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:
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Collaboration diagram for sc::MBPT2_R12:
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## 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| Marks all results as being out of date.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. More...
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. More...
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. More...
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. More...
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. More...
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
| 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...
Function & | operator= (const Function &)
Ref< SCMatrixKit > | matrixkit () const
| Return the SCMatrixKit used to construct vectors and matrices. More...
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.
RefSCVector | get_x () const
const RefSCVector & | get_x_no_copy () const
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 ()
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_matrixkit (const Ref< SCMatrixKit > &)
| Set the SCMatrixKit that should be used to construct the requisite vectors and matrices. More...
virtual void | set_dimension (const RefSCDimension &)
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. More...
virtual void | set_value (double)
virtual void | set_actual_value_accuracy (double)
virtual void | set_actual_gradient_accuracy (double)
virtual void | set_actual_hessian_accuracy (double)
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...

## 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. More...
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_

## Detailed Description

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

methods.

## Constructor & Destructor Documentation

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

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.

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.

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.

int sc::MBPT2_R12::value_implemented | ( |  | ) | const

virtual

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

Reimplemented from sc::MBPT2.

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

- mbptr12.h