sc_MBPT2_R12 - Man Page

MBPT2_R12 (StateIn &)
MBPT2_R12 (const Ref< KeyVal > &)
The KeyVal constructor.
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.
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Marks all results as being out of date.
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.
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.
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.
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.
void nuclear_repulsion_energy_gradient (double *g)
Computes the nuclear repulsion gradient.
virtual void nuclear_repulsion_energy_gradient (double **g)
Computes the nuclear repulsion gradient.
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.
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.
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.
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.
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 (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:
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.
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.
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.
virtual void save_vbase_state (StateOut &)
Save the virtual bases for the object.

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.
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.
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.

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

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.
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.

Protected Member Functions inherited from sc::RefCount
RefCount (const RefCount &)
RefCount & operator= (const RefCount &)

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.
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_.

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 Mo/ller-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 Mo/ller-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 Mo/ller-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.

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.

Returns the SO density.

Reimplemented from sc::MBPT2.

Reimplemented from sc::MBPT2.

Marks all results as being out of date. Any subsequent access to results will cause Compute::compute() to be called.

Reimplemented from sc::MBPT2.

Print information about the object.

Reimplemented from sc::MBPT2.

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.

Information about the availability of values, gradients, and hessians.

Reimplemented from sc::MBPT2.