| addModifierAfterInitialize() | ProtoMol::Integrator | [inline, protected, virtual] |
| addModifierBeforeInitialize() | ProtoMol::MOLLYIntegrator | [protected, virtual] |
| adjustAlias(T *obj) const | ProtoMol::Makeable | [inline, protected] |
| adjustWithDefaultParameters(std::vector< Value > &values, const Configuration *) const | ProtoMol::Makeable | [inline, virtual] |
| adoptMediForceModifier(Modifier *modifier) | ProtoMol::Integrator | |
| adoptPostDriftOrNextModifier(Modifier *modifier) | ProtoMol::Integrator | |
| adoptPostForceModifier(Modifier *modifier) | ProtoMol::Integrator | |
| adoptPostStepModifier(Modifier *modifier) | ProtoMol::Integrator | |
| adoptPreDriftOrNextModifier(Modifier *modifier) | ProtoMol::Integrator | |
| adoptPreForceModifier(Modifier *modifier) | ProtoMol::Integrator | |
| adoptPreStepModifier(Modifier *modifier) | ProtoMol::Integrator | |
| anyMediForceModify() const | ProtoMol::Integrator | [inline, protected] |
| anyPostDriftOrNextModify() const | ProtoMol::Integrator | [inline, protected] |
| anyPostForceModify() const | ProtoMol::Integrator | [inline, protected] |
| anyPostStepModify() const | ProtoMol::Integrator | [inline, protected] |
| anyPreDriftOrNextModify() const | ProtoMol::Integrator | [inline, protected] |
| anyPreForceModify() const | ProtoMol::Integrator | [inline, protected] |
| anyPreStepModify() const | ProtoMol::Integrator | [inline, protected] |
| averagingPositions() | ProtoMol::MOLLYIntegrator | |
| backward() | ProtoMol::Integrator | |
| bottom() | ProtoMol::Integrator | |
| bottom() const | ProtoMol::Integrator | |
| BSplineMOLLYIntegrator() | ProtoMol::BSplineMOLLYIntegrator | |
| BSplineMOLLYIntegrator(int cycles, const BSplineType &typeOfBSpline, Real mollyStepsize, ForceGroup *overloadedForces, StandardIntegrator *nextIntegrator) | ProtoMol::BSplineMOLLYIntegrator | |
| calcHessiansBondsAnglesHBonds() | ProtoMol::BSplineMOLLYIntegrator | [private] |
| calcMOLLYForcesHalfKickOneDrift() | ProtoMol::BSplineMOLLYIntegrator | [private] |
| calcMOLLYForcesOneKickOneDrift() | ProtoMol::BSplineMOLLYIntegrator | [private] |
| calculateForces() | ProtoMol::StandardIntegrator | [protected, virtual] |
| calculateMOLLYForcesBonded() | ProtoMol::BSplineMOLLYIntegrator | [private] |
| calculateMOLLYForcesHBonded() | ProtoMol::BSplineMOLLYIntegrator | [private] |
| checkParameters(std::string &errMsg, const std::vector< Value > &values) const | ProtoMol::Makeable | |
| checkParameters(const std::vector< Value > &values) const | ProtoMol::Makeable | |
| checkParameterTypes(const std::vector< Value > &values) const | ProtoMol::Makeable | |
| copy(T *obj) | ProtoMol::Makeable | [inline, static] |
| createRattleModifier(Real eps, int maxIter) | ProtoMol::Integrator | [virtual] |
| createShakeModifier(Real eps, int maxIter) | ProtoMol::Integrator | [virtual] |
| deleteExternalModifiers() | ProtoMol::Integrator | |
| deleteInternalModifiers() | ProtoMol::Integrator | [protected] |
| doAveragingPositions() | ProtoMol::BSplineMOLLYIntegrator | [private, virtual] |
| doDriftOrNextIntegrator() | ProtoMol::MTSIntegrator | [protected, virtual] |
| doHalfKick() | ProtoMol::StandardIntegrator | [protected, virtual] |
| doKick() | ProtoMol::StandardIntegrator | [protected, virtual] |
| doMake(std::string &errMsg, const std::vector< Value > &values, ForceGroup *fg, StandardIntegrator *nextIntegrator) const | ProtoMol::BSplineMOLLYIntegrator | [private, virtual] |
| doMollification(Vector3DBlock *preprocessedPositions) | ProtoMol::BSplineMOLLYIntegrator | [private, virtual] |
| doUncache() | ProtoMol::BSplineMOLLYIntegrator | [private, virtual] |
| forward() | ProtoMol::Integrator | |
| getAlias() const | ProtoMol::Makeable | |
| getBottomTimestep() const | ProtoMol::Integrator | [inline] |
| getDefinition() const | ProtoMol::Makeable | [virtual] |
| getForceGroup() const | ProtoMol::Integrator | [inline] |
| getForces() const | ProtoMol::Integrator | [inline] |
| getId() const | ProtoMol::Makeable | |
| getIdNoAlias() const | ProtoMol::BSplineMOLLYIntegrator | [inline, virtual] |
| getIntegratorDefinition() const | ProtoMol::Integrator | |
| getIntegratorDefinitionAll() const | ProtoMol::Integrator | |
| getParameters(std::vector< Parameter > ¶meters) const | ProtoMol::BSplineMOLLYIntegrator | [virtual] |
| ProtoMol::StandardIntegrator::getParameters() const | ProtoMol::Makeable | |
| getParameterSize() const | ProtoMol::BSplineMOLLYIntegrator | [inline, virtual] |
| getScope() const | ProtoMol::Integrator | [inline, virtual] |
| getText() const | ProtoMol::Makeable | [inline, virtual] |
| getTimestep() const | ProtoMol::MTSIntegrator | [inline, virtual] |
| init() | ProtoMol::BSplineMOLLYIntegrator | [private] |
| initialize(GenericTopology *topo, Vector3DBlock *positions, Vector3DBlock *velocities, ScalarStructure *energies) | ProtoMol::BSplineMOLLYIntegrator | [virtual] |
| initializeForces() | ProtoMol::StandardIntegrator | [protected, virtual] |
| initializeModifiers() | ProtoMol::Integrator | [protected] |
| Integrator() | ProtoMol::Integrator | |
| Integrator(ForceGroup *forceGroup) | ProtoMol::Integrator | |
| isforward() const | ProtoMol::Integrator | [inline] |
| keyword | ProtoMol::BSplineMOLLYIntegrator | [static] |
| level() const | ProtoMol::Integrator | |
| make(std::string &errMsg, const std::vector< Value > &values, ForceGroup *fg, StandardIntegrator *nextIntegrator) const | ProtoMol::MTSIntegrator | |
| mediForceModify() | ProtoMol::Integrator | [protected] |
| mollification() | ProtoMol::MOLLYIntegrator | |
| MOLLYIntegrator() | ProtoMol::MOLLYIntegrator | |
| MOLLYIntegrator(int cycles, ForceGroup *overloadedForces, StandardIntegrator *nextIntegrator) | ProtoMol::MOLLYIntegrator | |
| MTSIntegrator() | ProtoMol::MTSIntegrator | |
| MTSIntegrator(int cycles, ForceGroup *overloadedForces, StandardIntegrator *nextIntegrator) | ProtoMol::MTSIntegrator | |
| myAngle | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myAngleFilter | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myAngleIndexes | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myB | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myBond | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myBxAngle | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myCached | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myCoulomb | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myCycleLength | ProtoMol::MTSIntegrator | [protected] |
| myEnergies | ProtoMol::Integrator | [protected] |
| myForces | ProtoMol::Integrator | [protected] |
| myForcesToEvaluate | ProtoMol::Integrator | [protected] |
| myForward | ProtoMol::Integrator | [protected] |
| myHBondForces | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myLennardJones | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myMOLLYEnergies | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myMOLLYForces | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myMOLLYForcesBonded | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myMOLLYForcesHBonded | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myMOLLYPositions | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myMOLLYStepsize | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myMOLLYStepsizeP | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myMOLLYStepsizeSquare | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myMOLLYVelocities | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myNextIntegrator | ProtoMol::MTSIntegrator | [protected] |
| myNumIter | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myPositions | ProtoMol::Integrator | [protected] |
| myPreviousIntegrator | ProtoMol::StandardIntegrator | [protected] |
| myPxAngle | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myTopo | ProtoMol::Integrator | [protected] |
| myTypeOfBSpline | ProtoMol::BSplineMOLLYIntegrator | [private] |
| myVelocities | ProtoMol::Integrator | [protected] |
| myXxAngle | ProtoMol::BSplineMOLLYIntegrator | [private] |
| next() | ProtoMol::MTSIntegrator | [inline, virtual] |
| next() const | ProtoMol::MTSIntegrator | [inline, virtual] |
| postDriftOrNextModify() | ProtoMol::Integrator | [protected] |
| postForceModify() | ProtoMol::Integrator | [protected] |
| postStepModify() | ProtoMol::Integrator | [protected] |
| preDriftOrNextModify() | ProtoMol::Integrator | [protected] |
| preForceModify() | ProtoMol::Integrator | [protected] |
| preStepModify() | ProtoMol::Integrator | [protected] |
| previous() | ProtoMol::StandardIntegrator | [virtual] |
| previous() const | ProtoMol::StandardIntegrator | [virtual] |
| removeModifier(const Modifier *modifier) | ProtoMol::Integrator | |
| run(int numTimesteps) | ProtoMol::StandardIntegrator | [virtual] |
| scope | ProtoMol::Integrator | [static] |
| setAlias(const std::string &id) | ProtoMol::Makeable | |
| setMyNumIterMOLLYStepsize() | ProtoMol::BSplineMOLLYIntegrator | [private] |
| size() const | ProtoMol::Integrator | [inline] |
| StandardIntegrator() | ProtoMol::StandardIntegrator | |
| StandardIntegrator(ForceGroup *forceGroup) | ProtoMol::StandardIntegrator | |
| top() | ProtoMol::Integrator | |
| top() const | ProtoMol::Integrator | |
| uncache() | ProtoMol::Integrator | |
| updateB_Bx() | ProtoMol::BSplineMOLLYIntegrator | [private] |
| updateB_Bx_Px_for1Kick() | ProtoMol::BSplineMOLLYIntegrator | [private] |
| updateB_Bx_Px_for1stHalfKick() | ProtoMol::BSplineMOLLYIntegrator | [private] |
| updateXx() | ProtoMol::BSplineMOLLYIntegrator | [private] |
| ~BSplineMOLLYIntegrator() | ProtoMol::BSplineMOLLYIntegrator | [virtual] |
| ~Integrator() | ProtoMol::Integrator | [virtual] |
| ~Makeable() | ProtoMol::Makeable | [inline, virtual] |
| ~MOLLYIntegrator() | ProtoMol::MOLLYIntegrator | [virtual] |
| ~MTSIntegrator() | ProtoMol::MTSIntegrator | [virtual] |
Last update: . GNU GENERAL PUBLIC LICENSE, copyrighted by the University of Notre Dame and the University of
Bergen, Norway.
