sc_IntMolecularCoor3

sc::IntMolecularCoor::IntMolecularCoor (const Ref< KeyVal > &)

The KeyVal constructor.

variable

Gives a SetIntCoor object that specifies the internal coordinates that can be varied. If this is not given, the variable coordinates will be generated.

followed

Gives a IntCoor object that specifies a coordinate to used as the first coordinate in the variable coordinate list. The remaining coordinates will be automatically generated. The default is no followed coordinate. This option is usually used to set the initial search direction for a transition state optimization, where it is used in conjunction with the mode_following keyword read by the EFCOpt class.

fixed

Gives a SetIntCoor object that specifies the internal coordinates that will be fixed. The default is no fixed coordinates.

watched

Gives a SetIntCoor object that specifies internal coordinates that will be printed out whenever the coordinates are changed. The default is none.

have_fixed_values

If true, then values for the fixed coordinates must be given in fixed and an attempt will be made to displace the initial geometry to the given fixed values. The default is false.

extra_bonds

This is only read if the generator keyword is not given. It is a vector of atom numbers, where elements $(i-1) imes 2 + 1$ and $i imes 2$ specify the atoms which are bound in extra bond $i$. The extra_bonds keyword should only be needed for weakly interacting fragments, otherwise all the needed bonds will be found.

generator

Specifies an IntCoorGen object that creates simple, redundant internal coordinates. If this keyword is not given, then a vector giving extra bonds to be added is read from extra_bonds and this is used to create an IntCoorGen object.

decouple_bonds

Automatically generated internal coordinates are linear combinations of possibly any mix of simple internal coordinates. If decouple_bonds is true, an attempt will be made to form some of the internal coordinates from just stretch simple coordinates. The default is false.

decouple_bends

This is like decouple_bonds except it applies to the bend-like coordinates. The default is false.

max_update_disp

The maximum displacement to be used in the displacement to fixed internal coordinates values. Larger displacements will be broken into several smaller displacements and new coordinates will be formed for each of these displacments. This is only used when fixed and have_fixed_values are given. The default is 0.5.

max_update_steps

The maximum number of steps permitted to convert internal coordinate displacements to cartesian coordinate displacements. The default is 100.

update_bmat

Displacements in internal coordinates are converted to a cartesian displacements iteratively. If there are large changes in the cartesian coordinates during conversion, then recompute the $B$ matrix, which is using to do the conversion. The default is false.

only_totally_symmetric

If a simple test reveals that an internal coordinate is not totally symmetric, then it will not be added to the internal coordinate list. The default is true.

simple_tolerance

The internal coordinates are formed as linear combinations of simple, redundant internal coordinates. Coordinates with coefficients smaller then simple_tolerance will be omitted. The default is 1.0e-3.

cartesian_tolerance

The tolerance for conversion of internal coordinate displacements to cartesian displacements. The default is 1.0e-12.

form:print_simple

Print the simple internal coordinates. The default is false.

form:print_variable

Print the variable internal coordinates. The default is false.

form:print_constant

Print the constant internal coordinates. The default is false.

form:print_molecule

Print the molecule when forming coordinates. The default is false.

scale_bonds

Obsolete. The default value is 1.0.

scale_bends

Obsolete. The default value is 1.0.

scale_tors

Obsolete. The default value is 1.0.

scale_outs

Obsolete. The default value is 1.0.

symmetry_tolerance

Obsolete. The default is 1.0e-5.

coordinate_tolerance

Obsolete. The default is 1.0e-7.

virtual RefSCDimension sc::IntMolecularCoor::dim () [virtual]

These implement the virtual functions inherited from MolecularCoor.

Implements sc::MolecularCoor.

virtual void sc::IntMolecularCoor::form_coordinates (int keep_variable = 0) [pure virtual]

Actually form the variable and constant internal coordinates from the simple internal coordinates.

Implemented in sc::SymmMolecularCoor, and sc::RedundMolecularCoor.

virtual void sc::IntMolecularCoor::init () [protected], [virtual]

This is called by the constructors of classes derived from IntMolecularCoor. It initialized the lists of simple internal coordinates, and then calls the form_coordinates() member.

Reimplemented in sc::SymmMolecularCoor.

int sc::IntMolecularCoor::nconstrained () [virtual]

Returns the number of constrained coordinates.

Reimplemented from sc::MolecularCoor.

virtual void sc::IntMolecularCoor::print (std::ostream & = ExEnv::out0()) const [virtual]

Print the coordinate.

Implements sc::MolecularCoor.

Reimplemented in sc::SymmMolecularCoor.

virtual void sc::IntMolecularCoor::print_simples (std::ostream & = ExEnv::out0()) const [virtual]

Implements sc::MolecularCoor.

void sc::IntMolecularCoor::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::MolecularCoor.

Reimplemented in sc::SymmMolecularCoor, and sc::RedundMolecularCoor.

virtual int sc::IntMolecularCoor::to_cartesian (const Ref< Molecule > &, const RefSCVector & internal) [virtual]

Implements sc::MolecularCoor.

virtual int sc::IntMolecularCoor::to_cartesian (RefSCVector & cartesian, RefSCVector & internal) [virtual]

Convert the internal coordinate gradients in ``internal'' to Cartesian coordinates and copy these Cartesian coordinate gradients to ``cartesian''. Only the variable internal coordinate gradients are transformed.

Implements sc::MolecularCoor.

virtual int sc::IntMolecularCoor::to_cartesian (RefSymmSCMatrix & cartesian, RefSymmSCMatrix & internal) [virtual]

Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy the result tocartesian''. Only the variable internal coordinate force constants are transformed.

Implements sc::MolecularCoor.

virtual int sc::IntMolecularCoor::to_internal (RefSCVector & internal) [virtual]

Fill in the vector ``internal'' with the current internal coordinates. Note that this member will update the values of the variable internal coordinates.

Implements sc::MolecularCoor.

virtual int sc::IntMolecularCoor::to_internal (RefSCVector & internal, RefSCVector & cartesian) [virtual]

Convert the Cartesian coordinate gradients in ``cartesian'' to internal coordinates and copy these internal coordinate gradients to ``internal''. Only the variable internal coordinate gradients are calculated.

Implements sc::MolecularCoor.

virtual int sc::IntMolecularCoor::to_internal (RefSymmSCMatrix & internal, RefSymmSCMatrix & cartesian) [virtual]

Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy the result tointernal''. Only the variable internal coordinate force constants are calculated.

Implements sc::MolecularCoor.