sc_FinDispMolecularHessian - Man Page

FinDispMolecularHessian (const Ref< MolecularEnergy > &)
FinDispMolecularHessian (const Ref< KeyVal > &)
The FinDispMolecularHessian KeyVal constructor is used to generate a FinDispMolecularHessian object from the input.
FinDispMolecularHessian (StateIn &)
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.
RefSymmSCMatrix compute_hessian_from_gradients ()
These members are used to compute a cartesian hessian from gradients at finite displacements.
int ndisplace () const
int ndisplacements_done () const
RefSCMatrix displacements (int irrep) const
void displace (int disp)
void original_geometry ()
void set_gradient (int disp, const RefSCVector &grad)
void checkpoint_displacements (StateOut &)
void restore_displacements (StateIn &)
RefSymmSCMatrix cartesian_hessian ()
This returns the cartesian hessian.
void set_checkpoint (int c)
Set checkpoint option.
int checkpoint () const
Return the current value of the checkpoint option.
void set_energy (const Ref< MolecularEnergy > &energy)
Some MolecularHessian specializations require a molecular energy object.
MolecularEnergy * energy () const
This returns a MolecularEnergy object, if used by this specialization.
Ref< SCMatrixKit > matrixkit () const
RefSCDimension d3natom () const

Public Member Functions inherited from sc::MolecularHessian
MolecularHessian (const Ref< KeyVal > &)
The MolecularHessian KeyVal constructor is used to generate a MolecularHessian derivative object from the input.
MolecularHessian (StateIn &)
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.
RefSCDimension d3natom ()
Ref< SCMatrixKit > matrixkit () const

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.
virtual void print (std::ostream &=ExEnv::out0()) const
Print the object.

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 get_disp (int disp, int &irrep, int &index, double &coef)
void do_hess_for_irrep (int irrep, const RefSymmSCMatrix &dhessian, const RefSymmSCMatrix &xhessian)
void init ()
void restart ()

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 &)

Ref< MolecularEnergy > mole_
Ref< PointGroup > displacement_point_group_
Ref< PointGroup > original_point_group_
RefSCVector original_geometry_
double disp_
double accuracy_
int ndisp_
int nirrep_
int restart_
char * restart_file_
int checkpoint_
char * checkpoint_file_
int only_totally_symmetric_
int eliminate_cubic_terms_
int do_null_displacement_
int debug_
RefSCMatrix symbasis_
RefSCVector * gradients_

Protected Attributes inherited from sc::MolecularHessian
Ref< Molecule > mol_
RefSCDimension d3natom_
Ref< SCMatrixKit > matrixkit_

Static Public Member Functions inherited from sc::MolecularHessian

static RefSCMatrix cartesian_to_symmetry (const Ref< Molecule > &m, Ref< PointGroup > pg=0, Ref< SCMatrixKit > kit=0)
Find transformation matrix from cartesian to symmetry coordinates.
static void write_cartesian_hessian (const char *filename, const Ref< Molecule > &m, const RefSymmSCMatrix &hess)
Write the hessian in a simple text format.
static void read_cartesian_hessian (const char *filename, const Ref< Molecule > &m, const RefSymmSCMatrix &hess)
Read the hessian from a simple text format.

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)

The FinDispMolecularHessian KeyVal constructor is used to generate a FinDispMolecularHessian object from the input. It reads the keywords below.

KeywordTypeDefaultDescription

energyMolecularEnergynoneThis gives an object which will be used to compute the gradients needed to form the hessian. If this is not specified, the object using FinDispMolecularHessian will, in some cases, fill it in appropriately. However, even in these cases, it may be desirable to specify this keyword. For example, this could be used in an optimization to compute frequencies using a lower level of theory.

debugbooleanfalseIf true, print out debugging information.

point_groupPointGroupnoneThe point group to use for generating the displacements.

restartbooleantrueIf true, and a checkpoint file exists, restart from that file.

restart_filestring basename.ckpt.hessThe name of the file where checkpoint information is written to or read from.

checkpointbooleantrueIf true, checkpoint intermediate data.

only_totally_symmetricbooleanfalse If true, only follow totally symmetric displacments. The hessian will not be complete, but it has enough information to use it in a geometry optimization.

eliminate_cubic_termsbooleantrueIf true, then cubic terms will be eliminated. This requires that two displacements are done for each totally symmetric coordinate, rather than one. Setting this to false will reduce the accuracy, but the results will still probably be accurate enough for a geometry optimization.

do_null_displacementbooleantrueRun the calculation at the given geometry as well.

displacementdouble1.0e-2The size of the displacement in Bohr.

gradient_accuracydouble<td>displacement / 1000The accuracy to which the gradients will be computed.

This returns the cartesian hessian. If it has not yet been computed, it will be computed by finite displacements.

Implements sc::MolecularHessian.

This returns a MolecularEnergy object, if used by this specialization. Otherwise null is returned.

Reimplemented from sc::MolecularHessian.

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::SavableState.

Some MolecularHessian specializations require a molecular energy object. The default implementations of this ignores the argument.

Reimplemented from sc::MolecularHessian.