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Scine::Swoose
2.1.0
This is the SCINE module Swoose.
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Scine::Swoose
2.1.0
This is the SCINE module Swoose.
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LennardJonesEvaluator LennardJonesEvaluator.h. More...
#include <LennardJonesEvaluator.h>
Public Member Functions | |
| LennardJonesEvaluator (const Utils::PositionCollection &positions) | |
| Constructor from positions. | |
| double | evaluate (Utils::DerivativeCollection &derivatives) |
| This function evaluates and returns the energy for all LJ interactions and updates the derivatives. | |
| void | setCutOffRadius (std::shared_ptr< double > cutOffRadius) |
| Set the cut off radius for the electrostatic interactions. More... | |
| void | setParameters (std::shared_ptr< GaffParameters > parameters) |
| Setter for the parameter object. More... | |
| void | setAtomTypesHolder (std::shared_ptr< AtomTypesHolder > atomTypesHolder) |
| Setter for the atom types. More... | |
 Public Member Functions inherited from Scine::MolecularMechanics::InteractionExclusion | |
| InteractionExclusion (unsigned int nAtoms) | |
| Constructor. More... | |
| void | setExclusions (const Eigen::SparseMatrix< bool > &excludedPairs) |
| Setter for the exclusion matrix. More... | |
| void | addExclusions (const Eigen::SparseMatrix< bool > &excludedPairs) |
| Add new exclusions. More... | |
| void | addExclusions (const IndexedStructuralTopology &topology) |
| Add the exclusions encoded in the topology, e.g., 1-3 and 1-2 interactions. More... | |
| const Eigen::SparseMatrix< bool > & | getExclusions () |
| Getter for the exclusions. More... | |
| void | resetExclusions (unsigned int nAtoms) |
| Resize the exclusion matrix to the given number of atoms and remove all existing exlcuions. More... | |
| Public Member Functions inherited from Scine::MolecularMechanics::ScaledInteractions | |
| ScaledInteractions (unsigned int nAtoms) | |
| Constructor. More... | |
| void | setScaledInteractionPairs (const Eigen::SparseMatrix< bool > &pairs) |
| Setter for the scaling information. More... | |
| void | addScaledInteractionPairs (const Eigen::SparseMatrix< bool > &pairs) |
| Add new scaled interactions. More... | |
| void | addScaledInteractionPairs (const IndexedStructuralTopology &topology) |
| Add new scaled interactions from the topology, e.g., 1-4 interactions. More... | |
| const Eigen::SparseMatrix< bool > & | getScaledInteractionPairs () |
| Getter for scaling information. More... | |
| void | setInteractionScalingFactor (const double &factor) |
| Setter for the interaction scaling factor. More... | |
| double | getInteractionScalingFactor () |
| Getter for the interaction scaling factor. More... | |
| void | resetScaledInteractions (unsigned int nAtoms) |
| Resize the scaling information matrix to the nem number of atoms. More... | |
Friends | |
| class | Qmmm::InteractionTermEliminator |
LennardJonesEvaluator LennardJonesEvaluator.h.
This class evaluates the overall energy and derivatives of Lennard-Jones interactions.
| void Scine::MolecularMechanics::LennardJonesEvaluator::setAtomTypesHolder | ( | std::shared_ptr< AtomTypesHolder > | atomTypesHolder | ) |
Setter for the atom types.
| atomTypesHolder | The atom tyoes. |
| void Scine::MolecularMechanics::LennardJonesEvaluator::setCutOffRadius | ( | std::shared_ptr< double > | cutOffRadius | ) |
Set the cut off radius for the electrostatic interactions.
| cutOffRadius | The cut of radius in atomic units. |
| void Scine::MolecularMechanics::LennardJonesEvaluator::setParameters | ( | std::shared_ptr< GaffParameters > | parameters | ) |
Setter for the parameter object.
| parameters | The parameters. |
1.8.5 
