--- name: "sc_MolecularCoor" section: "3" platform: "linux" package: "libsc-doc" version: "2.3.1-22" release: "Debian 12 (Bookworm)" platforms: ["linux"] url: "https://new.carta.tech/sc_MolecularCoor" --- # sc\_MolecularCoor(3) The MolecularCoor abstract class describes the coordinate system used to describe a molecule. ## NAME sc::MolecularCoor - The **MolecularCoor** abstract class describes the coordinate system used to describe a molecule. ## SYNOPSIS `#include ` Inherits **sc::SavableState**. Inherited by **sc::CartMolecularCoor**, and **sc::IntMolecularCoor**. ### Public Member Functions **MolecularCoor** (**Ref**\< **Molecule** \> &)\ **MolecularCoor** (**StateIn** &)\ **MolecularCoor** (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. **RefSCDimension** **dim\_natom3** ()\ Returns a smart reference to an **SCDimension** equal to the number of atoms in the molecule times 3. **Ref**\< **Molecule** \> **molecule** () const\ Returns the molecule. virtual void **print** (std::ostream &=**ExEnv::out0**()) const =0\ Print the coordinate. virtual void **print\_simples** (std::ostream &=**ExEnv::out0**()) const =0\ virtual **RefSCDimension** **dim** ()=0\ Returns a smart reference to an **SCDimension** equal to the number of coordinates (be they Cartesian, internal, or whatever) that are being optimized. int **to\_cartesian** (const **RefSCVector** &internal)\ Given a set of displaced internal coordinates, update the cartesian coordinates of the **Molecule** contained herein. virtual int **to\_cartesian** (const **Ref**\< **Molecule** \> &mol, const **RefSCVector** &internal)=0\ virtual int **to\_internal** (**RefSCVector** &internal)=0\ Fill in the vector \`\`internal'' with the current internal coordinates. virtual int **to\_cartesian** (**RefSCVector** &cartesian, **RefSCVector** &internal)=0\ 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)=0\ Convert the Cartesian coordinate gradients in \`\`cartesian'' to internal coordinates and copy these internal coordinate gradients to \`\`internal''. virtual int **to\_cartesian** (**RefSymmSCMatrix** &cartesian, **RefSymmSCMatrix** &internal)=0\ Convert the internal coordinate Hessian `internal'' to Cartesian coordinates and copy the result to`cartesian''. virtual int **to\_internal** (**RefSymmSCMatrix** &internal, **RefSymmSCMatrix** &cartesian)=0\ Convert the Cartesian coordinate Hessian `cartesian'' to internal coordinates and copy the result to`internal''. virtual void **guess\_hessian** (**RefSymmSCMatrix** &hessian)=0\ Calculate an approximate hessian and place the result in \`\`hessian''. virtual **RefSymmSCMatrix** **inverse\_hessian** (**RefSymmSCMatrix** &)=0\ Given an Hessian, return the inverse of that hessian. virtual int **nconstrained** ()\ Returns the number of constrained coordinates. virtual **Ref**\< **NonlinearTransform** \> **change\_coordinates** ()\ When this is called, MoleculeCoor may select a new internal coordinate system and return a transform to it. **Ref**\< **SCMatrixKit** \> **matrixkit** () const\ ### Protected Attributes **Ref**\< **Molecule** \> **molecule\_**\ **RefSCDimension** **dnatom3\_**\ **Ref**\< **SCMatrixKit** \> **matrixkit\_**\ int **debug\_**\ ### Additional Inherited Members ## Detailed Description The **MolecularCoor** abstract class describes the coordinate system used to describe a molecule. It is used to convert a molecule's cartesian coordinates to and from this coordinate system. ## Constructor & Destructor Documentation ### sc::MolecularCoor::MolecularCoor (const Ref\< KeyVal \> &) The **KeyVal** constructor. - `molecule` A **Molecule** object. There is no default. - `debug` An integer which, if nonzero, will cause extra output. - `matrixkit` A **SCMatrixKit** object. It is usually unnecessary to give this keyword. - `natom3` An **SCDimension** object for the dimension of the vector of cartesian coordinates. It is usually unnecessary to give this keyword. ## Member Function Documentation ### virtual Ref\< NonlinearTransform \> sc::MolecularCoor::change\_coordinates ()` [virtual]` When this is called, MoleculeCoor may select a new internal coordinate system and return a transform to it. The default action is to not change anything and return an **IdentityTransform**. Reimplemented in **sc::SymmMolecularCoor**. ### virtual RefSCDimension sc::MolecularCoor::dim ()` [pure virtual]` Returns a smart reference to an **SCDimension** equal to the number of coordinates (be they Cartesian, internal, or whatever) that are being optimized. Implemented in **sc::IntMolecularCoor**, and **sc::CartMolecularCoor**. ### virtual void sc::MolecularCoor::guess\_hessian (RefSymmSCMatrix & hessian)` [pure virtual]` Calculate an approximate hessian and place the result in \`\`hessian''. Implemented in **sc::SymmMolecularCoor**, **sc::RedundMolecularCoor**, and **sc::CartMolecularCoor**. ### virtual RefSymmSCMatrix sc::MolecularCoor::inverse\_hessian (RefSymmSCMatrix &)` [pure virtual]` Given an Hessian, return the inverse of that hessian. For singular matrices this should return the generalized inverse. Implemented in **sc::SymmMolecularCoor**, **sc::RedundMolecularCoor**, and **sc::CartMolecularCoor**. ### virtual int sc::MolecularCoor::nconstrained ()` [virtual]` Returns the number of constrained coordinates. Reimplemented in **sc::IntMolecularCoor**. ### virtual void sc::MolecularCoor::print (std::ostream & = ExEnv::out0`()`) const` [pure virtual]` Print the coordinate. Reimplemented from **sc::DescribedClass**. Implemented in **sc::IntMolecularCoor**, **sc::SymmMolecularCoor**, and **sc::CartMolecularCoor**. ### void sc::MolecularCoor::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::SavableState**. Reimplemented in **sc::IntMolecularCoor**, **sc::SymmMolecularCoor**, **sc::RedundMolecularCoor**, and **sc::CartMolecularCoor**. ### int sc::MolecularCoor::to\_cartesian (const RefSCVector & internal) Given a set of displaced internal coordinates, update the cartesian coordinates of the **Molecule** contained herein. This function does not change the vector \`\`internal''. ### virtual int sc::MolecularCoor::to\_cartesian (RefSCVector & cartesian, RefSCVector & internal)` [pure 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. Implemented in **sc::IntMolecularCoor**, and **sc::CartMolecularCoor**. ### virtual int sc::MolecularCoor::to\_cartesian (RefSymmSCMatrix & cartesian, RefSymmSCMatrix & internal)` [pure virtual]` Convert the internal coordinate Hessian `internal'' to Cartesian coordinates and copy the result to`cartesian''. Only the variable internal coordinate force constants are transformed. Implemented in **sc::IntMolecularCoor**, and **sc::CartMolecularCoor**. ### virtual int sc::MolecularCoor::to\_internal (RefSCVector & internal)` [pure virtual]` Fill in the vector \`\`internal'' with the current internal coordinates. Note that this member will update the values of the variable internal coordinates. Implemented in **sc::IntMolecularCoor**, and **sc::CartMolecularCoor**. ### virtual int sc::MolecularCoor::to\_internal (RefSCVector & internal, RefSCVector & cartesian)` [pure 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. Implemented in **sc::IntMolecularCoor**, and **sc::CartMolecularCoor**. ### virtual int sc::MolecularCoor::to\_internal (RefSymmSCMatrix & internal, RefSymmSCMatrix & cartesian)` [pure virtual]` Convert the Cartesian coordinate Hessian `cartesian'' to internal coordinates and copy the result to`internal''. Only the variable internal coordinate force constants are calculated. Implemented in **sc::IntMolecularCoor**, and **sc::CartMolecularCoor**. ## Author Generated automatically by Doxygen for MPQC from the source code.