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

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Version 2.3.1                                    Sun Oct 4 2020                          sc::IntMolecularCoor(3)

Constructor & Destructor Documentation

sc::IntMolecularCoor::IntMolecularCoor(constRef<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.

Detailed Description

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

Member Function Documentation

virtualvoidsc::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.

   voidsc::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.

   virtualintsc::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.

   virtualintsc::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.

   virtualintsc::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.

   virtualintsc::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.

   virtualintsc::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.

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.

   PublicMemberFunctionsIntMolecularCoor (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 RefSCDimensiondim ()
           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.

   ProtectedMemberFunctions
       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.

   ProtectedAttributesRef< IntCoorGen > generator_RefSCDimensiondim_RefSCDimensiondvc_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_AdditionalInheritedMembers