ()
	Returns the SO density.
double	magnetic_moment () const
	Computes the S (or J) magnetic moment of the target state(s), in units of . More...
bool	analytic_gradient_implemented () const
	must overload this in a derived class if analytic gradient can be computed More...
int	value_implemented () const
void	set_desired_value_accuracy (double)
	set the value accuracy
void	symmetry_changed ()
	Call this if you have changed the molecular symmetry of the molecule contained by this MolecularEnergy.
void	obsolete ()
	Marks all results as being out of date. More...
void	print (std::ostream &o=ExEnv::out0()) const
	Print information about the object.
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)
void	orbitals (const SCVector3 &r, const RefSCMatrix &orbs, RefSCVector &values)
double	orbital_density (const SCVector3 &r, int iorb, const RefSCMatrix &orbs, double *orbval=0)
double	total_charge () const
	Returns the total charge of the system.
virtual RefSymmSCMatrix	ao_density ()
	Returns the AO density.
virtual RefSCMatrix	natural_orbitals ()
	Returns the natural orbitals, in SO basis.
virtual RefDiagSCMatrix	natural_density ()
	Returns the natural density (a diagonal matrix).
int	spin_polarized ()
	Return 1 if the magnetic moment != 0.
int	dk () const
	Returns the level the of the Douglas-Kroll approximation.
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_for_basis (const Ref< GaussianBasisSet > &bas, const Ref< GaussianBasisSet > &pbas=0)
	Returns the SO core Hamiltonian in the given basis and momentum basis. More...
virtual RefSymmSCMatrix	core_hamiltonian ()
	Returns the SO core Hamiltonian.
RefSymmSCMatrix	core_hamiltonian_nr (const Ref< GaussianBasisSet > &bas)
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 >	momentum_basis () const
	Returns the basis used for p^2 in the DK correction.
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.
virtual void	set_orthog_method (const OverlapOrthog::OrthogMethod &)
	(Re)Sets the orthogonalization method and makes this obsolete. More...
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.
void	writeorbitals ()
	output orbitals to some files to facilitate plotting, with the help of the WriteOrbital class.
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 &)
int	gradient_implemented () const
	Reports whether gradient is implemented either analytically or using MolecularGradient object. More...
int	hessian_implemented () const
	Reports whether hessian is implemented either analytically or using MolecularHessian object. More...
void	set_desired_gradient_accuracy (double acc)
	These functions overload their Function counterparts. More...
void	set_desired_hessian_accuracy (double acc)
void	set_molhess (const Ref< MolecularHessian > &molhess)
	Use this function to provide MolecularHessian object that will be used to compute hessian. More...
const Ref< MolecularHessian > &	molhess () const
RefSymmSCMatrix	hessian ()
	Will throw if hessian_implemented() returns 0.
void	set_molgrad (const Ref< MolecularGradient > &molgrad)
	Use this function to provide MolecularGradient object that will be used to compute gradient. More...
const Ref< MolecularGradient > &	molgrad () const
RefSCVector	gradient ()
	Will throw if gradient_implemented() returns 0.
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...
virtual void	purge ()
	This function purges any caches of data in MolecularEnergy. More...
const RefSCVector &	electric_field () const
	returns the electric field vector
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
int	gradient_needed () const
int	do_gradient (int)
virtual double	actual_gradient_accuracy () const
virtual double	desired_gradient_accuracy () const
AccResultRefSCVector &	gradient_result ()
int	hessian_needed () const
int	do_hessian (int)
virtual double	actual_hessian_accuracy () const
virtual double	desired_hessian_accuracy () const
AccResultRefSymmSCMatrix &	hessian_result ()
virtual bool	desired_value_accuracy_set_to_default () const
virtual bool	desired_gradient_accuracy_set_to_default () const
virtual bool	desired_hessian_accuracy_set_to_default () const
RefSCVector	get_x () const
const RefSCVector &	get_x_no_copy () const
void	print_desired_accuracy (std::ostream &=ExEnv::out0()) const
	similar to print(), but only prins desired accuracies
virtual bool	throw_if_tolerance_exceeded () const
	Overridden Compute member.
	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 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 MPQC__NOEXCEPT
	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.
Ref< DescribedClass >	ref ()
	Return this object wrapped up in a Ref smart pointer. More...
Public Member Functions inherited from sc::RefCount
size_t	identifier () const
	Return the unique identifier for this object that can be compared for different objects of different types. More...
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...

Protected Member Functions
void	init_variables ()
void	compute ()
	Recompute at least the results that have compute true and are not already computed. More...
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 ()
virtual bool	analytic_hessian_implemented () const
	must overload this in a derived class if analytic hessian can be computed More...
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 &)

Static Protected Member Functions
static double	ref_to_mp2_acc ()

Protected Attributes
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_
std::string	method_
std::string	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
ResultRefSCMatrix	natural_orbitals_
ResultRefDiagSCMatrix	natural_density_
Ref< GaussianBasisSet >	gbs_
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_.
bool	desired_value_accuracy_set_to_default_
bool	desired_gradient_accuracy_set_to_default_
bool	desired_hessian_accuracy_set_to_default_
bool	throw_if_tolerance_exceeded_

Additional Inherited Members
Static Public Member Functions inherited from sc::Wavefunction
static void	orbitals (const Ref< OrbitalSpace > &orbs, const std::vector< SCVector3 > &r, std::vector< double > &values)
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)

Detailed Description

The MBPT2 class implements several second-order perturbation theory methods.

Constructor & Destructor Documentation

MBPT2()

sc::MBPT2::MBPT2

(

const Ref< KeyVal > &

)

The KeyVal constructor.

reference

This gives the reference wavefunction. It must be an object of type CLSCF for closed-shell molecules and HSOSSCF for open-shell molecules. The is no default.

nfzc

The number of frozen core orbitals. The default is 0. If no atoms have an atomic number greater than 30, then the number of orbitals to be frozen can be automatically determined by specifying nfzc = auto.

nfzv

The number of frozen virtual orbitals. The default is 0.

memory

The amount of memory, in bytes, that each processor may use.

method

This gives a string that must take on one of the values below. The default is mp for closed-shell systems and zapt for open-shell systems.

mp

Use Møller-Plesset perturbation theory. This is only valid for closed-shell systems. Energies and gradients can be computed with this method.

opt1

Use the OPT1 variant of open-shell perturbation theory. Only energies can be computed for open-shell systems.

opt2

Use the OPT2 variant of open-shell perturbation theory. Only energies can be computed for open-shell systems.

zapt

Use the ZAPT variant of open-shell perturbation theory. Only energies can be computed for open-shell systems.

algorithm

This gives a string that must take on one of the values given below. The default is memgrp for closed-shell systems. For open-shell systems v1 is used for a small number of processors and v2 is used otherwise.

memgrp

Use the distributed shared memory algorithm (which uses a MemoryGrp object). This is only valid for MP2 energies and gradients.

v1

Use algorithm V1. Only energies can be computed. The maximum number of processors that can be utilized is the number of virtual orbitals. This algorithm computes few integrals than the others, but has higher communication requirements.

v2

Use algorithm V2. Only energies can be computed. The maximum number of processors that can be utilized is the number of shells.

v2lb

Use a modified V2 algorithm that may compute more two electron integrals, but may get better load balance on the part of the calculation. Only energies can be computed. This is recommended only for computations involving large molecules (where the transformation is dominant) on very many processors (approaching the number of shells).

The v1 and v2 algorithms are discussed in Ida M. B. Nielsen and Edward T. Seidl, J. Comp. Chem. 16, 1301 (1995). The memgrp algorithm is discussed in Ida M. B. Nielsen, Chem. Phys. Lett. 255, 210 (1996).

memorygrp

A MemoryGrp object is used by the memgrp algorithm. If this is not given the program will try to find an appropriate default.

dynamic

This boolean keyword specifies whether dynamic load balancing is used. The default is false.

Member Function Documentation

analytic_gradient_implemented()

bool sc::MBPT2::analytic_gradient_implemented ( ) const

virtual

must overload this in a derived class if analytic gradient can be computed

Returns

true (analytic gradient is available) or false (analytic gradient is not available, default)

Reimplemented from sc::MolecularEnergy.

Reimplemented in sc::MBPT2_R12.

compute()

void sc::MBPT2::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.

Implements sc::Compute.

Reimplemented in sc::MBPT2_R12.

magnetic_moment()

double sc::MBPT2::magnetic_moment ( ) const

virtual

Computes the S (or J) magnetic moment of the target state(s), in units of .

Can be evaluated from density and overlap, as;

(this->alpha_density() * this-> overlap()).trace() -
(this->beta_density() * this-> overlap()).trace()

but derived Wavefunction may have this value as user input.

Returns

the magnetic moment

Reimplemented from sc::Wavefunction.

obsolete()

void sc::MBPT2::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::Compute.

Reimplemented in sc::MBPT2_R12.

save_data_state()

void sc::MBPT2::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::MolecularEnergy.

Reimplemented in sc::MBPT2_R12.

value_implemented()

int sc::MBPT2::value_implemented ( ) const

virtual

Returns

1 (value implemented) or 0 (value not implemented, default). Must be overridden for the class to be useful.

Reimplemented from sc::Function.

Reimplemented in sc::MBPT2_R12.

---

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

• src/lib/chemistry/qc/mbpt/mbpt.h