Index

A

addForce() (espressopp.integrator.LBInit.espressopp.integrator.LBInit method) angle_between_vectors() (in module espressopp.external.transformations) Arcball (class in espressopp.external.transformations)

arcball_constrain_to_axis() (in module espressopp.external.transformations) arcball_map_to_sphere() (in module espressopp.external.transformations) arcball_nearest_axis() (in module espressopp.external.transformations)

C

call() (in module espressopp.pmi) clip_matrix() (in module espressopp.external.transformations) compose_matrix() (in module espressopp.external.transformations) compute() (espressopp.analysis.RadGyrXProfilePI.RadGyrXProfilePILocal method) computeEnergy() (espressopp.interaction.AngularPotential.espressopp.interaction.AngularPotential method) computeForce() (espressopp.interaction.AngularPotential.espressopp.interaction.AngularPotential method) computeKineticEnergy() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) computeMomentumDrift() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) computePositionDrift() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) computeRingEnergy() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method)

computeRingEnergyRaw() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) concatenate_matrices() (in module espressopp.external.transformations) connect() (in module espressopp.tools.vmd) convertTable() (in module espressopp.tools.gromacs) CoulombTruncated (class in espressopp.interaction.CoulombTruncated) CoulombTruncatedUniqueCharge (class in espressopp.interaction.CoulombTruncatedUniqueCharge) create() (in module espressopp.pmi) createCubic() (in module espressopp.tools.lattice) createDenVel() (espressopp.integrator.LBInit.espressopp.integrator.LBInit method) createDiamond() (in module espressopp.tools.lattice)

D

decompose_matrix() (in module espressopp.external.transformations) Default() (espressopp.standard_system.Default.espressopp.standard_system method) DihedralHarmonic (class in espressopp.interaction.DihedralHarmonic) DihedralHarmonicCos (class in espressopp.interaction.DihedralHarmonicCos)

DihedralHarmonicNCos (class in espressopp.interaction.DihedralHarmonicNCos) displacement (in module espressopp.integrator.MinimizeEnergy) down() (espressopp.external.transformations.Arcball method) drag() (espressopp.external.transformations.Arcball method)

E

Error espressopp.analysis.AdressDensity module espressopp.analysis.AdressDensity() (in module espressopp.analysis.AdressDensity) espressopp.analysis.AdressDensity.addExclusions() (in module espressopp.analysis.AdressDensity) espressopp.analysis.AdressDensity.compute() (in module espressopp.analysis.AdressDensity) espressopp.analysis.AllParticlePos module espressopp.analysis.AllParticlePos.gatherAllPositions() (in module espressopp.analysis.AllParticlePos) espressopp.analysis.AnalysisBase module espressopp.analysis.AnalysisBase.compute() (in module espressopp.analysis.AnalysisBase) espressopp.analysis.AnalysisBase.getAverageValue() (in module espressopp.analysis.AnalysisBase) espressopp.analysis.AnalysisBase.getNumberOfMeasurements() (in module espressopp.analysis.AnalysisBase) espressopp.analysis.AnalysisBase.performMeasurement() (in module espressopp.analysis.AnalysisBase) espressopp.analysis.AnalysisBase.reset() (in module espressopp.analysis.AnalysisBase) espressopp.analysis.Autocorrelation module espressopp.analysis.Autocorrelation() (in module espressopp.analysis.Autocorrelation) espressopp.analysis.Autocorrelation.clear() (in module espressopp.analysis.Autocorrelation) espressopp.analysis.Autocorrelation.compute() (in module espressopp.analysis.Autocorrelation) espressopp.analysis.Autocorrelation.gather() (in module espressopp.analysis.Autocorrelation) espressopp.analysis.CenterOfMass module espressopp.analysis.CenterOfMass() (in module espressopp.analysis.CenterOfMass) espressopp.analysis.CMVelocity module espressopp.analysis.CMVelocity (class in espressopp.analysis.CMVelocity) espressopp.analysis.CMVelocity.compute() (in module espressopp.analysis.CMVelocity) espressopp.analysis.CMVelocity.reset() (in module espressopp.analysis.CMVelocity) espressopp.analysis.ConfigsParticleDecomp module espressopp.analysis.ConfigsParticleDecomp() (in module espressopp.analysis.ConfigsParticleDecomp), [1] espressopp.analysis.ConfigsParticleDecomp.clear() (in module espressopp.analysis.ConfigsParticleDecomp) espressopp.analysis.ConfigsParticleDecomp.compute() (in module espressopp.analysis.ConfigsParticleDecomp) espressopp.analysis.ConfigsParticleDecomp.gather() (in module espressopp.analysis.ConfigsParticleDecomp) espressopp.analysis.ConfigsParticleDecomp.gatherFromFile() (in module espressopp.analysis.ConfigsParticleDecomp) espressopp.analysis.Configurations module espressopp.analysis.Configurations() (in module espressopp.analysis.Configurations) espressopp.analysis.Configurations.back() (in module espressopp.analysis.Configurations) espressopp.analysis.Configurations.clear() (in module espressopp.analysis.Configurations) espressopp.analysis.Configurations.gather() (in module espressopp.analysis.Configurations) espressopp.analysis.ConfigurationsExt module espressopp.analysis.ConfigurationsExt() (in module espressopp.analysis.ConfigurationsExt) espressopp.analysis.ConfigurationsExt.back() (in module espressopp.analysis.ConfigurationsExt) espressopp.analysis.ConfigurationsExt.clear() (in module espressopp.analysis.ConfigurationsExt) espressopp.analysis.ConfigurationsExt.gather() (in module espressopp.analysis.ConfigurationsExt) espressopp.analysis.Energy module espressopp.analysis.EnergyKin() (in module espressopp.analysis.Energy) espressopp.analysis.EnergyKin.compute() (in module espressopp.analysis.Energy) espressopp.analysis.EnergyPot() (in module espressopp.analysis.Energy) espressopp.analysis.EnergyPot.compute() (in module espressopp.analysis.Energy) espressopp.analysis.EnergyTot() (in module espressopp.analysis.Energy) espressopp.analysis.EnergyTot.compute() (in module espressopp.analysis.Energy) espressopp.analysis.IntraChainDistSq module espressopp.analysis.IntraChainDistSq() (in module espressopp.analysis.IntraChainDistSq) espressopp.analysis.IntraChainDistSq.compute() (in module espressopp.analysis.IntraChainDistSq) espressopp.analysis.LBOutput module espressopp.analysis.LBOutputScreen module espressopp.analysis.LBOutputScreen (class in espressopp.analysis.LBOutputScreen) espressopp.analysis.LBOutputVzInTime module espressopp.analysis.LBOutputVzInTime (class in espressopp.analysis.LBOutputVzInTime) espressopp.analysis.LBOutputVzOfX module espressopp.analysis.LBOutputVzOfX (class in espressopp.analysis.LBOutputVzOfX) espressopp.analysis.MaxPID module espressopp.analysis.MaxPID() (in module espressopp.analysis.MaxPID) espressopp.analysis.MeanSquareDispl module espressopp.analysis.MeanSquareDispl() (in module espressopp.analysis.MeanSquareDispl) espressopp.analysis.MeanSquareDispl.computeG2() (in module espressopp.analysis.MeanSquareDispl) espressopp.analysis.MeanSquareDispl.computeG3() (in module espressopp.analysis.MeanSquareDispl) espressopp.analysis.MeanSquareDispl.strange() (in module espressopp.analysis.MeanSquareDispl) espressopp.analysis.MeanSquareInternalDist module espressopp.analysis.MeanSquareInternalDist() (in module espressopp.analysis.MeanSquareInternalDist) espressopp.analysis.NeighborFluctuation module espressopp.analysis.NeighborFluctuation() (in module espressopp.analysis.NeighborFluctuation) espressopp.analysis.NPart module espressopp.analysis.NPart() (in module espressopp.analysis.NPart) espressopp.analysis.NPartSubregion module espressopp.analysis.NPartSubregion() (in module espressopp.analysis.NPartSubregion) espressopp.analysis.Observable module espressopp.analysis.Observable.compute() (in module espressopp.analysis.Observable) espressopp.analysis.OrderParameter module espressopp.analysis.OrderParameter() (in module espressopp.analysis.OrderParameter) espressopp.analysis.ParticleRadiusDistribution module espressopp.analysis.ParticleRadiusDistribution() (in module espressopp.analysis.ParticleRadiusDistribution) espressopp.analysis.PotentialEnergy module espressopp.analysis.PotentialEnergy() (in module espressopp.analysis.PotentialEnergy) espressopp.analysis.Pressure module espressopp.analysis.Pressure() (in module espressopp.analysis.Pressure) espressopp.analysis.PressureTensor module espressopp.analysis.PressureTensor() (in module espressopp.analysis.PressureTensor) espressopp.analysis.PressureTensorLayer module espressopp.analysis.PressureTensorLayer() (in module espressopp.analysis.PressureTensorLayer) espressopp.analysis.PressureTensorMultiLayer module espressopp.analysis.PressureTensorMultiLayer() (in module espressopp.analysis.PressureTensorMultiLayer) espressopp.analysis.RadGyrXProfilePI module espressopp.analysis.RadGyrXProfilePI() (in module espressopp.analysis.RadGyrXProfilePI) espressopp.analysis.RadialDistrF module espressopp.analysis.RadialDistrF() (in module espressopp.analysis.RadialDistrF) espressopp.analysis.RadialDistrF.compute() (in module espressopp.analysis.RadialDistrF) espressopp.analysis.RDFatomistic module espressopp.analysis.RDFatomistic() (in module espressopp.analysis.RDFatomistic) espressopp.analysis.RDFatomistic.compute() (in module espressopp.analysis.RDFatomistic) espressopp.analysis.RDFatomistic.computePathIntegral() (in module espressopp.analysis.RDFatomistic) espressopp.analysis.StaticStructF module espressopp.analysis.StaticStructF() (in module espressopp.analysis.StaticStructF) espressopp.analysis.StaticStructF.compute() (in module espressopp.analysis.StaticStructF) espressopp.analysis.StaticStructF.computeSingleChain() (in module espressopp.analysis.StaticStructF) espressopp.analysis.SubregionTracking module espressopp.analysis.SubregionTracking() (in module espressopp.analysis.SubregionTracking) espressopp.analysis.SystemMonitor module espressopp.analysis.SystemMonitor() (in module espressopp.analysis.SystemMonitor) espressopp.analysis.SystemMonitor.add_observable() (in module espressopp.analysis.SystemMonitor) espressopp.analysis.SystemMonitor.info() (in module espressopp.analysis.SystemMonitor) espressopp.analysis.SystemMonitorOutputCSV() (in module espressopp.analysis.SystemMonitor) espressopp.analysis.Temperature module espressopp.analysis.Temperature() (in module espressopp.analysis.Temperature) espressopp.analysis.Test module espressopp.analysis.Test() (in module espressopp.analysis.Test) espressopp.analysis.Velocities module espressopp.analysis.Velocities() (in module espressopp.analysis.Velocities) espressopp.analysis.Velocities.clear() (in module espressopp.analysis.Velocities) espressopp.analysis.Velocities.gather() (in module espressopp.analysis.Velocities) espressopp.analysis.VelocityAutocorrelation module espressopp.analysis.VelocityAutocorrelation() (in module espressopp.analysis.VelocityAutocorrelation) espressopp.analysis.Viscosity module espressopp.analysis.Viscosity() (in module espressopp.analysis.Viscosity) espressopp.analysis.Viscosity.compute() (in module espressopp.analysis.Viscosity) espressopp.analysis.Viscosity.gather() (in module espressopp.analysis.Viscosity) espressopp.analysis.XDensity module espressopp.analysis.XDensity() (in module espressopp.analysis.XDensity) espressopp.analysis.XDensity.compute() (in module espressopp.analysis.XDensity) espressopp.analysis.XPressure module espressopp.analysis.XPressure() (in module espressopp.analysis.XPressure) espressopp.analysis.XPressure.compute() (in module espressopp.analysis.XPressure) espressopp.analysis.XTemperature module espressopp.analysis.XTemperature() (in module espressopp.analysis.XTemperature) espressopp.analysis.XTemperature.compute() (in module espressopp.analysis.XTemperature) espressopp.bc.BC module espressopp.bc.BC (class in espressopp.bc.BC) espressopp.bc.OrthorhombicBC module espressopp.bc.SlabBC module espressopp.check.System module espressopp.Error() (in module espressopp.Exceptions) espressopp.esutil.Collectives module espressopp.esutil.GammaVariate module espressopp.esutil.GammaVariate() (in module espressopp.esutil.GammaVariate) espressopp.esutil.Grid module espressopp.esutil.NormalVariate module espressopp.esutil.NormalVariate() (in module espressopp.esutil.NormalVariate) espressopp.esutil.RNG module espressopp.esutil.UniformOnSphere module espressopp.Exceptions module espressopp.external.transformations module espressopp.FixedLocalTupleList module espressopp.FixedLocalTupleList() (in module espressopp.FixedLocalTupleList) espressopp.FixedLocalTupleList.addTuple() (in module espressopp.FixedLocalTupleList) espressopp.FixedLocalTupleList.getTuples() (in module espressopp.FixedLocalTupleList) espressopp.FixedLocalTupleList.size() (in module espressopp.FixedLocalTupleList) espressopp.FixedPairDistList module espressopp.FixedPairDistList() (in module espressopp.FixedPairDistList) espressopp.FixedPairDistList.add() (in module espressopp.FixedPairDistList) espressopp.FixedPairDistList.addPairs() (in module espressopp.FixedPairDistList) espressopp.FixedPairDistList.getDist() (in module espressopp.FixedPairDistList) espressopp.FixedPairDistList.getPairs() (in module espressopp.FixedPairDistList) espressopp.FixedPairDistList.getPairsDist() (in module espressopp.FixedPairDistList) espressopp.FixedPairDistList.size() (in module espressopp.FixedPairDistList) espressopp.FixedPairList module espressopp.FixedPairList() (in module espressopp.FixedPairList) espressopp.FixedPairList.add() (in module espressopp.FixedPairList) espressopp.FixedPairList.addBonds() (in module espressopp.FixedPairList) espressopp.FixedPairList.getBonds() (in module espressopp.FixedPairList) espressopp.FixedPairList.getLongtimeMaxBond() (in module espressopp.FixedPairList) espressopp.FixedPairList.remove() (in module espressopp.FixedPairList) espressopp.FixedPairList.resetLongtimeMaxBond() (in module espressopp.FixedPairList) espressopp.FixedPairList.size() (in module espressopp.FixedPairList) espressopp.FixedPairList.totalSize() (in module espressopp.FixedPairList) espressopp.FixedPairListAdress module espressopp.FixedPairListAdress() (in module espressopp.FixedPairListAdress) espressopp.FixedPairListAdress.add() (in module espressopp.FixedPairListAdress) espressopp.FixedPairListAdress.addBonds() (in module espressopp.FixedPairListAdress) espressopp.FixedPairListAdress.getBonds() (in module espressopp.FixedPairListAdress) espressopp.FixedPairListAdress.remove() (in module espressopp.FixedPairListAdress) espressopp.FixedQuadrupleAngleList module espressopp.FixedQuadrupleAngleList() (in module espressopp.FixedQuadrupleAngleList) espressopp.FixedQuadrupleAngleList.add() (in module espressopp.FixedQuadrupleAngleList) espressopp.FixedQuadrupleAngleList.addQuadruples() (in module espressopp.FixedQuadrupleAngleList) espressopp.FixedQuadrupleAngleList.getAngle() (in module espressopp.FixedQuadrupleAngleList) espressopp.FixedQuadrupleAngleList.getQuadruples() (in module espressopp.FixedQuadrupleAngleList) espressopp.FixedQuadrupleAngleList.getQuadruplesAngles() (in module espressopp.FixedQuadrupleAngleList) espressopp.FixedQuadrupleAngleList.size() (in module espressopp.FixedQuadrupleAngleList) espressopp.FixedQuadrupleList module espressopp.FixedQuadrupleList() (in module espressopp.FixedQuadrupleList) espressopp.FixedQuadrupleList.add() (in module espressopp.FixedQuadrupleList) espressopp.FixedQuadrupleList.addQuadruples() (in module espressopp.FixedQuadrupleList) espressopp.FixedQuadrupleList.getQuadruples() (in module espressopp.FixedQuadrupleList) espressopp.FixedQuadrupleList.remove() (in module espressopp.FixedQuadrupleList) espressopp.FixedQuadrupleList.size() (in module espressopp.FixedQuadrupleList) espressopp.FixedQuadrupleListAdress module espressopp.FixedQuadrupleListAdress() (in module espressopp.FixedQuadrupleListAdress) espressopp.FixedQuadrupleListAdress.add() (in module espressopp.FixedQuadrupleListAdress) espressopp.FixedQuadrupleListAdress.addQuadruples() (in module espressopp.FixedQuadrupleListAdress) espressopp.FixedQuadrupleListAdress.getQuadruples() (in module espressopp.FixedQuadrupleListAdress) espressopp.FixedQuadrupleListAdress.size() (in module espressopp.FixedQuadrupleListAdress) espressopp.FixedSingleList module espressopp.FixedSingleList() (in module espressopp.FixedSingleList) espressopp.FixedSingleList.add() (in module espressopp.FixedSingleList) espressopp.FixedSingleList.addSingles() (in module espressopp.FixedSingleList) espressopp.FixedSingleList.getSingles() (in module espressopp.FixedSingleList) espressopp.FixedSingleList.size() (in module espressopp.FixedSingleList) espressopp.FixedTripleAngleList module espressopp.FixedTripleAngleList() (in module espressopp.FixedTripleAngleList) espressopp.FixedTripleAngleList.add() (in module espressopp.FixedTripleAngleList) espressopp.FixedTripleAngleList.addTriples() (in module espressopp.FixedTripleAngleList) espressopp.FixedTripleAngleList.getAngle() (in module espressopp.FixedTripleAngleList) espressopp.FixedTripleAngleList.getTriples() (in module espressopp.FixedTripleAngleList) espressopp.FixedTripleAngleList.getTriplesAngles() (in module espressopp.FixedTripleAngleList) espressopp.FixedTripleAngleList.size() (in module espressopp.FixedTripleAngleList) espressopp.FixedTripleList module espressopp.FixedTripleList() (in module espressopp.FixedTripleList) espressopp.FixedTripleList.add() (in module espressopp.FixedTripleList) espressopp.FixedTripleList.addTriples() (in module espressopp.FixedTripleList) espressopp.FixedTripleList.getTriples() (in module espressopp.FixedTripleList) espressopp.FixedTripleList.remove() (in module espressopp.FixedTripleList) espressopp.FixedTripleList.size() (in module espressopp.FixedTripleList) espressopp.FixedTripleListAdress module espressopp.FixedTripleListAdress() (in module espressopp.FixedTripleListAdress) espressopp.FixedTripleListAdress.add() (in module espressopp.FixedTripleListAdress) espressopp.FixedTripleListAdress.addTriples() (in module espressopp.FixedTripleListAdress) espressopp.FixedTripleListAdress.remove() (in module espressopp.FixedTripleListAdress) espressopp.FixedTupleList module espressopp.FixedTupleList() (in module espressopp.FixedTupleList) espressopp.FixedTupleList.size() (in module espressopp.FixedTupleList) espressopp.FixedTupleListAdress module espressopp.FixedTupleListAdress() (in module espressopp.FixedTupleListAdress) espressopp.FixedTupleListAdress.addTuples() (in module espressopp.FixedTupleListAdress) espressopp.Int3D module espressopp.Int3D() (in module espressopp.Int3D) espressopp.Int3D.x() (in module espressopp.Int3D) espressopp.Int3D.y() (in module espressopp.Int3D) espressopp.Int3D.z() (in module espressopp.Int3D) espressopp.integrator.Adress module espressopp.integrator.Adress (class in espressopp.integrator.Adress) espressopp.integrator.AssociationReaction module espressopp.integrator.BerendsenBarostat module espressopp.integrator.BerendsenBarostat() (in module espressopp.integrator.BerendsenBarostat) espressopp.integrator.BerendsenBarostatAnisotropic module espressopp.integrator.BerendsenBarostatAnisotropic() (in module espressopp.integrator.BerendsenBarostatAnisotropic) espressopp.integrator.BerendsenThermostat module espressopp.integrator.BerendsenThermostat() (in module espressopp.integrator.BerendsenThermostat) espressopp.integrator.CapForce module espressopp.integrator.CapForce() (in module espressopp.integrator.CapForce) espressopp.integrator.DPDThermostat module espressopp.integrator.DPDThermostat() (in module espressopp.integrator.DPDThermostat) espressopp.integrator.EmptyExtension module espressopp.integrator.EmptyExtension() (in module espressopp.integrator.EmptyExtension) espressopp.integrator.ExtAnalyze module espressopp.integrator.ExtAnalyze() (in module espressopp.integrator.ExtAnalyze) espressopp.integrator.Extension module espressopp.integrator.Extension.connect() (in module espressopp.integrator.Extension) espressopp.integrator.Extension.disconnect() (in module espressopp.integrator.Extension) espressopp.integrator.ExtForce module espressopp.integrator.ExtForce() (in module espressopp.integrator.ExtForce) espressopp.integrator.FixPositions module espressopp.integrator.FixPositions() (in module espressopp.integrator.FixPositions) espressopp.integrator.FreeEnergyCompensation module espressopp.integrator.FreeEnergyCompensation() (in module espressopp.integrator.FreeEnergyCompensation) espressopp.integrator.FreeEnergyCompensation.addForce() (in module espressopp.integrator.FreeEnergyCompensation) espressopp.integrator.FreeEnergyCompensation.computeCompEnergy() (in module espressopp.integrator.FreeEnergyCompensation) espressopp.integrator.GeneralizedLangevinThermostat module espressopp.integrator.GeneralizedLangevinThermostat() (in module espressopp.integrator.GeneralizedLangevinThermostat) espressopp.integrator.GeneralizedLangevinThermostat.addCoeffs() (in module espressopp.integrator.GeneralizedLangevinThermostat) espressopp.integrator.Isokinetic module espressopp.integrator.Isokinetic() (in module espressopp.integrator.Isokinetic) espressopp.integrator.LangevinBarostat module espressopp.integrator.LangevinBarostat() (in module espressopp.integrator.LangevinBarostat) espressopp.integrator.LangevinThermostat module espressopp.integrator.LangevinThermostat() (in module espressopp.integrator.LangevinThermostat) espressopp.integrator.LangevinThermostat.addExclusions() (in module espressopp.integrator.LangevinThermostat) espressopp.integrator.LangevinThermostat1D module espressopp.integrator.LangevinThermostat1D() (in module espressopp.integrator.LangevinThermostat1D) espressopp.integrator.LangevinThermostatHybrid module espressopp.integrator.LangevinThermostatOnGroup module espressopp.integrator.LangevinThermostatOnGroup() (in module espressopp.integrator.LangevinThermostatOnGroup) espressopp.integrator.LangevinThermostatOnRadius module espressopp.integrator.LangevinThermostatOnRadius() (in module espressopp.integrator.LangevinThermostatOnRadius) espressopp.integrator.LangevinThermostatOnRadius.addExclusions() (in module espressopp.integrator.LangevinThermostatOnRadius) espressopp.integrator.LatticeBoltzmann module espressopp.integrator.LatticeBoltzmann (class in espressopp.integrator.LatticeBoltzmann) espressopp.integrator.LBInit module espressopp.integrator.LBInit (class in espressopp.integrator.LBInit) espressopp.integrator.LBInitConstForce module espressopp.integrator.LBInitPeriodicForce module espressopp.integrator.LBInitPopUniform module espressopp.integrator.LBInitPopWave module espressopp.integrator.MDIntegrator module espressopp.integrator.MDIntegrator.addExtension() (in module espressopp.integrator.MDIntegrator) espressopp.integrator.MDIntegrator.getExtension() (in module espressopp.integrator.MDIntegrator) espressopp.integrator.MDIntegrator.getNumberOfExtensions() (in module espressopp.integrator.MDIntegrator) espressopp.integrator.MDIntegrator.run() (in module espressopp.integrator.MDIntegrator) espressopp.integrator.MinimizeEnergy module espressopp.integrator.MinimizeEnergy() (in module espressopp.integrator.MinimizeEnergy) espressopp.integrator.MinimizeEnergy.run() (in module espressopp.integrator.MinimizeEnergy) espressopp.integrator.OnTheFlyFEC module espressopp.integrator.OnTheFlyFEC() (in module espressopp.integrator.OnTheFlyFEC) espressopp.integrator.OnTheFlyFEC.getBins() (in module espressopp.integrator.OnTheFlyFEC) espressopp.integrator.OnTheFlyFEC.getGap() (in module espressopp.integrator.OnTheFlyFEC) espressopp.integrator.OnTheFlyFEC.getSteps() (in module espressopp.integrator.OnTheFlyFEC) espressopp.integrator.OnTheFlyFEC.makeArrays() (in module espressopp.integrator.OnTheFlyFEC) espressopp.integrator.OnTheFlyFEC.resetCounter() (in module espressopp.integrator.OnTheFlyFEC) espressopp.integrator.OnTheFlyFEC.writeFEC() (in module espressopp.integrator.OnTheFlyFEC) espressopp.integrator.PIAdressIntegrator module espressopp.integrator.PIAdressIntegrator() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.computeKineticEnergy() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.computeMomentumDrift() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.computePositionDrift() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.computeRingEnergy() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.computeRingEnergyRaw() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getCentroidThermostat() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getClmassmultiplier() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getCMDparameter() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getConstKinMass() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getGamma() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getKTI() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getmStep() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getNtrotter() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getPILE() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getPILElambda() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getRealKinMass() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getSpeedup() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getsStep() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getTemperature() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getTimeStep() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getVerletList() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.getVerletlistBuilds() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setCentroidThermostat() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setClmassmultiplier() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setCMDparameter() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setConstKinMass() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setGamma() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setKTI() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setmStep() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setNtrotter() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setPILE() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setPILElambda() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setRealKinMass() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setSpeedup() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setsStep() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setTemperature() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setTimeStep() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.PIAdressIntegrator.setVerletList() (in module espressopp.integrator.PIAdressIntegrator) espressopp.integrator.Rattle module espressopp.integrator.Rattle() (in module espressopp.integrator.Rattle) espressopp.integrator.Rattle.addConstrainedBonds() (in module espressopp.integrator.Rattle) espressopp.integrator.Settle module espressopp.integrator.Settle() (in module espressopp.integrator.Settle) espressopp.integrator.Settle.addMolecules() (in module espressopp.integrator.Settle) espressopp.integrator.StochasticVelocityRescaling module espressopp.integrator.StochasticVelocityRescaling() (in module espressopp.integrator.StochasticVelocityRescaling) espressopp.integrator.TDforce module espressopp.integrator.TDforce() (in module espressopp.integrator.TDforce) espressopp.integrator.TDforce.addForce() (in module espressopp.integrator.TDforce) espressopp.integrator.TDforce.computeTDEnergy() (in module espressopp.integrator.TDforce) espressopp.integrator.VelocityVerlet module espressopp.integrator.VelocityVerlet() (in module espressopp.integrator.VelocityVerlet) espressopp.integrator.VelocityVerletOnGroup module espressopp.integrator.VelocityVerletOnGroup() (in module espressopp.integrator.VelocityVerletOnGroup) espressopp.integrator.VelocityVerletOnRadius module espressopp.integrator.VelocityVerletOnRadius() (in module espressopp.integrator.VelocityVerletOnRadius) espressopp.integrator.VelocityVerletRESPA module espressopp.integrator.VelocityVerletRESPA (class in espressopp.integrator.VelocityVerletRESPA) espressopp.integrator.VelocityVerletRESPA.getmultistep() (in module espressopp.integrator.VelocityVerletRESPA) espressopp.integrator.VelocityVerletRESPA.setmultistep() (in module espressopp.integrator.VelocityVerletRESPA) espressopp.interaction.AngularCosineSquared module espressopp.interaction.AngularCosineSquared (class in espressopp.interaction.AngularCosineSquared) espressopp.interaction.AngularHarmonic module espressopp.interaction.AngularHarmonic (class in espressopp.interaction.AngularHarmonic) espressopp.interaction.AngularPotential module espressopp.interaction.AngularPotential (class in espressopp.interaction.AngularPotential) espressopp.interaction.CellListCoulombKSpaceEwald() (in module espressopp.interaction.CoulombKSpaceEwald) espressopp.interaction.CellListCoulombKSpaceEwald.getFixedPairList() (in module espressopp.interaction.CoulombKSpaceEwald) espressopp.interaction.CellListCoulombKSpaceEwald.getPotential() (in module espressopp.interaction.CoulombKSpaceEwald) espressopp.interaction.CellListCoulombKSpaceP3M() (in module espressopp.interaction.CoulombKSpaceP3M) espressopp.interaction.CellListCoulombKSpaceP3M.getPotential() (in module espressopp.interaction.CoulombKSpaceP3M) espressopp.interaction.CellListCoulombTruncatedUniqueCharge() (in module espressopp.interaction.CoulombTruncatedUniqueCharge) espressopp.interaction.CellListCoulombTruncatedUniqueCharge.setPotential() (in module espressopp.interaction.CoulombTruncatedUniqueCharge) espressopp.interaction.CellListLennardJones() (in module espressopp.interaction.LennardJones) espressopp.interaction.CellListLennardJones.setPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.CellListLennardJonesAutoBonds() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.CellListLennardJonesAutoBonds.setPotential() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.CellListLennardJonesCapped() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.CellListLennardJonesCapped.getPotential() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.CellListLennardJonesCapped.setPotential() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.CellListLennardJonesEnergyCapped() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.CellListLennardJonesEnergyCapped.getPotential() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.CellListLennardJonesEnergyCapped.setPotential() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.CellListLennardJonesExpand() (in module espressopp.interaction.LennardJonesExpand) espressopp.interaction.CellListLennardJonesExpand.setPotential() (in module espressopp.interaction.LennardJonesExpand) espressopp.interaction.CellListLennardJonesGeneric() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.CellListLennardJonesGeneric.setPotential() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.CellListLennardJonesGromacs() (in module espressopp.interaction.LennardJonesGromacs) espressopp.interaction.CellListLennardJonesGromacs.setPotential() (in module espressopp.interaction.LennardJonesGromacs) espressopp.interaction.CellListLJcos() (in module espressopp.interaction.LJcos) espressopp.interaction.CellListLJcos.setPotential() (in module espressopp.interaction.LJcos) espressopp.interaction.CellListMorse() (in module espressopp.interaction.Morse) espressopp.interaction.CellListMorse.setPotential() (in module espressopp.interaction.Morse) espressopp.interaction.CellListReactionFieldGeneralized() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.CellListReactionFieldGeneralized.setPotential() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.CellListSoftCosine() (in module espressopp.interaction.SoftCosine) espressopp.interaction.CellListSoftCosine.setPotential() (in module espressopp.interaction.SoftCosine) espressopp.interaction.CellListStillingerWeberPairTerm() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.CellListStillingerWeberPairTerm.setPotential() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.CellListStillingerWeberPairTermCapped() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.CellListStillingerWeberPairTermCapped.setPotential() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.CellListTabulated() (in module espressopp.interaction.Tabulated) espressopp.interaction.CellListTabulated.setPotential() (in module espressopp.interaction.Tabulated) espressopp.interaction.CellListTersoffPairTerm() (in module espressopp.interaction.TersoffPairTerm) espressopp.interaction.CellListTersoffPairTerm.setPotential() (in module espressopp.interaction.TersoffPairTerm) espressopp.interaction.CellListZero() (in module espressopp.interaction.Zero) espressopp.interaction.CellListZero.setPotential() (in module espressopp.interaction.Zero) espressopp.interaction.ConstrainCOM module espressopp.interaction.ConstrainCOM() (in module espressopp.interaction.ConstrainCOM) espressopp.interaction.ConstrainRG module espressopp.interaction.ConstrainRG() (in module espressopp.interaction.ConstrainRG) espressopp.interaction.Cosine module espressopp.interaction.Cosine() (in module espressopp.interaction.Cosine) espressopp.interaction.CoulombKSpaceEwald module espressopp.interaction.CoulombKSpaceEwald() (in module espressopp.interaction.CoulombKSpaceEwald) espressopp.interaction.CoulombKSpaceP3M module espressopp.interaction.CoulombKSpaceP3M() (in module espressopp.interaction.CoulombKSpaceP3M) espressopp.interaction.CoulombRSpace module espressopp.interaction.CoulombRSpace() (in module espressopp.interaction.CoulombRSpace) espressopp.interaction.CoulombTruncated module espressopp.interaction.CoulombTruncated() (in module espressopp.interaction.CoulombTruncated) espressopp.interaction.CoulombTruncatedUniqueCharge module espressopp.interaction.CoulombTruncatedUniqueCharge() (in module espressopp.interaction.CoulombTruncatedUniqueCharge) espressopp.interaction.DihedralHarmonic module espressopp.interaction.DihedralHarmonic() (in module espressopp.interaction.DihedralHarmonic) espressopp.interaction.DihedralHarmonicCos module espressopp.interaction.DihedralHarmonicCos() (in module espressopp.interaction.DihedralHarmonicCos) espressopp.interaction.DihedralHarmonicNCos module espressopp.interaction.DihedralHarmonicNCos() (in module espressopp.interaction.DihedralHarmonicNCos) espressopp.interaction.DihedralPotential module espressopp.interaction.DihedralPotential.computeEnergy() (in module espressopp.interaction.DihedralPotential) espressopp.interaction.DihedralPotential.computeForce() (in module espressopp.interaction.DihedralPotential) espressopp.interaction.DihedralRB module espressopp.interaction.DihedralRB() (in module espressopp.interaction.DihedralRB) espressopp.interaction.FENE module espressopp.interaction.FENE (class in espressopp.interaction.FENE) espressopp.interaction.FENECapped module espressopp.interaction.FENECapped (class in espressopp.interaction.FENECapped) espressopp.interaction.FixedLocalTupleListConstrainCOM() (in module espressopp.interaction.ConstrainCOM) espressopp.interaction.FixedLocalTupleListConstrainCOM.getPotential() (in module espressopp.interaction.ConstrainCOM) espressopp.interaction.FixedLocalTupleListConstrainCOM.setCom() (in module espressopp.interaction.ConstrainCOM) espressopp.interaction.FixedLocalTupleListConstrainRG() (in module espressopp.interaction.ConstrainRG) espressopp.interaction.FixedLocalTupleListConstrainRG.getPotential() (in module espressopp.interaction.ConstrainRG) espressopp.interaction.FixedLocalTupleListConstrainRG.setRG() (in module espressopp.interaction.ConstrainRG) espressopp.interaction.FixedPairListCoulombTruncatedUniqueCharge() (in module espressopp.interaction.CoulombTruncatedUniqueCharge) espressopp.interaction.FixedPairListCoulombTruncatedUniqueCharge.setPotential() (in module espressopp.interaction.CoulombTruncatedUniqueCharge) espressopp.interaction.FixedPairListFENE (class in espressopp.interaction.FENE) espressopp.interaction.FixedPairListFENECapped (class in espressopp.interaction.FENECapped) espressopp.interaction.FixedPairListHarmonic() (in module espressopp.interaction.Harmonic) espressopp.interaction.FixedPairListHarmonic.getFixedPairList() (in module espressopp.interaction.Harmonic) espressopp.interaction.FixedPairListHarmonic.setFixedPairList() (in module espressopp.interaction.Harmonic) espressopp.interaction.FixedPairListHarmonic.setPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.FixedPairListLennardJones() (in module espressopp.interaction.LennardJones) espressopp.interaction.FixedPairListLennardJones.getFixedPairList() (in module espressopp.interaction.LennardJones) espressopp.interaction.FixedPairListLennardJones.getPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.FixedPairListLennardJones.setFixedPairList() (in module espressopp.interaction.LennardJones) espressopp.interaction.FixedPairListLennardJones.setPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.FixedPairListLennardJonesAutoBonds() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.FixedPairListLennardJonesAutoBonds.setPotential() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.FixedPairListLennardJonesCapped() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.FixedPairListLennardJonesCapped.getPotential() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.FixedPairListLennardJonesCapped.setPotential() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.FixedPairListLennardJonesEnergyCapped() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.FixedPairListLennardJonesEnergyCapped.getPotential() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.FixedPairListLennardJonesEnergyCapped.setPotential() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.FixedPairListLennardJonesExpand() (in module espressopp.interaction.LennardJonesExpand) espressopp.interaction.FixedPairListLennardJonesExpand.setPotential() (in module espressopp.interaction.LennardJonesExpand) espressopp.interaction.FixedPairListLennardJonesGeneric() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.FixedPairListLennardJonesGeneric.getFixedPairList() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.FixedPairListLennardJonesGeneric.getPotential() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.FixedPairListLennardJonesGeneric.setFixedPairList() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.FixedPairListLennardJonesGeneric.setPotential() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.FixedPairListLennardJonesGromacs() (in module espressopp.interaction.LennardJonesGromacs) espressopp.interaction.FixedPairListLennardJonesGromacs.setPotential() (in module espressopp.interaction.LennardJonesGromacs) espressopp.interaction.FixedPairListLJcos() (in module espressopp.interaction.LJcos) espressopp.interaction.FixedPairListLJcos.getFixedPairList() (in module espressopp.interaction.LJcos) espressopp.interaction.FixedPairListLJcos.setFixedPairList() (in module espressopp.interaction.LJcos) espressopp.interaction.FixedPairListLJcos.setPotential() (in module espressopp.interaction.LJcos) espressopp.interaction.FixedPairListMirrorLennardJones() (in module espressopp.interaction.MirrorLennardJones) espressopp.interaction.FixedPairListMirrorLennardJones.getFixedPairList() (in module espressopp.interaction.MirrorLennardJones) espressopp.interaction.FixedPairListMirrorLennardJones.getPotential() (in module espressopp.interaction.MirrorLennardJones) espressopp.interaction.FixedPairListMirrorLennardJones.setFixedPairList() (in module espressopp.interaction.MirrorLennardJones) espressopp.interaction.FixedPairListMirrorLennardJones.setPotential() (in module espressopp.interaction.MirrorLennardJones) espressopp.interaction.FixedPairListMorse() (in module espressopp.interaction.Morse) espressopp.interaction.FixedPairListMorse.setPotential() (in module espressopp.interaction.Morse) espressopp.interaction.FixedPairListPIadressTabulated() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListPIadressTabulated.getFixedPairList() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListPIadressTabulated.getFixedTupleList() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListPIadressTabulated.getNTrotter() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListPIadressTabulated.getPotential() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListPIadressTabulated.getSpeedup() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListPIadressTabulated.setFixedPairList() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListPIadressTabulated.setFixedTupleList() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListPIadressTabulated.setNTrotter() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListPIadressTabulated.setPotential() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListPIadressTabulated.setSpeedup() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListQuartic() (in module espressopp.interaction.Quartic) espressopp.interaction.FixedPairListQuartic.getFixedPairList() (in module espressopp.interaction.Quartic) espressopp.interaction.FixedPairListQuartic.setFixedPairList() (in module espressopp.interaction.Quartic) espressopp.interaction.FixedPairListQuartic.setPotential() (in module espressopp.interaction.Quartic) espressopp.interaction.FixedPairListSoftCosine() (in module espressopp.interaction.SoftCosine) espressopp.interaction.FixedPairListSoftCosine.setPotential() (in module espressopp.interaction.SoftCosine) espressopp.interaction.FixedPairListStillingerWeberPairTerm() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.FixedPairListStillingerWeberPairTerm.setPotential() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.FixedPairListStillingerWeberPairTermCapped() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.FixedPairListStillingerWeberPairTermCapped.setPotential() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.FixedPairListTabulated() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListTabulated.setPotential() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListTersoffPairTerm() (in module espressopp.interaction.TersoffPairTerm) espressopp.interaction.FixedPairListTersoffPairTerm.setPotential() (in module espressopp.interaction.TersoffPairTerm) espressopp.interaction.FixedPairListTypesCoulombTruncated() (in module espressopp.interaction.CoulombTruncated) espressopp.interaction.FixedPairListTypesCoulombTruncated.setPotential() (in module espressopp.interaction.CoulombTruncated) espressopp.interaction.FixedPairListTypesHarmonic() (in module espressopp.interaction.Harmonic) espressopp.interaction.FixedPairListTypesHarmonic.getFixedPairList() (in module espressopp.interaction.Harmonic) espressopp.interaction.FixedPairListTypesHarmonic.getPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.FixedPairListTypesHarmonic.setFixedPairList() (in module espressopp.interaction.Harmonic) espressopp.interaction.FixedPairListTypesHarmonic.setPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.FixedPairListTypesTabulated() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListTypesTabulated.setPotential() (in module espressopp.interaction.Tabulated) espressopp.interaction.FixedPairListZero() (in module espressopp.interaction.Zero) espressopp.interaction.FixedPairListZero.setPotential() (in module espressopp.interaction.Zero) espressopp.interaction.FixedQuadrupleListDihedralHarmonic() (in module espressopp.interaction.DihedralHarmonic) espressopp.interaction.FixedQuadrupleListDihedralHarmonic.getFixedQuadrupleList() (in module espressopp.interaction.DihedralHarmonic) espressopp.interaction.FixedQuadrupleListDihedralHarmonic.setPotential() (in module espressopp.interaction.DihedralHarmonic) espressopp.interaction.FixedQuadrupleListDihedralHarmonicCos() (in module espressopp.interaction.DihedralHarmonicCos) espressopp.interaction.FixedQuadrupleListDihedralHarmonicCos.getFixedQuadrupleList() (in module espressopp.interaction.DihedralHarmonicCos) espressopp.interaction.FixedQuadrupleListDihedralHarmonicCos.setPotential() (in module espressopp.interaction.DihedralHarmonicCos) espressopp.interaction.FixedQuadrupleListDihedralHarmonicNCos() (in module espressopp.interaction.DihedralHarmonicNCos) espressopp.interaction.FixedQuadrupleListDihedralHarmonicNCos.getFixedQuadrupleList() (in module espressopp.interaction.DihedralHarmonicNCos) espressopp.interaction.FixedQuadrupleListDihedralHarmonicNCos.setPotential() (in module espressopp.interaction.DihedralHarmonicNCos)

espressopp.interaction.FixedQuadrupleListDihedralRB() (in module espressopp.interaction.DihedralRB) espressopp.interaction.FixedQuadrupleListDihedralRB.getFixedQuadrupleList() (in module espressopp.interaction.DihedralRB) espressopp.interaction.FixedQuadrupleListDihedralRB.setPotential() (in module espressopp.interaction.DihedralRB) espressopp.interaction.FixedQuadrupleListOPLS() (in module espressopp.interaction.OPLS) espressopp.interaction.FixedQuadrupleListOPLS.setPotential() (in module espressopp.interaction.OPLS) espressopp.interaction.FixedQuadrupleListTabulatedDihedral() (in module espressopp.interaction.TabulatedDihedral) espressopp.interaction.FixedQuadrupleListTabulatedDihedral.setPotential() (in module espressopp.interaction.TabulatedDihedral) espressopp.interaction.FixedQuadrupleListTypesTabulatedDihedral() (in module espressopp.interaction.TabulatedDihedral), [1] espressopp.interaction.FixedQuadrupleListTypesTabulatedDihedral.setPotential() (in module espressopp.interaction.TabulatedDihedral) espressopp.interaction.FixedTripleListAngularCosineSquared (class in espressopp.interaction.AngularCosineSquared) espressopp.interaction.FixedTripleListAngularHarmonic (class in espressopp.interaction.AngularHarmonic) espressopp.interaction.FixedTripleListCosine() (in module espressopp.interaction.Cosine) espressopp.interaction.FixedTripleListCosine.getFixedTripleList() (in module espressopp.interaction.Cosine) espressopp.interaction.FixedTripleListCosine.setPotential() (in module espressopp.interaction.Cosine) espressopp.interaction.FixedTripleListPIadressTabulatedAngular() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListPIadressTabulatedAngular.getFixedTripleList() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListPIadressTabulatedAngular.getFixedTupleList() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListPIadressTabulatedAngular.getNTrotter() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListPIadressTabulatedAngular.getPotential() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListPIadressTabulatedAngular.getSpeedup() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListPIadressTabulatedAngular.setFixedTripleList() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListPIadressTabulatedAngular.setFixedTupleList() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListPIadressTabulatedAngular.setNTrotter() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListPIadressTabulatedAngular.setPotential() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListPIadressTabulatedAngular.setSpeedup() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListStillingerWeberTripleTerm() (in module espressopp.interaction.StillingerWeberTripleTerm) espressopp.interaction.FixedTripleListStillingerWeberTripleTerm.getFixedTripleList() (in module espressopp.interaction.StillingerWeberTripleTerm) espressopp.interaction.FixedTripleListStillingerWeberTripleTerm.setPotential() (in module espressopp.interaction.StillingerWeberTripleTerm) espressopp.interaction.FixedTripleListTabulatedAngular() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListTabulatedAngular.setPotential() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListTersoffTripleTerm() (in module espressopp.interaction.TersoffTripleTerm) espressopp.interaction.FixedTripleListTersoffTripleTerm.getFixedTripleList() (in module espressopp.interaction.TersoffTripleTerm) espressopp.interaction.FixedTripleListTersoffTripleTerm.setPotential() (in module espressopp.interaction.TersoffTripleTerm) espressopp.interaction.FixedTripleListTypesTabulatedAngular() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.FixedTripleListTypesTabulatedAngular.setPotential() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.GravityTruncated module espressopp.interaction.GravityTruncated() (in module espressopp.interaction.GravityTruncated) espressopp.interaction.Harmonic module espressopp.interaction.Harmonic() (in module espressopp.interaction.Harmonic) espressopp.interaction.HarmonicTrap module espressopp.interaction.HarmonicTrap() (in module espressopp.interaction.HarmonicTrap) espressopp.interaction.Interaction module espressopp.interaction.Interaction.bondType() (in module espressopp.interaction.Interaction) espressopp.interaction.Interaction.computeEnergy() (in module espressopp.interaction.Interaction) espressopp.interaction.Interaction.computeEnergyAA() (in module espressopp.interaction.Interaction) espressopp.interaction.Interaction.computeEnergyCG() (in module espressopp.interaction.Interaction) espressopp.interaction.Interaction.computeEnergyDeriv() (in module espressopp.interaction.Interaction) espressopp.interaction.Interaction.computeVirial() (in module espressopp.interaction.Interaction) espressopp.interaction.LennardJones module espressopp.interaction.LennardJones() (in module espressopp.interaction.LennardJones) espressopp.interaction.LennardJones93Wall module espressopp.interaction.LennardJones93Wall() (in module espressopp.interaction.LennardJones93Wall) espressopp.interaction.LennardJones93Wall.getParams() (in module espressopp.interaction.LennardJones93Wall) espressopp.interaction.LennardJones93Wall.setParams() (in module espressopp.interaction.LennardJones93Wall) espressopp.interaction.LennardJonesAutoBonds module espressopp.interaction.LennardJonesAutoBonds() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.LennardJonesCapped module espressopp.interaction.LennardJonesCapped() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.LennardJonesEnergyCapped module espressopp.interaction.LennardJonesEnergyCapped() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.LennardJonesExpand module espressopp.interaction.LennardJonesExpand() (in module espressopp.interaction.LennardJonesExpand) espressopp.interaction.LennardJonesGeneric module espressopp.interaction.LennardJonesGeneric() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.LennardJonesGromacs module espressopp.interaction.LennardJonesGromacs() (in module espressopp.interaction.LennardJonesGromacs) espressopp.interaction.LennardJonesSoftcoreTI module espressopp.interaction.LennardJonesSoftcoreTI() (in module espressopp.interaction.LennardJonesSoftcoreTI) espressopp.interaction.LennardJonesSoftcoreTI.addPids() (in module espressopp.interaction.LennardJonesSoftcoreTI) espressopp.interaction.LJcos module espressopp.interaction.LJcos() (in module espressopp.interaction.LJcos) espressopp.interaction.MirrorLennardJones module espressopp.interaction.MirrorLennardJones() (in module espressopp.interaction.MirrorLennardJones) espressopp.interaction.Morse module espressopp.interaction.Morse() (in module espressopp.interaction.Morse) espressopp.interaction.OPLS module espressopp.interaction.OPLS() (in module espressopp.interaction.OPLS) espressopp.interaction.Potential module espressopp.interaction.Potential.computeEnergy() (in module espressopp.interaction.Potential) espressopp.interaction.Potential.computeForce() (in module espressopp.interaction.Potential) espressopp.interaction.PotentialVSpherePair module espressopp.interaction.PotentialVSpherePair.computeEnergy() (in module espressopp.interaction.PotentialVSpherePair) espressopp.interaction.PotentialVSpherePair.computeForce() (in module espressopp.interaction.PotentialVSpherePair) espressopp.interaction.Quartic module espressopp.interaction.Quartic() (in module espressopp.interaction.Quartic) espressopp.interaction.ReactionFieldGeneralized module espressopp.interaction.ReactionFieldGeneralized() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.ReactionFieldGeneralizedTI module espressopp.interaction.ReactionFieldGeneralizedTI() (in module espressopp.interaction.ReactionFieldGeneralizedTI) espressopp.interaction.ReactionFieldGeneralizedTI.addPids() (in module espressopp.interaction.ReactionFieldGeneralizedTI) espressopp.interaction.SelfVSphere() (in module espressopp.interaction.VSphereSelf) espressopp.interaction.SelfVSphere.getPotential() (in module espressopp.interaction.VSphereSelf) espressopp.interaction.SelfVSphere.setPotential() (in module espressopp.interaction.VSphereSelf) espressopp.interaction.SingleParticleHarmonicTrap() (in module espressopp.interaction.HarmonicTrap) espressopp.interaction.SingleParticleHarmonicTrap.setPotential() (in module espressopp.interaction.HarmonicTrap) espressopp.interaction.SingleParticleLennardJones93Wall() (in module espressopp.interaction.LennardJones93Wall) espressopp.interaction.SingleParticleLennardJones93Wall.setPotential() (in module espressopp.interaction.LennardJones93Wall) espressopp.interaction.SingleParticlePotential module espressopp.interaction.SingleParticlePotential.computeEnergy() (in module espressopp.interaction.SingleParticlePotential) espressopp.interaction.SingleParticlePotential.computeForce() (in module espressopp.interaction.SingleParticlePotential) espressopp.interaction.SmoothSquareWell module espressopp.interaction.SoftCosine module espressopp.interaction.SoftCosine() (in module espressopp.interaction.SoftCosine) espressopp.interaction.StillingerWeberPairTerm module espressopp.interaction.StillingerWeberPairTerm() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.StillingerWeberPairTermCapped module espressopp.interaction.StillingerWeberPairTermCapped() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.StillingerWeberTripleTerm module espressopp.interaction.StillingerWeberTripleTerm() (in module espressopp.interaction.StillingerWeberTripleTerm) espressopp.interaction.Tabulated module espressopp.interaction.Tabulated() (in module espressopp.interaction.Tabulated) espressopp.interaction.TabulatedAngular module espressopp.interaction.TabulatedAngular() (in module espressopp.interaction.TabulatedAngular) espressopp.interaction.TabulatedDihedral module espressopp.interaction.TabulatedDihedral() (in module espressopp.interaction.TabulatedDihedral) espressopp.interaction.TersoffPairTerm module espressopp.interaction.TersoffPairTerm() (in module espressopp.interaction.TersoffPairTerm) espressopp.interaction.TersoffTripleTerm module espressopp.interaction.VerletListAdressATHarmonic() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListAdressATHarmonic.getPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListAdressATHarmonic.getVerletList() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListAdressATHarmonic.setPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListAdressATLenJonesReacFieldGen() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLenJonesReacFieldGen.setPotential1() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLenJonesReacFieldGen.setPotential2() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLennardJones() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLennardJones.getPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLennardJones.getVerletList() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLennardJones.setPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLJReacFieldGenHarmonic() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLJReacFieldGenHarmonic.setPotentialAT1() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLJReacFieldGenHarmonic.setPotentialAT2() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLJReacFieldGenHarmonic.setPotentialCG() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLJReacFieldGenTab() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLJReacFieldGenTab.setPotentialAT1() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLJReacFieldGenTab.setPotentialAT2() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATLJReacFieldGenTab.setPotentialCG() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressATReactionFieldGeneralized() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.VerletListAdressATReactionFieldGeneralized.getPotential() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.VerletListAdressATReactionFieldGeneralized.setPotential() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.VerletListAdressCGHarmonic() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListAdressCGHarmonic.getPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListAdressCGHarmonic.getVerletList() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListAdressCGHarmonic.setPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListAdressCGLennardJones() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressCGLennardJones.getPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressCGLennardJones.getVerletList() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressCGLennardJones.setPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressCGTabulated() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListAdressCGTabulated.getPotential() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListAdressCGTabulated.getVerletList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListAdressCGTabulated.setPotential() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListAdressLennardJones() (in module espressopp.interaction.LennardJones) (in module espressopp.interaction.LennardJonesSoftcoreTI) espressopp.interaction.VerletListAdressLennardJones.setPotentialAT() (in module espressopp.interaction.LennardJones) (in module espressopp.interaction.LennardJonesSoftcoreTI) espressopp.interaction.VerletListAdressLennardJones.setPotentialCG() (in module espressopp.interaction.LennardJones) (in module espressopp.interaction.LennardJonesSoftcoreTI) espressopp.interaction.VerletListAdressLennardJones2() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressLennardJones2.setPotentialAT() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressLennardJones2.setPotentialCG() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressLennardJonesAutoBonds() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.VerletListAdressLennardJonesAutoBonds.setPotential() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.VerletListAdressLennardJonesCapped() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListAdressLennardJonesCapped.getPotentialAT() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListAdressLennardJonesCapped.getPotentialCG() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListAdressLennardJonesCapped.setPotentialAT() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListAdressLennardJonesCapped.setPotentialCG() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListAdressLennardJonesEnergyCapped() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListAdressLennardJonesEnergyCapped.getPotentialAT() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListAdressLennardJonesEnergyCapped.getPotentialCG() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListAdressLennardJonesEnergyCapped.setPotentialAT() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListAdressLennardJonesEnergyCapped.setPotentialCG() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListAdressLennardJonesGeneric() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListAdressLennardJonesGeneric.setPotentialAT() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListAdressLennardJonesGeneric.setPotentialCG() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListAdressLennardJonesGeneric2() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListAdressLennardJonesGeneric2.setPotentialAT() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListAdressLennardJonesGeneric2.setPotentialCG() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListAdressLennardJonesHarmonic() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressLennardJonesHarmonic.setPotentialAT() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressLennardJonesHarmonic.setPotentialCG() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListAdressLJcos() (in module espressopp.interaction.LJcos) espressopp.interaction.VerletListAdressLJcos.setPotentialAT() (in module espressopp.interaction.LJcos) espressopp.interaction.VerletListAdressLJcos.setPotentialCG() (in module espressopp.interaction.LJcos) espressopp.interaction.VerletListAdressMorse() (in module espressopp.interaction.Morse) espressopp.interaction.VerletListAdressMorse.setPotentialAT() (in module espressopp.interaction.Morse) espressopp.interaction.VerletListAdressMorse.setPotentialCG() (in module espressopp.interaction.Morse) espressopp.interaction.VerletListAdressReactionFieldGeneralized() (in module espressopp.interaction.ReactionFieldGeneralized) (in module espressopp.interaction.ReactionFieldGeneralizedTI) espressopp.interaction.VerletListAdressReactionFieldGeneralized.setPotentialAT() (in module espressopp.interaction.ReactionFieldGeneralized) (in module espressopp.interaction.ReactionFieldGeneralizedTI) espressopp.interaction.VerletListAdressReactionFieldGeneralized.setPotentialCG() (in module espressopp.interaction.ReactionFieldGeneralized) (in module espressopp.interaction.ReactionFieldGeneralizedTI) espressopp.interaction.VerletListAdressStillingerWeberPairTerm() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.VerletListAdressStillingerWeberPairTerm.setPotentialAT() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.VerletListAdressStillingerWeberPairTerm.setPotentialCG() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.VerletListAdressStillingerWeberPairTermCapped() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.VerletListAdressStillingerWeberPairTermCapped.setPotentialAT() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.VerletListAdressStillingerWeberPairTermCapped.setPotentialCG() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.VerletListAdressTabulated() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListAdressTabulated.setPotentialAT() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListAdressTabulated.setPotentialCG() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListAdressZero() (in module espressopp.interaction.Zero) espressopp.interaction.VerletListAdressZero.setFixedTupleList() (in module espressopp.interaction.Zero) espressopp.interaction.VerletListAdressZero.setPotentialAT() (in module espressopp.interaction.Zero) espressopp.interaction.VerletListAdressZero.setPotentialCG() (in module espressopp.interaction.Zero) espressopp.interaction.VerletListCoulombRSpace() (in module espressopp.interaction.CoulombRSpace) espressopp.interaction.VerletListCoulombRSpace.getPotential() (in module espressopp.interaction.CoulombRSpace) espressopp.interaction.VerletListCoulombRSpace.getVerletList() (in module espressopp.interaction.CoulombRSpace) espressopp.interaction.VerletListCoulombRSpace.setPotential() (in module espressopp.interaction.CoulombRSpace) espressopp.interaction.VerletListCoulombTruncated() (in module espressopp.interaction.CoulombTruncated) espressopp.interaction.VerletListCoulombTruncated.getPotential() (in module espressopp.interaction.CoulombTruncated) espressopp.interaction.VerletListCoulombTruncated.setPotential() (in module espressopp.interaction.CoulombTruncated) espressopp.interaction.VerletListCoulombTruncatedUniqueCharge() (in module espressopp.interaction.CoulombTruncatedUniqueCharge) espressopp.interaction.VerletListCoulombTruncatedUniqueCharge.getPotential() (in module espressopp.interaction.CoulombTruncatedUniqueCharge) espressopp.interaction.VerletListCoulombTruncatedUniqueCharge.setPotential() (in module espressopp.interaction.CoulombTruncatedUniqueCharge) espressopp.interaction.VerletListGravityTruncated() (in module espressopp.interaction.GravityTruncated) espressopp.interaction.VerletListGravityTruncated.getPotential() (in module espressopp.interaction.GravityTruncated) espressopp.interaction.VerletListGravityTruncated.getVerletList() (in module espressopp.interaction.GravityTruncated) espressopp.interaction.VerletListGravityTruncated.setPotential() (in module espressopp.interaction.GravityTruncated) espressopp.interaction.VerletListHadressATHarmonic() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListHadressATHarmonic.getPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListHadressATHarmonic.getVerletList() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListHadressATHarmonic.setPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListHadressATLenJonesReacFieldGen() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLenJonesReacFieldGen.setPotential1() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLenJonesReacFieldGen.setPotential2() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLennardJones() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLennardJones.getPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLennardJones.getVerletList() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLennardJones.setPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLJReacFieldGenHarmonic() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLJReacFieldGenHarmonic.setPotentialAT1() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLJReacFieldGenHarmonic.setPotentialAT2() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLJReacFieldGenHarmonic.setPotentialCG() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLJReacFieldGenTab() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLJReacFieldGenTab.setPotentialAT1() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLJReacFieldGenTab.setPotentialAT2() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATLJReacFieldGenTab.setPotentialCG() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressATReactionFieldGeneralized() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.VerletListHadressATReactionFieldGeneralized.getPotential() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.VerletListHadressATReactionFieldGeneralized.setPotential() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.VerletListHadressCGHarmonic() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListHadressCGHarmonic.getPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListHadressCGHarmonic.getVerletList() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListHadressCGHarmonic.setPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListHadressCGLennardJones() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressCGLennardJones.getPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressCGLennardJones.getVerletList() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressCGLennardJones.setPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressCGTabulated() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListHadressCGTabulated.getPotential() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListHadressCGTabulated.getVerletList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListHadressCGTabulated.setPotential() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListHadressLennardJones() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressLennardJones.setPotentialAT() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressLennardJones.setPotentialCG() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressLennardJones2() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressLennardJones2.setPotentialAT() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressLennardJones2.setPotentialCG() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressLennardJonesAutoBonds() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.VerletListHadressLennardJonesAutoBonds.setPotential() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.VerletListHadressLennardJonesCapped() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListHadressLennardJonesCapped.getPotentialAT() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListHadressLennardJonesCapped.getPotentialCG() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListHadressLennardJonesCapped.setPotentialAT() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListHadressLennardJonesCapped.setPotentialCG() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListHadressLennardJonesEnergyCapped() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListHadressLennardJonesEnergyCapped.getPotentialAT() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListHadressLennardJonesEnergyCapped.getPotentialCG() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListHadressLennardJonesEnergyCapped.setPotentialAT() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListHadressLennardJonesEnergyCapped.setPotentialCG() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListHadressLennardJonesGeneric() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListHadressLennardJonesGeneric.setPotentialAT() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListHadressLennardJonesGeneric.setPotentialCG() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListHadressLennardJonesGeneric2() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListHadressLennardJonesGeneric2.setPotentialAT() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListHadressLennardJonesGeneric2.setPotentialCG() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListHadressLennardJonesHarmonic() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressLennardJonesHarmonic.setPotentialAT() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressLennardJonesHarmonic.setPotentialCG() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListHadressLJcos() (in module espressopp.interaction.LJcos) espressopp.interaction.VerletListHadressLJcos.setPotentialAT() (in module espressopp.interaction.LJcos) espressopp.interaction.VerletListHadressLJcos.setPotentialCG() (in module espressopp.interaction.LJcos) espressopp.interaction.VerletListHadressMorse() (in module espressopp.interaction.Morse) espressopp.interaction.VerletListHadressMorse.setPotentialAT() (in module espressopp.interaction.Morse) espressopp.interaction.VerletListHadressMorse.setPotentialCG() (in module espressopp.interaction.Morse) espressopp.interaction.VerletListHadressReactionFieldGeneralized() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.VerletListHadressReactionFieldGeneralized.setPotentialAT() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.VerletListHadressReactionFieldGeneralized.setPotentialCG() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.VerletListHadressStillingerWeberPairTerm() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.VerletListHadressStillingerWeberPairTerm.setPotentialAT() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.VerletListHadressStillingerWeberPairTerm.setPotentialCG() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.VerletListHadressStillingerWeberPairTermCapped() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.VerletListHadressStillingerWeberPairTermCapped.setPotentialAT() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.VerletListHadressStillingerWeberPairTermCapped.setPotentialCG() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.VerletListHadressTabulated() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListHadressTabulated.setPotentialAT() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListHadressTabulated.setPotentialCG() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListHadressZero() (in module espressopp.interaction.Zero) espressopp.interaction.VerletListHadressZero.setFixedTupleList() (in module espressopp.interaction.Zero) espressopp.interaction.VerletListHadressZero.setPotentialAT() (in module espressopp.interaction.Zero) espressopp.interaction.VerletListHadressZero.setPotentialCG() (in module espressopp.interaction.Zero) espressopp.interaction.VerletListHarmonic() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListHarmonic.getPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListHarmonic.setPotential() (in module espressopp.interaction.Harmonic) espressopp.interaction.VerletListLennardJones() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListLennardJones.getPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListLennardJones.getVerletList() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListLennardJones.setPotential() (in module espressopp.interaction.LennardJones) espressopp.interaction.VerletListLennardJonesAutoBonds() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.VerletListLennardJonesAutoBonds.getPotential() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.VerletListLennardJonesAutoBonds.getVerletList() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.VerletListLennardJonesAutoBonds.setPotential() (in module espressopp.interaction.LennardJonesAutoBonds) espressopp.interaction.VerletListLennardJonesCapped() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListLennardJonesCapped.getPotential() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListLennardJonesCapped.setPotential() (in module espressopp.interaction.LennardJonesCapped) espressopp.interaction.VerletListLennardJonesEnergyCapped() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListLennardJonesEnergyCapped.getPotential() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListLennardJonesEnergyCapped.setPotential() (in module espressopp.interaction.LennardJonesEnergyCapped) espressopp.interaction.VerletListLennardJonesExpand() (in module espressopp.interaction.LennardJonesExpand) espressopp.interaction.VerletListLennardJonesExpand.getPotential() (in module espressopp.interaction.LennardJonesExpand) espressopp.interaction.VerletListLennardJonesExpand.setPotential() (in module espressopp.interaction.LennardJonesExpand) espressopp.interaction.VerletListLennardJonesGeneric() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListLennardJonesGeneric.getPotential() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListLennardJonesGeneric.getVerletList() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListLennardJonesGeneric.setPotential() (in module espressopp.interaction.LennardJonesGeneric) espressopp.interaction.VerletListLennardJonesGromacs() (in module espressopp.interaction.LennardJonesGromacs) espressopp.interaction.VerletListLennardJonesGromacs.getPotential() (in module espressopp.interaction.LennardJonesGromacs) espressopp.interaction.VerletListLennardJonesGromacs.setPotential() (in module espressopp.interaction.LennardJonesGromacs) espressopp.interaction.VerletListLJcos() (in module espressopp.interaction.LJcos) espressopp.interaction.VerletListLJcos.getPotential() (in module espressopp.interaction.LJcos) espressopp.interaction.VerletListLJcos.getVerletList() (in module espressopp.interaction.LJcos) espressopp.interaction.VerletListLJcos.setPotential() (in module espressopp.interaction.LJcos) espressopp.interaction.VerletListMorse() (in module espressopp.interaction.Morse) espressopp.interaction.VerletListMorse.getPotential() (in module espressopp.interaction.Morse) espressopp.interaction.VerletListMorse.setPotential() (in module espressopp.interaction.Morse) espressopp.interaction.VerletListPIadressNoDriftTabulated() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressNoDriftTabulated.getFixedTupleList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressNoDriftTabulated.getNTrotter() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressNoDriftTabulated.getSpeedup() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressNoDriftTabulated.getVerletList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressNoDriftTabulated.setFixedTupleList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressNoDriftTabulated.setNTrotter() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressNoDriftTabulated.setPotential() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressNoDriftTabulated.setSpeedup() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressNoDriftTabulated.setVerletList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulated() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulated.getFixedTupleList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulated.getNTrotter() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulated.getSpeedup() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulated.getVerletList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulated.setFixedTupleList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulated.setNTrotter() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulated.setPotentialCL() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulated.setPotentialQM() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulated.setSpeedup() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulated.setVerletList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulatedLJ() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulatedLJ.getFixedTupleList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulatedLJ.getNTrotter() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulatedLJ.getSpeedup() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulatedLJ.getVerletList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulatedLJ.setFixedTupleList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulatedLJ.setNTrotter() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulatedLJ.setPotentialCL() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulatedLJ.setPotentialQM() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulatedLJ.setSpeedup() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListPIadressTabulatedLJ.setVerletList() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListReactionFieldGeneralized() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.VerletListReactionFieldGeneralized.getPotential() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.VerletListReactionFieldGeneralized.setPotential() (in module espressopp.interaction.ReactionFieldGeneralized) espressopp.interaction.VerletListSoftCosine() (in module espressopp.interaction.SoftCosine) espressopp.interaction.VerletListSoftCosine.setPotential() (in module espressopp.interaction.SoftCosine) espressopp.interaction.VerletListStillingerWeberPairTerm() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.VerletListStillingerWeberPairTerm.getPotential() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.VerletListStillingerWeberPairTerm.getVerletList() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.VerletListStillingerWeberPairTerm.setPotential() (in module espressopp.interaction.StillingerWeberPairTerm) espressopp.interaction.VerletListStillingerWeberPairTermCapped() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.VerletListStillingerWeberPairTermCapped.getCaprad() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.VerletListStillingerWeberPairTermCapped.getPotential() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.VerletListStillingerWeberPairTermCapped.getVerletList() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.VerletListStillingerWeberPairTermCapped.setPotential() (in module espressopp.interaction.StillingerWeberPairTermCapped) espressopp.interaction.VerletListStillingerWeberTripleTerm() (in module espressopp.interaction.StillingerWeberTripleTerm) espressopp.interaction.VerletListStillingerWeberTripleTerm.getPotential() (in module espressopp.interaction.StillingerWeberTripleTerm) espressopp.interaction.VerletListStillingerWeberTripleTerm.getVerletListTriple() (in module espressopp.interaction.StillingerWeberTripleTerm) espressopp.interaction.VerletListStillingerWeberTripleTerm.setPotential() (in module espressopp.interaction.StillingerWeberTripleTerm) espressopp.interaction.VerletListTabulated() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListTabulated.getPotential() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListTabulated.setPotential() (in module espressopp.interaction.Tabulated) espressopp.interaction.VerletListTersoffPairTerm() (in module espressopp.interaction.TersoffPairTerm) espressopp.interaction.VerletListTersoffPairTerm.getPotential() (in module espressopp.interaction.TersoffPairTerm) espressopp.interaction.VerletListTersoffPairTerm.getVerletList() (in module espressopp.interaction.TersoffPairTerm) espressopp.interaction.VerletListTersoffPairTerm.setPotential() (in module espressopp.interaction.TersoffPairTerm) espressopp.interaction.VerletListTersoffTripleTerm() (in module espressopp.interaction.TersoffTripleTerm) espressopp.interaction.VerletListTersoffTripleTerm.getPotential() (in module espressopp.interaction.TersoffTripleTerm) espressopp.interaction.VerletListTersoffTripleTerm.getVerletListTriple() (in module espressopp.interaction.TersoffTripleTerm) espressopp.interaction.VerletListTersoffTripleTerm.setPotential() (in module espressopp.interaction.TersoffTripleTerm) espressopp.interaction.VerletListVSpherePair() (in module espressopp.interaction.VSpherePair) espressopp.interaction.VerletListVSpherePair.getPotential() (in module espressopp.interaction.VSpherePair) espressopp.interaction.VerletListVSpherePair.getVerletList() (in module espressopp.interaction.VSpherePair) espressopp.interaction.VerletListVSpherePair.setPotential() (in module espressopp.interaction.VSpherePair) espressopp.interaction.VerletListZero() (in module espressopp.interaction.Zero) espressopp.interaction.VerletListZero.getPotential() (in module espressopp.interaction.Zero) espressopp.interaction.VerletListZero.setFixedTupleList() (in module espressopp.interaction.Zero) espressopp.interaction.VerletListZero.setPotential() (in module espressopp.interaction.Zero) espressopp.interaction.VSpherePair module espressopp.interaction.VSpherePair() (in module espressopp.interaction.VSpherePair) espressopp.interaction.VSphereSelf module espressopp.interaction.VSphereSelf() (in module espressopp.interaction.VSphereSelf) espressopp.interaction.Zero module espressopp.interaction.Zero() (in module espressopp.interaction.Zero) espressopp.io.DumpGRO module espressopp.io.DumpGRO() (in module espressopp.io.DumpGRO) espressopp.io.DumpGRO.dump() (in module espressopp.io.DumpGRO) espressopp.io.DumpGROAdress module espressopp.io.DumpGROAdress() (in module espressopp.io.DumpGROAdress) espressopp.io.DumpGROAdress.dump() (in module espressopp.io.DumpGROAdress) espressopp.io.DumpH5MD module espressopp.io.DumpH5MD() (in module espressopp.io.DumpH5MD) espressopp.io.DumpXYZ module espressopp.io.DumpXYZ() (in module espressopp.io.DumpXYZ) espressopp.io.DumpXYZ.dump() (in module espressopp.io.DumpXYZ) espressopp.MissingFixedPairList() (in module espressopp.Exceptions) espressopp.MultiSystem module espressopp.MultiSystem() (in module espressopp.MultiSystem) espressopp.MultiSystem.beginSystemDefinition() (in module espressopp.MultiSystem) espressopp.MultiSystem.runAnalysisNPart() (in module espressopp.MultiSystem) espressopp.MultiSystem.runAnalysisPotential() (in module espressopp.MultiSystem) espressopp.MultiSystem.runAnalysisTemperature() (in module espressopp.MultiSystem) espressopp.MultiSystem.runIntegrator() (in module espressopp.MultiSystem) espressopp.MultiSystem.setAnalysisNPart() (in module espressopp.MultiSystem) espressopp.MultiSystem.setAnalysisPotential() (in module espressopp.MultiSystem) espressopp.MultiSystem.setAnalysisTemperature() (in module espressopp.MultiSystem) espressopp.MultiSystem.setIntegrator() (in module espressopp.MultiSystem) espressopp.ParallelTempering module espressopp.ParallelTempering() (in module espressopp.ParallelTempering) espressopp.ParallelTempering.endDefiningSystem() (in module espressopp.ParallelTempering) espressopp.ParallelTempering.exchange() (in module espressopp.ParallelTempering) espressopp.ParallelTempering.getNumberOfCPUsPerSystem() (in module espressopp.ParallelTempering) espressopp.ParallelTempering.getNumberOfSystems() (in module espressopp.ParallelTempering) espressopp.ParallelTempering.run() (in module espressopp.ParallelTempering) espressopp.ParallelTempering.setAnalysisE() (in module espressopp.ParallelTempering) espressopp.ParallelTempering.setAnalysisNPart() (in module espressopp.ParallelTempering) espressopp.ParallelTempering.setAnalysisT() (in module espressopp.ParallelTempering) espressopp.ParallelTempering.setIntegrator() (in module espressopp.ParallelTempering) espressopp.ParallelTempering.startDefiningSystem() (in module espressopp.ParallelTempering) espressopp.Particle module espressopp.Particle (class in espressopp.Particle) espressopp.ParticleAccess module espressopp.ParticleAccess.perform_action() (in module espressopp.ParticleAccess) espressopp.ParticleDoesNotExistHere() (in module espressopp.Exceptions) espressopp.ParticleGroup module espressopp.ParticleGroup() (in module espressopp.ParticleGroup) espressopp.ParticleGroup.add() (in module espressopp.ParticleGroup) espressopp.ParticleGroup.has() (in module espressopp.ParticleGroup) espressopp.ParticleGroup.show() (in module espressopp.ParticleGroup) espressopp.ParticleGroup.size() (in module espressopp.ParticleGroup) espressopp.pmi module espressopp.Quaternion module espressopp.Real3D module espressopp.Real3D() (in module espressopp.Real3D) espressopp.Real3D.x() (in module espressopp.Real3D) espressopp.Real3D.y() (in module espressopp.Real3D) espressopp.Real3D.z() (in module espressopp.Real3D) espressopp.RealND module espressopp.RealND() (in module espressopp.RealND) espressopp.standard_system.Default module espressopp.standard_system.KGMelt module espressopp.standard_system.KGMelt() (in module espressopp.standard_system.KGMelt) espressopp.standard_system.LennardJones module espressopp.standard_system.LennardJones() (in module espressopp.standard_system.LennardJones) espressopp.standard_system.Minimal module espressopp.standard_system.Minimal() (in module espressopp.standard_system.Minimal) espressopp.standard_system.PolymerMelt module espressopp.standard_system.PolymerMelt() (in module espressopp.standard_system.PolymerMelt) espressopp.storage.DomainDecomposition module espressopp.storage.DomainDecomposition() (in module espressopp.storage.DomainDecomposition) espressopp.storage.DomainDecomposition.getCellGrid() (in module espressopp.storage.DomainDecomposition) espressopp.storage.DomainDecomposition.getNodeGrid() (in module espressopp.storage.DomainDecomposition) espressopp.storage.DomainDecompositionAdress module espressopp.storage.DomainDecompositionAdress() (in module espressopp.storage.DomainDecompositionAdress) espressopp.storage.DomainDecompositionNonBlocking module espressopp.storage.DomainDecompositionNonBlocking() (in module espressopp.storage.DomainDecompositionNonBlocking) espressopp.storage.Storage module espressopp.storage.Storage.addAdrATParticle() (in module espressopp.storage.Storage) espressopp.storage.Storage.addParticle() (in module espressopp.storage.Storage) espressopp.storage.Storage.addParticles() (in module espressopp.storage.Storage) espressopp.storage.Storage.clearSavedPositions() (in module espressopp.storage.Storage) espressopp.storage.Storage.getParticle() (in module espressopp.storage.Storage) espressopp.storage.Storage.getRealParticleIDs() (in module espressopp.storage.Storage) espressopp.storage.Storage.modifyParticle() (in module espressopp.storage.Storage) espressopp.storage.Storage.particleExists() (in module espressopp.storage.Storage) espressopp.storage.Storage.printRealParticles() (in module espressopp.storage.Storage) espressopp.storage.Storage.removeAllParticles() (in module espressopp.storage.Storage) espressopp.storage.Storage.removeParticle() (in module espressopp.storage.Storage) espressopp.storage.Storage.restorePositions() (in module espressopp.storage.Storage) espressopp.storage.Storage.savePositions() (in module espressopp.storage.Storage) espressopp.storage.Storage.setFixedTuplesAdress() (in module espressopp.storage.Storage) espressopp.System module espressopp.System() (in module espressopp.System) espressopp.System.addInteraction() (in module espressopp.System) espressopp.System.getAllInteractions() (in module espressopp.System) espressopp.System.getInteraction() (in module espressopp.System) espressopp.System.getNumberOfInteractions() (in module espressopp.System) espressopp.System.removeInteraction() (in module espressopp.System) espressopp.System.removeInteractionByName() (in module espressopp.System) espressopp.System.scaleVolume() (in module espressopp.System) espressopp.System.setTrace() (in module espressopp.System) espressopp.Tensor module espressopp.toInt3D() (in module espressopp.Int3D) espressopp.toInt3DFromVector() (in module espressopp.Int3D) espressopp.tools.analyse module espressopp.tools.applyBoreschRestraints() (in module espressopp.tools.prepareComplexMolecules) espressopp.tools.decomp module espressopp.tools.DumpConfigurations module espressopp.tools.espresso_old module espressopp.tools.findConstrainedBonds() (in module espressopp.tools.prepareComplexMolecules) espressopp.tools.getInternalNonbondedInteractions() (in module espressopp.tools.prepareComplexMolecules) espressopp.tools.gromacs module espressopp.tools.info module espressopp.tools.io_extended module espressopp.tools.lammps module espressopp.tools.lattice module espressopp.tools.pathintegral module espressopp.tools.pdb module espressopp.tools.pdbread() (in module espressopp.tools.pdb) espressopp.tools.pdbwrite() (in module espressopp.tools.pdb) espressopp.tools.povwrite module espressopp.tools.prepareAdress module espressopp.tools.prepareComplexMolecules module espressopp.tools.psf module espressopp.tools.psfread() (in module espressopp.tools.psf) espressopp.tools.psfwrite() (in module espressopp.tools.psf) espressopp.tools.readSimpleSystem() (in module espressopp.tools.prepareComplexMolecules) espressopp.tools.replicate module espressopp.tools.tabulated module espressopp.tools.timers module espressopp.tools.topology module espressopp.tools.topology_helper module espressopp.tools.units module espressopp.tools.velocities module espressopp.tools.vmd module espressopp.tools.warmup module espressopp.toReal3D() (in module espressopp.Real3D) espressopp.toReal3DFromVector() (in module espressopp.Real3D) espressopp.toRealND() (in module espressopp.RealND) espressopp.toRealNDFromVector() (in module espressopp.RealND) espressopp.UnknownParticleProperty() (in module espressopp.Exceptions) espressopp.VerletList module espressopp.VerletList() (in module espressopp.VerletList) espressopp.VerletList.exclude() (in module espressopp.VerletList) espressopp.VerletList.getAllPairs() (in module espressopp.VerletList) espressopp.VerletList.localSize() (in module espressopp.VerletList) espressopp.VerletList.totalSize() (in module espressopp.VerletList) espressopp.VerletListAdress module espressopp.VerletListAdress() (in module espressopp.VerletListAdress) espressopp.VerletListAdress.addAdrParticles() (in module espressopp.VerletListAdress) espressopp.VerletListAdress.exclude() (in module espressopp.VerletListAdress) espressopp.VerletListAdress.rebuild() (in module espressopp.VerletListAdress) espressopp.VerletListAdress.totalSize() (in module espressopp.VerletListAdress) espressopp.VerletListTriple module espressopp.VerletListTriple() (in module espressopp.VerletListTriple) espressopp.VerletListTriple.exclude() (in module espressopp.VerletListTriple) espressopp.VerletListTriple.getAllTriples() (in module espressopp.VerletListTriple) espressopp.VerletListTriple.localSize() (in module espressopp.VerletListTriple) espressopp.VerletListTriple.totalSize() (in module espressopp.VerletListTriple) espressopp.Version module espressopp.Version() (in module espressopp.Version) euler_from_matrix() (in module espressopp.external.transformations) euler_from_quaternion() (in module espressopp.external.transformations) euler_matrix() (in module espressopp.external.transformations) exec_() (in module espressopp.pmi)

F

f_max (in module espressopp.integrator.MinimizeEnergy) fastreadxyz() (in module espressopp.tools.DumpConfigurations) fastwritexyz() (in module espressopp.tools.DumpConfigurations) fastwritexyz_standard() (in module espressopp.tools.DumpConfigurations)

final_info() (in module espressopp.tools.analyse) finalizeWorkers() (in module espressopp.pmi) FixedQuadrupleListDihedralHarmonicLocal (class in espressopp.interaction.DihedralHarmonic) FixedQuadrupleListDihedralHarmonicNCosLocal (class in espressopp.interaction.DihedralHarmonicNCos) FixedTripleListPIadressTabulatedAngularLocal (class in espressopp.interaction.TabulatedAngular)

G

GammaVariate (class in espressopp.esutil.GammaVariate) gaussian() (in module espressopp.tools.velocities) getAllBonds() (in module espressopp.tools.info) getAllParticles() (in module espressopp.tools.info) getCentroidThermostat() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getClmassmultiplier() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getCMDparameter() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getConstKinMass() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getconstrain() (espressopp.external.transformations.Arcball method) getFixedPairList() (espressopp.interaction.FENE.espressopp.interaction.FixedPairListFENE method) (espressopp.interaction.FENECapped.espressopp.interaction.FixedPairListFENECapped method) getFixedQuadrupleList() (espressopp.interaction.DihedralHarmonic.FixedQuadrupleListDihedralHarmonicLocal method) (espressopp.interaction.DihedralHarmonicNCos.FixedQuadrupleListDihedralHarmonicNCosLocal method) getFixedTripleList() (espressopp.interaction.AngularCosineSquared.espressopp.interaction.FixedTripleListAngularCosineSquared method) (espressopp.interaction.AngularHarmonic.espressopp.interaction.FixedTripleListAngularHarmonic method) (espressopp.interaction.TabulatedAngular.FixedTripleListPIadressTabulatedAngularLocal method) getFixedTupleList() (espressopp.interaction.TabulatedAngular.FixedTripleListPIadressTabulatedAngularLocal method) getFoldedPosition() (espressopp.bc.BC.espressopp.bc.BC method) getGamma() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getKTI() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method)

getLBMom() (espressopp.integrator.LatticeBoltzmann.espressopp.integrator.LatticeBoltzmann method) getMinimumImageVector() (espressopp.bc.BC.espressopp.bc.BC method) getmStep() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getNtrotter() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getNTrotter() (espressopp.interaction.TabulatedAngular.FixedTripleListPIadressTabulatedAngularLocal method) getPILE() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getPILElambda() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getPotential() (espressopp.interaction.FENE.espressopp.interaction.FixedPairListFENE method) (espressopp.interaction.FENECapped.espressopp.interaction.FixedPairListFENECapped method) (espressopp.interaction.TabulatedAngular.FixedTripleListPIadressTabulatedAngularLocal method) getRandomPos() (espressopp.bc.BC.espressopp.bc.BC method) getRealKinMass() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getSpeedup() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) (espressopp.interaction.TabulatedAngular.FixedTripleListPIadressTabulatedAngularLocal method) getsStep() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getTemperature() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getTimeStep() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getUnfoldedPosition() (espressopp.bc.BC.espressopp.bc.BC method) getVerletList() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) getVerletlistBuilds() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) Grid (class in espressopp.esutil.Grid)

H

Harmonic (class in espressopp.interaction.Harmonic)

HarmonicTrap (class in espressopp.interaction.HarmonicTrap)

I

identity_matrix() (in module espressopp.external.transformations) import_() (in module espressopp.pmi) info() (in module espressopp.tools.analyse)

inverse_matrix() (in module espressopp.external.transformations) invoke() (in module espressopp.pmi) is_same_transform() (in module espressopp.external.transformations)

K

keepLBDump() (espressopp.integrator.LatticeBoltzmann.espressopp.integrator.LatticeBoltzmann method)

L

LennardJones (class in espressopp.interaction.LennardJones) LennardJones93Wall (class in espressopp.interaction.LennardJones93Wall) LennardJonesAutoBonds (class in espressopp.interaction.LennardJonesAutoBonds) LennardJonesCapped (class in espressopp.interaction.LennardJonesCapped) LennardJonesEnergyCapped (class in espressopp.interaction.LennardJonesEnergyCapped)

LennardJonesExpand (class in espressopp.interaction.LennardJonesExpand) LennardJonesGeneric (class in espressopp.interaction.LennardJonesGeneric) LennardJonesGromacs (class in espressopp.interaction.LennardJonesGromacs) LennardJonesSoftcoreTI (class in espressopp.interaction.LennardJonesSoftcoreTI) LJcos (class in espressopp.interaction.LJcos) locateItem() (espressopp.esutil.Collectives.espressopp.esutil method)

M

matrix() (espressopp.external.transformations.Arcball method) MirrorLennardJones (class in espressopp.interaction.MirrorLennardJones) MissingFixedPairList module espressopp.analysis.AdressDensity espressopp.analysis.AllParticlePos espressopp.analysis.AnalysisBase espressopp.analysis.Autocorrelation espressopp.analysis.CenterOfMass espressopp.analysis.CMVelocity espressopp.analysis.ConfigsParticleDecomp espressopp.analysis.Configurations espressopp.analysis.ConfigurationsExt espressopp.analysis.Energy espressopp.analysis.IntraChainDistSq espressopp.analysis.LBOutput espressopp.analysis.LBOutputScreen espressopp.analysis.LBOutputVzInTime espressopp.analysis.LBOutputVzOfX espressopp.analysis.MaxPID espressopp.analysis.MeanSquareDispl espressopp.analysis.MeanSquareInternalDist espressopp.analysis.NeighborFluctuation espressopp.analysis.NPart espressopp.analysis.NPartSubregion espressopp.analysis.Observable espressopp.analysis.OrderParameter espressopp.analysis.ParticleRadiusDistribution espressopp.analysis.PotentialEnergy espressopp.analysis.Pressure espressopp.analysis.PressureTensor espressopp.analysis.PressureTensorLayer espressopp.analysis.PressureTensorMultiLayer espressopp.analysis.RadGyrXProfilePI espressopp.analysis.RadialDistrF espressopp.analysis.RDFatomistic espressopp.analysis.StaticStructF espressopp.analysis.SubregionTracking espressopp.analysis.SystemMonitor espressopp.analysis.Temperature espressopp.analysis.Test espressopp.analysis.Velocities espressopp.analysis.VelocityAutocorrelation espressopp.analysis.Viscosity espressopp.analysis.XDensity espressopp.analysis.XPressure espressopp.analysis.XTemperature espressopp.bc.BC espressopp.bc.OrthorhombicBC espressopp.bc.SlabBC espressopp.check.System espressopp.esutil.Collectives espressopp.esutil.GammaVariate espressopp.esutil.Grid espressopp.esutil.NormalVariate espressopp.esutil.RNG espressopp.esutil.UniformOnSphere espressopp.Exceptions espressopp.external.transformations espressopp.FixedLocalTupleList espressopp.FixedPairDistList espressopp.FixedPairList espressopp.FixedPairListAdress espressopp.FixedQuadrupleAngleList espressopp.FixedQuadrupleList espressopp.FixedQuadrupleListAdress espressopp.FixedSingleList espressopp.FixedTripleAngleList espressopp.FixedTripleList espressopp.FixedTripleListAdress espressopp.FixedTupleList espressopp.FixedTupleListAdress espressopp.Int3D espressopp.integrator.Adress espressopp.integrator.AssociationReaction espressopp.integrator.BerendsenBarostat espressopp.integrator.BerendsenBarostatAnisotropic espressopp.integrator.BerendsenThermostat espressopp.integrator.CapForce espressopp.integrator.DPDThermostat espressopp.integrator.EmptyExtension espressopp.integrator.ExtAnalyze espressopp.integrator.Extension espressopp.integrator.ExtForce espressopp.integrator.FixPositions espressopp.integrator.FreeEnergyCompensation espressopp.integrator.GeneralizedLangevinThermostat espressopp.integrator.Isokinetic espressopp.integrator.LangevinBarostat espressopp.integrator.LangevinThermostat espressopp.integrator.LangevinThermostat1D espressopp.integrator.LangevinThermostatHybrid espressopp.integrator.LangevinThermostatOnGroup espressopp.integrator.LangevinThermostatOnRadius espressopp.integrator.LatticeBoltzmann espressopp.integrator.LBInit espressopp.integrator.LBInitConstForce espressopp.integrator.LBInitPeriodicForce espressopp.integrator.LBInitPopUniform espressopp.integrator.LBInitPopWave espressopp.integrator.MDIntegrator espressopp.integrator.MinimizeEnergy espressopp.integrator.OnTheFlyFEC espressopp.integrator.PIAdressIntegrator espressopp.integrator.Rattle espressopp.integrator.Settle espressopp.integrator.StochasticVelocityRescaling espressopp.integrator.TDforce espressopp.integrator.VelocityVerlet espressopp.integrator.VelocityVerletOnGroup espressopp.integrator.VelocityVerletOnRadius espressopp.integrator.VelocityVerletRESPA espressopp.interaction.AngularCosineSquared espressopp.interaction.AngularHarmonic espressopp.interaction.AngularPotential espressopp.interaction.ConstrainCOM espressopp.interaction.ConstrainRG espressopp.interaction.Cosine espressopp.interaction.CoulombKSpaceEwald espressopp.interaction.CoulombKSpaceP3M espressopp.interaction.CoulombRSpace espressopp.interaction.CoulombTruncated espressopp.interaction.CoulombTruncatedUniqueCharge espressopp.interaction.DihedralHarmonic espressopp.interaction.DihedralHarmonicCos espressopp.interaction.DihedralHarmonicNCos espressopp.interaction.DihedralPotential espressopp.interaction.DihedralRB espressopp.interaction.FENE espressopp.interaction.FENECapped espressopp.interaction.GravityTruncated espressopp.interaction.Harmonic espressopp.interaction.HarmonicTrap espressopp.interaction.Interaction espressopp.interaction.LennardJones espressopp.interaction.LennardJones93Wall espressopp.interaction.LennardJonesAutoBonds espressopp.interaction.LennardJonesCapped espressopp.interaction.LennardJonesEnergyCapped espressopp.interaction.LennardJonesExpand espressopp.interaction.LennardJonesGeneric espressopp.interaction.LennardJonesGromacs espressopp.interaction.LennardJonesSoftcoreTI espressopp.interaction.LJcos espressopp.interaction.MirrorLennardJones espressopp.interaction.Morse espressopp.interaction.OPLS espressopp.interaction.Potential espressopp.interaction.PotentialVSpherePair espressopp.interaction.Quartic espressopp.interaction.ReactionFieldGeneralized espressopp.interaction.ReactionFieldGeneralizedTI espressopp.interaction.SingleParticlePotential espressopp.interaction.SmoothSquareWell espressopp.interaction.SoftCosine espressopp.interaction.StillingerWeberPairTerm espressopp.interaction.StillingerWeberPairTermCapped espressopp.interaction.StillingerWeberTripleTerm espressopp.interaction.Tabulated espressopp.interaction.TabulatedAngular espressopp.interaction.TabulatedDihedral espressopp.interaction.TersoffPairTerm espressopp.interaction.TersoffTripleTerm espressopp.interaction.VSpherePair espressopp.interaction.VSphereSelf espressopp.interaction.Zero espressopp.io.DumpGRO espressopp.io.DumpGROAdress espressopp.io.DumpH5MD espressopp.io.DumpXYZ espressopp.MultiSystem espressopp.ParallelTempering espressopp.Particle espressopp.ParticleAccess espressopp.ParticleGroup espressopp.pmi espressopp.Quaternion espressopp.Real3D espressopp.RealND espressopp.standard_system.Default espressopp.standard_system.KGMelt espressopp.standard_system.LennardJones espressopp.standard_system.Minimal espressopp.standard_system.PolymerMelt espressopp.storage.DomainDecomposition espressopp.storage.DomainDecompositionAdress espressopp.storage.DomainDecompositionNonBlocking espressopp.storage.Storage espressopp.System espressopp.Tensor espressopp.tools.analyse espressopp.tools.decomp espressopp.tools.DumpConfigurations espressopp.tools.espresso_old espressopp.tools.gromacs espressopp.tools.info espressopp.tools.io_extended espressopp.tools.lammps espressopp.tools.lattice espressopp.tools.pathintegral espressopp.tools.pdb espressopp.tools.povwrite espressopp.tools.prepareAdress espressopp.tools.prepareComplexMolecules espressopp.tools.psf espressopp.tools.replicate espressopp.tools.tabulated espressopp.tools.timers espressopp.tools.topology espressopp.tools.topology_helper espressopp.tools.units espressopp.tools.velocities espressopp.tools.vmd espressopp.tools.warmup espressopp.VerletList espressopp.VerletListAdress espressopp.VerletListTriple espressopp.Version

Morse (class in espressopp.interaction.Morse) MultiSystem (class in espressopp.MultiSystem) MultiSystemLocal (class in espressopp.MultiSystem)

N

next() (espressopp.external.transformations.Arcball method)

NormalVariate (class in espressopp.esutil.NormalVariate) NPartSubregionLocal (class in espressopp.analysis.NPartSubregion)

O

OPLS (class in espressopp.interaction.OPLS)

orthogonalization_matrix() (in module espressopp.external.transformations) OrthorhombicBC() (espressopp.bc.OrthorhombicBC.espressopp.bc method)

P

ParticleDoesNotExistHere ParticleLocal (class in espressopp.Particle) PIAdressIntegratorLocal (class in espressopp.integrator.PIAdressIntegrator) place() (espressopp.external.transformations.Arcball method)

polymerRW() (in module espressopp.tools.topology) projection_from_matrix() (in module espressopp.external.transformations) projection_matrix() (in module espressopp.external.transformations) Proxy (class in espressopp.pmi)

Q

Quartic (class in espressopp.interaction.Quartic) quaternion_about_axis() (in module espressopp.external.transformations) quaternion_conjugate() (in module espressopp.external.transformations) quaternion_from_euler() (in module espressopp.external.transformations) quaternion_from_matrix() (in module espressopp.external.transformations)

quaternion_imag() (in module espressopp.external.transformations) quaternion_inverse() (in module espressopp.external.transformations) quaternion_matrix() (in module espressopp.external.transformations) quaternion_multiply() (in module espressopp.external.transformations) quaternion_real() (in module espressopp.external.transformations) quaternion_slerp() (in module espressopp.external.transformations)

R

RadGyrXProfilePILocal (class in espressopp.analysis.RadGyrXProfilePI) random_quaternion() (in module espressopp.external.transformations) random_rotation_matrix() (in module espressopp.external.transformations) random_vector() (in module espressopp.external.transformations) ReactionFieldGeneralized (class in espressopp.interaction.ReactionFieldGeneralized) ReactionFieldGeneralizedTI (class in espressopp.interaction.ReactionFieldGeneralizedTI) read() (in module espressopp.tools.espresso_old) (in module espressopp.tools.gromacs) readxyz() (in module espressopp.tools.DumpConfigurations) readxyzr() (in module espressopp.tools.DumpConfigurations)

receive() (in module espressopp.pmi) reduce() (in module espressopp.pmi) reflection_from_matrix() (in module espressopp.external.transformations) reflection_matrix() (in module espressopp.external.transformations) registerAtExit() (in module espressopp.pmi) replicate() (in module espressopp.tools.replicate) ReplicateParallel (class in espressopp.tools.replicate) RNG (class in espressopp.esutil.RNG) rotation_from_matrix() (in module espressopp.external.transformations) rotation_matrix() (in module espressopp.external.transformations)

S

saveLBConf() (espressopp.integrator.LatticeBoltzmann.espressopp.integrator.LatticeBoltzmann method) scale_from_matrix() (in module espressopp.external.transformations) scale_matrix() (in module espressopp.external.transformations) setaxes() (espressopp.external.transformations.Arcball method) setBoxL() (espressopp.bc.OrthorhombicBC.espressopp.bc.OrthorhombicBC method) (espressopp.bc.SlabBC.espressopp.bc.SlabBC method) setCentroidThermostat() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setClmassmultiplier() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setCMDparameter() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setConstKinMass() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setconstrain() (espressopp.external.transformations.Arcball method) setFixedPairList() (espressopp.interaction.FENE.espressopp.interaction.FixedPairListFENE method) (espressopp.interaction.FENECapped.espressopp.interaction.FixedPairListFENECapped method) setFixedTripleList() (espressopp.interaction.TabulatedAngular.FixedTripleListPIadressTabulatedAngularLocal method) setFixedTupleList() (espressopp.interaction.TabulatedAngular.FixedTripleListPIadressTabulatedAngularLocal method) setForce() (espressopp.integrator.LBInit.espressopp.integrator.LBInit method) setGamma() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setKTI() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setLBMom() (espressopp.integrator.LatticeBoltzmann.espressopp.integrator.LatticeBoltzmann method) setLennardJones14Interactions() (in module espressopp.tools.gromacs) setLennardJonesInteractions() (in module espressopp.tools.gromacs) setLennardJonesInteractionsTI() (in module espressopp.tools.gromacs) setmStep() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setNtrotter() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setNTrotter() (espressopp.interaction.TabulatedAngular.FixedTripleListPIadressTabulatedAngularLocal method) setPILE() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setPILElambda() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setPotential() (espressopp.interaction.AngularCosineSquared.espressopp.interaction.FixedTripleListAngularCosineSquared method) (espressopp.interaction.AngularHarmonic.espressopp.interaction.FixedTripleListAngularHarmonic method) (espressopp.interaction.DihedralHarmonic.FixedQuadrupleListDihedralHarmonicLocal method) (espressopp.interaction.DihedralHarmonicNCos.FixedQuadrupleListDihedralHarmonicNCosLocal method) (espressopp.interaction.FENE.espressopp.interaction.FixedPairListFENE method) (espressopp.interaction.FENECapped.espressopp.interaction.FixedPairListFENECapped method) (espressopp.interaction.TabulatedAngular.FixedTripleListPIadressTabulatedAngularLocal method)

setRealKinMass() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setSpeedup() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) (espressopp.interaction.TabulatedAngular.FixedTripleListPIadressTabulatedAngularLocal method) setsStep() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setTabulatedInteractions() (in module espressopp.tools.gromacs) setTemperature() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setTimeStep() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) setVerletList() (espressopp.integrator.PIAdressIntegrator.PIAdressIntegratorLocal method) shear_from_matrix() (in module espressopp.external.transformations) shear_matrix() (in module espressopp.external.transformations) show() (in module espressopp.tools.timers) SlabBC() (espressopp.bc.SlabBC.espressopp.bc method) SmoothSquareWell (class in espressopp.interaction.SmoothSquareWell) SoftCosine (class in espressopp.interaction.SoftCosine) startWorkerLoop() (in module espressopp.pmi) step (in module espressopp.integrator.MinimizeEnergy) StillingerWeberPairTerm (class in espressopp.interaction.StillingerWeberPairTerm) StillingerWeberPairTermCapped (class in espressopp.interaction.StillingerWeberPairTermCapped) StillingerWeberTripleTerm (class in espressopp.interaction.StillingerWeberTripleTerm) stopWorkerLoop() (in module espressopp.pmi) SubregionTrackingLocal (class in espressopp.analysis.SubregionTracking) superimposition_matrix() (in module espressopp.external.transformations) sync() (in module espressopp.pmi)

T

Tabulated (class in espressopp.interaction.Tabulated) TabulatedAngular (class in espressopp.interaction.TabulatedAngular) TabulatedDihedral (class in espressopp.interaction.TabulatedDihedral) TersoffPairTerm (class in espressopp.interaction.TersoffPairTerm) to_dict() (in module espressopp.tools.timers) toInt3D() (in module espressopp.Int3D) toInt3DFromVector() (in module espressopp.Int3D) toQuaternion() (in module espressopp.Quaternion)

toQuaternionFromVector() (in module espressopp.Quaternion) toReal3D() (in module espressopp.Real3D) toReal3DFromVector() (in module espressopp.Real3D) toRealND() (in module espressopp.RealND) toRealNDFromVector() (in module espressopp.RealND) toTensor() (in module espressopp.Tensor) toTensorFromVector() (in module espressopp.Tensor) translation_from_matrix() (in module espressopp.external.transformations) translation_matrix() (in module espressopp.external.transformations)

U

UniformOnSphere (class in espressopp.esutil.UniformOnSphere) unit_vector() (in module espressopp.external.transformations)

UnknownParticleProperty UserError

V

vector_norm() (in module espressopp.external.transformations) vector_product() (in module espressopp.external.transformations)

VSpherePair (class in espressopp.interaction.VSpherePair) VSphereSelf (class in espressopp.interaction.VSphereSelf)

W

warmup() (in module espressopp.tools.warmup)

writeTabFile() (in module espressopp.tools.tabulated) writexyz() (in module espressopp.tools.DumpConfigurations)

X

xyzfilewrite() (in module espressopp.tools.DumpConfigurations)

Z

Zero (class in espressopp.interaction.Zero)