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OpenMD::MolecularRestraint Class Reference
MolecularRestraint is the restraint (both positional and orientational) for the configuration of a flexible Molecule relative to some reference structure for the same Molecule. More...
#include <MolecularRestraint.hpp>
Inheritance diagram for OpenMD::MolecularRestraint:
Public Member Functions | |
| void | setReferenceStructure (std::vector< Vector3d > ref, Vector3d refCom) |
| void | calcForce (std::vector< Vector3d > struc, Vector3d molCom) |
| std::vector< Vector3d > | getRestraintForces () |
| Public Member Functions inherited from OpenMD::Restraint | |
| void | calcForce () |
| void | setReferenceStructure () |
| RealType | getUnscaledPotential () |
| RealType | getPotential () |
| void | setRestraintName (std::string name) |
| std::string | getRestraintName () |
| int | getRestraintType () |
| Returns the restraint type. | |
| void | setRestraintType (int restType) |
| Sets the restraint type. | |
| void | setScaleFactor (RealType sf) |
| void | setDisplacementForceConstant (RealType kDisp) |
| void | setDisplacementXForceConstant (RealType kDisp) |
| void | setDisplacementYForceConstant (RealType kDisp) |
| void | setDisplacementZForceConstant (RealType kDisp) |
| void | setAbsoluteForceConstant (RealType kAbs) |
| void | setTwistForceConstant (RealType kTwist) |
| void | setSwingXForceConstant (RealType kSwingX) |
| void | setSwingYForceConstant (RealType kSwingY) |
| void | setAbsolutePositionZ (RealType z0) |
| void | setRestrainedTwistAngle (RealType twist0) |
| void | setRestrainedSwingXAngle (RealType swingX0) |
| void | setRestrainedSwingYAngle (RealType swingY0) |
| void | setPrintRestraint (bool printRest) |
| RealType | getDisplacementForceConstant () |
| RealType | getDisplacementXForceConstant () |
| RealType | getDisplacementYForceConstant () |
| RealType | getDisplacementZForceConstant () |
| RealType | getAbsoluteForceConstant () |
| RealType | getAbsolutePositionZ () |
| RealType | getTwistForceConstant () |
| RealType | getSwingXForceConstant () |
| RealType | getSwingYForceConstant () |
| RealType | getRestrainedTwistAngle () |
| RealType | getRestrainedSwingXAngle () |
| RealType | getRestrainedSwingYAngle () |
| std::map< int, RealPair > | getRestraintInfo () |
| bool | getPrintRestraint () |
Additional Inherited Members | |
| Public Types inherited from OpenMD::Restraint | |
| enum | { rtDisplacement = 1 , rtDisplacementX = 2 , rtDisplacementY = 4 , rtDisplacementZ = 8 , rtAbsoluteZ = 16 , rtTwist = 32 , rtSwingX = 64 , rtSwingY = 128 } |
| using | RealPair = std::pair<RealType, RealType> |
| Protected Attributes inherited from OpenMD::Restraint | |
| RealType | scaleFactor_ |
| RealType | kDisp_ |
| RealType | kDispX_ |
| RealType | kDispY_ |
| RealType | kDispZ_ |
| RealType | kAbs_ |
| RealType | kTwist_ |
| RealType | kSwingX_ |
| RealType | kSwingY_ |
| RealType | pot_ |
| RealType | twist0_ |
| RealType | swingX0_ |
| RealType | swingY0_ |
| RealType | posZ0_ |
| bool | printRest_ |
| int | restType_ |
| std::string | restName_ |
| std::map< int, RealPair > | restInfo_ |
Detailed Description
MolecularRestraint is the restraint (both positional and orientational) for the configuration of a flexible Molecule relative to some reference structure for the same Molecule.
The angles that define the deflection away from the reference structure are the Euler angles taken from the rotation matrix that gives the lowest root mean square deviation (RMSD), while the displacement of the molecule is simply the displacement of the center of mass relative to the reference structure.
Definition at line 69 of file MolecularRestraint.hpp.
Constructor & Destructor Documentation
◆ MolecularRestraint()
|
inline |
Definition at line 71 of file MolecularRestraint.hpp.
Member Function Documentation
◆ calcForce()
| void OpenMD::MolecularRestraint::calcForce | ( | std::vector< Vector3d > | struc, |
| Vector3d | molCom ) |
dVdtwist = kTwist_ * sin(dTwist) ; p = kTwist_ * (1.0 - cos(dTwist) ) ;
dVdswingX = kSwingX_ * 2.0 * sin(2.0 * dSwingX); p = kSwingX_ * (1.0 - cos(2.0 * dSwingX));
dVdswingY = kSwingY_ * 2.0 * sin(2.0 * dSwingY); p = kSwingY_ * (1.0 - cos(2.0 * dSwingY));
Definition at line 59 of file MolecularRestraint.cpp.
References OpenMD::cross(), OpenMD::SquareMatrix3< Real >::determinant(), OpenMD::dot(), JAMA::SVD< Real >::getSingularValues(), OpenMD::Vector< Real, Dim >::length(), OpenMD::SquareMatrix3< Real >::toQuaternion(), OpenMD::Vector3< Real >::x(), OpenMD::Vector3< Real >::y(), and OpenMD::Vector3< Real >::z().
◆ getRestraintForces()
|
inline |
Definition at line 89 of file MolecularRestraint.hpp.
◆ setReferenceStructure()
|
inline |
Definition at line 73 of file MolecularRestraint.hpp.
The documentation for this class was generated from the following files:
- restraints/MolecularRestraint.hpp
- restraints/MolecularRestraint.cpp
