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

This is the complete list of members for ProtoMol::PaulTrapIntegrator, including all inherited members.
addModifierAfterInitialize()ProtoMol::STSIntegrator [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::STSIntegrator [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]
doDrift()ProtoMol::PaulTrapIntegrator [protected, virtual]
doDriftOrNextIntegrator()ProtoMol::STSIntegrator [protected, virtual]
doHalfKick()ProtoMol::StandardIntegrator [protected, virtual]
doKick()ProtoMol::StandardIntegrator [protected, virtual]
doMake(std::string &errMsg, const std::vector< Value > &values, ForceGroup *fg) const ProtoMol::PaulTrapIntegrator [private, virtual]
doUncache()ProtoMol::PaulTrapIntegrator [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::PaulTrapIntegrator [inline, virtual]
getIntegratorDefinition() const ProtoMol::Integrator
getIntegratorDefinitionAll() const ProtoMol::Integrator
getParameters(std::vector< Parameter > &parameters) const ProtoMol::PaulTrapIntegrator [virtual]
ProtoMol::StandardIntegrator::getParameters() const ProtoMol::Makeable
getParameterSize() const ProtoMol::PaulTrapIntegrator [inline, virtual]
getScope() const ProtoMol::Integrator [inline, virtual]
getText() const ProtoMol::Makeable [inline, virtual]
getTimestep() const ProtoMol::STSIntegrator [inline, virtual]
init()ProtoMol::PaulTrapIntegrator [private]
initialize(GenericTopology *topo, Vector3DBlock *positions, Vector3DBlock *velocities, ScalarStructure *energies)ProtoMol::PaulTrapIntegrator [virtual]
initializeForces()ProtoMol::StandardIntegrator [protected, virtual]
initializeModifiers()ProtoMol::Integrator [protected]
Integrator()ProtoMol::Integrator
Integrator(ForceGroup *forceGroup)ProtoMol::Integrator
isforward() const ProtoMol::Integrator [inline]
keywordProtoMol::PaulTrapIntegrator [static]
level() const ProtoMol::Integrator
make(std::string &errMsg, const std::vector< Value > &values, ForceGroup *fg) const ProtoMol::STSIntegrator
mediForceModify()ProtoMol::Integrator [protected]
myBathPositionProtoMol::PaulTrapIntegrator [private]
myBathVelocityProtoMol::PaulTrapIntegrator [private]
myCachedProtoMol::PaulTrapIntegrator [private]
myCountProtoMol::PaulTrapIntegrator [private]
myEnergiesProtoMol::Integrator [protected]
myForcesProtoMol::Integrator [protected]
myForcesToEvaluateProtoMol::Integrator [protected]
myForwardProtoMol::Integrator [protected]
myKeepProtoMol::PaulTrapIntegrator [private]
myLayerProtoMol::PaulTrapIntegrator [private]
myPartProtoMol::PaulTrapIntegrator [private]
myPartRealProtoMol::PaulTrapIntegrator [private]
myPositionsProtoMol::Integrator [protected]
myPreviousIntegratorProtoMol::StandardIntegrator [protected]
myRemoveAngularMotionProtoMol::PaulTrapIntegrator [private]
myRemoveCommonMotionProtoMol::PaulTrapIntegrator [private]
myTProtoMol::PaulTrapIntegrator [private]
myTemperatureProtoMol::PaulTrapIntegrator [private]
myThermalInertiaProtoMol::PaulTrapIntegrator [private]
myThermostatTypeProtoMol::PaulTrapIntegrator [private]
myTimeProtoMol::PaulTrapIntegrator [private]
myTopoProtoMol::Integrator [protected]
myVelocitiesProtoMol::Integrator [protected]
next()ProtoMol::STSIntegrator [inline, virtual]
next() const ProtoMol::STSIntegrator [inline, virtual]
PaulTrapIntegrator()ProtoMol::PaulTrapIntegrator
PaulTrapIntegrator(Real timestep, Real temperature, Real thermalInertia, Real bathPosition, Real bathVelocity, ThermostatType nvttype, Real part, const std::vector< Real > &time, const std::vector< Real > &t, ForceGroup *overloadedForces)ProtoMol::PaulTrapIntegrator
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]
scopeProtoMol::Integrator [static]
setAlias(const std::string &id)ProtoMol::Makeable
size() const ProtoMol::Integrator [inline]
StandardIntegrator()ProtoMol::StandardIntegrator
StandardIntegrator(ForceGroup *forceGroup)ProtoMol::StandardIntegrator
STSIntegrator()ProtoMol::STSIntegrator
STSIntegrator(Real timestep, ForceGroup *overloadedForces)ProtoMol::STSIntegrator
top()ProtoMol::Integrator
top() const ProtoMol::Integrator
uncache()ProtoMol::Integrator
~Integrator()ProtoMol::Integrator [virtual]
~Makeable()ProtoMol::Makeable [inline, virtual]
Last update: . GNU GENERAL PUBLIC LICENSE, copyrighted by the University of Notre Dame and the University of Bergen, Norway.