ProtoMol - an object-oriented component based framework for Molecular Dynamics simulations.
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ProtoMol::DihedralHMCIntegrator Member List

This is the complete list of members for ProtoMol::DihedralHMCIntegrator, including all inherited members.
addModifierAfterInitialize()ProtoMol::Integrator [inline, protected, virtual]
addModifierBeforeInitialize()ProtoMol::Integrator [inline, 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]
backward()ProtoMol::Integrator
bottom()ProtoMol::Integrator
bottom() const ProtoMol::Integrator
calculateForces()ProtoMol::StandardIntegrator [protected, virtual]
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]
DihedralHMCIntegrator()ProtoMol::DihedralHMCIntegrator
DihedralHMCIntegrator(int cycles, Real initialTemperature, bool randomCycLen, bool dihset, std::string dsetfile, bool angset, std::string asetfile, ForceGroup *overloadedForces, StandardIntegrator *nextIntegrator)ProtoMol::DihedralHMCIntegrator
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::DihedralHMCIntegrator [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::DihedralHMCIntegrator [inline, virtual]
getIntegratorDefinition() const ProtoMol::Integrator
getIntegratorDefinitionAll() const ProtoMol::Integrator
getParameters(std::vector< Parameter > &parameters) const ProtoMol::DihedralHMCIntegrator [virtual]
ProtoMol::StandardIntegrator::getParameters() const ProtoMol::Makeable
getParameterSize() const ProtoMol::DihedralHMCIntegrator [inline, virtual]
getScope() const ProtoMol::Integrator [inline, virtual]
getText() const ProtoMol::Makeable [inline, virtual]
getTimestep() const ProtoMol::MTSIntegrator [inline, virtual]
initialize(GenericTopology *topo, Vector3DBlock *positions, Vector3DBlock *velocities, ScalarStructure *energies)ProtoMol::DihedralHMCIntegrator [virtual]
initializeForces()ProtoMol::StandardIntegrator [protected, virtual]
initializeModifiers()ProtoMol::Integrator [protected]
Integrator()ProtoMol::Integrator
Integrator(ForceGroup *forceGroup)ProtoMol::Integrator
isforward() const ProtoMol::Integrator [inline]
keywordProtoMol::DihedralHMCIntegrator [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]
metropolisTest(Real newEnergy, Real oldEnergy, Real theTemperature, Real &acceptProb)ProtoMol::DihedralHMCIntegrator [protected]
MTSIntegrator()ProtoMol::MTSIntegrator
MTSIntegrator(int cycles, ForceGroup *overloadedForces, StandardIntegrator *nextIntegrator)ProtoMol::MTSIntegrator
myAnglesProtoMol::DihedralHMCIntegrator [protected]
myAnglesSetProtoMol::DihedralHMCIntegrator [protected]
myCycleLengthProtoMol::MTSIntegrator [protected]
myDhmcAnSetFileProtoMol::DihedralHMCIntegrator [protected]
myDhmcDiSetFileProtoMol::DihedralHMCIntegrator [protected]
myDihedralIndexProtoMol::DihedralHMCIntegrator [protected]
myDihedralsProtoMol::DihedralHMCIntegrator [protected]
myDihedralsSetProtoMol::DihedralHMCIntegrator [protected]
myEnergiesProtoMol::Integrator [protected]
myForcesProtoMol::Integrator [protected]
myForcesToEvaluateProtoMol::Integrator [protected]
myForwardProtoMol::Integrator [protected]
myInitialTemperatureProtoMol::DihedralHMCIntegrator [protected]
myNextIntegratorProtoMol::MTSIntegrator [protected]
myOldEnergiesProtoMol::DihedralHMCIntegrator [protected]
myOldPositionsProtoMol::DihedralHMCIntegrator [protected]
myOldVelocitiesProtoMol::DihedralHMCIntegrator [protected]
myPositionsProtoMol::Integrator [protected]
myPreviousIntegratorProtoMol::StandardIntegrator [protected]
myRandomCycLenProtoMol::DihedralHMCIntegrator [protected]
myTopoProtoMol::Integrator [protected]
myVelocitiesProtoMol::Integrator [protected]
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
restoreValues()ProtoMol::DihedralHMCIntegrator [protected]
run(int numTimesteps)ProtoMol::DihedralHMCIntegrator [virtual]
saveValues()ProtoMol::DihedralHMCIntegrator [protected]
scopeProtoMol::Integrator [static]
setAlias(const std::string &id)ProtoMol::Makeable
size() const ProtoMol::Integrator [inline]
StandardIntegrator()ProtoMol::StandardIntegrator
StandardIntegrator(ForceGroup *forceGroup)ProtoMol::StandardIntegrator
top()ProtoMol::Integrator
top() const ProtoMol::Integrator
uncache()ProtoMol::Integrator
~DihedralHMCIntegrator()ProtoMol::DihedralHMCIntegrator [virtual]
~Integrator()ProtoMol::Integrator [virtual]
~Makeable()ProtoMol::Makeable [inline, virtual]
~MTSIntegrator()ProtoMol::MTSIntegrator [virtual]
Last update: . GNU GENERAL PUBLIC LICENSE, copyrighted by the University of Notre Dame and the University of Bergen, Norway.