sc::IntMolecularCoor(3)

📦
version 2.3.1 · 5 versions
, in ubuntu jammy

🦋 sc::IntMolecularCoor(3) — internal coords are the moment 🦋

okay so this is the MPQC manual page for sc::IntMolecularCoor(3), and we're folding the manual name right in here at the top so it doesn't look like a dusty old header line, yk? This is part 1, and it's giving "abstract base class with a lot of options." No cap. Let's go. 💅

✨ NAME ✨

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

🌸 SYNOPSIS 🌸

#include <coor.h>
  • Inherits sc::MolecularCoor.
  • Inherited by sc::RedundMolecularCoor, and sc::SymmMolecularCoor.

🎀 Public Member Functions 🎀

  • IntMolecularCoor (StateIn &) — constructor from a StateIn. No extra blurb on this page, bestie.
  • IntMolecularCoor (Ref< Molecule > &mol) — constructor from a Ref< Molecule > &mol. Just the signature here.
  • IntMolecularCoor (const Ref< KeyVal > &) — The KeyVal constructor. Full deets are down in the constructor section, iykyk.
  • 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) — signature only on this page, no extra description.
  • 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 in internal to Cartesian coordinates and copy the result to cart.
  • virtual int to_internal (RefSymmSCMatrix &internal, RefSymmSCMatrix &cart) — Convert the Cartesian coordinate Hessian in cart to internal coordinates and copy the result to internal.
  • virtual void print (std::ostream &=ExEnv::out0()) const — Print the coordinate.
  • virtual void print_simples (std::ostream &=ExEnv::out0()) const — signature only, no extra description on this page.
  • virtual void print_variable (std::ostream &=ExEnv::out0()) const — signature only, no extra description on this page.
  • virtual void print_constant (std::ostream &=ExEnv::out0()) const — signature only, no extra description on this page.
  • 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) — signature only here, no extra blurb.
  • 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 🫶

The page has this heading, but no additional member list is shown here. That's the whole tea. 🍓

🌈 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.
These next ones are marked Obsolete in the original, bestie—so don't build your whole personality on them, but they're still part of the page. 💀
  • 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] — okay so this one is called by the constructors of classes derived from IntMolecularCoor. It gets the lists of simple internal coordinates initialized, and then it calls the form_coordinates() member. Reimplemented in sc::SymmMolecularCoor. ✨
  • void sc::IntMolecularCoor::save_data_state (StateOut &) [virtual] — bestie, this saves 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] — converts the internal coordinate gradients in internal to Cartesian coordinates, then copies those 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] — converts the internal coordinate Hessian internal to Cartesian coordinates and copies the result to cartesian. Only the variable internal coordinate force constants are transformed. Implements sc::MolecularCoor. 🦋
  • virtual int sc::IntMolecularCoor::to_internal (RefSCVector & internal) [virtual] — fills 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] — converts the Cartesian coordinate gradients in cartesian to internal coordinates and copies those 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] — converts the Cartesian coordinate Hessian cartesian to internal coordinates and copies the result to internal. Only the variable internal coordinate force constants are calculated. Implements sc::MolecularCoor. 👑

🎀 AUTHOR 🎀

Okay credits time, bestie 🫶: this page was generated automatically by Doxygen for MPQC from the source code. Version 2.3.1, dated Sun Oct 4 2020. Iconic. 💖✨

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