Ubuntu Manpage: sc::IntMolecularCoor - The IntMolecularCoor abstract class describes a molecule's

NAME

       sc::IntMolecularCoor - The IntMolecularCoor abstract class describes a molecule's
       coordinates in terms of internal coordinates.

SYNOPSIS

       #include <coor.h>

       Inherits sc::MolecularCoor.

       Inherited by sc::RedundMolecularCoor, and sc::SymmMolecularCoor.

   Public Member Functions
       IntMolecularCoor (StateIn &)
       IntMolecularCoor (Ref< Molecule > &mol)
       IntMolecularCoor (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.
       virtual void form_coordinates (int keep_variable=0)=0
           Actually form the variable and constant internal coordinates from the simple internal
           coordinates.
       virtual int all_to_cartesian (const Ref< Molecule > &, RefSCVector &internal)
           Like to_cartesians(), except all internal coordinates are considered, not just the
           variable ones.
       virtual int all_to_internal (const Ref< Molecule > &, RefSCVector &internal)
           Like to_internal(), except all internal coordinates are considered, not just the
           variable ones.
       virtual RefSCDimension dim ()
           These implement the virtual functions inherited from MolecularCoor.
       virtual int to_cartesian (const Ref< Molecule > &, const RefSCVector &internal)
       virtual int to_internal (RefSCVector &internal)
           Fill in the vector ``internal'' with the current internal coordinates.
       virtual int to_cartesian (RefSCVector &cartesian, RefSCVector &internal)
           Convert the internal coordinate gradients in ``internal'' to Cartesian coordinates and
           copy these Cartesian coordinate gradients to ``cartesian''.
       virtual int to_internal (RefSCVector &internal, RefSCVector &cartesian)
           Convert the Cartesian coordinate gradients in ``cartesian'' to internal coordinates
           and copy these internal coordinate gradients to ``internal''.
       virtual int to_cartesian (RefSymmSCMatrix &cart, RefSymmSCMatrix &internal)
           Convert the internal coordinate Hessian internal'' to Cartesian coordinates and copy
           the result tocartesian''.
       virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart)
           Convert the Cartesian coordinate Hessian cartesian'' to internal coordinates and copy
           the result tointernal''.
       virtual void print (std::ostream &=ExEnv::out0()) const
           Print the coordinate.
       virtual void print_simples (std::ostream &=ExEnv::out0()) const
       virtual void print_variable (std::ostream &=ExEnv::out0()) const
       virtual void print_constant (std::ostream &=ExEnv::out0()) const
       int nconstrained ()
           Returns the number of constrained coordinates.

   Protected Member Functions
       void form_K_matrix (RefSCDimension &dredundant, RefSCDimension &dfixed, RefSCMatrix &K,
           int *&is_totally_symmetric)
       virtual void init ()
           This is called by the constructors of classes derived from IntMolecularCoor.
       virtual void new_coords ()
           Allocates memory for the SetIntCoor's used to store the simple and internal
           coordinates.
       virtual void read_keyval (const Ref< KeyVal > &)
           Reads the KeyVal input.

   Protected Attributes
       Ref< IntCoorGen > generator_
       RefSCDimension dim_
       RefSCDimension dvc_
       Ref< SetIntCoor > variable_
       Ref< SetIntCoor > constant_
       Ref< SetIntCoor > fixed_
       Ref< SetIntCoor > watched_
       Ref< IntCoor > followed_
       Ref< SetIntCoor > bonds_
       Ref< SetIntCoor > bends_
       Ref< SetIntCoor > tors_
       Ref< SetIntCoor > outs_
       Ref< SetIntCoor > extras_
       Ref< SetIntCoor > all_
       int update_bmat_
       int only_totally_symmetric_
       double symmetry_tolerance_
       double simple_tolerance_
       double coordinate_tolerance_
       double cartesian_tolerance_
       double scale_bonds_
       double scale_bends_
       double scale_tors_
       double scale_outs_
       int nextra_bonds_
       int * extra_bonds_
       int given_fixed_values_
       int decouple_bonds_
       int decouple_bends_
       int max_update_steps_
       double max_update_disp_
       int form_print_simples_
       int form_print_variable_
       int form_print_constant_
       int form_print_molecule_

   Additional Inherited Members

Detailed Description

       The IntMolecularCoor abstract class describes a molecule's coordinates in terms of
       internal coordinates.

Constructor & Destructor Documentation

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 $iimes 2$ 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.

Member Function Documentation

   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.

   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::RedundMolecularCoor, and sc::SymmMolecularCoor.

   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.

Author

       Generated automatically by Doxygen for MPQC from the source code.