sc::IntMolecularCoor(3) MPQC sc::IntMolecularCoor(3)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 int sc::IntMolecularCoor::all_to_cartesian (const Ref< Molecule >
&, RefSCVector & internal) [virtual]
Like to_cartesians(), except all internal coordinates are considered,
not just the variable ones.
virtual int sc::IntMolecularCoor::all_to_internal (const Ref< Molecule > &,
RefSCVector & internal) [virtual]
Like to_internal(), except all internal coordinates are considered, not
just the variable ones.
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::RedundMolecularCoor, and sc::SymmMolecularCoor.
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.
virtual void sc::IntMolecularCoor::new_coords () [protected], [virtual]
Allocates memory for the SetIntCoor's used to store the simple and
internal coordinates.
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.
Version 2.3.1 Fri Feb 19 2016 sc::IntMolecularCoor(3)
